Measurement of the Neutron F2 Structure Function via Spectator Tagging with CLAS

NASA Astrophysics Data System (ADS)

Baillie, N.; Tkachenko, S.; Zhang, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Keppel, C. E.; Kuhn, S. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Adikaram, D.; Aghasyan, M.; Amaryan, M. J.; Anghinolfi, M.; Arrington, J.; Avakian, H.; Baghdasaryan, H.; Battaglieri, M.; Biselli, A. S.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Daniel, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Dey, B.; Djalali, C.; Dodge, G.; Domingo, J.; Doughty, D.; Dupre, R.; Dutta, D.; Ent, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fradi, A.; Gabrielyan, M. Y.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Graham, L.; Guegan, B.; Guidal, M.; Guler, N.; Guo, L.; Hafidi, K.; Heddle, D.; Hicks, K.; Holtrop, M.; Hungerford, E.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ispiryan, M.; Isupov, E. L.; Jawalkar, S. S.; Jo, H. S.; Kalantarians, N.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Klimenko, A.; Kubarovsky, V.; Kuleshov, S. V.; Kvaltine, N. D.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Mao, Y.; Markov, N.; McKinnon, B.; Mineeva, T.; Morrison, B.; Moutarde, H.; Munevar, E.; Nadel-Turonski, P.; Ni, A.; Niccolai, S.; Niculescu, I.; Niculescu, G.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L.; Park, K.; Park, S.; Pasyuk, E.; Anefalos Pereira, S.; Pisano, S.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Prok, Y.; Protopopescu, D.; Raue, B. A.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Schott, D.; Schumacher, R. A.; Seder, E.; Sharabian, Y. G.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Stoler, P.; Strauch, S.; Taiuti, M.; Tang, W.; Ungaro, M.; Vineyard, M. F.; Voutier, E.; Watts, D. P.; Weinstein, L. B.; Weygand, D. P.; Wood, M. H.; Zana, L.; Zhao, B.

2012-04-01

We report on the first measurement of the F2 structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲100MeV/c and their angles to ≳100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F2n data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65

Measurement of the neutron F 2 structure function via spectator tagging with CLAS

DOE PAGES

Baillie, N.; Tkachenko, S.; Zhang, J.; ...

2012-04-01

We report on the first measurement of the F 2 structure function of the neutron from semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≈< 100 MeV and their angles to ≈> 100 degrees relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F 2 n data collected cover the nucleon resonance and deep-inelastic regions over a wide range of x for 0.65 < Q 2 < 4.52 GeV 2, with uncertainties from nuclear correctionsmore » estimated to be less than a few percent. These measurements provide the first determination of the neutron to proton structure function ratio F 2 n/F 2 p at 0.2 ≈< x ≈< 0.8, essentially free of nuclear corrections.« less

Theoretical investigation of local proton conductance in the proton exchange membranes

NASA Astrophysics Data System (ADS)

Singh, Raman K.; Tsuneda, Takao; Miyatake, Kenji; Watanabe, Masahiro

2014-07-01

The hydrated structures of the proton exchange membranes were theoretically investigated using long-range corrected density functional theory to make clear why perfluorinated polymer membrane Nafion is superior to other membranes in the proton conductivity at low humidity. For exploring the possibility of the proton conductance in the vehicle mechanism with low hydration numbers, we examined the relay model of protonated water clusters between the sulfonic acid groups in Nafion and concluded that this relay model may contribute to the high proton conductivity of Nafion with less-hydrated sulfonic acid groups.

Scaling violations of the proton structure function F2 at small x

NASA Astrophysics Data System (ADS)

Abt, I.; Ahmed, T.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bärwolff, H.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bergstein, H.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Biddulph, P.; Binder, E.; Bischoff, A.; Bizot, J. C.; Blobel, V.; Borras, K.; Bosetti, P. C.; Boudry, V.; Bourdarios, C.; Brasse, F.; Braun, U.; Braunschweig, W.; Bruncko, D.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Colombo, M.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Danilov, M.; Dann, A. W. E.; Dau, W. D.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; Devel, M.; De Roeck, A.; Dingus, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Drescher, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebbinghaus, R.; Eberle, M.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellis, N. N.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Fensome, I. F.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Flauger, W.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Fuhrmann, P.; Gabathuler, E.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gellrich, A.; Gennis, M.; Genzel, H.; Gerhards, R.; Godfrey, L.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goodall, A. M.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Greif, H.; Grindhammer, G.; Gruber, C.; Haack, J.; Hajduk, L.; Hamon, O.; Handschuh, D.; Hanlon, E. M.; Hapke, M.; Harjes, J.; Haydar, R.; Haynes, W. J.; Heatherington, J.; Hedberg, V.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herma, R.; Herynek, I.; Hildesheim, W.; Hill, P.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Huet, Ph.; Hufnagel, H.; Huot, N.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kasarian, S.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Kaufmann, H. H.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Langkau, R.; Lanius, P.; Laporte, J. F.; Lebedev, A.; Leuschner, A.; Leverenz, C.; Levonian, S.; Lewin, D.; Ley, Ch.; Lindner, A.; Lindström, G.; Linsel, F.; Lipinski, J.; Loch, P.; Lohmander, H.; Lopez, G. C.; Lüers, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, A.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milone, V.; Monnier, E.; Moreau, F.; Moreels, J.; Morris, J. V.; Müller, K.; Murín, P.; Murray, S. A.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Niebergall, F.; Niebuhr, C.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Orenstein, S.; Ould-Saada, F.; Pascaud, C.; Patel, G. D.; Peppel, E.; Peters, S.; Phillips, H. T.; Phillips, J. P.; Pichler, Ch.; Pilgram, W.; Pitzl, D.; Prell, S.; Prosi, R.; Rädel, G.; Raupach, F.; Rauschnabel, K.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Robertson, S. M.; Robmann, P.; Roosen, R.; Rostovtsev, A.; Royon, C.; Rudowicz, M.; Ruffer, M.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Savitsky, M.; Schacht, P.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmitz, W.; Schöning, A.; Schröder, V.; Schulz, M.; Schwab, B.; Schwind, A.; Scobel, W.; Seehausen, U.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Smolik, L.; Soloviev, Y.; Spitzer, H.; Staroba, P.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stösslein, U.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Tichomirov, I.; Truöl, P.; Turnau, J.; Tutas, J.; Urban, L.; Usik, A.; Valkar, S.; Valkarova, A.; Vallée, C.; Van Esch, P.; Vartapetian, A.; Vazdik, Y.; Vecko, M.; Verrecchia, P.; Vick, R.; Villet, G.; Vogel, E.; Wacker, K.; Walker, I. W.; Walther, A.; Weber, G.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wolff, Th.; Womersley, L. A.; Wright, A. E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Závada, P.; Zeitnitz, C.; Ziaeepour, H.; Zimmer, M.; Zimmermann, W.; Zomer, F.; H1 Collaboration

1994-01-01

An analysis is presented of scaling violations of the proton structure function F2( x, Q2) measured with the H1 detector at HERA in the range of Bjorken x values between x = 3 × 10 -4 and 10 -2 for four-momentum transfers Q> 2 larger than 8.7 GeV 2. The structure function F2( x, Q2) is observed to rise linearly with ln Q2. Under the assumption that the observed scaling violations at small x ⩽ 0.01 are described correctly by perturbative QCD, an estimate is obtained of the gluon distribution function G( x, Q02) at Q22 = 20 GeV 2.

Measurement of the structure function of the nearly free neutron using spectator tagging in inelastic 2H(e ,e'ps )X scattering with CLAS

NASA Astrophysics Data System (ADS)

Tkachenko, S.; Baillie, N.; Kuhn, S. E.; Zhang, J.; Arrington, J.; Bosted, P.; Bültmann, S.; Christy, M. E.; Fenker, H.; Griffioen, K. A.; Kalantarians, N.; Keppel, C. E.; Melnitchouk, W.; Tvaskis, V.; Adhikari, K. P.; Aghasyan, M.; Amaryan, M. J.; Anefalos Pereira, S.; Avakian, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fleming, J. A.; Garillon, B.; Gevorgyan, N.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gothe, R. W.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Hicks, K.; Ho, D.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Jo, H. S.; Keller, D.; Khandaker, M.; Kim, A.; Kim, W.; King, P. M.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, V.; Kuleshov, S. V.; Lenisa, P.; Lewis, S.; Livingston, K.; Lu, H.; MacCormick, M.; MacGregor, I. J. D.; Markov, N.; Mayer, M.; McKinnon, B.; Mineeva, T.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munoz Camacho, C.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Phillips, J. J.; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Rimal, D.; Ripani, M.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Sabatié, F.; Schott, D.; Schumacher, R. A.; Seder, E.; Senderovich, I.; Sharabian, Y. G.; Simonyan, A.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S.; Stepanyan, S. S.; Strauch, S.; Tang, W.; Ungaro, M.; Vlassov, A. V.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D.; Wei, X.; Weinstein, L. B.; Wood, M. H.; Zana, L.; Zonta, I.; CLAS Collaboration

2014-04-01

Background: Much less is known about neutron structure than that of the proton due to the absence of free neutron targets. Neutron information is usually extracted from data on nuclear targets such as deuterium, requiring corrections for nuclear binding and nucleon off-shell effects. These corrections are model dependent and have significant uncertainties, especially for large values of the Bjorken scaling variable x . As a consequence, the same data can lead to different conclusions, for example, about the behavior of the d quark distribution in the proton at large x . Purpose: The Barely Off-shell Nucleon Structure experiment at Jefferson Lab measured the inelastic electron-deuteron scattering cross section, tagging spectator protons in coincidence with the scattered electrons. This method reduces nuclear binding uncertainties significantly and has allowed for the first time a (nearly) model-independent extraction of the neutron structure function F2(x ,Q2) in the resonance and deep-inelastic regions. Method: A novel compact radial time projection chamber was built to detect protons with momentum between 70 and 150 MeV/c and over a nearly 4 π angular range. For the extraction of the free-neutron structure function F2n, spectator protons at backward angles (>100∘ relative to the momentum transfer) and with momenta below 100 MeV/c were selected, ensuring that the scattering took place on a nearly free neutron. The scattered electrons were detected with Jefferson Lab's CLAS spectrometer, with data taken at beam energies near 2, 4, and 5 GeV. Results: The extracted neutron structure function F2n and its ratio to the inclusive deuteron structure function F2d are presented in both the resonance and the deep-inelastic regions for momentum transfer squared Q2 between 0.7 and 5 GeV2/c2 , invariant mass W between 1 and 2.7 GeV/c2 , and Bjorken x between 0.25 and 0.6 (in the deep-inelastic scattering region). The dependence of the semi-inclusive cross section on the spectator proton momentum and angle is investigated, and tests of the spectator mechanism for different kinematics are performed. Conclusions: Our data set on the structure function ratio F2n/F2d can be used to study neutron resonance excitations, test quark-hadron duality in the neutron, develop more precise parametrizations of structure functions, and investigate binding effects (including possible mechanisms for the nuclear EMC effect) and provide a first glimpse of the asymptotic behavior of d /u at x →1 .

Measurements of the separated longitudinal structure function FL from hydrogen and deuterium targets at low Q2

NASA Astrophysics Data System (ADS)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; Abbott, D.; Adams, G. S.; Afanasev, A.; Ahmidouch, A.; Angelescu, T.; Arrington, J.; Asaturyan, R.; Avery, S.; Baker, O. K.; Benmouna, N.; Berman, B. L.; Biselli, A.; Blok, H. P.; Boeglin, W. U.; Bosted, P. E.; Brash, E.; Breuer, H.; Chang, G.; Chant, N.; Christy, M. E.; Connell, S. H.; Dalton, M. M.; Danagoulian, S.; Day, D.; Dodario, T.; Dunne, J. A.; Dutta, D.; El Khayari, N.; Ent, R.; Fenker, H. C.; Frolov, V. V.; Gaskell, D.; Garrow, K.; Gilman, R.; Gueye, P.; Hafidi, K.; Hinton, W.; Holt, R. J.; Horn, T.; Huber, G. M.; Jackson, H.; Jiang, X.; Jones, M. K.; Joo, K.; Kelly, J. J.; Keppel, C. E.; Kuhn, J.; Kinney, E.; Klein, A.; Kubarovsky, V.; Liang, Y.; Lolos, G.; Lung, A.; Mack, D.; Malace, S.; Markowitz, P.; Mbianda, G.; McGrath, E.; Mckee, D.; Meekins, D. G.; Mkrtchyan, H.; Napolitano, J.; Navasardyan, T.; Niculescu, G.; Nozar, M.; Ostapenko, T.; Papandreou, Z.; Potterveld, D.; Reimer, P. E.; Reinhold, J.; Roche, J.; Rock, S. E.; Schulte, E.; Segbefia, E.; Smith, C.; Smith, G. R.; Stoler, P.; Tadevosyan, V.; Tang, L.; Telfeyan, J.; Todor, L.; Ungaro, M.; Uzzle, A.; Vidakovic, S.; Villano, A.; Vulcan, W. F.; Warren, G.; Wesselmann, F.; Wojtsekhowski, B.; Wood, S. A.; Yan, C.; Zihlmann, B.

2018-04-01

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. However, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q2<1 GeV2 , and compare them with parton distribution parametrization and kT factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q2 scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R , than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE PAGES

Tvaskis, V.; Tvaskis, A.; Niculescu, I.; ...

2018-04-26

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Measurements of the separated longitudinal structure function F L from hydrogen and deuterium targets at low Q 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tvaskis, V.; Tvaskis, A.; Niculescu, I.

Structure functions, as measured in lepton-nucleon scattering, have proven to be very useful in studying the partonic dynamics within the nucleon. Furthermore, it is experimentally difficult to separately determine the longitudinal and transverse structure functions, and consequently there are substantially less data available in particular for the longitudinal structure function. Here, we present separated structure functions for hydrogen and deuterium at low four-momentum transfer squared, Q 2 < 1 GeV 2, and compare them with parton distribution parametrization and k T factorization approaches. While differences are found, the parametrizations generally agree with the data, even at the very low-Q 2more » scale of the data. The deuterium data show a smaller longitudinal structure function and a smaller ratio of longitudinal to transverse cross section, R, than the proton. This suggests either an unexpected difference in R for the proton and the neutron or a suppression of the gluonic distribution in nuclei.« less

Subunit III-depleted cytochrome c oxidase provides insight into the process of proton uptake by proteins

PubMed Central

Varanasi, Lakshman; Hosler, Jonathan P.

2011-01-01

We review studies of subunit III-depleted cytochrome c oxidase (CcO III (−)) that elucidate the structural basis of steady-state proton uptake from solvent into an internal proton transfer pathway. The removal of subunit III from R. sphaeroides CcO makes proton uptake into the D pathway a rate-determining step, such that measurements of the pH dependence of steady-state O2 consumption can be used to compare the rate and functional pKa of proton uptake by D pathways containing different initial proton acceptors. The removal of subunit III also promotes spontaneous suicide inactivation by CcO, greatly shortening its catalytic lifespan. Because the probability of suicide inactivation is controlled by the rate at which the D pathway delivers protons to the active site, measurements of catalytic lifespan provide a second method to compare the relative efficacy of proton uptake by engineered CcO III (−) forms. These simple experimental systems have been used to explore general questions of proton uptake by proteins, such as the functional value of an initial proton acceptor, whether an initial acceptor must be surface-exposed, which side chains will function as initial proton acceptors and whether multiple acceptors can speed proton uptake. PMID:22023935

Measurement of the proton structure function F2 and σγ*ptot at low Q2 and very low x at HERA

NASA Astrophysics Data System (ADS)

Breitweg, J.; Derrick, M.; Krakauer, D.; Magill, S.; Mikunas, D.; Musgrave, B.; Repond, J.; Stanek, R.; Talaga, R. L.; Yoshida, R.; Zhang, H.; Mattingly, M. C. K.; Anselmo, F.; Antonioli, P.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Romeo, G. Cara; Castellini, G.; Cifarelli, L.; Cindolo, F.; Contin, A.; Corradi, M.; de Pasquale, S.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Palmonari, F.; Pesci, A.; Polini, A.; Ricci, F.; Sartorelli, G.; Garcia, Y. Zamora; Zichichi, A.; Amelung, C.; Bornheim, A.; Brock, I.; Coböken, K.; Crittenden, J.; Deffner, R.; Eckert, M.; Grothe, M.; Hartmann, H.; Heinloth, K.; Heinz, L.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Kerger, R.; Paul, E.; Pfeiffer, M.; Rembser, Ch.; Stamm, J.; Wedemeyer, R.; Wieber, H.; Bailey, D. S.; Campbell-Robson, S.; Cottingham, W. N.; Foster, B.; Hall-Wilton, R.; Hayes, M. E.; Heath, G. P.; Heath, H. F.; Piccioni, D.; Roff, D. G.; Tapper, R. J.; Arneodo, M.; Ayad, R.; Capua, M.; Garfagnini, A.; Iannotti, L.; Schioppa, M.; Susinno, G.; Kim, J. Y.; Lee, J. H.; Lim, I. T.; Pac, M. Y.; Caldwell, A.; Cartiglia, N.; Jing, Z.; Liu, W.; Mellado, B.; Parsons, J. A.; Ritz, S.; Sampson, S.; Sciulli, F.; Straub, P. B.; Zhu, Q.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Jakubowski, Z.; Przybycień, M. B.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Jeleń, J.; Kisielewska, D.; Kowalski, T.; Przybycień, M.; Rulikowska-Zarȩbska, E.; Suszycki, L.; Zajac, J.; Duliński, Z.; Kotański, A.; Abbiendi, G.; Bauerdick, L. A. T.; Behrens, U.; Beier, H.; Bienlein, J. K.; Cases, G.; Deppe, O.; Desler, K.; Drews, G.; Fricke, U.; Gilkinson, D. J.; Glasman, C.; Göttlicher, P.; Große-Knetter, J.; Haas, T.; Hain, W.; Hasell, D.; Johnson, K. F.; Kasemann, M.; Koch, W.; Kötz, U.; Kowalski, H.; Labs, J.; Lindemann, L.; Löhr, B.; Löwe, M.; Mańczak, O.; Milewski, J.; Monteiro, T.; Ng, J. S. T.; Notz, D.; Ohrenberg, K.; Park, I. H.; Pellegrino, A.; Pelucchi, F.; Piotrzkowski, K.; Roco, M.; Rohde, M.; Roldán, J.; Ryan, J. J.; Savin, A. A.; Schneekloth, U.; Selonke, F.; Surrow, B.; Tassi, E.; Voß, T.; Westphal, D.; Wolf, G.; Wollmer, U.; Youngman, C.; Żarnecki, A. F.; Zeuner, W.; Burow, B. D.; Grabosch, H. J.; Meyer, A.; Schlenstedt, S.; Barbagli, G.; Gallo, E.; Pelfer, P.; Maccarrone, G.; Votano, L.; Bamberger, A.; Eisenhardt, S.; Markun, P.; Trefzger, T.; Wölfle, S.; Bromley, J. T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Saxon, D. H.; Sinclair, L. E.; Strickland, E.; Utley, M. L.; Waugh, R.; Wilson, A. S.; Bohnet, I.; Gendner, N.; Holm, U.; Meyer-Larsen, A.; Salehi, H.; Wick, K.; Gladilin, L. K.; Horstmann, D.; Kçira, D.; Klanner, R.; Lohrmann, E.; Poelz, G.; Schott, W.; Zetsche, F.; Bacon, T. C.; Butterworth, I.; Cole, J. E.; Harris, V. L.; Howell, G.; Hung, B. H. Y.; Lamberti, L.; Long, K. R.; Miller, D. B.; Pavel, N.; Prinias, A.; Sedgbeer, J. K.; Sideris, D.; Whitfield, A. F.; Mallik, U.; Wang, S. M.; Wu, J. T.; Cloth, P.; Filges, D.; Fleck, J. I.; Ishii, T.; Kuze, M.; Nakao, M.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; An, S. H.; Lee, S. B.; Nam, S. W.; Park, H. S.; Park, S. K.; Barreiro, F.; Fernández, J. P.; García, G.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; Martínez, M.; del Peso, J.; Puga, J.; Terrón, J.; de Trocóniz, J. F.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Murray, W. N.; Ochs, A.; Riveline, M.; Stairs, D. G.; St-Laurent, M.; Ullmann, R.; Tsurugai, T.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Golubkov, Yu. A.; Khein, L. A.; Korotkova, N. A.; Korzhavina, I. A.; Kuzmin, V. A.; Lukina, O. Yu.; Proskuryakov, A. S.; Shcheglova, L. M.; Solomin, A. N.; Zotkin, S. A.; Bokel, C.; Botje, M.; Brümmer, N.; Chlebana, F.; Engelen, J.; Kooijman, P.; van Sighem, A.; Tiecke, H.; Tuning, N.; Verkerke, W.; Vossebeld, J.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Gilmore, J.; Ginsburg, C. M.; Kim, C. L.; Ling, T. Y.; Nylander, P.; Romanowski, T. A.; Blaikley, H. E.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Devenish, R. C. E.; Edmonds, J. K.; Harnew, N.; Lancaster, M.; McFall, J. D.; Nath, C.; Noyes, V. A.; Quadt, A.; Ruske, O.; Tickner, J. R.; Uijterwaal, H.; Walczak, R.; Waters, D. S.; Bertolin, A.; Brugnera, R.; Carlin, R.; dal Corso, F.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Feild, R. G.; Oh, B. Y.; Okrasiński, J. R.; Whitmore, J. J.; Iga, Y.; D'Agostini, G.; Marini, G.; Nigro, A.; Raso, M.; Hart, J. C.; McCubbin, N. A.; Shah, T. P.; Epperson, D.; Heusch, C.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Williams, D. C.; Schwarzer, O.; Walenta, A. H.; Abramowicz, H.; Briskin, G.; Dagan, S.; Doeker, T.; Kananov, S.; Levy, A.; Abe, T.; Fusayasu, T.; Inuzuka, M.; Nagano, K.; Suzuki, I.; Umemori, K.; Yamashita, T.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Matsushita, T.; Yamauchi, K.; Cirio, R.; Costa, M.; Ferrero, M. I.; Maselli, S.; Monaco, V.; Peroni, C.; Petrucci, M. C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Brkic, M.; Fagerstroem, C.-P.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Polenz, S.; Sampson, C. R.; Simmons, D.; Teuscher, R. J.; Butterworth, J. M.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Sutton, M. R.; Lu, B.; Mo, L. W.; Ciborowski, J.; Grzelak, G.; Kasprzak, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Pawlak, R.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Adamus, M.; Coldewey, C.; Eisenberg, Y.; Hochman, D.; Karshon, U.; Revel, D.; Badgett, W. F.; Chapin, D.; Cross, R.; Dasu, S.; Foudas, C.; Loveless, R. J.; Mattingly, S.; Reeder, D. D.; Smith, W. H.; Vaiciulis, A.; Wodarczyk, M.; Bhadra, S.; Frisken, W. R.; Khakzad, M.; Schmidke, W. B.

1997-02-01

A small electromagnetic sampling calorimeter, installed in the ZEUS experiment in 1995, significantly enhanced the acceptance for very low x and low Q2 inelastic neutral current scattering, e+p -> e+X, at HERA. A measurement of the proton structure function F2 and the total virtual photon-proton (γ*p) cross-section is presented for 0.11 <= Q2 <= 0.65 GeV2 and 2 × 10-6 <= x <= 6 × 10-5, corresponding to a range in the γ*p c.m. energy of 100 <= W <= 230 GeV. Comparisons with various models are also presented.

Resolving the negative potential side (n-side) water-accessible proton pathway of F-type ATP synthase by molecular dynamics simulations.

PubMed

Gohlke, Holger; Schlieper, Daniel; Groth, Georg

2012-10-19

The rotation of F(1)F(o)-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane F(o) domain, which is coupled to the ATP-producing F(1) domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the "locked" and "open" conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F(1)F(o)-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode.

Simulated infrared spectra of triflic acid during proton dissociation.

PubMed

Laflamme, Patrick; Beaudoin, Alexandre; Chapaton, Thomas; Spino, Claude; Soldera, Armand

2012-05-05

Vibrational analysis of triflic acid (TfOH) at different water uptakes was conducted. This molecule mimics the sulfonate end of the Nafion side-chain. As the proton leaves the sulfonic acid group, structural changes within the Nafion side-chain take place. They are revealed by signal shifts in the infrared spectrum. Molecular modeling is used to follow structural modifications that occur during proton dissociation. To confirm the accuracy of the proposed structures, infrared spectra were computed via quantum chemical modeling based on density functional theory. The requirement to use additional diffuse functions in the basis set is discussed. Comparison between simulated infrared spectra of 1 and 2 acid molecules with different water contents and experimental data was performed. An accurate description of infrared spectra for systems containing 2 TfOH was obtained. Copyright © 2012 Wiley Periodicals, Inc.

Structural characteristics of hydrated protons in the conductive channels: effects of confinement and fluorination studied by molecular dynamics simulation.

PubMed

Zhang, Ning; Song, Yuechun; Ruan, Xuehua; Yan, Xiaoming; Liu, Zhao; Shen, Zhuanglin; Wu, Xuemei; He, Gaohong

2016-09-21

The relationship between the proton conductive channel and the hydrated proton structure is of significant importance for understanding the deformed hydrogen bonding network of the confined protons which matches the nanochannel. In general, the structure of hydrated protons in the nanochannel of the proton exchange membrane is affected by several factors. To investigate the independent effect of each factor, it is necessary to eliminate the interference of other factors. In this paper, a one-dimensional carbon nanotube decorated with fluorine was built to investigate the independent effects of nanoscale confinement and fluorination on the structural properties of hydrated protons in the nanochannel using classical molecular dynamics simulation. In order to characterize the structure of hydrated protons confined in the channel, the hydrogen bonding interaction between water and the hydrated protons has been studied according to suitable hydrogen bond criteria. The hydrogen bond criteria were proposed based on the radial distribution function, angle distribution and pair-potential energy distribution. It was found that fluorination leads to an ordered hydrogen bonding structure of the hydrated protons near the channel surface, and confinement weakens the formation of the bifurcated hydrogen bonds in the radial direction. Besides, fluorination lowers the free energy barrier of hydronium along the nanochannel, but slightly increases the barrier for water. This leads to disintegration of the sequential hydrogen bond network in the fluorinated CNTs with small size. In the fluorinated CNTs with large diameter, the lower degree of confinement produces a spiral-like sequential hydrogen bond network with few bifurcated hydrogen bonds in the central region. This structure might promote unidirectional proton transfer along the channel without random movement. This study provides the cooperative effect of confinement dimension and fluorination on the structure and hydrogen bonding of the slightly acidic water in the nanoscale channel.

Spying on the neighbors' pool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xantheas, S. S.

2016-12-01

The structure and properties of the aqueous proton is of fundamental interest in many areas of chemistry and biology. Acids and bases are molecules that are able to transfer (donate / accept) a proton according to Brønsted and Lowry, a process that was further explained by Lewis in terms of changes in their electronic structure in an attempt to offer a generalization of the Arrhenius theory. Simple proton transfers or the ones coupled to an electron transfer determine speciation, valence and reactivity in aqueous media and explain electrochemical processes, while voltage-gated proton channels have severe implications to the function ofmore » a number of tissues and species.« less

Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase

PubMed Central

Pisliakov, Andrei V.; Hino, Tomoya; Shiro, Yoshitsugu; Sugita, Yuji

2012-01-01

Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb 3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. PMID:22956904

Measurement of the neutron F2 structure function via spectator tagging with CLAS.

PubMed

Baillie, N; Tkachenko, S; Zhang, J; Bosted, P; Bültmann, S; Christy, M E; Fenker, H; Griffioen, K A; Keppel, C E; Kuhn, S E; Melnitchouk, W; Tvaskis, V; Adhikari, K P; Adikaram, D; Aghasyan, M; Amaryan, M J; Anghinolfi, M; Arrington, J; Avakian, H; Baghdasaryan, H; Battaglieri, M; Biselli, A S; Branford, D; Briscoe, W J; Brooks, W K; Burkert, V D; Carman, D S; Celentano, A; Chandavar, S; Charles, G; Cole, P L; Contalbrigo, M; Crede, V; D'Angelo, A; Daniel, A; Dashyan, N; De Vita, R; De Sanctis, E; Deur, A; Dey, B; Djalali, C; Dodge, G; Domingo, J; Doughty, D; Dupre, R; Dutta, D; Ent, R; Egiyan, H; El Alaoui, A; El Fassi, L; Elouadrhiri, L; Eugenio, P; Fedotov, G; Fegan, S; Fradi, A; Gabrielyan, M Y; Gevorgyan, N; Gilfoyle, G P; Giovanetti, K L; Girod, F X; Gohn, W; Golovatch, E; Gothe, R W; Graham, L; Guegan, B; Guidal, M; Guler, N; Guo, L; Hafidi, K; Heddle, D; Hicks, K; Holtrop, M; Hungerford, E; Hyde, C E; Ilieva, Y; Ireland, D G; Ispiryan, M; Isupov, E L; Jawalkar, S S; Jo, H S; Kalantarians, N; Khandaker, M; Khetarpal, P; Kim, A; Kim, W; King, P M; Klein, A; Klein, F J; Klimenko, A; Kubarovsky, V; Kuleshov, S V; Kvaltine, N D; Livingston, K; Lu, H Y; MacGregor, I J D; Mao, Y; Markov, N; McKinnon, B; Mineeva, T; Morrison, B; Moutarde, H; Munevar, E; Nadel-Turonski, P; Ni, A; Niccolai, S; Niculescu, I; Niculescu, G; Osipenko, M; Ostrovidov, A I; Pappalardo, L; Park, K; Park, S; Pasyuk, E; Anefalos Pereira, S; Pisano, S; Pozdniakov, S; Price, J W; Procureur, S; Prok, Y; Protopopescu, D; Raue, B A; Ricco, G; Rimal, D; Ripani, M; Rosner, G; Rossi, P; Sabatié, F; Saini, M S; Salgado, C; Schott, D; Schumacher, R A; Seder, E; Sharabian, Y G; Sober, D I; Sokhan, D; Stepanyan, S; Stepanyan, S S; Stoler, P; Strauch, S; Taiuti, M; Tang, W; Ungaro, M; Vineyard, M F; Voutier, E; Watts, D P; Weinstein, L B; Weygand, D P; Wood, M H; Zana, L; Zhao, B

2012-04-06

We report on the first measurement of the F(2) structure function of the neutron from the semi-inclusive scattering of electrons from deuterium, with low-momentum protons detected in the backward hemisphere. Restricting the momentum of the spectator protons to ≲100 MeV/c and their angles to ≳100° relative to the momentum transfer allows an interpretation of the process in terms of scattering from nearly on-shell neutrons. The F(2)(n) data collected cover the nucleon-resonance and deep-inelastic regions over a wide range of Bjorken x for 0.65

Hydroxide diffuses slower than hydronium in water because its solvated structure inhibits correlated proton transfer

NASA Astrophysics Data System (ADS)

Chen, Mohan; Zheng, Lixin; Santra, Biswajit; Ko, Hsin-Yu; DiStasio, Robert A., Jr.; Klein, Michael L.; Car, Roberto; Wu, Xifan

2018-03-01

Proton transfer via hydronium and hydroxide ions in water is ubiquitous. It underlies acid-base chemistry, certain enzyme reactions, and even infection by the flu. Despite two centuries of investigation, the mechanism underlying why hydroxide diffuses slower than hydronium in water is still not well understood. Herein, we employ state-of-the-art density-functional-theory-based molecular dynamics—with corrections for non-local van der Waals interactions, and self-interaction in the electronic ground state—to model water and hydrated water ions. At this level of theory, we show that structural diffusion of hydronium preserves the previously recognized concerted behaviour. However, by contrast, proton transfer via hydroxide is less temporally correlated, due to a stabilized hypercoordination solvation structure that discourages proton transfer. Specifically, the latter exhibits non-planar geometry, which agrees with neutron-scattering results. Asymmetry in the temporal correlation of proton transfer leads to hydroxide diffusing slower than hydronium.

Determination of the parton distributions and structure functions of the proton from neutrino and antineutrino reactions on hydrogen and deuterium

NASA Astrophysics Data System (ADS)

Jones, G. T.; Jones, R. W. L.; Kennedy, B. W.; Klein, H.; Morrison, D. R. O.; Wachsmuth, H.; Miller, D. B.; Mobayyen, M. M.; Wainstein, S.; Aderholz, M.; Hantke, D.; Katz, U. F.; Kern, J.; Schmitz, N.; Wittek, W.; Borner, H. P.; Myatt, G.; Cooper-Sarkar, A. M.; Guy, J.; Venus, W.; Bullock, F. W.; Burke, S.

1994-12-01

This analysis is based on data from neutrino and antineutrino scattering on hydrogen and deuterium, obtained with BEBC in the (anti) neutrino wideband beam of the CERN SPS. The parton momentum distributions in the proton and the proton structure functions are determined in the range 0.01

The emerging structure of vacuolar ATPases.

PubMed

Drory, Omri; Nelson, Nathan

2006-10-01

Bioenergetics and physiology of primary pumps have been revitalized by new insights into the mechanism of energizing biomembranes. Structural information is becoming available, and the three-dimensional structure of F-ATPase is being resolved. The growing understanding of the fundamental mechanism of energy coupling may revolutionize our view of biological processes. The F- and V-ATPases (vacuolar-type ATPase) exhibit a common mechanical design in which nucleotide-binding on the catalytic sector, through a cycle of conformation changes, drives the transmembrane passage of protons by turning a membrane-embedded rotor. This motor can run in forward or reverse directions, hydrolyzing ATP as it pumps protons uphill or creating ATP as protons flow downhill. In contrast to F-ATPases, whose primary function in eukaryotic cells is to form ATP at the expense of the proton-motive force (pmf), V-ATPases function exclusively as an ATP-dependent proton pump. The pmf generated by V-ATPases in organelles and membranes of eukaryotic cells is utilized as a driving force for numerous secondary transport processes. V- and F-ATPases have similar structure and mechanism of action, and several of their subunits evolved from common ancestors. Electron microscopy studies of V-ATPase revealed its general structure at low resolution. Recently, several structures of V-ATPase subunits, solved by X-ray crystallography with atomic resolution, were published. This, together with electron microscopy low-resolution maps of the whole complex, and biochemistry cross-linking experiments, allows construction of a structural model for a part of the complex that may be used as a working hypothesis for future research.

Proton transport through aqueous Nafion membrane

NASA Astrophysics Data System (ADS)

Son, D. N.; Kasai, H.

2009-08-01

We introduce a new model for proton transport through a single proton-conducting channel of an aqueous Nafion membrane based on a mechanism in which protons move under electrostatic effect provided by the sulfonate ( SO3 -groups of the Nafion side chains, the spin effect of active components, the hydrogen bonding effect with water molecules, and the screening effect of water media. This model can describe the proton transport within various levels of humidification ranging from the low humidity to the high humidity as a function of operating temperature. At low humidity, this model approaches to the so-called surface mechanism, while at high humidity, it approaches the well-known Grotthuss one. Proton motion is considered as the transfer from cluster to cluster under a potential energy. A proton-proton interaction is comprised in the calculation. Using Green function method, we obtained the proton current as a function of the Nafion membrane temperature. We found that the lower the temperature, the higher the proton current transfer through the Nafion membrane in low temperatures compared to the critical point 10K, which separates magnetic regime from non-magnetic regime. The increasing of proton current at very low temperatures is attributed to the spin effect. As the membrane temperature is higher than 40 ° C , the decreasing of proton current is attributed to the loss of water uptake and the polymer contraction. The results of this study are qualitatively in good agreement with experiments. The expression for the critical temperature is also presented as a function of structural and tunable parameters, and interpreted by experimental data. in here

Quantum molecular dynamics study on the proton exchange, ionic structures, and transport properties of warm dense hydrogen-deuterium mixtures

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Zhi-Guo; Dai, Jia-Yu; Chen, Qi-Feng; Chen, Xiang-Rong

2018-06-01

Comprehensive knowledge of physical properties such as equation of state (EOS), proton exchange, dynamic structures, diffusion coefficients, and viscosities of hydrogen-deuterium mixtures with densities from 0.1 to 5 g /cm3 and temperatures from 1 to 50 kK has been presented via quantum molecular dynamics (QMD) simulations. The existing multi-shock experimental EOS provides an important benchmark to evaluate exchange-correlation functionals. The comparison of simulations with experiments indicates that a nonlocal van der Waals density functional (vdW-DF1) produces excellent results. Fraction analysis of molecules using a weighted integral over pair distribution functions was performed. A dissociation diagram together with a boundary where the proton exchange (H2+D2⇌2 HD ) occurs was generated, which shows evidence that the HD molecules form as the H2 and D2 molecules are almost 50% dissociated. The mechanism of proton exchange can be interpreted as a process of dissociation followed by recombination. The ionic structures at extreme conditions were analyzed by the effective coordination number model. High-order cluster, circle, and chain structures can be founded in the strongly coupled warm dense regime. The present QMD diffusion coefficient and viscosity can be used to benchmark two analytical one-component plasma (OCP) models: the Coulomb and Yukawa OCP models.

NMR studies on the structure and dynamics of lac operator DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, S.C.

Nuclear Magnetic Resonance spectroscopy was used to elucidate the relationships between structure, dynamics and function of the gene regulatory sequence corresponding to the lactose operon operator of Escherichia coli. The length of the DNA fragments examined varied from 13 to 36 base pair, containing all or part of the operator sequence. These DNA fragments are either derived genetically or synthesized chemically. Resonances of the imino protons were assigned by one dimensional inter-base pair nuclear Overhauser enhancement (NOE) measurements. Imino proton exchange rates were measured by saturation recovery methods. Results from the kinetic measurements show an interesting dynamic heterogeneity with amore » maximum opening rate centered about a GTG/CAC sequence which correlates with the biological function of the operator DNA. This particular three base pair sequence occurs frequently and often symmetrically in prokaryotic nd eukaryotic DNA sites where one anticipates specific protein interaction for gene regulation. The observed sequence dependent imino proton exchange rate may be a reflection of variation of the local structure of regulatory DNA. The results also indicate that the observed imino proton exchange rates are length dependent.« less

High performance, durable polymers including poly(phenylene)

DOEpatents

Fujimoto, Cy; Pratt, Harry; Anderson, Travis Mark

2017-02-28

The present invention relates to functionalized polymers including a poly(phenylene) structure. In some embodiments, the polymers and copolymers of the invention include a highly localized concentration of acidic moieties, which facilitate proton transport and conduction through networks formed from these polymers. In addition, the polymers can include functional moieties, such as electron-withdrawing moieties, to protect the polymeric backbone, thereby extending its durability. Such enhanced proton transport and durability can be beneficial for any high performance platform that employs proton exchange polymeric membranes, such as in fuel cells or flow batteries.

Fine Structure of Beta Decay Strength Function and Anisotropy of Isovector Nuclear Dencity Component Oscillations in Deformed Nuclei

NASA Astrophysics Data System (ADS)

Izosimov, I. N.; Solnyshkin, A. A.; Khushvaktov, J. H.; Vaganov, Yu. A.

2018-05-01

The experimental measurement data on the fine structure of beta-decay strength function S β( E) in spherical, transitional, and deformed nuclei are analyzed. Modern high-resolution nuclear spectroscopy methods made it possible to identify the splitting of peaks in S β( E) for deformed nuclei. By analogy with splitting of the peak of E1 giant dipole resonance (GDR) in deformed nuclei, the peaks in S β( E) are split into two components from the axial nuclear deformation. In this report, the fine structure of S β( E) is discussed. Splitting of the peaks connected with the oscillations of neutrons against protons (E1GDR), of proton holes against neutrons (peaks in S β( E) of β+/ EC-decay), and of protons against neutron holes (peaks in S β( E) of β--decay) is discussed.

Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE

PubMed Central

Wisedchaisri, Goragot; Park, Min-Sun; Iadanza, Matthew G.; Zheng, Hongjin; Gonen, Tamir

2014-01-01

The major facilitator superfamily (MFS) is the largest collection of structurally related membrane proteins that transport a wide array of substrates. The proton-coupled sugar transporter XylE is the first member of the MFS that has been structurally characterized in multiple transporting conformations, including both the outward and inward-facing states. Here we report the crystal structure of XylE in a new inward-facing open conformation, allowing us to visualize the rocker-switch movement of the N-domain against the C-domain during the transport cycle. Using molecular dynamics simulation, and functional transport assays, we describe the movement of XylE that facilitates sugar translocation across a lipid membrane and identify the likely candidate proton-coupling residues as the conserved Asp27 and Arg133. This study addresses the structural basis for proton-coupled substrate transport and release mechanism for the sugar porter family of proteins. PMID:25088546

IR spectrum of the protonated neurotransmitter 2-phenylethylamine: dispersion and anharmonicity of the NH3(+)-π interaction.

PubMed

Bouchet, Aude; Schütz, Markus; Chiavarino, Barbara; Crestoni, Maria Elisa; Fornarini, Simonetta; Dopfer, Otto

2015-10-21

The structure and dynamics of the highly flexible side chain of (protonated) phenylethylamino neurotransmitters are essential for their function. The geometric, vibrational, and energetic properties of the protonated neutrotransmitter 2-phenylethylamine (H(+)PEA) are characterized in the N-H stretch range by infrared photodissociation (IRPD) spectroscopy of cold ions using rare gas tagging (Rg = Ne and Ar) and anharmonic calculations at the B3LYP-D3/(aug-)cc-pVTZ level including dispersion corrections. A single folded gauche conformer (G) protonated at the basic amino group and stabilized by an intramolecular NH(+)-π interaction is observed. The dispersion-corrected density functional theory calculations reveal the important effects of dispersion on the cation-π interaction and the large vibrational anharmonicity of the NH3(+) group involved in the NH(+)-π hydrogen bond. They allow for assigning overtone and combination bands and explain anomalous intensities observed in previous IR multiple-photon dissociation spectra. Comparison with neutral PEA reveals the large effects of protonation on the geometric and electronic structure.

Analytic derivation of the next-to-leading order proton structure function F2p(x ,Q2) based on the Laplace transformation

NASA Astrophysics Data System (ADS)

Khanpour, Hamzeh; Mirjalili, Abolfazl; Tehrani, S. Atashbar

2017-03-01

An analytical solution based on the Laplace transformation technique for the Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution equations is presented at next-to-leading order accuracy in perturbative QCD. This technique is also applied to extract the analytical solution for the proton structure function, F2p(x ,Q2) , in the Laplace s space. We present the results for the separate parton distributions of all parton species, including valence quark densities, the antiquark and strange sea parton distribution functions (PDFs), and the gluon distribution. We successfully compare the obtained parton distribution functions and the proton structure function with the results from GJR08 [Gluck, Jimenez-Delgado, and Reya, Eur. Phys. J. C 53, 355 (2008)], 10.1140/epjc/s10052-007-0462-9 and KKT12 [Khanpour, Khorramian, and Tehrani, J. Phys. G 40, 045002 (2013)], 10.1088/0954-3899/40/4/045002 parametrization models as well as the x -space results using QCDnum code. Our calculations show a very good agreement with the available theoretical models as well as the deep inelastic scattering (DIS) experimental data throughout the small and large values of x . The use of our analytical solution to extract the parton densities and the proton structure function is discussed in detail to justify the analysis method, considering the accuracy and speed of calculations. Overall, the accuracy we obtain from the analytical solution using the inverse Laplace transform technique is found to be better than 1 part in 104 to 105. We also present a detailed QCD analysis of nonsinglet structure functions using all available DIS data to perform global QCD fits. In this regard we employ the Jacobi polynomial approach to convert the results from Laplace s space to Bjorken x space. The extracted valence quark densities are also presented and compared to the JR14, MMHT14, NNPDF, and CJ15 PDFs sets. We evaluate the numerical effects of target mass corrections (TMCs) and higher twist (HT) terms on various structure functions, and compare fits to data with and without these corrections.

The voltage-gated proton channel: a riddle, wrapped in a mystery, inside an enigma

PubMed Central

DeCoursey, Thomas E.

2016-01-01

The main properties of voltage gated proton channels are described, along with what is known about how the channel protein structure accomplishes these functions. Just as protons are unique among ions, proton channels are unique among ion channels. Their four transmembrane helices sense voltage, the pH gradient, and conduct protons exclusively. Selectivity is achieved by the unique ability of H3O+ to protonate an Asp-Arg salt bridge. Pathognomonic sensitivity of gating to the pH gradient ensures channel opening only when acid extrusion will result, which is crucial to most biological functions. An exception occurs in dinoflagellates in which H+ influx through HV1 triggers the bioluminescent flash. Pharmacological interventions that promise to ameliorate cancer, asthma, brain damage in ischemic stroke, Alzheimer’s disease, autoimmune diseases, and numerous other conditions, await future progress. PMID:25964989

A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein†

PubMed Central

Polishchuk, Alexei L.; Lear, James D.; Ma, Chunlong; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.

2010-01-01

The influenza A M2 protein exhibits inwardly rectifying, pH-activated proton transport that saturates at low pH. A comparison of high-resolution structures of the transmembrane domain at high and low pH suggests that pH-dependent conformational changes may facilitate proton conduction by alternately changing the accessibility of the N-terminal and C-terminal regions of the channel as a proton transits through the transmembrane domain. Here, we show that M2 functionally reconstituted in liposomes populates at least three different conformational states over a physiologically relevant pH range, with transition midpoints that are consistent with previously reported His37 pKas. We then develop and test two similar, quantitative mechanistic models of proton transport, where protonation shifts the equilibrium between structural states having different proton affinities and solvent accessibilities. The models account well for a collection of experimental data sets over a wide range of pHs and voltages and require only a small number of adjustable parameters to accurately describe the data. While the kinetic models do not require any specific conformation for the protein, they nevertheless are consistent with a large body of structural information based on high-resolution NMR and crystallographic structures, optical spectroscopy, and MD calculations. PMID:20968306

Test of New Readout Electronics for the BONuS12 Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ehrhart, Mathieu

For decades, electron-proton scattering experiments have been providing a large amount of data on the proton structure function. However, because of the instability of free neutrons, fewer experiments have been able to study the neutron structure function. The BONuS collaboration at Jefferson Laboratory addresses this challenge by scattering electrons off a deuterium target, using a RTPC capable of detecting the low-momentum spectator protons near the target. Events of electrons scattering on almost free neutrons are selected by constraining the spectator protons to very low momenta and very backward scattering angles. In 2005, BONuS successfully measured the neutron structure with scatteringmore » electrons of up to 5.3 GeV energy. An extension of this measurement has been approved using the newly upgraded 12 GeV electron beam and CLAS12 (CEBAF Large Acceptance Spectrometer). For this new set of measurements, a new RTPC detector using GEM trackers is being developed to allow measurements of spectator protons with momenta as low as 70 MeV/c. The new RTPC will use a new readout electronic system, which is also used by other trackers in CLAS12. This thesis will present the first tests of this electronics using a previously built RTPC of similar design.« less

Test of New Readout Electronics for the Bonus12 Experiment

NASA Astrophysics Data System (ADS)

Ehrhart, Mathieu

For decades, electron-proton scattering experiments have been providing a large amount of data on the proton structure function. However, because of the instability of free neutrons, fewer experiments have been able to study the neutron structure function. The BONuS collaboration at Jefferson Laboratory addresses this challenge by scattering electrons off a deuterium target, using a RTPC capable of detecting the low-momentum spectator protons near the target. Events of electrons scattering on almost free neutrons are selected by constraining the spectator protons to very low momenta and very backward scattering angles. In 2005, BONuS successfully measured the neutron structure with scattering electrons of up to 5.3 GeV energy. An extension of this measurement has been approved using the newly upgraded 12 GeV electron beam and CLAS12 (CEBAF Large Acceptance Spectrometer). For this new set of measurements, a new RTPC detector using GEM trackers is being developed to allow measurements of spectator protons with momenta as low as 70 MeV/c. The new RTPC will use a new readout electronic system, which is also used by other trackers in CLAS12. This thesis will present the first tests of this electronics using a previously built RTPC of similar design.

A measurement of the proton structure function F2( x, Q2)

NASA Astrophysics Data System (ADS)

Ahmed, T.; Aid, S.; Akhundov, A.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bergstein, H.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegge, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Danilov, M.; Dau, W. D.; Daum, K.; David, M.; Deffur, E.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, V.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herma, R.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Linsel, F.; Lipinski, J.; List, B.; Loch, P.; Lohmander, H.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Savitsky, M.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Seehausen, U.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Soloviev, Y.; Spiekermann, J.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taylor, R. E.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Vecko, M.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Winde, M.; Winter, G.-G.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

A measurement of the proton structure function F2( x, Q2) is reported for momentum transfers squared Q2 between 4.5 GeV 2 and 1600 GeV 2 and for Bjorken x between 1.8 × 10 -14 and 0.13 using data collected by the HERA experiment H1 in 1993. It is observed that F2 increases significantly with decreasing x, confirming our previous measurement made with one tenth of the data available in this analysis. The Q2 dependence is approximately logarithmic over the full kinematic range covered. The subsample of deep inelastic events with a large pseudo-rapidity gap in the hadronic energy flow close to the proton remnant is used to measure the "diffractive" contribution to F2.

Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents

DOE PAGES

McNally, Joshua S.; Noll, Bruce; Orme, Christopher J.; ...

2015-05-04

Here, a density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An x-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction withmore » the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo-six membered ring which included both protons.« less

Intramolecular cation-π interactions in protonated phenylalanine derivatives.

PubMed

Fu, Weiqiang; Carr, Patrick J J; Lecours, Michael J; Burt, Michael; Marta, Rick A; Steinmetz, Vincent; Fillion, Eric; McMahon, Terrance B; Hopkins, W Scott

2016-12-21

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm -1 region show that protonation is localized on the amine group in all cases. Intramolecular cation-π interactions between the ammonium group and the phenyl ring heavily influence molecular geometries and properties such as gas phase basicity and proton affinity. By varying substituents on the phenyl ring, one can sensitively tune the cation-π interaction and, therefore, the molecular structure and properties. Variations in molecular structures and properties as a function of phenyl ring substitution are shown to correlate with substituent Hammett parameters.

Density Functional Calculations for the Neutron Star Matter at Subnormal Density

NASA Astrophysics Data System (ADS)

Kashiwaba, Yu; Nakatsukasa, Takashi

The pasta phases of nuclear matter, whose existence is suggested at low density, may influence observable properties of neutron stars. In order to investigate properties of the neutron star matter, we calculate self-consistent solutions for the ground states of slab-like phase using the microscopic density functional theory with Bloch wave functions. The calculations are performed at each point of fixed average density and proton fraction (\\bar{ρ },Yp), varying the lattice constant of the unit cell. For small Yp values, the dripped neutrons emerge in the ground state, while the protons constitute the slab (crystallized) structure. The shell effect of protons affects the thickness of the slab nuclei.

Determination of the longitudinal proton structure function FL(x,Q2) at low x

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arndt, C.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Blümlein, J.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; de Roeck, A.; de Wolf, E. A.; Dirkmann, M.; Dixon, P.; di Nezza, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Erdmann, W.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krehbiel, H.; Krücker, D.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Levonian, S.; Lindström, G.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Noyes, G. W.; Nunnemann, T.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Reinshagen, S.; Riemersma, S.; Rick, H.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steiner, H.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tutas, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; van Esch, P.; van Mechelen, P.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wünsch, E.; ŽáČek, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; Zuber, K.; Zurnedden, M.

1997-02-01

A measurement of the inclusive cross section for the deep-inelastic scattering of positrons off protons at HERA is presented at momentum transfers 8.5 <= Q2 <= 35 GeV2 and large inelasticity = 0.7, i.e. for the Bjorken-x range 0.00013 <= x <= 0.00055. Using a next-to-leading order QCD fit to the structure function F2 at lower y values, the contribution of F2 to the measured cross section at high y is calculated and, by subtraction, the longitudinal structure function FL is determined for the first time with an average value of FL = 0.52+/-0.03 (stat)+0.25-0.22 (syst) at Q2 = 15.4 GeV2 and x = 0.000243.

NMR and rotational angles in solution conformation of polypeptides

NASA Astrophysics Data System (ADS)

Bystrov, V. F.

1985-01-01

Professor San-Ichiro Mizushima and Professor Yonezo Morino's classical contributions provided unique means and firm basis for understanding of conformational states and internal rotation in polypeptide molecules. Now the NMR spectroscopy is the best choice to study molecular conformation, mechanism of action and structure-functional relationships of peptide and proteins in solution under conditions approaching those of their physiological environments. Crucial details of spatial structure and interactions of these molecules in solution are revealed by using proton-proton and carbon-proton vicinal coupling constants, proton nuclear Overhauser effect and spectral perturbation techniques. The results of NMR conformational analysis are presented for valinomycin "bracelet", gramicidin A double helices, honey-bee neurotoxin apamin, scorpion insectotoxins and snake neurotoxins of long and short types.

A proton wire and water channel revealed in the crystal structure of isatin hydrolase.

PubMed

Bjerregaard-Andersen, Kaare; Sommer, Theis; Jensen, Jan K; Jochimsen, Bjarne; Etzerodt, Michael; Morth, J Preben

2014-08-01

The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolase converts isatin to isatinate and belongs to a novel family of metalloenzymes that include the bacterial kynurenine formamidase. The product state, mimicked by bound thioisatinate, reveals a water molecule that bridges the thioisatinate to a proton wire in an adjacent water channel and thus allows the proton released by the reaction to escape only when the product is formed. The functional proton wire present in isatin hydrolase isoform b represents a unique catalytic feature common to all hydrolases is here trapped and visualized for the first time. The local molecular environment required to coordinate thioisatinate allows stronger and more confident identification of orthologous genes encoding isatin hydrolases within the prokaryotic kingdom. The isatin hydrolase orthologues found in human gut bacteria raise the question as to whether the indole-3-acetic acid degradation pathway is present in human gut flora. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Characterizing the proton loading site in cytochrome c oxidase.

PubMed

Lu, Jianxun; Gunner, M R

2014-08-26

Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, Cu(B), Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1-4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.

Characterizing the proton loading site in cytochrome c oxidase

PubMed Central

Lu, Jianxun; Gunner, M. R.

2014-01-01

Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, CuB, Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1–4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded. PMID:25114210

Polarization phenomena in quantum chromodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brodsky, S.J.

1994-12-01

The author discusses a number of interrelated hadronic spin effects which test fundamental features of perturbative and nonperturbative QCD. For example, the anomalous magnetic moment of the proton and the axial coupling g{sub A} on the nucleon are shown to be related to each other for fixed proton radius, independent of the form of the underlying three-quark relativistic quark wavefunction. The renormalization scale and scheme ambiguities for the radiative corrections to the Bjorken sum rule for the polarized structure functions can be eliminated by using commensurate scale relations with other observables. Other examples include (a) new constraints on the shapemore » and normalization of the polarized quark and gluon structure functions of the proton at large and small x{sub bj}; (b) consequences of the principle of hadron retention in high x{sub F} inclusive reactions; (c) applications of hadron helicity conservation to high momentum transfer exclusive reactions; and (d) the dependence of nuclear structure functions and shadowing on virtual photon polarization. The author also discusses the implications of a number of measurements which are in striking conflict with leading-twist perturbative QCD predictions, such as the extraordinarily large spin correlation A{sub NN} observed in large angle proton-proton scattering, the anomalously large {rho}{pi} branching ratio of the J/{psi}, and the rapidly changing polarization dependence of both J/{psi} and continuum lepton pair hadroproduction observed at large x{sub F}. The azimuthal angular dependence of the Drell-Yan process is shown to be highly sensitive to the projectile distribution amplitude, the fundamental valence light-cone wavefunction of the hadron.« less

A measurement of the proton structure function F2( x, Q2) at low x and low Q2 at HERA

NASA Astrophysics Data System (ADS)

Adloff, C.; Aid, S.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Bassler, U.; Beck, H. P.; Beck, M.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Borras, K.; Botterweck, F.; Boudry, V.; Bourov, S.; Braemer, A.; Braunschweig, W.; Brisson, V.; Brückner, W.; Bruel, P.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Dollfus, C.; Donovan, K. T.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Gruber, A.; Gruber, C.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jacquet, M.; Jaffre, M.; Janoth, J.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kaufmann, O.; Kausch, M.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Laforge, B.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Levonian, S.; Lindstroem, M.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Walter, T.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Newton, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nowak, G.; Nunnemann, T.; Nyberg-Werther, M.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Prell, S.; Rabbertz, K.; Rädel, G.; Reimer, P.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schoeffel, L.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stöβlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Valĺee, C.; Van Esch, P.; Van Mechelen, P.; Vandenplas, D.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Wallny, R.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1997-02-01

The results of a measurement of the proton structure function F2( x, Q2) and the virtual photon-proton cross section are reported for momentum transfers squared Q2 between 0.35 GeV 2 and 3.5 GeV 2 and for Bjorken- x values down to 6 × 10 -6 using data collected by the HERA experiment H1 in 1995. The data represent an increase in kinematic reach to lower x and Q2 values of about a factor of 5 compared to previous H1 measurements. Including measurements from fixed target experiments the rise of F2 with decreasing x is found to be less steep for the lowest Q2 values measured. Phenomenological models at low Q2 are compared with the data.

Structural and mechanistic basis of proton-coupled metal ion transport in the SLC11/NRAMP family

PubMed Central

Ehrnstorfer, Ines A.; Manatschal, Cristina; Arnold, Fabian M.; Laederach, Juerg; Dutzler, Raimund

2017-01-01

Secondary active transporters of the SLC11/NRAMP family catalyse the uptake of iron and manganese into cells. These proteins are highly conserved across all kingdoms of life and thus likely share a common transport mechanism. Here we describe the structural and functional properties of the prokaryotic SLC11 transporter EcoDMT. Its crystal structure reveals a previously unknown outward-facing state of the protein family. In proteoliposomes EcoDMT mediates proton-coupled uptake of manganese at low micromolar concentrations. Mutants of residues in the transition-metal ion-binding site severely affect transport, whereas a mutation of a conserved histidine located near this site results in metal ion transport that appears uncoupled to proton transport. Combined with previous results, our study defines the conformational changes underlying transition-metal ion transport in the SLC11 family and it provides molecular insight to its coupling to protons. PMID:28059071

Sensors and regulators of intracellular pH.

PubMed

Casey, Joseph R; Grinstein, Sergio; Orlowski, John

2010-01-01

Protons dictate the charge and structure of macromolecules and are used as energy currency by eukaryotic cells. The unique function of individual organelles therefore depends on the establishment and stringent maintenance of a distinct pH. This, in turn, requires a means to sense the prevailing pH and to respond to deviations from the norm with effective mechanisms to transport, produce or consume proton equivalents. A dynamic, finely tuned balance between proton-extruding and proton-importing processes underlies pH homeostasis not only in the cytosol, but in other cellular compartments as well.

Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine.

PubMed

Bythell, Benjamin J; Csonka, István P; Suhai, Sándor; Barofsky, Douglas F; Paizs, Béla

2010-11-25

The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.

Proton transfer from imidazole to chloranil studied by FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Sharma, Amit

2018-05-01

Imidazole is incorporated into many important biological molecules. The most obvious is the amino acid histidine, which has an imidazole side chain. Histidine is present in many proteins and enzymes and plays a vital part in the structure and binding functions of hemoglobin. Therefore it is important to study its proton transfer property. In the present work proton transfer from imidazole to chloranil is investigated by Fourier Transform Infra red Spectroscopy.

Constraints on the large-x d/u ratio from electron--nucleus scattering at x>1

DOE Office of Scientific and Technical Information (OSTI.GOV)

O. Hen, A. Accardi, W. Melnitchouk and E. Piasetzky

2011-12-01

Recently the ratio of neutron to proton structure functions F{sub 2}{sup n}/F{sub 2}{sup p} was extracted from a phenomenological correlation between the strength of the nuclear EMC effect and inclusive electron-nucleus cross section ratios at x > 1. Within conventional models of nuclear smearing, this 'in-medium correction' (IMC) extraction constrains the size of nuclear effects in the deuteron structure functions, from which the neutron structure function F{sub 2}{sup n} is usually extracted. The IMC data determine the resulting proton d/u quark distribution ratio, extrapolated to x = 1, to be 0.23 {+-} 0.09 with a 90% confidence level. This ismore » well below the SU(6) symmetry limit of 1/2 and significantly above the scalar diquark dominance limit of 0.« less

NMR Stratagems for the Study of Multiple Kinetic Hydrogen/Deuterium Isotope Effectsof Proton Exchange. Example: Di-p-fluorophenylformamidine/THF

NASA Astrophysics Data System (ADS)

Limbach, Hans-Heinrich; Meschede, Ludger; Scherer, Gerd

1989-05-01

Stratagems are presented for the determination of kinetic isotope effects of proton exchange reactions by dynamic NMR spectroscopy. In such experiments, lineshape analyses and/or polarization transfer experiments are performed on the exchanging protons or deuterons as well as on remote spins, as a function of the deuterium fraction in the mobile proton sites. These methods are NMR analogs of previous proton inventory techniques involving classical kinetic methods. A theory is developed in order to derive the kinetic isotope effects as well as the number of transferred protons from the experimental NMR spectra. The technique is then applied to the problem of proton exchange in the system 15N,15N'-di-p-fluorophenylibrmamidine, a nitrogen analog of formic acid, dissolved in tetrahydrofuran-d8 (THF). DFFA forms two conformers in THF to which s-trans and s-cis structures have been assigned. Only the s-trans conformer is able to dimerize and exchange protons. Lineshape simulations and magnetization transfer experiments were carried out at 189,2 K, at a concentration of 0.02 mol l-1, as a function of the deuterium fraction D in the 1H-15N sites. Using 1H NMR spectroscopy, a linear dependence of the inverse proton lifetimes on D was observed. From this it was concluded that two protons are transported in the rate limiting step of the proton exchange. This result is expected for a double proton transfer in an s-trans dimer with a cyclic structure. The full kinetic HH/HD/DD isotope effects of 233:11:1 at 189 K were determined through 19F NMR experiments on the same samples. The deviation from the rule of geometric mean, although substantial, is much smaller than found in previous studies of intramolecular HH transfer reactions. Possible causes of this effect are discussed.

Electron and proton absorption calculations for a graphite/epoxy composite model. [large space structures

NASA Technical Reports Server (NTRS)

Long, E. R., Jr.

1979-01-01

The Bethe-Bloch stopping power relations for inelastic collisions were used to determine the absorption of electron and proton energy in cured neat epoxy resin and the absorption of electron energy in a graphite/epoxy composite. Absorption of electron energy due to bremsstrahlung was determined. Electron energies from 0.2 to 4.0 MeV and proton energies from 0.3 to 1.75 MeV were used. Monoenergetic electron energy absorption profiles for models of pure graphite, cured neat epoxy resin, and graphite/epoxy composites are reported. A relation is determined for depth of uniform energy absorption in a composite as a function of fiber volume fraction and initial electron energy. Monoenergetic proton energy absorption profiles are reported for the neat resin model. A relation for total proton penetration in the epoxy resin as a function of initial proton energy is determined. Electron energy absorption in the composite due to bremsstrahlung is reported. Electron and proton energy absorption profiles in cured neat epoxy resin are reported for environments approximating geosynchronous earth orbit.

CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease.

PubMed

Jentsch, Thomas J; Pusch, Michael

2018-07-01

CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals, ClC-1, -2, -Ka/-Kb are plasma membrane Cl - channels, whereas ClC-3 through ClC-7 are 2Cl - /H + -exchangers in endolysosomal membranes. Biological roles of CLCs were mostly studied in mammals, but also in plants and model organisms like yeast and Caenorhabditis elegans. CLC Cl - channels have roles in the control of electrical excitability, extra- and intracellular ion homeostasis, and transepithelial transport, whereas anion/proton exchangers influence vesicular ion composition and impinge on endocytosis and lysosomal function. The surprisingly diverse roles of CLCs are highlighted by human and mouse disorders elicited by mutations in their genes. These pathologies include neurodegeneration, leukodystrophy, mental retardation, deafness, blindness, myotonia, hyperaldosteronism, renal salt loss, proteinuria, kidney stones, male infertility, and osteopetrosis. In this review, emphasis is laid on biophysical structure-function analysis and on the cell biological and organismal roles of mammalian CLCs and their role in disease.

REVIEWS OF TOPICAL PROBLEMS Molecular energy transducers of the living cell. Proton ATP synthase: a rotating molecular motor

NASA Astrophysics Data System (ADS)

Romanovsky, Yurii M.; Tikhonov, Alexander N.

2010-12-01

The free energy released upon the enzymatic hydrolysis of adenosine triphosphate (ATP) is the main source of energy for the functioning of the living cell and all multicellular organisms. The overwhelming majority of ATP molecules are formed by proton ATP synthases, which are the smallest macromolecular electric motors in Nature. This paper reviews the modern concepts of the molecular structure and functioning of the proton ATP synthase, and real-time biophysical experiments on the rotation of the 'rotor' of this macromolecular motor. Some mathematical models describing the operation of this nanosized macromolecular machine are described.

Protomers of benzocaine: solvent and permittivity dependence.

PubMed

Warnke, Stephan; Seo, Jongcheol; Boschmans, Jasper; Sobott, Frank; Scrivens, James H; Bleiholder, Christian; Bowers, Michael T; Gewinner, Sandy; Schöllkopf, Wieland; Pagel, Kevin; von Helden, Gert

2015-04-01

The immediate environment of a molecule can have a profound influence on its properties. Benzocaine, the ethyl ester of para-aminobenzoic acid that finds an application as a local anesthetic, is found to adopt in its protonated form at least two populations of distinct structures in the gas phase, and their relative intensities strongly depend on the properties of the solvent used in the electrospray ionization process. Here, we combine IR-vibrational spectroscopy with ion mobility-mass spectrometry to yield gas-phase IR spectra of simultaneously m/z and drift-time-resolved species of benzocaine. The results allow for an unambiguous identification of two protomeric species: the N- and O-protonated forms. Density functional theory calculations link these structures to the most stable solution and gas-phase structures, respectively, with the electric properties of the surrounding medium being the main determinant for the preferred protonation site. The fact that the N-protonated form of benzocaine can be found in the gas phase is owed to kinetic trapping of the solution-phase structure during transfer into the experimental setup. These observations confirm earlier studies on similar molecules where N- and O-protonation have been suggested.

The use of neutron scattering to determine the functional structure of glycoside hydrolase.

PubMed

Nakamura, Akihiko; Ishida, Takuya; Samejima, Masahiro; Igarashi, Kiyohiko

2016-10-01

Neutron diffraction provides different information from X-ray diffraction, because neutrons are scattered by atomic nuclei, whereas X-rays are scattered by electrons. One of the key advantages of neutron crystallography is the ability to visualize hydrogen and deuterium atoms, making it possible to observe the protonation state of amino acid residues, hydrogen bonds, networks of water molecules and proton relay pathways in enzymes. But, because of technical difficulties, less than 100 enzyme structures have been evaluated by neutron crystallography to date. In this review, we discuss the advantages and disadvantages of neutron crystallography as a tool to investigate the functional structure of glycoside hydrolases, with some examples. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of convection electric field on the distribution of ring current type protons

NASA Technical Reports Server (NTRS)

Grebowsky, J. M.; Chen, A. J.

1975-01-01

The topology of the boundaries of penetration (or, inversely, the boundaries of the forbidden regions) of 90-deg pitch-angle equatorial protons with energies less than 100 keV are explored for an equatorial convection E-field which is directed in general from dawn to dusk. Due to the dependence of drift path on energy (or magnetic moment), complex structural features are expected in the proton energy spectra detected by satellites since the penetration distance of a proton is not a monotonically increasing or decreasing function of energy. During a storm when the convection E is enhanced, model calculations predict elongations of the forbidden regions analogous to tail extensions of the plasmasphere. Following a reduction in the convection field, spiral-structured forbidden regions can occur. Structural features inherent to large-scale convection field changes may be seen in the nose-like proton spectrograms observed near dusk by instrumentation on Explorer 45. These nose events are modelled by using an electric field model developed originally by Volland (1973). The strength of the field is related to the Kp index through night-time equatorial plasmapause measurements.

Quark-hadron duality constraints on $$\\gamma Z$$ box corrections to parity-violating elastic scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hall, Nathan L.; Blunden, Peter G.; Melnitchouk, Wally

2015-12-08

We examine the interference \\gamma Z box corrections to parity-violating elastic electron--proton scattering in the light of the recent observation of quark-hadron duality in parity-violating deep-inelastic scattering from the deuteron, and the approximate isospin independence of duality in the electromagnetic nucleon structure functions down to Q 2 \\approx 1 GeV 2. Assuming that a similar behavior also holds for the \\gamma Z proton structure functions, we find that duality constrains the γ Z box correction to the proton's weak charge to be Re V γ Z V = (5.4 \\pm 0.4) \\times 10 -3 at the kinematics of the Qmore » weak experiment. Within the same model we also provide estimates of the γ Z corrections for future parity-violating experiments, such as MOLLER at Jefferson Lab and MESA at Mainz.« less

Longitudinal double-spin asymmetry A1p and spin-dependent structure function g1p of the proton at small values of x and Q2

NASA Astrophysics Data System (ADS)

Aghasyan, M.; Alexeev, M. G.; Alexeev, G. D.; Amoroso, A.; Andrieux, V.; Anfimov, N. V.; Anosov, V.; Antoshkin, A.; Augsten, K.; Augustyniak, W.; Austregesilo, A.; Azevedo, C. D. R.; Badełek, B.; Balestra, F.; Ball, M.; Barth, J.; Beck, R.; Bedfer, Y.; Bernhard, J.; Bicker, K.; Bielert, E. R.; Birsa, R.; Bodlak, M.; Bordalo, P.; Bradamante, F.; Bressan, A.; Büchele, M.; Burtsev, V. E.; Capozza, L.; Chang, W.-C.; Chatterjee, C.; Chiosso, M.; Choi, I.; Chumakov, A. G.; Chung, S.-U.; Cicuttin, A.; Crespo, M. L.; Dalla Torre, S.; Dasgupta, S. S.; Dasgupta, S.; Denisov, O. Yu.; Dhara, L.; Donskov, S. V.; Doshita, N.; Dreisbach, Ch.; Dünnweber, W.; Dusaev, R. R.; Dziewiecki, M.; Efremov, A.; Eversheim, P. D.; Faessler, M.; Ferrero, A.; Finger, M.; Finger, M.; Fischer, H.; Franco, C.; Du Fresne von Hohenesche, N.; Friedrich, J. M.; Frolov, V.; Fuchey, E.; Gautheron, F.; Gavrichtchouk, O. P.; Gerassimov, S.; Giarra, J.; Giordano, F.; Gnesi, I.; Gorzellik, M.; Grasso, A.; Gridin, A.; Grosse Perdekamp, M.; Grube, B.; Grussenmeyer, T.; Guskov, A.; Hahne, D.; Hamar, G.; von Harrach, D.; Heinsius, F. H.; Heitz, R.; Herrmann, F.; Horikawa, N.; D'Hose, N.; Hsieh, C.-Y.; Huber, S.; Ishimoto, S.; Ivanov, A.; Iwata, T.; Jary, V.; Joosten, R.; Jörg, P.; Kabuß, E.; Kerbizi, A.; Ketzer, B.; Khaustov, G. V.; Khokhlov, Yu. A.; Kisselev, Yu.; Klein, F.; Koivuniemi, J. H.; Kolosov, V. N.; Kondo, K.; Königsmann, K.; Konorov, I.; Konstantinov, V. F.; Kotzinian, A. M.; Kouznetsov, O. M.; Kral, Z.; Krämer, M.; Kremser, P.; Krinner, F.; Kroumchtein, Z. V.; Kulinich, Y.; Kunne, F.; Kurek, K.; Kurjata, R. P.; Kuznetsov, I. I.; Kveton, A.; Lednev, A. A.; Levchenko, E. A.; Levillain, M.; Levorato, S.; Lian, Y.-S.; Lichtenstadt, J.; Longo, R.; Lyubovitskij, V. E.; Maggiora, A.; Magnon, A.; Makins, N.; Makke, N.; Mallot, G. K.; Mamon, S. A.; Marianski, B.; Martin, A.; Marzec, J.; Matoušek, J.; Matsuda, H.; Matsuda, T.; Meshcheryakov, G. V.; Meyer, M.; Meyer, W.; Mikhailov, Yu. V.; Mikhasenko, M.; Mitrofanov, E.; Mitrofanov, N.; Miyachi, Y.; Moretti, A.; Nagaytsev, A.; Nerling, F.; Neyret, D.; Nový, J.; Nowak, W.-D.; Nukazuka, G.; Nunes, A. S.; Olshevsky, A. G.; Orlov, I.; Ostrick, M.; Panzieri, D.; Parsamyan, B.; Paul, S.; Peng, J.-C.; Pereira, F.; Pešek, M.; Pešková, M.; Peshekhonov, D. V.; Pierre, N.; Platchkov, S.; Pochodzalla, J.; Polyakov, V. A.; Pretz, J.; Quaresma, M.; Quintans, C.; Ramos, S.; Regali, C.; Reicherz, G.; Riedl, C.; Rogacheva, N. S.; Ryabchikov, D. I.; Rybnikov, A.; Rychter, A.; Salac, R.; Samoylenko, V. D.; Sandacz, A.; Santos, C.; Sarkar, S.; Savin, I. A.; Sawada, T.; Sbrizzai, G.; Schiavon, P.; Schmidt, K.; Schmieden, H.; Schönning, K.; Seder, E.; Selyunin, A.; Silva, L.; Sinha, L.; Sirtl, S.; Slunecka, M.; Smolik, J.; Srnka, A.; Steffen, D.; Stolarski, M.; Subrt, O.; Sulc, M.; Suzuki, H.; Szabelski, A.; Szameitat, T.; Sznajder, P.; Tasevsky, M.; Tessaro, S.; Tessarotto, F.; Thiel, A.; Tomsa, J.; Tosello, F.; Tskhay, V.; Uhl, S.; Vasilishin, B. I.; Vauth, A.; Veloso, J.; Vidon, A.; Virius, M.; Wallner, S.; Weisrock, T.; Wilfert, M.; Windmolders, R.; Ter Wolbeek, J.; Zaremba, K.; Zavada, P.; Zavertyaev, M.; Zemlyanichkina, E.; Ziembicki, M.; Compass Collaboration

2018-06-01

We present a precise measurement of the proton longitudinal double-spin asymmetry A1p and the proton spin-dependent structure function g1p at photon virtualities 0.006(GeV / c) 2

Electronic band structure effects in the stopping of protons in copper [Electronic band structure non-linear effects in the stopping of protons in copper

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

2016-10-05

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Insights into proton translocation in cbb3 oxidase from MD simulations.

PubMed

Carvalheda, Catarina A; Pisliakov, Andrei V

2017-05-01

Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb 3 ) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb 3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337. Copyright © 2017 Elsevier B.V. All rights reserved.

Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).

PubMed

Godwin, Ryan C; Melvin, Ryan L; Gmeiner, William H; Salsbury, Freddie R

2017-01-31

Zinc-finger proteins are regulators of critical signaling pathways for various cellular functions, including apoptosis and oncogenesis. Here, we investigate how binding site protonation states and zinc coordination influence protein structure, dynamics, and ultimately function, as these pivotal regulatory proteins are increasingly important for protein engineering and therapeutic discovery. To better understand the thermodynamics and dynamics of the zinc finger of NEMO (NF-κB essential modulator), as well as the role of zinc, we present results of 20 μs molecular dynamics trajectories, 5 μs for each of four active site configurations. Consistent with experimental evidence, the zinc ion is essential for mechanical stabilization of the functional, folded conformation. Hydrogen bond motifs are unique for deprotonated configurations yet overlap in protonated cases. Correlated motions and principal component analysis corroborate the similarity of the protonated configurations and highlight unique relationships of the zinc-bound configuration. We hypothesize a potential mechanism for zinc binding from results of the thiol configurations. The deprotonated, zinc-bound configuration alone predominantly maintains its tertiary structure throughout all 5 μs and alludes rare conformations potentially important for (im)proper zinc-finger-related protein-protein or protein-DNA interactions.

IR spectral assignments for the hydrated excess proton in liquid water.

PubMed

Biswas, Rajib; Carpenter, William; Fournier, Joseph A; Voth, Gregory A; Tokmakoff, Andrei

2017-04-21

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm -1 for every local proton configuration, with the region 2000-2600 cm -1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H + ⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H 5 O2+moiety.

IR spectral assignments for the hydrated excess proton in liquid water

NASA Astrophysics Data System (ADS)

Biswas, Rajib; Carpenter, William; Fournier, Joseph A.; Voth, Gregory A.; Tokmakoff, Andrei

2017-04-01

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5+O2 moiety.

Comparative analysis of proton- and neutron-halo breakups

NASA Astrophysics Data System (ADS)

Mukeru, B.

2018-06-01

A detailed analysis of the proton- and neutron-halo breakup cross sections is presented. Larger neutron-halo breakup cross sections than proton-halo breakup cross sections are obtained. This is found to be mainly due to the projectile structure, namely the ground state wave function and the dipole electric response function. It is also found that the continuum–continuum couplings are stronger in the proton-halo breakup than in the neutron-halo breakup. The increase of proton- and neutron-halo ground state separation energy slightly strengthens these couplings in the proton- and neutron-halo total and nuclear breakups, while they are weakened in the proton- and neutron-halo Coulomb breakups. The Coulomb-nuclear interference remains strongly destructive in both proton- and neutron-halo breakups and this is independent of the ground state separation energy. The results also show that the increase of the neutron-halo ground state separation energy decreases significantly the agreement between the proton- and neutron-halo breakup cross sections, both qualitatively and quantitatively. It is obtained that when the proton-halo ground state separation energy is increased by a factor of 4.380, the proton-halo breakup cross section is reduced by a factor of 4.392, indicating a clear proportionality. However, when the neutron-halo ground state separation energy is increased by the same factor, the neutron-halo total breakup cross section is reduced by a factor of 8.522.

Piston-assisted proton pumping in Complex I of mitochondria membranes

NASA Astrophysics Data System (ADS)

Mourokh, Lev; Filonenko, Ilan

2014-03-01

Proton-pumping mechanism of Complex I remains mysterious because its electron and proton paths are well separated and the direct Coulomb interaction seems to be negligible. The structure of this enzyme was resolved very recently and its functionality was connected the shift of the helix HL. We model the helix as a piston oscillating between the protons and electrons. We assume that positive charges are accumulated near the edges of the helix. In the oxidized state, the piston is attracted to electrons, so its distance to the proton sites increases, the energy of these sites decreases and the sites can be populated. When electrons proceed to the drain, elastic forces return the piston to the original position and the energies of populated proton sites increase, so the protons can be transferred to the positive site of the membrane. In this work, we explore a simplified model when the interaction of the piston with electrons is replaced by a periodic force. We derive quantum Heisenberg equations for the proton operators and solve them jointly with the Langevin equation for the piston position. We show that the proton pumping is possible in such structure with parameters closely resembling the real system. We also address the feasibility of using such mechanism in nanoelectronics.

X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O 2 -reduction states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia

2015-11-26

During X-ray data collection from a multicopper oxidase (MCO) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the X-ray-induced reduction of O 2 to 2H 2O at the trinuclear copper cluster (TNC) of the enzyme. In this work, 12 crystallographic structures of Thermus thermophilus HB27 multicopper oxidase (Tth-MCO) in holo, apo and Hg-bound forms and with different X-ray absorbed doses have been determined. In holo Tth -MCO structures with four Cu atoms, the proton-donor residue Glu451 involved in O 2 reduction was found in a double conformation: Glu451a (~7 Åmore » from the TNC) and Glu451b (~4.5 Å from the TNC). A positive peak of electron density above 3.5σ in anF o-F c map for Glu451a O ε2 indicates the presence of a carboxyl functional group at the side chain, while its significant absence in Glu451b strongly suggests a carboxylate functional group. In contrast, for apo Tth -MCO and in Hg-bound structures neither the positive peak nor double conformations were observed. Together, these observations provide the first structural evidence for a proton-relay mechanism in the MCO family and also support previous studies indicating that Asp106 does not provide protons for this mechanism. In addition, eight composite structures (Tth -MCO-C1–8) with different X-ray-absorbed doses allowed the observation of different O 2-reduction states, and a total depletion of T2Cu at doses higher than 0.2 MGy showed the high susceptibility of this Cu atom to radiation damage, highlighting the importance of taking radiation effects into account in biochemical interpretations of an MCO structure.« less

Spin dependent structure function g1 of the deuteron and the proton

NASA Astrophysics Data System (ADS)

Klostermann, L.

1995-05-01

This thesis presents a study on the spin structure of the nucleon, via deep inelastic scattering (DIS) of polarized muons on polarized proton and deuterium targets. The work was done in the Spin Muon Collaboration (SMC) at CERN in Geneva. From the asymmetry in the scattering cross section for nucleon and lepton spins parallel and anti-parallel, one can determine the spin dependent structure function g(sub 1), which contains information on the quark and gluon spin distribution functions. The interpretation in the frame work of the quark parton model (QPM) of earlier results on g(sub 1, sup d) by the European Muon Collaboration (EMC), gave an indication that only a small fraction of the proton spin, compatible with zero, is carried by the spins of the constituent quarks. The SMC was set up to check this unexpected result with improved accuracy, and to combine measurements of g(sub 1, sup p) and g(sub 1, sup d) to test a fundamental sum rule in quantum chromodynamics (QCD), the Bjorken sum rule. The SMC results presented in this thesis are based on data taken in 1992 using a polarized deuterium target and polarized muons with an incident energy of 100 GeV, and 1993 data with a proton target and an incident muon energy of 190 GeV. Using all available data, the fundamental Bjorken sum rule has now been verified at the one standard deviation level to within 16% of its theoretical value.

A measurement and QCD analysis of the proton structure function F2 ( x, Q2) at HERA

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Bähr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançoni, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; BurgerF. W. Büsser, J.; Buniatian, A.; Burke, S.; Burton, M. J.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Cousinou, M.-C.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davis, C. L.; Delcourt, B.; De Roeck, A.; De Wolf, E. A.; Dirkmann, M.; Dixon, P.; Di Nezza, P.; Dlugosz, W.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Fahr, A. B.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Glazov, A.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Golec-Biernat, K.; Gonzalez-Pineiro, B.; Gorelov, I.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Griffiths, R.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hampel, M.; Haynes, W. J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johannsen, K.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kander, M.; Kant, D.; Kaschowitz, R.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbie, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Lacour, D.; Laforge, B.; Lander, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Laporte, J.-F.; Lebedev, A.; Lehner, F.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindström, G.; Lindstroem, M.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Lohmander, H.; Lomas, J. W.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, G.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Merz, T.; Meyer, A.; MeyerH. Meyer, A.; Meyer, J.; Meyer, P.-O.; Migliori, A.; Mikocki, S.; Milstead, D.; Moeck, J.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, D.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Pawletta, H.; Peppel, E.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Rick, H.; Riech, V.; Riedlberger, J.; Riepenhausen, F.; Riess, S.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Sahlmann, N.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleif, S.; Schleper, P.; von Schlippe, W.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, H.; Specka, A.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Squinabl, F.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Steiner, H.; Stella, B.; Stellberger, A.; Stier, J.; Stiewe, J.; Stößlein, U.; Stolze, K.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Vandenplas, D.; Van Esch, P.; Van Mechelen, P.; Vazdik, Y.; Verrecchi, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walther, A.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wünsch, E.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zomer, F.; Zsembery, J.; Zuber, K.; zurNedden, M.; Kaufmannxa, O.; H1 Collaboration

1996-02-01

A new measurement of the proton structure function F2 ( x, Q2) is reported for momentum transfers squared Q2 between ].5 GeV 2 and 5000 GeV 2 and for Bjorken x between 3 · 10 -5 and 0.32 using data collected by the HERA experiment H1 in 1994. The data represent an increase in statistics by a factor of ten with respect to the analysis of the 1993 data. Substantial extension of the kinematic range towards low Q2 and x has been achieved using dedicated data samples and events with initial state photon radiation. The structure function is found to increase significantly with decreasing x, even in the lowest accessible Q2 region. The data are well described by a Next to Leading Order QCD fit and the gluon density is extracted.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Imker,H.; Fedorov, A.; Fedorov, E.

D-Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme, is the paradigm member of the recently recognized mechanistically diverse RuBisCO superfamily. The RuBisCO reaction is initiated by abstraction of the proton from C3 of the D-ribulose 1,5-bisphosphate substrate by a carbamate oxygen of carboxylated Lys 201 (spinach enzyme). Heterofunctional homologues of RuBisCO found in species of Bacilli catalyze the tautomerization ('enolization') of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P) in the methionine salvage pathway in which 5-methylthio-D-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine [Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N., and Yokota, A. (2003) A functional link between RuBisCO-likemore » protein of Bacillus and photosynthetic RuBisCO, Science 302, 286-290]. The reaction catalyzed by this 'enolase' is accomplished by abstraction of a proton from C1 of the DK-MTP 1-P substrate to form the tautomerized product, a conjugated enol. Because the RuBisCO- and 'enolase'-catalyzed reactions differ in the regiochemistry of proton abstraction but are expected to share stabilization of an enolate anion intermediate by coordination to an active site Mg{sup 2+}, we sought to establish structure-function relationships for the 'enolase' reaction so that the structural basis for the functional diversity could be established. We determined the stereochemical course of the reaction catalyzed by the 'enolases' from Bacillus subtilis and Geobacillus kaustophilus. Using stereospecifically deuterated samples of an alternate substrate derived from D-ribose (5-OH group instead of the 5-methylthio group in MTR) as well as of the natural DK-MTP 1-P substrate, we determined that the 'enolase'-catalyzed reaction involves abstraction of the 1-proS proton. We also determined the structure of the activated 'enolase' from G. kaustophilus (carboxylated on Lys 173) liganded with Mg{sup 2+} and 2,3-diketohexane 1-phosphate, a stable alternate substrate. The stereospecificity of proton abstraction restricts the location of the general base to the N-terminal {alpha}+ {beta} domain instead of the C-terminal ({beta}/{alpha}){sub 8}-barrel domain that contains the carboxylated Lys 173. Lys 98 in the N-terminal domain, conserved in all 'enolases', is positioned to abstract the 1-proS proton. Consistent with this proposed function, the K98A mutant of the G. kaustophilus 'enolase' is unable to catalyze the 'enolase' reaction. Thus, we conclude that this functionally divergent member of the RuBisCO superfamily uses the same structural strategy as RuBisCO for stabilizing the enolate anion intermediate, i.e., coordination to an essential Mg{sup 2+}, but the proton abstraction is catalyzed by a different general base.« less

A detailed study of the proton structure functions in deep inelastic muon-proton scattering

NASA Astrophysics Data System (ADS)

Aubert, J. J.; Bassompierre, G.; Becks, K. H.; Best, C.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Broll, C.; Brown, S.; Carr, J.; Clifft, R. W.; Cobb, J. H.; Coignet, G.; Combley, F.; D'Agostini, G.; Dau, W. D.; Davies, J. K.; Déclais, Y.; Dobinson, R. W.; Dosselli, U.; Drees, J.; Edwards, A. W.; Edwards, M.; Favier, J.; Ferrero, M. I.; Flauger, W.; Gabathuler, E.; Gamet, R.; Gayler, J.; Gerhardt, V.; Gössling, C.; Haas, J.; Hamacher, K.; Hayman, P.; Henckes, M.; Korbel, V.; Landgraf, U.; Leenen, M.; Maire, M.; Mohr, W.; Montgomery, H. E.; Moser, K.; Mount, R. P.; Nassalski, J.; Norton, P. R.; McNicholas, J.; Osborne, A. M.; Payre, P.; Peroni, C.; Pessard, H.; Pietrzyk, U.; Rith, K.; Schneegans, M.; Sloan, T.; Stier, H. E.; Stockhausen, W.; Thénard, J. M.; Thompson, J. C.; Urban, L.; Wahlen, H.; Whalley, M.; Williams, W. S. C.; Williamson, J.; Wimpenny, S. J.; European Muon Collaboration

1985-09-01

The x and Q2 dependence of the single photon exchange cross section d 2σ/d Q2d x and the proton structure functions F2( x, Q2) and R( x, Q2) have been measured in deep inelastic muon proton scattering in the region 0.02 < x < 0.8 and 3 < Q2 < 190 GeV 2. By comparing data at different incident muon energies R was found to have little kinematic dependence and an average value of -0.010 ± 0.037 (stat.) ± 0.102 (stat.). The observed deviations from scaling gave the value of Λ overlineMS, the QCD mass scale parameter, to be 105 -45+55 (stat.) -45+85 (syst.) MeV. The fraction of the momentum of the nucleon carried by gluons was found to be ˜56% at Q2˜22.5 GeV 2. It is shown that to obtain a description of the data for F2( x, Q2) together with that measured in deep inelastic electron-proton scattering at lower Q2 it is necessary to include additional higher twist contributions. The value of Λ overlineMS remains unchanged with the inclusion of these contributions which were found to have an x-dependence of the form x3/(1 - x).

Decoupling of the Leading Order DGLAP Evolution Equation with Spin Dependent Structure Functions

NASA Astrophysics Data System (ADS)

Azadbakht, F. Teimoury; Boroun, G. R.

2018-02-01

We propose an analytical solution for DGLAP evolution equations with polarized splitting functions at the Leading Order (LO) approximation based on the Laplace transform method. It is shown that the DGLAP evolution equations can be decoupled completely into two second order differential equations which then are solved analytically by using the initial conditions δ FS(x,Q2)=F[partial δ FS0(x), δ FS0(x)] and {δ G}(x,Q2)=G[partial δ G0(x), δ G0(x)]. We used this method to obtain the polarized structure function of the proton as well as the polarized gluon distribution function inside the proton and compared the numerical results with experimental data of COMPASS, HERMES, and AAC'08 Collaborations. It was found that there is a good agreement between our predictions and the experiments.

Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions

PubMed Central

Dellisanti, Cosma D.; Ghosh, Borna; Hanson, Susan M.; Raspanti, James M.; Grant, Valerie A.; Diarra, Gaoussou M.; Schuh, Abby M.; Satyshur, Kenneth; Klug, Candice S.; Czajkowski, Cynthia

2013-01-01

Pentameric ligand-gated ion channels (pLGICs) are neurotransmitter-activated receptors that mediate fast synaptic transmission. In pLGICs, binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and, in the continued presence of neurotransmitter, the channels desensitize (close). The flexible loops in each subunit that connect the extracellular binding domain (loops 2, 7, and 9) to the transmembrane channel domain (M2–M3 loop) are essential for coupling ligand binding to channel gating. Comparing the crystal structures of two bacterial pLGIC homologues, ELIC and the proton-activated GLIC, suggests channel gating is associated with rearrangements in these loops, but whether these motions accurately predict the motions in functional lipid-embedded pLGICs is unknown. Here, using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and functional GLIC channels reconstituted into liposomes, we examined if, and how far, the loops at the ECD/TMD gating interface move during proton-dependent gating transitions from the resting to desensitized state. Loop 9 moves ∼9 Å inward toward the channel lumen in response to proton-induced desensitization. Loop 9 motions were not observed when GLIC was in detergent micelles, suggesting detergent solubilization traps the protein in a nonactivatable state and lipids are required for functional gating transitions. Proton-induced desensitization immobilizes loop 2 with little change in position. Proton-induced motion of the M2–M3 loop was not observed, suggesting its conformation is nearly identical in closed and desensitized states. Our experimentally derived distance measurements of spin-labeled GLIC suggest ELIC is not a good model for the functional resting state of GLIC, and that the crystal structure of GLIC does not correspond to a desensitized state. These findings advance our understanding of the molecular mechanisms underlying pLGIC gating. PMID:24260024

Density Functional Theory Investigation of Proton Diffusion in Tungsten Oxide And Its Hydrates

NASA Astrophysics Data System (ADS)

Lin, Hao

Fast proton conduction mechanism is of key importance for achieving high performance in fuel cell membranes, batteries, supercapacitors, and electrochromic materials. Enhanced proton diffusion is often observed in hydrated materials where it is thought to occur via the famous Grotthuss mechanism through pathways formed by structural water. Using first-principles calculations, we demonstrate that proton diffusion in tungsten oxide dihydrate (WO3·2H 2O), a known good proton conductor, takes place within the layers of corner-sharing WO6 octahedra without direct involvement of structural water. The calculated proton migration barrier in WO3·2H 2O is in good agreement with the experimental value inferred from the temperature dependence of conductivity. The preferred proton diffusion path in WO3·2H2O is essentially the same as in gamma-WO 3. In contrast to the small intercalation voltages calculated for WO 3 and WO3·2H2O, we find that proton absorption in the monohydrate WO3·H2O is energetically highly favorable. However, strong proton-proton repulsion limits the equilibrium H content at zero voltage. We find a fast one-dimensional diffusion channel in WO3·H2O at dilute proton concentrations, but much higher barriers are expected at near-equilibrium concentrations due to strong repulsive interactions with other protons. Our results illustrate that low proton diffusion barriers and low insertion voltages both contribute to fast proton transport in bulk WO3·2H2O and gamma-WO 3.

Enhanced Spectral Anisotropies Near the Proton-Cyclotron Scale: Possible Two-Component Structure in Hall-FLR MHD Turbulence Simulations

NASA Technical Reports Server (NTRS)

Ghosh, Sanjoy; Goldstein, Melvyn L.

2011-01-01

Recent analysis of the magnetic correlation function of solar wind fluctuations at 1 AU suggests the existence of two-component structure near the proton-cyclotron scale. Here we use two-and-one-half dimensional and three-dimensional compressible MHD models to look for two-component structure adjacent the proton-cyclotron scale. Our MHD system incorporates both Hall and Finite Larmor Radius (FLR) terms. We find that strong spectral anisotropies appear adjacent the proton-cyclotron scales depending on selections of initial condition and plasma beta. These anisotropies are enhancements on top of related anisotropies that appear in standard MHD turbulence in the presence of a mean magnetic field and are suggestive of one turbulence component along the inertial scales and another component adjacent the dissipative scales. We compute the relative strengths of linear and nonlinear accelerations on the velocity and magnetic fields to gauge the relative influence of terms that drive the system with wave-like (linear) versus turbulent (nonlinear) dynamics.

Hard exclusive pion electroproduction at backward angles with CLAS

DOE PAGES

Park, K.; Guidal, M.; Gothe, R. W.; ...

2018-03-09

We report on the first measurement of cross sections for exclusive deeply virtual pion electroproduction off the proton,more » $$e p \\to e^\\prime n \\pi^+$$, above the resonance region at backward pion center-of-mass angles. The $$\\varphi^*_{\\pi}$$-dependent cross sections were measured, from which we extracted three combinations of structure functions of the proton. Our results are compatible with calculations based on nucleon-to-pion transition distribution amplitudes (TDAs) and shed new light on nucleon structure.« less

Modeling the Proton Radiation Belt With Van Allen Probes Relativistic Electron-Proton Telescope Data

NASA Technical Reports Server (NTRS)

Kanekal, S. G.; Li, X.; Baker, D. N.; Selesnick, R. S.; Hoxie, V. C.

2018-01-01

An empirical model of the proton radiation belt is constructed from data taken during 2013-2017 by the Relativistic Electron-Proton Telescopes on the Van Allen Probes satellites. The model intensity is a function of time, kinetic energy in the range 18-600 megaelectronvolts, equatorial pitch angle, and L shell of proton guiding centers. Data are selected, on the basis of energy deposits in each of the nine silicon detectors, to reduce background caused by hard proton energy spectra at low L. Instrument response functions are computed by Monte Carlo integration, using simulated proton paths through a simplified structural model, to account for energy loss in shielding material for protons outside the nominal field of view. Overlap of energy channels, their wide angular response, and changing satellite orientation require the model dependencies on all three independent variables be determined simultaneously. This is done by least squares minimization with a customized steepest descent algorithm. Model uncertainty accounts for statistical data error and systematic error in the simulated instrument response. A proton energy spectrum is also computed from data taken during the 8 January 2014 solar event, to illustrate methods for the simpler case of an isotropic and homogeneous model distribution. Radiation belt and solar proton results are compared to intensities computed with a simplified, on-axis response that can provide a good approximation under limited circumstances.

Modeling the Proton Radiation Belt With Van Allen Probes Relativistic Electron-Proton Telescope Data

NASA Astrophysics Data System (ADS)

Selesnick, R. S.; Baker, D. N.; Kanekal, S. G.; Hoxie, V. C.; Li, X.

2018-01-01

An empirical model of the proton radiation belt is constructed from data taken during 2013-2017 by the Relativistic Electron-Proton Telescopes on the Van Allen Probes satellites. The model intensity is a function of time, kinetic energy in the range 18-600 MeV, equatorial pitch angle, and L shell of proton guiding centers. Data are selected, on the basis of energy deposits in each of the nine silicon detectors, to reduce background caused by hard proton energy spectra at low L. Instrument response functions are computed by Monte Carlo integration, using simulated proton paths through a simplified structural model, to account for energy loss in shielding material for protons outside the nominal field of view. Overlap of energy channels, their wide angular response, and changing satellite orientation require the model dependencies on all three independent variables be determined simultaneously. This is done by least squares minimization with a customized steepest descent algorithm. Model uncertainty accounts for statistical data error and systematic error in the simulated instrument response. A proton energy spectrum is also computed from data taken during the 8 January 2014 solar event, to illustrate methods for the simpler case of an isotropic and homogeneous model distribution. Radiation belt and solar proton results are compared to intensities computed with a simplified, on-axis response that can provide a good approximation under limited circumstances.

Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

PubMed Central

2015-01-01

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment. PMID:24960612

Proton transfer pathways, energy landscape, and kinetics in creatine-water systems.

PubMed

Ivchenko, Olga; Whittleston, Chris S; Carr, Joanne M; Imhof, Petra; Goerke, Steffen; Bachert, Peter; Wales, David J

2014-02-27

We study the exchange processes of the metabolite creatine, which is present in both tumorous and normal tissues and has NH2 and NH groups that can transfer protons to water. Creatine produces chemical exchange saturation transfer (CEST) contrast in magnetic resonance imaging (MRI). The proton transfer pathway from zwitterionic creatine to water is examined using a kinetic transition network constructed from the discrete path sampling approach and an approximate quantum-chemical energy function, employing the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. The resulting potential energy surface is visualized by constructing disconnectivity graphs. The energy landscape consists of two distinct regions corresponding to the zwitterionic creatine structures and deprotonated creatine. The activation energy that characterizes the proton transfer from the creatine NH2 group to water was determined from an Arrhenius fit of rate constants as a function of temperature, obtained from harmonic transition state theory. The result is in reasonable agreement with values obtained in water exchange spectroscopy (WEX) experiments.

The mechanism of protein export enhancement by the SecDF membrane component

PubMed Central

Tsukazaki, Tomoya; Nureki, Osamu

2011-01-01

Protein transport across membranes is a fundamental and essential cellular activity in all organisms. In bacteria, protein export across the cytoplasmic membrane, driven by dynamic interplays between the protein-conducting SecYEG channel (Sec translocon) and the SecA ATPase, is enhanced by the proton motive force (PMF) and a membrane-integrated Sec component, SecDF. However, the structure and function of SecDF have remained unclear. We solved the first crystal structure of SecDF, consisting of a pseudo-symmetrical 12-helix transmembrane domain and two protruding periplasmic domains. Based on the structural features, we proposed that SecDF functions as a membrane-integrated chaperone, which drives protein movement without using the major energetic currency, ATP, but with remarkable cycles of conformational changes, powered by the proton gradient across the membrane. By a series of biochemical and biophysical approaches, several functionally important residues in the transmembrane region have been identified and our model of the SecDF function has been verified. PMID:27857601

Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.

PubMed

Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H-J

2015-12-04

Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg(82) and Thr(201), linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg(82)-Thr(201) hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity*

PubMed Central

Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H.-J.

2015-01-01

Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg82 and Thr201, linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg82–Thr201 hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping. PMID:26483542

Proton transfer and protein quake in photoreceptor activation

NASA Astrophysics Data System (ADS)

Xie, Aihua

2002-03-01

Proteins are able to perform an enormous variety of functions, while using only a limited number of underlying processes. One of these is proton transfer, found in a range of receptors and enzymes. It is conceivable that proton transfer is essential in biological energy transduction, but it is less evident how proton transfer is employed in receptor activation during biological signal transduction. An important question regarding receptor activation is how a localized event of detecting a stimulus at the active site drives global conformational changes involving protein surface for signal relay. We will present structural, kinetic and energetic studies on the activation mechanism of a prototype PAS domain photoreceptor, photoactive yellow protein (PYP). Our data reveal that the putative signaling state of PYP upon absorption of a blue photon is formed during a large-amplitude protein quake triggered by the formation of a new buried charge in a hydrophobic pocket at the active site of PYP via intramolecular proton transfer. This mechanism for protein quakes driven by proton transfer and electrostatic interactions may play roles during the functioning of other receptor proteins and non-receptor proteins that require large conformational changes.

Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family

PubMed Central

Marreiros, Bruno C.; Sena, Filipa V.; Sousa, Filipe M.; Oliveira, A. Sofia F.; Soares, Cláudio M.; Batista, Ana P.; Pereira, Manuela M.

2017-01-01

Type II NADH:quinone oxidoreductases (NDH-2s) are membrane proteins involved in respiratory chains. These proteins contribute indirectly to the establishment of the transmembrane difference of electrochemical potential by catalyzing the reduction of quinone by oxidation of NAD(P)H. NDH-2s are widespread enzymes being present in the three domains of life. In this work, we explored the catalytic mechanism of NDH-2 by investigating the common elements of all NDH-2s, based on the rationale that conservation of such elements reflects their structural/functional importance. We observed conserved sequence motifs and structural elements among 1762 NDH-2s. We identified two proton pathways possibly involved in the protonation of the quinone. Our results led us to propose the first catalytic mechanism for NDH-2 family, in which a conserved glutamate residue, E172 (in NDH-2 from Staphylococcus aureus) plays a key role in proton transfer to the quinone pocket. This catalytic mechanism may also be extended to the other members of the two-Dinucleotide Binding Domains Flavoprotein (tDBDF) superfamily, such as sulfide:quinone oxidoreductases. PMID:28181562

The Structure of the Proton

DOE R&D Accomplishments Database

Chambers, E. E.; Hofstadter, R.

1956-04-01

The structure and size of the proton have been studied by means of the methods of high-energy electron scattering. The elastic scattering of electrons from protons in polyethylene has been investigated at the following energies in the laboratory system: 200, 300, 400, 500, 550 Mev. The range of laboratory angles examined has been 30 degrees to 135 degrees. At the largest angles and the highest energy, the cross section for scattering shows a deviation below that expected from a point proton by a factor of about nine. The magnitude and variation with angle of the deviations determine a structure factor for the proton, and thereby determine the size and shape of the charge and magnetic-moment distributions within the proton. An interpretation, consistent at all energies and angles and agreeing with earlier results from this laboratory, fixes the rms radius at 0.77 {plus or minus} 0.10 x 10{sup -13} cm for each of the charge and moment distributions. The shape of the density function is not far from a Gaussian with rms radius 0.70 x 10{sup -13} cm or an exponential with rms radius 0.80 x 10 {sup -13} cm. An equivalent interpretation of the experiments would ascribe the apparent size to a breakdown of the Coulomb law and the conventional theory of electromagnetism.

Decoupling the NLO-coupled QED⊗QCD, DGLAP evolution equations, using Laplace transform method

NASA Astrophysics Data System (ADS)

Mottaghizadeh, Marzieh; Eslami, Parvin; Taghavi-Shahri, Fatemeh

2017-05-01

We analytically solved the QED⊗QCD-coupled DGLAP evolution equations at leading order (LO) quantum electrodynamics (QED) and next-to-leading order (NLO) quantum chromodynamics (QCD) approximations, using the Laplace transform method and then computed the proton structure function in terms of the unpolarized parton distribution functions. Our analytical solutions for parton densities are in good agreement with those from CT14QED (1.2952 < Q2 < 1010) (Ref. 6) global parametrizations and APFEL (A PDF Evolution Library) (2 < Q2 < 108) (Ref. 4). We also compared the proton structure function, F2p(x,Q2), with the experimental data released by the ZEUS and H1 collaborations at HERA. There is a nice agreement between them in the range of low and high x and Q2.

Structure and Dynamics Investigations of Sr/Ca-Doped LaPO 4 Proton Conductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

al-Wahish, Amal; al-Binni, U.; Tetard, L.

Proton conductors loom out of the pool of candidate materials with great potential to boost hydrogen alternatives to fossil-based resources for energy. Acceptor doped lanthanum orthophosphates are considered for solid oxide fuel cells (SOFCs) for their potential stability and conductivity at high temperature. By exploring the crystal and defect structure of x% Sr/Ca-doped LaPO 4 with different nominal Sr/Ca concentrations (x = 0 – 10) with Neutron powder diffraction (NPD) and X-ray powder diffraction (XRD), we confirm that Sr/Ca-doped LaPO 4 can exist as self-supported structures at high temperatures during solid oxide fuel cell operation. Thermal stability, surface topography, sizemore » distribution are also studied to better understand the proton conductivity for dry and wet compounds obtained at sintering temperatures ranging from 1200 to 1400 °C using a combination of scanning electron microscopy (SEM), Atomic Force Microscopy (AFM), Fourier transform infrared spectroscopy (FTIR) and electrochemical impedance spectroscopy (EIS). In conclusion, the results suggest that Sr doped samples exhibit the highest proton conductivity of our samples and illustrate the impact of material design and versatile characterization schemes on the development of proton conductors with superior functionality.« less

Tautomeric transformation of temozolomide, their proton affinities and chemical reactivities: A theoretical approach.

PubMed

Sang-Aroon, Wichien; Ruangpornvisuti, Vithaya; Amornkitbamrung, Vittaya

2016-05-01

The gas-phase geometry optimizations of bare, mono- and dihydrated complexes of temozolomide isomers were carried out using density functional calculation at the M06-2X/6-31+G(d,p) level of the theory. The structures and protonation energies of protonated species of temozolomide are reported. Chemical indices of all isomers and protonated species are also reported. Energies, thermodynamic quantities, rate constants and equilibrium constants of tautomeric and rotameric transformations of all isomers I1↔TZM↔HIa↔HIb↔I2↔I3 in bare and hydrated systems were obtained. Copyright © 2016 Elsevier Inc. All rights reserved.

Stability of proton-bound clusters of alkyl alcohols, aldehydes and ketones in Ion Mobility Spectrometry.

PubMed

Jurado-Campos, Natividad; Garrido-Delgado, Rocío; Martínez-Haya, Bruno; Eiceman, Gary A; Arce, Lourdes

2018-08-01

Significant substances in emerging applications of ion mobility spectrometry such as breath analysis for clinical diagnostics and headspace analysis for food purity include low molar mass alcohols, ketones, aldehydes and esters which produce mobility spectra containing protonated monomers and proton-bound dimers. Spectra for all n- alcohols, aldehydes and ketones from carbon number three to eight exhibited protonated monomers and proton-bound dimers with ion drift times of 6.5-13.3 ms at ambient pressure and from 35° to 80 °C in nitrogen. Only n-alcohols from 1-pentanol to 1-octanol produced proton-bound trimers which were sufficiently stable to be observed at these temperatures and drift times of 12.8-16.3 ms. Polar functional groups were protected in compact structures in ab initio models for proton-bound dimers of alcohols, ketones and aldehydes. Only alcohols formed a V-shaped arrangement for proton-bound trimers strengthening ion stability and lifetime. In contrast, models for proton-bound trimers of aldehydes and ketones showed association of the third neutral through weak, non-specific, long-range interactions consistent with ion dissociation in the ion mobility drift tube before arriving at the detector. Collision cross sections derived from reduced mobility coefficients in nitrogen gas atmosphere support the predicted ion structures and approximate degrees of hydration. Copyright © 2018 Elsevier B.V. All rights reserved.

Determination of the proton spin structure functions for 0.05

NASA Astrophysics Data System (ADS)

Fersch, R. G.; Guler, N.; Bosted, P.; Deur, A.; Griffioen, K.; Keith, C.; Kuhn, S. E.; Minehart, R.; Prok, Y.; Adhikari, K. P.; Adhikari, S.; Akbar, Z.; Amaryan, M. J.; Anefalos Pereira, S.; Asryan, G.; Avakian, H.; Ball, J.; Balossino, I.; Baltzell, N. A.; Battaglieri, M.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Thanh Cao, Frank; Carman, D. S.; Careccia, S.; Celentano, A.; Chandavar, S.; Charles, G.; Chetry, T.; Ciullo, G.; Clark, L.; Colaneri, L.; Cole, P. L.; Compton, N.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Djalali, C.; Dodge, G. E.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fanchini, E.; Fedotov, G.; Filippi, A.; Fleming, J. A.; Forest, T. A.; Garçon, M.; Gavalian, G.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gleason, C.; Golovatch, E.; Gothe, R. W.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Heddle, D.; Hicks, K.; Holtrop, M.; Hughes, S. M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jenkins, D.; Joo, K.; Keller, D.; Khachatryan, G.; Khachatryan, M.; Khandaker, M.; Kim, A.; Kim, W.; Klein, A.; Klein, F. J.; Kubarovsky, V.; Lagerquist, V. G.; Lanza, L.; Lenisa, P.; Livingston, K.; Lu, H. Y.; McKinnon, B.; Meyer, C. A.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Movsisyan, A.; Munoz Camacho, C.; Murdoch, G.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Paolone, M.; Paremuzyan, R.; Park, K.; Pasyuk, E.; Phelps, W.; Pierce, J.; Pisano, S.; Pogorelko, O.; Price, J. W.; Protopopescu, D.; Raue, B. A.; Ripani, M.; Riser, D.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Sabatié, F.; Salgado, C.; Schumacher, R. A.; Sharabian, Y. G.; Simonyan, A.; Skorodumina, Iu.; Smith, G. D.; Sokhan, D.; Sparveris, N.; Stankovic, I.; Stepanyan, S.; Strakovsky, I. I.; Strauch, S.; Taiuti, M.; Tian, Ye; Torayev, B.; Ungaro, M.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Wei, X.; Weinstein, L. B.; Zachariou, N.; Zhang, J.; CLAS Collaboration

2017-12-01

We present the results of our final analysis of the full data set of g1p(Q2) , the spin structure function of the proton, collected using CLAS at Jefferson Laboratory in 2000-2001. Polarized electrons with energies of 1.6, 2.5, 4.2, and 5.7 GeV were scattered from proton targets (NH153 dynamically polarized along the beam direction) and detected with CLAS. From the measured double spin asymmetries, we extracted virtual photon asymmetries A1p and A2p and spin structure functions g1p and g2p over a wide kinematic range (0.05 GeV2

An overview of recent nucleon spin structure measurements at Jefferson Lab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Allada, Kalyan

2016-02-01

Jefferson Lab have made significant contributions to improve our knowledge of the longitudinal spin structure by measuring polarized structure functions, g1 and g2, down to Q2 = 0.02 GeV2. The low Q2 data is especially useful in testing the Chiral Perturbation theory (cPT) calculations. The spin-dependent sum rules and the spin polarizabilities, constructed from the moments of g1 and g2, provide an important tool to study the longitudinal spin structure. We will present an overview of the experimental program to measure these structure functions at Jefferson Lab, and present some recent results on the neutron polarizabilities, proton g1 at lowmore » Q2, and proton and neutron d2 measurement. In addition to this, we will discuss the transverse spin structure of the nucleon which can be accessed using chiral-odd transversity distribution (h1), and show some results from measurements done on polarized 3He target in Hall A.« less

Structure and Function of the Bi-Directional Bacterial Flagellar Motor

PubMed Central

Morimoto, Yusuke V.; Minamino, Tohru

2014-01-01

The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor–stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor. PMID:24970213

Structure and function of the bi-directional bacterial flagellar motor.

PubMed

Morimoto, Yusuke V; Minamino, Tohru

2014-02-18

The bacterial flagellum is a locomotive organelle that propels the bacterial cell body in liquid environments. The flagellum is a supramolecular complex composed of about 30 different proteins and consists of at least three parts: a rotary motor, a universal joint, and a helical filament. The flagellar motor of Escherichia coli and Salmonella enterica is powered by an inward-directed electrochemical potential difference of protons across the cytoplasmic membrane. The flagellar motor consists of a rotor made of FliF, FliG, FliM and FliN and a dozen stators consisting of MotA and MotB. FliG, FliM and FliN also act as a molecular switch, enabling the motor to spin in both counterclockwise and clockwise directions. Each stator is anchored to the peptidoglycan layer through the C-terminal periplasmic domain of MotB and acts as a proton channel to couple the proton flow through the channel with torque generation. Highly conserved charged residues at the rotor-stator interface are required not only for torque generation but also for stator assembly around the rotor. In this review, we will summarize our current understanding of the structure and function of the proton-driven bacterial flagellar motor.

Polarized structure functions in a constituent quark scenario

NASA Astrophysics Data System (ADS)

Scopetta, Sergio; Vento, Vicente; Traini, Marco

1998-12-01

Using a simple picture of the constituent quark as a composite system of point-like partons, we construct the polarized parton distributions by a convolution between constituent quark momentum distributions and constituent quark structure functions. Using unpolarized data to fix the parameters we achieve good agreement with the polarization experiments for the proton, while not so for the neutron. By relaxing our assumptions for the sea distributions, we define new quark functions for the polarized case, which reproduce well the proton data and are in better agreement with the neutron data. When our results are compared with similar calculations using non-composite constituent quarks the accord with the experiments of the present scheme is impressive. We conclude that, also in the polarized case, DIS data are consistent with a low energy scenario dominated by composite constituents of the nucleon.

Proteorhodopsins: an array of physiological roles?

PubMed

Fuhrman, Jed A; Schwalbach, Michael S; Stingl, Ulrich

2008-06-01

Metagenomic analyses have revealed widespread and diverse retinal-binding rhodopsin proteins (named proteorhodopsins) among numerous marine bacteria and archaea, which has challenged the notion that solar energy can only enter marine ecosystems by chlorophyll-based photosynthesis. Most marine proteorhodopsins share structural and functional similarities with archaeal bacteriorhodopsins, which generate proton motive force via light-activated proton pumping, thereby ultimately powering ATP production. This suggests an energetic role for proteorhodopsins. However, results from a growing number of investigations do not readily fit this model, which indicates that proteorhodopsins could have a range of physiological functions.

Proton environment of reduced Rieske iron-sulfur cluster probed by two-dimensional ESEEM spectroscopy

PubMed Central

Kolling, Derrick R. J.; Samoilova, Rimma I.; Shubin, Alexander A.; Crofts, Antony R.; Dikanov, Sergei A.

2008-01-01

The proton environment of the reduced [2Fe-2S] cluster in the water-soluble head domain of the Rieske iron—sulfur protein (ISF) from the cytochrome bc1 complex of Rhodobacter sphaeroides has been studied by orientation-selected X-band 2D ESEEM. The 2D spectra show multiple cross-peaks from protons, with considerable overlap. Samples in which 1H2O water was replaced by 2H2O were used to determine which of the observed peaks belong to exchangeable protons, likely involved in hydrogen bonds in the neighborhood of the cluster. By correlating the cross-peaks from 2D spectra recorded at different parts of the EPR spectrum, lines from nine distinct proton signals were identified. Assignment of the proton signals was based on a point-dipole model for interaction with electrons of Fe(III) and Fe(II) ions, using the high-resolution structure of ISF from Rb. sphaeroides. Analysis of experimental and calculated tensors has led us to conclude that even 2D spectra do not completely resolve all contributions from nearby protons. Particularly, the seven resolved signals from non-exchangeable protons could be produced by at least thirteen protons. The contributions from exchangeable protons were resolved by difference spectra (1H2O minus 2H2O), and assigned to two groups of protons with distinct anisotropic hyperfine values. The largest measured coupling exceeded any calculated value. This discrepancy could result from limitations of the point dipole approximation in dealing with the distribution of spin density over the sulfur atoms of the cluster and the cysteine ligands, or from differences between the structure in solution and the crystallographic structure. The approach demonstrated here provides a paradigm for a wide range of studies in which hydrogen-bonding interactions with metallic centers has a crucial role in understanding of function. PMID:19099453

Protons in non-ionic aqueous reverse micelles.

PubMed

Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

2007-05-03

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

Nitrogen K-edge x-ray absorption near edge structure of pyrimidine-containing nucleotides in aqueous solution

NASA Astrophysics Data System (ADS)

Shimada, Hiroyuki; Minami, Hirotake; Okuizumi, Naoto; Sakuma, Ichiro; Ukai, Masatoshi; Fujii, Kentaro; Yokoya, Akinari; Fukuda, Yoshihiro; Saitoh, Yuji

2015-05-01

X-ray absorption near edge structure (XANES) was measured at energies around the N K-edge of the pyrimidine-containing nucleotides, cytidine 5'-monophosphate (CMP), 2'-deoxythymidine 5'-monophosphate (dTMP), and uridine 5'-monophosphate (UMP), in aqueous solutions and in dried films under various pH conditions. The features of resonant excitations below the N K-edge in the XANES spectra for CMP, dTMP, and UMP changed depending on the pH of the solutions. The spectral change thus observed is systematically explained by the chemical shift of the core-levels of N atoms in the nucleobase moieties caused by structural changes due to protonation or deprotonation at different proton concentrations. This interpretation is supported by the results of theoretical calculations using density functional theory for the corresponding nucleobases in the neutral and protonated or deprotonated forms.

Nitrogen K-edge x-ray absorption near edge structure of pyrimidine-containing nucleotides in aqueous solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shimada, Hiroyuki, E-mail: hshimada@cc.tuat.ac.jp; Minami, Hirotake; Okuizumi, Naoto

2015-05-07

X-ray absorption near edge structure (XANES) was measured at energies around the N K-edge of the pyrimidine-containing nucleotides, cytidine 5′-monophosphate (CMP), 2′-deoxythymidine 5′-monophosphate (dTMP), and uridine 5′-monophosphate (UMP), in aqueous solutions and in dried films under various pH conditions. The features of resonant excitations below the N K-edge in the XANES spectra for CMP, dTMP, and UMP changed depending on the pH of the solutions. The spectral change thus observed is systematically explained by the chemical shift of the core-levels of N atoms in the nucleobase moieties caused by structural changes due to protonation or deprotonation at different proton concentrations.more » This interpretation is supported by the results of theoretical calculations using density functional theory for the corresponding nucleobases in the neutral and protonated or deprotonated forms.« less

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller than ˜ 10 H2O/SO 3-, which is consistent with experimental observations. The sulfonate groups are also found to have influence on the proton hopping directions. The temperature and water content effects on the PT pathways are also investigated. The morphological effects on proton solvation and transport in hydrated Nafion are investigated, by using the SCI-MS-EVB method. Two of the most significant morphological models of Nafion, the lamellar model and the cylinder model, are selected. The two models exhibit distinct PT patterns, which result in different proton diffusion rates. In both models, the interaction between protons and the sulfonate groups are proven to be the key to determining PT behavior. The proton solvation structure change as a function of the distance between protons and sulfonate groups has been analyzed. It is found that the increase of water cylinder radius or water layer height leads to the presence of more protons around the sulfonate groups. Furthermore, at a lower hydration level, the increased amount of protons around the sulfonate groups consists of more Zundel-like structures, which is influenced by the distinct morphological structures of Nafion.

Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP γ-Phosphate*

PubMed Central

Knihtila, Ryan; Holzapfel, Genevieve; Weiss, Kevin; Meilleur, Flora; Mattos, Carla

2015-01-01

RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated γ-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the start of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. The neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases. PMID:26515069

Neutron crystal structure of RAS GTPase puts in question the protonation state of the GTP γ-phosphate

DOE PAGES

Knihtila, Ryan; Holzapfel, Genevieve; Weiss, Kevin; ...

2015-10-29

RAS GTPase is a prototype for nucleotide-binding proteins that function by cycling between GTP and GDP, with hydrogen atoms playing an important role in the GTP hydrolysis mechanism. It is one of the most well studied proteins in the superfamily of small GTPases, which has representatives in a wide range of cellular functions. These proteins share a GTP-binding pocket with highly conserved motifs that promote hydrolysis to GDP. The neutron crystal structure of RAS presented here strongly supports a protonated gamma-phosphate at physiological pH. This counters the notion that the phosphate groups of GTP are fully deprotonated at the startmore » of the hydrolysis reaction, which has colored the interpretation of experimental and computational data in studies of the hydrolysis mechanism. As a result, the neutron crystal structure presented here puts in question our understanding of the pre-catalytic state associated with the hydrolysis reaction central to the function of RAS and other GTPases.« less

Measurement of the deuteron structure function F2 in the resonance region and evaluation of its moments

NASA Astrophysics Data System (ADS)

Osipenko, M.; Ricco, G.; Simula, S.; Battaglieri, M.; Ripani, M.; Adams, G.; Ambrozewicz, P.; Anghinolfi, M.; Asavapibhop, B.; Asryan, G.; Audit, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Barrow, S.; Batourine, V.; Beard, K.; Bedlinskiy, I.; Bektasoglu, M.; Bellis, M.; Benmouna, N.; Biselli, A. S.; Bonner, B. E.; Bouchigny, S.; Boiarinov, S.; Bradford, R.; Branford, D.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Butuceanu, C.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Cazes, A.; Chen, S.; Cole, P. L.; Coleman, A.; Coltharp, P.; Cords, D.; Corvisiero, P.; Crabb, D.; Cummings, J. P.; de Sanctis, E.; Devita, R.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; Deur, A.; Dharmawardane, K. V.; Djalali, C.; Dodge, G. E.; Donnelly, J.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dytman, S.; Dzyubak, O. P.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Empl, A.; Eugenio, P.; Fatemi, R.; Fedotov, G.; Feuerbach, R. J.; Forest, T. A.; Funsten, H.; Garçon, M.; Gavalian, G.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gordon, C. I. O.; Gothe, R. W.; Griffioen, K. A.; Guidal, M.; Guillo, M.; Guler, N.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hakobyan, R. S.; Hardie, J.; Heddle, D.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Hu, J.; Huertas, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Joo, K.; Juengst, H. G.; Kellie, J. D.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Klusman, M.; Kossov, M.; Kramer, L. H.; Kubarovsky, V.; Kuhn, J.; Kuhn, S. E.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Lee, T.; Li, Ji; Lima, A. C. S.; Livingston, K.; Lukashin, K.; Manak, J. J.; Marchand, C.; McAleer, S.; McKinnon, B.; McNabb, J. W. C.; Mecking, B. A.; Mehrabyan, S.; Melone, J. J.; Mestayer, M. D.; Meyer, C. A.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morand, L.; Morrow, S. A.; Mueller, J.; Mutchler, G. S.; Nadel-Turonski, P.; Napolitano, J.; Nasseripour, R.; Nefedov, G.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Philips, S. A.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Polli, E.; Pozdniakov, S.; Preedom, B. M.; Price, J. W.; Prok, Y.; Protopopescu, D.; Qin, L. M.; Raue, B. A.; Riccardi, G.; Ritchie, B. G.; Ronchetti, F.; Rosner, G.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Shaw, J.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Stoler, P.; Strauch, S.; Suleiman, R.; Taiuti, M.; Taylor, S.; Tedeschi, D. J.; Thoma, U.; Thompson, R.; Tkabladze, A.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Weinstein, L. B.; Weygand, D. P.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zana, L.; Zhang, J.

2006-04-01

Inclusive electron scattering off the deuteron has been measured to extract the deuteron structure function F2 with the CEBAF Large Acceptance Spectrometer (CLAS) at the Thomas Jefferson National Accelerator Facility. The measurement covers the entire resonance region from the quasielastic peak up to the invariant mass of the final-state hadronic system W≃2.7 GeV with four-momentum transfers Q2 from 0.4 to 6 (GeV/c)2. These data are complementary to previous measurements of the proton structure function F2 and cover a similar two-dimensional region of Q2 and Bjorken variable x. Determination of the deuteron F2 over a large x interval including the quasielastic peak as a function of Q2, together with the other world data, permit a direct evaluation of the structure function moments for the first time. By fitting the Q2 evolution of these moments with an OPE-based twist expansion we have obtained a separation of the leading twist and higher twist terms. The observed Q2 behavior of the higher twist contribution suggests a partial cancelation of different higher twists entering into the expansion with opposite signs. This cancelation, found also in the proton moments, is a manifestation of the “duality” phenomenon in the F2 structure function.

Recent progress in computational approaches to studying the M2 proton channel and its implication to drug design against influenza viruses.

PubMed

Du, Qi-Shi; Huang, Ri-Bo

2012-05-01

For quite a long period of time in history, many intense efforts have been made to determine the 3D (three-dimensional) structure of the M2 proton channel. The reason why the M2 proton channel has attracted so many attentions is because (1) it is the key for really understanding the life cycle of influenza viruses, and (2) it is indispensable for conducting rational drug design against the flu viruses. Recently, the long-sough 3D structures of the M2 proton channels for both influenza A and B viruses were consecutively successfully determined by the high-resolution NMR spectroscopy (Schnell J.R. and Chou, J.J., Nature, 2008, 451: 591-595; Wang, J., Pielak, R.M., McClintock, M.A., and Chou, J.J., Nature Structural & Molecular Biology, 2009,16: 1267-1271). Such a milestone work has provided a solid structural basis for in-depth understanding the action mechanism of the M2 channel and rationally designing effective drugs against influenza viruses. This review is devoted to, with the focus on the M2 proton channel of influenza A, addressing a series of relevant problems, such as how to correctly understand the novel allosteric inhibition mechanism inferred from the NMR structure that is completely different from the traditional view, what the possible impacts are to the previous functional studies in this area, and what kind of new strategy can be stimulated for drug development against influenza.

Long-Range Near-Side Angular Correlations in Proton-Proton Interactions in CMS.

ScienceCinema

None

2017-12-09

The CMS Collaboration Results on two-particle angular correlations for charged particles emitted in proton-proton collisions at center of mass energies of 0.9, 2.36 and 7TeV over a broad range of pseudorapidity (?) and azimuthal angle (f) are presented using data collected with the CMS detector at the LHC. Short-range correlations in ??, which are studied in minimum bias events, are characterized using a simple independent cluster parameterization in order to quantify their strength (cluster size) and their extent in ? (cluster decay width). Long-range azimuthal correlations are studied more differentially as a function of charged particle multiplicity and particle transverse momentum using a 980nb-1 data set at 7TeV. In high multiplicity events, a pronounced structure emerges in the two-dimensional correlation function for particles in intermediate pT’s of 1-3GeV/c, 2.0< |??|<4.8 and ?f˜0. This is the ?rst observation of such a ridge-like feature in two-particle correlation functions in pp or p-pbar collisions. EVO Universe, password "seminar"; Phone Bridge ID: 2330444 Password: 5142

Deprotonation and protonation of humic acids as a strategy for the technological development of pH-responsive nanoparticles with fungicidal potential.

PubMed

Motta, F L; Melo, B A G; Santana, M H A

2016-12-25

Humic acids (HAs) are macromolecules of undefined compositions that vary with origin, the process by which they are obtained and functional groups present in their structure, such as quinones, phenols, and carboxylic acids. In addition to agriculture, there is an increased interest in HAs due to their important pharmacological effects. However, HAs are not readily soluble in water at physiological pH, which may limit their bioavailability. Although primary aggregation forms non-uniform pseudo-micelles, the presence of ionisable groups in the HA molecule makes pH an environmental stimulus for controlled aggregation and precipitation. The aim of this work was to induce HA deprotonation and protonation, without compromising their colloidal dispersion, by means of pH changes as a strategy to produce nanoparticles. Deprotonation and protonation were achieved by treating HAs with sodium hydroxide and acetic acid, respectively, at various concentrations. Non pH-treated HAs at the same concentrations were used as control. The evolution of the treatments was monitored by pH changes in bulk solutions as a function of time. At equilibrium, the conformation of the colloidal structures was characterised by the predominant mean diameter, polydispersity index and absorbance of the solutions. The zeta potential was also measured in protonation assays. Moreover, the fungicidal activity of the nanoparticles was evaluated on the mycelial growth of three fungal genera. The results showed the pH decrease or increment as a function of the balance between hydroxyl and carboxyl groups and of the diffusion rate inside the structures. Deprotonation followed by protonation produced nanosized (100-200nm), electrostatically stable (-30mV) and pH-responsive particles with a polydispersity index <0.5. The protonated nanoparticles significantly inhibited (P≤0.05) the mycelial growth of Candida albicans in vitro, when compared with control, and the fungicidal activity was dose-dependent. No activity was observed for the deprotonated HAs nanoparticles. These results show that deprotonation followed by protonation is an easy and useful strategy for the controlled production of HA nanoparticles, which exhibit a tendency to elicit fungicidal effects, with potential to develop new classes of cosmetics and pharmaceuticals. Copyright © 2016 Elsevier B.V. All rights reserved.

Faster proton transfer dynamics of water on SnO2 compared to TiO2.

PubMed

Kumar, Nitin; Kent, Paul R C; Bandura, Andrei V; Kubicki, James D; Wesolowski, David J; Cole, David R; Sofo, Jorge O

2011-01-28

Proton jump processes in the hydration layer on the iso-structural TiO(2) rutile (110) and SnO(2) cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O-H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates.

Inward H+ pump xenorhodopsin: Mechanism and alternative optogenetic approach.

PubMed

Shevchenko, Vitaly; Mager, Thomas; Kovalev, Kirill; Polovinkin, Vitaly; Alekseev, Alexey; Juettner, Josephine; Chizhov, Igor; Bamann, Christian; Vavourakis, Charlotte; Ghai, Rohit; Gushchin, Ivan; Borshchevskiy, Valentin; Rogachev, Andrey; Melnikov, Igor; Popov, Alexander; Balandin, Taras; Rodriguez-Valera, Francisco; Manstein, Dietmar J; Bueldt, Georg; Bamberg, Ernst; Gordeliy, Valentin

2017-09-01

Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina ( Ns XeR) and suggest a mechanism of inward proton pumping. We demonstrate that the Ns XeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.

Building a stable RNA U-turn with a protonated cytidine

PubMed Central

Gottstein-Schmidtke, Sina R.; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E.; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-01-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5′-UNR-3′ (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3′ phosphate group of the R residue as well as a hydrogen bond between the 2′-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3′ from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. PMID:24951555

Multiscale modeling and computation of nano-electronic transistors and transmembrane proton channels

NASA Astrophysics Data System (ADS)

Chen, Duan

The miniaturization of nano-scale electronic transistors, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. In biology, proton dynamics and transport across membrane proteins are of paramount importance to the normal function of living cells. Similar physical characteristics are behind the two subjects, and model simulations share common mathematical interests/challenges. In this thesis work, multiscale and multiphysical models are proposed to study the mechanisms of nanotransistors and proton transport in transmembrane at the atomic level. For nano-electronic transistors, we introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential. This framework enables us to put microscopic and macroscopic descriptions on an equal footing at nano-scale. Additionally, this model includes layered structures and random doping effect of nano-transistors. For transmembrane proton channels, we describe proton dynamics quantum mechanically via a density functional approach while implicitly treat numerous solvent molecules as a dielectric continuum. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered in atomic details. We formulate a total free energy functional to include kinetic and potential energies of protons, as well as electrostatic energy of all other ions on an equal footing. For both nano-transistors and proton channels systems, the variational principle is employed to derive nonlinear governing equations. The Poisson-Kohn-Sham equations are derived for nano-transistors while the generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained for proton channels. Related numerical challenges in simulations are addressed: the matched interface and boundary (MIB) method, the Dirichlet-to-Neumann mapping (DNM) technique, and the Krylov subspace and preconditioner theory are introduced to improve the computational efficiency of the Poisson-type equation. The quantum transport theory is employed to solve the Kohn-Sham equation. The Gummel iteration and relaxation technique are utilized for overall self-consistent iterations. Finally, applications are considered and model validations are verified by realistic nano-transistors and transmembrane proteins. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our threedimensional numerical simulations. For these devices, the current uctuation and voltage threshold lowering effect induced by discrete dopants are explored. For proton transport, a realistic channel protein, the Gramicidin A (GA) is used to demonstrate the performance of the proposed proton channel model and validate the efficiency of the proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. Proton channel conductances are studied over a number of applied voltages and reference concentrations. Comparisons with experimental data are utilized to verify our model predictions.

Facile synthesis of polypyrrole functionalized nickel foam with catalytic activity comparable to Pt for the poly-generation of hydrogen and electricity

NASA Astrophysics Data System (ADS)

Tang, Tiantian; Li, Kan; Shen, Zhemin; Sun, Tonghua; Wang, Yalin; Jia, Jinping

2016-01-01

Polypyrrole functionalized nickel foam is facilely prepared through the potentiostatic electrodeposition. The PPy-functionalized Ni foam functions as a hydrogen-evolution cathode in a rotating disk photocatalytic fuel cell, in which hydrogen energy and electric power are generated by consuming organic wastes. The PPy-functionalized Ni foam cathode exhibits stable catalytic activities after thirteen continuous runs. Compared with net or plate structure, the Ni foam with a unique three-dimensional reticulate structure is conducive to the electrodeposition of PPy. Compared with Pt-group electrode, PPy-coated Ni foam shows a satisfactory catalytic performance for the H2 evolution. The combination of PPy and Ni forms a synergistic effect for the rapid trapping and removal of proton from solution and the catalytic reduction of proton to hydrogen. The PPy-functionalized Ni foam could be applied in photocatalytic and photoelectrochemical generation of H2. In all, we report a low cost, high efficient and earth abundant PPy-functionalized Ni foam with a satisfactory catalytic activities comparable to Pt for the practical application of poly-generation of hydrogen and electricity.

Using Gas-Phase Guest-Host Chemistry to Probe the Structures of b Ions of Peptides

NASA Astrophysics Data System (ADS)

Somogyi, Árpád; Harrison, Alex G.; Paizs, Béla

2012-12-01

Middle-sized b n ( n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b n ( n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b n ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b n ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b 4 , b 5 , and b 7 ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N+-H…O H-bonds; this stabilization is much stronger for macrocyclic b n isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b 9 , b 9 -A, and b 9 -2A of A8YA, and b 13 of A20YVFL are observed indicating that even these large b-type ions form macrocyclic structures.

Determination of the proton spin structure functions for 0.05 < Q 2 < 5 GeV 2 using CLAS

DOE PAGES

Fersch, R. G.; Guler, N.; Bosted, P.; ...

2017-12-27

In this work, we present the results of our final analysis of the full data set of gmore » $$p\\atop{1}$$ (Q 2), the spin structure function of the proton, collected using CLAS at Jefferson Laboratory in 2000–2001. Polarized electrons with energies of 1.6, 2.5, 4.2, and 5.7 GeV were scattered from proton targets ( 15NH 3 dynamically polarized along the beam direction) and detected with CLAS. From the measured double spin asymmetries, we extracted virtual photon asymmetries A$$p\\atop{1}$$ and A$$p\\atop{2}$$ and spin structure functions g$$p\\atop{1}$$ and g$$p\\atop{2}$$ over a wide kinematic range (0.05 GeV 2 < Q 2 < 5 GeV 2 and 1.08 GeV < W < 3 GeV) and calculated moments of g$$p\\atop{1}$$. We compare our final results with various theoretical models and expectations, as well as with parametrizations of the world data. Lastly, our data, with their precision and dense kinematic coverage, are able to constrain fits of polarized parton distributions, test pQCD predictions for quark polarizations at large x, offer a better understanding of quark-hadron duality, and provide more precise values of higher twist matrix elements in the framework of the operator product expansion.« less

Measurement of the diffractive structure function in deep inelastic scattering at HERA

NASA Astrophysics Data System (ADS)

Derrick, M.; Krakauer, D.; Magill, S.; Mikunas, D.; Musgrave, B.; Repond, J.; Stanek, R.; Talaga, R. L.; Zhang, H.; Ayad, R.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Bruni, P.; Cara Romeo, G.; Castellini, G.; Chiarini, M.; Cifarelli, L.; Cindolo, F.; Contin, A.; Corradi, M.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Nemoz, C.; Palmonari, F.; Polini, A.; Sartorelli, G.; Timellini, R.; Zamora Garcia, Y.; Zichichi, A.; Bargende, A.; Crittenden, J.; Desch, K.; Diekmann, B.; Doeker, T.; Eckert, M.; Feld, L.; Frey, A.; Geerts, M.; Geitz, G.; Grothe, M.; Hartmann, H.; Heinloth, H.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Mari, S. M.; Mass, A.; Mengel, S.; Mollen, J.; Paul, E.; Rembser, Ch.; Schramm, D.; Stamm, J.; Wedemeyer, R.; Campbell-Robson, S.; Cassidy, A.; Dyce, N.; Foster, B.; George, S.; Gilmore, R.; Heath, G. P.; Heath, H. F.; Llewellyn, T. J.; Morgado, C. J. S.; Norman, D. J. P.; O'Mara, J. A.; Tapper, R. J.; Wilson, S. S.; Yoshida, R.; Rau, R. R.; Arneodo, M.; Capua, M.; Garfagnini, A.; Iannotti, L.; Schioppa, M.; Susinno, G.; Bernstein, A.; Caldwell, A.; Cartiglia, N.; Parsons, J. A.; Ritz, S.; Sciulli, F.; Straub, P. B.; Wai, L.; Yang, S.; Zhu, Q.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Piotrzkowski, K.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Jeleń, K.; Kisielewska, D.; Kowalski, T.; Rulikowska-Zarębska, E.; Suszycki, L.; Zając, J.; Kotański, A.; Przybycień, M.; Bauerdick, L. A. T.; Behrens, U.; Beier, H.; Bienlein, J. K.; Coldewey, C.; Deppe, O.; Desler, K.; Drews, G.; Flasiński, M.; Gilkinson, D. J.; Glasman, C.; Göttlicher, P.; Große-Knetter, J.; Gutjahr, B.; Haas, T.; Hain, W.; Hasell, D.; Heßling, H.; Iga, Y.; Joos, P.; Kasemann, M.; Klanner, R.; Koch, W.; Köpke, L.; Kötz, U.; Kowalski, H.; Labs, J.; Ladage, A.; Löhr, B.; Löwe, M.; Lüke, D.; Mainusch, J.; Mańczak, O.; Monteiro, T.; Ng, J. S. T.; Nickel, S.; Notz, D.; Ohrenberg, K.; Roco, M.; Rohde, M.; Roldán, J.; Schneekloth, U.; Schulz, W.; Selonke, F.; Stiliaris, E.; Surrow, B.; Voß, T.; Westphal, D.; Wolf, G.; Youngman, C.; Zhou, J. F.; Grabosch, H. J.; Kharchilava, A.; Leich, A.; Mattingly, M. C. K.; Meyer, A.; Schlenstedt, S.; Wulff, N.; Barbagli, G.; Pelfer, P.; Anzivino, G.; Maccarrone, G.; de Pasquale, S.; Votano, L.; Bamberger, A.; Eisenhardt, S.; Freidhof, A.; Söldner-Rembold, S.; Schroeder, J.; Trefzger, T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Fleck, J. I.; Saxon, D. H.; Utley, M. L.; Wilson, A. S.; Dannemann, A.; Holm, U.; Horstmann, D.; Neumann, T.; Sinkus, R.; Wick, K.; Badura, E.; Burow, B. D.; Hagge, L.; Lohrmann, E.; Milewski, J.; Nakahata, M.; Pavel, N.; Poelz, G.; Schott, W.; Zetsche, F.; Bacon, T. C.; Butterworth, I.; Gallo, E.; Harris, V. L.; Hung, B. Y. H.; Long, K. R.; Miller, D. B.; Morawitz, P. P. O.; Prinias, A.; Sedgbeer, J. K.; Whitfield, A. F.; Mallik, U.; McCliment, E.; Wang, M. Z.; Wang, S. M.; Wu, J. T.; Zhang, Y.; Cloth, P.; Filges, D.; An, S. H.; Hong, S. M.; Nam, S. W.; Park, S. K.; Suh, M. H.; Yon, S. H.; Imlay, R.; Kartik, S.; Kim, H.-J.; McNeil, R. R.; Metcalf, W.; Nadendla, V. K.; Barreiro, F.; Cases, G.; Fernandez, J. P.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; Martinez, M.; Del Peso, J.; Puga, J.; Terron, J.; de Trocóniz, J. F.; Smith, G. R.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Matthews, C. G.; Patel, P. M.; Sinclair, L. E.; Stairs, D. G.; St. Laurent, M.; Ullmann, R.; Zacek, G.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Gladilin, L. K.; Golubkov, Yu. A.; Kobrin, V. D.; Korzhavina, I. A.; Kuzmin, V. A.; Lukina, O. Yu.; Proskuryakov, A. S.; Savin, A. A.; Shcheglova, L. M.; Solomin, A. N.; Zotov, N. P.; Botje, M.; Chlebana, F.; Dake, A.; Engelen, J.; de Kamps, M.; Kooijman, P.; Kruse, A.; Tiecke, H.; Verkerke, W.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; van Woudenberg, R.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Honscheid, K.; Li, C.; Ling, T. Y.; McLean, K. W.; Murray, W. N.; Park, I. H.; Romanowski, T. A.; Seidlein, R.; Bailey, D. S.; Byrne, A.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Devenish, R. C. E.; Harnew, N.; Lancaster, M.; Lindemann, L.; McFall, J. D.; Nath, C.; Noyes, V. A.; Quadt, A.; Tickner, J. R.; Uijterwaal, H.; Walczak, R.; Waters, D. S.; Wilson, F. F.; Yip, T.; Abbiendi, G.; Bertolin, A.; Brugnera, R.; Carlin, R.; Dal Corso, F.; de Giorgi, M.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Butterworth, J. M.; Feild, R. G.; Oh, B. Y.; Whitmore, J. J.; D'Agostini, G.; Marini, G.; Nigro, A.; Tassi, E.; Hart, J. C.; McCubbin, N. A.; Prytz, K.; Shah, T. P.; Short, T. L.; Barberis, E.; Dubbs, T.; Heusch, C.; van Hook, M.; Hubbard, B.; Lockman, W.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Biltzinger, J.; Seifert, R. J.; Schwarzer, O.; Walenta, A. H.; Zech, G.; Abramowicz, H.; Briskin, G.; Dagan, S.; Levy, A.; Hasegawa, T.; Hazumi, M.; Ishii, T.; Kuze, M.; Mine, S.; Nagasawa, Y.; Nakao, M.; Suzuki, I.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; Chiba, M.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Nakamitsu, Y.; Yamauchi, K.; Cirio, R.; Costa, M.; Ferrero, M. I.; Lamberti, L.; Maselli, S.; Peroni, C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Bandyopadhyay, D.; Benard, F.; Brkic, M.; Crombie, M. B.; Gingrich, D. M.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Sampson, C. R.; Teuscher, R. J.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Blankenship, K.; Lu, B.; Mo, L. W.; Bogusz, W.; Charchula, K.; Ciborowski, J.; Gajewski, J.; Grzelak, G.; Kasprzak, M.; Krzyżanowski, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Żarnecki, A. F.; Adamus, M.; Eisenberg, Y.; Karshon, U.; Revel, D.; Zer-Zion, D.; Ali, I.; Badgett, W. F.; Behrens, B.; Dasu, S.; Fordham, C.; Foudas, C.; Goussiou, A.; Loveless, R. J.; Reeder, D. D.; Silverstein, S.; Smith, W. H.; Vaiciulis, A.; Wodarczyk, M.; Tsurugai, T.; Bhadra, S.; Cardy, M. L.; Fagerstroem, C.-P.; Frisken, W. R.; Furutani, K. M.; Khakzad, M.; Schmidke, W. B.

1995-12-01

This paper presents an analysis of the inclusive properties of diffractive deep inelastic scattering events produced in ep interactions at HERA. The events are characterised by a rapidity gap between the outgoing proton system and the remaining hadronic system. Inclusive distributions are presented and compared with Monte Carlo models for diffractive processes. The data are consistent with models where the pomeron structure function has a hard and a soft contribution. The diffractive structure function is measured as a function of x ℙ, the momentum fraction lost by the proton, of β, the momentum fraction of the struck quark with respect to x ℙ, and of Q 2 in the range 6.3·10-4< x ℙ <10-2, 0.1<β<0.8 and 8< Q 2<100 GeV2. The dependence is consistent with the form x ℙ where a=1.30±0.08(stat) {-0.14/+0.08} (sys) in all bins of β and Q 2. In the measured Q 2 range, the diffractive structure function approximately scales with Q 2 at fixed β. In an Ingelman-Schlein type model, where commonly used pomeron flux factor normalisations are assumed, it is found that the quarks within the pomeron do not saturate the momentum sum rule.

Revealing proton shape fluctuations with incoherent diffraction at high energy

DOE PAGES

Mantysaari, H.; Schenke, B.

2016-08-30

The di erential cross section of exclusive di ractive vector meson production in electron proton collisions carries important information on the geometric structure of the proton. More speci cally, the coherent cross section as a function of the transferred transverse momentum is sensitive to the size of the proton, while the incoherent, or proton dissociative cross section is sensitive to uctuations of the gluon distribution in coordinate space. We show that at high energies the experimentally measured coherent and incoherent cross sections for the production of J= mesons are very well reproduced within the color glass condensate framework when strongmore » geometric uctuations of the gluon distribution in the proton are included. For meson production we also nd reasonable agreement. We study in detail the dependence of our results on various model parameters, including the average proton shape, analyze the e ect of saturation scale and color charge uctuations and constrain the degree of geometric uctuations.« less

A precision measurement of the spin structure functions g

NASA Astrophysics Data System (ADS)

Toole, Terrence S.

In Experiment E155 at the Stanford Linear Accelerator Center, the spin dependent structure function g1(x, Q 2) was measured for both the proton and deuteron. This was accomplished by scattering 48.3 GeV highly polarized electrons (0.813 +/- 0.020) off polarized 15NH3 (proton) and 6LiD (deuteron) targets. Data were collected in March and April of 1997 using three fixed angle, momentum analyzing spectrometers centered at 2.75°, 5.5°, and 10.5°. This enabled a kinematic coverage of 0.01 < x < 0.9 and 1 GeV2 < Q2 < 40 GeV2. At an average Q2 of 5 GeV2, the integrals in the measured region were ∑0.0140.9 g1 (x)dx = 0.119 +/- 0.002(stat.) +/- 0.009(syst.) for the proton and 0.043 +/- 0.003(stat.) +/- 0.003(syst.) for the deuteron. Using a perturbative QCD analysis which included a global data set, the results were found to be consistent with the Bjorken Sum Rule. Asymmetry measurements also were made using photoproduced hadrons. Data were collected concurrently with the g1 data. For the proton, the asymmetries were small and non-zero. The deuteron measurements were consistent with zero.

Review. The mammalian proton-coupled peptide cotransporter PepT1: sitting on the transporter-channel fence?

PubMed

Meredith, David

2009-01-27

The proton-coupled di- and tripeptide transporter PepT1 (SLC15a1) is the major route by which dietary nitrogen is taken up from the small intestine, as well as being the route of entry for important therapeutic (pro)drugs such as the beta-lactam antibiotics, angiotensin-converting enzyme inhibitors and antiviral and anti-cancer agents. PepT1 is a member of the major facilitator superfamily of 12 transmembrane domain transporter proteins. Expression studies in Xenopus laevis on rabbit PepT1 that had undergone site-directed mutagenesis of a conserved arginine residue (arginine282 in transmembrane domain 7) to a glutamate revealed that this residue played a role in the coupling of proton and peptide transport and prevented the movement of non-coupled ions during the transporter cycle. Mutations of arginine282 to other non-positive residues did not uncouple proton-peptide cotransport, but did allow additional ion movements when substrate was added. By contrast, mutations to positive residues appeared to function the same as wild-type. These findings are discussed in relation to the functional role that arginine282 may play in the way PepT1 operates, together with structural information from the homology model of PepT1 based on the Escherichia coli lactose permease crystal structure.

Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus

PubMed Central

Khurana, Ekta; Peraro, Matteo Dal; DeVane, Russell; Vemparala, Satyavani; DeGrado, William F.; Klein, Michael L.

2009-01-01

The M2 protein of the influenza A virus is activated by low endosomal pH and performs the essential function of proton transfer into the viral interior. The resulting decrease in pH within the virion is essential for the uncoating and further replication of the viral genetic material. The x-ray crystal [Stouffer AL, et al. (2008) Nature 451:596–599] and solution NMR [Schnell JR, Chou JJ (2008) Nature 451:591–595] structures of the transmembrane region of the M2 homo-tetrameric bundle both revealed pores with narrow constrictions at one end, leaving a question as to how protons enter the channel. His-37, which is essential for proton-gating and selective conduction of protons, lies in the pore of the crystallographic and NMR structures. Here, we explore the different protonation states of the His-37 residues of the M2 bundle in a bilayer using molecular dynamics (MD) simulations. When the His-37 residues are neutral, the protein prefers an Openout-Closedin conformation in which the channel is open to the environment on the outside of the virus but closed to the interior environment of the virus. Diffusion of protons into the channel from the outside of the virus and protonation of His-37 residues in the tetramer stabilizes an oppositely gated Closedout-Openin conformation. Thus, protons might be conducted through a transporter-like mechanism, in which the protein alternates between Openout-Closedin and Closedout-Openin conformations, and His-37 is protonated/deprotonated during each turnover. The transporter-like mechanism is consistent with the known properties of the M2 bundle, including its relatively low rate of proton flux and its strong rectifying behavior. PMID:19144924

SU(2) Flavor Asymmetry of the Proton Sea in Chiral Effective Theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKenney, J. R.; Sato Gonzalez, Nobuo; Melnitchouk, Wally

We refine the computation of themore » $$\\bar{d}$$ - $$\\bar{u}$$ flavor asymmetry in the proton sea with a complementary effort to reveal the dynamics of pion exchange in high-energy processes. In particular, we discuss the efficacy of pion exchange models to simultaneously describe leading neutron electroproduction at HERA along with the $$\\bar{d}$$ - $$\\bar{u}$$ flavor asymmetry in the proton. A detailed χ 2 analysis of the ZEUS and H1 data, when combined with constraints on the pion flux from Drell-Yan data, allows regions of applicability of one-pion exchange to be delineated. Based on the fit results, we also address a possible estimate for leading proton structure functions in upcoming tagged deep-inelastic scattering experiments at Jefferson Lab on the deuteron with forward protons.« less

Electronic-structure and quantum dynamical study of the photochromism of the aromatic Schiff base salicylideneaniline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ortiz-Sanchez, Juan Manuel; Gelabert, Ricard; Moreno, Miquel

2008-12-07

The ultrafast proton transfer dynamics of salicylideneaniline has been theoretically analyzed in the ground and first singlet excited electronic states using density functional theory (DFT) and time-dependent DFT calculations, which predict a ({pi},{pi}*) barrierless excited state intramolecular proton transfer (ESIPT). In addition to this, the photochemistry of salicylideneaniline is experimentally known to present fast depopulation processes of the photoexcited species before and after the proton transfer reaction. Such processes are explained by means of conical intersections between the ground and first singlet ({pi},{pi}*) excited electronic states. The electronic energies obtained by the time-dependent density functional theory formalism have been fittedmore » to a monodimensional potential energy surface in order to perform quantum dynamics study of the processes. Our results show that the proton transfer and deactivation of the photoexcited species before the ESIPT processes are completed within 49.6 and 37.7 fs, respectively, which is in remarkable good agreement with experiments.« less

Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.

PubMed

Mazhab-Jafari, Mohammad T; Rohou, Alexis; Schmidt, Carla; Bueler, Stephanie A; Benlekbir, Samir; Robinson, Carol V; Rubinstein, John L

2016-11-03

Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V 1 region drives proton translocation through the membrane-embedded V O region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V 1 and V O regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the V O complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac 8 c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.

Structure Functions of Bound Neutrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sebastian Kuhn

2005-04-01

We describe an experiment measuring electron scattering on a neutron bound in deuterium with coincident detection of a fast, backward-going spectator proton. Our data map out the relative importance of the pure PWIA spectator mechanism and final state interactions in various kinematic regions, and give a first glimpse of the modification of the structure function of a bound neutron as a function of its off-shell mass. We also discuss a new experimental program to study the structure of a free neutron by extending the same technique to much lower spectator momenta.

Conductivity equations of protons transporting through 2D crystals obtained with the rate process theory and free volume concept

NASA Astrophysics Data System (ADS)

Hao, Tian; Xu, Yuanze; Hao, Ting

2018-04-01

The Eyring's rate process theory and free volume concept are employed to treat protons (or other particles) transporting through a 2D (two dimensional) crystal like graphene and hexagonal boron nitride. The protons are assumed to be activated first in order to participate conduction and the conduction rate is dependent on how much free volume available in the system. The obtained proton conductivity equations show that only the number of conduction protons, proton size and packing structure, and the energy barrier associated with 2D crystals are critical; the quantization conductance is unexpectedly predicted with a simple Arrhenius type temperature dependence. The predictions agree well with experimental observations and clear out many puzzles like much smaller energy barrier determined from experiments than from the density function calculations and isotope separation rate independent of the energy barrier of 2D crystals, etc. Our work may deepen our understandings on how protons transport through a membrane and has direct implications on hydrogen related technology and proton involved bioprocesses.

Moments of the spin structure functions g1p and g1d for 0.05

NASA Astrophysics Data System (ADS)

Clas Collaboration; Prok, Y.; Bosted, P.; Burkert, V. D.; Deur, A.; Dharmawardane, K. V.; Dodge, G. E.; Griffioen, K. A.; Kuhn, S. E.; Minehart, R.; Adams, G.; Amaryan, M. J.; Anghinolfi, M.; Asryan, G.; Audit, G.; Avakian, H.; Bagdasaryan, H.; Baillie, N.; Ball, J. P.; Baltzell, N. A.; Barrow, S.; Battaglieri, M.; Beard, K.; Bedlinskiy, I.; Bektasoglu, M.; Bellis, M.; Benmouna, N.; Berman, B. L.; Biselli, A. S.; Blaszczyk, L.; Boiarinov, S.; Bonner, B. E.; Bouchigny, S.; Bradford, R.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Bültmann, S.; Butuceanu, C.; Calarco, J. R.; Careccia, S. L.; Carman, D. S.; Casey, L.; Cazes, A.; Chen, S.; Cheng, L.; Cole, P. L.; Collins, P.; Coltharp, P.; Cords, D.; Corvisiero, P.; Crabb, D.; Crede, V.; Cummings, J. P.; Dale, D.; Dashyan, N.; de Masi, R.; de Vita, R.; de Sanctis, E.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; Dhuga, K. S.; Dickson, R.; Djalali, C.; Doughty, D.; Dugger, M.; Dytman, S.; Dzyubak, O. P.; Egiyan, H.; Egiyan, K. S.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fatemi, R.; Fedotov, G.; Feldman, G.; Fersh, R. G.; Feuerbach, R. J.; Forest, T. A.; Fradi, A.; Funsten, H.; Garçon, M.; Gavalian, G.; Gevorgyan, N.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Golovatch, E.; Gothe, R. W.; Guidal, M.; Guillo, M.; Guler, N.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Hardie, J.; Hassall, N.; Heddle, D.; Hersman, F. W.; Hicks, K.; Hleiqawi, I.; Holtrop, M.; Huertas, M.; Hyde-Wright, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Ito, M. M.; Jenkins, D.; Jo, H. S.; Johnstone, J. R.; Joo, K.; Juengst, H. G.; Kalantarians, N.; Keith, C. D.; Kellie, J. D.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klusman, M.; Kossov, M.; Krahn, Z.; Kramer, L. H.; Kubarovsky, V.; Kuhn, J.; Kuleshov, S. V.; Kuznetsov, V.; Lachniet, J.; Laget, J. M.; Langheinrich, J.; Lawrence, D.; Li, Ji; Lima, A. C. S.; Livingston, K.; Lu, H. Y.; Lukashin, K.; MacCormick, M.; Marchand, C.; Markov, N.; Mattione, P.; McAleer, S.; McKinnon, B.; McNabb, J. W. C.; Mecking, B. A.; Mestayer, M. D.; Meyer, C. A.; Mibe, T.; Mikhailov, K.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morand, L.; Moreno, B.; Moriya, K.; Morrow, S. A.; Moteabbed, M.; Mueller, J.; Munevar, E.; Mutchler, G. S.; Nadel-Turonski, P.; Nasseripour, R.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niroula, M. R.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Osipenko, M.; Ostrovidov, A. I.; Park, K.; Pasyuk, E.; Paterson, C.; Pereira, S. Anefalos; Philips, S. A.; Pierce, J.; Pivnyuk, N.; Pocanic, D.; Pogorelko, O.; Popa, I.; Pozdniakov, S.; Preedom, B. M.; Price, J. W.; Procureur, S.; Protopopescu, D.; Qin, L. M.; Raue, B. A.; Riccardi, G.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Rosner, G.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Salamanca, J.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Schumacher, R. A.; Seely, M. L.; Serov, V. S.; Sharabian, Y. G.; Sharov, D.; Shaw, J.; Shvedunov, N. V.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Sokhan, D.; Stavinsky, A.; Stepanyan, S. S.; Stepanyan, S.; Stokes, B. E.; Stoler, P.; Strakovsky, I. I.; Strauch, S.; Suleiman, R.; Taiuti, M.; Tedeschi, D. J.; Tkabladze, A.; Tkachenko, S.; Todor, L.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Watts, D. P.; Weinstein, L. B.; Weygand, D. P.; Williams, M.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zana, L.; Zhang, J.; Zhao, B.; Zhao, Z. W.

2009-02-01

The spin structure functions g for the proton and the deuteron have been measured over a wide kinematic range in x and Q using 1.6 and 5.7 GeV longitudinally polarized electrons incident upon polarized NH3 and ND3 targets at Jefferson Lab. Scattered electrons were detected in the CEBAF Large Acceptance Spectrometer, for 0.05

Production of W + W - pairs via γ * γ * → W + W - subprocess with photon transverse momenta

NASA Astrophysics Data System (ADS)

Łuszczak, Marta; Schäfer, Wolfgang; Szczurek, Antoni

2018-05-01

We discuss production of W + W - pairs in proton-proton collisions induced by two-photon fusion including, for a first time, transverse momenta of incoming photons. The unintegrated inelastic fluxes (related to proton dissociation) of photons are calculated based on modern parametrizations of deep inelastic structure functions in a broad range of their arguments ( x and Q 2). In our approach we can get separate contributions of different W helicities states. Several one- and two-dimensional differential distributions are shown and discussed. The present results are compared to the results of previous calculations within collinear factorization approach. Similar results are found except of some observables such as e.g. transverse momentum of the pair of W + and W -. We find large contributions to the cross section from the region of large photon virtualities. We show decomposition of the total cross section as well as invariant mass distribution into the polarisation states of both W bosons. The role of the longitudinal F L structure function is quantified. Its inclusion leads to a 4-5% decrease of the cross section, almost independent of M WW .

Persistent gastro-oesophageal reflux symptoms despite proton pump inhibitor therapy

PubMed Central

Ang, Daphne; How, Choon How; Ang, Tiing Leong

2016-01-01

About one-third of patients with suspected gastro-oesophageal reflux disease (GERD) do not respond symptomatically to proton pump inhibitors (PPIs). Many of these patients do not suffer from GERD, but may have underlying functional heartburn or atypical chest pain. Other causes of failure to respond to PPIs include inadequate acid suppression, non-acid reflux, oesophageal hypersensitivity, oesophageal dysmotility and psychological comorbidities. Functional oesophageal tests can exclude cardiac and structural causes, as well as help to confi rm or exclude GERD. The use of PPIs should only be continued in the presence of acid reflux or oesophageal hypersensitivity for acid reflux-related events that is proven on functional oesophageal tests. PMID:27779277

Persistent gastro-oesophageal reflux symptoms despite proton pump inhibitor therapy.

PubMed

Ang, Daphne; How, Choon How; Ang, Tiing Leong

2016-10-01

About one-third of patients with suspected gastro-oesophageal reflux disease (GERD) do not respond symptomatically to proton pump inhibitors (PPIs). Many of these patients do not suffer from GERD, but may have underlying functional heartburn or atypical chest pain. Other causes of failure to respond to PPIs include inadequate acid suppression, non-acid reflux, oesophageal hypersensitivity, oesophageal dysmotility and psychological comorbidities. Functional oesophageal tests can exclude cardiac and structural causes, as well as help to confi rm or exclude GERD. The use of PPIs should only be continued in the presence of acid reflux or oesophageal hypersensitivity for acid reflux-related events that is proven on functional oesophageal tests. Copyright: © Singapore Medical Association.

Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form.

PubMed

Shevchenko, Vitaly; Gushchin, Ivan; Polovinkin, Vitaly; Round, Ekaterina; Borshchevskiy, Valentin; Utrobin, Petr; Popov, Alexander; Balandin, Taras; Büldt, Georg; Gordeliy, Valentin

2014-01-01

Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas

2016-11-16

MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic mechanism requires multiple proton-transfer events. Of particular interest is the protonation state of residue D198, which possesses a pKa above 8 and functions as a general acid to initiate the enzymatic reaction. In this study we present three corefined neutron/X-ray crystal structures of wild-type HpMTAN cocrystallized with S-adenosylhomocysteine (SAH), Formycinmore » A (FMA), and (3R,4S)-4-(4-Chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine (p-ClPh-Thio-DADMe-ImmA) as well as one neutron/X-ray crystal structure of an inactive variant (HpMTAN-D198N) cocrystallized with SAH. These results support a mechanism of D198 pKa elevation through the unexpected sharing of a proton with atom N7 of the adenine moiety possessing unconventional hydrogen-bond geometry. Additionally, the neutron structures also highlight active site features that promote the stabilization of the transition state and slight variations in these interactions that result in 100-fold difference in binding affinities between the DADMe-ImmA and ImmA analogs.« less

Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas

MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic mechanism requires multiple proton-transfer events. Of particular interest is the protonation state of residue D198, which possesses a pK a above 8 and functions as a general acid to initiate the enzymatic reaction. In this study we present three corefined neutron/X-ray crystal structures of wild-type HpMTAN cocrystallized with S-adenosylhomocysteine (SAH),more » Formycin A (FMA), and (3R,4S)-4-(4-Chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine (p-ClPh-Thio-DADMe-ImmA) as well as one neutron/X-ray crystal structure of an inactive variant (HpMTAN-D198N) cocrystallized with SAH. These results support a mechanism of D198 pKa elevation through the unexpected sharing of a proton with atom N7 of the adenine moiety possessing unconventional hydrogen-bond geometry. Additionally, the neutron structures also highlight active site features that promote the stabilization of the transition state and slight variations in these interactions that result in 100-fold difference in binding affinities between the DADMe-ImmA and ImmA analogs.« less

Neutron structures of the Helicobacter pylori 5'-methylthioadenosine nucleosidase highlight proton sharing and protonation states

DOE PAGES

Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas; ...

2016-10-01

MTAN (5'-methylthioadenosine nucleosidase) catalyzes the hydrolysis of the N-ribosidic bond of a variety of adenosine-containing metabolites. The Helicobacter pylori MTAN (HpMTAN) hydrolyzes 6-amino-6-deoxyfutalosine in the second step of the alternative menaquinone biosynthetic pathway. Substrate binding of the adenine moiety is mediated almost exclusively by hydrogen bonds, and the proposed catalytic mechanism requires multiple proton-transfer events. Of particular interest is the protonation state of residue D198, which possesses a pK a above 8 and functions as a general acid to initiate the enzymatic reaction. In this study we present three corefined neutron/X-ray crystal structures of wild-type HpMTAN cocrystallized with S-adenosylhomocysteine (SAH),more » Formycin A (FMA), and (3R,4S)-4-(4-Chlorophenylthiomethyl)-1-[(9-deaza-adenin-9-yl)methyl]-3-hydroxypyrrolidine (p-ClPh-Thio-DADMe-ImmA) as well as one neutron/X-ray crystal structure of an inactive variant (HpMTAN-D198N) cocrystallized with SAH. These results support a mechanism of D198 pKa elevation through the unexpected sharing of a proton with atom N7 of the adenine moiety possessing unconventional hydrogen-bond geometry. Additionally, the neutron structures also highlight active site features that promote the stabilization of the transition state and slight variations in these interactions that result in 100-fold difference in binding affinities between the DADMe-ImmA and ImmA analogs.« less

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba 2In 2O 4(OH) 2 Structure and Dynamics

DOE PAGES

Dervisoglu, Riza; Middlemiss, Derek S.; Blanc, Frederic; ...

2015-05-01

Here, a structural characterization of the hydrated form of the brownmillerite-type phase Ba 2In 2O 5, Ba 2In 2O 4(OH) 2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics 2004, 170, 25–32) using X-ray and neutron studies. Calculationsmore » of possible proton arrangements within the partially occupied layer of Ba 2In 2O 4(OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H– 17O double resonance experiments.« less

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics.

PubMed

Dervişoğlu, Rıza; Middlemiss, Derek S; Blanc, Frédéric; Lee, Yueh-Lin; Morgan, Dane; Grey, Clare P

2015-06-09

A structural characterization of the hydrated form of the brownmillerite-type phase Ba 2 In 2 O 5 , Ba 2 In 2 O 4 (OH) 2 , is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H 2 O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25-32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba 2 In 2 O 4 (OH) 2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1 H and 17 O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1 H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1 H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17 O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1 H- 17 O double resonance experiments.

Joint Experimental and Computational 17O and 1H Solid State NMR Study of Ba2In2O4(OH)2 Structure and Dynamics

PubMed Central

2015-01-01

A structural characterization of the hydrated form of the brownmillerite-type phase Ba2In2O5, Ba2In2O4(OH)2, is reported using experimental multinuclear NMR spectroscopy and density functional theory (DFT) energy and GIPAW NMR calculations. When the oxygen ions from H2O fill the inherent O vacancies of the brownmillerite structure, one of the water protons remains in the same layer (O3) while the second proton is located in the neighboring layer (O2) in sites with partial occupancies, as previously demonstrated by Jayaraman et al. (Solid State Ionics2004, 170, 25−32) using X-ray and neutron studies. Calculations of possible proton arrangements within the partially occupied layer of Ba2In2O4(OH)2 yield a set of low energy structures; GIPAW NMR calculations on these configurations yield 1H and 17O chemical shifts and peak intensity ratios, which are then used to help assign the experimental MAS NMR spectra. Three distinct 1H resonances in a 2:1:1 ratio are obtained experimentally, the most intense resonance being assigned to the proton in the O3 layer. The two weaker signals are due to O2 layer protons, one set hydrogen bonding to the O3 layer and the other hydrogen bonding alternately toward the O3 and O1 layers. 1H magnetization exchange experiments reveal that all three resonances originate from protons in the same crystallographic phase, the protons exchanging with each other above approximately 150 °C. Three distinct types of oxygen atoms are evident from the DFT GIPAW calculations bare oxygens (O), oxygens directly bonded to a proton (H-donor O), and oxygen ions that are hydrogen bonded to a proton (H-acceptor O). The 17O calculated shifts and quadrupolar parameters are used to assign the experimental spectra, the assignments being confirmed by 1H–17O double resonance experiments. PMID:26321789

Models for the a subunits of the Thermus thermophilus V/A-ATPase and Saccharomyces cerevisiae V-ATPase enzymes by cryo-EM and evolutionary covariance

PubMed Central

Schep, Daniel G.; Rubinstein, John L.

2016-01-01

Rotary ATPases couple ATP synthesis or hydrolysis to proton translocation across a membrane. However, understanding proton translocation has been hampered by a lack of structural information for the membrane-embedded a subunit. The V/A-ATPase from the eubacterium Thermus thermophilus is similar in structure to the eukaryotic V-ATPase but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. We determined the T. thermophilus V/A-ATPase structure by cryo-EM at 6.4 Å resolution. Evolutionary covariance analysis allowed tracing of the a subunit sequence within the map, providing a complete model of the rotary ATPase. Comparing the membrane-embedded regions of the T. thermophilus V/A-ATPase and eukaryotic V-ATPase from Saccharomyces cerevisiae allowed identification of the α-helices that belong to the a subunit and revealed the existence of previously unknown subunits in the eukaryotic enzyme. Subsequent evolutionary covariance analysis enabled construction of a model of the a subunit in the S. cerevisae V-ATPase that explains numerous biochemical studies of that enzyme. Comparing the two a subunit structures determined here with a structure of the distantly related a subunit from the bovine F-type ATP synthase revealed a conserved pattern of residues, suggesting a common mechanism for proton transport in all rotary ATPases. PMID:26951669

Biomimetics of [NiFe]-Hydrogenase: Nickel- or Iron-Centered Proton Reduction Catalysis?

PubMed

Tang, Hao; Hall, Michael B

2017-12-13

The [NiFe] hydrogenase (H2ase) has been characterized in the Ni-R state with a hydride bridging between Fe and Ni but displaced toward the Ni. In nearly all of the synthetic Ni-R models reported so far, the hydride ligand is either displaced toward Fe, or terminally bound to Fe. Recently, a structural and functional [NiFe]-H2ase mimic ( Nat. Chem. 2016 , 8 , 1054 - 1060 ) was reported to produce H 2 catalytically via EECC mechanism through a Ni-centered hydride intermediate like the enzyme. Here, a comprehensive DFT study shows a much lower energy route via an E[ECEC] mechanism through an Fe-centered hydride intermediate. Although catalytic H 2 production occurs at the potential corresponding to the complex's second reduction, a third electron is needed to induce the second proton addition from the weak acid. The first two-electron reductions and a proton addition produce a semibridging hydride with a short Fe-H bond like other structured [NiFe]-biomimetics, but this species is not basic enough to add another proton from the weak acid without the third electron. The calculated mechanism provides insight into the origin of this structure in the enzyme.

Removal of distal protein–water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability

PubMed Central

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L.; Widersten, Mikael

2008-01-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro186, Leu266, His269, and the His153 imidazole. The hydroxyl of Tyr149 is also an integrated component of the chain, which leads to the hydroxyl of Tyr154. Available data suggest that Tyr154 functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 Å resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k cat/K M was similar or slightly increased compared with the wild-type reactions. k cat for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K M. Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k cat but lowered thermostability. PMID:18515642

Building a stable RNA U-turn with a protonated cytidine.

PubMed

Gottstein-Schmidtke, Sina R; Duchardt-Ferner, Elke; Groher, Florian; Weigand, Julia E; Gottstein, Daniel; Suess, Beatrix; Wöhnert, Jens

2014-08-01

The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone. © 2014 Gottstein-Schmidtke et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability.

PubMed

Thomaeus, Ann; Naworyta, Agata; Mowbray, Sherry L; Widersten, Mikael

2008-07-01

A putative proton wire in potato soluble epoxide hydrolase 1, StEH1, was identified and investigated by means of site-directed mutagenesis, steady-state kinetic measurements, temperature inactivation studies, and X-ray crystallography. The chain of hydrogen bonds includes five water molecules coordinated through backbone carbonyl oxygens of Pro(186), Leu(266), His(269), and the His(153) imidazole. The hydroxyl of Tyr(149) is also an integrated component of the chain, which leads to the hydroxyl of Tyr(154). Available data suggest that Tyr(154) functions as a final proton donor to the anionic alkylenzyme intermediate formed during catalysis. To investigate the role of the putative proton wire, mutants Y149F, H153F, and Y149F/H153F were constructed and purified. The structure of the Y149F mutant was solved by molecular replacement and refined to 2.0 A resolution. Comparison with the structure of wild-type StEH1 revealed only subtle structural differences. The hydroxyl group lost as a result of the mutation was replaced by a water molecule, thus maintaining a functioning hydrogen bond network in the proton wire. All mutants showed decreased catalytic efficiencies with the R,R-enantiomer of trans-stilbene oxide, whereas with the S,S-enantiomer, k (cat)/K (M) was similar or slightly increased compared with the wild-type reactions. k (cat) for the Y149F mutant with either TSO enantiomer was increased; thus the lowered enzyme efficiencies were due to increases in K (M). Thermal inactivation studies revealed that the mutated enzymes were more sensitive to elevated temperatures than the wild-type enzyme. Hence, structural alterations affecting the hydrogen bond chain caused increases in k (cat) but lowered thermostability.

Mechanism of electrocatalytic hydrogen production by a di-iron model of iron-iron hydrogenase: a density functional theory study of proton dissociation constants and electrode reduction potentials.

PubMed

Surawatanawong, Panida; Tye, Jesse W; Darensbourg, Marcetta Y; Hall, Michael B

2010-03-28

Simple dinuclear iron dithiolates such as (mu-SCH2CH2CH2S)[Fe(CO)3]2, (1) and (mu-SCH2CH2S)[Fe(CO)3]2 (2) are functional models for diiron-hydrogenases, [FeFe]-H2ases, that catalyze the reduction of protons to H2. The mechanism of H2 production with 2 as the catalyst and with both toluenesulfonic (HOTs) and acetic (HOAc) acids as the H+ source in CH3CN solvent has been examined by density functional theory (DFT). Proton dissociation constants (pKa) and electrode reduction potentials (E(o)) are directly computed and compared to the measured pKa of HOTs and HOAc acids and the experimental reduction potentials. Computations show that when the strong acid, HOTs, is used as a proton source the one-electron reduced species 2- can be protonated to form a bridging hydride complex as the most stable structure. Then, this species can be reduced and protonated to form dihydrogen and regenerate 2. This cycle produces H2 via an ECEC process at an applied potential of -1.8 V vs. Fc/Fc+. A second faster process opens for this system when the species produced at the ECEC step above is further reduced and H2 release returns the system to 2- rather than 2, an E[CECE] process. On the other hand, when the weak acid, HOAc, is the proton source a more negative applied reduction potential (-2.2 V vs. Fc/Fc+) is necessary. At this potential two one-electron reductions yield the dianion 2(2-) before the first protonation, which in this case occurs on the thiolate. Subsequent reduction and protonation form dihydrogen and regenerate 2- through an E[ECEC] process.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE PAGES

Park, Kiyoung; Li, Ning; Kwak, Yeonju; ...

2017-05-01

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Kiyoung; Li, Ning; Kwak, Yeonju

Binuclear non-heme iron enzymes activate O 2 for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O 2. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reactionmore » shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. As a result, this activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.« less

Computer Modeling of the Earliest Cellular Structures and Functions

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl

2000-01-01

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

The Hydric Effect in Inorganic Nanomaterials for Nanoelectronics and Energy Applications.

PubMed

Sun, Xu; Guo, Yuqiao; Wu, Changzheng; Xie, Yi

2015-07-08

Protons, as one of the world's smallest ions, are able to trigger the charge effect without obvious lattice expansion inside inorganic materials, offering a unique and important test-bed for controlling their diverse functionalities. Arising from the high chemical reactivity of hydrogen (easily losing an electron) with various main group anions (easily accepting a proton), the hydric effect provides a convenient and environmentally benign route to bring about fascinating new physicochemical properties, as well as to create new inorganic structures based on the "old lattice" without dramatically destroying the pristine structure, covering most inorganic materials. Moreover, hydrogen atoms tend to bond with anions or to produce intrinsic defects, both of which are expected to inject extra electrons into lattice framework, promising advances in control of bandgap, spin behavior, and carrier concentration, which determine functionality for wide applications. In this review article, recently developed effective hydric strategies are highlighted, which include the conventional hydric reaction under high temperature or room temperature, proton irradiation or hydrogen plasma treatment, and gate-electrolyte-driven adsorption or doping. The diverse physicochemical properties brought by the hydric effect via modulation of the intrinsic electronic structure are also summarized, finding wide applications in nanoelectronics, energy applications, and catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multidrug efflux transporter, AcrB--the pumping mechanism.

PubMed

Murakami, Satoshi

2008-08-01

Resistance nodulation cell division (RND) transporters are one of the main causes of the bacterial multidrug resistance. They pump a wide range of antibiotics out of the cell by proton motive force. AcrB is the major RND transporter in Escherichia coli. Recently, the crystal structures of AcrB have been determined by different space groups. All these structures are consistent with asymmetric trimer. Each monomer has different conformation corresponding to one of the three functional states of the transport cycle. Transporting hydrophobic drug was bound in the periplasmic domain on one of the three monomers. The transport pathway with alternating access mechanism is located at the hydrophilic domain protruded into the periplasmic space while this mechanism of other transporter families like ATP binding cassette (ABC) and major facilitator superfamily (MFS) transporter is located in the membrane-embedded region. For the RND, protonation might also take place asymmetrically at the functionally important charged residues in the transmembrane (TM) region. The structures indicate that drugs are transported by a three-step functional rotation in which substrates undergo ordered binding change.

Ligand versus metal protonation of an iron hydrogenase active site mimic.

PubMed

Eilers, Gerriet; Schwartz, Lennart; Stein, Matthias; Zampella, Giuseppe; de Gioia, Luca; Ott, Sascha; Lomoth, Reiner

2007-01-01

The protonation behavior of the iron hydrogenase active-site mimic [Fe2(mu-adt)(CO)4(PMe3)2] (1; adt=N-benzyl-azadithiolate) has been investigated by spectroscopic, electrochemical, and computational methods. The combination of an adt bridge and electron-donating phosphine ligands allows protonation of either the adt nitrogen to give [Fe2(mu-Hadt)(CO)4(PMe3)2]+ ([1 H]+), the Fe-Fe bond to give [Fe2(mu-adt)(mu-H)(CO)4(PMe3)2]+ ([1 Hy]+), or both sites simultaneously to give [Fe2(mu-Hadt)(mu-H)(CO)4(PMe3)2]2+ ([1 HHy]2 +). Complex 1 and its protonation products have been characterized in acetonitrile solution by IR, (1)H, and (31)P NMR spectroscopy. The solution structures of all protonation states feature a basal/basal orientation of the phosphine ligands, which contrasts with the basal/apical structure of 1 in the solid state. Density functional calculations have been performed on all protonation states and a comparison between calculated and experimental spectra confirms the structural assignments. The ligand protonated complex [1 H]+ (pKa=12) is the initial, metastable protonation product while the hydride [1 Hy]+ (pKa=15) is the thermodynamically stable singly protonated form. Tautomerization of cation [1 H]+ to [1 Hy]+ does not occur spontaneously. However, it can be catalyzed by HCl (k=2.2 m(-1) s(-1)), which results in the selective formation of cation [1 Hy]+. The protonations of the two basic sites have strong mutual effects on their basicities such that the hydride (pK(a)=8) and the ammonium proton (pK(a)=5) of the doubly protonated cationic complex [1 HHy]2+ are considerably more acidic than in the singly protonated analogues. The formation of dication [1 HHy]2+ from cation [1 H]+ is exceptionally slow with perchloric or trifluoromethanesulfonic acid (k=0.15 m(-1) s(-1)), while the dication is formed substantially faster (k>10(2) m(-1) s(-1)) with hydrobromic acid. Electrochemically, 1 undergoes irreversible reduction at -2.2 V versus ferrocene, and this potential shifts to -1.6, -1.1, and -1.0 V for the cationic complexes [1 H]+, [1 Hy]+, and [1 HHy]2+, respectively, upon protonation. The doubly protonated form [1 HHy]2+ is reduced at less negative potential than all previously reported hydrogenase models, although catalytic proton reduction at this potential is characterized by slow turnover.

The determination of the in situ structure by nuclear spin contrast variation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stuhrmann, H.B.; Nierhaus, K.H.

1994-12-31

Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

PubMed

Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

2014-02-01

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Antiplasmodial Drugs in the Gas Phase: A CID and DFT Study of Quinolon-4( 1H)-Imine Derivatives

NASA Astrophysics Data System (ADS)

Amorim Madeira, Paulo J.; Sitoe, Ana Raquel Fernandes; Gonçalves, Daniel; Rodrigues, Tiago; Guedes, Rita C.; Lopes, Francisca; Moreira, Rui; Bronze, M. Rosário

2014-09-01

The gas-phase behavior of 12 quinolon-4( 1H)-imine derivatives with antiplasmodial activity was investigated using electrospray ionization tandem mass spectrometry together with collision induced dissociation and density functional theory (DFT) calculations. The most probable protonation site was predicted by calculating the proton affinity (PA) values for each possible protonation site and it was found to be the imine nitrogen for all compounds under study. Fragmentation pathways of the protonated molecules were proposed and the assignment of product ion structures was performed taking into account theoretical calculations. The nature of the quinoline substituent was found to influence the gas-phase behavior of the compounds under study. The data acquired allowed to bracket the proton affinity of the quinolin-4-imine scaffold, which can be a useful starting point to choose appropriate references for determining PA values of this scaffold.

DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase.

PubMed

Lintuluoto, Masami; Lintuluoto, Juha M

2016-01-12

Dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.

Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates

NASA Astrophysics Data System (ADS)

Vener, M. V.; Chernyshov, I. Yu.; Rykounov, A. A.; Filarowski, A.

2018-01-01

Crystalline HCl and CF3SO3H hydrates serve as excellent model systems for protonated water and perfluorosulphonic acid membranes, respectively. They contain characteristic H3O+, H5О+2, H7О+3 and H3O+(H2O)3 (the Eigen cation) structures. The properties of these cations in the crystalline hydrates of strong monobasic acids are studied by solid-state density function theory (DFT). Simultaneous consideration of the HCl and CF3SO3H hydrates reveals the impact of the size of a counter ion and the crystalline environment on the structure and infrared active bands of the simplest proton hydrates. The H7O+3 structure is very sensitive to the size of the counter ion and symmetry of the local environment. This makes it virtually impossible to identify the specific features of H7O+3 in molecular crystals. The H3O+ ion can be treated as the Eigen-like cation in the crystalline state. Structural, infrared and electron-density features of H5О+2 and the Eigen cation are virtually insensitive to the size of the counter ion and the symmetry of the local crystalline environment. These cations can be considered as the simplest stable proton hydrates in the condensed phase. Finally, the influence of the Grimme correction on the structure and harmonic frequencies of the molecular crystals with short (strong) intermolecular O-H···O bonds is discussed.

Peptides at Membrane Surfaces and their Role in the Origin of Life

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, D. (Technical Monitor)

2002-01-01

All ancestors of contemporary cells (protocells) had to transport ions and organic matter across membranous walls, capture and utilize energy and transduce environmental signals. In modern organisms, all these functions are preformed by membrane proteins. We make the parsimonious assumption that in the protobiological milieu the same functions were carried out by their simple analogs - peptides. This, however, required that simple peptides could self-organize into ordered, functional structures. In a series of detailed, molecular-level computer simulations we demonstrated how this is possible. One example is the peptide (LSLLLSL)3 which forms a trameric bundle capable of transporting protons across membranes. Another example is the transmembrane pore of the influenza M2 protein. This aggregate of four identical alpha-helices, each built of 25 amino acids, forms an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism in this channel. The channel can be re-engineered into a simple proton pump.

Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.

PubMed

ten Brink, Tim; Exner, Thomas E

2009-06-01

In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers.

Exceptionally High Proton and Lithium Cation Gas-Phase Basicity of the Anti-Diabetic Drug Metformin.

PubMed

Raczyńska, Ewa D; Gal, Jean-François; Maria, Pierre-Charles; Michalec, Piotr; Zalewski, Marcin

2017-11-16

Substituted biguanides are known for their biological effect, and a few of them are used as drugs, the most prominent example being metformin (1,1-dimethylbiguanide, IUPAC name: N,N-dimethylimidodicarbonimidic diamide). Because of the presence of hydrogen atoms at the amino groups, biguanides exhibit a multiple tautomerism. This aspect of their structures was examined in detail for unsubstituted biguanide and metformin in the gas phase. At the density functional theory (DFT) level {essentially B3LYP/6-311+G(d,p)}, the most stable structures correspond to the conjugated, push-pull, system (NR 2 )(NH 2 )C═N-C(═NH)NH 2 (R = H, CH 3 ), further stabilized by an internal hydrogen bond. The structural and energetic aspects of protonation and lithium cation adduct formation of biguanide and metformin was examined at the same level of theory. The gas-phase protonation energetics reveal that the more stable tautomer is protonated at the terminal imino C═NH site, still with an internal hydrogen bond maintaining the structure of the neutral system. The calculated proton affinity and gas-phase basicity of the two molecules reach the domain of superbasicity. By contrast, the lithium cation prefers to bind the less stable, not fully conjugated, tautomer (NR 2 )C(═NH)-NH-C(═NH)NH 2 of biguanides, in which the two C═NH groups are separated by NH. This less stable form of biguanides binds Li + as a bidentate ligand, in agreement with what was reported in the literature for other metal cations in the solid phase. The quantitative assessment of resonance in biguanide, in metformin and in their protonated forms, using the HOMED and HOMA indices, reveals an increase in electron delocalization upon protonation. On the contrary, the most stable lithium cation adducts are less conjugated than the stable neutral biguanides, because the metal cation is better coordinated by the not-fully conjugated bidentate tautomer.

A new screening method for flunitrazepam in vodka and tequila by fluorescence spectroscopy.

PubMed

Leesakul, Nararak; Pongampai, Sirintip; Kanatharana, Proespichaya; Sudkeaw, Pravit; Tantirungrotechai, Yuthana; Buranachai, Chittanon

2013-01-01

A new screening method for flunitrazepam in colourless alcoholic beverages based on a spectroscopic technique is proposed. Absorption and steady-state fluorescence of flunitrazepam and its protonated form with various acids were investigated. The redshift of the wavelength of maximum absorption was distinctively observed in protonated flunitrazepam. An emissive fluorescence at 472 nm was detected in colourless spirits (vodka and tequila) at room temperature. 2-M perchloric acid was the most appropriated proton source. By using electron ionization mass spectrometry and time-dependent density functional theory calculations, the possible structure of protonated flunitrazepam was identified to be 2-nitro-N-methylacridone, an acridone derivative as opposed to 2-methylamino-5-nitro-2'-fluorobenzophenone, a benzophenone derivative. Copyright © 2012 John Wiley & Sons, Ltd.

Energy dependence of the ridge in high multiplicity proton-proton collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dusling, Kevin; Tribedy, Prithwish; Venugopalan, Raju

2016-01-27

In this study, we demonstrate that the recent measurement of azimuthally collimated, long-range rapidity (“ridge”) correlations in √s=13 TeV proton-proton (p+p) collisions by the ATLAS Collaboration at the LHC are in agreement with expectations from the color glass condensate effective theory of high-energy QCD. The observation that the integrated near-side yield as a function of multiplicity is independent of collision energy is a natural consequence of the fact that multiparticle production is driven by a single semihard saturation scale in the color glass condensate framework. We argue further that the azimuthal structure of these recent ATLAS ridge measurements strongly constrainsmore » hydrodynamic interpretations of such correlations in high-multiplicity p+p collisions.« less

Measurement of the structure function of the nearly free neutron using spectator tagging in inelastic H 2 ( e , e ' p s ) X scattering with CLAS

DOE PAGES

Tkachenko, S.; Baillie, N.; Kuhn, S. E.; ...

2014-04-24

In this study, much less is known about neutron structure than that of the proton due to the absence of free neutron targets. Neutron information is usually extracted from data on nuclear targets such as deuterium, requiring corrections for nuclear binding and nucleon off-shell effects. These corrections are model dependent and have significant uncertainties, especially for large values of the Bjorken scaling variable x. As a consequence, the same data can lead to different conclusions, for example, about the behavior of the d quark distribution in the proton at large x.

A spectroscopic investigation of the Schiff base reprotonation mechanism of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Russell, Terence Stephen

This thesis reports time-resolved visible spectroscopy experiments performed on the light-driven proton pumping protein, bacteriorhodopsin (bR), and a number of artificially produced analogs. These analogs comprise a variety of single and double amino acid substitutions produced in several of the residues previously implicated in proton transport in bR. Also addressed are the results of resonance Raman and FTIR difference spectroscopy which provide information about the vibrational modes of the protein. The results from these experiments confirm aspects of both structural and functional models of bR based on previous electron diffraction and spectroscopic data. During a phase of the proton pumping photocycle in bR known as Schiff base reprotonation (also referred to as M intermediate decay), a proton is transferred over a 12 A distance from a proton donor residue (Asp-96) to the light-absorbing active site. The behavior of the M intermediate was monitored by time-resolved visible spectroscopy. In the single substitution known as D96N, the Asp-96 residue was replaced with a less efficient proton donor, asparagine. This mutant exhibited an M intermediate which decayed slowly in comparison to that of wild-type bR. However, this effect was reversed with the double substitution, T46D/D96N. This result indicates that the proton donor group can be moved to another nearby location and still yield a system functionally similar to the native protein. Replacement of the donor group with a histidine, His-96, resulted in a photocycle similar to D96N above pH 7. However, below this pH, the M intermediate is not detected. FTIR difference spectroscopy indicates that the protonation state of the substituted His-96 residue influences the structure of the active site of bR which suggests that a proton that is associated with His-96 may move towards the active site and thereby block M intermediate formation. Finally, the residue Thr-89 was replaced with an asparagine. This substitution altered not only the vibrational modes of the protein but also its visible absorption, which indicates that Thr-89 interacts directly with the active site of bR. These results are used to correct and extend an overall molecular model of the proton transport mechanism in bacteriorhodopsin.

Surface proton transport of fully protonated poly(aspartic acid) thin films on quartz substrates

NASA Astrophysics Data System (ADS)

Nagao, Yuki; Kubo, Takahiro

2014-12-01

Thin film structure and the proton transport property of fully protonated poly(aspartic acid) (P-Asp100) have been investigated. An earlier study assessed partially protonated poly(aspartic acid), highly oriented thin film structure and enhancement of the internal proton transport. In this study of P-Asp100, IR p-polarized multiple-angle incidence resolution (P-MAIR) spectra were measured to investigate the thin film structure. The obtained thin films, with thicknesses of 120-670 nm, had no oriented structure. Relative humidity dependence of the resistance, proton conductivity, and normalized resistance were examined to ascertain the proton transport property of P-Asp100 thin films. The obtained data showed that the proton transport of P-Asp100 thin films might occur on the surface, not inside of the thin film. This phenomenon might be related with the proton transport of the biological system.

Multidrug Transport Protein NorM from Vibrio cholerae Simultaneously Couples to Sodium- and Proton-Motive Force*

PubMed Central

Jin, Yoonhee; Nair, Asha; van Veen, Hendrik W.

2014-01-01

Membrane transporters belonging to the multidrug and toxic compound extrusion family mediate the efflux of unrelated pharmaceuticals from the interior of the cell in organisms ranging from bacteria to human. These proteins are thought to fall into two classes that couple substrate efflux to the influx of either Na+ or H+. We studied the energetics of drug extrusion by NorM from Vibrio cholerae in proteoliposomes in which purified NorM protein was functionally reconstituted in an inside-out orientation. We establish that NorM simultaneously couples to the sodium-motive force and proton-motive force, and biochemically identify protein regions and residues that play important roles in Na+ or H+ binding. As the positions of protons are not available in current medium and high-resolution crystal structures of multidrug and toxic compound extrusion transporters, our findings add a previously unrecognized parameter to mechanistic models based of these structures. PMID:24711447

Structure evolution of mononuclear tungsten and molybdenum species in the protonation process: Insight from FPMD and DFT calculations

NASA Astrophysics Data System (ADS)

Zhang, Ning; Yi, Haibo; Zeng, Dewen; Zhao, Zhongwei; Wang, Wenlei; Costanzo, Francesca

2018-03-01

In this work, we apply static density functional theory (DFT) calculations, as well as classical and first-principles molecular dynamics (FPMD) simulations, using the free-energy perturbation method to study the protonation ability, active site and structures of W(VI) and Mo(VI) in acidic aqueous solution. Using FPMD simulations, utilizing the pKa's calculation technique, we concluded that the octahedral WO2(OH)2(H2O)2 is the true formula for tungstic acid (H2WO4), and the hydroxyl ligands are the acidic site. This aqueous structure of H2WO4 is analogous to the previously reported structure of molybdic acid (H2MoO4). The FPMD trajectories of the tungstic acid deprotonation show that the mono-protonated monotungstate ion (HWO4-) may partially exist as a five-coordinated WO3(OH)(H2O)- species except for the four-coordinated WO3(OH)- species. This result is supported by DFT calculations, with an isoenergetic point (ΔE = 1.9 kcal·mol-1) for the WO3(OH)(H2O)- and WO3(OH)- species, when explicit solvent molecules are taken into account. In contrast, for the H2MoO4 acid, FPMD trajectories during the deprotonation process show that two H2O ligands immediately escape from the first coordinated sphere of Mo(VI) to form the four-coordinated MoO3(OH)- species. This difference indicates that structural expansion of W(VI) began in the first protonated step, while that of Mo(VI) only occurs in the second step. In addition, our calculated first and second acid constants for tungstic acid are higher than previously reported values for molybdic acid. This result suggests that WO42- is more easily protonated than the MoO42- anion in the same acidic solution, which is further confirmed by DFT calculations of hydrated oxoanions and its protonated species, based upon the hydration energy.

Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE

PubMed Central

Ke, Meng; Jiang, Xin; Yan, Nieng

2017-01-01

GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE. Using molecular dynamics simulations, we evaluated the free energy profiles of the transition between inward- and outward-facing conformations for the apo proteins. Our results revealed the correlation between the protonation state and conformational preference in XylE, which is supported by the crystal structures. In addition, our simulations suggested a thermodynamic difference between XylE and GLUT1 that cannot be explained by the single residue variation at the protonation site. To understand the molecular basis, we applied Bayesian network models to analyze the alteration in the architecture of the hydrogen bond networks during conformational transition. The models and subsequent experimental validation suggest that multiple residue substitutions are required to produce the thermodynamic and functional distinction between XylE and GLUT1. Despite the lack of simulation studies with substrates, these computational and biochemical characterizations provide unprecedented insight into the mechanistic difference between proton symporters and uniporters. PMID:28617850

Advances in structural and functional analysis of membrane proteins by electron crystallography

PubMed Central

Wisedchaisri, Goragot; Reichow, Steve L.; Gonen, Tamir

2011-01-01

Summary Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. PMID:22000511

Advances in structural and functional analysis of membrane proteins by electron crystallography.

PubMed

Wisedchaisri, Goragot; Reichow, Steve L; Gonen, Tamir

2011-10-12

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. Copyright © 2011 Elsevier Ltd. All rights reserved.

Precision measurements of g1 of the proton and of the deuteron with 6 GeV electrons

NASA Astrophysics Data System (ADS)

Prok, Y.; Bosted, P.; Kvaltine, N.; Adhikari, K. P.; Adikaram, D.; Aghasyan, M.; Amaryan, M. J.; Anderson, M. D.; Anefalos Pereira, S.; Avakian, H.; Baghdasaryan, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Biselli, A. S.; Bono, J.; Briscoe, W. J.; Brock, J.; Brooks, W. K.; Bültmann, S.; Burkert, V. D.; Carlin, C.; Carman, D. S.; Celentano, A.; Chandavar, S.; Colaneri, L.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crabb, D.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dupre, R.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Fedotov, G.; Fegan, S.; Fersch, R.; Fleming, J. A.; Forest, T. A.; Garçon, M.; Garillon, B.; Gevorgyan, N.; Ghandilyan, Y.; Gilfoyle, G. P.; Girod, F. X.; Giovanetti, K. L.; Goetz, J. T.; Gohn, W.; Gothe, R. W.; Griffioen, K. A.; Guegan, B.; Guler, N.; Hafidi, K.; Hanretty, C.; Harrison, N.; Hattawy, M.; Hicks, K.; Ho, D.; Holtrop, M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jawalkar, S.; Jiang, X.; Jo, H. S.; Joo, K.; Kalantarians, N.; Keith, C.; Keller, D.; Khandaker, M.; Kim, A.; Kim, W.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, V.; Kuhn, S. E.; Kuleshov, S. V.; Lenisa, P.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Markov, N.; Mayer, M.; McKinnon, B.; Meekins, D.; Mineeva, T.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Movsisyan, A.; Munevar, E.; Munoz Camacho, C.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L. L.; Paremuzyan, R.; Park, K.; Peng, P.; Phillips, J. J.; Pierce, J.; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Protopopescu, D.; Puckett, A. J. R.; Raue, B. A.; Rimal, D.; Ripani, M.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Schott, D.; Schumacher, R. A.; Seder, E.; Sharabian, Y. G.; Simonyan, A.; Smith, C.; Smith, G.; Sober, D. I.; Sokhan, D.; Stepanyan, S. S.; Stepanyan, S.; Strakovsky, I. I.; Strauch, S.; Sytnik, V.; Taiuti, M.; Tang, W.; Tkachenko, S.; Ungaro, M.; Vernarsky, B.; Vlassov, A. V.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D. P.; Weinstein, L. B.; Zachariou, N.; Zana, L.; Zhang, J.; Zhao, B.; Zhao, Z. W.; Zonta, I.; CLAS Collaboration

2014-08-01

The inclusive polarized structure functions of the proton and deuteron, g1p and g1d, were measured with high statistical precision using polarized 6 GeV electrons incident on a polarized ammonia target in Hall B at Jefferson Laboratory. Electrons scattered at laboratory angles between 18 and 45 degrees were detected using the CEBAF Large Acceptance Spectrometer (CLAS). For the usual deep inelastic region kinematics, Q2>1 GeV2 and the final-state invariant mass W >2 GeV, the ratio of polarized to unpolarized structure functions g1/F1 is found to be nearly independent of Q2 at fixed x. Significant resonant structure is apparent at values of W up to 2.3 GeV. In the framework of perturbative quantum chromodynamics, the high-W results can be used to better constrain the polarization of quarks and gluons in the nucleon, as well as high-twist contributions.

Precision measurements of g1 of the proton and the deuteron with 6 GeV electrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prok, Yelena; Bosted, Peter; Kvaltine, Nicholas

2014-08-01

The inclusive polarized structure functions of the proton and deuteron, g1p and g1d, were measured with high statistical precision using polarized 6 GeV electrons incident on a polarized ammonia target in Hall B at Jefferson Laboratory. Electrons scattered at lab angles between 18 and 45 degrees were detected using the CEBAF Large Acceptance Spectrometer (CLAS). For the usual DIS kinematics, Q^2>1 GeV^2 and the final-state invariant mass W>2 GeV, the ratio of polarized to unpolarized structure functions g1/F1 is found to be nearly independent of Q^2 at fixed x. Significant resonant structure is apparent at values of W up tomore » 2.3 GeV. In the framework of perturbative QCD, the high-W results can be used to better constrain the polarization of quarks and gluons in the nucleon, as well as high-twist contributions.« less

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

⁵¹V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site.

PubMed

Gupta, Rupal; Hou, Guangjin; Renirie, Rokus; Wever, Ron; Polenova, Tatyana

2015-04-29

Vanadium-dependent haloperoxidases (VHPOs) perform two-electron oxidation of halides using hydrogen peroxide. Their mechanism, including the factors determining the substrate specificity and the pH-dependence of the catalytic rates, is poorly understood. The vanadate cofactor in the active site of VHPOs contains "spectroscopically silent" V(V), which does not change oxidation state during the reaction. We employed an NMR crystallography approach based on (51)V magic angle spinning NMR spectroscopy and Density Functional Theory, to gain insights into the structure and coordination environment of the cofactor in the resting state of vanadium-dependent chloroperoxidases (VCPO). The cofactor environments in the wild-type VCPO and its P395D/L241V/T343A mutant exhibiting 5-100-fold improved catalytic activity are examined at various pH values. Optimal sensitivity attained due to the fast MAS probe technologies enabled the assignment of the location and number of protons on the vanadate as a function of pH. The vanadate cofactor changes its protonation from quadruply protonated at pH 6.3 to triply protonated at pH 7.3 to doubly protonated at pH 8.3. In contrast, in the mutant, the vanadate protonation is the same at pH 5.0 and 8.3, and the cofactor is doubly protonated. This methodology to identify the distinct protonation environments of the cofactor, which are also pH-dependent, could help explain the different reactivities of the wild-type and mutant VCPO and their pH-dependence. This study demonstrates that (51)V-based NMR crystallography can be used to derive the detailed coordination environments of vanadium centers in large biological molecules.

Water channel structures analysed by electron crystallography.

PubMed

Tani, Kazutoshi; Fujiyoshi, Yoshinori

2014-05-01

The mechanisms underlying water transport through aquaporin (AQP) have been debated for two decades. The water permeation phenomenon of AQP seems inexplicable because the Grotthuss mechanism does not allow for simultaneous fast water permeability and inhibition of proton transfer through the hydrogen bonds of water molecules. The AQP1 structure determined by electron crystallography provided the first insights into the proton exclusion mechanism despite fast water permeation. Although several studies have provided clues about the mechanism based on the AQP structure, each proposed mechanism remains incomplete. The present review is focused on AQP function and structure solved by electron crystallography in an attempt to fill the gaps between the findings in the absence and presence of lipids. Many AQP structures can be superimposed regardless of the determination method. The AQP fold is preserved even under conditions lacking lipids, but the water arrangement in the channel pore differs. The differences might be explained by dipole moments formed by the two short helices in the lipid bilayer. In addition, structure analyses of double-layered two-dimensional crystals of AQP suggest an array formation and cell adhesive function. Electron crystallography findings not only have contributed to resolve some of the water permeation mechanisms, but have also elucidated the multiple functions of AQPs in the membrane. The roles of AQPs in the brain remain obscure, but their multiple activities might be important in the regulation of brain and other biological functions. This article is part of a Special Issue entitled Aquaporins. © 2013.

Investigation of the 9B nucleus and its cluster-nucleon correlations

NASA Astrophysics Data System (ADS)

Zhao, Qing; Ren, Zhongzhou; Lyu, Mengjiao; Horiuchi, Hisashi; Funaki, Yasuro; Röpke, Gerd; Schuck, Peter; Tohsaki, Akihiro; Xu, Chang; Yamada, Taiichi; Zhou, Bo

2018-05-01

In order to study the correlations between clusters and nucleons in light nuclei, we formulate a new superposed Tohsaki-Horiuchi-Schuck-Röpke (THSR) wave function which describes both spatially large spreading and cluster-correlated dynamics of valence nucleons. Using this new THSR wave function, the binding energy of 9B is significantly improved in comparison with our previous studies. We calculate the excited states of 9B and obtain an energy spectrum of 9B which is consistent with the experimental results. This includes the prediction of the first 1 /2+ excited state of 9B which is not yet fixed experimentally. We study the proton dynamics in 9B and find that the cluster-proton correlation plays an essential role for the proton dynamics in the ground state of 9B. Furthermore, we discuss the density distribution of the valence proton with special attention to its tail structure. Finally, the resonance nature of excited states of 9B is illustrated comparing root-mean-square radii between the ground and excited states.

Revisit the landscape of protonated water clusters H+(H2O)n with n = 10-17: An ab initio global search.

PubMed

Shi, Ruili; Li, Keyao; Su, Yan; Tang, Lingli; Huang, Xiaoming; Sai, Linwei; Zhao, Jijun

2018-05-07

Using a genetic algorithm incorporated with density functional theory, we explore the ground state structures of protonated water clusters H + (H 2 O) n with n = 10-17. Then we re-optimize the isomers at B97-D/aug-cc-pVDZ level of theory. The extra proton connects with a H 2 O molecule to form a H 3 O + ion in all H + (H 2 O) 10-17 clusters. The lowest-energy structures adopt a monocage form at n = 10-16 and core-shell structure at n = 17 based on the MP2/aug-cc-pVTZ//B97-D/aug-cc-pVDZ+ZPE single-point-energy calculation. Using second-order vibrational perturbation theory, we further calculate the infrared spectra with anharmonic correction for the ground state structures of H + (H 2 O) 10-17 clusters at the PBE0/aug-cc-pVDZ level. The anharmonic correction to the spectra is crucial since it reproduces the experimental results quite well. The extra proton weakens the O-H bond strength in the H 3 O + ion since the Wiberg bond order of the O-H bond in the H 3 O + ion is smaller than that in H 2 O molecules, which causes a red shift of the O-H stretching mode in the H 3 O + ion.

Revisit the landscape of protonated water clusters H+(H2O)n with n = 10-17: An ab initio global search

NASA Astrophysics Data System (ADS)

Shi, Ruili; Li, Keyao; Su, Yan; Tang, Lingli; Huang, Xiaoming; Sai, Linwei; Zhao, Jijun

2018-05-01

Using a genetic algorithm incorporated with density functional theory, we explore the ground state structures of protonated water clusters H+(H2O)n with n = 10-17. Then we re-optimize the isomers at B97-D/aug-cc-pVDZ level of theory. The extra proton connects with a H2O molecule to form a H3O+ ion in all H+(H2O)10-17 clusters. The lowest-energy structures adopt a monocage form at n = 10-16 and core-shell structure at n = 17 based on the MP2/aug-cc-pVTZ//B97-D/aug-cc-pVDZ+ZPE single-point-energy calculation. Using second-order vibrational perturbation theory, we further calculate the infrared spectra with anharmonic correction for the ground state structures of H+(H2O)10-17 clusters at the PBE0/aug-cc-pVDZ level. The anharmonic correction to the spectra is crucial since it reproduces the experimental results quite well. The extra proton weakens the O-H bond strength in the H3O+ ion since the Wiberg bond order of the O-H bond in the H3O+ ion is smaller than that in H2O molecules, which causes a red shift of the O-H stretching mode in the H3O+ ion.

Functional diversity of potassium channel voltage-sensing domains.

PubMed

Islas, León D

2016-01-01

Voltage-gated potassium channels or Kv's are membrane proteins with fundamental physiological roles. They are composed of 2 main functional protein domains, the pore domain, which regulates ion permeation, and the voltage-sensing domain, which is in charge of sensing voltage and undergoing a conformational change that is later transduced into pore opening. The voltage-sensing domain or VSD is a highly conserved structural motif found in all voltage-gated ion channels and can also exist as an independent feature, giving rise to voltage sensitive enzymes and also sustaining proton fluxes in proton-permeable channels. In spite of the structural conservation of VSDs in potassium channels, there are several differences in the details of VSD function found across variants of Kvs. These differences are mainly reflected in variations in the electrostatic energy needed to open different potassium channels. In turn, the differences in detailed VSD functioning among voltage-gated potassium channels might have physiological consequences that have not been explored and which might reflect evolutionary adaptations to the different roles played by Kv channels in cell physiology.

Functional diversity of potassium channel voltage-sensing domains

PubMed Central

Islas, León D.

2016-01-01

Abstract Voltage-gated potassium channels or Kv's are membrane proteins with fundamental physiological roles. They are composed of 2 main functional protein domains, the pore domain, which regulates ion permeation, and the voltage-sensing domain, which is in charge of sensing voltage and undergoing a conformational change that is later transduced into pore opening. The voltage-sensing domain or VSD is a highly conserved structural motif found in all voltage-gated ion channels and can also exist as an independent feature, giving rise to voltage sensitive enzymes and also sustaining proton fluxes in proton-permeable channels. In spite of the structural conservation of VSDs in potassium channels, there are several differences in the details of VSD function found across variants of Kvs. These differences are mainly reflected in variations in the electrostatic energy needed to open different potassium channels. In turn, the differences in detailed VSD functioning among voltage-gated potassium channels might have physiological consequences that have not been explored and which might reflect evolutionary adaptations to the different roles played by Kv channels in cell physiology. PMID:26794852

Quantum Dynamics in Continuum for Proton Transport I: Basic Formulation.

PubMed

Chen, Duan; Wei, Guo-Wei

2013-01-01

Proton transport is one of the most important and interesting phenomena in living cells. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins. We describe proton dynamics quantum mechanically via a density functional approach while implicitly model other solvent ions as a dielectric continuum to reduce the number of degrees of freedom. The densities of all other ions in the solvent are assumed to obey the Boltzmann distribution. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic level. We formulate a total free energy functional to put proton kinetic and potential energies as well as electrostatic energy of all ions on an equal footing. The variational principle is employed to derive nonlinear governing equations for the proton transport system. Generalized Poisson-Boltzmann equation and Kohn-Sham equation are obtained from the variational framework. Theoretical formulations for the proton density and proton conductance are constructed based on fundamental principles. The molecular surface of the channel protein is utilized to split the discrete protein domain and the continuum solvent domain, and facilitate the multiscale discrete/continuum/quantum descriptions. A number of mathematical algorithms, including the Dirichlet to Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to demonstrate the performance of the proposed proton transport model and validate the efficiency of proposed mathematical algorithms. The electrostatic characteristics of the GA channel is analyzed with a wide range of model parameters. The proton conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and validates the proposed model.

Structure and dynamics of [3.3]paracyclophane as studied by nuclear magnetic resonance and density functional theory calculations.

PubMed

Dodziuk, Helena; Szymański, Sławomir; Jaźwiński, Jarosław; Marchwiany, Maciej E; Hopf, Henning

2010-09-30

Strained cyclophanes with small (-CH(2)-)(n) bridges connecting two benzene rings are interesting objects of basic research, mostly because of the nonplanarity of the rings and of interference of π-electrons of the latter. For title [3.3]paracyclophane, in solutions occurring in two interconverting cis and trans conformers, the published nuclear magnetic resonance (NMR) data are incomplete and involve its partially deuterated isotopomers. In this paper, variable-temperature NMR studies of its perprotio isotopomer combined with DFT quantum chemical calculations provide a complete characterization of the solution structure, NMR parameters, and interconversion of the cis and trans isomers of the title compound. Using advanced methods of spectral analysis, total quantitative interpretation of its proton NMR spectra in both the static and dynamic regimes is conducted. In particular, not only the geminal but also all of the vicinal J(HH) values for the bridge protons are determined, and for the first time, complete Arrhenius data for the interconversion process are reported. The experimental proton and carbon chemical shifts and the (n)J(HH), (1)J(CH), and (1)J(CC) coupling constants are satisfactorily reproduced theoretically by the values obtained from the density functional theory calculations.

WE-H-BRA-01: BEST IN PHYSICS (THERAPY): Nano-Dosimetric Kinetic Model for Variable Relative Biological Effectiveness of Proton and Ion Beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abolfath, R; Bronk, L; Titt, U.

2016-06-15

Purpose: Recent clonogenic cell survival and γH2AX studies suggest proton relative biological effectiveness (RBE) may be a non-linear function of linear energy transfer (LET) in the distal edge of the Bragg peak and beyond. We sought to develop a multiscale model to account for non-linear response phenomena to aid in the optimization of intensity-modulated proton therapy. Methods: The model is based on first-principle simulations of proton track structures, including secondary ions, and an analytical derivation of the dependence on particle LET of the linear-quadratic (LQ) model parameters α and β. The derived formulas are an extension of the microdosimetric kineticmore » (MK) model that captures dissipative track structures and non-Poissonian distribution of DNA damage at the distal edge of the Bragg peak and beyond. Monte Carlo simulations were performed to confirm the non-linear dose-response characteristics arising from the non-Poisson distribution of initial DNA damage. Results: In contrast to low LET segments of the proton depth dose, from the beam entrance to the Bragg peak, strong deviations from non-dissipative track structures and Poisson distribution in the ionization events in the Bragg peak distal edge govern the non-linear cell response and result in the transformation α=(1+c-1 L) α-x+2(c-0 L+c-2 L^2 )(1+c-1 L) β-x and β=(1+c-1 L)^2 β-x. Here L is the charged particle LET, and c-0,c-1, and c-2 are functions of microscopic parameters and can be served as fitting parameters to the cell-survival data. In the low LET limit c-1, and c-2 are negligible hence the linear model proposed and used by Wilkins-Oelfke for the proton treatment planning system can be retrieved. The present model fits well the recent clonogenic survival data measured recently in our group in MDACC. Conclusion: The present hybrid method provides higher accuracy in calculating the RBE-weighted dose in the target and normal tissues.« less

The gluon density of the proton at low x from a QCD analysis of F2

NASA Astrophysics Data System (ADS)

Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; Barschke, R.; Bartel, W.; Barth, M.; Bassler, U.; Beck, H. P.; Behrend, H.-J.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bernet, R.; Bertrand-Coremans, G.; Besançon, M.; Beyer, R.; Biddulph, P.; Bispham, P.; Bizot, J. C.; Blobel, V.; Borras, K.; Botterweck, F.; Boudry, V.; Braemer, A.; Brasse, F.; Braunschweig, W.; Brisson, V.; Bruncko, D.; Brune, C.; Buchholz, R.; Büngener, L.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burton, M.; Buschhorn, G.; Campbell, A. J.; Carli, T.; Charles, F.; Charlet, M.; Clarke, D.; Clegg, A. B.; Clerbaux, B.; Colombo, M.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Courau, A.; Coutures, Ch.; Cozzika, G.; Criegee, L.; Cussans, D. G.; Cvach, J.; Dagoret, S.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Delcourt, B.; Del Buono, L.; De Roeck, A.; De Wolf, E. A.; Di Nezza, P.; Dollfus, C.; Dowell, J. D.; Dreis, H. B.; Droutskoi, A.; Duboc, J.; Düllmann, D.; Dünger, O.; Duhm, H.; Ebert, J.; Ebert, T. R.; Eckerlin, G.; Efremenko, V.; Egli, S.; Ehrlichmann, H.; Eichenberger, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Ellison, R. J.; Elsen, E.; Erdmann, M.; Erdmann, W.; Evrard, E.; Favart, L.; Fedotov, A.; Feeken, D.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Flamm, K.; Fleischer, M.; Flieser, M.; Flügge, G.; Fomenko, A.; Fominykh, B.; Forbush, M.; Formánek, J.; Foster, J. M.; Franke, G.; Fretwurst, E.; Gabathuler, E.; Gabathuler, K.; Gamerdinger, K.; Garvey, J.; Gayler, J.; Gebauer, M.; Gellrich, A.; Genzel, H.; Gerhards, R.; Goerlach, U.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Goldner, D.; Gonzalez-Pineiro, B.; Gorelov, I.; Goritchev, P.; Grab, C.; Grässler, H.; Grässler, R.; Greenshaw, T.; Grindhammer, G.; Gruber, A.; Gruber, C.; Haack, J.; Haidt, D.; Hajduk, L.; Hamon, O.; Hampel, M.; Hanlon, E. M.; Hapke, M.; Haynes, W. J.; Heatherington, J.; Heinzelmann, G.; Henderson, R. C. W.; Henschel, H.; Herynek, I.; Hess, M. F.; Hildesheim, W.; Hill, P.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoeger, K. C.; Höppner, M.; Horisberger, R.; Hudgson, V. L.; Huet, Ph.; Hütte, M.; Hufnagel, H.; Ibbotson, M.; Itterbeck, H.; Jabiol, M.-A.; Jacholkowska, A.; Jacobsson, C.; Jaffre, M.; Janoth, J.; Jansen, T.; Jönsson, L.; Johnson, D. P.; Johnson, L.; Jung, H.; Kalmus, P. I. P.; Kant, D.; Kaschowitz, R.; Kasselmann, P.; Kathage, U.; Katzy, J.; Kaufmann, H. H.; Kazarian, S.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Ko, W.; Köhler, T.; Köhne, J. H.; Kolanoski, H.; Kole, F.; Kolya, S. D.; Korbel, V.; Korn, M.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, U.; Krüner-Marquis, U.; Kubenka, J. P.; Küster, H.; Kuhlen, M.; Kurča, T.; Kurzhöfer, J.; Kuznik, B.; Lacour, D.; Lamarche, F.; Lander, R.; Landon, M. P. J.; Lange, W.; Lanius, P.; Laporte, J.-F.; Lebedev, A.; Leverenz, C.; Levonian, S.; Ley, Ch.; Lindner, A.; Lindström, G.; Link, J.; Linsel, F.; Lipinski, J.; List, B.; Lobo, G.; Loch, P.; Lohmander, H.; Lomas, J.; Lopez, G. C.; Lubimov, V.; Lüke, D.; Magnussen, N.; Malinovski, E.; Mani, S.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martens, J.; Martin, R.; Martyn, H.-U.; Martyniak, J.; Masson, S.; Mavroidis, T.; Maxfield, S. J.; McMahon, S. J.; Mehta, A.; Meier, K.; Mercer, D.; Merz, T.; Meyer, C. A.; Meyer, H.; Meyer, J.; Migliori, A.; Mikocki, S.; Milstead, D.; Moreau, F.; Morris, J. V.; Mroczko, E.; Müller, G.; Müller, K.; Murín, P.; Nagovizin, V.; Nahnhauer, R.; Naroska, B.; Naumann, Th.; Newman, P. R.; Newton, D.; Neyret, D.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Nisius, R.; Nowak, G.; Noyes, G. W.; Nyberg-Werther, M.; Oakden, M.; Oberlack, H.; Obrock, U.; Olsson, J. E.; Ozerov, D.; Panaro, E.; Panitch, A.; Pascaud, C.; Patel, G. D.; Peppel, E.; Perez, E.; Phillips, J. P.; Pichler, Ch.; Pieuchot, A.; Pitzl, D.; Pope, G.; Prell, S.; Prosi, R.; Rabbertz, K.; Rädel, G.; Raupach, F.; Reimer, P.; Reinshagen, S.; Ribarics, P.; Rick, H.; Riech, V.; Riedlberger, J.; Riess, S.; Rietz, M.; Rizvi, E.; Robertson, S. M.; Robmann, P.; Roloff, H. E.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rüter, K.; Rusakov, S.; Rybicki, K.; Rylko, R.; Sahlmann, N.; Sanchez, E.; Sankey, D. P. C.; Schacht, P.; Schiek, S.; Schleper, P.; von Schlippe, W.; Schmidt, C.; Schmidt, D.; Schmidt, G.; Schöning, A.; Schröder, V.; Schuhmann, E.; Schwab, B.; Schwind, A.; Sefkow, F.; Seidel, M.; Sell, R.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shooshtari, H.; Shtarkov, L. N.; Siegmon, G.; Siewert, U.; Sirois, Y.; Skillicorn, I. O.; Smirnov, P.; Smith, J. R.; Solochenko, V.; Soloviev, Y.; Spiekermann, J.; Spielman, S.; Spitzer, H.; Starosta, R.; Steenbock, M.; Steffen, P.; Steinberg, R.; Stella, B.; Stephens, K.; Stier, J.; Stiewe, J.; Stösslein, U.; Stolze, K.; Strachota, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Tapprogge, S.; Tchernyshov, V.; Thiebaux, C.; Thompson, G.; Truöl, P.; Turnau, J.; Tutas, J.; Uelkes, P.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Mechelen, P.; Vartapetian, A.; Vazdik, Y.; Verrecchia, P.; Villet, G.; Wacker, K.; Wagener, A.; Wagener, M.; Walker, I. W.; Walther, A.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wellisch, H. P.; West, L. R.; Willard, S.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wright, A. E.; Wünsch, E.; Wulff, N.; Yiou, T. P.; Žáček, J.; Zarbock, D.; Zhang, Z.; Zhokin, A.; Zimmer, M.; Zimmermann, W.; Zomer, F.; Zuber, K.; H1 Collaboration

1995-02-01

We present a QCD analysis of the proton structure function F2 measured by the H1 experiment at HERA, combined with data from previous fixed target experiments. The gluon density is extracted from the scaling violations of F2 in the range 2 · 10 -4 < x < 3 · 10 -2 and compared with an approximate solution of the QCD evolution equations. The gluon density is found to rise steeply with decreasing x.

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

PubMed Central

Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2014-01-01

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

Dosimetric feasibility of 4DCT-ventilation imaging guided proton therapy for locally advanced non-small-cell lung cancer.

PubMed

Huang, Qijie; Jabbour, Salma K; Xiao, Zhiyan; Yue, Ning; Wang, Xiao; Cao, Hongbin; Kuang, Yu; Zhang, Yin; Nie, Ke

2018-04-25

The principle aim of this study is to incorporate 4DCT ventilation imaging into functional treatment planning that preserves high-functioning lung with both double scattering and scanning beam techniques in proton therapy. Eight patients with locally advanced non-small-cell lung cancer were included in this study. Deformable image registration was performed for each patient on their planning 4DCTs and the resultant displacement vector field with Jacobian analysis was used to identify the high-, medium- and low-functional lung regions. Five plans were designed for each patient: a regular photon IMRT vs. anatomic proton plans without consideration of functional ventilation information using double scattering proton therapy (DSPT) and intensity modulated proton therapy (IMPT) vs. functional proton plans with avoidance of high-functional lung using both DSPT and IMPT. Dosimetric parameters were compared in terms of tumor coverage, plan heterogeneity, and avoidance of normal tissues. Our results showed that both DSPT and IMPT plans gave superior dose advantage to photon IMRTs in sparing low dose regions of the total lung in terms of V5 (volume receiving 5Gy). The functional DSPT only showed marginal benefit in sparing high-functioning lung in terms of V5 or V20 (volume receiving 20Gy) compared to anatomical plans. Yet, the functional planning in IMPT delivery, can further reduce the low dose in high-functioning lung without degrading the PTV dosimetric coverages, compared to anatomical proton planning. Although the doses to some critical organs might increase during functional planning, the necessary constraints were all met. Incorporating 4DCT ventilation imaging into functional proton therapy is feasible. The functional proton plans, in intensity modulated proton delivery, are effective to further preserve high-functioning lung regions without degrading the PTV coverage.

Gating Topology of the Proton-Coupled Oligopeptide Symporters

PubMed Central

Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

2015-01-01

Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

Artificial synapse network on inorganic proton conductor for neuromorphic systems.

PubMed

Zhu, Li Qiang; Wan, Chang Jin; Guo, Li Qiang; Shi, Yi; Wan, Qing

2014-01-01

The basic units in our brain are neurons, and each neuron has more than 1,000 synapse connections. Synapse is the basic structure for information transfer in an ever-changing manner, and short-term plasticity allows synapses to perform critical computational functions in neural circuits. Therefore, the major challenge for the hardware implementation of neuromorphic computation is to develop artificial synapse network. Here in-plane lateral-coupled oxide-based artificial synapse network coupled by proton neurotransmitters are self-assembled on glass substrates at room-temperature. A strong lateral modulation is observed due to the proton-related electrical-double-layer effect. Short-term plasticity behaviours, including paired-pulse facilitation, dynamic filtering and spatiotemporally correlated signal processing are mimicked. Such laterally coupled oxide-based protonic/electronic hybrid artificial synapse network proposed here is interesting for building future neuromorphic systems.

Effect of in-medium nucleon-nucleon cross section on proton-proton momentum correlation in intermediate-energy heavy-ion collisions

NASA Astrophysics Data System (ADS)

Wang, Ting-Ting; Ma, Yu-Gang; Zhang, Chun-Jian; Zhang, Zheng-Qiao

2018-03-01

The proton-proton momentum correlation function from different rapidity regions is systematically investigated for the Au + Au collisions at different impact parameters and different energies from 400 A MeV to 1500 A MeV in the framework of the isospin-dependent quantum molecular dynamics model complemented by the Lednický-Lyuboshitz analytical method. In particular, the in-medium nucleon-nucleon cross-section dependence of the correlation function is brought into focus, while the impact parameter and energy dependence of the momentum correlation function are also explored. The sizes of the emission source are extracted by fitting the momentum correlation functions using the Gaussian source method. We find that the in-medium nucleon-nucleon cross section obviously influences the proton-proton momentum correlation function, which is from the whole-rapidity or projectile or target rapidity region at smaller impact parameters, but there is no effect on the mid-rapidity proton-proton momentum correlation function, which indicates that the emission mechanism differs between projectile or target rapidity and mid-rapidity protons.

A comparative study between para-aminophenyl and ortho-aminophenyl benzothiazoles using NMR and DFT calculations.

PubMed

Pierens, G K; Venkatachalam, T K; Reutens, D

2014-08-01

Ortho-substituted and para-substituted aminophenyl benzothiazoles were synthesised and characterised using NMR spectroscopy. A comparison of the proton chemical shift values reveals significant differences in the observed chemical shift values for the NH protons indicating the presence of a hydrogen bond in all ortho-substituted compounds as compared to the para compounds. The presence of intramolecular hydrogen bond in the ortho amino substituted aminophenyl benzothiazole forces the molecule to be planar which may be an additional advantage in developing these compounds as Alzheimer's imaging agent because the binding to amyloid fibrils prefers planar compounds. The splitting pattern of the methylene proton next to the amino group also showed significant coupling to the amino proton consistent with the notion of the existence of slow exchange and hydrogen bond in the ortho-substituted compounds. This is further verified by density functional theory calculations which yielded a near planar low energy conformer for all the o-aminophenyl benzothiazoles and displayed a hydrogen bond from the amine proton to the nitrogen of the thiazole ring. A detailed analysis of the (1)H, (13)C and (15)N NMR chemical shifts and density functional theory calculated structures of the compounds are described. Copyright © 2014 John Wiley & Sons, Ltd.

Dynamics and Structure of Point Defects in Forsterite: ab initio calculations

NASA Astrophysics Data System (ADS)

Churakov, S.; Khisina, N.; Urusov, V.; Wirth, R.

2001-12-01

OH-bearing fluid inclusions in Fo92 forsterite samples from peridotite nodule 9206 (Udachnaja kimberlite pipe)[1] were documented recently based on TEM and IR studies. The Fourier transform of diffraction pattern from the inclusions exhibited a pattern, which is interpreted as ordered planar (2H)xMg defects. In this study the structure and dynamics of protons associated with Mg(1), Mg(2) vacancies and interstitial polyhedrons ordered in a (100) plane corresponding to double unite cell periodicity of the forsterite lattice has been investigated by ab initio quantum mechanic calculations. Static structure optimizations and ab-initio molecular dynamics (MD) simulations have been performed using the CPMD density functional code[2]. The calculations were accomplished with the BLYP-functional utilizing the generalized gradient approximation. Non-local Goedecker-type pseudopotentials[3] have been applied to account for core electrons. Valence electron orbitals were approximated by plane wave expansion up to 70 Ry energy cutoff. The energy of static structures was sampled on 2x2x2 Monkhorst-Pack mesh[4]. During the structure relaxation parameters of an orthorhombic 2x1x2 supercell contaning 116 atoms corresponding to Mg28Si16O64H8 hydrous olivine was fixed at experimental values of a=9.524Å b=10.225Å and c=11.988Å relative to the Pbnm space group. Series of NVT-MD calculations were performed at 1000 K on 2x1x1 supercell with 58 atoms using four chain Nose thermostat. Randomly disturbed optimized structures were used as initial configuration for MD runs. The 1ps system equilibration is followed by trajectory production over 5 ps interval. A point energy sampling was applied in all MD calculations. A series of geometry optimizations, starting with various initial position of protons in Mg(1), Mg(2) and interstitial sites were carried out to obtain a structure with the lowest lattice energy. It was found that structures with protons completely located within the M1-polyhedron vacancies have lower energies then any other associated with M2 and interstitial polyhedrons. For protons associated with vacancies several configurations with small energy difference have been found. These configurations suggest a possible binding of the protons to O1, O2 and O3 sites including the formation of water-like HOH complexes. The MD simulations shows that protons can move easily within the vacant polyhedron to form covalent OH bonds at various oxygen sites. The protons initially located in interstitial positions of fosterite lattice were found to migrate in vacant polyhedra. References [1] Khisina, N.R. & Wirth, R. (2001): Hydrous olivine (Mg,Fe)2-xvxSiO4H2x - a new DHMS phase of variable composition observed as nanometer-size precipitation in mantle olivine. PCM, submitted [2] Hutter J. et al.: CPMD v. 4.0, MPI fuer Festkoerperforschung and IBM Zuerich Research Laboratory 1995-2000 [3] Goedecker S., Teter M. and Hutter J. (1996) Separable dual-space Gaussian pseudopotentials. Phys.Rev. B, 54(3) 1703-1710 [4] Monkhorst H.J. and Pack D. 1975 Special points for Brellouin-zone intagration. Phys. Rev B,13,5188-5192

Phenomenology of leading nucleon production in e p collisions at HERA in the framework of fracture functions

NASA Astrophysics Data System (ADS)

Shoeibi, Samira; Taghavi-Shahri, F.; Khanpour, Hamzeh; Javidan, Kurosh

2018-04-01

In recent years, several experiments at the e-p collider HERA have collected high precision deep-inelastic scattering (DIS) data on the spectrum of leading nucleon carrying a large fraction of the proton's energy. In this paper, we have analyzed recent experimental data on the production of forward protons and neutrons in DIS at HERA in the framework of a perturbative QCD. We propose a technique based on the fractures functions framework, and extract the nucleon fracture functions (FFs) M2(n /p )(x ,Q2;xL) from global QCD analysis of DIS data measured by the ZEUS Collaboration at HERA. We have shown that an approach based on the fracture functions formalism allows us to phenomenologically parametrize the nucleon FFs. Considering both leading neutron as well as leading proton production data at HERA, we present the results for the separate parton distributions for all parton species, including valence quark densities, the antiquark densities, the strange sea distribution, and the gluon distribution functions. We proposed several parametrizations for the nucleon FFs and open the possibility of these asymmetries. The obtained optimum set of nucleon FFs is accompanied by Hessian uncertainty sets which allow one to propagate uncertainties to other observables interest. The extracted results for the t -integrated leading neutron F2LN (3 )(x ,Q2;xL) and leading proton F2LP (3 )(x ,Q2;xL) structure functions are in good agreement with all data analyzed, for a wide range of fractional momentum variable x as well as the longitudinal momentum fraction xL.

pKa Modulation of the Acid/Base Catalyst within GH32 and GH68: A Role in Substrate/Inhibitor Specificity?

PubMed Central

Yuan, Shuguang; Le Roy, Katrien; Venken, Tom; Lammens, Willem; Van den Ende, Wim; De Maeyer, Marc

2012-01-01

Glycoside hydrolases of families 32 (GH32) and 68 (GH68) belong to clan GH-J, containing hydrolytic enzymes (sucrose/fructans as donor substrates) and fructosyltransferases (sucrose/fructans as donor and acceptor substrates). In GH32 members, some of the sugar substrates can also function as inhibitors, this regulatory aspect further adding to the complexity in enzyme functionalities within this family. Although 3D structural information becomes increasingly available within this clan and huge progress has been made on structure-function relationships, it is not clear why some sugars bind as inhibitors without being catalyzed. Conserved aspartate and glutamate residues are well known to act as nucleophile and acid/bases within this clan. Based on the available 3D structures of enzymes and enzyme-ligand complexes as well as docking simulations, we calculated the pKa of the acid-base before and after substrate binding. The obtained results strongly suggest that most GH-J members show an acid-base catalyst that is not sufficiently protonated before ligand entrance, while the acid-base can be fully protonated when a substrate, but not an inhibitor, enters the catalytic pocket. This provides a new mechanistic insight aiming at understanding the complex substrate and inhibitor specificities observed within the GH-J clan. Moreover, besides the effect of substrate entrance on its own, we strongly suggest that a highly conserved arginine residue (in the RDP motif) rather than the previously proposed Tyr motif (not conserved) provides the proton to increase the pKa of the acid-base catalyst. PMID:22662155

Parton distributions in the LHC era

NASA Astrophysics Data System (ADS)

Del Debbio, Luigi

2018-03-01

Analyses of LHC (and other!) experiments require robust and statistically accurate determinations of the structure of the proton, encoded in the parton distribution functions (PDFs). The standard description of hadronic processes relies on factorization theorems, which allow a separation of process-dependent short-distance physics from the universal long-distance structure of the proton. Traditionally the PDFs are obtained from fits to experimental data. However, understanding the long-distance properties of hadrons is a nonperturbative problem, and lattice QCD can play a role in providing useful results from first principles. In this talk we compare the different approaches used to determine PDFs, and try to assess the impact of existing, and future, lattice calculations.

FTIR Studies of Internal Water Molecules of Bacteriorhodopsin: Structural Analysis of Halide-bound D85S and D212N Mutants in the Schiff Base Region

NASA Astrophysics Data System (ADS)

Shibata, Mikihiro; Kandori, Hideki

2007-12-01

Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of C1- brings different effects for pumping functions in mutants at D85 and D212 position. While C1--bound D85T and D85S pump C1-, photovoltage measurements suggested that C1--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed.

Molecular dynamics analysis of stabilities of the telomeric Watson-Crick duplex and the associated i-motif as a function of pH and temperature.

PubMed

Panczyk, Tomasz; Wolski, Pawel

2018-06-01

This work deals with a molecular dynamics analysis of the protonated and deprotonated states of the natural sequence d[(CCCTAA) 3 CCCT] of the telomeric DNA forming the intercalated i-motif or paired with the sequence d[(CCCTAA) 3 CCCT] and forming the Watson-Crick (WC) duplex. By utilizing the amber force field for nucleic acids we built the i-motif and the WC duplex either with native cytosines or using their protonated forms. We studied, by applying molecular dynamics simulations, the role of hydrogen bonds between cytosines or in cytosine-guanine pairs in the stabilization of both structures in the physiological fluid. We found that hydrogen bonds exist in the case of protonated i-motif and in the standard form of the WC duplex. They, however, vanish in the case of the deprotonated i-motif and protonated form of the WC duplex. By determining potentials of mean force in the enforced unwrapping of these structures we found that the protonated i-motif is thermodynamically the most stable. Its deprotonation leads to spontaneous and observed directly in the unbiased calculations unfolding of the i-motif to the hairpin structure at normal temperature. The WC duplex is stable in its standard form and its slight destabilization is observed at the acidic pH. However, the protonated WC duplex unwraps very slowly at 310 K and its decomposition was not observed in the unbiased calculations. At higher temperatures (ca. 400 K or more) the WC duplex unwraps spontaneously. Copyright © 2018. Published by Elsevier B.V.

Human neuronal uncoupling proteins 4 and 5 (UCP4 and UCP5): structural properties, regulation, and physiological role in protection against oxidative stress and mitochondrial dysfunction.

PubMed

Ramsden, David B; Ho, Philip W-L; Ho, Jessica W-M; Liu, Hui-Fang; So, Danny H-F; Tse, Ho-Man; Chan, Koon-Ho; Ho, Shu-Leong

2012-07-01

Uncoupling proteins (UCPs) belong to a large family of mitochondrial solute carriers 25 (SLC25s) localized at the inner mitochondrial membrane. UCPs transport protons directly from the intermembrane space to the matrix. Of five structural homologues (UCP1 to 5), UCP4 and 5 are principally expressed in the central nervous system (CNS). Neurons derived their energy in the form of ATP that is generated through oxidative phosphorylation carried out by five multiprotein complexes (Complexes I-V) embedded in the inner mitochondrial membrane. In oxidative phosphorylation, the flow of electrons generated by the oxidation of substrates through the electron transport chain to molecular oxygen at Complex IV leads to the transport of protons from the matrix to the intermembrane space by Complex I, III, and IV. This movement of protons to the intermembrane space generates a proton gradient (mitochondrial membrane potential; MMP) across the inner membrane. Complex V (ATP synthase) uses this MMP to drive the conversion of ADP to ATP. Some electrons escape to oxygen-forming harmful reactive oxygen species (ROS). Proton leakage back to the matrix which bypasses Complex V resulting in a major reduction in ROS formation while having a minimal effect on MMP and hence, ATP synthesis; a process termed "mild uncoupling." UCPs act to promote this proton leakage as means to prevent excessive build up of MMP and ROS formation. In this review, we discuss the structure and function of mitochondrial UCPs 4 and 5 and factors influencing their expression. Hypotheses concerning the evolution of the two proteins are examined. The protective mechanisms of the two proteins against neurotoxins and their possible role in regulating intracellular calcium movement, particularly with regard to the pathogenesis of Parkinson's disease are discussed.

Electron attachment to the guanine-cytosine nucleic acid base pair and the effects of monohydration and proton transfer.

PubMed

Gupta, Ashutosh; Jaeger, Heather M; Compaan, Katherine R; Schaefer, Henry F

2012-05-17

The guanine-cytosine (GC) radical anion and its interaction with a single water molecule is studied using ab initio and density functional methods. Z-averaged second-order perturbation theory (ZAPT2) was applied to GC radical anion for the first time. Predicted spin densities show that the radical character is localized on cytosine. The Watson-Crick monohydrated GC anion is compared to neutral GC·H2O, as well as to the proton-transferred analogue on the basis of structural and energetic properties. In all three systems, local minima are identified that correspond to water positioned in the major and minor grooves of macromolecular DNA. On the anionic surface, two novel structures have water positioned above or below the GC plane. On the neutral and anionic surfaces, the global minimum can be described as water interacting with the minor groove. These structures are predicted to have hydration energies of 9.7 and 11.8 kcal mol(-1), respectively. Upon interbase proton-transfer (PT), the anionic global minimum has water positioned in the major groove, and the hydration energy increases to 13.4 kcal mol(-1). PT GC·H2O(•-) has distonic character; the radical character resides on cytosine, while the negative charge is localized on guanine. The effects of proton transfer are further investigated through the computed adiabatic electron affinities (AEA) of GC and monohydrated GC, and the vertical detachment energies (VDE) of the corresponding anions. Monohydration increases the AEAs and VDEs by only 0.1 eV, while proton-transfer increases the VDEs substantially (0.8 eV). The molecular charge distribution of monohydrated guanine-cytosine radical anion depends heavily on interbase proton transfer.

Proton NMR studies of functionalized nanoparticles in aqueous environments

NASA Astrophysics Data System (ADS)

Tataurova, Yulia Nikolaevna

Nanoscience is an emerging field that can provide potential routes towards addressing critical issues such as clean and sustainable energy, environmental remediation and human health. Specifically, porous nanomaterials, such as zeolites and mesoporous silica, are found in a wide range of applications including catalysis, drug delivery, imaging, environmental protection, and sensing. The characterization of the physical and chemical properties of nanocrystalline materials is essential to the realization of these innovative applications. The great advantage of porous nanocrystals is their increased external surface area that can control their biological, chemical and catalytic activities. Specific functional groups synthesized on the surface of nanoparticles are able to absorb heavy metals from the solution or target disease cells, such as cancer cells. In these studies, three main issues related to functionalized nanomaterials will be addressed through the application of nuclear magnetic resonance (NMR) techniques including: 1) surface composition and structure of functionalized nanocrystalline particles; 2) chemical properties of the guest molecules on the surface of nanomaterials, and 3) adsorption and reactivity of surface bound functional groups. Nuclear magnetic resonance (NMR) is one of the major spectroscopic techniques available for the characterization of molecular structure and conformational dynamics with atomic level detail. This thesis deals with the application of 1H solution state NMR to porous nanomaterial in an aqueous environment. Understanding the aqueous phase behavior of functionalized nanomaterials is a key factor in the design and development of safe nanomaterials because their interactions with living systems are always mediated through the aqueous phase. This is often due to a lack of fundamental knowledge in interfacial chemical and physical phenomena that occur on the surface of nanoparticles. The use of solution NMR spectroscopy results in high-resolution NMR spectra. This technique is selective for protons on the surface organic functional groups due to their motional averaging in solution. In this study, 1H solution NMR spectroscopy was used to investigate the interface of the organic functional groups in D2O. The pKa for these functional groups covalently bound to the surface of nanoparticles was determined using an NMR-pH titration method based on the variation in the proton chemical shift for the alkyl group protons closest to the amine group with pH. The adsorption of toxic contaminants (chromate and arsenate anions) on the surface of functionalized silicalite-1 and mesoporous silica nanoparticles has been studied by 1H solution NMR spectroscopy. With this method, the surface bound contaminants are detected. The analysis of the intensity and position of these peaks allows quantitative assessment of the relative amounts of functional groups with adsorbed metal ions. These results demonstrate the sensitivity of solution NMR spectroscopy to the electronic environment and structure of the surface functional groups on porous nanomaterials.

Measurements of the u valence quark distribution function in the proton and u quark fragmentation functions

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Badelek, B.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I. G.; Blum, D.; Böhm, E.; De Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S. C.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffre, M.; Jacholkowska, A.; Janata, F.; Jancso, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, A.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettingale, J.; Pietrzyk, B.; Poensgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Scholz, M.; Schouten, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thenard, J. M.; Thompson, J. C.; De la Torre, A.; Toth, J.; Urban, L.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.; European Muon Collaboration

1989-07-01

A new determination of the u valence quark distribution function in the proton is obtained from the analysis of identified charged pions, kaons, protons and antiprotons produced in muon-proton and muon-deuteron scattering. The comparison with results obtained in inclusive deep inelastic lepton-nucleon scattering provides a further test of the quark-parton model. The u quark fragmentation functions into positive and negative pions, kaons, protons and antiprotons are also measured.

Nuclear quantum fluctuations in ice I(h).

PubMed

Moreira, Pedro Augusto Franco Pinheiro; de Koning, Maurice

2015-10-14

We discuss the role of nuclear quantum fluctuations in ice Ih, focusing on the hydrogen-bond (HB) structure and the molecular dipole-moment distribution. For this purpose we carry out DFT-based first-principles molecular dynamics and path-integral molecular dynamics simulations at T = 100 K. We analyze the HB structure in terms of a set of parameters previously employed to characterize molecular structures in the liquid phase and compute the molecular dipole moments using the maximally-localized Wannier functions. The results show that the protons experience very large digressions driven by quantum fluctuations, accompanied by major rearrangements in the electronic density. As a result of these protonic quantum fluctuations the molecular dipole-moment distribution is substantially broadened as well as shifted to a larger mean value when compared to the results obtained when such fluctuations are neglected. In terms of dielectric constants, the reconciliation between the greater mean dipole moment and experimental indications that the dielectric constant of H2O ice is lower than that of D2O ice would indicate that the topology of the HB network is sensitive to protonic quantum fluctuations.

Measurement of the inclusive jet cross section at D0 Run II (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agram, Jean-Laurent

2004-12-17

This work describes the measurement of inclusive jets cross section in the DØ experiment. This cross section is computed as a function of jet transverse momentum, in several rapidity intervals. This quantity is sensitive to the proton structure and is crucial for the determination of parton distribution functions (PDF), essentially for the gluon at high proton momentum fraction. The measurement presented here gives the first values obtained for Tevatron Run II for the cross section in several rapidity intervals, for an integrated luminosity of 143 pb -1. The results are in agreement, within the uncertainties, with theoretical Standard Model predictions,more » showing no evidence for new physics.« less

HERAFitter: Open source QCD fit project

DOE PAGES

Alekhin, S.; Behnke, O.; Belov, P.; ...

2015-07-01

HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodologicalmore » options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options.« less

Protonation States in molecular dynamics simulations of peptide folding and binding.

PubMed

Ben-Shimon, Avraham; Shalev, Deborah E; Niv, Masha Y

2013-01-01

Peptides are important signaling modules, acting both as individual hormones and as parts of larger molecules, mediating their protein-protein interactions. Many peptidic and peptidomimetic drugs have reached the marketplace and opportunities for peptide-based drug discovery are on the rise. pH-dependent behavior of peptides is well documented in the context of misfolding diseases and peptide translocation. Changes in the protonation states of peptide residues often have a crucial effect on a peptide's structure, dynamics and function, which may be exploited for biotechnological applications. The current review surveys the increasing levels of sophistication in the treatment of protonation states in computational studies involving peptides. Specifically we describe I) the common practice of assigning a single protonation state and using it throughout the dynamic simulation, II) approaches that consider multiple protonation states and compare computed observables to experimental ones, III) constant pH molecular dynamics methods that couple changes in protonation states with conformational dynamics "on the fly". Applications of conformational dynamics treatment of peptides in the context of binding, folding and interactions with the membrane are presented, illustrating the growing body of work in this field and highlighting the importance of careful handling of protonation states of peptidic residues.

Radicalization and Radical Catalysis of Biomass Sugars: Insights from First-principles Studies.

PubMed

Yang, Gang; Zhu, Chang; Zou, Xianli; Zhou, Lijun

2016-07-13

Ab initio and density functional calculations are conducted to investigate the radicalization processes and radical catalysis of biomass sugars. Structural alterations due to radicalization generally focus on the radicalized sites, and radicalization affects H-bonds in D-fructofuranose more than in D-glucopyranose, potentially with outcome of new H-bonds. Performances of different functionals and basis sets are evaluated for all radicalization processes, and enthalpy changes and Gibbs free energies for these processes are presented with high accuracy, which can be referenced for subsequent experimental and theoretical studies. It shows that radicalization can be utilized for direct transformation of biomass sugars, and for each sugar, C rather than O sites are always preferred for radicalization, thus suggesting the possibility to activate C-H bonds of biomass sugars. Radical catalysis is further combined with Brønsted acids, and it clearly states that functionalization fundamentally regulates the catalytic effects of biomass sugars. In presence of explicit water molecules, functionalization significantly affects the activation barriers and reaction energies of protonation rather than dehydration steps. Tertiary butyl and phenyl groups with large steric hindrances or hydroxyl and amino groups resulting in high stabilities for protonation products drive the protonation steps to occur facilely at ambient conditions.

Volutin granules of Eimeria parasites are acidic compartments and have physiological and structural characteristics similar to acidocalcisomes

PubMed Central

Medeiros, Lia Carolina Soares; Gomes, Fabio; Maciel, Luis Renato Maia; Seabra, Sergio Henrique; Docampo, Roberto; Moreno, Silvia; Plattner, Helmut; Hentschel, Joachim; Kawazoe, Urara; Barrabin, Hector; de Souza, Wanderley; DaMatta, Renato Augusto; Miranda, Kildare

2012-01-01

The structural organization of parasites has been the subject of investigation by many groups and has lead to the identification of structures and metabolic pathways that may represent targets for anti-parasitic drugs. A specific group of organelles named acidocalcisomes has been identified in a number of organisms, including the apicomplexan parasites such as Toxoplasma and Plasmodium, where they have been shown to be involved in cation homeostasis, polyphosphate metabolism, and osmoregulation. Their structural counterparts in the apicomplexan parasite Eimeria have not been fully characterized. In this work, the ultrastructural and chemical properties of acidocalcisomes in Eimeria were characterized. Electron microscopy analysis of Eimeria parasites showed the dense organelles called volutin granules similar to acidocalcisomes. Immunolocalization of the vacuolar proton pyrophosphatase, considered as a marker for acidocalcisomes, showed labeling in vesicles of size and distribution similar to the dense organelles seen by electron microscopy. Spectrophotometric measurements of the kinetics of proton uptake showed a vacuolar proton pyrophosphatase activity. X-ray mapping revealed significant amounts of Na, Mg, P, K, Ca, and Zn in their matrix. The results suggest that volutin granules of Eimeria parasites are acidic, dense organelles and possess structural and chemical properties analogous to those of other acidocalcisomes, suggesting a similar functional role in these parasites. PMID:21699625

Computational study of the structure-free radical scavenging relationship of procyanidins.

PubMed

Mendoza-Wilson, Ana María; Castro-Arredondo, Sergio Ivan; Balandrán-Quintana, René Renato

2014-10-15

Procyanidins (PCs) are effective free radical scavengers, however, their antioxidant ability is variable because they have different degrees of polymerisation, are composed by distinct types of subunits and are very susceptible to changes in conformation. In this work the structure-free radical scavenging relationship of monomers, dimers and trimers of PCs was studied through the hydrogen atom transfer (HAT), sequential proton-loss electron-transfer (SPLET) and single electron transfer followed by proton transfer (SET-PT) mechanisms in aqueous phase, employing the Density Functional Theory (DFT) computational method. The structure-free radical scavenging relationship of PCs showed a very similar behaviour in HAT and SET-PT mechanisms, but very different in the SPLET mechanism. The structural factor that showed more effects on the ability of PCs to scavenge free radicals in aqueous phase was the conformation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Evaluating the quality of NMR structures by local density of protons.

PubMed

Ban, Yih-En Andrew; Rudolph, Johannes; Zhou, Pei; Edelsbrunner, Herbert

2006-03-01

Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. 2005 Wiley-Liss, Inc.

The response of a thermoluminescent dosimeter to low energy protons in the range 30-100 keV.

PubMed

Chu, T C; Lin, S Y; Hsu, C C; Li, J P

2001-11-01

This study demonstrates the thermoluminescence (TL) response of CaF2:Tm (commercial name TLD-300) to 30-100 keV protons which were generated by means of a Cockcroft-Walton accelerator. The phenomenon in which the total thermoluminescent output from CaF2:Tm (TLD-300) decreases with proton energy from 30 to 100 keV (with increase of LET) can be interpreted by the track structure theory (TST). The analysis of the glow peaks: P2 (131 degrees C), P3 (153.5 degrees C) and P6 (259 degrees C), of TLD-300 show the oscillatory decreasing phenomenon as a function of incident proton energy, which can be interpreted with the TST and the oscillatory emission of electrons in a thermoluminescent dosimeter (TLD) that is caused by resonant or quasi-resonant charge transfer in ion-atom interactions in this TLD-300.

Methylmercury chloride damage to the adult rat hippocampus cannot be detected by proton magnetic resonance spectroscopy

PubMed Central

Lu, Zhiyan; Wu, Jinwei; Cheng, Guangyuan; Tian, Jianying; Lu, Zeqing; Bi, Yongyi

2014-01-01

Previous studies have found that methylmercury can damage hippocampal neurons and accordingly cause cognitive dysfunction. However, a non-invasive, safe and accurate detection method for detecting hippocampal injury has yet to be developed. This study aimed to detect methylmercury-induced damage on hippocampal tissue using proton magnetic resonance spectroscopy. Rats were given a subcutaneous injection of 4 and 2 mg/kg methylmercury into the neck for 50 consecutive days. Water maze and pathology tests confirmed that cognitive function had been impaired and that the ultrastructure of hippocampal tissue was altered after injection. The results of proton magnetic resonance spectroscopy revealed that the nitrogen-acetyl aspartate/creatine, choline complex/creatine and myoinositol/creatine ratio in rat hippocampal tissue were unchanged. Therefore, proton magnetic resonance spectroscopy can not be used to determine structural damage in the adult rat hippocampus caused by methylmercury chloride. PMID:25368649

Catalytic Activity and Proton Translocation of Reconstituted Respiratory Complex I Monitored by Surface-Enhanced Infrared Absorption Spectroscopy.

PubMed

Gutiérrez-Sanz, Oscar; Forbrig, Enrico; Batista, Ana P; Pereira, Manuela M; Salewski, Johannes; Mroginski, Maria A; Götz, Robert; De Lacey, Antonio L; Kozuch, Jacek; Zebger, Ingo

2018-05-22

Respiratory complex I (CpI) is a key player in the way organisms obtain energy, being an energy transducer, which couples nicotinamide adenine dinucleotide (NADH)/quinone oxidoreduction with proton translocation by a mechanism that remains elusive so far. In this work, we monitored the function of CpI in a biomimetic, supported lipid membrane system assembled on a 4-aminothiophenol (4-ATP) self-assembled monolayer by surface-enhanced infrared absorption spectroscopy. 4-ATP serves not only as a linker molecule to a nanostructured gold surface but also as pH sensor, as indicated by concomitant density functional theory calculations. In this way, we were able to monitor NADH/quinone oxidoreduction-induced transmembrane proton translocation via the protonation state of 4-ATP, depending on the net orientation of CpI molecules induced by two complementary approaches. An associated change of the amide I/amide II band intensity ratio indicates conformational modifications upon catalysis which may involve movements of transmembrane helices or other secondary structural elements, as suggested in the literature [ Di Luca , Proc. Natl. Acad. Sci. U.S.A. , 2017 , 114 , E6314 - E6321 ].

Protonation of Excited State Pyrene-1-Carboxylate by Phosphate and Organic Acids in Aqueous Solution Studied by Fluorescence Spectroscopy

PubMed Central

Zelent, Bogumil; Vanderkooi, Jane M.; Coleman, Ryan G.; Gryczynski, Ignacy; Gryczynski, Zygmunt

2006-01-01

Pyrene-1-carboxylic acid has a pK of 4.0 in the ground state and 8.1 in the singlet electronic excited state. In the pH range of physiological interest (pH ∼5–8), the ground state compound is largely ionized as pyrene-1-carboxylate, but protonation of the excited state molecule occurs when a proton donor reacts with the carboxylate during the excited state lifetime of the fluorophore. Both forms of the pyrene derivatives are fluorescent, and in this work the protonation reaction was measured by monitoring steady-state and time-resolved fluorescence. The rate of protonation of pyrene-COO− by acetic, chloroacetic, lactic, and cacodylic acids is a function of ΔpK, as predicted by Marcus theory. The rate of proton transfer from these acids saturates at high concentration, as expected for the existence of an encounter complex. Trihydrogen-phosphate is a much better proton donor than dihydrogen- and monohydrogen-phosphate, as can be seen by the pH dependence. The proton-donating ability of phosphate does not saturate at high concentrations, but increases with increasing phosphate concentration. We suggest that enhanced rate of proton transfer at high phosphate concentrations may be due to the dual proton donating and accepting nature of phosphate, in analogy to the Grotthuss mechanism for proton transfer in water. It is suggested that in molecular structures containing multiple phosphates, such as membrane surfaces and DNA, proton transfer rates will be enhanced by this mechanism. PMID:16920831

Structural elucidation of direct analysis in real time ionized nerve agent simulants with infrared multiple photon dissociation spectroscopy.

PubMed

Rummel, Julia L; Steill, Jeffrey D; Oomens, Jos; Contreras, Cesar S; Pearson, Wright L; Szczepanski, Jan; Powell, David H; Eyler, John R

2011-06-01

Infrared multiple photon dissociation (IRMPD) was used to generate vibrational spectra of ions produced with a direct analysis in real time (DART) ionization source coupled to a 4.7 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The location of protonation on the nerve agent simulants diisopropyl methylphosphonate (DIMP) and dimethyl methylphosphonate (DMMP) was studied while solutions of the compounds were introduced for extended periods of time with a syringe pump. Theoretical vibrational spectra were generated with density functional theory calculations. Visual comparison of experimental mid-IR IRMPD spectra and theoretical spectra could not establish definitively if a single structure or a mixture of conformations was present for the protonated parent of each compound. However, theoretical calculations, near-ir IRMPD spectra, and frequency-to-frequency and statistical comparisons indicated that the protonation site for both DIMP and DMMP was predominantly, if not exclusively, the phosphonyl oxygen instead of one of the oxygen atoms with only single bonds.

Multidrug transport protein norM from vibrio cholerae simultaneously couples to sodium- and proton-motive force.

PubMed

Jin, Yoonhee; Nair, Asha; van Veen, Hendrik W

2014-05-23

Membrane transporters belonging to the multidrug and toxic compound extrusion family mediate the efflux of unrelated pharmaceuticals from the interior of the cell in organisms ranging from bacteria to human. These proteins are thought to fall into two classes that couple substrate efflux to the influx of either Na(+) or H(+). We studied the energetics of drug extrusion by NorM from Vibrio cholerae in proteoliposomes in which purified NorM protein was functionally reconstituted in an inside-out orientation. We establish that NorM simultaneously couples to the sodium-motive force and proton-motive force, and biochemically identify protein regions and residues that play important roles in Na(+) or H(+) binding. As the positions of protons are not available in current medium and high-resolution crystal structures of multidrug and toxic compound extrusion transporters, our findings add a previously unrecognized parameter to mechanistic models based of these structures. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.; Vincenzi, Donald L. (Technical Monitor)

2001-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. In the absence of any record of the earliest ancestors of contemporary cells, protocells, the most direct way to test our understanding of their characteristics is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs of molecules that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing and storing energy, and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following, questions about these proteins: (1) How do small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides aggregate to form membrane-spannin(y structures (e.g., channels)? (3) By what mechanisms do such aggregates perform their functions? The simulations are performed using the molecular dynamics (MD) method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated directly in real space while long-range forces are evaluated in reciprocal space, usually using a particle-mesh algorithm which is of order O(NlnN). Currently, a time step of 2 femtoseconds is typically used, thereby making studies of problems occurring on multi-nanosecond time scales (10(exp 6) - 10(exp 8) time steps) accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude. Such an extension requires both algorithmic improvements and codes scalable to a large number of parallel processors. Work in this direction is in progress. Two specific series of simulations that demonstrate how peptides self-organize and function in membranes are discussed. In one series of simulations, it was shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and, simultaneously, fold into two different helical structures, which remain in equilibrium. Once in the membrane, the peptides can readily change their orientation, especially in response to local electric fields. This structural and orientational flexibility of peptides with changing conditions may have provided a mechanism of transmitting signals between the environment and the interior of the protocell. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations demonstrate that protons move through the gate by a "shuttle" mechanism, wherein one histidine is protonated on the extracellular side and, subsequently, the proton bound on the opposite side is released.

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Multifactorial Resistance of Bacillus subtilis Spores to High-Energy Proton Radiation: Role of Spore Structural Components and the Homologous Recombination and Non-Homologous End Joining DNA Repair Pathways

PubMed Central

Reitz, Günther; Li, Zuofeng; Klein, Stuart; Nicholson, Wayne L.

2012-01-01

Abstract The space environment contains high-energy charged particles (e.g., protons, neutrons, electrons, α-particles, heavy ions) emitted by the Sun and galactic sources or trapped in the radiation belts. Protons constitute the majority (87%) of high-energy charged particles. Spores of Bacillus species are one of the model systems used for astro- and radiobiological studies. In this study, spores of different Bacillus subtilis strains were used to study the effects of high energetic proton irradiation on spore survival. Spores of the wild-type B. subtilis strain [mutants deficient in the homologous recombination (HR) and non-homologous end joining (NHEJ) DNA repair pathways and mutants deficient in various spore structural components such as dipicolinic acid (DPA), α/β-type small, acid-soluble spore protein (SASP) formation, spore coats, pigmentation, or spore core water content] were irradiated as air-dried multilayers on spacecraft-qualified aluminum coupons with 218 MeV protons [with a linear energy transfer (LET) of 0.4 keV/μm] to various final doses up to 2500 Gy. Spores deficient in NHEJ- and HR-mediated DNA repair were significantly more sensitive to proton radiation than wild-type spores, indicating that both HR and NHEJ DNA repair pathways are needed for spore survival. Spores lacking DPA, α/β-type SASP, or with increased core water content were also significantly more sensitive to proton radiation, whereas the resistance of spores lacking pigmentation or spore coats was essentially identical to that of the wild-type spores. Our results indicate that α/β-type SASP, core water content, and DPA play an important role in spore resistance to high-energy proton irradiation, suggesting their essential function as radioprotectants of the spore interior. Key Words: Bacillus—Spores—DNA repair—Protection—High-energy proton radiation. Astrobiology 12, 1069–1077. PMID:23088412

Functional complementation of yeast cytosolic pyrophosphatase by bacterial and plant H+-translocating pyrophosphatases.

PubMed

Perez-Castineira, Jose R; Lopez-Marques, Rosa L; Villalba, Jose M; Losada, Manuel; Serrano, Aurelio

2002-12-10

Two types of proteins that hydrolyze inorganic pyrophosphate (PPi), very different in both amino acid sequence and structure, have been characterized to date: soluble and membrane-bound proton-pumping pyrophosphatases (sPPases and H(+)-PPases, respectively). sPPases are ubiquitous proteins that hydrolyze PPi releasing heat, whereas H+-PPases, so far unidentified in animal and fungal cells, couple the energy of PPi hydrolysis to proton movement across biological membranes. The budding yeast Saccharomyces cerevisiae has two sPPases that are located in the cytosol and in the mitochondria. Previous attempts to knock out the gene coding for a cytosolic sPPase (IPP1) have been unsuccessful, thus suggesting that this protein is essential for growth. Here, we describe the generation of a conditional S. cerevisiae mutant (named YPC-1) whose functional IPP1 gene is under the control of a galactose-dependent promoter. Thus, YPC-1 cells become growth arrested in glucose but they regain the ability to grow on this carbon source when transformed with autonomous plasmids bearing diverse foreign H+-PPase genes under the control of a yeast constitutive promoter. The heterologously expressed H+-PPases are distributed among different yeast membranes, including the plasma membrane, functional complementation by these integral membrane proteins being consistently sensitive to external pH. These results demonstrate that hydrolysis of cytosolic PPi is essential for yeast growth and that this function is not substantially affected by the intrinsic characteristics of the PPase protein that accomplishes it. Moreover, this is, to our knowledge, the first direct evidence that H+-PPases can mediate net hydrolysis of PPi in vivo. YPC-1 mutant strain constitutes a convenient expression system to perform studies aimed at the elucidation of the structure-function relationships of this type of proton pumps.

Proton-coupled electron transfer in the catalytic cycle of Alcaligenes xylosoxidans copper-dependent nitrite reductase.

PubMed

Leferink, Nicole G H; Han, Cong; Antonyuk, Svetlana V; Heyes, Derren J; Rigby, Stephen E J; Hough, Michael A; Eady, Robert R; Scrutton, Nigel S; Hasnain, S Samar

2011-05-17

We demonstrated recently that two protons are involved in reduction of nitrite to nitric oxide through a proton-coupled electron transfer (ET) reaction catalyzed by the blue Cu-dependent nitrite reductase (Cu NiR) of Alcaligenes xylosoxidans (AxNiR). Here, the functionality of two putative proton channels, one involving Asn90 and the other His254, is studied using single (N90S, H254F) and double (N90S--H254F) mutants. All mutants studied are active, indicating that protons are still able to reach the active site. The H254F mutation has no effect on the catalytic activity, while the N90S mutation results in ~70% decrease in activity. Laser flash-photolysis experiments show that in H254F and wild-type enzyme electrons enter at the level of the T1Cu and then redistribute between the two Cu sites. Complete ET from T1Cu to T2Cu occurs only when nitrite binds at the T2Cu site. This indicates that substrate binding to T2Cu promotes ET from T1Cu, suggesting that the enzyme operates an ordered mechanism. In fact, in the N90S and N90S--H254F variants, where the T1Cu site redox potential is elevated by ∼60 mV, inter-Cu ET is only observed in the presence of nitrite. From these results it is evident that the Asn90 channel is the main proton channel in AxNiR, though protons can still reach the active site if this channel is disrupted. Crystallographic structures provide a clear structural rationale for these observations, including restoration of the proton delivery via a significant movement of the loop connecting the T1Cu ligands Cys130 and His139 that occurs on binding of nitrite. Notably, a role for this loop in facilitating interaction of cytochrome c(551) with Cu NiR has been suggested previously based on a crystal structure of the binary complex.

Protonated sugars: vibrational spectroscopy and conformational structure of protonated O-methyl α-D-galactopyranoside

NASA Astrophysics Data System (ADS)

Rudić, Svemir; Xie, Hong-bin; Gerber, R. Benny; Simons, John P.

2012-08-01

'Bridging' protons provide a common structural motif in biological assemblies such as proton wires and proton-bound dimers. Here we present a 'proof-of-principle' computational and vibrational spectroscopic investigation of an 'intra-molecular proton-bound dimer,' O-methyl α-D-galactopyranoside (αMeGal-H+), generated in the gas phase through photo-ionisation of its complex with phenol in a molecular beam. Its vibrational spectrum corresponds well with a classical molecular dynamics simulation conducted 'on-the-fly' and also with the lowest-energy structures predicted by DFT and ab initio calculations. They reveal proton-bound structures that bridge neighbouring pairs of oxygen atoms, preferentially O6 and O4, linked together within the carbohydrate scaffold. Motivated by the possibility of an entry into the microscopic mechanism of its acid (or enzyme)-catalysed hydrolysis, we also report the corresponding predictions for its singly hydrated complex.

Surface Protonation at the Rutile (110) Interface: Explicit Incorporation of Solvation Structure within the Refined MUSIC Model Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Machesky, Michael L.; Predota, M.; Wesolowski, David J

The detailed solvation structure at the (110) surface of rutile ({alpha}-TiO{sub 2}) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming thatmore » the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 {angstrom} of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 C that agrees quantitatively with the experimentally determined value (5.4 {+-} 0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pH{sub znpc} values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pH{sub znpc} value of the rutile (110) surface at 25 C into quantitative agreement with the experimental value (4.8 {+-} 0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite ({alpha}-SnO{sub 2}) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.« less

Surface protonation at the rutile (110) interface: explicit incorporation of solvation structure within the refined MUSIC model framework.

PubMed

Machesky, Michael L; Predota, Milan; Wesolowski, David J; Vlcek, Lukas; Cummings, Peter T; Rosenqvist, Jörgen; Ridley, Moira K; Kubicki, James D; Bandura, Andrei V; Kumar, Nitin; Sofo, Jorge O

2008-11-04

The detailed solvation structure at the (110) surface of rutile (alpha-TiO2) in contact with bulk liquid water has been obtained primarily from experimentally verified classical molecular dynamics (CMD) simulations of the ab initio-optimized surface in contact with SPC/E water. The results are used to explicitly quantify H-bonding interactions, which are then used within the refined MUSIC model framework to predict surface oxygen protonation constants. Quantum mechanical molecular dynamics (QMD) simulations in the presence of freely dissociable water molecules produced H-bond distributions around deprotonated surface oxygens very similar to those obtained by CMD with nondissociable SPC/E water, thereby confirming that the less computationally intensive CMD simulations provide accurate H-bond information. Utilizing this H-bond information within the refined MUSIC model, along with manually adjusted Ti-O surface bond lengths that are nonetheless within 0.05 A of those obtained from static density functional theory (DFT) calculations and measured in X-ray reflectivity experiments (as well as bulk crystal values), give surface protonation constants that result in a calculated zero net proton charge pH value (pHznpc) at 25 degrees C that agrees quantitatively with the experimentally determined value (5.4+/-0.2) for a specific rutile powder dominated by the (110) crystal face. Moreover, the predicted pHznpc values agree to within 0.1 pH unit with those measured at all temperatures between 10 and 250 degrees C. A slightly smaller manual adjustment of the DFT-derived Ti-O surface bond lengths was sufficient to bring the predicted pHznpcvalue of the rutile (110) surface at 25 degrees C into quantitative agreement with the experimental value (4.8+/-0.3) obtained from a polished and annealed rutile (110) single crystal surface in contact with dilute sodium nitrate solutions using second harmonic generation (SHG) intensity measurements as a function of ionic strength. Additionally, the H-bond interactions between protolyzable surface oxygen groups and water were found to be stronger than those between bulk water molecules at all temperatures investigated in our CMD simulations (25, 150 and 250 degrees C). Comparison with the protonation scheme previously determined for the (110) surface of isostructural cassiterite (alpha-SnO2) reveals that the greater extent of H-bonding on the latter surface, and in particular between water and the terminal hydroxyl group (Sn-OH) results in the predicted protonation constant for that group being lower than for the bridged oxygen (Sn-O-Sn), while the reverse is true for the rutile (110) surface. These results demonstrate the importance of H-bond structure in dictating surface protonation behavior, and that explicit use of this solvation structure within the refined MUSIC model framework results in predicted surface protonation constants that are also consistent with a variety of other experimental and computational data.

Molecular differences between deuterated and protonated polystyrenes using reversed-phase high-performance liquid chromatography.

PubMed

Kayillo, Sindy; Gray, Michael J; Shalliker, R Andrew; Dennis, Gary R

2005-05-06

Isotopic substitution is a technique used to highlight particular bonds within a molecule for kinetic, spectroscopic and structure analysis. It is presumed that although some properties such as stretching frequencies will not be the same for substituted analogues, the chemical interactions will not vary appreciably as a function of labelling. Reversed-phase liquid chromatography has been used to demonstrate that there are significant differences between the chromatographic behaviour of a sequence of deuterated and protonated oligomeric polystyrenes. Two-dimensional reversed-phase liquid chromatography was used to show that even the diasteromers of the oligomers (n = 5) have retention mechanisms that are dependent on the subtle changes to the molecular conformation and electronic structure, which are a consequence of deuteration.

Origins of Protons in C-H Bond Insertion Products of Phenols: Proton-Self-Sufficient Function via Water Molecules.

PubMed

Luo, Zhoujie; Gao, Ya; Zhu, Tong; Zhang, John Zenghui; Xia, Fei

2017-08-31

Water molecules can serve as proton shuttles for proton transfer in the C-H bond insertion reactions catalyzed by transition metal complexes. Recently, the control experiments performed for C-H bond insertion of phenol and anisol by gold carbenes show that large discrepancy exists in the yields of hydrogenated and deuterated products. Thus, we conducted a detailed theoretical analysis on the function of water molecules in the C-H bond insertion reactions. The comparison of calculated results and control experiments indicates that the solution water molecules play a crucial role of proton shuttle in C-H bond insertion. In particular, it was found that the hydroxyl groups in phenols were capable of donating protons via water shuttles for the production of C-H products, which had a substantial influence on the yields of inserted products. The hydroxyl groups instead of C-H bonds in phenols function like "proton reservoirs" in the C-H bond insertion, which we call the "proton self-sufficient" (PSS) function of phenol. The PSS function of phenol indicates that the substrates with and without proton reservoirs will lead to different C-H bond insertion products.

Short Carboxylic Acid–Carboxylate Hydrogen Bonds Can Have Fully Localized Protons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15–0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor–acceptor distance criteria for amore » LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [O–O> = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O–O distance with increasing H-bond donor pK a. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid–carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.« less

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

PubMed

Lin, Jiusheng; Pozharski, Edwin; Wilson, Mark A

2017-01-17

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨d O-O ⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pK a . This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Pseudomonas aeruginosa overexpression system of nitric oxide reductase for in vivo and in vitro mutational analyses.

PubMed

Yamagiwa, Raika; Kurahashi, Takuya; Takeda, Mariko; Adachi, Mayuho; Nakamura, Hiro; Arai, Hiroyuki; Shiro, Yoshitsugu; Sawai, Hitomi; Tosha, Takehiko

2018-05-01

Membrane-integrated nitric oxide reductase (NOR) reduces nitric oxide (NO) to nitrous oxide (N 2 O) with protons and electrons. This process is essential for the elimination of the cytotoxic NO that is produced from nitrite (NO 2 - ) during microbial denitrification. A structure-guided mutagenesis of NOR is required to elucidate the mechanism for NOR-catalyzed NO reduction. We have already solved the crystal structure of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa. In this study, we then constructed its expression system using cNOR-gene deficient and wild-type strains for further functional study. Characterizing the variants of the five conserved Glu residues located around the heme/non-heme iron active center allowed us to establish how the anaerobic growth rate of cNOR-deficient strains expressing cNOR variants correlates with the in vitro enzymatic activity of the variants. Since bacterial strains require active cNOR to eliminate cytotoxic NO and to survive under denitrification conditions, the anaerobic growth rate of a strain with a cNOR variant is a good indicator of NO decomposition capability of the variants and a marker for the screening of functionally important residues without protein purification. Using this in vivo screening system, we examined the residues lining the putative proton transfer pathways for NO reduction in cNOR, and found that the catalytic protons are likely transferred through the Glu57 located at the periplasmic protein surface. The homologous cNOR expression system developed here is an invaluable tool for facile identification of crucial residues in vivo, and for further in vitro functional and structural studies. Copyright © 2018 Elsevier B.V. All rights reserved.

Calcium binding and transport by coenzyme Q.

PubMed

Bogeski, Ivan; Gulaboski, Rubin; Kappl, Reinhard; Mirceski, Valentin; Stefova, Marina; Petreska, Jasmina; Hoth, Markus

2011-06-22

Coenzyme Q10 (CoQ10) is one of the essential components of the mitochondrial electron-transport chain (ETC) with the primary function to transfer electrons along and protons across the inner mitochondrial membrane (IMM). The concomitant proton gradient across the IMM is essential for the process of oxidative phosphorylation and consequently ATP production. Cytochrome P450 (CYP450) monoxygenase enzymes are known to induce structural changes in a variety of compounds and are expressed in the IMM. However, it is unknown if CYP450 interacts with CoQ10 and how such an interaction would affect mitochondrial function. Using voltammetry, UV-vis spectrometry, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), fluorescence microscopy and high performance liquid chromatography-mass spectrometry (HPLC-MS), we show that both CoQ10 and its analogue CoQ1, when exposed to CYP450 or alkaline media, undergo structural changes through a complex reaction pathway and form quinone structures with distinct properties. Hereby, one or both methoxy groups at positions 2 and 3 on the quinone ring are replaced by hydroxyl groups in a time-dependent manner. In comparison with the native forms, the electrochemically reduced forms of the new hydroxylated CoQs have higher antioxidative potential and are also now able to bind and transport Ca(2+) across artificial biomimetic membranes. Our results open new perspectives on the physiological importance of CoQ10 and its analogues, not only as electron and proton transporters, but also as potential regulators of mitochondrial Ca(2+) and redox homeostasis.

Identification of prominence ejecta by the proton distribution function and magnetic fine structure in ICMEs in the inner heliosphere

NASA Astrophysics Data System (ADS)

Marsch, Eckart; Yao, Shuo; Tu, Chuanyi; Schwenn, Rainer

This work presents in-situ solar wind observations of three magnetic clouds that contain certain cold high-density material, when Helios 2 was located at 0.3 AU, on 9 May 1979, 0.5 AU on 30 March 1976, and 0.7 AU on 24 December 1978, respectively. In the cold high-density regions embedded in the ICMEs we find that (1) the number density of protons is higher than in other regions inside the magnetic cloud (MC), (2)the possible existence of He+, (3) the thermal velocity distribution functions (VDFs) are more isotropic and appear to be colder than in the other regions of the MC, and the proton temperature is lower than that of the ambient plasma, (4) the associated magnetic field configuration can for all three MC events be identified as a flux rope. This cold high-density region is located at the polarity inversion line in the center of the bipolar structure of the MC magnetic field (consistent with previous work of solar observation that a prominence lies over the neutral line of the related bipolar solar magnetic field ). It is the first time that prominence ejecta are identified by both the plasma and magnetic field features inside 1 AU, and that thermal ion velocity distribution functions are used to investigate the microstate of the prominence material. Overall, our in situ observations are consistent with the three-part CME models.

Web application for studying the free energy of binding and protonation states of protein-ligand complexes based on HINT

PubMed Central

Bayden, Alexander S.; Fornabaio, Micaela; Scarsdale, J. Neel

2009-01-01

A public web server performing computational titration at the active site in a protein-ligand complex has been implemented. This calculation is based on the Hydropathic INTeraction (HINT) noncovalent force field. From 3D coordinate data for the protein, ligand and bridging waters (if available), the server predicts the best combination of protonation states for each ionizable residue and/or ligand functional group as well as the Gibbs free energy of binding for the ionization-optimized protein-ligand complex. The 3D structure for the modified molecules is available as output. In addition, a graph depicting how this energy changes with acidity, i.e., as a function of added protons, can be obtained. This data may prove to be of use in preparing models for virtual screening and molecular docking. A few illustrative examples are presented. In β secretase (2va7) computational titration flipped the amide groups of Gln12 and Asn37 and protonated a ligand amine yielding an improvement of 6.37 kcal mol−1 in the protein-ligand binding score. Protonation of Glu139 in mutant HIV-1 reverse transcriptase (2opq) allows a water bridge between the protein and inhibitor that increases the protein-ligand interaction score by 0.16 kcal mol−1. In human sialidase NEU2 complexed with an isobutyl ether mimetic inhibitor (2f11) computational titration suggested that protonating Glu218, deprotonating Arg237, flipping the amide bond on Tyr334, and optimizing the positions of several other polar protons would increase the protein-ligand interaction score by 0.71 kcal mol−1. PMID:19554265

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle*

PubMed Central

Yano, Naomine; Muramoto, Kazumasa; Shimada, Atsuhiro; Takemura, Shuhei; Baba, Junpei; Fujisawa, Hidenori; Mochizuki, Masao; Shinzawa-Itoh, Kyoko; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, Shinya

2016-01-01

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H3O+ through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O2 bound to heme a3. To block backward proton movement, the water channel remains closed after O2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu198, which bridges the Mg2+ and CuA (the initial electron acceptor from cytochrome c) sites, suggest that the CuA-Glu198-Mg2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg2+-containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO. PMID:27605664

The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle.

PubMed

Yano, Naomine; Muramoto, Kazumasa; Shimada, Atsuhiro; Takemura, Shuhei; Baba, Junpei; Fujisawa, Hidenori; Mochizuki, Masao; Shinzawa-Itoh, Kyoko; Yamashita, Eiki; Tsukihara, Tomitake; Yoshikawa, Shinya

2016-11-11

Bovine heart cytochrome c oxidase (CcO) pumps four proton equivalents per catalytic cycle through the H-pathway, a proton-conducting pathway, which includes a hydrogen bond network and a water channel operating in tandem. Protons are transferred by H 3 O + through the water channel from the N-side into the hydrogen bond network, where they are pumped to the P-side by electrostatic repulsion between protons and net positive charges created at heme a as a result of electron donation to O 2 bound to heme a 3 To block backward proton movement, the water channel remains closed after O 2 binding until the sequential four-proton pumping process is complete. Thus, the hydrogen bond network must collect four proton equivalents before O 2 binding. However, a region with the capacity to accept four proton equivalents was not discernable in the x-ray structures of the hydrogen bond network. The present x-ray structures of oxidized/reduced bovine CcO are improved from 1.8/1.9 to 1.5/1.6 Å resolution, increasing the structural information by 1.7/1.6 times and revealing that a large water cluster, which includes a Mg 2+ ion, is linked to the H-pathway. The cluster contains enough proton acceptor groups to retain four proton equivalents. The redox-coupled x-ray structural changes in Glu 198 , which bridges the Mg 2+ and Cu A (the initial electron acceptor from cytochrome c) sites, suggest that the Cu A -Glu 198 -Mg 2+ system drives redox-coupled transfer of protons pooled in the water cluster to the H-pathway. Thus, these x-ray structures indicate that the Mg 2+ -containing water cluster is the crucial structural element providing the effective proton pumping in bovine CcO. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A Dosimetric Comparison of Proton and Intensity-Modulated Photon Radiotherapy for Pediatric Parameningeal Rhabdomyosarcomas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kozak, Kevin R.; Adams, Judith; Krejcarek, Stephanie J.

Purpose: We compared tumor and normal tissue dosimetry of proton radiation therapy with intensity-modulated radiation therapy (IMRT) for pediatric parameningeal rhabdomyosarcomas (PRMS). Methods and Materials: To quantify dosimetric differences between contemporary proton and photon treatment for pediatric PRMS, proton beam plans were compared with IMRT plans. Ten patients treated with proton radiation therapy at Massachusetts General Hospital had IMRT plans generated. To facilitate dosimetric comparisons, clinical target volumes and normal tissue volumes were held constant. Plans were optimized for target volume coverage and normal tissue sparing. Results: Proton and IMRT plans provided acceptable and comparable target volume coverage, with atmore » least 99% of the CTV receiving 95% of the prescribed dose in all cases. Improved dose conformality provided by proton therapy resulted in significant sparing of all examined normal tissues except for ipsilateral cochlea and mastoid; ipsilateral parotid gland sparing was of borderline statistical significance (p = 0.05). More profound sparing of contralateral structures by protons resulted in greater dose asymmetry between ipsilateral and contralateral retina, optic nerves, cochlea, and mastoids; dose asymmetry between ipsilateral and contralateral parotids was of borderline statistical significance (p = 0.05). Conclusions: For pediatric PRMS, superior normal tissue sparing is achieved with proton radiation therapy compared with IMRT. Because of enhanced conformality, proton plans also demonstrate greater normal tissue dose distribution asymmetry. Longitudinal studies assessing the impact of proton radiotherapy and IMRT on normal tissue function and growth symmetry are necessary to define the clinical consequences of these differences.« less

Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

PubMed

Graziani, F R; Bauer, J D; Murillo, M S

2014-09-01

Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.

PREFACE: Transport phenomena in proton conducting media Transport phenomena in proton conducting media

NASA Astrophysics Data System (ADS)

Eikerling, Michael

2011-06-01

Proton transport phenomena are of paramount importance for acid-base chemistry, energy transduction in biological organisms, corrosion processes, and energy conversion in electrochemical systems such as polymer electrolyte fuel cells. The relevance for such a plethora of materials and systems, and the ever-lasting fascination with the highly concerted nature of underlying processes drive research across disciplines in chemistry, biology, physics and chemical engineering. A proton never travels alone. Proton motion is strongly correlated with its environment, usually comprised of an electrolyte and a solid or soft host material. For the transport in nature's most benign proton solvent and shuttle, water that is, insights from ab initio simulations, matured over the last 15 years, have furnished molecular details of the structural diffusion mechanism of protons. Excess proton movement in water consists of sequences of Eigen-Zundel-Eigen transitions, triggered by hydrogen bond breaking and making in the surrounding water network. Nowadays, there is little debate about the validity of this mechanism in water, which bears a stunning resemblance to the basic mechanistic picture put forward by de Grotthuss in 1806. While strong coupling of an excess proton with degrees of freedom of solvent and host materials facilitates proton motion, this coupling also creates negative synergies. In general, proton mobility in biomaterials and electrochemical proton conducting media is highly sensitive to the abundance and structure of the proton solvent. In polymer electrolyte membranes, in which protons are bound to move in nano-sized water-channels, evaporation of water or local membrane dehydration due to electro-osmotic coupling are well-known phenomena that could dramatically diminish proton conductivity. Contributions in this special issue address various vital aspects of the concerted nature of proton motion and they elucidate important structural and dynamic effects of solvent, charge-bearing species at interfaces and porous host materials on proton transport properties. As a common thread, articles in this special issue contribute to understanding the functionality provided by complex materials, beyond hydrogen bond fluctuations in water. The first group of articles (Smirnov et al, Henry et al, Medvedev and Stuchebrukhov) elucidates various aspects of the impact of local structural fluctuations, hydrogen bonding and long-range electrostatic forces on proton transfer across and at the surface of mitochondrial membranes. The second group of articles (Ilhan and Spohr, Allahyarov et al and Idupulapati et al) employ molecular dynamics simulations to rationalize vital dependencies of proton transport mechanisms in aqueous-based polymer electrolyte membranes on the nanoporous, phase-separated ionomer morphology, and on the level of hydration. The articles by Gebel et al, Boillat et al, and Aleksandrova et al employ small angle neutron scattering, neutron radiography, and electrochemical atomic force microscopy, respectively, to obtain detailed insights into the kinetics of water sorption, water distribution, water transport properties, as well as spatial maps of proton conductivity in fuel cell membranes. The contribution of Paschos et al provides a comprehensive review of phosphate-based solid state protonic conductors for intermediate temperature fuel cells. The topic of proton conductive materials for high-temperature, water-free operation of fuel cells is continued in the article of Verbraeken et al which addresses synthesis and characterization of a proton conducting perovskite. The guest editor wishes to acknowledge and thank all contributing authors for their commitment to this special issue. Moreover, I would like to thank the staff at IOP Publishing for coordinating submission and refereeing processes. Finally, for the readers, I hope that this special issue will be a valuable and stimulating source of insights into the versatile and eminently important field of transport phenomena in proton conducting media. Complex dynamics of fluids in disordered and crowded environments contents Electrostatic models of electron-driven proton transfer across a lipid membrane Anatoly Yu Smirnov, Lev G Mourokh and Franco Nori Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase Rowan M Henry, David Caplan, Elisa Fadda and Régis Pomès Proton diffusion along biological membranes E S Medvedev and A A Stuchebrukhov Ab initio molecular dynamics of proton networks in narrow polymer electrolyte pores Mehmet A Ilhan and Eckhard Spohr A simulation study of field-induced proton-conduction pathways in dry ionomers Elshad Allahyarov, Philip L Taylor and Hartmut Löwen Molecular structure and transport dynamics in perfluoro sulfonyl imide membranes Nagesh Idupulapati, Ram Devanathan and Michel Dupuis The kinetics of water sorption in Nafion membranes: a small-angle neutron scattering study Gérard Gebel, Sandrine Lyonnard, Hakima Mendil-Jakani and Arnaud Morin Using 2H labeling with neutron radiography for the study of solid polymer electrolyte water transport properties P Boillat, P Oberholzer, B C Seyfang, A Kästner, R Perego, G G Scherer, E H Lehmann and A Wokaun Spatial distribution and dynamics of proton conductivity in fuel cell membranes: potential and limitations of electrochemical atomic force microscopy measurements E Aleksandrova, S Hink, R Hiesgen and E Roduner A review on phosphate based, solid state, protonic conductors for intermediate temperature fuel cells O Paschos, J Kunze, U Stimming and F Maglia A structural study of the proton conducting B-site ordered perovskite Ba3Ca1.18Ta1.82O8.73 Maarten C Verbraeken, Hermenegildo A L Viana, Philip Wormald and John T S Irvine

Exclusive single pion electroproduction off the proton in the high-lying resonances at Q2 < 5 GeV2 from CLAS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Kijun

The differential cross sections and structure functions for the exclusive electroproduction process ep --> e'n pi+ were measured in the range of the invariantmass for the np+ system 1.6 GeV lte W lte 2.0 GeV, and the photon virtuality 1.8 GeV2 lte Q2 lte 4.0 GeV2 using CLAS at Jefferson Lab. For the first time, these kinematics are probed in the exclusive p+ production from the protons with nearly full coverage in the azimuthal and polar angles of the np+ center-of-mass system. In this analysis, approximately 39,000 differential cross-section data points in terms of W, Q2, cosq theta* _ pi,more » and phi*_p-, were obtained. The preliminary differential cross section and structure function analyses are carried out, which allow us to extract the helicity amplitudes in high-lying resonances.« less

Polarized deep inelastic scattering off the neutron from gauge/string duality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao Jianhua; Mou Zonggang; Department of Physics, Shandong University, Jinan, Shandong, 250100

2010-05-01

We investigate deep inelastic scattering off the polarized 'neutron' using gauge/string duality. The 'neutron' corresponds to a supergravity mode of the neutral dilatino. Through introducing the Pauli interaction term into the action in AdS{sub 5} space, we calculate the polarized deep inelastic structure functions of the 'neutron' in supergravity approximation at large t' Hooft coupling {lambda} and finite x with {lambda}{sup -1/2}<

Revealing an outward-facing open conformational state in a CLC Cl –/H + exchange transporter

DOE PAGES

Khantwal, Chandra M.; Abraham, Sherwin J.; Han, Wei; ...

2016-01-22

CLC secondary active transporters exchange Cl - for H + . Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Glu ex ) upon its protonation. Using 19 F NMR, we show that as [H + ] is increased to protonate Glu ex and enrich the outward-facing state, a residue ~20 Å away from Glu ex , near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that themore » cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function.« less

Perfluoroalkyl phosphonic and phosphinic acids as proton conductors for anhydrous proton-exchange membranes.

PubMed

Herath, Mahesha B; Creager, Stephen E; Kitaygorodskiy, Alex; DesMarteau, Darryl D

2010-09-10

A study of proton-transport rates and mechanisms under anhydrous conditions using a series of acid model compounds, analogous to comb-branch perfluorinated ionomers functionalized with phosphonic, phosphinic, sulfonic, and carboxylic acid protogenic groups, is reported. Model compounds are characterized with respect to proton conductivity, viscosity, proton, and anion (conjugate base) self-diffusion coefficients, and Hammett acidity. The highest conductivities, and also the highest viscosities, are observed for the phosphonic and phosphinic acid model compounds. Arrhenius analysis of conductivity and viscosity for these two acids reveals much lower activation energies for ion transport than for viscous flow. Additionally, the proton self-diffusion coefficients are much higher than the conjugate-base self-diffusion coefficients for these two acids. Taken together, these data suggest that anhydrous proton transport in the phosphonic and phosphinic acid model compounds occurs primarily by a structure-diffusion, hopping-based mechanism rather than a vehicle mechanism. Further analysis of ionic conductivity and ion self-diffusion rates by using the Nernst-Einstein equation reveals that the phosphonic and phosphinic acid model compounds are relatively highly dissociated even under anhydrous conditions. In contrast, sulfonic and carboxylic acid-based systems exhibit relatively low degrees of dissociation under anhydrous conditions. These findings suggest that fluoroalkyl phosphonic and phosphinic acids are good candidates for further development as anhydrous, high-temperature proton conductors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malik, Radhika; Viola, Ronald E.

2010-10-28

The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2 {angstrom} resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg{sup 2+} and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identificationmore » of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH.« less

Novel Composite Proton Exchange Membrane with Connected Long-Range Ionic Nanochannels Constructed via Exfoliated Nafion-Boron Nitride Nanocomposite.

PubMed

Jia, Wei; Tang, Beibei; Wu, Peiyi

2017-05-03

Nafion-boron nitride (NBN) nanocomposites with a Nafion-functionalized periphery are prepared via a convenient and ecofriendly Nafion-assisted water-phase exfoliation method. Nafion and the boron nitride nanosheet present strong interactions in the NBN nanocomposite. Then the NBN nanocomposites were blended with Nafion to prepare NBN Nafion composite proton exchange membranes (PEMs). NBN nanocomposites show good dispersibility and have a noticeable impact on the aggregation structure of the Nafion matrix. Connected long-range ionic nanochannels containing exaggerated (-SO 3 - ) n ionic clusters are constructed during the membrane-forming process via the hydrophilic and H-bonding interactions between NBN nanocomposites and Nafion matrix. The addition of NBN nanocomposites with sulfonic groups also provides additional proton transportation spots and enhances the water uptake of the composite PEMs. The proton conductivity of the NBN Nafion composite PEMs is significantly increased under various conditions relative to that of recast Nafion. At 80 °C-95% relative humidity, the proton conductivity of 0.5 NBN Nafion is 0.33 S·cm -1 , 6 times that of recast Nafion under the same conditions.

Radicalization and Radical Catalysis of Biomass Sugars: Insights from First-principles Studies

PubMed Central

Yang, Gang; Zhu, Chang; Zou, Xianli; Zhou, Lijun

2016-01-01

Ab initio and density functional calculations are conducted to investigate the radicalization processes and radical catalysis of biomass sugars. Structural alterations due to radicalization generally focus on the radicalized sites, and radicalization affects H-bonds in D-fructofuranose more than in D-glucopyranose, potentially with outcome of new H-bonds. Performances of different functionals and basis sets are evaluated for all radicalization processes, and enthalpy changes and Gibbs free energies for these processes are presented with high accuracy, which can be referenced for subsequent experimental and theoretical studies. It shows that radicalization can be utilized for direct transformation of biomass sugars, and for each sugar, C rather than O sites are always preferred for radicalization, thus suggesting the possibility to activate C-H bonds of biomass sugars. Radical catalysis is further combined with Brønsted acids, and it clearly states that functionalization fundamentally regulates the catalytic effects of biomass sugars. In presence of explicit water molecules, functionalization significantly affects the activation barriers and reaction energies of protonation rather than dehydration steps. Tertiary butyl and phenyl groups with large steric hindrances or hydroxyl and amino groups resulting in high stabilities for protonation products drive the protonation steps to occur facilely at ambient conditions. PMID:27405843

The nitric-oxide reductase from Paracoccus denitrificans uses a single specific proton pathway.

PubMed

ter Beek, Josy; Krause, Nils; Reimann, Joachim; Lachmann, Peter; Ädelroth, Pia

2013-10-18

The NO reductase from Paracoccus denitrificans reduces NO to N2O (2NO + 2H(+) + 2e(-) → N2O + H2O) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent NO reductase; cNOR). cNORs are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the O2-reducing, proton-pumping respiratory enzymes. In contrast, although NO reduction is as exergonic as O2 reduction, there are no protons pumped in cNOR, and in addition, protons needed for NO reduction are derived from the periplasmic solution (no contribution to the electrochemical gradient is made). cNOR thus only needs to transport protons from the periplasm into the active site without the requirement to control the timing of opening and closing (gating) of proton pathways as is needed in a proton pump. Based on the crystal structure of a closely related cNOR and molecular dynamics simulations, several proton transfer pathways were suggested, and in principle, these could all be functional. In this work, we show that residues in one of the suggested pathways (denoted pathway 1) are sensitive to site-directed mutation, whereas residues in the other proposed pathways (pathways 2 and 3) could be exchanged without severe effects on turnover activity with either NO or O2. We further show that electron transfer during single-turnover reduction of O2 is limited by proton transfer and can thus be used to study alterations in proton transfer rates. The exchange of residues along pathway 1 showed specific slowing of this proton-coupled electron transfer as well as changes in its pH dependence. Our results indicate that only pathway 1 is used to transfer protons in cNOR.

Electrogenic steps of light-driven proton transport in ESR, a retinal protein from Exiguobacterium sibiricum.

PubMed

Siletsky, Sergey A; Mamedov, Mahir D; Lukashev, Evgeniy P; Balashov, Sergei P; Dolgikh, Dmitriy A; Rubin, Andrei B; Kirpichnikov, Mikhail P; Petrovskaya, Lada E

2016-11-01

A retinal protein from Exiguobacterium sibiricum (ESR) functions as a light-driven proton pump. Unlike other proton pumps, it contains Lys96 instead of a usual carboxylic residue in the internal proton donor site. Nevertheless, the reprotonation of the Schiff base occurs fast, indicating that Lys96 facilitates proton transfer from the bulk. In this study we examined kinetics of light-induced transmembrane electrical potential difference, ΔΨ, generated in proteoliposomes reconstituted with ESR. We show that total magnitude of ΔΨ is comparable to that produced by bacteriorhodopsin but its kinetic components and their pH dependence are substantially different. The results are in agreement with the earlier finding that proton uptake precedes reprotonation of the Schiff base in ESR, suggesting that Lys96 is unprotonated in the initial state and gains a proton transiently in the photocycle. The electrogenic phases and the photocycle transitions related to proton transfer from the bulk to the Schiff base are pH dependent. At neutral pH, they occur with τ 0.5ms and 4.5ms. At alkaline pH, the fast component ceases and Schiff base reprotonation slows. At pH8.4, a spectrally silent electrogenic component with τ 0.25ms is detected, which can be attributed to proton transfer from the bulk to Lys96. At pH5.1, the amplitude of ΔΨ decreases 10 fold, reflecting a decreased yield and rate of proton transfer, apparently from protonation of the acceptor (Asp85-His57 pair) in the initial state. The features of the photoelectric potential generation correlate with the ESR structure and proposed mechanism of proton transfer. Copyright © 2016 Elsevier B.V. All rights reserved.

Charge structure of the hadronic final state in deep-inelastic muon-nucleon scattering

NASA Astrophysics Data System (ADS)

Arneodo, M.; Arvidson, A.; Aubert, J. J.; Bedełek, J.; Beaufays, J.; Bee, C. P.; Benchouk, C.; Berghoff, G.; Bird, I.; Blum, D.; Böhm, E.; de Bouard, X.; Brasse, F. W.; Braun, H.; Broll, C.; Brown, S.; Brück, H.; Calen, H.; Chima, J. S.; Ciborowski, J.; Clifft, R.; Coignet, G.; Combley, F.; Coughlan, J.; D'Agostini, G.; Dahlgren, S.; Dengler, F.; Derado, I.; Dreyer, T.; Drees, J.; Düren, M.; Eckardt, V.; Edwards, A.; Edwards, M.; Ernst, T.; Eszes, G.; Favier, J.; Ferrero, M. I.; Figiel, J.; Flauger, W.; Foster, J.; Ftáčnik, J.; Gabathuler, E.; Gajewski, J.; Gamet, R.; Gayler, J.; Geddes, N.; Grafström, P.; Grard, F.; Haas, J.; Hagberg, E.; Hasert, F. J.; Hayman, P.; Heusse, P.; Jaffré, M.; Jachołkowska, A.; Janata, F.; Jancsó, G.; Johnson, A. S.; Kabuss, E. M.; Kellner, G.; Korbel, V.; Krüger, J.; Kullander, S.; Landgraf, U.; Lanske, D.; Loken, J.; Long, K.; Maire, M.; Malecki, P.; Manz, A.; Maselli, S.; Mohr, W.; Montanet, F.; Montgomery, H. E.; Nagy, E.; Nassalski, J.; Norton, P. R.; Oakham, F. G.; Osborne, A. M.; Pascaud, C.; Pawlik, B.; Payre, P.; Peroni, C.; Peschel, H.; Pessard, H.; Pettinghale, J.; Pietrzyk, B.; Pietrzyk, U.; Pönsgen, B.; Pötsch, M.; Renton, P.; Ribarics, P.; Rith, K.; Rondio, E.; Sandacz, A.; Scheer, M.; Schlagböhmer, A.; Schiemann, H.; Schmitz, N.; Schneegans, M.; Schneider, A.; Scholz, M.; Schröder, T.; Schultze, K.; Sloan, T.; Stier, H. E.; Studt, M.; Taylor, G. N.; Thénard, J. M.; Thompson, J. C.; de La Torre, A.; Toth, J.; Urban, L.; Wallucks, W.; Whalley, M.; Wheeler, S.; Williams, W. S. C.; Wimpenny, S. J.; Windmolders, R.; Wolf, G.

1988-09-01

The general charge properties of the hadronic final state produced in μ + p and μ + d interactions at 280 GeV are investigated. Quark charge retention and local charge compensation is observed. The ratio F {2/ n }/ F {2/ p } of the neutron to proton structure function is derived from the measurement of the average hadronic charge in μ d interactions.

Virtual Compton scattering and the generalized polarizabilities of the proton at Q2=0.92 and 1.76 GeV2

NASA Astrophysics Data System (ADS)

Fonvieille, H.; Laveissière, G.; Degrande, N.; Jaminion, S.; Jutier, C.; Todor, L.; Di Salvo, R.; Van Hoorebeke, L.; Alexa, L. C.; Anderson, B. D.; Aniol, K. A.; Arundell, K.; Audit, G.; Auerbach, L.; Baker, F. T.; Baylac, M.; Berthot, J.; Bertin, P. Y.; Bertozzi, W.; Bimbot, L.; Boeglin, W. U.; Brash, E. J.; Breton, V.; Breuer, H.; Burtin, E.; Calarco, J. R.; Cardman, L. S.; Cavata, C.; Chang, C.-C.; Chen, J.-P.; Chudakov, E.; Cisbani, E.; Dale, D. S.; de Jager, C. W.; De Leo, R.; Deur, A.; d'Hose, N.; Dodge, G. E.; Domingo, J. J.; Elouadrhiri, L.; Epstein, M. B.; Ewell, L. A.; Finn, J. M.; Fissum, K. G.; Fournier, G.; Frois, B.; Frullani, S.; Furget, C.; Gao, H.; Gao, J.; Garibaldi, F.; Gasparian, A.; Gilad, S.; Gilman, R.; Glamazdin, A.; Glashausser, C.; Gomez, J.; Gorbenko, V.; Grenier, P.; Guichon, P. A. M.; Hansen, J. O.; Holmes, R.; Holtrop, M.; Howell, C.; Huber, G. M.; Hyde, C. E.; Incerti, S.; Iodice, M.; Jardillier, J.; Jones, M. K.; Kahl, W.; Kato, S.; Katramatou, A. T.; Kelly, J. J.; Kerhoas, S.; Ketikyan, A.; Khayat, M.; Kino, K.; Kox, S.; Kramer, L. H.; Kumar, K. S.; Kumbartzki, G.; Kuss, M.; Leone, A.; LeRose, J. J.; Liang, M.; Lindgren, R. A.; Liyanage, N.; Lolos, G. J.; Lourie, R. W.; Madey, R.; Maeda, K.; Malov, S.; Manley, D. M.; Marchand, C.; Marchand, D.; Margaziotis, D. J.; Markowitz, P.; Marroncle, J.; Martino, J.; McCormick, K.; McIntyre, J.; Mehrabyan, S.; Merchez, F.; Meziani, Z. E.; Michaels, R.; Miller, G. W.; Mougey, J. Y.; Nanda, S. K.; Neyret, D.; Offermann, E. A. J. M.; Papandreou, Z.; Pasquini, B.; Perdrisat, C. F.; Perrino, R.; Petratos, G. G.; Platchkov, S.; Pomatsalyuk, R.; Prout, D. L.; Punjabi, V. A.; Pussieux, T.; Quémenér, G.; Ransome, R. D.; Ravel, O.; Real, J. S.; Renard, F.; Roblin, Y.; Rowntree, D.; Rutledge, G.; Rutt, P. M.; Saha, A.; Saito, T.; Sarty, A. J.; Serdarevic, A.; Smith, T.; Smirnov, G.; Soldi, K.; Sorokin, P.; Souder, P. A.; Suleiman, R.; Templon, J. A.; Terasawa, T.; Tieulent, R.; Tomasi-Gustaffson, E.; Tsubota, H.; Ueno, H.; Ulmer, P. E.; Urciuoli, G. M.; Vanderhaeghen, M.; Van der Meer, R. L. J.; Van De Vyver, R.; Vernin, P.; Vlahovic, B.; Voskanyan, H.; Voutier, E.; Watson, J. W.; Weinstein, L. B.; Wijesooriya, K.; Wilson, R.; Wojtsekhowski, B. B.; Zainea, D. G.; Zhang, W.-M.; Zhao, J.; Zhou, Z.-L.

2012-07-01

Virtual Compton scattering (VCS) on the proton has been studied at the Jefferson Laboratory using the exclusive photon electroproduction reaction ep→epγ. This paper gives a detailed account of the analysis which has led to the determination of the structure functions PLL-PTT/ɛ and PLT and the electric and magnetic generalized polarizabilities (GPs) αE(Q2) and βM(Q2) at values of the four-momentum transfer squared Q2=0.92 and 1.76 GeV2. These data, together with the results of VCS experiments at lower momenta, help building a coherent picture of the electric and magnetic GPs of the proton over the full measured Q2 range and point to their nontrivial behavior.

Extraction of the gluon density of the proton at x

NASA Astrophysics Data System (ADS)

Derrick, M.; Krakauer, D.; Magill, S.; Musgrave, B.; Repond, J.; Schlereth, J.; Stanek, R.; Talaga, R. L.; Thron, J.; Arzarello, F.; Ayad, R.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Bruni, P.; Cara Romeo, G.; Castellini, G.; Chiarini, M.; Cifarelli, L.; Cindolo, F.; Ciralli, F.; Contin, A.; D'Auria, S.; Frasconi, F.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Nemoz, C.; Palmonari, F.; Polini, A.; Sartorelli, G.; Timellini, R.; Zamora Garcia, Y.; Zichichi, A.; Bargende, A.; Crittenden, J.; Desch, K.; Diekmann, B.; Doeker, T.; Eckert, M.; Feld, L.; Frey, A.; Geerts, M.; Geitz, G.; Grothe, M.; Hartmann, H.; Haun, D.; Heinloth, K.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Mari, S. M.; Mass, A.; Mengel, S.; Mollen, J.; Paul, E.; Rembser, Ch.; Schattevoy, R.; Schramm, D.; Stamm, J.; Wedemeyer, R.; Campbell-Robson, S.; Cassidy, A.; Dyce, N.; Foster, B.; George, S.; Gilmore, R.; Heath, G. P.; Heath, H. F.; Llewellyn, T. J.; Morgado, C. J. S.; Norman, D. J. P.; O'Mara, J. A.; Tapper, R. J.; Wilson, S. S.; Yoshida, R.; Rau, R. R.; Arneodo, M.; Iannotti, L.; Schioppa, M.; Susinno, G.; Bernstein, A.; Caldwell, A.; Parsons, J. A.; Ritz, S.; Sciulli, F.; Straub, P. B.; Wai, L.; Yang, S.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Piotrzkowski, K.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Eskreys, K.; Jelén, K.; Kisielewska, D.; Kowalski, T.; Rulikowska-Zarȩbska, E.; Suszycki, L.; Zajaç, J.; Kȩdzierski, T.; Kotański, A.; Przybycień, M.; Bauerdick, L. A. T.; Behrens, U.; Bienlein, J. K.; Böttcher, S.; Coldewey, C.; Drews, G.; Flasiński, M.; Gilkinson, D. J.; Göttlicher, P.; Gutjahr, B.; Haas, T.; Hain, W.; Hasell, D.; Heβling, H.; Hultschig, H.; Iga, Y.; Joos, P.; Kasemann, M.; Klanner, R.; Koch, W.; Köpke, L.; Kötz, U.; Kowalski, H.; Kröger, W.; Krüger, J.; Labs, J.; Ladage, A.; Löhr, B.; Löwe, M.; Lüke, D.; Mańczak, O.; Ng, J. S. T.; Nickel, S.; Notz, D.; Ohrenberg, K.; Roco, M.; Rohde, M.; Roldán, J.; Schneekloth, U.; Schulz, W.; Selonke, F.; Stiliaris, E.; Voβ, T.; Westphal, D.; Wolf, G.; Youngman, C.; Grabosch, H. J.; Leich, A.; Meyer, A.; Rethfeldt, C.; Schlenstedt, S.; Barbagli, G.; Pelfer, P.; Anzivino, G.; Maccarrone, G.; De Pasquale, S.; Qian, S.; Votano, L.; Bamberger, A.; Freidhof, A.; Poser, T.; Söldner-Rembold, S.; Schroeder, J.; Theisen, G.; Trefzger, T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Fleck, I.; Jamieson, V. A.; Saxon, D. H.; Utley, M. L.; Wilson, A. S.; Dannemann, A.; Holm, U.; Horstmann, D.; Kammerlocher, H.; Krebs, B.; Neumann, T.; Sinkus, R.; Wick, K.; Badura, E.; Burow, B. D.; Fürtjes, A.; Hagge, L.; Lohrmann, E.; Mainusch, J.; Milewski, J.; Nakahata, M.; Pavel, N.; Poelz, G.; Schott, W.; Terron, J.; Zetsche, F.; Bacon, T. C.; Beuselinck, R.; Butterworth, I.; Gallo, E.; Harris, V. L.; Hung, B. H.; Long, K. R.; Miller, D. B.; Morawitz, P. P. O.; Prinias, A.; Sedgbeer, J. K.; Whitfield, A. F.; Mallik, U.; McCliment, E.; Wang, M. Z.; Wang, S. M.; Wu, J. T.; Zhang, Y.; Cloth, P.; Filges, D.; An, S. H.; Hong, S. M.; Nam, S. W.; Park, S. K.; Suh, M. H.; Yon, S. H.; Imlay, R.; Kartik, S.; Kim, H.-J.; McNeil, R. R.; Metcalf, W.; Nadendla, V. K.; Barreiro, F.; Cases, G.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; del Peso, J.; Puga, J.; de Trocóniz, J. F.; Ikraiam, F.; Mayer, J. K.; Smith, G. R.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Matthews, C. G.; Patel, P. M.; Sinclair, L. E.; Stairs, D. G.; St. Laurent, M.; Ullmann, R.; Zacek, G.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Gladilin, L. K.; Golubkov, Y. A.; Kobrin, V. D.; Kuzmin, V. A.; Proskuryakov, A. S.; Savin, A. A.; Shcheglova, L. M.; Solomin, A. N.; Zotov, N. P.; Bentvelsen, S.; Botje, M.; Chlebana, F.; Dake, A.; Engelen, J.; de Jong, P.; de Kamps, M.; Kooijman, P.; Kruse, A.; O'Dell, V.; Tenner, A.; Tiecke, H.; Verkerke, W.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; van Woudenberg, R.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Honscheid, K.; Li, C.; Ling, T. Y.; McLean, K. W.; Murray, W. N.; Park, I. H.; Romanowski, T. A.; Seidlein, R.; Bailey, D. S.; Blair, G. A.; Byrne, A.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Daniels, D.; Devenish, R. C. E.; Harnew, N.; Lancaster, M.; Luffman, P. E.; Lindemann, L.; McFall, J.; Nath, C.; Quadt, A.; Uijterwaal, H.; Walczak, R.; Wilson, F. F.; Yip, T.; Abbiendi, G.; Bertolin, A.; Brugnera, R.; Carlin, R.; Dal Corso, F.; De Giorgi, M.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Butterworth, J. M.; Feild, R. G.; Oh, B. Y.; Whitmore, J. J.; D'Agostini, G.; Iori, M.; Marini, G.; Mattioli, M.; Nigro, A.; Tassi, E.; Hart, J. C.; McCubbin, N. A.; Prytz, K.; Shah, T. P.; Short, T. L.; Barberis, E.; Cartiglia, N.; Dubbs, T.; Heusch, C.; Van Hook, M.; Hubbard, B.; Lockman, W.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Biltzinger, J.; Seifert, R. J.; Walenta, A. H.; Zech, G.; Abramowicz, H.; Briskin, G.; Dagan, S.; Levy, A.; Hasegawa, T.; Hazumi, M.; Ishii, T.; Kuze, M.; Mine, S.; Nagasawa, Y.; Nagira, T.; Nakao, M.; Suzuki, I.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; Chiba, M.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Nagayama, S.; Nakamitsu, Y.; Cirio, R.; Costa, M.; Ferrero, M. I.; Lamberti, L.; Maselli, S.; Peroni, C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Bandyopadhyay, D.; Benard, F.; Brkic, M.; Crombie, M. B.; Gingrich, D. M.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Sampson, C. R.; Teuscher, R. J.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Blankenship, K.; Kochocki, J.; Lu, B.; Mo, L. W.; Bogusz, W.; Charchuł; a, K.; Ciborowski, J.; Gajewski, J.; Grzelak, G.; Kasprzak, M.; Krzyżanowski, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Zarnecki, A. F.; Adamus, M.; Eisenberg, Y.; Glasman, C.; Karshon, U.; Revel, D.; Shapira, A.; Ali, I.; Behrens, B.; Dasu, S.; Fordham, C.; Foudas, C.; Goussiou, A.; Loveless, R. J.; Reeder, D. D.; Silverstein, S.; Smith, W. H.; Tsurugai, T.; Bhadra, S.; Frisken, W. R.; Furutani, K. M.; Zeus Collaboration

1995-02-01

The gluon momentum density xg( x, Q2) of the proton was extracted at Q2 = 20 GeV 2 for small values of x between 4 × 10 -4 and 10 -2 from the scaling violations of the proton structure function F2 measured recently by ZEUS in deep inelastic neutral current ep scattering at HERA. The extraction was performed in two ways. Firstly, using a global NLO fit to the ZEUS data on F2 at low x constrained by measurementsfrom NMC at larger x; and secondly using published approximate methods for the solution of the GLAP QCD evolution equations. Consistent results are obtained. A substantial increase of the gluon density is found at small x in comparison with the NMC result obtained at larger values of x.

Two-proton radioactivity with 2p halo in light mass nuclei A = 18-34

NASA Astrophysics Data System (ADS)

Saxena, G.; Kumawat, M.; Kaushik, M.; Jain, S. K.; Aggarwal, Mamta

2017-12-01

Two-proton radioactivity with 2p halo is reported theoretically in light mass nuclei A = 18- 34. We predict 19Mg, 22Si, 26S, 30Ar and 34Ca as promising candidates of ground state 2p-radioactivity with S2p < 0 and Sp > 0. Observation of extended tail of spatial charge density distribution, larger charge radius and study of proton single particle states, Fermi energy and the wave functions indicate 2p halo like structure which supports direct 2p emission. The Coulomb and centrifugal barriers in experimentally identified 2p unbound 22Si show a quasi-bound state that ensures enough life time for such experimental probes. Our predictions are in good accord with experimental and other theoretical data available so far.

Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.

Molecular Modeling of Lipid Aggregates: Theory and Application

NASA Astrophysics Data System (ADS)

Fenner, Joel Stewart

The ability of cell membranes to perform a wide variety of biological functions stems from the organization and composition of its molecular constituents. There are many engineering applications, such as liposome drug delivery carriers, whose functionality takes advantage of the structure to function relationship of lipid membranes. The fundamental understanding of the relationship between the thermodynamic behavior and structure of lipid membranes and the molecular properties of their lipid constituents is crucial to the successful design of lipid related applications. However, information about how the local microscopic composition of lipid membranes responds to the presence of proteins and nanomaterials is challenging given the intrinsic experimental and theoretical difficulties of studying such small-scale systems. The present work generalizes a self consistent mean field theory for the study of the thermodynamic and structural behavior of lipid bilayers as a function of its molecular composition and physicochemical environments. This novel molecular theory provides with the ability of performing systematic thermodynamic calculations at relatively low computational costs while considering a detailed molecular description of the system under study. The competition of all relevant molecular interactions, such as electrostatics, vdW and chemical equilibria, in the membrane system is described. The developed molecular theory is applied to study how the protonation state of pH-sensitive amphiphiles in a membrane system affects the membrane's morphology. The molecular theory results demonstrate that the protonation state of ionizable groups within amphiphilic membranes shows a highly complex non-monotonic dependence on bulk salt concentration and pH strength. This result suggests that information about the pKa of the molecules is not sufficient to predict the protonation state of the ionizable groups in the membrane system. The molecular theory is also applied to study how the presence of proteins or functionalized nanoparticles near a multicomponent membrane surface leads to changes in its local membrane composition. The results support an electrostatic dependent recruitment mechanism of oncogenic RhoA proteins to the cell membrane. Finally, the molecular theory results describe how nanoparticle functionality and/or membrane molecular composition can be tuned to enhance or suppress nanoparticle adsorption on to phospholipid membranes.

Towards a unified description of total and diffractive structure functions at DESY HERA in the QCD dipole picture

NASA Astrophysics Data System (ADS)

Bialas, A.; Peschanski, R.; Royon, Ch.

1998-06-01

It is argued that the QCD dipole picture allows us to build a unified theoretical description, based on Balitskii-Fadin-Kuraev-Lipatov dynamics, of the total and diffractive nucleon structure functions. This description is in qualitative agreement with the present collection of data obtained by the H1 Collaboration. More precise theoretical estimates, in particular the determination of the normalizations and proton transverse momentum behavior of the diffractive components, are shown to be required in order to reach definite conclusions.

Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.

2014-01-15

Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistentmore » hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.

PubMed

Chen, Duan; Chen, Zhan; Wei, Guo-Wei

2012-01-01

Proton transport plays an important role in biological energy transduction and sensory systems. Therefore, it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic, and quantum descriptions, assisted with the evolution, formation, and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free-energy functional to put proton kinetic and potential energies, the free energy of all other ions, and the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation, and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet-to-Neumann mapping, matched interface and boundary method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The gramicidin A channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model. Copyright © 2011 John Wiley & Sons, Ltd.

Proceedings of the Ringberg Workshop New Trends in HERA Physics 2005

NASA Astrophysics Data System (ADS)

Grindhammer, G.; Ochs, W.; Kniehl, B. A.; Kramer, G.

2006-04-01

1. Proton structure. Proton structure measurements at high Q2 and large x / Katarzyna Wichmann. Electroweak physics at HERA / Joachim Meyer. Inclusive low Q2 measurements at HERA / Victor Lendermann. Resummed perturbative evolution at high energy / Richard Ball. Colour dipole phenomenology / Graham Shaw -- 2. Spin physics. Exclusive reactions at HERMES / Frank Ellinghaus. Transverse spin effects in single and double hadron electroproduction at HERMES / Benedikt Zihlmann. Present understanding of the nucleon spin structure in view of recent experiments / Andreas Metz -- 3. Production of Hadrons and Jets. Measurements of [symbol] and parton distribution functions using HERA jet data / Amanda Cooper-Sarkar. A new parton shower algorithm: shower evolution, matching at leading and next-to-leading order level / Zóltan Nagy. Jet production at HERA / Dan Traynor. Multi-jet production in lepton-proton scattering with next-to-leading order accuracy / Zóltan Trócsányi. Dijet rates with symmetric [symbol] cuts / Andrea Banfi. QCD dynamics from forward hadron and jet measurements / Lidia Goerlich. Light-hadron electroproduction at next-to-leading order and implications / Bernd Kniehl. Particle production and fragmentation / David Saxon. Soft gluon logarithmic resummation and hadron mass effects in single hadron inclusive production / Simon Albino -- 4. Heavy-flavour production. Heavy-flavour photo- and electroproduction at NLO / Ingo Schienbein. Physics with charm quarks at HERA / John Loizides. Beauty production at HERA / Olaf Behnke. J/[symbol] photoproduction at next-to-leading order / Luminita Mihaila. J/[symbol] photoproduction at large z in soft collinear effective theory / Sean Fleming -- 5. Diffractive ep Scattering. Exclusive and inclusive diffraction at HERA / Henri Kowalski. Diffractive production of vector mesons and the gluon at small x / Thomas Teubner. Inclusive diffraction / Laurent Favart. From factorization to its breaking in diffractive dijet production / Michael Klasen. Diffractive parton density functions / Graeme Watt -- 6. Beyond the standard model. Beyond the standard model at HERA: status and prospects / Emmanuelle Perez -- 7. Resonances and diquarks. New resonances in the hadronic final state at HERA / Katsuo Tokushuku. Hadron systematics and emergent diquarks / Frank Wilczek -- 8. Future projects. Importance of a measurement of [symbol] at HERA / Robert Thorne. Measurement of the longitudinal proton structure function at low x at HERA / Joël Feltesse. HERA and the LHC / Albert De Roeck -- List of participants.

Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli.

PubMed

Bagramyan, K; Trchounian, A

2003-11-01

Formate hydrogen lyase from Escherichia coli is a membrane-bound complex that oxidizes formic acid to carbon dioxide and molecular hydrogen. Under anaerobic growth conditions and fermentation of sugars (glucose), it exists in two forms. One form is constituted by formate dehydrogenase H and hydrogenase 3, and the other one is the same formate dehydrogenase and hydrogenase 4; the presence of small protein subunits, carriers of electrons, is also probable. Other proteins may also be involved in formation of the enzyme complex, which requires the presence of metal (nickel-cobalt). Its formation also depends on the external pH and the presence of formate. Activity of both forms requires F(0)F(1)-ATPase; this explains dependence of the complex functioning on proton-motive force. It is also possible that the formate hydrogen lyase complex will exhibit its own proton-translocating function.

Hard exclusive pion electroproduction at backward angles with CLAS

NASA Astrophysics Data System (ADS)

Park, K.; Guidal, M.; Gothe, R. W.; Pire, B.; Semenov-Tian-Shansky, K.; Laget, J.-M.; Adhikari, K. P.; Adhikari, S.; Akbar, Z.; Avakian, H.; Ball, J.; Balossino, I.; Baltzell, N. A.; Barion, L.; Battaglieri, M.; Bedlinskiy, I.; Biselli, A. S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Cao, F. T.; Carman, D. S.; Celentano, A.; Charles, G.; Chetry, T.; Ciullo, G.; Clark, L.; Cole, P. L.; Contalbrigo, M.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Defurne, M.; Deur, A.; Djalali, C.; Dupre, R.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Elouadrhiri, L.; Eugenio, P.; Fedotov, G.; Fersch, R.; Filippi, A.; Garçon, M.; Ghandilyan, Y.; Gilfoyle, G. P.; Girod, F. X.; Golovatch, E.; Griffioen, K. A.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Hattawy, M.; Heddle, D.; Hicks, K.; Holtrop, M.; Hyde, C. E.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jenkins, D.; Johnston, S.; Joo, K.; Kabir, M. L.; Keller, D.; Khachatryan, G.; Khachatryan, M.; Khandaker, M.; Kim, W.; Klein, F. J.; Kubarovsky, V.; Kuhn, S. E.; Lanza, L.; Livingston, K.; MacGregor, I. J. D.; Markov, N.; McKinnon, B.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Munoz Camacho, C.; Nadel-Turonski, P.; Niccolai, S.; Niculescu, G.; Osipenko, M.; Paolone, M.; Paremuzyan, R.; Pasyuk, E.; Phelps, W.; Pogorelko, O.; Poudel, J.; Price, J. W.; Prok, Y.; Protopopescu, D.; Ripani, M.; Rizzo, A.; Rossi, P.; Sabatié, F.; Salgado, C.; Schumacher, R. A.; Sharabian, Y.; Skorodumina, Iu.; Smith, G. D.; Sokhan, D.; Sparveris, N.; Stepanyan, S.; Strakovsky, I. I.; Strauch, S.; Taiuti, M.; Tan, J. A.; Ungaro, M.; Voskanyan, H.; Voutier, E.; Wei, X.; Zachariou, N.; Zhang, J.

2018-05-01

We report on the first measurement of cross sections for exclusive deeply virtual pion electroproduction off the proton, ep →e‧ nπ+, above the resonance region at backward pion center-of-mass angles. The φπ* -dependent cross sections were measured, from which we extracted three combinations of structure functions of the proton. Our results are compatible with calculations based on nucleon-to-pion transition distribution amplitudes (TDAs). These non-perturbative objects are defined as matrix elements of three-quark-light-cone-operators and characterize partonic correlations with a particular emphasis on baryon charge distribution inside a nucleon.

Human neuronal uncoupling proteins 4 and 5 (UCP4 and UCP5): structural properties, regulation, and physiological role in protection against oxidative stress and mitochondrial dysfunction

PubMed Central

Ramsden, David B; Ho, Philip W-L; Ho, Jessica W-M; Liu, Hui-Fang; So, Danny H-F; Tse, Ho-Man; Chan, Koon-Ho; Ho, Shu-Leong

2012-01-01

Uncoupling proteins (UCPs) belong to a large family of mitochondrial solute carriers 25 (SLC25s) localized at the inner mitochondrial membrane. UCPs transport protons directly from the intermembrane space to the matrix. Of five structural homologues (UCP1 to 5), UCP4 and 5 are principally expressed in the central nervous system (CNS). Neurons derived their energy in the form of ATP that is generated through oxidative phosphorylation carried out by five multiprotein complexes (Complexes I–V) embedded in the inner mitochondrial membrane. In oxidative phosphorylation, the flow of electrons generated by the oxidation of substrates through the electron transport chain to molecular oxygen at Complex IV leads to the transport of protons from the matrix to the intermembrane space by Complex I, III, and IV. This movement of protons to the intermembrane space generates a proton gradient (mitochondrial membrane potential; MMP) across the inner membrane. Complex V (ATP synthase) uses this MMP to drive the conversion of ADP to ATP. Some electrons escape to oxygen-forming harmful reactive oxygen species (ROS). Proton leakage back to the matrix which bypasses Complex V resulting in a major reduction in ROS formation while having a minimal effect on MMP and hence, ATP synthesis; a process termed “mild uncoupling.” UCPs act to promote this proton leakage as means to prevent excessive build up of MMP and ROS formation. In this review, we discuss the structure and function of mitochondrial UCPs 4 and 5 and factors influencing their expression. Hypotheses concerning the evolution of the two proteins are examined. The protective mechanisms of the two proteins against neurotoxins and their possible role in regulating intracellular calcium movement, particularly with regard to the pathogenesis of Parkinson's disease are discussed. PMID:22950050

A transparent electrochromic metal-insulator switching device with three-terminal transistor geometry

NASA Astrophysics Data System (ADS)

Katase, Takayoshi; Onozato, Takaki; Hirono, Misako; Mizuno, Taku; Ohta, Hiromichi

2016-05-01

Proton and hydroxyl ion play an essential role for tuning functionality of oxides because their electronic state can be controlled by modifying oxygen off-stoichiometry and/or protonation. Tungsten trioxide (WO3), a well-known electrochromic (EC) material for smart window, is a wide bandgap insulator, whereas it becomes a metallic conductor HxWO3 by protonation. Although one can utilize electrochromism together with metal-insulator (MI) switching for one device, such EC-MI switching cannot be utilized in current EC devices because of their two-terminal structure with parallel-plate configuration. Here we demonstrate a transparent EC-MI switchable device with three-terminal TFT-type structure using amorphous (a-) WO3 channel layer, which was fabricated on glass substrate at room temperature. We used water-infiltrated nano-porous glass, CAN (calcium aluminate with nano-pores), as a liquid-leakage-free solid gate insulator. At virgin state, the device was fully transparent in the visible-light region. For positive gate voltage, the active channel became dark blue, and electrical resistivity of the a-WO3 layer drastically decreased with protonation. For negative gate voltage, deprotonation occurred and the active channel returned to transparent insulator. Good cycleability of the present transparent EC-MI switching device would have potential for the development of advanced smart windows.

TURBULENCE-GENERATED PROTON-SCALE STRUCTURES IN THE TERRESTRIAL MAGNETOSHEATH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vörös, Zoltán; Narita, Yasuhito; Yordanova, Emiliya

2016-03-01

Recent results of numerical magnetohydrodynamic simulations suggest that in collisionless space plasmas, turbulence can spontaneously generate thin current sheets. These coherent structures can partially explain the intermittency and the non-homogenous distribution of localized plasma heating in turbulence. In this Letter, Cluster multi-point observations are used to investigate the distribution of magnetic field discontinuities and the associated small-scale current sheets in the terrestrial magnetosheath downstream of a quasi-parallel bow shock. It is shown experimentally, for the first time, that the strongest turbulence-generated current sheets occupy the long tails of probability distribution functions associated with extremal values of magnetic field partial derivatives.more » During the analyzed one-hour time interval, about a hundred strong discontinuities, possibly proton-scale current sheets, were observed.« less

Inhomogeneous kinetic effects related to intermittent magnetic discontinuities

NASA Astrophysics Data System (ADS)

Greco, A.; Valentini, F.; Servidio, S.; Matthaeus, W. H.

2012-12-01

A connection between kinetic processes and two-dimensional intermittent plasma turbulence is observed using direct numerical simulations of a hybrid Vlasov-Maxwell model, in which the Vlasov equation is solved for protons, while the electrons are described as a massless fluid. During the development of turbulence, the proton distribution functions depart from the typical configuration of local thermodynamic equilibrium, displaying statistically significant non-Maxwellian features. In particular, temperature anisotropy and distortions are concentrated near coherent structures, generated as the result of the turbulent cascade, such as current sheets, which are nonuniformly distributed in space. Here, the partial variance of increments (PVI) method has been employed to identify high magnetic stress regions within a two-dimensional turbulent pattern. A quantitative association between non-Maxwellian features and coherent structures is established.

The Synthesis, Structures, and Chemical Properties of Macrocyclic Ligands Covalently Bonded into Layered Arrays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clearfield, Abraham

2014-11-01

In this part of the proposal we have concentrated on the surface functionalization of α-zirconium phosphate of composition Zr(O3POH)2•H2O. It is a layered compound that can be prepared as particles as small as 30 nm to single crystals in the range of cm. This compound is an ion exchanger with a capacity of 6.64 meq per gram. It finds use as a catalyst, proton conductor, sensors, biosensors, in kidney dialysis and drug delivery. By functionalizing the surface additional uses are contemplated as will be described. The layers consist of the metal, with 4+ charge, that is positioned slightly above andmore » below the mean layer plane and bridged by three of the four phosphate oxygens. The remaining POH groups point into the interlayer space creating double rows of POH groups but single arrays on the surface layers. The surface groups are reactive and we were able to bond silanes, isocyanates, epoxides, acrylates ` and phosphates to the surface POH groups. The layers are easily exfoliated or filled with ions by ion exchange or molecules by intercalation reactions. Highlights of our work include, in addition to direct functionalization of the surfaces, replacement of the protons on the surface with ions of different charge. This allows us to bond phosphates, biophosphates, phosphonic acids and alcohols to the surface. By variation of the ion charge of the ions that replace the surface protons, different surface structures are obtained. We have already shown that polymer fillers, catalysts and Janus particles may be prepared. The combination of surface functionalization with the ability to insert molecules and ions between the layers allow for a rich development of numerous useful other applications as well as nano-surface chemistry.« less

Density functional theory study of defect energies and space charge distribution at a solid-oxide electrolyte surface

NASA Astrophysics Data System (ADS)

Han, Chu; Bongiorno, Angelo

2014-03-01

Yttrium-doped barium zirconate (BZY) is a proton conducting electrolyte forming a class of novel materials for new generation of solid oxide fuel cells, for hydrogen separation and purification, and for electrolysis of water. Here we use density functional theory calculations to compute the energy of protons and oxygen vacancies at the surface and in the bulk of lightly Y-doped BZY materials. We found that protons are energetically more stable at the surface termination than in the bulk of BZY by about 1 eV. In contrast, doubly-positively charged oxygen vacancies are found to form iso-energetic defects at both the terminal surface layer and in the bulk of BZY, while in the sub-surface region the defect energy raises by about 1 eV with respect to the value in the bulk. The energetic behavior of protons and oxygen vacancies in the near surface region of BZY is attributed to the competition of strain and electrostatic effects. Lattice model representations of BZY surfaces are then used in combination with Monte Carlo simulations to solve the Poisson-Boltzmann equation and investigate the implication of the results above on the structure of the space charge region at the surface of BZY materials.

Longitudinal Double-Spin Asymmetry ALL for Inclusive Jet Production in Polarized Proton Collisions at √s = 510 GeV

NASA Astrophysics Data System (ADS)

Quintero, Amilkar; STAR Collaboration

2017-09-01

The STAR experiment at the Relativistic Heavy-Ion Collider (RHIC) at Brookhaven National Laboratory is carrying out a spin physics program in high-energy polarized proton collisions at center of mass energies up to 510 GeV, to gain a deeper insight into the spin structure and dynamics of the proton. The polarized gluon distribution function can be constrained in longitudinally polarized proton collisions through jet / di-jet production. Recent global analyses, which include results of the measurement of ALL for inclusive jet production at 200 GeV at mid-rapidity at the STAR experiment, provide evidence of a non-zero gluon polarization in the measured range of partonic momentum fraction of approximately 0.05

The tropolone-isobutylamine complex: a hydrogen-bonded troponoid without dominant π-π interactions.

PubMed

Vealey, Zachary N; Mercado, Brandon Q; Vaccaro, Patrick H

2016-10-01

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π-π, C-H...π, or ion-π interactions. The organic salt (TrOH·iBA) formed by a facile proton-transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7-oxocyclohepta-1,3,5-trien-1-olate, C 4 H 12 N + ·C 7 H 5 O 2 - , has been investigated by X-ray crystallography, with complementary quantum-chemical and statistical-database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice-packing phenomena. The crystal structure deduced from low-temperature diffraction measurements displays extensive hydrogen-bonding networks, yet shows little evidence of the aryl forces (viz. π-π, C-H...π, and ion-π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton-donating and proton-accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven-membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen-bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor-acceptor distances of any troponoid-based complex, combined with unambiguous signatures of enhanced proton-delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.

Search for the X (5568 ) State Decaying into Bs0π± in Proton-Proton Collisions at √{s }=8 TeV

NASA Astrophysics Data System (ADS)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Ambrogi, F.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Escalante Del Valle, A.; Flechl, M.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Grossmann, J.; Hrubec, J.; Jeitler, M.; König, A.; Krammer, N.; Krätschmer, I.; Liko, D.; Madlener, T.; Mikulec, I.; Pree, E.; Rad, N.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Spanring, M.; Spitzbart, D.; Waltenberger, W.; Wittmann, J.; Wulz, C.-E.; Zarucki, M.; Chekhovsky, V.; Mossolov, V.; Suarez Gonzalez, J.; De Wolf, E. A.; Di Croce, D.; Janssen, X.; Lauwers, J.; Van Haevermaet, H.; Van Mechelen, P.; Van Remortel, N.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; De Bruyn, I.; De Clercq, J.; Deroover, K.; Flouris, G.; Lontkovskyi, D.; Lowette, S.; Marchesini, I.; Moortgat, S.; Moreels, L.; Python, Q.; Skovpen, K.; Tavernier, S.; Van Doninck, W.; Van Mulders, P.; Van Parijs, I.; Beghin, D.; Bilin, B.; Brun, H.; Clerbaux, B.; De Lentdecker, G.; Delannoy, H.; Dorney, B.; Fasanella, G.; Favart, L.; Goldouzian, R.; Grebenyuk, A.; Kalsi, A. K.; Lenzi, T.; Luetic, J.; Maerschalk, T.; Marinov, A.; Seva, T.; Starling, E.; Vander Velde, C.; Vanlaer, P.; Vannerom, D.; Yonamine, R.; Zenoni, F.; Cornelis, T.; Dobur, D.; Fagot, A.; Gul, M.; Khvastunov, I.; Poyraz, D.; Roskas, C.; Salva, S.; Tytgat, M.; Verbeke, W.; Zaganidis, N.; Bakhshiansohi, H.; Bondu, O.; Brochet, S.; Bruno, G.; Caputo, C.; Caudron, A.; David, P.; De Visscher, S.; Delaere, C.; Delcourt, M.; Francois, B.; Giammanco, A.; Komm, M.; Krintiras, G.; Lemaitre, V.; Magitteri, A.; Mertens, A.; Musich, M.; Piotrzkowski, K.; Quertenmont, L.; Saggio, A.; Vidal Marono, M.; Wertz, S.; Zobec, J.; Aldá Júnior, W. L.; Alves, F. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Hensel, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Coelho, E.; Da Costa, E. M.; Da Silveira, G. G.; De Jesus Damiao, D.; Fonseca De Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Melo De Almeida, M.; Mora Herrera, C.; Mundim, L.; Nogima, H.; Sanchez Rosas, L. J.; Santoro, A.; Sznajder, A.; Thiel, M.; Tonelli Manganote, E. J.; Torres Da Silva De Araujo, F.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; Tomei, T. R. Fernandez Perez; Gregores, E. M.; Mercadante, P. G.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Misheva, M.; Rodozov, M.; Shopova, M.; Sultanov, G.; Dimitrov, A.; Litov, L.; Pavlov, B.; Petkov, P.; Fang, W.; Gao, X.; Yuan, L.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Chen, Y.; Jiang, C. H.; Leggat, D.; Liao, H.; Liu, Z.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Yazgan, E.; Zhang, H.; Zhang, S.; Zhao, J.; Ban, Y.; Chen, G.; Li, J.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Zhang, F.; Wang, Y.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; González Hernández, C. F.; Ruiz Alvarez, J. D.; Segura Delgado, M. A.; Courbon, B.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Sculac, T.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Ferencek, D.; Kadija, K.; Mesic, B.; Starodumov, A.; Susa, T.; Ather, M. W.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Finger, M.; Finger, M.; Carrera Jarrin, E.; El-khateeb, E.; Ellithi Kamel, A.; Mahrous, A.; Dewanjee, R. K.; Kadastik, M.; Perrini, L.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Kirschenmann, H.; Pekkanen, J.; Voutilainen, M.; Havukainen, J.; Heikkilä, J. K.; Järvinen, T.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Laurila, S.; Lehti, S.; Lindén, T.; Luukka, P.; Siikonen, H.; Tuominen, E.; Tuominiemi, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Faure, J. L.; Ferri, F.; Ganjour, S.; Ghosh, S.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Kucher, I.; Leloup, C.; Locci, E.; Machet, M.; Malcles, J.; Negro, G.; Rander, J.; Rosowsky, A.; Sahin, M. Ö.; Titov, M.; Abdulsalam, A.; Amendola, C.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Charlot, C.; Granier de Cassagnac, R.; Jo, M.; Lisniak, S.; Lobanov, A.; Martin Blanco, J.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Stahl Leiton, A. G.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Zghiche, A.; Agram, J.-L.; Andrea, J.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Jansová, M.; Le Bihan, A.-C.; Tonon, N.; Van Hove, P.; Gadrat, S.; Beauceron, S.; Bernet, C.; Boudoul, G.; Chierici, R.; Contardo, D.; Depasse, P.; El Mamouni, H.; Fay, J.; Finco, L.; Gascon, S.; Gouzevitch, M.; Grenier, G.; Ille, B.; Lagarde, F.; Laktineh, I. B.; Lethuillier, M.; Mirabito, L.; Pequegnot, A. L.; Perries, S.; Popov, A.; Sordini, V.; Vander Donckt, M.; Viret, S.; Toriashvili, T.; Tsamalaidze, Z.; Autermann, C.; Feld, L.; Kiesel, M. K.; Klein, K.; Lipinski, M.; Preuten, M.; Schomakers, C.; Schulz, J.; Teroerde, M.; Zhukov, V.; Albert, A.; Dietz-Laursonn, E.; Duchardt, D.; Endres, M.; Erdmann, M.; Erdweg, S.; Esch, T.; Fischer, R.; Güth, A.; Hamer, M.; Hebbeker, T.; Heidemann, C.; Hoepfner, K.; Knutzen, S.; Merschmeyer, M.; Meyer, A.; Millet, P.; Mukherjee, S.; Pook, T.; Radziej, M.; Reithler, H.; Rieger, M.; Scheuch, F.; Teyssier, D.; Thüer, S.; Flügge, G.; Kargoll, B.; Kress, T.; Künsken, A.; Müller, T.; Nehrkorn, A.; Nowack, A.; Pistone, C.; Pooth, O.; Stahl, A.; Aldaya Martin, M.; Arndt, T.; Asawatangtrakuldee, C.; Beernaert, K.; Behnke, O.; Behrens, U.; Bermúdez Martínez, A.; Bin Anuar, A. A.; Borras, K.; Botta, V.; Campbell, A.; Connor, P.; Contreras-Campana, C.; Costanza, F.; Diez Pardos, C.; Eckerlin, G.; Eckstein, D.; Eichhorn, T.; Eren, E.; Gallo, E.; Garay Garcia, J.; Geiser, A.; Grados Luyando, J. M.; Grohsjean, A.; Gunnellini, P.; Guthoff, M.; Harb, A.; Hauk, J.; Hempel, M.; Jung, H.; Kasemann, M.; Keaveney, J.; Kleinwort, C.; Korol, I.; Krücker, D.; Lange, W.; Lelek, A.; Lenz, T.; Leonard, J.; Lipka, K.; Lohmann, W.; Mankel, R.; Melzer-Pellmann, I.-A.; Meyer, A. B.; Mittag, G.; Mnich, J.; Mussgiller, A.; Ntomari, E.; Pitzl, D.; Raspereza, A.; Savitskyi, M.; Saxena, P.; Shevchenko, R.; Stefaniuk, N.; Van Onsem, G. P.; Walsh, R.; Wen, Y.; Wichmann, K.; Wissing, C.; Zenaiev, O.; Aggleton, R.; Bein, S.; Blobel, V.; Centis Vignali, M.; Dreyer, T.; Garutti, E.; Gonzalez, D.; Haller, J.; Hinzmann, A.; Hoffmann, M.; Karavdina, A.; Klanner, R.; Kogler, R.; Kovalchuk, N.; Kurz, S.; Lapsien, T.; Marconi, D.; Meyer, M.; Niedziela, M.; Nowatschin, D.; Pantaleo, F.; Peiffer, T.; Perieanu, A.; Scharf, C.; Schleper, P.; Schmidt, A.; Schumann, S.; Schwandt, J.; Sonneveld, J.; Stadie, H.; Steinbrück, G.; Stober, F. M.; Stöver, M.; Tholen, H.; Troendle, D.; Usai, E.; Vanhoefer, A.; Vormwald, B.; Akbiyik, M.; Barth, C.; Baselga, M.; Baur, S.; Butz, E.; Caspart, R.; Chwalek, T.; Colombo, F.; De Boer, W.; Dierlamm, A.; Faltermann, N.; Freund, B.; Friese, R.; Giffels, M.; Harrendorf, M. A.; Hartmann, F.; Heindl, S. M.; Husemann, U.; Kassel, F.; Kudella, S.; Mildner, H.; Mozer, M. U.; Müller, Th.; Plagge, M.; Quast, G.; Rabbertz, K.; Schröder, M.; Shvetsov, I.; Sieber, G.; Simonis, H. J.; Ulrich, R.; Wayand, S.; Weber, M.; Weiler, T.; Williamson, S.; Wöhrmann, C.; Wolf, R.; Anagnostou, G.; Daskalakis, G.; Geralis, T.; Kyriakis, A.; Loukas, D.; Topsis-Giotis, I.; Karathanasis, G.; Kesisoglou, S.; Panagiotou, A.; Saoulidou, N.; Kousouris, K.; Evangelou, I.; Foudas, C.; Gianneios, P.; Katsoulis, P.; Kokkas, P.; Mallios, S.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Strologas, J.; Triantis, F. A.; Tsitsonis, D.; Csanad, M.; Filipovic, N.; Pasztor, G.; Surányi, O.; Veres, G. 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R.; Williams, T.; Auzinger, G.; Bainbridge, R.; Borg, J.; Breeze, S.; Buchmuller, O.; Bundock, A.; Casasso, S.; Citron, M.; Colling, D.; Corpe, L.; Dauncey, P.; Davies, G.; De Wit, A.; Della Negra, M.; Di Maria, R.; Elwood, A.; Haddad, Y.; Hall, G.; Iles, G.; James, T.; Lane, R.; Laner, C.; Lyons, L.; Magnan, A.-M.; Malik, S.; Mastrolorenzo, L.; Matsushita, T.; Nash, J.; Nikitenko, A.; Palladino, V.; Pesaresi, M.; Raymond, D. M.; Richards, A.; Rose, A.; Scott, E.; Seez, C.; Shtipliyski, A.; Summers, S.; Tapper, A.; Uchida, K.; Vazquez Acosta, M.; Virdee, T.; Wardle, N.; Winterbottom, D.; Wright, J.; Zenz, S. C.; Cole, J. E.; Hobson, P. R.; Khan, A.; Kyberd, P.; Reid, I. D.; Teodorescu, L.; Zahid, S.; Borzou, A.; Call, K.; Dittmann, J.; Hatakeyama, K.; Liu, H.; Pastika, N.; Smith, C.; Bartek, R.; Dominguez, A.; Buccilli, A.; Cooper, S. 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A.; Hanson, G.; Heilman, J.; Karapostoli, G.; Kennedy, E.; Lacroix, F.; Long, O. R.; Olmedo Negrete, M.; Paneva, M. I.; Si, W.; Wang, L.; Wei, H.; Wimpenny, S.; Yates, B. R.; Branson, J. G.; Cittolin, S.; Derdzinski, M.; Gerosa, R.; Gilbert, D.; Hashemi, B.; Holzner, A.; Klein, D.; Kole, G.; Krutelyov, V.; Letts, J.; Masciovecchio, M.; Olivito, D.; Padhi, S.; Pieri, M.; Sani, M.; Sharma, V.; Tadel, M.; Vartak, A.; Wasserbaech, S.; Wood, J.; Würthwein, F.; Yagil, A.; Zevi Della Porta, G.; Amin, N.; Bhandari, R.; Bradmiller-Feld, J.; Campagnari, C.; Dishaw, A.; Dutta, V.; Franco Sevilla, M.; Gouskos, L.; Heller, R.; Incandela, J.; Ovcharova, A.; Qu, H.; Richman, J.; Stuart, D.; Suarez, I.; Yoo, J.; Anderson, D.; Bornheim, A.; Lawhorn, J. M.; Newman, H. B.; Nguyen, T.; Pena, C.; Spiropulu, M.; Vlimant, J. R.; Xie, S.; Zhang, Z.; Zhu, R. Y.; Andrews, M. B.; Ferguson, T.; Mudholkar, T.; Paulini, M.; Russ, J.; Sun, M.; Vogel, H.; Vorobiev, I.; Weinberg, M.; Cumalat, J. P.; Ford, W. T.; Jensen, F.; Johnson, A.; Krohn, M.; Leontsinis, S.; Mulholland, T.; Stenson, K.; Wagner, S. R.; Alexander, J.; Chaves, J.; Chu, J.; Dittmer, S.; Mcdermott, K.; Mirman, N.; Patterson, J. R.; Quach, D.; Rinkevicius, A.; Ryd, A.; Skinnari, L.; Soffi, L.; Tan, S. M.; Tao, Z.; Thom, J.; Tucker, J.; Wittich, P.; Zientek, M.; Abdullin, S.; Albrow, M.; Alyari, M.; Apollinari, G.; Apresyan, A.; Apyan, A.; Banerjee, S.; Bauerdick, L. A. T.; Beretvas, A.; Berryhill, J.; Bhat, P. C.; Bolla, G.; Burkett, K.; Butler, J. N.; Canepa, A.; Cerati, G. B.; Cheung, H. W. K.; Chlebana, F.; Cremonesi, M.; Duarte, J.; Elvira, V. D.; Freeman, J.; Gecse, Z.; Gottschalk, E.; Gray, L.; Green, D.; Grünendahl, S.; Gutsche, O.; Harris, R. M.; Hasegawa, S.; Hirschauer, J.; Hu, Z.; Jayatilaka, B.; Jindariani, S.; Johnson, M.; Joshi, U.; Klima, B.; Kreis, B.; Lammel, S.; Lincoln, D.; Lipton, R.; Liu, M.; Liu, T.; Lopes De Sá, R.; Lykken, J.; Maeshima, K.; Magini, N.; Marraffino, J. M.; Mason, D.; McBride, P.; Merkel, P.; Mrenna, S.; Nahn, S.; O'Dell, V.; Pedro, K.; Prokofyev, O.; Rakness, G.; Ristori, L.; Schneider, B.; Sexton-Kennedy, E.; Soha, A.; Spalding, W. J.; Spiegel, L.; Stoynev, S.; Strait, J.; Strobbe, N.; Taylor, L.; Tkaczyk, S.; Tran, N. V.; Uplegger, L.; Vaandering, E. W.; Vernieri, C.; Verzocchi, M.; Vidal, R.; Wang, M.; Weber, H. A.; Whitbeck, A.; Acosta, D.; Avery, P.; Bortignon, P.; Bourilkov, D.; Brinkerhoff, A.; Carnes, A.; Carver, M.; Curry, D.; Field, R. D.; Furic, I. K.; Gleyzer, S. V.; Joshi, B. M.; Konigsberg, J.; Korytov, A.; Kotov, K.; Ma, P.; Matchev, K.; Mei, H.; Mitselmakher, G.; Shi, K.; Sperka, D.; Terentyev, N.; Thomas, L.; Wang, J.; Wang, S.; Yelton, J.; Joshi, Y. R.; Linn, S.; Markowitz, P.; Rodriguez, J. L.; Ackert, A.; Adams, T.; Askew, A.; Hagopian, S.; Hagopian, V.; Johnson, K. F.; Kolberg, T.; Martinez, G.; Perry, T.; Prosper, H.; Saha, A.; Santra, A.; Sharma, V.; Yohay, R.; Baarmand, M. M.; Bhopatkar, V.; Colafranceschi, S.; Hohlmann, M.; Noonan, D.; Roy, T.; Yumiceva, F.; Adams, M. R.; Apanasevich, L.; Berry, D.; Betts, R. R.; Cavanaugh, R.; Chen, X.; Evdokimov, O.; Gerber, C. E.; Hangal, D. A.; Hofman, D. J.; Jung, K.; Kamin, J.; Sandoval Gonzalez, I. D.; Tonjes, M. B.; Trauger, H.; Varelas, N.; Wang, H.; Wu, Z.; Zhang, J.; Bilki, B.; Clarida, W.; Dilsiz, K.; Durgut, S.; Gandrajula, R. P.; Haytmyradov, M.; Khristenko, V.; Merlo, J.-P.; Mermerkaya, H.; Mestvirishvili, A.; Moeller, A.; Nachtman, J.; Ogul, H.; Onel, Y.; Ozok, F.; Penzo, A.; Snyder, C.; Tiras, E.; Wetzel, J.; Yi, K.; Blumenfeld, B.; Cocoros, A.; Eminizer, N.; Fehling, D.; Feng, L.; Gritsan, A. V.; Maksimovic, P.; Roskes, J.; Sarica, U.; Swartz, M.; Xiao, M.; You, C.; Al-bataineh, A.; Baringer, P.; Bean, A.; Boren, S.; Bowen, J.; Castle, J.; Khalil, S.; Kropivnitskaya, A.; Majumder, D.; Mcbrayer, W.; Murray, M.; Royon, C.; Sanders, S.; Schmitz, E.; Tapia Takaki, J. D.; Wang, Q.; Ivanov, A.; Kaadze, K.; Maravin, Y.; Mohammadi, A.; Saini, L. K.; Skhirtladze, N.; Rebassoo, F.; Wright, D.; Anelli, C.; Baden, A.; Baron, O.; Belloni, A.; Eno, S. C.; Feng, Y.; Ferraioli, C.; Hadley, N. J.; Jabeen, S.; Jeng, G. Y.; Kellogg, R. G.; Kunkle, J.; Mignerey, A. C.; Ricci-Tam, F.; Shin, Y. H.; Skuja, A.; Tonwar, S. C.; Abercrombie, D.; Allen, B.; Azzolini, V.; Barbieri, R.; Baty, A.; Bi, R.; Brandt, S.; Busza, W.; Cali, I. A.; D'Alfonso, M.; Demiragli, Z.; Gomez Ceballos, G.; Goncharov, M.; Hsu, D.; Hu, M.; Iiyama, Y.; Innocenti, G. M.; Klute, M.; Kovalskyi, D.; Lee, Y.-J.; Levin, A.; Luckey, P. D.; Maier, B.; Marini, A. C.; Mcginn, C.; Mironov, C.; Narayanan, S.; Niu, X.; Paus, C.; Roland, C.; Roland, G.; Salfeld-Nebgen, J.; Stephans, G. S. F.; Tatar, K.; Velicanu, D.; Wang, J.; Wang, T. W.; Wyslouch, B.; Benvenuti, A. C.; Chatterjee, R. M.; Evans, A.; Hansen, P.; Hiltbrand, J.; Kalafut, S.; Kubota, Y.; Lesko, Z.; Mans, J.; Nourbakhsh, S.; Ruckstuhl, N.; Rusack, R.; Turkewitz, J.; Wadud, M. A.; Acosta, J. G.; Oliveros, S.; Avdeeva, E.; Bloom, K.; Claes, D. R.; Fangmeier, C.; Golf, F.; Gonzalez Suarez, R.; Kamalieddin, R.; Kravchenko, I.; Monroy, J.; Siado, J. E.; Snow, G. R.; Stieger, B.; Dolen, J.; Godshalk, A.; Harrington, C.; Iashvili, I.; Nguyen, D.; Parker, A.; Rappoccio, S.; Roozbahani, B.; Alverson, G.; Barberis, E.; Freer, C.; Hortiangtham, A.; Massironi, A.; Morse, D. M.; Orimoto, T.; Teixeira De Lima, R.; Trocino, D.; Wamorkar, T.; Wang, B.; Wisecarver, A.; Wood, D.; Bhattacharya, S.; Charaf, O.; Hahn, K. A.; Mucia, N.; Odell, N.; Schmitt, M. H.; Sung, K.; Trovato, M.; Velasco, M.; Bucci, R.; Dev, N.; Hildreth, M.; Hurtado Anampa, K.; Jessop, C.; Karmgard, D. J.; Kellams, N.; Lannon, K.; Li, W.; Loukas, N.; Marinelli, N.; Meng, F.; Mueller, C.; Musienko, Y.; Planer, M.; Reinsvold, A.; Ruchti, R.; Siddireddy, P.; Smith, G.; Taroni, S.; Wayne, M.; Wightman, A.; Wolf, M.; Woodard, A.; Alimena, J.; Antonelli, L.; Bylsma, B.; Durkin, L. S.; Flowers, S.; Francis, B.; Hart, A.; Hill, C.; Ji, W.; Liu, B.; Luo, W.; Winer, B. L.; Wulsin, H. W.; Cooperstein, S.; Driga, O.; Elmer, P.; Hardenbrook, J.; Hebda, P.; Higginbotham, S.; Kalogeropoulos, A.; Lange, D.; Luo, J.; Marlow, D.; Mei, K.; Ojalvo, I.; Olsen, J.; Palmer, C.; Piroué, P.; Stickland, D.; Tully, C.; Malik, S.; Norberg, S.; Barker, A.; Barnes, V. E.; Das, S.; Folgueras, S.; Gutay, L.; Jha, M. K.; Jones, M.; Jung, A. W.; Khatiwada, A.; Miller, D. H.; Neumeister, N.; Peng, C. C.; Qiu, H.; Schulte, J. F.; Sun, J.; Wang, F.; Xiao, R.; Xie, W.; Cheng, T.; Parashar, N.; Stupak, J.; Chen, Z.; Ecklund, K. M.; Freed, S.; Geurts, F. J. M.; Guilbaud, M.; Kilpatrick, M.; Li, W.; Michlin, B.; Padley, B. P.; Roberts, J.; Rorie, J.; Shi, W.; Tu, Z.; Zabel, J.; Zhang, A.; Bodek, A.; de Barbaro, P.; Demina, R.; Duh, Y. t.; Ferbel, T.; Galanti, M.; Garcia-Bellido, A.; Han, J.; Hindrichs, O.; Khukhunaishvili, A.; Lo, K. H.; Tan, P.; Verzetti, M.; Ciesielski, R.; Goulianos, K.; Mesropian, C.; Agapitos, A.; Chou, J. P.; Gershtein, Y.; Gómez Espinosa, T. A.; Halkiadakis, E.; Heindl, M.; Hughes, E.; Kaplan, S.; Kunnawalkam Elayavalli, R.; Kyriacou, S.; Lath, A.; Montalvo, R.; Nash, K.; Osherson, M.; Saka, H.; Salur, S.; Schnetzer, S.; Sheffield, D.; Somalwar, S.; Stone, R.; Thomas, S.; Thomassen, P.; Walker, M.; Delannoy, A. G.; Heideman, J.; Riley, G.; Rose, K.; Spanier, S.; Thapa, K.; Bouhali, O.; Castaneda Hernandez, A.; Celik, A.; Dalchenko, M.; De Mattia, M.; Delgado, A.; Dildick, S.; Eusebi, R.; Gilmore, J.; Huang, T.; Kamon, T.; Mueller, R.; Pakhotin, Y.; Patel, R.; Perloff, A.; Perniè, L.; Rathjens, D.; Safonov, A.; Tatarinov, A.; Ulmer, K. A.; Akchurin, N.; Damgov, J.; De Guio, F.; Dudero, P. R.; Faulkner, J.; Gurpinar, E.; Kunori, S.; Lamichhane, K.; Lee, S. W.; Libeiro, T.; Mengke, T.; Muthumuni, S.; Peltola, T.; Undleeb, S.; Volobouev, I.; Wang, Z.; Greene, S.; Gurrola, A.; Janjam, R.; Johns, W.; Maguire, C.; Melo, A.; Ni, H.; Padeken, K.; Sheldon, P.; Tuo, S.; Velkovska, J.; Xu, Q.; Arenton, M. W.; Barria, P.; Cox, B.; Hirosky, R.; Joyce, M.; Ledovskoy, A.; Li, H.; Neu, C.; Sinthuprasith, T.; Wang, Y.; Wolfe, E.; Xia, F.; Harr, R.; Karchin, P. E.; Poudyal, N.; Sturdy, J.; Thapa, P.; Zaleski, S.; Brodski, M.; Buchanan, J.; Caillol, C.; Dasu, S.; Dodd, L.; Duric, S.; Gomber, B.; Grothe, M.; Herndon, M.; Hervé, A.; Hussain, U.; Klabbers, P.; Lanaro, A.; Levine, A.; Long, K.; Loveless, R.; Ruggles, T.; Savin, A.; Smith, N.; Smith, W. H.; Taylor, D.; Woods, N.; CMS Collaboration

2018-05-01

A search for resonancelike structures in the Bs0π± invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at √{s }=8 TeV , corresponding to an integrated luminosity of 19.7 fb-1 . The Bs0 mesons are reconstructed in the decay chain Bs0→J /ψ ϕ , with J /ψ →μ+μ- and ϕ →K+K-. The Bs0π± invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed Bs0 and π± candidates. Upper limits are set on the relative production rates of the X (5568 ) and Bs0 states times the branching fraction of the decay X (5568 )±→Bs0π± . In addition, upper limits are obtained as a function of the mass and the natural width of possible exotic states decaying into Bs0π±.

Proton Affinities of Anionic Bases:  Trends Across the Periodic Table, Structural Effects, and DFT Validation.

PubMed

Swart, Marcel; Bickelhaupt, F Matthias

2006-03-01

We have carried out an extensive exploration of the gas-phase basicity of archetypal anionic bases across the periodic system using the generalized gradient approximation of density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities:  BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 1.6 kcal/mol for the proton affinity at 0 K with respect to high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the anionic conjugate bases of all main-group-element hydrides of groups 14-17 and periods 2-6. We have also studied the effect of stepwise methylation of the protophilic center of the second- and third-period bases.

Molecular switching behavior in isosteric DNA base pairs.

PubMed

Jissy, A K; Konar, Sukanya; Datta, Ayan

2013-04-15

The structures and proton-coupled behavior of adenine-thymine (A-T) and a modified base pair containing a thymine isostere, adenine-difluorotoluene (A-F), are studied in different solvents by dispersion-corrected density functional theory. The stability of the canonical Watson-Crick base pair and the mismatched pair in various solvents with low and high dielectric constants is analyzed. It is demonstrated that A-F base pairing is favored in solvents with low dielectric constant. The stabilization and conformational changes induced by protonation are also analyzed for the natural as well as the mismatched base pair. DNA sequences capable of changing their sequence conformation on protonation are used in the construction of pH-based molecular switches. An acidic medium has a profound influence in stabilizing the isostere base pair. Such a large gain in stability on protonation leads to an interesting pH-controlled molecular switch, which can be incorporated in a natural DNA tract. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measurement of the Transverse Single-Spin Asymmetry in p↑+p →W±/Z0 at RHIC

NASA Astrophysics Data System (ADS)

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; Aggarwal, M. M.; Ahammed, Z.; Alekseev, I.; Aparin, A.; Arkhipkin, D.; Aschenauer, E. C.; Attri, A.; Averichev, G. S.; Bai, X.; Bairathi, V.; Banerjee, A.; Bellwied, R.; Bhasin, A.; Bhati, A. K.; Bhattarai, P.; Bielcik, J.; Bielcikova, J.; Bland, L. C.; Bordyuzhin, I. G.; Bouchet, J.; Brandenburg, J. D.; Brandin, A. V.; Bunzarov, I.; Butterworth, J.; Caines, H.; Calderón de la Barca Sánchez, M.; Campbell, J. M.; Cebra, D.; Chakaberia, I.; Chaloupka, P.; Chang, Z.; Chattopadhyay, S.; Chen, X.; Chen, J. H.; Cheng, J.; Cherney, M.; Christie, W.; Contin, G.; Crawford, H. J.; Das, S.; De Silva, L. C.; Debbe, R. R.; Dedovich, T. G.; Deng, J.; Derevschikov, A. A.; di Ruzza, B.; Didenko, L.; Dilks, C.; Dong, X.; Drachenberg, J. L.; Draper, J. E.; Du, C. M.; Dunkelberger, L. E.; Dunlop, J. C.; Efimov, L. G.; Engelage, J.; Eppley, G.; Esha, R.; Evdokimov, O.; Eyser, O.; Fatemi, R.; Fazio, S.; Federic, P.; Fedorisin, J.; Feng, Z.; Filip, P.; Fisyak, Y.; Flores, C. E.; Fulek, L.; Gagliardi, C. A.; Garand, D.; Geurts, F.; Gibson, A.; Girard, M.; Greiner, L.; Grosnick, D.; Gunarathne, D. S.; Guo, Y.; Gupta, A.; Gupta, S.; Guryn, W.; Hamad, A.; Hamed, A.; Haque, R.; Harris, J. W.; He, L.; Heppelmann, S.; Heppelmann, S.; Hirsch, A.; Hoffmann, G. W.; Hofman, D. J.; Horvat, S.; Huang, X.; Huang, H. Z.; Huang, B.; Huang, T.; Huck, P.; Humanic, T. J.; Igo, G.; Jacobs, W. W.; Jang, H.; Jentsch, A.; Jia, J.; Jiang, K.; Judd, E. G.; Kabana, S.; Kalinkin, D.; Kang, K.; Kauder, K.; Ke, H. W.; Keane, D.; Kechechyan, A.; Khan, Z. H.; Kikoła, D. P.; Kisel, I.; Kisiel, A.; Kochenda, L.; Koetke, D. D.; Kosarzewski, L. K.; Kraishan, A. F.; Kravtsov, P.; Krueger, K.; Kumar, L.; Lamont, M. A. C.; Landgraf, J. M.; Landry, K. D.; Lauret, J.; Lebedev, A.; Lednicky, R.; Lee, J. H.; Li, C.; Li, Y.; Li, W.; Li, X.; Li, X.; Lin, T.; Lisa, M. A.; Liu, F.; Ljubicic, T.; Llope, W. J.; Lomnitz, M.; Longacre, R. S.; Luo, X.; Ma, R.; Ma, L.; Ma, G. L.; Ma, Y. G.; Magdy, N.; Majka, R.; Manion, A.; Margetis, S.; Markert, C.; McDonald, D.; Meehan, K.; Mei, J. C.; Minaev, N. G.; Mioduszewski, S.; Mishra, D.; Mohanty, B.; Mondal, M. M.; Morozov, D. A.; Mustafa, M. K.; Nandi, B. K.; Nasim, Md.; Nayak, T. K.; Nigmatkulov, G.; Niida, T.; Nogach, L. V.; Noh, S. Y.; Novak, J.; Nurushev, S. B.; Odyniec, G.; Ogawa, A.; Oh, K.; Okorokov, V. A.; Olvitt, D.; Page, B. S.; Pak, R.; Pan, Y. X.; Pandit, Y.; Panebratsev, Y.; Pawlik, B.; Pei, H.; Perkins, C.; Pile, P.; Pluta, J.; Poniatowska, K.; Porter, J.; Posik, M.; Poskanzer, A. M.; Pruthi, N. K.; Putschke, J.; Qiu, H.; Quintero, A.; Ramachandran, S.; Raniwala, R.; Raniwala, S.; Ray, R. L.; Ritter, H. G.; Roberts, J. B.; Rogachevskiy, O. V.; Romero, J. L.; Roy, A.; Ruan, L.; Rusnak, J.; Rusnakova, O.; Sahoo, N. R.; Sahu, P. K.; Sakrejda, I.; Salur, S.; Sandweiss, J.; Sarkar, A.; Schambach, J.; Scharenberg, R. P.; Schmah, A. M.; Schmidke, W. B.; Schmitz, N.; Seger, J.; Seyboth, P.; Shah, N.; Shahaliev, E.; Shanmuganathan, P. V.; Shao, M.; Sharma, M. K.; Sharma, B.; Shen, W. Q.; Shi, Z.; Shi, S. S.; Shou, Q. Y.; Sichtermann, E. P.; Sikora, R.; Simko, M.; Singha, S.; Skoby, M. J.; Smirnov, D.; Smirnov, N.; Solyst, W.; Song, L.; Sorensen, P.; Spinka, H. M.; Srivastava, B.; Stanislaus, T. D. S.; Stepanov, M.; Stock, R.; Strikhanov, M.; Stringfellow, B.; Sumbera, M.; Summa, B.; Sun, Y.; Sun, Z.; Sun, X. M.; Surrow, B.; Svirida, D. N.; Tang, A. H.; Tang, Z.; Tarnowsky, T.; Tawfik, A.; Thäder, J.; Thomas, J. H.; Timmins, A. R.; Tlusty, D.; Todoroki, T.; Tokarev, M.; Trentalange, S.; Tribble, R. E.; Tribedy, P.; Tripathy, S. K.; Tsai, O. D.; Ullrich, T.; Underwood, D. G.; Upsal, I.; Van Buren, G.; van Nieuwenhuizen, G.; Vandenbroucke, M.; Varma, R.; Vasiliev, A. N.; Vertesi, R.; Videbæk, F.; Vokal, S.; Voloshin, S. A.; Vossen, A.; Wang, J. S.; Wang, Y.; Wang, F.; Wang, Y.; Wang, H.; Wang, G.; Webb, J. C.; Webb, G.; Wen, L.; Westfall, G. D.; Wieman, H.; Wissink, S. W.; Witt, R.; Wu, Y.; Xiao, Z. G.; Xie, X.; Xie, W.; Xin, K.; Xu, N.; Xu, Y. F.; Xu, Z.; Xu, Q. H.; Xu, J.; Xu, H.; Yang, Q.; Yang, Y.; Yang, S.; Yang, Y.; Yang, C.; Yang, Y.; Ye, Z.; Ye, Z.; Yepes, P.; Yi, L.; Yip, K.; Yoo, I.-K.; Yu, N.; Zbroszczyk, H.; Zha, W.; Zhang, S.; Zhang, Z.; Zhang, S.; Zhang, J. B.; Zhang, Y.; Zhang, J.; Zhang, J.; Zhang, X. P.; Zhao, J.; Zhong, C.; Zhou, L.; Zhu, X.; Zoulkarneeva, Y.; Zyzak, M.; STAR Collaboration

2016-04-01

We present the measurement of the transverse single-spin asymmetry of weak boson production in transversely polarized proton-proton collisions at √{s }=500 GeV by the STAR experiment at RHIC. The measured observable is sensitive to the Sivers function, one of the transverse-momentum-dependent parton distribution functions, which is predicted to have the opposite sign in proton-proton collisions from that observed in deep inelastic lepton-proton scattering. These data provide the first experimental investigation of the nonuniversality of the Sivers function, fundamental to our understanding of QCD.

WE-EF-303-08: Proton Radiography Using Pencil Beam Scanning and Novel Micromegas Detectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolney, D; Lustig, R; Teo, B

Purpose: While the energy of therapeutic proton beams can be adjusted to penetrate to any given depth in water, range uncertainties arise in patients due in part to imprecise knowledge of the stopping power of protons in human tissues. Proton radiography is one approach to reduce the beam range uncertainty, thereby allowing for a reduction in treatment margins and dose escalation. Methods: The authors have adapted a novel detector technology based on Micromesh Gaseous Structure (“Micromegas”) for proton therapy beams and have demonstrated fine spatial and time resolution of magnetically scanned proton pencil beams, as well as wide dynamic rangemore » for dosimetry. In this work, proton radiographs were obtained using Micromegas 2D planes positioned downstream of solid water assemblies. The position-sensitive monitor chambers in the IBA proton delivery nozzle provide the beam entrance position. Results: Radiography with Micromegas detectors and actively scanned beams provide spatial resolution of up to 300 µm and water-equivalent thickness (WET) resolution as good as 0.02% (60 µm out of 31 cm total thickness), with the dose delivered to the patient kept below 2 cGy. The spatial resolution as a function of sample rate and number of delivered protons is found to be near the theoretical Cramer-Rao lower bound. Using the CR bound, we argue that the imaging dose could be further lowered to 1 mGy, while still achieving sub-mm spatial resolution, by relatively simple instrumentation upgrades and beam delivery modifications. Conclusion: For proton radiography, high spatial and WET resolution can be achieved, with minimal additional dose to patient, by using magnetically scanned proton pencil beams and Micromegas detectors.« less

SU-C-207A-02: Proton Radiography Using Pencil Beam Scanning and a Novel, Low-Cost Range Telescope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dolney, D; Mayers, G; Newcomer, M

Purpose: While the energy of therapeutic proton beams can be adjusted to penetrate to any given depth in water, range uncertainties arise in patients due in part to imprecise knowledge of the stopping power of protons in human tissues [1]. Proton radiography is one approach to reduce the beam range uncertainty [2], thereby allowing for a reduction in treatment margins and dose escalation. Methods: The authors have adapted a novel detector technology based on Micromesh Gaseous Structure (“Micromegas”) for proton therapy beams and have demonstrated fine spatial and time resolution of magnetically scanned proton pencil beams, as well as widemore » dynamic range for dosimetry [3]. The authors have constructed a prototype imaging system comprised of 5 Micromegas layers. Proton radiographs were obtained downstream of solid water assemblies. The position-sensitive monitor chambers in the IBA proton delivery nozzle provide the beam entrance position. Results: Our technique achieves spatial resolution as low as 300 µm and water-equivalent thickness (WET) resolution as good as 0.02% (60 µm out of 31 cm total thickness). The dose delivered to the patient is kept below 2 cGy. The spatial resolution as a function of sample rate and number of delivered protons is found to be near the theoretical Cramer-Rao lower bound. By extrapolating the CR bound, we argue that the imaging dose could be further lowered to 1 mGy, while still achieving submillimeter spatial resolution, by achievable instrumentation and beam delivery modifications. Conclusion: For proton radiography, high spatial and WET resolution can be achieved, with minimal additional dose to patient, by using magnetically scanned proton pencil beams and Micromegas detectors.« less

Proton storage site in bacteriorhodopsin: new insights from QM/MM simulations of microscopic pKa and infrared spectra

PubMed Central

Goyal, Puja; Ghosh, Nilanjan; Phatak, Prasad; Clemens, Maike; Gaus, Michael; Elstner, Marcus; Cui, Qiang

2011-01-01

Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as PRG would require the protein to raise the pKa of a hydronium by almost 11 pKa units, which is difficult considering known cases of pKa shifts in proteins. Our recent QM/MM simulations suggested an alternative “intermolecular proton bond” model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pKa values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting x-ray structure and nuclear quantum effects, the “intermolecular proton bond” model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the “intermolecular proton bond” model is likely applicable to PRG in biomolecular proton pumps in general. PMID:21761868

Alternative initial proton acceptors for the D pathway of Rhodobacter sphaeroides cytochrome c oxidase

PubMed Central

Varanasi, Lakshman; Hosler, Jonathan

2011-01-01

In order to characterize protein structures that control proton uptake, forms of cytochrome c oxidase (CcO) containing a carboxyl or a thiol group in line with the initial, internal waters of the D pathway for proton transfer have been assayed in the presence and absence of subunit III. Subunit III provides approximately half of the protein surrounding the entry region of the D pathway. The mutant N139D-D132N contains a carboxyl group 6Å within the D pathway and lacks the normal, surface-exposed proton acceptor, Asp-132. With subunit III, the steady-state activity of this mutant is slow but once subunit III is removed its activity is the same as wild-type CcO lacking subunit III (∼1800 H+ s-1). Thus, a carboxyl group ∼25% within the pathway enhances proton uptake even though the carboxyl has no direct contact with bulk solvent. Protons from solvent apparently move to internal Asp-139 through a short file of waters, normally blocked by subunit III. Cysteine-139 also supports rapid steady-state proton uptake, demonstrating that an anion other than a carboxyl can attract and transfer protons into the D pathway. When both Asp-132 and Asp/Cys-139 are present, the removal of subunit III increases CcO activity to rates greater than that of normal CcO due to simultaneous proton uptake by two initial acceptors. The results show how the environment of the initial proton acceptor for the D pathway in these CcO forms dictates the pH range of CcO activity, with implications for the function of Asp-132, the normal proton acceptor. PMID:21344856

Assessment of the Density Functional Tight Binding Method for Protic Ionic Liquids

PubMed Central

2015-01-01

Density functional tight binding (DFTB), which is ∼100–1000 times faster than full density functional theory (DFT), has been used to simulate the structure and properties of protic ionic liquid (IL) ions, clusters of ions and the bulk liquid. Proton affinities for a wide range of IL cations and anions determined using DFTB generally reproduce G3B3 values to within 5–10 kcal/mol. The structures and thermodynamic stabilities of n-alkyl ammonium nitrate clusters (up to 450 quantum chemical atoms) predicted with DFTB are in excellent agreement with those determined using DFT. The IL bulk structure simulated using DFTB with periodic boundary conditions is in excellent agreement with published neutron diffraction data. PMID:25328497

Ab Initio Molecular Dynamics of Uranium Incorporated in Goethite (α-FeOOH): Interpretation of X-ray Absorption Spectroscopy of Trace Polyvalent Metals.

PubMed

Kerisit, Sebastien; Bylaska, Eric J; Massey, Michael S; McBriarty, Martin E; Ilton, Eugene S

2016-11-21

Incorporation of economically or environmentally consequential polyvalent metals into iron (oxyhydr)oxides has applications in environmental chemistry, remediation, and materials science. A primary tool for characterizing the local coordination environment of such metals, and therefore building models to predict their behavior, is extended X-ray absorption fine structure spectroscopy (EXAFS). Accurate structural information can be lacking yet is required to constrain and inform data interpretation. In this regard, ab initio molecular dynamics (AIMD) was used to calculate the local coordination environment of minor amounts of U incorporated in the structure of goethite (α-FeOOH). U oxidation states (VI, V, and IV) and charge compensation schemes were varied. Simulated trajectories were used to calculate the U L III -edge EXAFS function and fit experimental EXAFS data for U incorporated into goethite under reducing conditions. Calculations that closely matched the U EXAFS of the well-characterized mineral uraninite (UO 2 ), and constrained the S 0 2 parameter to be 0.909, validated the approach. The results for the U-goethite system indicated that U(V) substituted for structural Fe(III) in octahedral uranate coordination. Charge balance was achieved by the loss of one structural proton coupled to addition of one electron into the solid (-1 H + , +1 e - ). The ability of AIMD to model higher energy states thermally accessible at room temperature is particularly relevant for protonated systems such as goethite, where proton transfers between adjacent octahedra had a dramatic effect on the calculated EXAFS. Vibrational effects as a function of temperature were also estimated using AIMD, allowing separate quantification of thermal and configurational disorder. In summary, coupling AIMD structural modeling and EXAFS experiments enables modeling of the redox behavior of polyvalent metals that are incorporated in conductive materials such as iron (oxyhydr)oxides, with applications over a broad swath of chemistry and materials science.

Ab Initio Molecular Dynamics of Uranium Incorporated in Goethite (α-FeOOH): Interpretation of X-ray Absorption Spectroscopy of Trace Polyvalent Metals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerisit, Sebastien; Bylaska, Eric J.; Massey, Michael S.

2016-11-21

Incorporation of economically or environmentally consequential polyvalent metals into iron (oxyhydr)oxides has applications in environmental chemistry, remediation, and materials science. A primary tool for characterizing the local coordination environment of such metals, and therefore building models to predict their behavior, is extended X-ray absorption fine structure spectroscopy (EXAFS). Accurate structural information can be lacking, yet is required to constrain and inform data interpretation. In this regard, ab initio molecular dynamics (AIMD) was used to calculate the local coordination environment of minor amounts of U incorporated in the structure of goethite (α-FeOOH). U oxidation state (VI, V, and IV) and chargemore » compensation scheme (CCS) were varied. Simulated trajectories were used to calculate the U LIII-edge EXAFS function and fit experimental EXAFS data for U incorporated into goethite under reducing conditions. Calculations that closely matched the U EXAFS of the well-characterized mineral uraninite (UO2), and constrained the S02 parameter to be 0.909, validated the approach. The results for the U-goethite system indicated that U(V) substituted for structural Fe(III) in octahedral uranate coordination. Charge balance was achieved by the loss of one structural proton coupled to injection of one electron into the solid (–1 H+, + 1 e-). The ability of AIMD to model higher-energy states thermally accessible at room temperature is particularly relevant for protonated systems such as goethite, where proton transfers between adjacent octahedra had a dramatic effect on the calculated EXAFS. Vibrational effects as a function of temperature were also estimated using AIMD, allowing separate quantification of thermal and configurational disorder. In summary, coupling AIMD structural modeling and EXAFS experiments enables modeling of the redox behavior of polyvalent metals that are incorporated in conductive materials such as iron (oxyhydr)oxides, with applications over a broad swath of chemistry and materials science.« less

Protons and how they are transported by proton pumps.

PubMed

Buch-Pedersen, M J; Pedersen, B P; Veierskov, B; Nissen, P; Palmgren, M G

2009-01-01

The very high mobility of protons in aqueous solutions demands special features of membrane proton transporters to sustain efficient yet regulated proton transport across biological membranes. By the use of the chemical energy of ATP, plasma-membrane-embedded ATPases extrude protons from cells of plants and fungi to generate electrochemical proton gradients. The recently published crystal structure of a plasma membrane H(+)-ATPase contributes to our knowledge about the mechanism of these essential enzymes. Taking the biochemical and structural data together, we are now able to describe the basic molecular components that allow the plasma membrane proton H(+)-ATPase to carry out proton transport against large membrane potentials. When divergent proton pumps such as the plasma membrane H(+)-ATPase, bacteriorhodopsin, and F(O)F(1) ATP synthase are compared, unifying mechanistic premises for biological proton pumps emerge. Most notably, the minimal pumping apparatus of all pumps consists of a central proton acceptor/donor, a positively charged residue to control pK(a) changes of the proton acceptor/donor, and bound water molecules to facilitate rapid proton transport along proton wires.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokosawa, A.

The first polarized collider where we collide 250-GeV/c beams of 70% polarized protons at high luminosity is under construction. This will allow a determination of the nucleon spin-dependent structure functions over a large range in x and a collection of sufficient W and Z events to investigate extremely interesting spin-related phenomena.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokosawa, A.

The first polarized collider where one collides 250-GeV/c beams of 70% polarized protons at high luminosity is under construction. This will allow a determination of the nucleon spin-dependent structure functions over a large range in x and a collection of sufficient W and Z events to investigate extremely interesting spin-related phenomena.

Proton conducting membrane for fuel cells

DOEpatents

Colombo, Daniel G.; Krumpelt, Michael; Myers, Deborah J.; Kopasz, John P.

2005-12-20

An ion conducting membrane comprising dendrimeric polymers covalently linked into a network structure. The dendrimeric polymers have acid functional terminal groups and may be covalently linked via linking compounds, cross-coupling reactions, or copolymerization reactions. The ion conducting membranes may be produced by various methods and used in fuel cells.

Proton conducting membrane for fuel cells

DOEpatents

Colombo, Daniel G.; Krumpelt, Michael; Myers, Deborah J.; Kopasz, John P.

2007-03-27

An ion conducting membrane comprising dendrimeric polymers covalently linked into a network structure. The dendrimeric polymers have acid functional terminal groups and may be covalently linked via linking compounds, cross-coupling reactions, or copolymerization reactions. The ion conducting membranes may be produced by various methods and used in fuel cells.

The influence of the local structure on proton transport in a solid oxide proton conductor La 0.8 Ba 1.2 GaO 3.9

DOE PAGES

Cheng, Yongqiang; Balachandran, Janakiraman; Bi, Zhonghe; ...

2017-07-18

The local structure around the mobile ions influences their dynamics. The knowledge about the relationship between these properties is of fundamental importance and may lead the way for development of improved solid state ionic conductors. Here, we use inelastic neutron scattering and ab initio modeling to study a representative proton conductor, La 0.8Ba 1.2GaO 3.9, where different local structures are possible for the same stoichiometry. The intrinsic correlations between the local bonding environment and the dynamical behavior of protons are presented. In particular, we identify how the local Ba/La concentration affects the proton vibrational frequencies, hydrogen bond strength, O–H rotationsmore » and in turn long-range proton mobility. Furthermore, possible mechanism for proton transport, through the inter-tetrahedral bond switching, O–H rotations and tetrahedral reorientation is anticipated.« less

New insight into the properties of proton conducting oxides from neutron total scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Proffen, Thomas E; Kim, Hyunjeong; Malavasi, Lorenzo

In recent years there has been a growing interest in searching for new proton conducting materials that could be successfully used in medium temperature solid oxide fuel cells (SOFC). In particular, proton conducting oxides have been the subject of a massive research activity. Among the most promising oxide the acceptor doped cerates appears to be those most appealing in view of practical applications. A relevant aspect of these materials is the investigation of the local distortion of the structure arising from water incorporation. This kind of study is of great help in defining how the structure changes in order tomore » accommodate the proton which is usually thought to enter the structure in form of hydroxyl group where the oxygen vacancy results from the acceptor doping on the Ce site. Atomistic simulation work confirmed that the preferential location of dopant ions is on the Ce site. To the best of our knowledge the only experimental work addressing the role of dopant and water incorporation on the local structure of V-doped cerates is a X-ray absorption spectroscopy (XAS) work carried out by Longo and coworkers at the Y K-edge. The main conclusion of that work was the observation that Y-doping induces a distortion of the parent BaCe0{sub 3} structure resulting in a significantly distorted Y local environment. However, local structure information derived from XAS study does not provide a direct structural information and depends strongly upon the model used to calcualte theoretical {chi}(k) which is not unique. Moreover, the XAS analysis usually provide significant information only up to the second shell. As a consequence, a more reliable and useful technique to investigate the local arrangement in these proton conducting oxides appears to be the Pair Distribution Function (PDF) analysis derived from total neutron scattering measurements. In the present work we investigated the pure BaCeO{sub 3} and the acceptor doped BaCe{sub 0.90}Y{sub 0.10}O{sub 2.85} compounds. In both cases the samples have been measured at room temperature and after being exposed to dry and wet air (humidification attained through bubbling air in D{sub 2}O). Aim of this work is to look at the effect of Y-doping and water doping on the local structure of the above mentioned samples.« less

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate.

PubMed

Bouchet, Aude; Schütz, Markus; Dopfer, Otto

2016-01-18

Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structure–property reduced order model for viscosity prediction in single-component CO 2 -binding organic liquids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cantu, David C.; Malhotra, Deepika; Koech, Phillip K.

2016-01-01

CO2 capture from power generation with aqueous solvents remains energy intensive due to the high water content of the current technology, or the high viscosity of non-aqueous alternatives. Quantitative reduced models, connecting molecular structure to bulk properties, are key for developing structure-property relationships that enable molecular design. In this work, we describe such a model that quantitatively predicts viscosities of CO2 binding organic liquids (CO2BOLs) based solely on molecular structure and the amount of bound CO2. The functional form of the model correlates the viscosity with the CO2 loading and an electrostatic term describing the charge distribution between the CO2-bearingmore » functional group and the proton-receiving amine. Molecular simulations identify the proton shuttle between these groups within the same molecule to be the critical indicator of low viscosity. The model, developed to allow for quick screening of solvent libraries, paves the way towards the rational design of low viscosity non-aqueous solvent systems for post-combustion CO2 capture. Following these theoretical recommendations, synthetic efforts of promising candidates and viscosity measurement provide experimental validation and verification.« less

Development of Colle-Salvetti type electron-nucleus correlation functional for MC-DFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Udagawa, Taro; Tsuneda, Takao; Tachikawa, Masanori

2015-12-31

A Colle-Salvetti type electron-nucleus correlation functional for multicomponent density-functional theory is proposed. We demonstrate that our correlation functional quantitatively reproduces the quantum nuclear effects of protons; the mean absolute deviation value is 2.8 millihartrees for the optimized structure of hydrogen-containing molecules. We also show other practical calculations with our new electron-deuteron and electron-triton correlation functionals. Since this functional is derived without any unphysical assumption, the strategy taken in this development will be a promising recipe to make new functionals for the potentials of other particles’ interactions.

Structural stability of anhydrous proton conducting SrZr0.9Er0.1O3-δ perovskite ceramic vs. protonation/deprotonation cycling: Neutron diffraction and Raman studies

NASA Astrophysics Data System (ADS)

Slodczyk, Aneta; Colomban, Philippe; Upasen, Settakorn; Grasset, Frédéric; André, Gilles

2015-08-01

Long-term chemical and structural stability of an ion conducting ceramic is one of the main criteria for its selection as an electrolytic membrane in energy plant devices. Consequently, medium density SrZr0.9Er0.1O3-δ (SZE) anhydrous proton conducting ceramic - a potential electrolyte of SOFC/PCFC, was analysed by neutron diffraction between room temperature and 900 °C. After the first heating/cooling cycle, the ceramic pieces were exposed to water vapour pressure in an autoclave (500 °C, 40 bar, 7 days) in order to incorporate protonic species; the protonated compound was then again analysed by neutron diffraction. This procedure was repeated two times. At each step, the sample was also controlled by TGA and Raman spectroscopy. These studies allow the first comprehensive comparison of structural and chemical stability during the protonation/deprotonation cycling. The results reveal good structural stability, although an irreversible small contraction of the unit-cell volume and local structure modifications near Zr/ErO5[] octahedra are detected after the first protonation. After the second protonation easy ceramic crumbling under a stress is observed because of the presence of secondary phases (SrCO3, Sr(OH)2) well detected by Raman scattering and TGA. The role of crystallographic purity, substituting element and residual porosity in the proton conducting perovskite electrolyte stability is discussed.

The effect of protonation on the thermal isomerization of stilbazolium betaines

NASA Astrophysics Data System (ADS)

Tavan, Paul; Schulten, Klaus

1984-09-01

MINDOC calculations have been carried out on the protonated and unprotonated forms of a stilbazolium betaine. The results show (1) a strong increase by 24 kcal/mol of the torsional barrier around the central bond upon protonation, (2) polar structures for the protonated as well as the unprotonated forms, and (3) strong alterations of the polar structure of the latter during isomerization, and predict a higher pK value for the cis isomer, particularly, in the case of less polar and less protonic solvents.

Formation of M-Like Intermediates in Proteorhodopsin in Alkali Solutions (pH ≥ ∼8.5) Where the Proton Release Occurs First in Contrast to the Sequence at Lower pH.

PubMed

Tamogami, Jun; Sato, Keitaro; Kurokawa, Sukuna; Yamada, Takumi; Nara, Toshifumi; Demura, Makoto; Miyauchi, Seiji; Kikukawa, Takashi; Muneyuki, Eiro; Kamo, Naoki

2016-02-23

Proteorhodopsin (PR) is an outward light-driven proton pump observed in marine eubacteria. Despite many structural and functional similarities to bacteriorhodopsin (BR) in archaea, which also acts as an outward proton pump, the mechanism of the photoinduced proton release and uptake is different between two H(+)-pumps. In this study, we investigated the pH dependence of the photocycle and proton transfer in PR reconstituted with the phospholipid membrane under alkaline conditions. Under these conditions, as the medium pH increased, a blue-shifted photoproduct (defined as Ma), which is different from M, with a pKa of ca. 9.2 was produced. The sequence of the photoinduced proton uptake and release during the photocycle was inverted with the increase in pH. A pKa value of ca. 9.5 was estimated for this inversion and was in good agreement with the pKa value of the formation of Ma (∼ 9.2). In addition, we measured the photoelectric current generated by PRs attached to a thin polymer film at varying pH. Interestingly, increases in the medium pH evoked bidirectional photocurrents, which may imply a possible reversal of the direction of the proton movement at alkaline pH. On the basis of these findings, a putative photocycle and proton transfer scheme in PR under alkaline pH conditions was proposed.

Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site

PubMed Central

Sigala, Paul A.; Fafarman, Aaron T.; Schwans, Jason P.; Fried, Stephen D.; Fenn, Timothy D.; Caaveiro, Jose M. M.; Pybus, Brandon; Ringe, Dagmar; Petsko, Gregory A.; Boxer, Steven G.; Herschlag, Daniel

2013-01-01

Hydrogen bond networks are key elements of protein structure and function but have been challenging to study within the complex protein environment. We have carried out in-depth interrogations of the proton transfer equilibrium within a hydrogen bond network formed to bound phenols in the active site of ketosteroid isomerase. We systematically varied the proton affinity of the phenol using differing electron-withdrawing substituents and incorporated site-specific NMR and IR probes to quantitatively map the proton and charge rearrangements within the network that accompany incremental increases in phenol proton affinity. The observed ionization changes were accurately described by a simple equilibrium proton transfer model that strongly suggests the intrinsic proton affinity of one of the Tyr residues in the network, Tyr16, does not remain constant but rather systematically increases due to weakening of the phenol–Tyr16 anion hydrogen bond with increasing phenol proton affinity. Using vibrational Stark spectroscopy, we quantified the electrostatic field changes within the surrounding active site that accompany these rearrangements within the network. We were able to model these changes accurately using continuum electrostatic calculations, suggesting a high degree of conformational restriction within the protein matrix. Our study affords direct insight into the physical and energetic properties of a hydrogen bond network within a protein interior and provides an example of a highly controlled system with minimal conformational rearrangements in which the observed physical changes can be accurately modeled by theoretical calculations. PMID:23798390

Inspection of anode and field wires for the COMPASS drift chamber, DC5, with Environmental Scanning Electron Microscope

NASA Astrophysics Data System (ADS)

Cyuzuzo, Sonia

2014-09-01

The COMPASS experiment at CERN uses a secondary pion beam from the Super Proton Synchrotron (SPS) at CERN to explore the spin structure of nucleons. A new drift chamber, DC5, will be integrated into the COMPASS spectrometer to replace an aging straw tube detector. DC5 will detect muon pairs from Drell-Yan scattering of a pion-beam off a transversely polarized proton target. This data will be used to determine the correlation between transverse proton spin and the intrinsic transverse momentum of up-quarks inside the proton, the Sivers effect. DC5 is a large area planar drift chamber with 8 layers of anode-frames made of G10 fiberglass-epoxy. The G10 frames support printed circuit boards for soldering 20 μm diameter anode and 100 μm diameter field wires. The anode planes are sandwiched by 13 graphite coated Mylar cathode planes. To ensure a well-functioning of DC5, the wires were carefully tested. An optical inspection and a spectral analysis was performed with an Environmental Scanning Electron Microscope (ESEM) to verify the composition and dimensions and the integrity of the gold plating on the surface of these wires. The spectra of the wires were studied at 10 and 30 keV. The COMPASS experiment at CERN uses a secondary pion beam from the Super Proton Synchrotron (SPS) at CERN to explore the spin structure of nucleons. A new drift chamber, DC5, will be integrated into the COMPASS spectrometer to replace an aging straw tube detector. DC5 will detect muon pairs from Drell-Yan scattering of a pion-beam off a transversely polarized proton target. This data will be used to determine the correlation between transverse proton spin and the intrinsic transverse momentum of up-quarks inside the proton, the Sivers effect. DC5 is a large area planar drift chamber with 8 layers of anode-frames made of G10 fiberglass-epoxy. The G10 frames support printed circuit boards for soldering 20 μm diameter anode and 100 μm diameter field wires. The anode planes are sandwiched by 13 graphite coated Mylar cathode planes. To ensure a well-functioning of DC5, the wires were carefully tested. An optical inspection and a spectral analysis was performed with an Environmental Scanning Electron Microscope (ESEM) to verify the composition and dimensions and the integrity of the gold plating on the surface of these wires. The spectra of the wires were studied at 10 and 30 keV. Acknowledging NSF and UIUC.

Measurements of the vector boson production with the ATLAS detector

NASA Astrophysics Data System (ADS)

Lapertosa, A.

2018-01-01

Measurements of the Drell-Yan production of W and Z bosons at the LHC provide a benchmark of our understanding of perturbative QCD and probe the proton structure in a unique way. The ATLAS collaboration has performed new high precision measurements at a center-of-mass energy of 7 TeV. The measurements are performed for W+, W- and Z bosons integrated and as a function of the boson or lepton rapidity and the Z mass. Unprecedented precision is reached and strong constraints on Parton Distribution Functions, in particular the strange density are found. Z boson cross sections are also measured at center-of-mass energies of 8 TeV and 13 TeV, and cross-section ratios to the top-quark pair production have been derived. This ratio measurement leads to a cancellation of systematic effects and allows for a high precision comparison to the theory predictions. The production of jets in association with vector bosons is a further important process to study perturbative QCD in a multi-scale environment. The ATLAS collaboration has performed new measurements of Z boson plus jets cross sections, differential in several kinematic variables, in proton-proton collision data taken at a center-of-mass energy of 13 TeV. The measurements are compared to state-of-the art theory predictions. They are sensitive to higher-order pQCD effects, probe flavour and mass schemes and can be used to constrain the proton structure. In addition, a new measurement of the splitting scales of the kt jet-clustering algorithm for final states containing a Z boson candidate at a center-of-mass energy of 8 TeV is presented.

The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation.

PubMed

Oksanen, Esko; Blakeley, Matthew P; El-Hajji, Mohamed; Ryde, Ulf; Budayova-Spano, Monika

2014-01-01

Urate oxidase transforms uric acid to 5-hydroxyisourate without the help of cofactors, but the catalytic mechanism has remained enigmatic, as the protonation state of the substrate could not be reliably deduced. We have determined the neutron structure of urate oxidase, providing unique information on the proton positions. A neutron crystal structure inhibited by a chloride anion at 2.3 Å resolution shows that the substrate is in fact 8-hydroxyxanthine, the enol tautomer of urate. We have also determined the neutron structure of the complex with the inhibitor 8-azaxanthine at 1.9 Å resolution, showing the protonation states of the K10-T57-H256 catalytic triad. Together with X-ray data and quantum chemical calculations, these structures allow us to identify the site of the initial substrate protonation and elucidate why the enzyme is inhibited by a chloride anion.

Multicomponent density functional theory embedding formulation.

PubMed

Culpitt, Tanner; Brorsen, Kurt R; Pak, Michael V; Hammes-Schiffer, Sharon

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF(-) molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Multicomponent density functional theory embedding formulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density ismore » separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.« less

Blackbody Infrared Radiative Dissociation of Bradykinin and Its Analogues: Energetics, Dynamics, and Evidence for Salt-Bridge Structures in the Gas Phase

PubMed Central

Schnier, Paul D.; Price, William D.; Jockusch, Rebecca A.

2005-01-01

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (Ea) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 105 to 1012 s−1, respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 108 and 1012 s−1, respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 104. This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an Ea of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 ± 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the Ea of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s−1. This modification also dramatically changes the dissociation products. Similar results are observed for [Ala6]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure. PMID:16525512

Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kovalevsky, Andrey, E-mail: ayk@lanl.gov; Chatake, Toshiyuki; Shibayama, Naoya

2010-11-01

Using neutron diffraction analysis, the protonation states of 35 of 38 histidine residues were determined for the deoxy form of normal human adult hemoglobin. Distal and buried histidines may contribute to the increased affinity of the deoxy state for hydrogen ions and its decreased affinity for oxygen compared with the oxygenated form. The protonation states of the histidine residues key to the function of deoxy (T-state) human hemoglobin have been investigated using neutron protein crystallography. These residues can reversibly bind protons, thereby regulating the oxygen affinity of hemoglobin. By examining the OMIT F{sub o} − F{sub c} and 2F{sub o}more » − F{sub c} neutron scattering maps, the protonation states of 35 of the 38 His residues were directly determined. The remaining three residues were found to be disordered. Surprisingly, seven pairs of His residues from equivalent α or β chains, αHis20, αHis50, αHis58, αHis89, βHis63, βHis143 and βHis146, have different protonation states. The protonation of distal His residues in the α{sub 1}β{sub 1} heterodimer and the protonation of αHis103 in both subunits demonstrates that these residues may participate in buffering hydrogen ions and may influence the oxygen binding. The observed protonation states of His residues are compared with their ΔpK{sub a} between the deoxy and oxy states. Examination of inter-subunit interfaces provided evidence for interactions that are essential for the stability of the deoxy tertiary structure.« less

Measurement of the Transverse Single-Spin Asymmetry in p ↑ + p → W ± / Z 0 at RHIC

DOE PAGES

Adamczyk, L.; Adkins, J. K.; Agakishiev, G.; ...

2016-04-01

In this paper, we present the measurement of the transverse single-spin asymmetry of weak boson production in transversely polarized proton-proton collisions at √s = 500 GeV by the STAR experiment at RHIC. The measured observable is sensitive to the Sivers function, one of the transverse-momentum-dependent parton distribution functions, which is predicted to have the opposite sign in proton-proton collisions from that observed in deep inelastic lepton-proton scattering. In conclusion, these data provide the first experimental investigation of the nonuniversality of the Sivers function, fundamental to our understanding of QCD.

Proton transfer and hydrogen bonding in the organic solid state: a combined XRD/XPS/ssNMR study of 17 organic acid-base complexes.

PubMed

Stevens, Joanna S; Byard, Stephen J; Seaton, Colin C; Sadiq, Ghazala; Davey, Roger J; Schroeder, Sven L M

2014-01-21

The properties of nitrogen centres acting either as hydrogen-bond or Brønsted acceptors in solid molecular acid-base complexes have been probed by N 1s X-ray photoelectron spectroscopy (XPS) as well as (15)N solid-state nuclear magnetic resonance (ssNMR) spectroscopy and are interpreted with reference to local crystallographic structure information provided by X-ray diffraction (XRD). We have previously shown that the strong chemical shift of the N 1s binding energy associated with the protonation of nitrogen centres unequivocally distinguishes protonated (salt) from hydrogen-bonded (co-crystal) nitrogen species. This result is further supported by significant ssNMR shifts to low frequency, which occur with proton transfer from the acid to the base component. Generally, only minor chemical shifts occur upon co-crystal formation, unless a strong hydrogen bond is formed. CASTEP density functional theory (DFT) calculations of (15)N ssNMR isotropic chemical shifts correlate well with the experimental data, confirming that computational predictions of H-bond strengths and associated ssNMR chemical shifts allow the identification of salt and co-crystal structures (NMR crystallography). The excellent agreement between the conclusions drawn by XPS and the combined CASTEP/ssNMR investigations opens up a reliable avenue for local structure characterization in molecular systems even in the absence of crystal structure information, for example for non-crystalline or amorphous matter. The range of 17 different systems investigated in this study demonstrates the generic nature of this approach, which will be applicable to many other molecular materials in organic, physical, and materials chemistry.

Gas-phase ion-molecule reactions for the identification of the sulfone functionality in protonated analytes in a linear quadrupole ion trap mass spectrometer.

PubMed

Tang, Weijuan; Sheng, Huaming; Kong, John Y; Yerabolu, Ravikiran; Zhu, Hanyu; Max, Joann; Zhang, Minli; Kenttämaa, Hilkka I

2016-06-30

The oxidation of sulfur atoms is an important biotransformation pathway for many sulfur-containing drugs. In order to rapidly identify the sulfone functionality in drug metabolites, a tandem mass spectrometric method based on ion-molecule reactions was developed. A phosphorus-containing reagent, trimethyl phosphite (TMP), was allowed to react with protonated analytes with various functionalities in a linear quadrupole ion trap mass spectrometer. The reaction products and reaction efficiencies were measured. Only protonated sulfone model compounds were found to react with TMP to form a characteristic [TMP adduct-MeOH] product ion. All other protonated compounds investigated, with functionalities such as sulfoxide, N-oxide, hydroxylamino, keto, carboxylic acid, and aliphatic and aromatic amino, only react with TMP via proton transfer and/or addition. The specificity of the reaction was further demonstrated by using a sulfoxide-containing anti-inflammatory drug, sulindac, as well as its metabolite sulindac sulfone. A method based on functional group-selective ion-molecule reactions in a linear quadrupole ion trap mass spectrometer has been demonstrated for the identification of the sulfone functionality in protonated analytes. A characteristic [TMP adduct-MeOH] product ion was only formed for the protonated sulfone analytes. The applicability of the TMP reagent in identifying sulfone functionalities in drug metabolites was also demonstrated. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

NASA Astrophysics Data System (ADS)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-05-01

We report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experiments and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Finally, the observed frequencies of the Nsbnd H and Osbnd H stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE PAGES

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-03-08

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

A-Site Cation Substitutions in Strained Y-Doped BaZrO 3 Multilayer Films Leading to Fast Proton Transport Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aruta, Carmela; Han, Chu; Zhou, Si

Proton-conducting perovskite oxides form a class of solid electrolytes for novel electrochemical devices operating at moderate temperatures. Here, we use hard X-ray photoelectron spectroscopy, scanning transmission electron microscopy, and density functional theory calculations to investigate the structure and elucidate the origin of the fast proton transport properties of strained ultrathin films of Y-doped BaZrO 3 grown by pulsed lased deposition on NdGaO 3. Our study shows that our BaZr 0.8Y 0.2O 3 films incorporate a significant amount of Y dopants, and to a lesser extent also Zr ions, substituting for Ba 2+, and that these substitutional defects agglomerate forming columnarmore » regions crossing vertically from the surface to the interface the entire film. In conclusion, our calculations also show that, in regions rich in Y substitutions for both Zr and Ba, the proton transfer process involves nearly zero-energy barriers, indicating that A-site cation substitutions by Y lead to fast transport pathways and hence are responsible for the previously observed enhanced values of the proton conductivity of these perovskite oxide films.« less

Probing the Repulsive Core of the Nucleon-Nucleon Interaction via the 4He(e,e`pN) Triple-Coincidence Reaction

DOE PAGES

Korover, Igor; Muangma, Navaphon; Hen, Or; ...

2014-07-01

We studied simultaneously the 4He(e,e'p), 4He(e,e'pp), and 4He(e,e'pn) reactions at Q 2=2 [GeV/c] 2 and x B >1, for a (e,e'p) missing-momentum range of 400 to 830 MeV/c. The knocked-out proton was detected in coincidence with a proton or neutron recoiling almost back to back to the missing momentum, leaving the residual A=2 system at low excitation energy. These data were used to identify two-nucleon short-range correlated pairs and to deduce their isospin structure as a function of missing momentum in a region where the nucleon-nucleon force is expected to change from predominantly tensor to repulsive. Neutron-proton pairs dominate themore » high-momentum tail of the nucleon momentum distributions, but their abundance is reduced as the nucleon momentum increases beyond ~500 MeV/c. The extracted fraction of proton-proton pairs is small and almost independent of the missing momentum in the range we studied. Our data are compared with ab-initio calculations of two-nucleon momentum distributions in 4He.« less

{ital D}({ital e},{ital e}`{ital p}) longitudinal-transverse separation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jordan, D.; Alarcon, R.; Beck, R.

1995-05-10

A Rosenbluth separation of the longitudinal and transverse structure functions in the {ital D}({ital e},{ital e}`{ital p}) reaction has been performed in parallel kinematics at {vert_bar}{ital {rvec q}}{vert_bar}=400 MeV/{ital c} and initial proton momentum centered at 50 MeV/{ital c}. The data are compared to a nonrelativistic calculation which includes effects due to final state interactions, meson exchange currents, and isobar configurations. The data are also compared to the results of two previous structure function separations. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

IR spectroscopy of protonation in benzene-water nanoclusters: hydronium, zundel, and eigen at a hydrophobic interface.

PubMed

Cheng, Timothy C; Bandyopadhyay, Biswajit; Mosley, Jonathan D; Duncan, Michael A

2012-08-08

The structure of ions in water at a hydrophobic interface influences important processes throughout chemistry and biology. However, experiments to measure these structures are limited by the distribution of configurations present and the inability to selectively probe the interfacial region. Here, protonated nanoclusters containing benzene and water are produced in the gas phase, size-selected, and investigated with infrared laser spectroscopy. Proton stretch, free OH, and hydrogen-bonding vibrations uniquely define protonation sites and hydrogen-bonding networks. The structures consist of protonated water clusters binding to the hydrophobic interface of neutral benzene via one or more π-hydrogen bonds. Comparison to the spectra of isolated hydronium, zundel, or eigen ions reveals the inductive effects and local ordering induced by the interface. The structures and interactions revealed here represent key features expected for aqueous hydrophobic interfaces.

4D dose calculation and delivery with interplay effects between respiratory motion and uniform scanning proton beam

NASA Astrophysics Data System (ADS)

Zhao, Qingya

2011-12-01

Proton radiotherapy has advantages to deliver accurate high conformal radiation dose to the tumor while sparing the surrounding healthy tissue and critical structures. However, the treatment effectiveness is degraded greatly due to patient free breathing during treatment delivery. Motion compensation for proton radiotherapy is especially challenging as proton beam is more sensitive to the density change along the beam path. Tumor respiratory motion during treatment delivery will affect the proton dose distribution and the selection of optimized parameters for treatment planning, which has not been fully addressed yet in the existing approaches for proton dose calculation. The purpose of this dissertation is to develop an approach for more accurate dose delivery to a moving tumor in proton radiotherapy, i.e., 4D proton dose calculation and delivery, for the uniform scanning proton beam. A three-step approach has been carried out to achieve this goal. First, a solution for the proton output factor calculation which will convert the prescribed dose to machine deliverable monitor unit for proton dose delivery has been proposed and implemented. The novel sector integration method is accurate and time saving, which considers the various beam scanning patterns and treatment field parameters, such as aperture shape, aperture size, measuring position, beam range, and beam modulation. Second, tumor respiratory motion behavior has been statistically characterized and the results have been applied to advanced image guided radiation treatment. Different statistical analysis and correlation discovery approaches have been investigated. The internal / external motion correlation patterns have been simulated, analyzed, and applied in a new hybrid gated treatment to improve the target coverage. Third, a dose calculation method has been developed for 4D proton treatment planning which integrates the interplay effects of tumor respiratory motion patterns and proton beam delivery mechanism. These three steps provide an innovative integrated framework for accurate 4D proton dose calculation and treatment planning for a moving tumor, which extends the functionalities of existing 3D planning systems. In short, this dissertation work addresses a few important problems for effective proton radiotherapy to a moving target. The outcomes of the dissertation are very useful for motion compensation with advanced image guided proton treatment.

The Mirror Nuclei 3H and 3He Program at JLab

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomez, Javier

2017-02-28

Jefferson Lab plans to carry out in the near future a group of four experiments involving the mirror nuclei 3H and 3He, using electron beam energies of up to 11 GeV. Our experiments aim to, (A) extract the deep inelastic neutron to proton structure function ratio Fmore » $$n\\atop{2}$$F$$p\\atop{2}$$ (and u / d quark distributions) for 0.2 ≤ x ≤ 0.9 , (B) study the isospin structure of two-nucleon and search for three-nucleon Short Range Correlations (SRC) for x < 3 , (C) measure the proton momentum distribution of both nuclei at $x = 1.2$ to further our understanding of SRCs in the few-body and (D) extract the charge radii of both nuclei at Q 2 ≤ 0.1 GeV 2.« less

Coronal magnetic structure and the latitude and longitude distribution of energetic particles, 1-5 AU

NASA Technical Reports Server (NTRS)

Roelof, E. C.; Mitchell, D. G.

1979-01-01

The relation of the coronal magnetic field structure to the distribution of approximately 1 MeV protons in interplanetary space between 1 and 5 AU is discussed. After ordering the interplanetary data by its estimated coronal emission source location in heliographic coordinates, the multispacecraft measured proton fluxes are compared with coronal magnetic field structure infrared as observed in soft X-ray photographs and potential field calculations. Evidence for the propagation and possible acceleration of solar flare protons on high magnetic loop structure in the corona is presented. Further, it is shown that corotating proton flux enhancements are associated with regions of low coronal X-ray emission (including coronal holes), usually in association with solar wind stream structure.

Transient low-barrier hydrogen bond in the photoactive state of green fluorescent protein.

PubMed

Nadal-Ferret, Marc; Gelabert, Ricard; Moreno, Miquel; Lluch, José M

2015-12-14

In this paper, we have analyzed the feasibility of spontaneous proton transfer in GFP at the Franck-Condon region directly after photoexcitation. Computation of a sizeable portion of the potential energy surface at the Franck-Condon region of A the structure shows the process of proton transfer to be unfavorable by 3 kcal mol(-1) in S1 if no further structural relaxation is permitted. The ground vibrational state is found to lie above the potential energy barrier of the proton transfer in both S0 and S1. Expectation values of the geometry reveal that the proton shared between the chromophore and W22, and the proton shared between Ser205 and Glu222 are very close to the center of the respective hydrogen bonds, giving support to the claim that the first transient intermediate detected after photoexcitation (I0*) has characteristics similar to those of a low-barrier hydrogen bond [Di Donato et al., Phys. Chem. Chem. Phys., 2012, 13, 16295]. A quantum dynamical calculation of the evolution in the excited state shows an even larger probability of finding those two protons close to the center compared to in the ground state, but no formation of the proton-transferred product is observed. A QM/MM photoactive state geometry optimization, initiated using a configuration obtained by taking the A minimum and moving the protons to the product side, yields a minimum energy structure with the protons transferred and in which the His148 residue is substantially closer to the now anionic chromophore. These results indicate that: (1) proton transfer is not possible if structural relaxation of the surroundings of the chromophore is prevented; (2) protons H1 and H3 especially are found very close to the point halfway between the donor and acceptor after photoexcitation when the zero-point energy is considered; (3) a geometrical parameter exists (the His148-Cro distance) under which the structure with the protons transferred is not a minimum, and that, if included, should lead to the fluorescing I* structure. The existence of an oscillating stationary state between the reactants and products of the triple proton transfer reaction can explain the dual emission reported for the I0* intermediate of wtGFP.

Structural dependence of the multi-functionalized carbon nanotubes to the substituents on the grafted diazo compounds

NASA Astrophysics Data System (ADS)

Amiri, Rahebeh; Rasouli, Sousan; Ghasemi, Alireza; Eghbali, Babak; Mohammadi, Soutodeh

2014-05-01

Systematic studies on the covalent functionalization of multi-walled carbon nanotubes were performed by a series of azo molecules with different substituents. For this investigation, 4-substituted diazonium reagents have been used in the reaction with the functionalized multi-walled carbon nanotubes. We analyzed the effect of the substituted groups on the diazo component affinity in the grafting. Also, the structural differences of the final products were evaluated by visual dispersion test, UV-Vis absorption. Fourier transforms infrared, Raman, and several complementary techniques (scanning electron microscopy, thermal gravimetric analysis, and colorimetry test). Nuclear magnetic resonance spectroscopy has been used to confirm the allylic protons attached to the surface of carbon nanotubes after functionalization.

A density functional theory study of the structure of pure-silica and aluminium-substituted MFI nanosheets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernandez-Tamargo, Carlos E.; Roldan, Alberto; School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT

The layered MFI zeolite allows a straightforward hierarchization of the pore system which accelerates mass transfer and increases its lifetime as a catalyst. Here, we present a theoretical study of the structural features of the pure-silica and aluminium-substituted MFI nanosheets. We have analysed the effects of aluminium substitution on the vibrational properties of silanols as well as the features of protons as counter-ions. The formation of the two-dimensional system did not lead to appreciable distortions within the framework. Moreover, the effects on the structure due to the aluminium dopants were the same in both the bulk and the slab. Themore » principal differences were related to the silanol groups that form hydrogen-bonds with neighbouring aluminium-substituted silanols, whereas intra-framework hydrogen-bonds increase the stability of aluminium-substituted silanols toward dehydration. Thus, we have complemented previous experimental and theoretical studies, showing the lamellar MFI zeolite to be a very stable material of high crystallinity regardless of its very thin structure. - Graphical abstract: The structure of MFI zeolite nanosheet was investigated using Density Functional Theory. The results showed no differences against the bulk-type material upon aluminium doping. The aluminium-substituted silanol dehydrates toward a more stable configuration composed by a water molecule adsorbed on a Lewis centre. - Highlights: • MFI nanosheets with variable thicknesses were characterised using DFT calculations. • The distortions in the nanosheets after Al substitution reproduced those of the bulk. • H-bonds were only observed between silanol groups when the Al substitution took place. • The kinetic of the Al-silanol dehydration is dependent on intra-framework H-bonds. • Lewis acids with adsorbed water are more stable than Al-silanols. • The proton accessibility was related to the framework O atom binding the proton.« less

FTIR spectroscopic study on individual amino acid residues in the proton pumping process of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Liu, Xiaomei

1998-05-01

My thesis project has concentrated on clarifying the role of individual amino acids such as tyrosine, arginine and threonine in the active proton transferring process of Bacteriorhodopsin(bR). BR is a protein found in the purple membrane of Halobacteria salinarium. The main function of bR is to transfer a proton from the interior side of the cell to the external medium upon illumination by visible light. BR belongs to a family of retinal- containing membrane proteins which includes rhodopsin, a visual receptor found in the eye, and sensory rhodopsin I, a light receptor for phototaxis found in H. salinarium. Complete understanding of the proton transferring mechanism of bR can help explain the energy transduction and active ion transport in biological systems. This information also provides insight into other members of the retinal-containing protein family. To study the behavior of a single amino acid in a protein which consists of 248 amino acids, I employed the Fourier transform infrared (FTIR) difference spectroscopy technique. This was combined with the recently developed genetic engineering method of site directed isotope labeling (SDIL). As complementary work, I also characterized the vibrational properties of individual amino acids in various environments. Because of the high resolution and sensitivity of FTIR difference spectroscopy, along with the ability of SDIL to detect structural changes at the single amino acid level, we are able to determine changes in the structure of specific amino acids at different steps in bR photocycle. My research results provide strong evidence for a proton pump model. This model predicts the participation of tyrosine 185 and one or more threonines in a hydrogen bonded chain which can transfer proton across the membrane. My data also suggest a more accurate model for the proton release step which involves arginine 82.

Structure, stability, thermodynamic properties, and IR spectra of the protonated water decamer H+(H2O)10.

PubMed

Karthikeyan, S; Kim, Kwang S

2009-08-13

Protonated water clusters H+(H2O)n favor two-dimensional (2D) structures for n < or = 7 at low temperatures. At 0 K, the 2D and three-dimensional (3D) structures for n = 8 are almost isoenergetic, and the 3D structures for n > 9 tend to be more stable. However, for n = 9, the netlike structures are likely to be more stable above 150 K. In this regard, we investigate the case of n = 10 to find which structure is more stable between the 3D structure and the netlike structure around 150 and 250 K. We use density functional theory, Møller-Plesset second-order perturbation theory, and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). At the complete basis set limit for the CCSD(T) level of theory, three isomers of 3D cage structure are much more stable in zero point energy corrected binding energy and in free binding energies at 150 K than the lowest energy netlike structures, while the netlike structure would be more stable around approximately 250 K. The predicted vibrational spectra are in good agreement with the experiment. One of the three isomers explains the experimental IR observation of an acceptor (A) type peak of a dangling hydrogen atom.

A Novel Unitized Regenerative Proton Exchange Membrane Fuel Cell

NASA Technical Reports Server (NTRS)

Murphy, O. J.; Cisar, A. J.; Gonzalez-Martin, A.; Salinas, C. E.; Simpson, S. F.

1996-01-01

A difficulty encountered in designing a unitized regenerative proton exchange membrane (PEM) fuel cell lies in the incompatibility of electrode structures and electrocatalyst materials optimized for either of the two functions (fuel cell or electrolyzer) with the needs of the other function. This difficulty is compounded in previous regenerative fuel cell designs by the fact that water, which is needed for proton conduction in the PEM during both modes of operation, is the reactant supplied to the anode in the electrolyzer mode of operation and the product formed at the cathode in the fuel cell mode. Drawbacks associated with existing regenerative fuel cells have been addressed. In a first innovation, electrodes function either as oxidation electrodes (hydrogen ionization or oxygen evolution) or as reduction electrodes (oxygen reduction or hydrogen evolution) in the fuel cell and electrolyzer modes, respectively. Control of liquid water within the regenerative fuel cell has been brought about by a second innovation. A novel PEM has been developed with internal channels that permit the direct access of water along the length of the membrane. Lateral diffusion of water along the polymer chains of the PEM provides the water needed at electrode/PEM interfaces. Fabrication of the novel single cell unitized regenerative fuel cell and results obtained on testing it are presented.

A novel unitized regenerative proton exchange membrane fuel cell

NASA Technical Reports Server (NTRS)

Murphy, O. J.; Cisar, A. J.; Gonzalez-Martin, A.; Salinas, C. E.; Simpson, S. F.

1995-01-01

A difficulty encountered in designing a unitized regenerative proton exchange membrane (PEM) fuel cell lies in the incompatibility of electrode structures and electrocatalyst materials optimized for either of the two functions (fuel cell or electrolyzer) with the needs of the other function. This difficulty is compounded in previous regenerative fuel cell designs by the fact that water, which is needed for proton conduction in the PEM during both modes of operation, is the reactant supplied to the anode in the electrolyzer mode of operation and the product formed at the cathode in the fuel cell mode. Drawbacks associated with existing regenerative fuel cells have been addressed in work performed at Lynntech. In a first innovation, electrodes function either as oxidation electrodes (hydrogen ionization or oxygen evolution) or as reduction electrodes (oxygen reduction or hydrogen evolution) in the fuel cell and electrolyzer modes, respectively. Control of liquid water within the regenerative fuel cell has been brought about by a second innovation. A novel PEM has been developed with internal channels that permit the direct access of water along the length of the membrane. Lateral diffusion of water along the polymer chains of the PEM provides the water needed at electrode/PEM interfaces. Fabrication of the novel unitized regenerative fuel cell and results obtained on testing it will be presented.

Searches for New Physics Using High Mass Dimuons at the CDF II Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karagoz Unel, Muge

2004-12-01

This work describes the measurement of inclusive jets cross section in the D0 experiment. This cross section is computed as a function of jet transverse momentum, in several rapidity intervals. This quantity is sensitive to the proton structure and is crucial for the determination of parton distribution functions (PDF), essentially for the gluon at high proton momentum fraction. The measurement presented here gives the first values obtained for Tevatron Run II for the cross section in several rapidity intervals, for an integrated luminosity of 143 pb -1. The results are in agreement, within the uncertainties, with theoretical Standard Model predictions,more » showing no evidence for new physics. This work points out the aspects of the detector which need better understanding to reach Run I precision and to constrain the PDFs.« less

First measurement of the beam asymmetry in photoproduction off the proton near threshold

NASA Astrophysics Data System (ADS)

Levi Sandri, P.; Mandaglio, G.; De Leo, V.; Bartalini, O.; Bellini, V.; Bocquet, J.-P.; Capogni, M.; Curciarello, F.; Didelez, J.-P.; D'Angelo, A.; Di Salvo, R.; Fantini, A.; Franco, D.; Gervino, G.; Ghio, F.; Girolami, B.; Giusa, A.; Lapik, A.; Lleres, A.; Mammoliti, F.; Manganaro, M.; Moricciani, D.; Mushkarenkov, A.; Nedorezov, V.; Randieri, C.; Rebreyend, D.; Rudnev, N.; Russo, G.; Schaerf, C.; Sperduto, M.-L.; Sutera, M.-C.; Turinge, A.; Vegna, V.; Zonta, I.

2015-07-01

The beam asymmetry in photoproduction off the proton was measured at the GrAAL polarised photon beam with incoming photon energies of 1.461 and 1.480 GeV. For both energies the asymmetry as a function of the meson production angle shows a clear structure, more pronounced at the lowest one, with a change of sign around . The observed behaviour is compatible with P-wave D-wave (or S-wave F-wave) interference, the closer to threshold the stronger. The results are compared to the existing state-of-the-art calculations that fail to account for the data.

Target and double spin asymmetries of deeply virtual π0 production with a longitudinally polarized proton target and CLAS

NASA Astrophysics Data System (ADS)

Kim, A.; Avakian, H.; Burkert, V.; Joo, K.; Kim, W.; Adhikari, K. P.; Akbar, Z.; Anefalos Pereira, S.; Badui, R. A.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Boiarinov, S.; Bosted, P.; Briscoe, W. J.; Brooks, W. K.; Bültmann, S.; Cao, T.; Carman, D. S.; Celentano, A.; Chandavar, S.; Charles, G.; Chetry, T.; Colaneri, L.; Cole, P. L.; Compton, N.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Djalali, C.; Egiyan, H.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fedotov, G.; Fersch, R.; Filippi, A.; Fleming, J. A.; Fradi, A.; Garc con, M.; Ghandilyan, Y.; Gilfoyle, G. P.; Giovanetti, K. L.; Girod, F. X.; Gohn, W.; Golovatch, E.; Gothe, R. W.; Griffioen, K. A.; Guo, L.; Hafidi, K.; Hanretty, C.; Hattawy, M.; Heddle, D.; Hicks, K.; Holtrop, M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Jenkins, D.; Jiang, H.; Jo, H. S.; Joosten, S.; Keller, D.; Khachatryan, G.; Khandaker, M.; Klein, A.; Klein, F. J.; Kubarovsky, V.; Kuhn, S. E.; Kuleshov, S. V.; Lanza, L.; Lenisa, P.; Lu, H. Y.; MacGregor, I. J. D.; Markov, N.; Mattione, P.; McCracken, M. E.; McKinnon, B.; Mokeev, V.; Movsisyan, A.; Munevar, E.; Nadel-Turonski, P.; Net, L. A.; Niccolai, S.; Osipenko, M.; Ostrovidov, A. I.; Paolone, M.; Park, K.; Pasyuk, E.; Phelps, W.; Pisano, S.; Pogorelko, O.; Price, J. W.; Prok, Y.; Ripani, M.; Rizzo, A.; Rosner, G.; Rossi, P.; Roy, P.; Salgado, C.; Schumacher, R. A.; Seder, E.; Sharabian, Y. G.; Skorodumina, Iu.; Smith, G. D.; Sokhan, D.; Sparveris, N.; Stepanyan, S.; Stoler, P.; Strakovsky, I. I.; Strauch, S.; Sytnik, V.; Taiuti, M.; Torayev, B.; Ungaro, M.; Voskanyan, H.; Voutier, E.; Watts, D. P.; Wei, X.; Weinstein, L. B.; Zachariou, N.; Zana, L.; Zhang, J.

2017-05-01

The target and double spin asymmetries of the exclusive pseudoscalar channel e → p → → epπ0 were measured for the first time in the deep-inelastic regime using a longitudinally polarized 5.9 GeV electron beam and a longitudinally polarized proton target at Jefferson Lab with the CEBAF Large Acceptance Spectrometer (CLAS). The data were collected over a large kinematic phase space and divided into 110 four-dimensional bins of Q2, xB, -t and ϕ. Large values of asymmetry moments clearly indicate a substantial contribution to the polarized structure functions from transverse virtual photon amplitudes. The interpretation of experimental data in terms of generalized parton distributions (GPDs) provides the first insight on the chiral-odd GPDs H˜T and ET, and complement previous measurements of unpolarized structure functions sensitive to the GPDs HT and EbarT. These data provide a crucial input for parametrizations of essentially unknown chiral-odd GPDs and will strongly influence existing theoretical calculations based on the handbag formalism.

Revealing an outward-facing open conformational state in a CLC Cl–/H+ exchange transporter

PubMed Central

Khantwal, Chandra M; Abraham, Sherwin J; Han, Wei; Jiang, Tao; Chavan, Tanmay S; Cheng, Ricky C; Elvington, Shelley M; Liu, Corey W; Mathews, Irimpan I; Stein, Richard A; Mchaourab, Hassane S; Tajkhorshid, Emad; Maduke, Merritt

2016-01-01

CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20 Å away from Gluex, near the subunit interface, moves from buried to solvent-exposed. Consistent with functional relevance of this motion, constriction via inter-subunit cross-linking reduces transport. Molecular dynamics simulations indicate that the cross-link dampens extracellular gate-opening motions. In support of this model, mutations that decrease steric contact between Helix N (part of the extracellular gate) and Helix P (at the subunit interface) remove the inhibitory effect of the cross-link. Together, these results demonstrate the formation of a previously uncharacterized 'outward-facing open' state, and highlight the relevance of global structural changes in CLC function. DOI: http://dx.doi.org/10.7554/eLife.11189.001 PMID:26799336

Investigation of evolution-related aspects of bacterial rhodopsins

NASA Technical Reports Server (NTRS)

1994-01-01

We have investigated evolution-related aspects of bacterial rhodopsins, the unique retinal-based energy transducing systems of halophilic archae. The approach was to describe both structural and functional aspects: the structure by sequencing genes to explore which regions are conserved, and the function by comparing proton and chloride transport in the closely related systems, bacteriorhodopsin and halorhodopsin, respectively. In the latter, we have made a good start toward the ultimate goal of separating the attributes of the general principles of retinal-based ionic pumps from those of the specific ion specificities, by determining the thermodynamics of the internal steps of the protein-mediated active transport process, as well as some of the intraprotein ion-transfer steps. Our present emphasis is on continuing to acquire the tools for studying what distinguishes proton transport from chloride transport. We consider it important, therefore, that we have been able to provide firm mathematical grounds for the kinetics analyses which underlies these studies. Our molecular biological studies have received a great boost from the expression vector for the bop gene based on a halobacterial plasmid, that we recently developed.

Target and double spin asymmetries of deeply virtual π 0 production with a longitudinally polarized proton target and CLAS

DOE PAGES

Kim, A.; Avakian, H.; Burkert, V.; ...

2017-02-22

The target and double spin asymmetries of the exclusive pseudoscalar channelmore » $$\\vec e\\vec p\\to ep\\pi^0$$ were measured for the first time in the deep-inelastic regime using a longitudinally polarized 5.9 GeV electron beam and a longitudinally polarized proton target at Jefferson Lab with the CEBAF Large Acceptance Spectrometer (CLAS). The data were collected over a large kinematic phase space and divided into 110 four-dimensional bins of $Q^2$, $$x_B$$, $-t$ and $$\\phi$$. Large values of asymmetry moments clearly indicate a substantial contribution to the polarized structure functions from transverse virtual photon amplitudes. The interpretation of experimental data in terms of generalized parton distributions (GPDs) provides the first insight on the chiral-odd GPDs $$\\tilde{H}_T$$ and $$E_T$$, and complement previous measurements of unpolarized structure functions sensitive to the GPDs $$H_T$$ and $$\\bar E_T$$. Finally, these data provide necessary constraints for chiral-odd GPD parametrizations and will strongly influence existing theoretical handbag models.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yokosawa, A.

The first polarized collider, where we collide 250 GeV/c beams of 70% polarized protons at high luminosity, is under construction. This will allow a determination of the nuclear spin-dependent structure functions over a large range in x, and a collection of sufficient W and Z events to investigate extremely interesting spin-related phenomena. For these measurements, two major RHIC detectors will be used simultaneously whose functions are complimentary. Expected event rates given in this paper are for the STAR detector.

Quantum chemical ab initio prediction of proton exchange barriers between CH{sub 4} and different H-zeolites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, Christian; Sauer, Joachim, E-mail: js@chemie.hu-berlin.de

2015-09-14

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, thismore » difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.« less

A new numerical method for inverse Laplace transforms used to obtain gluon distributions from the proton structure function

NASA Astrophysics Data System (ADS)

Block, Martin M.; Durand, Loyal

2011-11-01

We recently derived a very accurate and fast new algorithm for numerically inverting the Laplace transforms needed to obtain gluon distributions from the proton structure function F2^{γ p}(x,Q2). We numerically inverted the function g( s), s being the variable in Laplace space, to G( v), where v is the variable in ordinary space. We have since discovered that the algorithm does not work if g( s)→0 less rapidly than 1/ s as s→∞, e.g., as 1/ s β for 0< β<1. In this note, we derive a new numerical algorithm for such cases, which holds for all positive and non-integer negative values of β. The new algorithm is exact if the original function G( v) is given by the product of a power v β-1 and a polynomial in v. We test the algorithm numerically for very small positive β, β=10-6 obtaining numerical results that imitate the Dirac delta function δ( v). We also devolve the published MSTW2008LO gluon distribution at virtuality Q 2=5 GeV2 down to the lower virtuality Q 2=1.69 GeV2. For devolution, β is negative, giving rise to inverse Laplace transforms that are distributions and not proper functions. This requires us to introduce the concept of Hadamard Finite Part integrals, which we discuss in detail.

Consecutive Fragmentation Mechanisms of Protonated Ferulic Acid Probed by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations

NASA Astrophysics Data System (ADS)

Martens, Sabrina M.; Marta, Rick A.; Martens, Jonathan K.; McMahon, Terry B.

2012-10-01

Protonated ferulic acid and its principle fragment ion have been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311 + G(d,p) level of theory. Due to its extensively conjugated structure, protonated ferulic acid is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. The first pathway involves proton transfer, resulting in the loss of water and subsequently carbon monoxide, producing fragment ions m/z 177 and 149, respectively. Optimization of m/z 177 yields a species containing an acylium group, which is supported by a diagnostic peak in the IRMPD spectrum at 2168 cm-1. The second pathway involves an alternate proton transfer leading to loss of methanol and rearrangement to a five-membered ring.

Properties of Hermean plasma belt: Numerical simulations and comparison with MESSENGER data

NASA Astrophysics Data System (ADS)

Herčík, David; Trávníček, Pavel M.; Å tverák, Å. těpán.; Hellinger, Petr

2016-01-01

Using a global hybrid model and test particle simulations we present a detailed analysis of the Hermean plasma belt structure. We investigate characteristic properties of quasi-trapped particle population characteristics and its behavior under different orientations of the interplanetary magnetic field. The plasma belt region is constantly supplied with solar wind protons via magnetospheric flanks and tail current sheet region. Protons inside the plasma belt region are quasi-trapped in the magnetic field of Mercury and perform westward drift along the planet. This region is well separated by a magnetic shell and has higher average temperatures and lower bulk proton current densities than the surrounding area. On the dayside the population exhibits loss cone distribution function matching the theoretical loss cone angle. The simulation results are in good agreement with in situ observations of MESSENGER's (MErcury Surface Space ENvironment GEochemistry, and Ranging) MAG and FIPS instruments.

QCD and Standard Model Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gagliardi, Carl A

Our group has focused on using jets in STAR to investigate the longitudinal and transverse spin structure of the proton. We performed measurements of the longitudinal double-spin asymmetry for inclusive jet production that provide the strongest evidence to date that the gluons in the proton with x>0.05 are polarized. We also made the first observation of the Collins effect in pp collisions, thereby providing an important test of the universality of the Collins fragmentation function and opening a new tool to probe quark transversity in the proton. Our studies of forward rapidity electromagnetic jet-like events raise serious question whether themore » large transverse spin asymmetries that have been seen for forward inclusive hadron production arise from conventional 2 → 2 parton scattering. This is the final technical report for DOE Grant DE-FG02-93ER40765. It covers activities during the period January 1, 2015 through November 30, 2016.« less

Effect of protonation and deprotonation on the gas-phase reactivity of fluorinated 1,2,4-triazines.

PubMed

Giorgi, Gianluca; Palumbo Piccionello, Antonio; Pace, Andrea; Buscemi, Silvestre

2008-05-01

Positive and negative electrospray mass spectrometry (MS), in-time and in-space MS(n) experiments, high-resolution and accurate mass measurements obtained with an Orbitrap, together with density functional theory calculations have been used to study the gas-phase ion chemistry of a series of fluorinated 1,2,4-triazines. As a result of low-energy collision-induced dissociations, occurring in an ion trap and in a triple quadrupole, their protonated and deprotonated molecules show interesting features depending on the nature and structure of the precursor ions. The occurrence of elimination/hydration reactions produced by positive ions in the ion trap is noteworthy. Decompositions of deprotonated molecules, initiated by elimination of a hydroxyl radical from [M-H](-), are dominated by radical anions. Theoretical calculations have allowed us to obtain information on atom sites involved in the protonation and deprotonation reactions.

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

PubMed

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport.

PubMed

Komarov, Pavel V; Khalatur, Pavel G; Khokhlov, Alexei R

2013-01-01

Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25-50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity.

Structural characterization/correlation of calorimetric properties of coal fluids: Final report, September 1, 1985--August 31, 1988

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, IR, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined. 8 refs.« less

Structural characterization/correlation of calorimetric properties of coal fluids: Second annual report, September 1, 1986-August 31, 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal fluids and their molecular functional group composition. Coal fluid samples which have had their calorimetric properties measured are characterized using proton NMR, ir, and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal fluid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for ideal gas heat capacities are then examined withinmore » an existing equation of state methodology to determine an optimal correlation. The optimal correlation for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model is examined.« less

Structural characterization/correlation of calorimetric properties of coal fluids. First annual report, September 1, 1985-August 31, 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starling, K.E.; Mallinson, R.G.; Li, M.H.

The objective of this research is to examine the relationship between the calorimetric properties of coal liquids and their molecular functional group composition. Coal liquid samples which have had their calorimetric properties measured are characterized using proton NMR, ir and elemental analysis. These characterizations are then used in a chemical structural model to determine the composition of the coal liquid in terms of the important molecular functional groups. These functional groups are particularly important in determining the intramolecular based properties of a fluid, such as ideal gas heat capacities. Correlational frameworks for heat capacities will then be examined within anmore » existing equation of state methodology to determine an optimal correlation. Also, the optimal recipe for obtaining the characterization/chemical structure information and the sensitivity of the correlation to the characterization and structural model will be examined and determined. 7 refs.« less

Structure Elucidation of the Diagnostic Product Ion at m/z 97 Derived from Androst-4-en-3-One-Based Steroids by ESI-CID and IRMPD Spectroscopy

NASA Astrophysics Data System (ADS)

Thevis, Mario; Beuck, Simon; Höppner, Sebastian; Thomas, Andreas; Held, Joseph; Schäfer, Mathias; Oomens, Jos; Schänzer, Wilhelm

2012-03-01

Structure elucidation of steroids by mass spectrometry has been of great importance to various analytical arenas and numerous studies were conducted to provide evidence for the composition and origin of (tandem) mass spectrometry-derived product ions used to characterize and identify steroidal substances. The common product ion at m/z 97 generated from androst-4-ene-3-one analogs has been subject of various studies, including stable isotope-labeling and (high resolution/high accuracy) tandem mass spectrometry, but its gas-phase structure has never been confirmed. Using high resolution/high accuracy mass spectrometry and low resolution tandem mass spectrometry, density functional theory (DFT) calculation, and infrared multiple photon dissociation (IRMPD) spectroscopy employing a free electron laser, the structure of m/z 97 derived from testosterone was assigned to protonated 3-methyl-2-cyclopenten-1-one. This ion was identified in a set of six cyclic C6H9O+ isomers as computed at the B3LYP/6-311++G(2d,2p) level of theory (protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one and 2-cyclohexen-1-one). Product ions of m/z 97 obtained from MS2 and MS3 experiments of protonated 3-methyl-2-cyclopenten-1-one, 2-methyl-2-cyclopenten-1-one, 2-cyclohexen-1-one, and testosterone corroborated the suggested gas-phase ion structure, which was eventually substantiated by IRMPD spectroscopy yielding a spectrum that convincingly matched the predicted counterpart. Finally, the dissociation pathway of the protonated molecule of testosterone to m/z 97 was revisited and an alternative pathway was suggested that considers the exclusion of C-10 along with the inclusion of C-5, which was experimentally demonstrated with stable isotope labeling.

Search for the X(5568) state decaying into $$\\mathrm{B}^{0}_{\\mathrm{s}}\\pi^{\\pm}$$ in proton-proton collisions at $$\\sqrt{s} = $$ 8 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, Albert M; et al.

2018-05-19

A search for resonancelike structures in the Bs0π± invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at s=8  TeV, corresponding to an integrated luminosity of 19.7  fb-1. The Bs0 mesons are reconstructed in the decay chain Bs0→J/ψϕ, with J/ψ→μ+μ- and ϕ→K+K-. The Bs0π± invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed Bs0 and π± candidates. Upper limits are set on the relative production rates of the X(5568) and Bs0 states times the branching fraction of the decay X(5568)±→Bs0π±. In addition, upper limits are obtained as amore » function of the mass and the natural width of possible exotic states decaying into Bs0π±.« less

Search for the X ( 5568 ) State Decaying into B s 0 π ± in Proton-Proton Collisions at s = 8 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sirunyan, A. M.; Tumasyan, A.; Adam, W.

Here, a search for resonancelike structures in the B 0 sπ ± invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at √s = 8 TeV, corresponding to an integrated luminosity of 19.7 fb –1. The B 0 s mesons are reconstructed in the decay chain B 0 s → J/ψΦ, with J/ψ → μ +μ – and Φ → K +K –. The B 0 sπ ± invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed B 0 s and π ± candidates. Upper limitsmore » are set on the relative production rates of the X(5568) and B 0 s states times the branching fraction of the decay X(5568) ± → B 0 sπ ±. In addition, upper limits are obtained as a function of the mass and the natural width of possible exotic states decaying into B 0 sπ ±.« less

Search for the X ( 5568 ) State Decaying into B s 0 π ± in Proton-Proton Collisions at s = 8 TeV

DOE PAGES

Sirunyan, A. M.; Tumasyan, A.; Adam, W.; ...

2018-05-18

Here, a search for resonancelike structures in the B 0 sπ ± invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at √s = 8 TeV, corresponding to an integrated luminosity of 19.7 fb –1. The B 0 s mesons are reconstructed in the decay chain B 0 s → J/ψΦ, with J/ψ → μ +μ – and Φ → K +K –. The B 0 sπ ± invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed B 0 s and π ± candidates. Upper limitsmore » are set on the relative production rates of the X(5568) and B 0 s states times the branching fraction of the decay X(5568) ± → B 0 sπ ±. In addition, upper limits are obtained as a function of the mass and the natural width of possible exotic states decaying into B 0 sπ ±.« less

Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

PubMed

Swart, Marcel; Rösler, Ernst; Bickelhaupt, F Matthias

2006-10-01

We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases. Copyright 2006 Wiley Periodicals, Inc.

Search for the X(5568) State Decaying into B_{s}^{0}π^{±} in Proton-Proton Collisions at sqrt[s]=8  TeV.

PubMed

Sirunyan, A M; Tumasyan, A; Adam, W; Ambrogi, F; Asilar, E; Bergauer, T; Brandstetter, J; Brondolin, E; Dragicevic, M; Erö, J; Escalante Del Valle, A; Flechl, M; Friedl, M; Frühwirth, R; Ghete, V M; Grossmann, J; Hrubec, J; Jeitler, M; König, A; Krammer, N; Krätschmer, I; Liko, D; Madlener, T; Mikulec, I; Pree, E; Rad, N; Rohringer, H; Schieck, J; Schöfbeck, R; Spanring, M; Spitzbart, D; Waltenberger, W; Wittmann, J; Wulz, C-E; Zarucki, M; Chekhovsky, V; Mossolov, V; Suarez Gonzalez, J; De Wolf, E A; Di Croce, D; Janssen, X; Lauwers, J; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Abu Zeid, S; Blekman, F; D'Hondt, J; De Bruyn, I; De Clercq, J; Deroover, K; Flouris, G; Lontkovskyi, D; Lowette, S; Marchesini, I; Moortgat, S; Moreels, L; Python, Q; Skovpen, K; Tavernier, S; Van Doninck, W; Van Mulders, P; Van Parijs, I; Beghin, D; Bilin, B; Brun, H; Clerbaux, B; De Lentdecker, G; Delannoy, H; Dorney, B; Fasanella, G; Favart, L; Goldouzian, R; Grebenyuk, A; Kalsi, A K; Lenzi, T; Luetic, J; Maerschalk, T; Marinov, A; Seva, T; Starling, E; Vander Velde, C; Vanlaer, P; Vannerom, D; Yonamine, R; Zenoni, F; Cornelis, T; Dobur, D; Fagot, A; Gul, M; Khvastunov, I; Poyraz, D; Roskas, C; Salva, S; Tytgat, M; Verbeke, W; Zaganidis, N; Bakhshiansohi, H; Bondu, O; Brochet, S; Bruno, G; Caputo, C; Caudron, A; David, P; De Visscher, S; Delaere, C; Delcourt, M; Francois, B; Giammanco, A; Komm, M; Krintiras, G; Lemaitre, V; Magitteri, A; Mertens, A; Musich, M; Piotrzkowski, K; Quertenmont, L; Saggio, A; Vidal Marono, M; Wertz, S; Zobec, J; Aldá Júnior, W L; Alves, F L; Alves, G A; Brito, L; Correa Martins Junior, M; Hensel, C; Moraes, A; Pol, M E; Rebello Teles, P; Belchior Batista Das Chagas, E; Carvalho, W; Chinellato, J; Coelho, E; Da Costa, E M; Da Silveira, G G; De Jesus Damiao, D; Fonseca De Souza, S; Huertas Guativa, L M; Malbouisson, H; Melo De Almeida, M; Mora Herrera, C; Mundim, L; Nogima, H; Sanchez Rosas, L J; Santoro, A; Sznajder, A; Thiel, M; Tonelli Manganote, E J; Torres Da Silva De Araujo, F; 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Musella, P; Nessi-Tedaldi, F; Pandolfi, F; Pata, J; Pauss, F; Perrin, G; Perrozzi, L; Quittnat, M; Reichmann, M; Sanz Becerra, D A; Schönenberger, M; Shchutska, L; Tavolaro, V R; Theofilatos, K; Vesterbacka Olsson, M L; Wallny, R; Zhu, D H; Aarrestad, T K; Amsler, C; Canelli, M F; De Cosa, A; Del Burgo, R; Donato, S; Galloni, C; Hreus, T; Kilminster, B; Pinna, D; Rauco, G; Robmann, P; Salerno, D; Schweiger, K; Seitz, C; Takahashi, Y; Zucchetta, A; Candelise, V; Chang, Y H; Cheng, K Y; Doan, T H; Jain, Sh; Khurana, R; Kuo, C M; Lin, W; Pozdnyakov, A; Yu, S S; Kumar, Arun; Chang, P; Chao, Y; Chen, K F; Chen, P H; Fiori, F; Hou, W-S; Hsiung, Y; Liu, Y F; Lu, R-S; Paganis, E; Psallidas, A; Steen, A; Tsai, J F; Asavapibhop, B; Kovitanggoon, K; Singh, G; Srimanobhas, N; Bat, A; Boran, F; Cerci, S; Damarseckin, S; Demiroglu, Z S; Dozen, C; Dumanoglu, I; Girgis, S; Gokbulut, G; Guler, Y; Hos, I; Kangal, E E; Kara, O; Kayis Topaksu, A; Kiminsu, U; Oglakci, M; Onengut, G; Ozdemir, K; Sunar Cerci, D; 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Vlimant, J R; Xie, S; Zhang, Z; Zhu, R Y; Andrews, M B; Ferguson, T; Mudholkar, T; Paulini, M; Russ, J; Sun, M; Vogel, H; Vorobiev, I; Weinberg, M; Cumalat, J P; Ford, W T; Jensen, F; Johnson, A; Krohn, M; Leontsinis, S; Mulholland, T; Stenson, K; Wagner, S R; Alexander, J; Chaves, J; Chu, J; Dittmer, S; Mcdermott, K; Mirman, N; Patterson, J R; Quach, D; Rinkevicius, A; Ryd, A; Skinnari, L; Soffi, L; Tan, S M; Tao, Z; Thom, J; Tucker, J; Wittich, P; Zientek, M; Abdullin, S; Albrow, M; Alyari, M; Apollinari, G; Apresyan, A; Apyan, A; Banerjee, S; Bauerdick, L A T; Beretvas, A; Berryhill, J; Bhat, P C; Bolla, G; Burkett, K; Butler, J N; Canepa, A; Cerati, G B; Cheung, H W K; Chlebana, F; Cremonesi, M; Duarte, J; Elvira, V D; Freeman, J; Gecse, Z; Gottschalk, E; Gray, L; Green, D; Grünendahl, S; Gutsche, O; Harris, R M; Hasegawa, S; Hirschauer, J; Hu, Z; Jayatilaka, B; Jindariani, S; Johnson, M; Joshi, U; Klima, B; Kreis, B; Lammel, S; Lincoln, D; Lipton, R; Liu, M; Liu, T; Lopes De Sá, R; Lykken, J; Maeshima, K; Magini, N; Marraffino, J M; Mason, D; McBride, P; Merkel, P; Mrenna, S; Nahn, S; O'Dell, V; Pedro, K; Prokofyev, O; Rakness, G; Ristori, L; Schneider, B; Sexton-Kennedy, E; Soha, A; Spalding, W J; Spiegel, L; Stoynev, S; Strait, J; Strobbe, N; Taylor, L; Tkaczyk, S; Tran, N V; Uplegger, L; Vaandering, E W; Vernieri, C; Verzocchi, M; Vidal, R; Wang, M; Weber, H A; Whitbeck, A; Acosta, D; Avery, P; Bortignon, P; Bourilkov, D; Brinkerhoff, A; Carnes, A; Carver, M; Curry, D; Field, R D; Furic, I K; Gleyzer, S V; Joshi, B M; Konigsberg, J; Korytov, A; Kotov, K; Ma, P; Matchev, K; Mei, H; Mitselmakher, G; Shi, K; Sperka, D; Terentyev, N; Thomas, L; Wang, J; Wang, S; Yelton, J; Joshi, Y R; Linn, S; Markowitz, P; Rodriguez, J L; Ackert, A; Adams, T; Askew, A; Hagopian, S; Hagopian, V; Johnson, K F; Kolberg, T; Martinez, G; Perry, T; Prosper, H; Saha, A; Santra, A; Sharma, V; Yohay, R; Baarmand, M M; Bhopatkar, V; Colafranceschi, S; Hohlmann, M; Noonan, D; Roy, T; Yumiceva, F; Adams, M R; Apanasevich, L; Berry, D; Betts, R R; Cavanaugh, R; Chen, X; Evdokimov, O; Gerber, C E; Hangal, D A; Hofman, D J; Jung, K; Kamin, J; Sandoval Gonzalez, I D; Tonjes, M B; Trauger, H; Varelas, N; Wang, H; Wu, Z; Zhang, J; Bilki, B; Clarida, W; Dilsiz, K; Durgut, S; Gandrajula, R P; Haytmyradov, M; Khristenko, V; Merlo, J-P; Mermerkaya, H; Mestvirishvili, A; Moeller, A; Nachtman, J; Ogul, H; Onel, Y; Ozok, F; Penzo, A; Snyder, C; Tiras, E; Wetzel, J; Yi, K; Blumenfeld, B; Cocoros, A; Eminizer, N; Fehling, D; Feng, L; Gritsan, A V; Maksimovic, P; Roskes, J; Sarica, U; Swartz, M; Xiao, M; You, C; Al-Bataineh, A; Baringer, P; Bean, A; Boren, S; Bowen, J; Castle, J; Khalil, S; Kropivnitskaya, A; Majumder, D; Mcbrayer, W; Murray, M; Royon, C; Sanders, S; Schmitz, E; Tapia Takaki, J D; Wang, Q; Ivanov, A; Kaadze, K; Maravin, Y; Mohammadi, A; Saini, L K; Skhirtladze, N; Rebassoo, F; Wright, D; Anelli, C; Baden, A; Baron, O; Belloni, A; Eno, S C; Feng, Y; Ferraioli, C; Hadley, N J; Jabeen, S; Jeng, G Y; Kellogg, R G; Kunkle, J; Mignerey, A C; Ricci-Tam, F; Shin, Y H; Skuja, A; Tonwar, S C; Abercrombie, D; Allen, B; Azzolini, V; Barbieri, R; Baty, A; Bi, R; Brandt, S; Busza, W; Cali, I A; D'Alfonso, M; Demiragli, Z; Gomez Ceballos, G; Goncharov, M; Hsu, D; Hu, M; Iiyama, Y; Innocenti, G M; Klute, M; Kovalskyi, D; Lee, Y-J; Levin, A; Luckey, P D; Maier, B; Marini, A C; Mcginn, C; Mironov, C; Narayanan, S; Niu, X; Paus, C; Roland, C; Roland, G; Salfeld-Nebgen, J; Stephans, G S F; Tatar, K; Velicanu, D; Wang, J; Wang, T W; Wyslouch, B; Benvenuti, A C; Chatterjee, R M; Evans, A; Hansen, P; Hiltbrand, J; Kalafut, S; Kubota, Y; Lesko, Z; Mans, J; Nourbakhsh, S; Ruckstuhl, N; Rusack, R; Turkewitz, J; Wadud, M A; Acosta, J G; Oliveros, S; Avdeeva, E; Bloom, K; Claes, D R; Fangmeier, C; Golf, F; Gonzalez Suarez, R; Kamalieddin, R; Kravchenko, I; Monroy, J; Siado, J E; Snow, G R; Stieger, B; Dolen, J; Godshalk, A; Harrington, C; Iashvili, I; Nguyen, D; Parker, A; Rappoccio, S; Roozbahani, B; Alverson, G; Barberis, E; Freer, C; Hortiangtham, A; Massironi, A; Morse, D M; Orimoto, T; Teixeira De Lima, R; Trocino, D; Wamorkar, T; Wang, B; Wisecarver, A; Wood, D; Bhattacharya, S; Charaf, O; Hahn, K A; Mucia, N; Odell, N; Schmitt, M H; Sung, K; Trovato, M; Velasco, M; Bucci, R; Dev, N; Hildreth, M; Hurtado Anampa, K; Jessop, C; Karmgard, D J; Kellams, N; Lannon, K; Li, W; Loukas, N; Marinelli, N; Meng, F; Mueller, C; Musienko, Y; Planer, M; Reinsvold, A; Ruchti, R; Siddireddy, P; Smith, G; Taroni, S; Wayne, M; Wightman, A; Wolf, M; Woodard, A; Alimena, J; Antonelli, L; Bylsma, B; Durkin, L S; Flowers, S; Francis, B; Hart, A; Hill, C; Ji, W; Liu, B; Luo, W; Winer, B L; Wulsin, H W; Cooperstein, S; Driga, O; Elmer, P; Hardenbrook, J; Hebda, P; Higginbotham, S; Kalogeropoulos, A; Lange, D; Luo, J; Marlow, D; Mei, K; Ojalvo, I; Olsen, J; Palmer, C; Piroué, P; Stickland, D; Tully, C; Malik, S; Norberg, S; Barker, A; Barnes, V E; Das, S; Folgueras, S; Gutay, L; Jha, M K; Jones, M; Jung, A W; Khatiwada, A; Miller, D H; Neumeister, N; Peng, C C; Qiu, H; Schulte, J F; Sun, J; Wang, F; Xiao, R; Xie, W; Cheng, T; Parashar, N; Stupak, J; Chen, Z; Ecklund, K M; Freed, S; Geurts, F J M; Guilbaud, M; Kilpatrick, M; Li, W; Michlin, B; Padley, B P; Roberts, J; Rorie, J; Shi, W; Tu, Z; Zabel, J; Zhang, A; Bodek, A; de Barbaro, P; Demina, R; Duh, Y T; Ferbel, T; Galanti, M; Garcia-Bellido, A; Han, J; Hindrichs, O; Khukhunaishvili, A; Lo, K H; Tan, P; Verzetti, M; Ciesielski, R; Goulianos, K; Mesropian, C; Agapitos, A; Chou, J P; Gershtein, Y; Gómez Espinosa, T A; Halkiadakis, E; Heindl, M; Hughes, E; Kaplan, S; Kunnawalkam Elayavalli, R; Kyriacou, S; Lath, A; Montalvo, R; Nash, K; Osherson, M; Saka, H; Salur, S; Schnetzer, S; Sheffield, D; Somalwar, S; Stone, R; Thomas, S; Thomassen, P; Walker, M; Delannoy, A G; Heideman, J; Riley, G; Rose, K; Spanier, S; Thapa, K; Bouhali, O; Castaneda Hernandez, A; Celik, A; Dalchenko, M; De Mattia, M; Delgado, A; Dildick, S; Eusebi, R; Gilmore, J; Huang, T; Kamon, T; Mueller, R; Pakhotin, Y; Patel, R; Perloff, A; Perniè, L; Rathjens, D; Safonov, A; Tatarinov, A; Ulmer, K A; Akchurin, N; Damgov, J; De Guio, F; Dudero, P R; Faulkner, J; Gurpinar, E; Kunori, S; Lamichhane, K; Lee, S W; Libeiro, T; Mengke, T; Muthumuni, S; Peltola, T; Undleeb, S; Volobouev, I; Wang, Z; Greene, S; Gurrola, A; Janjam, R; Johns, W; Maguire, C; Melo, A; Ni, H; Padeken, K; Sheldon, P; Tuo, S; Velkovska, J; Xu, Q; Arenton, M W; Barria, P; Cox, B; Hirosky, R; Joyce, M; Ledovskoy, A; Li, H; Neu, C; Sinthuprasith, T; Wang, Y; Wolfe, E; Xia, F; Harr, R; Karchin, P E; Poudyal, N; Sturdy, J; Thapa, P; Zaleski, S; Brodski, M; Buchanan, J; Caillol, C; Dasu, S; Dodd, L; Duric, S; Gomber, B; Grothe, M; Herndon, M; Hervé, A; Hussain, U; Klabbers, P; Lanaro, A; Levine, A; Long, K; Loveless, R; Ruggles, T; Savin, A; Smith, N; Smith, W H; Taylor, D; Woods, N

2018-05-18

A search for resonancelike structures in the B_{s}^{0}π^{±} invariant mass spectrum is performed using proton-proton collision data collected by the CMS experiment at the LHC at sqrt[s]=8  TeV, corresponding to an integrated luminosity of 19.7  fb^{-1}. The B_{s}^{0} mesons are reconstructed in the decay chain B_{s}^{0}→J/ψϕ, with J/ψ→μ^{+}μ^{-} and ϕ→K^{+}K^{-}. The B_{s}^{0}π^{±} invariant mass distribution shows no statistically significant peaks for different selection requirements on the reconstructed B_{s}^{0} and π^{±} candidates. Upper limits are set on the relative production rates of the X(5568) and B_{s}^{0} states times the branching fraction of the decay X(5568)^{±}→B_{s}^{0}π^{±}. In addition, upper limits are obtained as a function of the mass and the natural width of possible exotic states decaying into B_{s}^{0}π^{±}.

Infrared renormalons and single meson production in proton-proton collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmadov, A. I.; Aydin, Coskun; Hakan, Yilmaz A.

2009-07-01

In this article, we investigate the contribution of the higher-twist Feynman diagrams to the large-p{sub T} inclusive pion production cross section in proton-proton collisions and present the general formulas for the higher-twist differential cross sections in the case of the running coupling and frozen coupling approaches. The structure of infrared renormalon singularities of the higher-twist subprocess cross section and the resummed expression (the Borel sum) for it are found. We compared the resummed higher-twist cross sections with the ones obtained in the framework of the frozen coupling approach and leading-twist cross section. We obtain, that ratio R=({sigma}{sub {pi}{sup +}}{sup HT}){supmore » res}/({sigma}{sub {pi}{sup +}}{sup HT}){sup 0}, for all values of the transverse momentum p{sub T} of the pion identically equivalent to ratio r=({delta}{sub {pi}}{sup HT}){sup res}/({delta}{sub {pi}}{sup HT}){sup 0}. It is shown that the resummed result depends on the choice of the meson wave functions used in calculation. Phenomenological effects of the obtained results are discussed.« less

Deep Proton Writing for the rapid prototyping of polymer micro-components for optical interconnects and optofluidics

NASA Astrophysics Data System (ADS)

Van Erps, Jürgen; Vervaeke, Michael; Ottevaere, Heidi; Hermanne, Alex; Thienpont, Hugo

2013-07-01

The use of photonics in data communication and numerous other industrial applications brought plenty of prospects for innovation and opened up different unexplored market opportunities. This is a major driving force for the fabrication of micro-optical and micro-mechanical structures and their accurate alignment and integration into opto-mechanical modules and systems. To this end, we present Deep Proton Writing (DPW) as a powerful rapid prototyping technology for such micro-components. The DPW process consists of bombarding polymer samples (PMMA or SU-8) with swift protons, which results after chemical processing steps in high-quality micro-optical components. One of the strengths of the DPW micro-fabrication technology is the ability to fabricate monolithic building blocks that include micro-optical and mechanical functionalities which can be precisely integrated into more complex photonic systems. In this paper we comment on how we shifted from using 8.3 to 16.5 MeV protons for DPW and give some examples of micro-optical and micro-mechanical components recently fabricated through DPW, targeting applications in optical interconnections and in optofluidics.

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Melchior, Jan-Patrick; Frick, Bernhard

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

On the nanosecond proton dynamics in phosphoric acid–benzimidazole and phosphoric acid–water mixtures

DOE PAGES

Melchior, Jan-Patrick; Frick, Bernhard

2017-09-22

Combining 1H-NMR, 17O-NMR, and high-resolution backscattering QENS hydrodynamic and structural proton transport in phosphoric acid is separated. The rate limiting steps for structural proton diffusion in mixtures of acid with Brønsted bases are found to occur below the nanosecond timescale.

Proton spin structure from measurable parton distributions.

PubMed

Ji, Xiangdong; Xiong, Xiaonu; Yuan, Feng

2012-10-12

We present a systematic study of the proton spin structure in terms of measurable parton distributions. For a transversely polarized proton, we derive a polarization sum rule from the leading generalized parton distributions appearing in hard exclusive processes. For a longitudinally polarized proton, we obtain a helicity decomposition from well-known quark and gluon helicity distributions and orbital angular-momentum contributions. The latter are shown to be related to measurable subleading generalized parton distributions and quantum-phase space Wigner distributions.

Infrared photodissociation spectroscopy of protonated neurotransmitters in the gas phase

NASA Astrophysics Data System (ADS)

MacLeod, N. A.; Simons, J. P.

2007-03-01

Protonated neurotransmitters have been produced in the gas phase via a novel photochemical scheme: complexes of the species of interest, 1-phenylethylamine, 2-amino-1-phenylethanol and the diastereo-isomers, ephedrine and pseudoephedrine, with a suitable proton donor, phenol (or indole), are produced in a supersonic expansion and ionized by resonant two photon ionization of the donor. Efficient proton transfer generates the protonated neurotransmitters, complexed to a phenoxy radical. Absorption of infrared radiation, and subsequent evaporation of the phenoxy tag, coupled with time of flight mass spectrometry, provides vibrational spectra of the protonated (and also hydrated) complexes for comparison with the results of quantum chemical computation. Comparison with the conformational structures of the neutral neurotransmitters (established previously) reveals the effect of protonation on their structure. The photochemical proton transfer strategy allows spectra to be recorded from individual laser shots and their quality compares favourably with that obtained using electro-spray or matrix assisted laser desorption ion sources.

Minima in generalized oscillator strengths for initially excited hydrogen-like atoms

NASA Technical Reports Server (NTRS)

Matsuzawa, M.; Omidvar, K.; Inokuti, M.

1976-01-01

Generalized oscillator strengths for transitions from an initially excited state of a hydrogenic atom to final states (either discrete or continuum) have complicated structures, including minima and shoulders, as functions of the momentum transfer. Extensive calculations carried out in the present work have revealed certain systematics of these structures. Some implications of the minima to the energy dependence of the inner-shell ionization cross section of heavy atoms by proton impact are discussed.

Optical potentials for nuclear level structures and nucleon interactions data of tin isotopes based on the soft-rotator model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Jeong-Yeon; Hahn, Insik; Kim, Yeongduk

2009-06-15

The soft-rotator model is applied to self-consistent analyses of the nuclear level structures and the nucleon interaction data of the even-even Sn isotopes, {sup 116}Sn, {sup 118}Sn, {sup 120}Sn, and {sup 122}Sn. The model successfully describes low-lying collective levels of these isotopes, which exhibit neither typical rotational nor harmonic vibrational structures. The experimental nucleon interaction data--total neutron cross sections, proton reaction cross sections, and nucleon elastic and inelastic scattering data--are well described up to 200 MeV in a coupled-channels optical model approach. For the calculations, nuclear wave functions for the Sn isotopes are taken from the nonaxial soft-rotator model withmore » the model parameters adjusted to fit the measured low-lying collective level structures. We find that the {beta}{sub 2} and {beta}{sub 3} deformations for incident protons are larger than those for incident neutrons by {approx}15%, which is clear evidence of the deviation from the pure collective model for these isotopes.« less

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding.

PubMed

Adrian, Michael; Winnerdy, Fernaldo Richtia; Heddi, Brahim; Phan, Anh Tuân

2017-08-22

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Novel structure design of composite proton exchange membranes with continuous and through-membrane proton-conducting channels

NASA Astrophysics Data System (ADS)

Wang, Hang; Tang, Chenxiao; Zhuang, Xupin; Cheng, Bowen; Wang, Wei; Kang, Weimin; Li, Hongjun

2017-10-01

The primary goal of this study is to develop a high-performanced proton exchange membrane with the characteristics of through-membrane and continuous solution blown nanofibers as proton-conducting channels. The curled sulfonated phenolphthalein poly (ether sulfone) and poly (vinylidene fluoride) nanofibers were separately fabricated through the solution blowing process which is a new nanofiber fabricating method with high productivity, then they were fabricated into a sandwich-structured mat. Then this sandwich-structured mat was hot-pressed to form the designed structure using different melting temperatures of the two polymers by melting and making poly (vinylidene fluoride) flow into the phenolphthalein poly (ether sulfone) nanofiber mat. The characteristics of the composite membrane, such as morphology and performance of the membrane, were investigated. The characterization results proved the successful preparation of the membrane structure. Performance results showed that the novel structured membrane with through-membrane nanofibers significantly improved water swelling and methanol permeability, though its conductivity is lower than that of Nafion, the cell performance showed comparable results. Therefore, the novel structure design can be considered as a promising method for preparing of proton exchange membranes.

Preparation, characterization and application of novel proton conducting ceramics

NASA Astrophysics Data System (ADS)

Wang, Siwei

Due to the immediate energy shortage and the requirement of environment protection nowadays, the efficient, effective and environmental friendly use of current energy sources is urgent. Energy conversion and storage is thus an important focus both for industry and academia. As one of the hydrogen energy related materials, proton conducting ceramics can be applied in solid oxide fuel cells and steam electrolysers, as well as high temperature hydrogen separation membranes and hydrogen sensors. For most of the practical applications, both high proton conductivity and chemical stability are desirable. However, the state-of-the-art proton conducting ceramics are facing great challenges in simultaneously fulfilling conductivity and stability requirements for practical applications. Consequently, understanding the properties for the proton conducting ceramics and developing novel materials that possess both high proton conductivity and enhanced chemical stability have both scientific and practical significances. The objective of this study is to develop novel proton conducting ceramics, either by evaluating the doping effects on the state-of-the-art simple perovskite structured barium cerates, or by investigating novel complex perovskite structured Ba3Ca1.18Nb1.82O 9-delta based proton conductors as potential proton conducting ceramics with improved proton conductivity and enhanced chemical stability. Different preparation methods were compared, and their influence on the structure, including the bulk and grain boundary environment has been investigated. In addition, the effects of microstructure on the electrical properties of the proton conducting ceramics have also been characterized. The solid oxide fuel cell application for the proton conducting ceramics performed as electrolyte membranes has been demonstrated.

Structural insights into electron transfer in caa3-type cytochrome oxidase

PubMed Central

Lyons, Joseph A.; Aragão, David; Slattery, Orla; Pisliakov, Andrei V.; Soulimane, Tewfik; Caffrey, Martin

2012-01-01

Summary Paragraph Cytochrome c oxidase is a member of the heme copper oxidase superfamily (HCO)1. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c2–4. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented. PMID:22763450

Expanding the View of Proton Pumping in Cytochrome c Oxidase through Computer Simulation

PubMed Central

Peng, Yuxing; Voth, Gregory A.

2011-01-01

In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are transported by the Grotthuss shuttling via hydrogen-bonded water molecules and protonatable residues. Proton transport through the D-pathway is a complicated process that is highly sensitive to alterations in the amino acids or the solvation structure in the channel, both of which can inhibit proton pumping and enzymatic activity. Simulations of proton transport in the hydrophobic cavity showed a clear redox state dependence. To study the mechanism of proton pumping in CcO, multi-state empirical valence bond (MS-EVB) simulations have been conducted, focusing on the proton transport through the D-pathway and the hydrophobic cavity next to the binuclear center. The hydration structures, transport pathways, effects of residues, and free energy surfaces of proton transport were revealed in these MS-EVB simulations. The mechanistic insight gained from them is herein reviewed and placed in context for future studies. PMID:22178790

Generation of the neutron response function of an NE213 scintillator for fusion applications

NASA Astrophysics Data System (ADS)

Binda, F.; Eriksson, J.; Ericsson, G.; Hellesen, C.; Conroy, S.; Nocente, M.; Sundén, E. Andersson; JET Contributors

2017-09-01

In this work we present a method to evaluate the neutron response function of an NE213 liquid scintillator. This method is particularly useful when the proton light yield function of the detector has not been measured, since it is based on a proton light yield function taken from literature, MCNPX simulations, measurements of gamma-rays from a calibration source and measurements of neutrons from fusion experiments with ohmic plasmas. The inclusion of the latter improves the description of the proton light yield function in the energy range of interest (around 2.46 MeV). We apply this method to an NE213 detector installed at JET, inside the radiation shielding of the magnetic proton recoil (MPRu) spectrometer, and present the results from the calibration along with some examples of application of the response function to perform neutron emission spectroscopy (NES) of fusion plasmas. We also investigate how the choice of the proton light yield function affects the NES analysis, finding that the result does not change significantly. This points to the fact that the method for the evaluation of the neutron response function is robust and gives reliable results.

Effects of Alternating Hydrogenated and Protonated Segments in polymers on their Wettability.

NASA Astrophysics Data System (ADS)

Smith, Dennis; Traiphol, Rakchart; Cheng, Gang; Perahia, Dvora

2003-03-01

Polymers consisting of alternating hydrogenated and fluorinated segments exhibit unique interfacial characteristics governed by the components that dominate the interface. Presence of fluorine reduces the interfacial energy and is expected to decrease the adhesion to the polymer surface. Thin liquid crystalline (LC) layers of 4,4?-octyl-cyanobiphenyl, cast on top of a polymeric layer consisting of alternating methylstylbine protonated segments bridged by a fluorinated group was used as a mechanistic tool to study of interfacial effects on three parameters: wetting, interfacial alignment and surface induces structures. The liquid crystal cast on a low interfacial energy fluorinated polymeric film exhibits bulk homeotropic alignment as expected. However it fully wetted the polymer surface despite the incompatibility of the protonated LC and mainly fluorinated polymer interface. Further more, it was found to stabilize the interfacial Semitic layers to a higher temperature and induce different surface ordering that was not observed at the same temperature neither in the bulk nor at the interfaces with silicon or glass surface. These results indicate that the interfacial interactions of polymers with liquid crystals are a complex function of both surface energies and the interfacial structure of the polymer.

Mercury's plasma belt: hybrid simulations results compared to in-situ measurements

NASA Astrophysics Data System (ADS)

Hercik, D.; Travnicek, P. M.; Schriver, D.; Hellinger, P.

2012-12-01

The presence of plasma belt and trapped particles region in the Mercury's inner magnetosphere has been questionable due to small dimensions of the magnetosphere of Mercury compared to Earth, where these regions are formed. Numerical simulations of the solar wind interaction with Mercury's magnetic field suggested that such a structure could be found also in the vicinity of Mercury. These results has been recently confirmed also by MESSENGER observations. Here we present more detailed analysis of the plasma belt structure and quasi-trapped particle population characteristics and behaviour under different orientations of the interplanetary magnetic field.The plasma belt region is constantly supplied with solar wind protons via magnetospheric flanks and tail current sheet region. Protons inside the plasma belt region are quasi-trapped in the magnetic field of Mercury and perform westward drift along the planet. This region is well separated by a magnetic shell and has higher average temperatures and lower bulk proton current densities than surrounding area. On the day side the population exhibits loss cone distribution function matching the theoretical loss cone angle. Simulations results are also compared to in-situ measurements acquired by MESSENGER MAG and FIPS instruments.

Photoinduced electron transfer and fluorophore motion as a probe of the conformational dynamics of membrane proteins: application to the influenza a M2 proton channel.

PubMed

Rogers, Julie M G; Polishchuk, Alexei L; Guo, Lin; Wang, Jun; DeGrado, William F; Gai, Feng

2011-04-05

The structure and function of the influenza A M2 proton channel have been the subject of intensive investigations in recent years because of their critical role in the life cycle of the influenza virus. Using a truncated version of the M2 proton channel (i.e., M2TM) as a model, here we show that fluctuations in the fluorescence intensity of a dye reporter that arise from both fluorescence quenching via the mechanism of photoinduced electron transfer (PET) by an adjacent tryptophan (Trp) residue and local motions of the dye molecule can be used to probe the conformational dynamics of membrane proteins. Specifically, we find that the dynamics of the conformational transition between the N-terminal open and C-terminal open states of the M2TM channel occur on a timescale of about 500 μs and that the binding of either amantadine or rimantadine does not inhibit the pH-induced structural equilibrium of the channel. These results are consistent with the direct occluding mechanism of inhibition which suggests that the antiviral drugs act by sterically occluding the channel pore.

Effective-range function methods for charged particle collisions

NASA Astrophysics Data System (ADS)

Gaspard, David; Sparenberg, Jean-Marc

2018-04-01

Different versions of the effective-range function method for charged particle collisions are studied and compared. In addition, a novel derivation of the standard effective-range function is presented from the analysis of Coulomb wave functions in the complex plane of the energy. The recently proposed effective-range function denoted as Δℓ [Ramírez Suárez and Sparenberg, Phys. Rev. C 96, 034601 (2017), 10.1103/PhysRevC.96.034601] and an earlier variant [Hamilton et al., Nucl. Phys. B 60, 443 (1973), 10.1016/0550-3213(73)90193-4] are related to the standard function. The potential interest of Δℓ for the study of low-energy cross sections and weakly bound states is discussed in the framework of the proton-proton S10 collision. The resonant state of the proton-proton collision is successfully computed from the extrapolation of Δℓ instead of the standard function. It is shown that interpolating Δℓ can lead to useful extrapolation to negative energies, provided scattering data are known below one nuclear Rydberg energy (12.5 keV for the proton-proton system). This property is due to the connection between Δℓ and the effective-range function by Hamilton et al. that is discussed in detail. Nevertheless, such extrapolations to negative energies should be used with caution because Δℓ is not analytic at zero energy. The expected analytic properties of the main functions are verified in the complex energy plane by graphical color-based representations.

Gompertz type dechanneling functions for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels

NASA Astrophysics Data System (ADS)

Petrović, S.; Erić, M.; Kokkoris, M.; Nešković, N.

2007-03-01

In this work the energy dependences of the Gompertz type sigmoidal dechanneling function parameters for protons in <1 0 0>, <1 1 0> and <1 1 1> Si crystal channels is investigated theoretically. The proton energy range considered is between 1 and 10 MeV. The original dechanneling functions are generated using a realistic Monte Carlo computer simulation code. We show that the Gompertz type dechanneling function, having two parameters, lc and k, representing the dechanneling range and rate, respectively, approximate accurately the original dechanneling function. It is also shown that the energy dependences of parameters lc and k can be approximated by a linear function and a sum of two exponential functions, respectively. The results obtained can be used for accurate reproduction of experimental proton channeling spectra recorded in the backscattering geometry.

Synthesis and characterizations of novel polymer electrolytes

NASA Astrophysics Data System (ADS)

Chanthad, Chalathorn

Polymer electrolytes are an important component of many electrochemical devices. The ability to control the structures, properties, and functions of polymer electrolytes remains a key subject for the development of next generation functional polymers. Taking advantage of synthetic strategies is a promising approach to achieve the desired chemical structures, morphologies, thermal, mechanical, and electrochemical properties. Therefore, the major goal of this thesis is to develop synthetic methods for of novel proton exchange membranes and ion conductive membranes. In Chapter 2, new classes of fluorinated polymer- polysilsesquioxane nanocomposites have been designed and synthesized. The synthetic method employed includes radical polymerization using the functional benzoyl peroxide initiator for the telechelic fluorinated polymers with perfluorosulfonic acids in the side chains and a subsequent in-situ sol-gel condensation of the prepared triethoxylsilane-terminated fluorinated polymers with alkoxide precursors. The properties of the composite membranes have been studied as a function of the content and structure of the fillers. The proton conductivity of the prepared membranes increases steadily with the addition of small amounts of the polysilsesquioxane fillers. In particular, the sulfopropylated polysilsesquioxane based nanocomposites display proton conductivities greater than Nafion. This is attributed to the presence of pendant sulfonic acids in the fillers, which increases ion-exchange capacity and offers continuous proton transport channels between the fillers and the polymer matrix. The methanol permeability of the prepared membranes has also been examined. Lower methanol permeability and higher electrochemical selectivity than those of Nafion have been demonstrated in the polysilsesquioxane based nanocomposites. In Chapter 3, the synthesis of a new class of ionic liquid-containing triblock copolymers with fluoropolymer mid-block and imidazolium methacrylate end-blocks is described for the first time. The synthetic strategy involves the preparation of the telechelic fluoropolymers using a functional benzoyl peroxide initiator as the macro-chain transfer agent for subsequent RAFT polymerization of the imidazolium methacrylate monomer. As revealed in DSC, SAXS and dielectric relaxation spectroscopy (DRS) measurements, there was no microphase separation in the triblock copolymers, likely due to solubility of ionic liquid moieties in the fluoropolymer matrix. The anionic counterion has direct impact on the thermal properties, ionic conductivity and segmental dynamics of the polymers. The temperature dependence of the ionic conductivity is well described by the Vogel-Tamman-Fulcher model, suggesting that ion motion is closely coupled to segmental motion. In Chapter 4 and 5, new solid electrolytes for lithium cations have been synthesized by catalyzed hydrosilylation reaction involving hydrogen atoms of polysiloxane and polyhedral oligomeric silsesquioxane (POSS) and double bonds of vinyl tris17-bromo-3,6,9,12,15- pentaoxaheptadecan-1-ol silane. The obtained structures are based on branched or dendritic with ionic liquid-ethylene oxide oligomer. High room temperature ionic conductivities have been obtained in the range of 10-4-10-5 can be regarded as solid electrolytes. This is attributed to the high concentration of ions from ionic liquid moieties in the tripodand molecule, high segmental mobility, and high ion dissociation from ethylene oxide spacers. The influence of anion structures and lithium salts and concentration has been investigated.

A study of nuclear structure for 244Cm, 241Am, 238Pu, 210Po, 147Pm, 137Cs, 90Sr and 63Ni nuclei used in nuclear battery

NASA Astrophysics Data System (ADS)

Artun, Ozan

2017-07-01

In this paper, we intend to extend the nuclear data of 244Cm, 241Am, 238Pu, 210Po, 147Pm, 137Cs, 90Sr and 63Ni nuclei used in nuclear battery technology, because, these nuclei are quite important for space investigations in radioisotope thermoelectric generator (RTG) and for microelectronic technologies in betavoltaic batteries. Therefore, the nuclear structure properties of nuclei such as separation energies, neutron skin thicknesses, proton, charge and neutron density distributions as a function of radius, the root mean square (rms) proton, charge and neutron radii, binding energies per particle, have been investigated by Hartree-Fock with eight different Skyrme forces. The obtained results have been compared with the experimental data in literature and relativistic mean field theory (RMFT) results.

Electron Emission from Amorphous Solid Water Induced by Passage of Energetic Protons and Fluorine Ions

PubMed Central

Toburen, L. H.; McLawhorn, S. L.; McLawhorn, R. A.; Carnes, K. D.; Dingfelder, M.; Shinpaugh, J. L.

2013-01-01

Absolute doubly differential electron emission yields were measured from thin films of amorphous solid water (ASW) after the transmission of 6 MeV protons and 19 MeV (1 MeV/nucleon) fluorine ions. The ASW films were frozen on thin (1-μm) copper foils cooled to approximately 50 K. Electrons emitted from the films were detected as a function of angle in both the forward and backward direction and as a function of the film thickness. Electron energies were determined by measuring the ejected electron time of flight, a technique that optimizes the accuracy of measuring low-energy electron yields, where the effects of molecular environment on electron transport are expected to be most evident. Relative electron emission yields were normalized to an absolute scale by comparison of the integrated total yields for proton-induced electron emission from the copper substrate to values published previously. The absolute doubly differential yields from ASW are presented along with integrated values, providing single differential and total electron emission yields. These data may provide benchmark tests of Monte Carlo track structure codes commonly used for assessing the effects of radiation quality on biological effectiveness. PMID:20681805

EFFECTIVE HYPERFINE-STRUCTURE FUNCTIONS OF AMMONIA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Augustovičová, L.; Soldán, P.; Špirko, V., E-mail: spirko@marge.uochb.cas.cz

The hyperfine structure of the rotation-inversion ( v {sub 2} = 0{sup +}, 0{sup −}, 1{sup +}, 1{sup −}) states of the {sup 14}NH{sub 3} and {sup 15}NH{sub 3} ammonia isotopomers is rationalized in terms of effective (ro-inversional) hyperfine-structure (hfs) functions. These are determined by fitting to available experimental data using the Hougen’s effective hyperfine-structure Hamiltonian within the framework of the non-rigid inverter theory. Involving only a moderate number of mass independent fitting parameters, the fitted hfs functions provide a fairly close reproduction of a large majority of available experimental data, thus evidencing adequacy of these functions for reliable prediction.more » In future experiments, this may help us derive spectroscopic constants of observed inversion and rotation-inversion transitions deperturbed from hyperfine effects. The deperturbed band centers of ammonia come to the forefront of fundamental physics especially as the probes of a variable proton-to-electron mass ratio.« less

Femtochemistry of Intramolecular Charge and Proton Transfer Reactions in Solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Douhal, Abderrazzak; Sanz, Mikel; Carranza, Maria Angeles

2005-03-17

We report on the first observation of ultrafast intramolecular charge- and proton-transfer reactions in 4'-dimethylaminoflavonol (DAMF) in solution. Upon femtosecond excitation of a non-planar structure of DMAF in apolar medium, the intramolecular charge transfer (ICT) does not occur, and a slow (2 ps) proton motion takes place. However, in polar solvents, the ICT is very fast (100-200 fs) and the produced structure is stabilized that proton motion takes place in few or tens of ps.

A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

DOE PAGES

He, Bo; Dai, Jing; Zherebetskyy, Danylo; ...

2015-03-31

Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing,more » but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.« less

Measurement of the Structure Function Ratio $$F^{\\eta}_2$$ /$$ F^p_2$$ in Muon - Nucleon Scattering at Low $x$ and $$Q^{2}$$

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spentzouris, Panagiotis

1994-12-01

The ratio of the neutron to proton structure functions,more » $$F^{\\eta}_2$$ / $$F^p_2$$, from scattering of 470 GeV muons on liquid hydrogen and deuterium targets, is measured at very small-x and $Q^2$ , using the Fermilab E665 spectrometer. The results presented cover the region 0.000004 < x < 0.3 and $Q^2$ > 0.001 $GeV^2$ , three orders of magnitude lower in z than previous fixed-target experiments, and with higher average Q2 in the overlap region....« less

Hydrogens detected by subatomic resolution protein crystallography in a [NiFe] hydrogenase.

PubMed

Ogata, Hideaki; Nishikawa, Koji; Lubitz, Wolfgang

2015-04-23

The enzyme hydrogenase reversibly converts dihydrogen to protons and electrons at a metal catalyst. The location of the abundant hydrogens is of key importance for understanding structure and function of the protein. However, in protein X-ray crystallography the detection of hydrogen atoms is one of the major problems, since they display only weak contributions to diffraction and the quality of the single crystals is often insufficient to obtain sub-ångström resolution. Here we report the crystal structure of a standard [NiFe] hydrogenase (∼91.3 kDa molecular mass) at 0.89 Å resolution. The strictly anoxically isolated hydrogenase has been obtained in a specific spectroscopic state, the active reduced Ni-R (subform Ni-R1) state. The high resolution, proper refinement strategy and careful modelling allow the positioning of a large part of the hydrogen atoms in the structure. This has led to the direct detection of the products of the heterolytic splitting of dihydrogen into a hydride (H(-)) bridging the Ni and Fe and a proton (H(+)) attached to the sulphur of a cysteine ligand. The Ni-H(-) and Fe-H(-) bond lengths are 1.58 Å and 1.78Å, respectively. Furthermore, we can assign the Fe-CO and Fe-CN(-) ligands at the active site, and can obtain the hydrogen-bond networks and the preferred proton transfer pathway in the hydrogenase. Our results demonstrate the precise comprehensive information available from ultra-high-resolution structures of proteins as an alternative to neutron diffraction and other methods such as NMR structural analysis.

Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase.

PubMed

Schnier, P D; Price, W D; Jockusch, R A; Williams, E R

1996-07-31

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.

Exchangers man the pumps: Functional interplay between proton pumps and proton-coupled Ca(2+) exchangers

USDA-ARS?s Scientific Manuscript database

Tonoplast-localised proton-coupled Ca(2+) transporters encoded by cation/H(+) exchanger (CAX) genes play a critical role in sequestering Ca(2+) into the vacuole. These transporters may function in coordination with Ca(2+) release channels, to shape stimulus-induced cytosolic Ca(2+) elevations. Recen...

Response functions of Fuji imaging plates to monoenergetic protons in the energy range 0.6-3.2 MeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonnet, T.; Denis-Petit, D.; Gobet, F.

2013-01-15

We have measured the responses of Fuji MS, SR, and TR imaging plates (IPs) to protons with energies ranging from 0.6 to 3.2 MeV. Monoenergetic protons were produced with the 3.5 MV AIFIRA (Applications Interdisciplinaires de Faisceaux d'Ions en Region Aquitaine) accelerator at the Centre d'Etudes Nucleaires de Bordeaux Gradignan (CENBG). The IPs were irradiated with protons backscattered off a tantalum target. We present the photo-stimulated luminescence response of the IPs together with the fading measurements for these IPs. A method is applied to allow correction of fading effects for variable proton irradiation duration. Using the IP fading corrections, amore » model of the IP response function to protons was developed. The model enables extrapolation of the IP response to protons up to proton energies of 10 MeV. Our work is finally compared to previous works conducted on Fuji TR IP response to protons.« less

Analyzing powers in the three-body break-up reactions from 3overlineHe + 2H

NASA Astrophysics Data System (ADS)

Okumuşoǧlu, Nazmi T.; Basak, A. K.; Blyth, C. O.

1980-11-01

Analyzing powers and cross sections of the 2H( 3overlineHe, pp ) 3H, 2H( 3overlineHe, pt) 1H and2H( 3overlineHe, p 3He) n reactions have been measured as a function of the energy of the detected proton. Two of the outgoing particles were identified and detected in coincidence with several forward-angle geometries. The analyzing powers found were generally small but non-zero. However, at kinematical conditions favoring the final-state interactions between proton and triton (or neutron and helion) large values up to 0.4 were found. The results are discussed with respect to the level structure of 4He.

Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Qi; Underwood, Tracy S.A.; Kung, Jong

2016-05-01

Purpose: Clinical proton beam therapy has been based on the use of a generic relative biological effectiveness (RBE) of ∼1.1. However, emerging data have suggested that Fanconi anemia (FA) and homologous recombination pathway defects can lead to a variable RBE, at least in vitro. We investigated the role of SLX4 (FANCP), which acts as a docking platform for the assembly of multiple structure-specific endonucleases, in the response to proton irradiation. Methods and Materials: Isogenic cell pairs for the study of SLX4, XPF/ERCC1, MUS81, and SLX1 were irradiated at the mid-spread-out Bragg peak of a clinical proton beam (linear energy transfer 2.5 keV/μm)more » or with 250 kVp x-rays, and the clonogenic survival fractions were determined. To estimate the RBE of the protons relative to cobalt-60 photons (Co60Eq), we assigned a RBE(Co60Eq) of 1.1 to x-rays to correct the physical dose measured. Standard DNA repair foci assays were used to monitor the damage responses, and the cell cycle distributions were assessed by flow cytometry. The poly(ADP-ribose) polymerase inhibitor olaparib was used for comparison. Results: Loss of SLX4 function resulted in an enhanced proton RBE(Co60Eq) of 1.42 compared with 1.11 for wild-type cells (at a survival fraction of 0.1; P<.05), which correlated with increased persistent DNA double-strand breaks in cells in the S/G{sub 2} phase. Genetic analysis identified the SLX4-binding partner MUS81 as a mediator of resistance to proton radiation. Both proton irradiation and olaparib treatment resulted in a similar prolonged accumulation of RAD51 foci in SLX4/MUS81-deficient cells, suggesting a common defect in the repair of DNA replication fork-associated damage. Conclusions: A defect in the FA pathway at the level of SLX4 results in hypersensitivity to proton radiation, which is, at least in part, due to impaired MUS81-mediated processing of replication forks that stall at clustered DNA damage. In vivo and clinical studies are needed to confirm these findings in human cancers.« less

Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation.

PubMed

Liu, Qi; Underwood, Tracy S A; Kung, Jong; Wang, Meng; Lu, Hsiao-Ming; Paganetti, Harald; Held, Kathryn D; Hong, Theodore S; Efstathiou, Jason A; Willers, Henning

2016-05-01

Clinical proton beam therapy has been based on the use of a generic relative biological effectiveness (RBE) of ∼1.1. However, emerging data have suggested that Fanconi anemia (FA) and homologous recombination pathway defects can lead to a variable RBE, at least in vitro. We investigated the role of SLX4 (FANCP), which acts as a docking platform for the assembly of multiple structure-specific endonucleases, in the response to proton irradiation. Isogenic cell pairs for the study of SLX4, XPF/ERCC1, MUS81, and SLX1 were irradiated at the mid-spread-out Bragg peak of a clinical proton beam (linear energy transfer 2.5 keV/μm) or with 250 kVp x-rays, and the clonogenic survival fractions were determined. To estimate the RBE of the protons relative to cobalt-60 photons (Co60Eq), we assigned a RBE(Co60Eq) of 1.1 to x-rays to correct the physical dose measured. Standard DNA repair foci assays were used to monitor the damage responses, and the cell cycle distributions were assessed by flow cytometry. The poly(ADP-ribose) polymerase inhibitor olaparib was used for comparison. Loss of SLX4 function resulted in an enhanced proton RBE(Co60Eq) of 1.42 compared with 1.11 for wild-type cells (at a survival fraction of 0.1; P<.05), which correlated with increased persistent DNA double-strand breaks in cells in the S/G2 phase. Genetic analysis identified the SLX4-binding partner MUS81 as a mediator of resistance to proton radiation. Both proton irradiation and olaparib treatment resulted in a similar prolonged accumulation of RAD51 foci in SLX4/MUS81-deficient cells, suggesting a common defect in the repair of DNA replication fork-associated damage. A defect in the FA pathway at the level of SLX4 results in hypersensitivity to proton radiation, which is, at least in part, due to impaired MUS81-mediated processing of replication forks that stall at clustered DNA damage. In vivo and clinical studies are needed to confirm these findings in human cancers. Copyright © 2016 Elsevier Inc. All rights reserved.

Modeling of S-Nitrosothiol-Thiol Reactions of Biological Significance: HNO Production by S-Thiolation Requires a Proton Shuttle and Stabilization of Polar Intermediates.

PubMed

Ivanova, Lena V; Cibich, Daniel; Deye, Gregory; Talipov, Marat R; Timerghazin, Qadir K

2017-04-18

Nitroxyl (HNO), a reduced form of the important gasotransmitter nitric oxide, exhibits its own unique biological activity. A possible biological pathway of HNO formation is the S-thiolation reaction between thiols and S-nitrosothiols (RSNOs). Our density functional theory (DFT) calculations suggested that S-thiolation proceeds through a proton transfer from the thiol to the RSNO nitrogen atom, which increases electrophilicity of the RSNO sulfur, followed by nucleophilic attack by thiol, yielding a charge-separated zwitterionic intermediate structure RSS + (R)N(H)O - (Zi), which decomposes to yield HNO and disulfide RSSR. In the gas phase, the proton transfer and the S-S bond formation are asynchronous, resulting in a high activation barrier (>40 kcal mol -1 ), making the reaction infeasible. However, the barrier can decrease below the S-N bond dissociation energy in RSNOs (≈30 kcal mol -1 ) upon transition into an aqueous environment that stabilizes Zi and provides a proton shuttle to synchronize the proton transfer and the S-S bond formation. These mechanistic features suggest that S-thiolation can easily lend itself to enzymatic catalysis and thus can be a possible route of endogenous HNO production. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Space Environment Effects on Flexible, Low-Voltage Organic Thin-Film Transistors.

PubMed

Basiricò, Laura; Basile, Alberto Francesco; Cosseddu, Piero; Gerardin, Simone; Cramer, Tobias; Bagatin, Marta; Ciavatti, Andrea; Paccagnella, Alessandro; Bonfiglio, Annalisa; Fraboni, Beatrice

2017-10-11

Organic electronic devices fabricated on flexible substrates are promising candidates for applications in environments where flexible, lightweight, and radiation hard materials are required. In this work, device parameters such as threshold voltage, charge mobility, and trap density of 13-bis(triisopropylsilylethynyl)pentacene (TIPS-pentacene)-based organic thin-film transistors (OTFTs) have been monitored for performing electrical measurements before and after irradiation by high-energy protons. The observed reduction of charge carrier mobility following irradiation can be only partially ascribed to the increased trap density. Indeed, we used other techniques to identify additional effects induced by proton irradiation in such devices. Atomic force microscopy reveals morphological defects occurring in the organic dielectric layer induced by the impinging protons, which, in turn, induce a strain on the TIPS-pentacene crystallites lying above. The effects of this strain are investigated by density functional theory simulations of two model structures, which describe the TIPS-pentacene crystalline films at equilibrium and under strain. The two different density of states distributions in the valence band have been correlated with the photocurrent spectra acquired before and after proton irradiation. We conclude that the degradation of the dielectric layer and the organic semiconductor sensitivity to strain are the two main phenomena responsible for the reduction of OTFT mobility after proton irradiation.

Synthesis, characterization, crystal structure and solution studies of a novel proton transfer (charge transfer) complex of 2,2‧-dipyridylamine with 2,6-pyridine dicarboxylic acid

NASA Astrophysics Data System (ADS)

Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Zarghampour, Fereshteh; Moghimi, Abolghasem; García-Granda, Santiago; Mendoza-Meroño, Rafael

2015-06-01

Reaction between 2,2‧-dipyridylamine (DPA) and 2,6-pyridine dicarboxylic acid (dipicolinic acid, dipicH2), in water results in the formation of a proton transfer or charge transfer (CT) complex, (DPAH)+(dipicH)-·H2O, 1. The characterization was performed using 1H NMR and FTIR spectroscopy, elemental analysis and X-ray crystallography. The crystal system is triclinic with space group P1. The structural investigations exhibit that the hydrogen bonds and π-π stacking interactions stabilize the crystal structure of proton transfer complex. The protonation constants of 2,6-pyridine dicarboxylic acid, 2,2‧-dipyridylamine and the equilibrium constants for dipic-DPA (1:1) proton transfer system were calculated by potentiometric pH titration method using Hyperquad2008 program. The stoichiometries of the proton transfer species in solution was in agreement with the solid state result.

Crystal structure of acetanilide at 15 and 295 K by neutron diffraction. Lack of evidence for proton transfer along the N-H...O hydrogen bond

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, S.W.; Eckert, J.; Barthes, M.

1995-11-02

The crystal structure of acetanilide C{sub 8}H{sub 9}NO, M{sub r} = 135.17, orthorhombic, space group Pbca, Z=8, has been determined from neutron diffraction data at 15 and 295 K. The crystal data obtained are presented. This new investigation of the structure of acetanilide has been undertaken in order to assess a recent suggestion that confirmational substates in the amide proton position may be responsible for the vibrational anomalies. We found no evidence for multiple conformations or transfer along the N-H...O hydrogen bond of the amide proton at either temperature. However the intramolecular O...H6 distance from O to the nearest phenylmore » ring proton is unusually short and the amide proton has relatively close contacts with one of the phenyl and one of the methyl protons, which may well affect the vibrational parameters of the respective molecular groups. 44 refs., 6 figs., 5 tabs.« less

Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR

NASA Astrophysics Data System (ADS)

Lange, Adam; Giller, Karin; Hornig, Sönke; Martin-Eauclaire, Marie-France; Pongs, Olaf; Becker, Stefan; Baldus, Marc

2006-04-01

The active site of potassium (K+) channels catalyses the transport of K+ ions across the plasma membrane-similar to the catalytic function of the active site of an enzyme-and is inhibited by toxins from scorpion venom. On the basis of the conserved structures of K+ pore regions and scorpion toxins, detailed structures for the K+ channel-scorpion toxin binding interface have been proposed. In these models and in previous solution-state nuclear magnetic resonance (NMR) studies using detergent-solubilized membrane proteins, scorpion toxins were docked to the extracellular entrance of the K+ channel pore assuming rigid, preformed binding sites. Using high-resolution solid-state NMR spectroscopy, here we show that high-affinity binding of the scorpion toxin kaliotoxin to a chimaeric K+ channel (KcsA-Kv1.3) is associated with significant structural rearrangements in both molecules. Our approach involves a combined analysis of chemical shifts and proton-proton distances and demonstrates that solid-state NMR is a sensitive method for analysing the structure of a membrane protein-inhibitor complex. We propose that structural flexibility of the K+ channel and the toxin represents an important determinant for the high specificity of toxin-K+ channel interactions.

Hydrogen bonding and spin density distribution in the QB semiquinone of bacterial reaction centers and comparison with the QA site

PubMed Central

Martin, Erik; Samoilova, Rimma I.; Narasimhulu, Kupala V.; Lin, Tzu-Jen; O’Malley, Patrick J.; Wraight, Colin A.; Dikanov, Sergei A.

2011-01-01

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (QA) and secondary (QB) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the QA and QB sites, using samples of 15N-labeled reaction centers, with the native high spin Fe2+ exchanged for diamagnetic Zn2+, prepared in 1H2O and 2H2O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the QA SQ by Flores et al. (Biophys. J. 2007, 92, 671–682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6–5.4 MHz. HYSCORE was then applied to the QB SQ where we found proton lines corresponding to T~5.2, 3.7 MHz and T~1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the QB site, were used to assign the observed couplings to specific hydrogen bonding interactions with the QB SQ. These calculations allow us to assign the T=5.2 MHz proton to the His-L190 NδH…O4 (carbonyl) hydrogen bonding interaction. The T =3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the QB site show less asymmetric distribution of unpaired spin density over the SQ than seen for the QA site, consistent with available experimental data for 13C and 17O carbonyl hyperfine couplings. The implications of these interactions for QB function and comparisons with the QA site are discussed. PMID:21417328

A determination of the charm content of the proton: The NNPDF Collaboration.

PubMed

Ball, Richard D; Bertone, Valerio; Bonvini, Marco; Carrazza, Stefano; Forte, Stefano; Guffanti, Alberto; Hartland, Nathan P; Rojo, Juan; Rottoli, Luca

2016-01-01

We present an unbiased determination of the charm content of the proton, in which the charm parton distribution function (PDF) is parametrized on the same footing as the light quarks and the gluon in a global PDF analysis. This determination relies on the NLO calculation of deep-inelastic structure functions in the FONLL scheme, generalized to account for massive charm-initiated contributions. When the EMC charm structure function dataset is included, it is well described by the fit, and PDF uncertainties in the fitted charm PDF are significantly reduced. We then find that the fitted charm PDF vanishes within uncertainties at a scale [Formula: see text] GeV for all [Formula: see text], independent of the value of [Formula: see text] used in the coefficient functions. We also find some evidence that the charm PDF at large [Formula: see text] and low scales does not vanish, but rather has an "intrinsic" component, very weakly scale dependent and almost independent of the value of [Formula: see text], carrying less than [Formula: see text] of the total momentum of the proton. The uncertainties in all other PDFs are only slightly increased by the inclusion of fitted charm, while the dependence of these PDFs on [Formula: see text] is reduced. The increased stability with respect to [Formula: see text] persists at high scales and is the main implication of our results for LHC phenomenology. Our results show that if the EMC data are correct, then the usual approach in which charm is perturbatively generated leads to biased results for the charm PDF, though at small x this bias could be reabsorbed if the uncertainty due to the charm mass and missing higher orders were included. We show that LHC data for processes, such as high [Formula: see text] and large rapidity charm pair production and [Formula: see text] production, have the potential to confirm or disprove the implications of the EMC data.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Experimental observation of acoustic emissions generated by a pulsed proton beam from a hospital-based clinical cyclotron.

PubMed

Jones, Kevin C; Vander Stappen, François; Bawiec, Christopher R; Janssens, Guillaume; Lewin, Peter A; Prieels, Damien; Solberg, Timothy D; Sehgal, Chandra M; Avery, Stephen

2015-12-01

To measure the acoustic signal generated by a pulsed proton spill from a hospital-based clinical cyclotron. An electronic function generator modulated the IBA C230 isochronous cyclotron to create a pulsed proton beam. The acoustic emissions generated by the proton beam were measured in water using a hydrophone. The acoustic measurements were repeated with increasing proton current and increasing distance between detector and beam. The cyclotron generated proton spills with rise times of 18 μs and a maximum measured instantaneous proton current of 790 nA. Acoustic emissions generated by the proton energy deposition were measured to be on the order of mPa. The origin of the acoustic wave was identified as the proton beam based on the correlation between acoustic emission arrival time and distance between the hydrophone and proton beam. The acoustic frequency spectrum peaked at 10 kHz, and the acoustic pressure amplitude increased monotonically with increasing proton current. The authors report the first observation of acoustic emissions generated by a proton beam from a hospital-based clinical cyclotron. When modulated by an electronic function generator, the cyclotron is capable of creating proton spills with fast rise times (18 μs) and high instantaneous currents (790 nA). Measurements of the proton-generated acoustic emissions in a clinical setting may provide a method for in vivo proton range verification and patient monitoring.

Voltage-gated proton channel in a dinoflagellate

PubMed Central

Smith, Susan M. E.; Morgan, Deri; Musset, Boris; Cherny, Vladimir V.; Place, Allen R.; Hastings, J. Woodland; DeCoursey, Thomas E.

2011-01-01

Fogel and Hastings first hypothesized the existence of voltage-gated proton channels in 1972 in bioluminescent dinoflagellates, where they were thought to trigger the flash by activating luciferase. Proton channel genes were subsequently identified in human, mouse, and Ciona intestinalis, but their existence in dinoflagellates remained unconfirmed. We identified a candidate proton channel gene from a Karlodinium veneficum cDNA library based on homology with known proton channel genes. K. veneficum is a predatory, nonbioluminescent dinoflagellate that produces toxins responsible for fish kills worldwide. Patch clamp studies on the heterologously expressed gene confirm that it codes for a genuine voltage-gated proton channel, kHV1: it is proton-specific and activated by depolarization, its gH–V relationship shifts with changes in external or internal pH, and mutation of the selectivity filter (which we identify as Asp51) results in loss of proton-specific conduction. Indirect evidence suggests that kHV1 is monomeric, unlike other proton channels. Furthermore, kHV1 differs from all known proton channels in activating well negative to the Nernst potential for protons, EH. This unique voltage dependence makes the dinoflagellate proton channel ideally suited to mediate the proton influx postulated to trigger bioluminescence. In contrast to vertebrate proton channels, whose main function is acid extrusion, we propose that proton channels in dinoflagellates have fundamentally different functions of signaling and excitability. PMID:22006335

Atom redistribution and multilayer structure in NiTi shape memory alloy induced by high energy proton irradiation

NASA Astrophysics Data System (ADS)

Wang, Haizhen; Yi, Xiaoyang; Zhu, Yingying; Yin, Yongkui; Gao, Yuan; Cai, Wei; Gao, Zhiyong

2017-10-01

The element distribution and surface microstructure in NiTi shape memory alloys exposed to 3 MeV proton irradiation were investigated. Redistribution of the alloying element and a clearly visible multilayer structure consisting of three layers were observed on the surface of NiTi shape memory alloys after proton irradiation. The outermost layer consists primarily of a columnar-like TiH2 phase with a tetragonal structure, and the internal layer is primarily comprised of a bcc austenite phase. In addition, the Ti2Ni phase, with an fcc structure, serves as the transition layer between the outermost and internal layer. The above-mentioned phenomenon is attributed to the preferential sputtering of high energy protons and segregation induced by irradiation.

Gluon structure function of a color dipole in the light-cone limit of lattice QCD

NASA Astrophysics Data System (ADS)

Grünewald, D.; Ilgenfritz, E.-M.; Pirner, H. J.

2009-10-01

We calculate the gluon structure function of a color dipole in near-light-cone SU(2) lattice QCD as a function of xB. The quark and antiquark are external nondynamical degrees of freedom which act as sources of the gluon string configuration defining the dipole. We compute the color dipole matrix element of transversal chromo-electric and chromo-magnetic field operators separated along a direction close to the light cone, the Fourier transform of which is the gluon structure function. As vacuum state in the pure glue sector, we use a variational ground state of the near-light-cone Hamiltonian. We derive a recursion relation for the gluon structure function on the lattice similar to the perturbative Dokshitzer-Gribov-Lipatov-Altarelli-Parisi equation. It depends on the number of transversal links assembling the Schwinger string of the dipole. Fixing the mean momentum fraction of the gluons to the “experimental value” in a proton, we compare our gluon structure function for a dipole state with four links with the next-to-leading-order MRST 2002 and the CTEQ AB-0 parametrizations at Q2=1.5GeV2. Within the systematic uncertainty we find rather good agreement. We also discuss the low xB behavior of the gluon structure function in our model calculation.

Protonation-dependent conformational dynamics of the multidrug transporter EmrE

PubMed Central

Dastvan, Reza; Mishra, Smriti; Meiler, Jens; Mchaourab, Hassane S.

2016-01-01

The small multidrug transporter from Escherichia coli, EmrE, couples the energetically uphill extrusion of hydrophobic cations out of the cell to the transport of two protons down their electrochemical gradient. Although principal mechanistic elements of proton/substrate antiport have been described, the structural record is limited to the conformation of the substrate-bound state, which has been shown to undergo isoenergetic alternating access. A central but missing link in the structure/mechanism relationship is a description of the proton-bound state, which is an obligatory intermediate in the transport cycle. Here we report a systematic spin labeling and double electron electron resonance (DEER) study that uncovers the conformational changes of EmrE subsequent to protonation of critical acidic residues in the context of a global description of ligand-induced structural rearrangements. We find that protonation of E14 leads to extensive rotation and tilt of transmembrane helices 1–3 in conjunction with repacking of loops, conformational changes that alter the coordination of the bound substrate and modulate its access to the binding site from the lipid bilayer. The transport model that emerges from our data posits a proton-bound, but occluded, resting state. Substrate binding from the inner leaflet of the bilayer releases the protons and triggers alternating access between inward- and outward-facing conformations of the substrate-loaded transporter, thus enabling antiport without dissipation of the proton gradient. PMID:26787875

Six-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Yuewei; Gralla, Edith Butler; Schumacher, Mikhail

Reduction of superoxide (O{sub 2}{sup -}) by manganese-containing superoxide dismutase occurs through either a 'prompt protonation' pathway, or an 'inner-sphere' pathway, with the latter leading to formation of an observable Mn-peroxo complex. We recently reported that wild-type (WT) manganese superoxide dismutases (MnSODs) from Saccharomyces cerevisiae and Candida albicans are more gated toward the 'prompt protonation' pathway than human and bacterial MnSODs and suggested that this could result from small structural changes in the second coordination sphere of manganese. We report here that substitution of a second-sphere residue, Tyr34, by phenylalanine (Y34F) causes the MnSOD from S. cerevisiae to react exclusivelymore » through the 'inner-sphere' pathway. At neutral pH, we have a surprising observation that protonation of the Mn-peroxo complex in the mutant yeast enzyme occurs through a fast pathway, leading to a putative six-coordinate Mn3+ species, which actively oxidizes O{sub 2}{sup -} in the catalytic cycle. Upon increasing pH, the fast pathway is gradually replaced by a slow proton-transfer pathway, leading to the well-characterized five-coordinate Mn{sup 3+}. We here propose and compare two hypothetical mechanisms for the mutant yeast enzyme, diffeeing in the structure of the Mn-peroxo complex yet both involving formation of the active six-coordinate Mn{sup 3+} and proton transfer from a second-sphere water molecule, which has substituted for the -OH of Tyr34, to the Mn-peroxo complex. Because WT and the mutant yeast MnSOD both rest in the 2+ state and become six-coordinate when oxidized up from Mn{sup 2+}, six-coordinate Mn{sup 3+} species could also actively function in the mechanism of WT yeast MnSODs.« less

Detection analysis of surface hydroxyl active sites and simulation calculation of the surface dissociation constants of aqueous diatomite suspensions

NASA Astrophysics Data System (ADS)

Ma, Shu-Cui; Wang, Zhi-Gang; Zhang, Ji-Lin; Sun, De-Hui; Liu, Gui-Xia

2015-02-01

The surface properties of the diatomite were investigated using nitrogen adsorption/deadsorption isotherms, TG-DSC, FTIR, and XPS, and surface protonation-deprotonation behavior was determined by continuous acid-base potentiometric titration technique. The diatomite sample with porous honeycomb structure has a BET specific surface area of 10.21 m2/g and large numbers of surface hydroxyl functional groups (i.e. tbnd Si-OH, tbnd Fe-OH, and tbnd Al-OH). These surface hydroxyls can be protonated or deprotonated depending on the pH of the suspension. The experimental potentiometric data in two different ionic strength solutions (0.1 and 0.05 mol/L NaCl) were fitted using ProtoFit GUI V2.1 program by applying diffuse double layer model (DLM) with three amphoteric sites and minimizing the sum of squares between a dataset derivative function and a model derivative function. The optimized surface parameters (i.e. surface dissociation constants (log K1, log K2) and surface site concentrations (log C)) of the sample were obtained. Based on the optimized surface parameters, the surface species distribution was calculated using Program-free PHREEQC 3.1.2. Thus, this work reveals considerable new information about surface protonation-deprotonation processes and surface adsorptive behaviors of the diatomite, which helps us to effectively use the cheap and cheerful diatomite clay adsorbent.

Differences in the phenotypic effects of mutations in homologous MrpA and MrpD subunits of the multi-subunit Mrp-type Na+/H+ antiporter.

PubMed

Morino, Masato; Ogoda, Shinichiro; Krulwich, Terry Ann; Ito, Masahiro

2017-01-01

Mrp antiporters are the sole antiporters in the Cation/Proton Antiporter 3 family of transporter databases because of their unusual structural complexity, 6-7 hydrophobic proteins that function as a hetero-oligomeric complex. The two largest and homologous subunits, MrpA and MrpD, are essential for antiport activity and have direct roles in ion transport. They also show striking homology with proton-conducting, membrane-embedded Nuo subunits of respiratory chain complex I of bacteria, e.g., Escherichia coli. MrpA has the closest homology to the complex I NuoL subunit and MrpD has the closest homology to the complex I NuoM and N subunits. Here, introduction of mutations in MrpD, in residues that are also present in MrpA, led to defects in antiport function and/or complex formation. No significant phenotypes were detected in strains with mutations in corresponding residues of MrpA, but site-directed changes in the C-terminal region of MrpA had profound effects, showing that the MrpA C-terminal region has indispensable roles in antiport function. The results are consistent with a divergence in adaptations that support the roles of MrpA and MrpD in secondary antiport, as compared to later adaptations supporting homologs in primary proton pumping by the respiratory chain complex I.

Uridine Nucleoside Thiation: Gas-Phase Structures and Energetics

NASA Astrophysics Data System (ADS)

Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

2016-06-01

The naturally occurring thiated uridine nucleosides, 4-thiouridine (s4Urd) and 2-thiouridine (s2Urd), play important roles in the function and analysis of a variety of RNAs. 2-Thiouridine and its C5 modified analogues are commonly found in tRNAs and are believed to play an important role in codon recognition possibly due to their different structure, which has been shown by NMR to be predominantly C3'-endo. 2-Thiouridine may also play an important role in facilitating nonenzymatic RNA replication and transcription. 4-Thiouridine is a commonly used photoactivatable crosslinker that is often used to study RNA-RNA and RNA-protein cross-linking behavior. Differences in the base pairing between uracil and 4-thiouracil with adenine and guanine are an important factor in their role as a cross linker. The photoactivity of s4Urd may also aid in preventing near-UV lethality in cells. An understanding of their intrinsic structure in the gas-phase may help further elucidate the roles these modified nucleosides play in the regulation of RNAs. In this work, infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of s2Urd and s4Urd were collected in the IR fingerprint region. Structural information is determined by comparison with theoretical linear IR spectra generated from density functional theory calculations using molecular modeling to generate low-energy candidate structures. Present results are compared with analogous results for the protonated forms of uridine and 2'-deoxyuridine as well as solution phase NMR data and crystal structures.

Protonic transport through solitons in hydrogen-bonded systems

NASA Astrophysics Data System (ADS)

Kavitha, L.; Jayanthi, S.; Muniyappan, A.; Gopi, D.

2011-09-01

We offer an alternative route for investigating soliton solutions in hydrogen-bonded (HB) chains. We invoke the modified extended tangent hyperbolic function method coupled with symbolic computation to solve the governing equation of motion for proton dynamics. We investigate the dynamics of proton transfer in HB chains through bell-shaped soliton excitations, which trigger the bio-energy transport in most biological systems. This solitonic mechanism of proton transfer could play functional roles in muscular contraction, enzymatic activity and oxidative phosphorylation.

Spin-isospin excitation of 3He with three-proton final state

NASA Astrophysics Data System (ADS)

Ishikawa, Souichi

2018-01-01

Spin-isospin excitation of the {}^3He nucleus by a proton-induced charge exchange reaction, {}^3He(p,n)ppp, at forward neutron scattering angle is studied in a plane wave impulse approximation (PWIA). In PWIA, cross sections of the reaction are written in terms of proton-neutron scattering amplitudes and response functions of the transition from {}3He to the three-proton state by spin-isospin transition operators. The response functions are calculated with realistic nucleon-nucleon potential models using a Faddeev three-body method. Calculated cross sections agree with available experimental data in substance. Possible effects arising from the uncertainty of proton-neutron amplitudes and three-nucleon interactions in the three-proton system are examined.

Molecular Simulations in Astrobiology

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.; Schweighofer, Karl; Chipot, Christophe; New, Michael H.

2000-01-01

One of the main goals of astrobiology is to understand the origin of cellular life. The most direct approach to this problem is to construct laboratory models of protocells. Such efforts, currently underway in the NASA Astrobiology Program, are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures that are capable of performing protocellular functions. Many of these functions, such as importing nutrients, capturing energy and responding to changes in the environment, are carried out by proteins bound to membranes. We use computer simulations to address the following questions about these proteins: (1) How do small proteins self-organize into ordered structures at water-membrane interfaces and insert into membranes? (2) How do peptides form membrane-spanning structures (e.g. channels)? (3) By what mechanisms do such structures perform their functions? The simulations are performed using the molecular dynamics method. In this method, Newton's equations of motion for each atom in the system are solved iteratively. At each time step, the forces exerted on each atom by the remaining atoms are evaluated by dividing them into two parts. Short-range forces are calculated in real space while long-range forces are evaluated in reciprocal space, using a particle-mesh algorithm which is of order O(NInN). With a time step of 2 femtoseconds, problems occurring on multi-nanosecond time scales (10(exp 6)-10(exp 8) time steps) are accessible. To address a broader range of problems, simulations need to be extended by three orders of magnitude, which requires algorithmic improvements and codes scalable to a large number of processors. Work in this direction is in progress. Two series of simulations are discussed. In one series, it is shown that nonpolar peptides, disordered in water, translocate to the nonpolar interior of the membrane and fold into helical structures (see Figure). Once in the membrane, the peptides exhibit orientational flexibility with changing conditions, which may have provided a mechanism of transmitting signals between the protocell and its environment. In another series of simulations, the mechanism by which a simple protein channel efficiently mediates proton transport across membranes was investigated. This process is a key step in cellular bioenergetics. In the channel under study, proton transport is gated by four histidines that occlude the channel pore. The simulations identify the mechanisms by which protons move through the gate.

The F-ATPase operon from the oral streptococci S. mutans and S. sanguis: How structure relates to function

NASA Astrophysics Data System (ADS)

Kuhnert, Wendi Lee

1999-10-01

The oral microbe, Streptococcus mutans is known to be a primary contributor to the most common infection in humans, dental caries. In the plaque environment, resident bacteria metabolize dietary sucrose which results in the production of organic acids and a decrease in plaque pH. The proton-translocating ATPase (F-ATPase) protects the bacteria from acidification by extruding protons, at the expense of ATP, to maintain an internal pH which is more neutral than the external environment. Examination of this enzyme will help us to gain insight regarding its contribution to the aciduricity characteristics of oral bacteria. In this work, our goal was to begin the molecular dissection of the mechanism by which streptococcal ATPases are regulated and function enzymatically. Sequence analysis of the F-ATPase from the non-pathogenic S. sanguis revealed that the structural genes are homologous to S. mutans as well as other sequenced F-ATPases. Cloned subunits were functionally similar as shown by complementing E. coli ATPase mutants. S. sanguis/E. coli hybrid enzymes hydrolyzed ATP, but proton conduction was uncoupled as demonstrated with inhibition studies. Transcriptional regulation of the F-ATPase operon from S. mutans was examined using chloramphenicol acetyltransferase gene fusions. Fusions containing 136 bp of DNA upstream of the promoter showed higher levels of expression as compared to those with only 16 bp. Similar to ATPase enzymatic activity, CAT expression also increased during growth at low pH. Analysis of RNA demonstrated that ATPase mRNA levels were higher at low pH, which supported the CAT activity data. Therefore, the F-ATPase from S. mutans was regulated, at least partially, by both the DNA located upstream of the promoter as well as by pH. Examination of structural models of the F-ATPase from the pathogenic oral organisms S. mutans and Lactobacillus casei and the non- pathogenic S. sanguis showed that the differences noted in the sequence of the catalytic β subunit do not result in structural alterations. Therefore, the contribution that the F-ATPase makes towards the aciduricity of the oral streptococci is linked to its increased expression at low pH or perhaps to structural differences in the other, less-conserved, domains of the enzyme.

The General Base in the Thymidylate Synthase Catalyzed Proton Abstraction

PubMed Central

Ghosh, Ananda K.; Islam, Zahidul; Krueger, Jonathan; Abeysinghe, Don Thelma; Kohen, Amnon

2015-01-01

The enzyme thymidylate synthase (TSase), an important chemotherapeutic drug target, catalyzes the formation of 2′-deoxythymidine-5′-monophosphate (dTMP), a precursor of one of the DNA building blocks. TSase catalyzes a multi-step mechanism that includes the abstraction of a proton from the C5 of the substrate 2′-deoxyuridine-5′-monophosphate (dUMP). Previous studies on ecTSase proposed that an active-site residue, Y94 serves the role of the general base abstracting this proton. However, since Y94 is neither very basic, nor connected to basic residues, nor located close enough to the pyrimidine proton to be abstracted, the actual identity of this base remains enigmatic. Based on crystal structures, an alternative hypothesis is that the nearest potential proton-acceptor of C5 of dUMP is a water molecule that is part of a hydrogen bond (H-bond) network comprised of several water molecules and several protein residues including H147, E58, N177, and Y94. Here, we examine the role of the residue Y94 in the proton abstraction step by removing its hydroxyl group (Y94F mutant). We investigated the effect of the mutation on the temperature dependence of intrinsic kinetic isotope effects (KIEs) and found that these KIEs are more temperature dependent than those of the wild-type enzyme (WT). These results suggest that the phenolic –OH of Y94 is a component of the transition state for the proton abstraction step. The findings further support the hypothesis that no single functional group is the general base, but a network of bases and hydroxyls (from water molecules and tyrosine) sharing H-bonds across the active site can serve the role of the general base to remove the pyrimidine proton. PMID:25912171

A Two-Fluid, MHD Coronal Model

NASA Technical Reports Server (NTRS)

Suess, Steven T.; Wang, A.-H.; Wu, S. T.; Poletto, G.; McComas, D. J.

1998-01-01

We describe first results from a numerical two-fluid MHD model of the global structure of the solar corona. The model is two-fluid in the sense that it accounts for the collisional energy exchange between protons and electrons. As in our single-fluid model, volumetric heat and momentum sources are required to produce high speed wind from coronal holes, low speed wind above streamers, and mass fluxes similar to the empirical solar wind. By specifying different proton and electron heating functions we obtain a high proton temperature in the coronal hole and a relatively low proton temperature in the streamer (in comparison with the electron temperature). This is consistent with inferences from SOHO/UVCS, and with the Ulysses/SWOOPS proton and electron temperature measurements which we show from the fast latitude scan. The density in the coronal hole between 2 solar radii and 5 solar radii (2RS and 5RS) is similar to the density reported from SPARTAN 201-01 measurements by Fisher and Guhathakurta. The proton mass flux scaled to 1 AU is 2.4 x 10(exp 8)/sq cm s, which is consistent with Ulysses observations. Inside the closed field region, the density is sufficiently high so that the simulation gives equal proton and electron temperatures due to the high collision rate. In open field regions (in the coronal hole and above the streamer) the proton and electron temperatures differ by varying amounts. In the streamer, the temperature and density are similar to those reported empirically by Li et al and the plasma beta is larger than unity everywhere above approx. 1.5 R(sub s), as it is in all other MHD coronal streamer models.

Decoding the spectroscopic features and time scales of aqueous proton defects

NASA Astrophysics Data System (ADS)

Napoli, Joseph A.; Marsalek, Ondrej; Markland, Thomas E.

2018-06-01

Acid solutions exhibit a variety of complex structural and dynamical features arising from the presence of multiple interacting reactive proton defects and counterions. However, disentangling the transient structural motifs of proton defects in the water hydrogen bond network and the mechanisms for their interconversion remains a formidable challenge. Here, we use simulations treating the quantum nature of both the electrons and nuclei to show how the experimentally observed spectroscopic features and relaxation time scales can be elucidated using a physically transparent coordinate that encodes the overall asymmetry of the solvation environment of the proton defect. We demonstrate that this coordinate can be used both to discriminate the extremities of the features observed in the linear vibrational spectrum and to explain the molecular motions that give rise to the interconversion time scales observed in recent nonlinear experiments. This analysis provides a unified condensed-phase picture of the proton structure and dynamics that, at its extrema, encompasses proton sharing and spectroscopic features resembling the limiting Eigen [H3O(H2O)3]+ and Zundel [H(H2O)2]+ gas-phase structures, while also describing the rich variety of interconverting environments in the liquid phase.

Is nucleon spin structure inconsistent with the constituent quark model?

NASA Astrophysics Data System (ADS)

Qing, Di; Chen, Xiang-Song; Wang, Fan

1998-12-01

Proton spin structure discovered in polarized deep inelastic scattering is shown to be consistent with the valence-sea quark mixing constituent quark model. The relativistic correction and quark-antiquark pair creation (annihilation) terms inherently involved in the quark axial vector current suppress the quark spin contribution to the proton spin. The relativistic quark orbital angular momentum provides compensative terms to keep the proton spin 12 untouched. The tensor charge of the proton is predicted to have a similar but smaller suppression. An explanation on why baryon magnetic moments can be parametrized by the naive quark model spin content as well as the spin structure discovered in polarized deep inelastic scattering is given.

Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases.

PubMed

Zhou, Wenchang; Leone, Vanessa; Krah, Alexander; Faraldo-Gómez, José D

2017-04-20

Recent years have witnessed a renewed interest in the ATP synthase as a drug target against human pathogens. Indeed, clinical, biochemical, and structural data indicate that hydrophobic inhibitors targeting the membrane-embedded proton-binding sites of the c-subunit ring could serve as last-resort antibiotics against multidrug resistant strains. However, because inhibition of the mitochondrial ATP synthase in humans is lethal, it is essential that these inhibitors be not only potent but also highly selective for the bacterial enzyme. To this end, a detailed understanding of the structure of this protein target is arguably instrumental. Here, we use computational methods to predict the atomic structures of the proton-binding sites in two prototypical c-rings: that of the ATP synthase from Saccharomyces cerevisiae, which is a model system for mitochondrial enzymes, and that from Escherichia coli, which can be pathogenic for humans. Our study reveals the structure of these binding sites loaded with protons and in the context of the membrane, that is, in the state that would mediate the recognition of a potential inhibitor. Both structures reflect a mode of proton coordination unlike those previously observed in other c-ring structures, whether experimental or modeled.

Proton clouds to measure long-range contacts between nonexchangeable side chain protons in solid-state NMR.

PubMed

Sinnige, Tessa; Daniëls, Mark; Baldus, Marc; Weingarth, Markus

2014-03-26

We show that selective labeling of proteins with protonated amino acids embedded in a perdeuterated matrix, dubbed 'proton clouds', provides general access to long-range contacts between nonexchangeable side chain protons in proton-detected solid-state NMR, which is important to study protein tertiary structure. Proton-cloud labeling significantly improves spectral resolution by simultaneously reducing proton line width and spectral crowding despite a high local proton density in clouds. The approach is amenable to almost all canonical amino acids. Our method is demonstrated on ubiquitin and the β-barrel membrane protein BamA.

Ocean acidification affects marine chemical communication by changing structure and function of peptide signalling molecules.

PubMed

Roggatz, Christina C; Lorch, Mark; Hardege, Jörg D; Benoit, David M

2016-12-01

Ocean acidification is a global challenge that faces marine organisms in the near future with a predicted rapid drop in pH of up to 0.4 units by the end of this century. Effects of the change in ocean carbon chemistry and pH on the development, growth and fitness of marine animals are well documented. Recent evidence also suggests that a range of chemically mediated behaviours and interactions in marine fish and invertebrates will be affected. Marine animals use chemical cues, for example, to detect predators, for settlement, homing and reproduction. But, while effects of high CO 2 conditions on these behaviours are described across many species, little is known about the underlying mechanisms, particularly in invertebrates. Here, we investigate the direct influence of future oceanic pH conditions on the structure and function of three peptide signalling molecules with an interdisciplinary combination of methods. NMR spectroscopy and quantum chemical calculations were used to assess the direct molecular influence of pH on the peptide cues, and we tested the functionality of the cues in different pH conditions using behavioural bioassays with shore crabs (Carcinus maenas) as a model system. We found that peptide signalling cues are susceptible to protonation in future pH conditions, which will alter their overall charge. We also show that structure and electrostatic properties important for receptor binding differ significantly between the peptide forms present today and the protonated signalling peptides likely to be dominating in future oceans. The bioassays suggest an impaired functionality of the signalling peptides at low pH. Physiological changes due to high CO 2 conditions were found to play a less significant role in influencing the investigated behaviour. From our results, we conclude that the change of charge, structure and consequently function of signalling molecules presents one possible mechanism to explain altered behaviour under future oceanic pH conditions. © 2016 John Wiley & Sons Ltd.

Insight into proton transfer in phosphotungstic acid functionalized mesoporous silica-based proton exchange membrane fuel cells.

PubMed

Zhou, Yuhua; Yang, Jing; Su, Haibin; Zeng, Jie; Jiang, San Ping; Goddard, William A

2014-04-02

We have developed for fuel cells a novel proton exchange membrane (PEM) using inorganic phosphotungstic acid (HPW) as proton carrier and mesoporous silica as matrix (HPW-meso-silica) . The proton conductivity measured by electrochemical impedance spectroscopy is 0.11 S cm(-1) at 90 °C and 100% relative humidity (RH) with a low activation energy of ∼14 kJ mol(-1). In order to determine the energetics associated with proton migration within the HPW-meso-silica PEM and to determine the mechanism of proton hopping, we report density functional theory (DFT) calculations using the generalized gradient approximation (GGA). These DFT calculations revealed that the proton transfer process involves both intramolecular and intermolecular proton transfer pathways. When the adjacent HPWs are close (less than 17.0 Å apart), the calculated activation energy for intramolecular proton transfer within a HPW molecule is higher (29.1-18.8 kJ/mol) than the barrier for intermolecular proton transfer along the hydrogen bond. We find that the overall barrier for proton movement within the HPW-meso-silica membranes is determined by the intramolecular proton transfer pathway, which explains why the proton conductivity remains unchanged when the weight percentage of HPW on meso-silica is above 67 wt %. In contrast, the activation energy of proton transfer on a clean SiO2 (111) surface is computed to be as high as ∼40 kJ mol(-1), confirming the very low proton conductivity on clean silica surfaces observed experimentally.

Contributions of the Histidine Side Chain and the N-terminal α-Amino Group to the Binding Thermodynamics of Oligopeptides to Nucleic Acids as a Function of pH

PubMed Central

Ballin, Jeff D.; Prevas, James P.; Ross, Christina R.; Toth, Eric A.; Wilson, Gerald M.; Record, M. Thomas

2010-01-01

Interactions of histidine with nucleic acid phosphates and histidine pKa shifts make important contributions to many protein-nucleic acid binding processes. To characterize these phenomena in simplified systems, we quantified binding of a histidine-containing model peptide HWKK (+NH3-His-Trp-Lys-Lys-NH2) and its lysine analog KWKK (+NH3-Lys-Trp-Lys-Lys-NH2) to a single-stranded RNA model, polyuridylate (polyU), by changes in tryptophan fluorescence as a function of salt concentration and pH. For both HWKK and KWKK, equilibrium binding constants, Kobs, and magnitudes of log-log salt derivatives SKobs ≡ (∂logKobs/∂log[Na+]), decreased with increasing pH in the manner expected for a titration curve model in which deprotonation of the histidine and α-amino groups weakens binding and reduces its salt-dependence. Fully protonated HWKK and KWKK exhibit the same Kobs and SKobs within uncertainty, and these SKobs values are consistent with limiting-law polyelectrolyte theory for +4 cationic oligopeptides binding to single-stranded nucleic acids. The pH-dependence of HWKK binding to polyU provides no evidence for pKa shifts nor any requirement for histidine protonation, in stark contrast to the thermodynamics of coupled protonation often seen for these cationic residues in the context of native protein structure where histidine protonation satisfies specific interactions (e.g., salt-bridge formation) within highly complementary binding interfaces. The absence of pKa shifts in our studies indicates that additional Coulombic interactions across the nonspecific-binding interface between RNA and protonated histidine or the α-amino group are not sufficient to promote proton uptake for these oligopeptides. We present our findings in the context of hydration models for specific versus nonspecific nucleic acid binding. PMID:20108951

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

PubMed

Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

2017-08-03

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

Role of transmembrane segment 5 of the plant vacuolar H+-pyrophosphatase.

PubMed

Van, Ru C; Pan, Yih J; Hsu, Shen H; Huang, Yun T; Hsiao, Yi Y; Pan, Rong L

2005-08-15

Vacuolar H+-translocating inorganic pyrophosphatase (V-PPase; EC 3.6.1.1) is a homodimeric proton translocase consisting of a single type of polypeptide with a molecular mass of approximately 81 kDa. Topological analysis tentatively predicts that mung bean V-PPase contains 14 transmembrane domains. Alignment analysis of V-PPase demonstrated that the transmembrane domain 5 (TM5) of the enzyme is highly conserved in plants and located at the N-terminal side of the putative substrate-binding loop. The hydropathic analysis of V-PPase showed a relatively lower degree of hydrophobicity in the TM5 region as compared to other domains. Accordingly, it appears that TM5 is probably involved in the proton translocation of V-PPase. In this study, we used site-directed mutagenesis to examine the functional role of amino acid residues in TM5 of V-PPase. A series of mutants singly replaced by alanine residues along TM5 were constructed and over-expressed in Saccharomyces cerevisiae; they were then used to determine their enzymatic activities and proton translocations. Our results indicate that several mutants displayed minor variations in enzymatic properties, while others including those mutated at E225, a GYG motif (residues from 229 to 231), A238, and R242, showed a serious decline in enzymatic activity, proton translocation, and coupling efficiency of V-PPase. Moreover, the mutation at Y230 relieved several cation effects on the V-PPase. The GYG motif presumably plays a significant role in maintaining structure and function of V-PPase.

Evidence from in Situ X-ray Absorption Spectroscopy for the Involvement of Terminal Disulfide in the Reduction of Protons by an Amorphous Molybdenum Sulfide Electrocatalyst

DOE PAGES

Lassalle-Kaiser, Benedikt; Merki, Daniel; Vrubel, Heron; ...

2015-11-26

The reduction of protons into dihydrogen is important because of its potential use in a wide range of energy applications. The preparation of efficient and cheap catalysts for this reaction is one of the issues that need to be tackled to allow the widespread use of hydrogen as an energy carrier. In this paper, we report the study of an amorphous molybdenum sulfide (MoS x) proton reducing electrocatalyst under functional conditions, using in situ X-ray absorption spectroscopy. We probed the local and electronic structures of both the molybdenum and sulfur elements for the as prepared material as well as themore » precatalytic and catalytic states. The as prepared material is very similar to MoS 3 and remains unmodified under functional conditions (pH = 2 aqueous HNO 3) in the precatalytic state (+0.3 V vs RHE). In its catalytic state (-0.3 V vs RHE), the film is reduced to an amorphous form of MoS 2 and shows spectroscopic features that indicate the presence of terminal disulfide units. These units are formed concomitantly with the release of hydrogen, and we suggest that the rate-limiting step of the HER is the reduction and protonation of these disulfide units. In conclusion, these results show the implication of terminal disulfide chemical motifs into HER driven by transition-metal sulfides and provide insight into their reaction mechanism.« less

The photon content of the proton

NASA Astrophysics Data System (ADS)

Manohar, Aneesh V.; Nason, Paolo; Salam, Gavin P.; Zanderighi, Giulia

2017-12-01

The photon PDF of the proton is needed for precision comparisons of LHC cross sections with theoretical predictions. In a recent paper, we showed how the photon PDF could be determined in terms of the electromagnetic proton structure functions F 2 and F L measured in electron-proton scattering experiments, and gave an explicit formula for the PDF including all terms up to next-to-leading order. In this paper we give details of the derivation. We obtain the photon PDF using the factorisation theorem and applying it to suitable BSM hard scattering processes. We also obtain the same PDF in a process-independent manner using the usual definition of PDFs in terms of light-cone Fourier transforms of products of operators. We show how our method gives an exact representation for the photon PDF in terms of F 2 and F L , valid to all orders in QED and QCD, and including all non-perturbative corrections. This representation is then used to give an explicit formula for the photon PDF to one order higher than our previous result. We also generalise our results to obtain formulæ for the polarised photon PDF, as well as the photon TMDPDF. Using our formula, we derive the P γ i subset of DGLAP splitting functions to order αα s and α 2, which agree with known results. We give a detailed explanation of the approach that we follow to determine a photon PDF and its uncertainty within the above framework.

Interaction of water with (silico)aluminophosphate zeotypes: a comparative investigation using dispersion-corrected DFT.

PubMed

Fischer, Michael

2016-06-21

Porous aluminophosphates (AlPOs) and silicoaluminophosphates (SAPOs) with zeolite-like structures have received considerable attention as potential adsorbents for heat transformation applications using water adsorption/desorption cycles. Since a detailed experimental characterisation of the water adsorption properties has only been performed for some of these materials, such as AlPO-18 (AEI topology) and SAPO-34 (CHA topology), more systematic insights regarding the influence of the pore topology and (for SAPOs) the arrangement of the framework protons on the affinity towards water are lacking. To study the relationships between structure and properties in more detail, the interaction of water with six structurally different AlPOs (with AEI, AFX, CHA, ERI, GIS, RHO topologies) and their SAPO analogues was investigated using dispersion-corrected density-functional theory (DFT-D) calculations. Different possible locations of silicon atoms and charge-balancing protons were considered for the SAPO systems. The calculations for SAPOs at low water loadings (one H2O molecule per framework proton) revealed that the interaction energies exhibit a considerable variation, ranging from -75 to -100 kJ mol(-1) (per water molecule). The differences in interaction energy were rationalised with the different structural environment of the framework protons at which the water molecules are adsorbed. At high water uptakes (near saturation), interaction energies in the range of -65 kJ mol(-1) were obtained for all AlPOs, and there was no evidence for a marked influence of pore size and/or topology on the interaction strength. The interaction of water with SAPOs was found to be approximately 5 kJ mol(-1) stronger than for AlPOs due to an increased contribution of electrostatic interactions. An analysis of the structural changes upon water adsorption revealed striking differences between the distinct topologies, with the materials with GIS and RHO topologies being distorted much more drastically than the systems based on double six-ring (d6r) units. Moreover, the direct coordination of water molecules to framework aluminium atoms occurs more frequently in these materials, an observation that points towards a reduced structural stability upon hydration.

Proton affinity determinations and proton-bound dimer structure indications in C2 to C15, (alpha),(omega)-alkyldiamines

NASA Technical Reports Server (NTRS)

Karpas, Z.; Harden, C. S.; Smith, P. B. W.

1995-01-01

The 'kinetic method' was used to determine the proton affinity (PA) of a,coalkyldiamines from collision induced dissociation (CID) studies of protonated heterodimers. These PA values were consistently lower than those reported in the proton affinity scale. The apparent discrepancy was rationalized in terms of differences in the conformation of the protonated diamine monomers. The minimum energy species, formed by equilibrium proton transfer processes, have a cyclic conformation and the ion charge is shared by both amino-groups which are bridged by the proton. On the other hand, the species formed through dissociation of protonated dimers have a linear structure and the charge is localized on one of the amino-groups. Thus, the difference in the PA values obtained by both methods is a measure of the additional stability acquired by the protonated diamines through cyclization and charge delocalization. The major collision dissociation pathway of the protonated diamine monomers involved elimination of an ammonia moiety. Other reactions observed included loss of the second amino-group and several other bond cleavages. CID of the protonated dimers involved primarily formation of a protonated monomer through cleavage of the weaker hydrogen bond and subsequently loss of ammonia at higher collision energies. As observed from the CID studies, doubly charged ions were also formed from the diamines under conditions of the electrospray ionization.

Optimal Control-Enabled Imaging and Spectroscopy using a Nanowire Magnetic Resonance Force Microscope

NASA Astrophysics Data System (ADS)

Rose, William; Haas, Holger; Chen, Angela; Cory, David; Budakian, Raffi

Magnetic resonance imaging (MRI) is a powerful non-invasive technique that has transformed our ability to study the structure and function of biological systems. Key to its success has been the unique ability to combine imaging with magnetic resonance spectroscopy. Although it remains a significant challenge, there is considerable interest in extending MRI spectroscopy to the nanometer scale because it would provide a fundamentally new route for determining the structure and function of complex biomolecules. We present data taken with a nanowire magnetic resonance force microscopy (MRFM) setup. We show how the capabilities of this very sensitive spin-detection system can be extended to include spectroscopy and nanometer-scale imaging by combining optimal control theory (OCT) techniques with magic echo sequences. We apply OCT-based dynamical-decoupling pulses to nanoscale ensembles of proton spins in polystyrene, and demonstrate a 500-fold line-narrowing of the proton spin resonance, from 30 kHz to 60 Hz. We further demonstrate 1-D imaging over a 35-nm region with an average voxel size of 2.2 nm. Funding provided by the U.S. Army Research Office, Grant No. W911NF-12-1-0341.

A Precision Measurement of the Spin Structure Function g{sub 1}(x,Q{sup 2}) for the Proton and Deuteron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, Gregory

A precision measurement of the spin structure function g{sub 1}(x,Q{sup 2}) for both the proton and deuteron was made using deep inelastic scattering of the 48.35 GeV polarized electron beam at the Stanford Linear Accelerator Center. The kinematic range of the measurement was 0.014 < x < 0.9 and 1 (GeV/c){sup 2} < Q{sup 2} < 40 (GeV/c){sup 2}. Solid {sup 15}NH{sub 3} and {sup 6}Li{sup 2}H were used as target materials. The beam polarization of 0.81 {+-} 0.02 was measured using Moeller polarimetry. The scattered electron events were accumulated in three magnetic spectrometers at fixed angles of 2.75{sup o},more » 5.5{sup o}, and 10.5{sup o}. Data were obtained with the target polarization direction both parallel and transverse to the beam direction. Together with existing world data, the g{sub 1}(x,Q{sup 2}) results were fit in a well-established next-to-leading order QCD formalism, and are consistent with the Bjorken sum rule.« less

Selective heteronuclear Hartmann-Hahn: A multiple-pulse sequence for selective magnetization transfer in the structural elucidation of “isotagged” oligosaccharides

NASA Astrophysics Data System (ADS)

Meng, Xi; Nguyen, William H.; Nowick, James S.; Shaka, A. J.

2010-03-01

A new selective heteronuclear Hartmann-Hahn (SHEHAHA) multiple-pulse mixing sequence is proposed for the solution structure elucidation of milligram amounts of peracetylated oligosaccharides in which the acetyl groups are enriched in carbon-13, so-called “isotags”. SHEHAHA accomplishes exclusive in-phase magnetization transfer between the isotag carbonyl 13C and the proximal proton on the sugar ring. Relayed transfer around the sugar rings by proton-proton TOCSY is suppressed, while the heteronuclear transfer from the labeled carbonyl carbon to the proximal ring proton is maintained. The sequence is broadband in the sense that all acetyl groups simultaneously give good signal transfer to their respective nearest proton neighbors. The 1H-detected spectra have decent sensitivity and excellent resolution, giving patterns that unambiguously identify common structural subunits in human glycans. Peracetylated maltitol is shown as a test case of the method. Lineshapes are pure absorption, allowing facile measurement of vicinal proton-proton couplings. Linkage points can be deduced, and the 2D correlation spectra may be useful for more ambitious prediction algorithms and machine identification by a spectral database.

Shrink-wrapping water to conduct protons

NASA Astrophysics Data System (ADS)

Shimizu, George K. H.

2017-11-01

For proton-conducting metal-organic frameworks (MOFs) to find application as the electrolyte in proton-exchange membrane fuel cells, materials with better stability and conductivity are required. Now, a structurally flexible MOF that is also highly stable is demonstrated to possess high proton conductivity over a range of humidities.

Low-temperature nanodoping of protonated LiNbO3 crystals by univalent ions

NASA Astrophysics Data System (ADS)

Borodin, Yu. V.

2015-01-01

In the nanocomposite model developed here, crystals are treated as subordinate aggregate of pro- ton-selected structural elements, their blocks, and proton-containing quantum sublattices with preferred transport effects separating them. The formation of stratified reversible hexagonal structures is accompanied with protonation and formation of a dense network of H-bonds ensuring the nanocomposite properties. Nanodoping with H+ ions occurs during processing of crystals and glasses in melts as well as in aqueous solutions of Ag, Tl, Rb, and Cs salts. The isotope exchange H+ ↔ D+ and ion exchange H+ ↔ M+ lead to nanodoping of protonated materials with D+ and M+ ions. This is manifested especially clearly in Li-depleted nonequilibrium LiNbO3 and LiTaO3 crystals. Low-temperature proton-ion nanodoping over superlattices is a basically new approach to analysis of the structure and properties of extremely nonequilibrium materials.

Proton transfer in the K-channel analog of B-type Cytochrome c oxidase from Thermus thermophilus.

PubMed

Woelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-Walter

2014-11-04

A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers.

Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilus

PubMed Central

Woelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-Walter

2014-01-01

A key enzyme in aerobic metabolism is cytochrome c oxidase (CcO), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. Substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. The well-studied A-type CcO uses two different entry channels for protons: the D-channel for all pumped and two consumed protons, and the K-channel for the other two consumed protons. In contrast, the B-type CcO uses only a single proton input channel for all consumed and pumped protons. It has the same location as the A-type K-channel (and thus is named the K-channel analog) without sharing any significant sequence homology. In this study, we performed molecular-dynamics simulations and electrostatic calculations to characterize the K-channel analog in terms of its energetic requirements and functionalities. The function of Glu-15B as a proton sink at the channel entrance is demonstrated by its rotational movement out of the channel when it is deprotonated and by its high pKA value when it points inside the channel. Tyr-244 in the middle of the channel is identified as the valve that ensures unidirectional proton transfer, as it moves inside the hydrogen-bond gap of the K-channel analog only while being deprotonated. The electrostatic energy landscape was calculated for all proton-transfer steps in the K-channel analog, which functions via proton-hole transfer. Overall, the K-channel analog has a very stable geometry without large energy barriers. PMID:25418102

Roles of Chemical Functionality and Pore Curvature in the Design of Nanoporous Proton Conductors

DOE PAGES

Jackson, Grayson L.; Perroni, Dominic V.; Mahanthappa, Mahesh K.

2017-10-03

Nanoporous proton-transporting media are critical components in fuel cells and other electrochemical devices, yet general molecular design criteria for new materials with enhanced performance remain obscure. Aqueous lyotropic liquid crystals (LLCs) comprise a platform for detailed studies of the molecular-level features governing proton transport in monodisperse, water-filled nanopores lined with well-defined chemical functionalities. Here, we report new alkylsulfonic acid LLCs that exhibit H+ conductivities as high as σ = 380 mS/cm at 80°C, which rival those of more acidic, perfluorinated polymers, thus demonstrating that the acidity of the pore functionality is not the sole determinant of proton transport. Direct experimentalmore » comparisons of LLCs with convex and concave nanopores of similar dimensions indicate that H+ conductivities therein sensitively depend on the hydration state of the acid functionalities and the pore curvature. These experiments suggest that judicious manipulation of pore curvature provides a new means for optimizing the activities of proton-exchange membranes and nanoporous solid acid catalysts.« less

Isomers and conformational barriers of gas phase nicotine, nornicotine and their protonated forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshida, Tomoki; Farone, William A.; Xantheas, Sotiris S.

We report extensive conformational searches of the neutral nicotine, nornicotine and their protonated analogs that are based on ab-initio second order Møller-Plesset perturbation (MP2) electronic structure calculations. Initial searches were performed with the 6-31G(d,p) and the energetics of the most important structures were further refined from geometry optimizations with the aug-cc-pVTZ basis set. Based on the calculated free energies at T=298 K for the gas phase molecules, neutral nicotine has two dominant trans conformers, whereas neutral nornicotine is a mixture of several conformers. For nicotine, the protonation on both the pyridine and the pyrrolidine sites is energetically competitive, whereas nornicotinemore » prefers protonation on the pyridine nitrogen. The protonated form of nicotine is mainly a mixture of two pyridine-protonated trans conformers and two pyrrolidine-protonated trans conformers, whereas the protonated form of nornicotine is a mixture of four pyridine-protonated trans conformers. Nornicotine is conformationally more flexible than nicotine, however it is less protonated at the biologically important pyrrolidine nitrogen site. The lowest energy isomers for each case were found to interconvert via low (< 6 kcal/mol) rotational barriers around the pyridine-pyrrolidine bond.« less

Random and Block Sulfonated Polyaramides as Advanced Proton Exchange Membranes

DOE PAGES

Kinsinger, Corey L.; Liu, Yuan; Liu, Feilong; ...

2015-10-09

We present here the experimental and computational characterization of two novel copolyaramide proton exchange membranes (PEMs) with higher conductivity than Nafion at relatively high temperatures, good mechanical properties, high thermal stability, and the capability to operate in low humidity conditions. The random and block copolyaramide PEMs are found to possess different ion exchange capacities (IEC) in addition to subtle structural and morphological differences, which impact the stability and conductivity of the membranes. SAXS patterns indicate the ionomer peak for the dry block copolymer resides at q = 0.1 Å –1, which increases in amplitude when initially hydrated to 25% relativemore » humidity, but then decrease in amplitude with additional hydration. This pattern is hypothesized to signal the transport of water into the polymer matrix resulting in a reduced degree of phase separation. Coupled to these morphological changes, the enhanced proton transport characteristics and structural/mechanical stability for the block copolymer are hypothesized to be primarily due to the ordered structure of ionic clusters that create connected proton transport pathways while reducing swelling upon hydration. Interestingly, the random copolymer did not possess an ionomer peak at any of the hydration levels investigated, indicating a lack of any significant ionomer structure. The random copolymer also demonstrated higher proton conductivity than the block copolymer, which is opposite to the trend normally seen in polymer membranes. However, it has reduced structural/mechanical stability as compared to the block copolymer. In conclusion, this reduction in stability is due to the random morphology formed by entanglements of polymer chains and the adverse swelling characteristics upon hydration. Therefore, the block copolymer with its enhanced proton conductivity characteristics, as compared to Nafion, and favorable structural/mechanical stability, as compared to the random copolymer, represents a viable alternative to current proton exchange membranes.« less

Intermediate temperature proton conductors for PEM fuel cells based on phosphonic acid as protogenic group: a progress report.

PubMed

Steininger, H; Schuster, M; Kreuer, K D; Kaltbeitzel, A; Bingöl, B; Meyer, W H; Schauff, S; Brunklaus, G; Maier, J; Spiess, H W

2007-04-21

The melting behaviour and transport properties of straight chain alkanes mono- and difunctionalized with phosphonic acid groups have been investigated as a function of their length. The increase of melting temperature and decrease of proton conductivity with increasing chain length is suggested to be the consequence of an increasing ordering of the alkane segments which constrains the free aggregation of the phosphonic acid groups. However, the proton mobility is reduced to a greater extent than the proton diffusion coefficient indicating an increasing cooperativity of proton transport with increasing length of the alkane segment. The results clearly indicate that the "spacer concept", which had been proven successful in the optimization of the proton conductivity of heterocycle based systems, fails in the case of phosphonic acid functionalized polymers. Instead, a very high concentration of phosphonic acid functional groups forming "bulky" hydrogen bonded aggregates is suggested to be essential for obtaining very high proton conductivity. Aggregation is also suggested to reduce condensation reactions generally observed in phosphonic acid containing systems. On the basis of this understanding, the proton conductivities of poly(vinyl phosphonic acid) and poly(meta-phenylene phosphonic acid) are discussed. Though both polymers exhibit a substantial concentration of phosphonic acid groups, aggregation seems to be constrained to such an extent that intrinsic proton conductivity is limited to values below sigma = 10(-3) S cm(-1) at T = 150 degrees C. The results suggest that different immobilization concepts have to be developed in order to minimize the conductivity reduction compared to the very high intrinsic proton conductivity of neat phosphonic acid under quasi dry conditions. In the presence of high water activities, however, (as usually present in PEM fuel cells) the very high ion exchange capacities (IEC) possible for phosphonic acid functionalized ionomers (IEC >10 meq g(-1)) may allow for high proton conductivities in the intermediate temperature range (T approximately 120 -160 degrees C).

Pion, Kaon, Proton and Antiproton Production in Proton-Proton Collisions

NASA Technical Reports Server (NTRS)

Norbury, John W.; Blattnig, Steve R.

2008-01-01

Inclusive pion, kaon, proton, and antiproton production from proton-proton collisions is studied at a variety of proton energies. Various available parameterizations of Lorentz-invariant differential cross sections as a function of transverse momentum and rapidity are compared with experimental data. The Badhwar and Alper parameterizations are moderately satisfactory for charged pion production. The Badhwar parameterization provides the best fit for charged kaon production. For proton production, the Alper parameterization is best, and for antiproton production the Carey parameterization works best. However, no parameterization is able to fully account for all the data.

Experimental observation of acoustic emissions generated by a pulsed proton beam from a hospital-based clinical cyclotron

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jones, Kevin C.; Solberg, Timothy D.; Avery, Stephen, E-mail: Stephen.Avery@uphs.upenn.edu

Purpose: To measure the acoustic signal generated by a pulsed proton spill from a hospital-based clinical cyclotron. Methods: An electronic function generator modulated the IBA C230 isochronous cyclotron to create a pulsed proton beam. The acoustic emissions generated by the proton beam were measured in water using a hydrophone. The acoustic measurements were repeated with increasing proton current and increasing distance between detector and beam. Results: The cyclotron generated proton spills with rise times of 18 μs and a maximum measured instantaneous proton current of 790 nA. Acoustic emissions generated by the proton energy deposition were measured to be onmore » the order of mPa. The origin of the acoustic wave was identified as the proton beam based on the correlation between acoustic emission arrival time and distance between the hydrophone and proton beam. The acoustic frequency spectrum peaked at 10 kHz, and the acoustic pressure amplitude increased monotonically with increasing proton current. Conclusions: The authors report the first observation of acoustic emissions generated by a proton beam from a hospital-based clinical cyclotron. When modulated by an electronic function generator, the cyclotron is capable of creating proton spills with fast rise times (18 μs) and high instantaneous currents (790 nA). Measurements of the proton-generated acoustic emissions in a clinical setting may provide a method for in vivo proton range verification and patient monitoring.« less

Spectroscopic, DFT, and XRD Studies of Hydrogen Bonds in N-Unsubstituted 2-Aminobenzamides.

PubMed

Mphahlele, Malose Jack; Maluleka, Marole Maria; Rhyman, Lydia; Ramasami, Ponnadurai; Mampa, Richard Mokome

2017-01-04

The structures of the mono- and the dihalogenated N -unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (¹H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)-NH₂ single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the ¹H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide ( ABB ) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar-NH₂ single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer ( A ) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

PubMed Central

Komarov, Pavel V; Khokhlov, Alexei R

2013-01-01

Summary Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the membrane. For the water/Nafion systems containing more than 4 million atoms, it is found that the observed microphase-segregated morphology can be classified as bicontinuous: both majority (hydrophobic) and minority (hydrophilic) subphases are 3D continuous and organized in an irregular ordered pattern, which is largely similar to that known for a bicontinuous double-diamond structure. The characteristic size of the connected hydrophilic channels is about 25–50 Å, depending on the water content. A thermodynamic decomposition of the potential of mean force and the calculated spectral densities of the hindered translational motions of cations reveal that ion association observed with decreasing temperature is largely an entropic effect related to the loss of low-frequency modes. Based on the results from the atomistic simulation of the morphology of Nafion, we developed a realistic model of ion-conducting hydrophilic channel within the Nafion membrane and studied it with quantum molecular dynamics. The extensive 120 ps-long density functional theory (DFT)-based simulations of charge migration in the 1200-atom model of the nanochannel consisting of Nafion chains and water molecules allowed us to observe the bimodality of the van Hove autocorrelation function, which provides the direct evidence of the Grotthuss bond-exchange (hopping) mechanism as a significant contributor to the proton conductivity. PMID:24205452

The extraction of the spin structure function, g2 (and g1) at low Bjorken x

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ndukum, Luwani Z.

2015-08-01

The Spin Asymmetries of the Nucleon Experiment (SANE) used the Continuous Electron Beam Accelerator Facility at Jefferson Laboratory in Newport News, VA to investigate the spin structure of the proton. The experiment measured inclusive double polarization electron asymmetries using a polarized electron beam, scattered off a solid polarized ammonia target with target polarization aligned longitudinal and near transverse to the electron beam, allowing the extraction of the spin asymmetries A1 and A2, and spin structure functions g1 and g2. Polarized electrons of energies of 4.7 and 5.9 GeV were used. The scattered electrons were detected by a novel, non-magnetic arraymore » of detectors observing a four-momentum transfer range of 2.5 to 6.5 GeV*V. This document addresses the extraction of the spin asymmetries and spin structure functions, with a focus on spin structure function, g2 (and g1) at low Bjorken x. The spin structure functions were measured as a function of x and W in four Q square bins. A full understanding of the low x region is necessary to get clean results for SANE and extend our understanding of the kinematic region at low x.« less

WE-AB-202-04: Statistical Evaluation of Lung Function Using 4DCT Ventilation Imaging: Proton Therapy VS IMRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Q; Zhang, M; Chen, T

Purpose: Variation in function of different lung regions has been ignored so far for conventional lung cancer treatment planning, which may lead to higher risk of radiation induced lung disease. 4DCT based lung ventilation imaging provides a novel yet convenient approach for lung functional imaging as 4DCT is taken as routine for lung cancer treatment. Our work aims to evaluate the impact of accounting for spatial heterogeneity in lung function using 4DCT based lung ventilation imaging for proton and IMRT plans. Methods: Six patients with advanced stage lung cancer of various tumor locations were retrospectively evaluated for the study. Protonmore » and IMRT plans were designed following identical planning objective and constrains for each patient. Ventilation images were calculated from patients’ 4DCT using deformable image registration implemented by Velocity AI software based on Jacobian-metrics. Lung was delineated into two function level regions based on ventilation (low and high functional area). High functional region was defined as lung ventilation greater than 30%. Dose distribution and statistics in different lung function area was calculated for patients. Results: Variation in dosimetric statistics of different function lung region was observed between proton and IMRT plans. In all proton plans, high function lung regions receive lower maximum dose (100.2%–108.9%), compared with IMRT plans (106.4%–119.7%). Interestingly, three out of six proton plans gave higher mean dose by up to 2.2% than IMRT to high function lung region. Lower mean dose (lower by up to 14.1%) and maximum dose (lower by up to 9%) were observed in low function lung for proton plans. Conclusion: A systematic approach was developed to generate function lung ventilation imaging and use it to evaluate plans. This method hold great promise in function analysis of lung during planning. We are currently studying more subjects to evaluate this tool.« less

2.5 dimension structures in deep proton lithography

NASA Astrophysics Data System (ADS)

Kasztelanic, Rafal

2006-04-01

There are several technologies for cheap mass fabrication of microelements. One of them is deep proton lithography, used for the fabrication of elements of high structural depth. In this technology, accelerated protons are usually focused or formed by a mask to light a target. The energy of the proton beam is enough for all the protons to get through the target, losing only a part of their kinesthetic energy. Protons leaving the target are counted in various ways, thanks to which it is possible to estimate the energy deposed inside the target. In the next step chemical development is used to get rid of the radiated part of the target. With the use of this method, various 2D microelements can be obtained and the proton beam plays the role of a knife, cutting out the required shapes from the material. However, in order to make elements of modified surface (2.5D surface) it is necessary to change the energy of the proton beam or to change the dose deposed inside the material. The current article presents a proposal of creating simple 2.5D structures with the use of the method modifying the deposed does. This entails the modification of the deep proton lithography setup, which results moving the part for measuring the deposed dose of energy before the target. Additionally, the new deep proton lithography setup operates in the air. This article presents the results of simulations, as well as experimental results for such a setup built for the tandem accelerator in Erlangen, Germany.

Separated structure functions for exclusive K+Λ and K+Σ0 electroproduction at 5.5 GeV measured with CLAS

NASA Astrophysics Data System (ADS)

Carman, D. S.; Park, K.; Raue, B. A.; Adhikari, K. P.; Adikaram, D.; Aghasyan, M.; Amaryan, M. J.; Anderson, M. D.; Anefalos Pereira, S.; Anghinolfi, M.; Avakian, H.; Baghdasaryan, H.; Ball, J.; Baltzell, N. A.; Battaglieri, M.; Batourine, V.; Bedlinskiy, I.; Biselli, A. S.; Bono, J.; Boiarinov, S.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Celentano, A.; Chandavar, S.; Charles, G.; Cole, P. L.; Contalbrigo, M.; Cortes, O.; Crede, V.; D'Angelo, A.; Dashyan, N.; De Vita, R.; De Sanctis, E.; Deur, A.; Djalali, C.; Doughty, D.; Dupre, R.; El Alaoui, A.; El Fassi, L.; Eugenio, P.; Fedotov, G.; Fegan, S.; Fersch, R.; Fleming, J. A.; Fradi, A.; Gabrielyan, M. Y.; Gevorgyan, N.; Giovanetti, K. L.; Girod, F. X.; Goetz, J. T.; Gohn, W.; Gothe, R. W.; Griffioen, K. A.; Guegan, B.; Guidal, M.; Guo, L.; Hafidi, K.; Hakobyan, H.; Hanretty, C.; Harrison, N.; Heddle, D.; Hicks, K.; Ho, D.; Holtrop, M.; Ilieva, Y.; Ireland, D. G.; Ishkhanov, B. S.; Isupov, E. L.; Jo, H. S.; Joo, K.; Keller, D.; Khandaker, M.; Khetarpal, P.; Kim, A.; Kim, W.; Klein, A.; Klein, F. J.; Koirala, S.; Kubarovsky, A.; Kubarovsky, V.; Kuleshov, S. V.; Kvaltine, N. D.; Lewis, S.; Livingston, K.; Lu, H. Y.; MacGregor, I. J. D.; Mao, Y.; Martinez, D.; Mayer, M.; McKinnon, B.; Mestayer, M. D.; Meyer, C. A.; Mineeva, T.; Mirazita, M.; Mokeev, V.; Montgomery, R. A.; Moutarde, H.; Munevar, E.; Munoz Camacho, C.; Nadel-Turonski, P.; Nasseripour, R.; Nepali, C. S.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Osipenko, M.; Ostrovidov, A. I.; Pappalardo, L. L.; Paremuzyan, R.; Park, S.; Pasyuk, E.; Phelps, E.; Phillips, J. J.; Pisano, S.; Pogorelko, O.; Pozdniakov, S.; Price, J. W.; Procureur, S.; Prok, Y.; Protopopescu, D.; Puckett, A. J. R.; Ricco, G.; Rimal, D.; Ripani, M.; Rosner, G.; Rossi, P.; Sabatié, F.; Saini, M. S.; Salgado, C.; Saylor, N. A.; Schott, D.; Schumacher, R. A.; Seder, E.; Seraydaryan, H.; Sharabian, Y. G.; Smith, G. D.; Sober, D. I.; Sokhan, D.; Stepanyan, S. S.; Stepanyan, S.; Stoler, P.; Strakovsky, I. I.; Strauch, S.; Taiuti, M.; Tang, W.; Taylor, C. E.; Tian, Y.; Tkachenko, S.; Trivedi, A.; Ungaro, M.; Vernarsky, B.; Voskanyan, H.; Voutier, E.; Walford, N. K.; Watts, D.; Weinstein, L. B.; Wood, M. H.; Zachariou, N.; Zana, L.; Zhang, J.; Zhao, Z. W.; Zonta, I.

2013-02-01

We report measurements of the exclusive electroproduction of K+Λ and K+Σ0 final states from an unpolarized proton target using the CLAS detector at the Thomas Jefferson National Accelerator Facility. The separated structure functions σU, σLT, σTT, and σLT' were extracted from the Φ-dependent differential cross sections acquired with a longitudinally polarized 5.499 GeV electron beam. The data span a broad range of momentum transfers Q2 from 1.4 to 3.9 GeV2, invariant energy W from threshold to 2.6 GeV, and nearly the full center-of-mass angular range of the kaon. The separated structure functions provide an unprecedented data sample, which, in conjunction with other meson photo- and electroproduction data, will help to constrain the higher-level analyses being performed to search for missing baryon resonances.

A modular, energy-based approach to the development of nickel containing molecular electrocatalysts for hydrogen production and oxidation.

PubMed

Shaw, Wendy J; Helm, Monte L; DuBois, Daniel L

2013-01-01

This review discusses the development of molecular electrocatalysts for H2 production and oxidation based on nickel. A modular approach is used in which the structure of the catalyst is divided into first, second, and outer coordination spheres. The first coordination sphere consists of the ligands bound directly to the metal center, and this coordination sphere can be used to control such factors as the presence or absence of vacant coordination sites, redox potentials, hydride donor abilities and other important thermodynamic parameters. The second coordination sphere includes functional groups such as pendent acids or bases that can interact with bound substrates such as H2 molecules and hydride ligands, but that do not form strong bonds with the metal center. These functional groups can play diverse roles such as assisting the heterolytic cleavage of H2, controlling intra- and intermolecular proton transfer reactions, and providing a physical pathway for coupling proton and electron transfer reactions. By controlling both the hydride donor ability of the catalysts using the first coordination sphere and the proton donor abilities of the functional groups in the second coordination sphere, catalysts can be designed that are biased toward H2 production, oxidation, or bidirectional (catalyzing both H2 oxidation and production). The outer coordination sphere is defined as that portion of the catalytic system that is beyond the second coordination sphere. This coordination sphere can assist in the delivery of protons and electrons to and from the catalytically active site, thereby adding another important avenue for controlling catalytic activity. Many features of these simple catalytic systems are good models for enzymes, and these simple systems provide insights into enzyme function and reactivity that may be difficult to probe in enzymes. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Proton-Induced Conductivity Enhancement in AlGaN/GaN HEMT Devices

NASA Astrophysics Data System (ADS)

Lee, In Hak; Lee, Chul; Choi, Byoung Ki; Yun, Yeseul; Chang, Young Jun; Jang, Seung Yup

2018-04-01

We investigated the influence of proton irradiation on the AlGaN/GaN high-electron-mobility transistor (HEMT) devices. Unlike previous studies on the degradation behavior upon proton irradiation, we observed improvements in their electrical conductivity and carrier concentration of up to 25% for the optimal condition. As we increased the proton dose, the carrier concentration and the mobility showed a gradual increase and decrease, respectively. From the photoluminescence measurements, we observed a reduction in the near-band-edge peak of GaN ( 366 nm), which correlate on the observed electrical properties. However, neither the Raman nor the X-ray diffraction analysis showed any changes, implying a negligible influence of protons on the crystal structures. We demonstrated that high-energy proton irradiation could be utilized to modify the transport properties of HEMT devices without damaging their crystal structures.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

Measurement of the stochastic radial dose distribution for a 30-MeV proton beam using a wall-less tissue-equivalent proportional counter

PubMed Central

Tsuda, S.; Sato, T.; Ogawa, T.

2016-01-01

The frequency distribution of the lineal energy, y, of a 30-MeV proton beam was measured as a function of the radial distance from the beam path, and the dosed mean of y,y¯D, was obtained to investigate the radial dependence of y¯D. A wall-less tissue-equivalent proportional counter, in a cylindrical volume with simulated diameters of 0.36, 0.72 and 1.44 µm was used for the measurement of y distributions, yf(y). The measured values of yf(y) summed in the radial direction agreed fairly well with the corresponding data taken from the microdosimetric calculations using the PHITS code. The y¯D value of the 30-MeV proton beam presented its smallest value at r = 0.0 and gradually increased with radial distance, and the y¯D values of heavy ions such as iron showed rapid decrease with radial distance. This experimental result demonstrated that the stochastic deposited energy distribution of high-energy protons in the microscopic region is rather constant in the core as well as in the penumbra region of the track structure. PMID:25956785

Theoretical Investigation of oxides for batteries and fuel cell applications

NASA Astrophysics Data System (ADS)

Ganesh, Panchapakesan; Lubimtsev, Andrew A.; Balachandran, Janakiraman

I will present theoretical studies of Li-ion and proton-conducting oxides using a combination of theory and computations that involve Density Functional Theory based atomistic modeling, cluster-expansion based studies, global optimization, high-throughput computations and machine learning based investigation of ionic transport in oxide materials. In Li-ion intercalated oxides, we explain the experimentally observed (Nature Materials 12, 518-522 (2013)) 'intercalation pseudocapacitance' phenomenon, and explain why Nb2O5 is special to show this behavior when Li-ions are intercalated (J. Mater. Chem. A, 2013,1, 14951-14956), but not when Na-ions are used. In addition, we explore Li-ion intercalation theoretically in VO2 (B) phase, which is somewhat structurally similar to Nb2O5 and predict an interesting role of site-trapping on the voltage and capacity of the material, validated by ongoing experiments. Computations of proton conducting oxides explain why Y-doped BaZrO3 , one of the fastest proton conducting oxide, shows a decrease in conductivity above 20% Y-doping. Further, using high throughput computations and machine learning tools we discover general principles to improve proton conductivity. Acknowledgements: LDRD at ORNL and CNMS at ORNL

pH sensing characteristics and biosensing application of solution-gated reduced graphene oxide field-effect transistors.

PubMed

Sohn, Il-Yung; Kim, Duck-Jin; Jung, Jin-Heak; Yoon, Ok Ja; Thanh, Tien Nguyen; Quang, Trung Tran; Lee, Nae-Eung

2013-07-15

Solution-gated reduced graphene oxide field-effect transistors (R-GO FETs) were investigated for pH sensing and biochemical sensing applications. A channel of a networked R-GO film formed by self-assembly was incorporated as a sensing layer into a solution-gated FET structure for pH sensing and the detection of acetylcholine (Ach), which is a neurotransmitter in the nerve system, through enzymatic reactions. The fabricated R-GO FET was sensitive to protons (H(+)) with a pH sensitivity of 29 mV/pH in terms of the shift of the charge neutrality point (CNP), which is attributed to changes in the surface potential caused by the interaction of protons with OH surface functional groups present on the R-GO surface. The R-GO FET immobilized with acetylcholinesterase (AchE) was used to detect Ach in the concentration range of 0.1-10mM by sensing protons generated during the enzymatic reactions. The results indicate that R-GO FETs provide the capability to detect protons, demonstrating their applicability as a biosensing device for enzymatic reactions. Copyright © 2013 Elsevier B.V. All rights reserved.

Conformational sensitivity of conjugated poly(ethylene oxide)-poly(amidoamine) molecules to cations adducted upon electrospray ionization - a mass spectrometry, ion mobility and molecular modeling study.

PubMed

Tintaru, Aura; Chendo, Christophe; Wang, Qi; Viel, Stéphane; Quéléver, Gilles; Peng, Ling; Posocco, Paola; Pricl, Sabrina; Charles, Laurence

2014-01-15

Tandem mass spectrometry and ion mobility spectrometry experiments were performed on multiply charged molecules formed upon conjugation of a poly(amidoamine) (PAMAM) dendrimer with a poly(ethylene oxide) (PEO) linear polymer to evidence any conformational modification as a function of their charge state (2+ to 4+) and of the adducted cation (H(+)vs Li(+)). Experimental findings were rationalized by molecular dynamics simulations. The G0 PAMAM head-group could accommodate up to three protons, with protonated terminal amine group enclosed in a pseudo 18-crown-6 ring formed by the PEO segment. This particular conformation enabled a hydrogen bond network which allowed long-range proton transfer to occur during collisionally activated dissociation. In contrast, lithium adduction was found to mainly occur onto oxygen atoms of the polyether, each Li(+) cation being coordinated by a 12-crown-4 pseudo structure. As a result, for the studied polymeric segment (Mn=1500gmol(-1)), PEO-PAMAM hybrid molecules exhibited a more expanded shape when adducted to lithium as compared to proton. Copyright © 2013 Elsevier B.V. All rights reserved.

Nonlinear optical properties of rhenium(I) complexes: Influence of the extended π-conjugated connectors and proton abstraction.

PubMed

Yu, Hai-Ling; Hong, Bo; Yang, Ning; Zhao, Hong-Yan

2015-09-01

The photoinduced proton-coupled electron transfer chemistry is very crucial to the development of nonlinear optical (NLO) materials with large first hyperpolarizability contrast. We have performed a systematic investigation on the geometric structures, NLO switching, and simulated absorption spectra of rhenium(I) complexes via density functional theory (DFT). The results show that the first hyperpolarizabilities (βvec) increase remarkably with further extending of the organic connectors. In addition, the solvent leads to a slight enhancement of the hyperpolarizability and frequency dependent hyperpolarizability. Furthermore, the proton abstraction plays an important role in tuning the second-order NLO response. It is found that deprotonation not only increases the absolute value of βvec but also changes the sign of βvec from positive to negative. This different sign can be explained by the opposite dipole moments. The efficient enhancement of first hyperpolarizability is attributed to the better delocalization of the π-electron system and the more obvious degree of charge transfer. Therefore, these kinds of complexes might be promising candidates for designed as proton driven molecular second-order NLO switching. Copyright © 2015 Elsevier Inc. All rights reserved.

Structure of the membrane domain of respiratory complex I.

PubMed

Efremov, Rouslan G; Sazanov, Leonid A

2011-08-07

Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.

Applying Occam's Razor To The Proton Radius Puzzle

NASA Astrophysics Data System (ADS)

Higinbotham, Douglas

2016-09-01

Over the past five decades, ever more complex mathematical functions have been used to extract the radius of the proton from electron scattering data. For example, in 1963 the proton radius was extracted with linear and quadratic fits of low Q2 data (< 3 fm-2) and by 2014 a non-linear regression of two tenth order power series functions with thirty-one normalization parameters and data out to 25 fm-2 was used. But for electron scattering, the radius of the proton is determined by extracting the slope of the charge form factor at a Q2 of zero. By using higher precision data than was available in 1963 and focusing on the low Q2 data from 1974 to today, we find extrapolating functions consistently produce a proton radius of around 0.84 fm. A result that is in agreement with modern Lamb shift measurements.

Influence of aminosilane precursor concentration on physicochemical properties of composite Nafion membranes for vanadium redox flow battery applications

NASA Astrophysics Data System (ADS)

Kondratenko, Mikhail S.; Karpushkin, Evgeny A.; Gvozdik, Nataliya A.; Gallyamov, Marat O.; Stevenson, Keith J.; Sergeyev, Vladimir G.

2017-02-01

A series of composite proton-exchange membranes have been prepared via sol-gel modification of commercial Nafion membranes with [N-(2-aminoethyl)-3-aminopropyl]trimethoxysilane. The structure and physico-chemical properties (water uptake, ion-exchange capacity, vanadyl ion permeability, and proton conductivity) of the prepared composite membranes have been studied as a function of the precursor loading (degree of the membrane modification). If the amount of the precursor is below 0.4/1 M ratio of the amino groups of the precursor to the sulfonic groups of Nafion, the composite membranes exhibit decreased vanadium ion permeability while having relatively high proton conductivity. With respect to the use of a non-modified Nafion membrane, the performance of the composite membrane with an optimum precursor loading in a single-cell vanadium redox flow battery demonstrates enhanced energy efficiency in 20-80 mA cm-2 current density range. The maximum efficiency increase of 8% is observed at low current densities.

Measurement of D ∗ meson cross sections at HERA and determination of the gluon density in the proton using NLO QCD

NASA Astrophysics Data System (ADS)

Adloff, C.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Bate, P.; Beck, M.; Beglarian, A.; Behnke, O.; Behrend, H.-J.; Beier, C.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Biddulph, P.; Bizot, J. C.; Boudry, V.; Braunschweig, W.; Brisson, V.; Brown, D. P.; Brückner, W.; Bruel, P.; Bruncko, D.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Burrage, A.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Chabert, E.; Charlet, M.; Clarke, D.; Clerbaux, B.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cvach, J.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davidsson, M.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Demirchyan, R.; Diaconu, C.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Donovan, K. T.; Dowell, J. D.; Droutskoi, A.; Ebert, J.; Eckerlin, G.; Eckstein, D.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Enzenberger, M.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Fleischer, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gassner, J.; Gayler, J.; Gerhards, R.; Ghazaryan, S.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haustein, V.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Hengstmann, S.; Henschel, H.; Heremans, R.; Herynek, I.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoffmann, D.; Horisberger, R.; Hurling, S.; Ibbotson, M.; İşsever, Ç.; Jacquet, M.; Jaffre, M.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jones, M.; Jung, H.; Kästli, H. K.; Kander, M.; Kant, D.; Kapichine, M.; Karlsson, M.; Karschnik, O.; Katzy, J.; Kaufmann, O.; Kausch, M.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, K.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Lahmann, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Lendermann, V.; Levonian, S.; Lindstroem, M.; List, B.; Lobo, G.; Lobodzinska, E.; Lubimov, V.; Lüders, S.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martin, G.; Martyn, H.-U.; Martyniak, J.; Maxfield, S. J.; McMahon, T. R.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Mikocki, S.; Milstead, D.; Moeck, J.; Mohr, R.; Mohrdieck, S.; Moreau, F.; Morris, J. V.; Müller, D.; Müller, K.; Murin, P.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nikitin, D.; Nix, O.; Nowak, G.; Nunnemann, T.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panassik, V.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Rabbertz, K.; Rauschenberger, J.; Reimer, P.; Reisert, B.; Reyna, D.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Scheins, J.; Schilling, F.-P.; Schleif, S.; Schleper, P.; Schmidt, D.; Schmidt, D.; Schoeffel, L.; Schröder, V.; Schultz-Coulon, H.-C.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Sirois, Y.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Spaskov, V.; Specka, A.; Spiekermann, J.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stiewe, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Swart, M.; Tapprogge, S.; Taševský, M.; Tchernshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Udluft, S.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Haecke, A.; Van Mechelen, P.; Vazdik, Y.; Villet, G.; Wacker, K.; Wallny, R.; Walter, T.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wittmann, E.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žaček, J.; Zálešak, J.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1999-04-01

With the H1 detector at the ep collider HERA, D ∗ meson production cross sections have been measured in deep inelastic scattering with four-momentum transfers Q2 > 3 GeV 2 and in photoproduction at energies around Wγp ≈ 88 GeV and 194 GeV. Next-to-Leading Order QCD calculations are found to describe the differential cross sections within theoretical and experimental uncertainties. Using these calculations, the NLO gluon momentum distribution in the proton, xgg( xg), has been extracted in the momentum fraction range 7.5 × 10 -4 < xg < 4 × 10 -2 at average scales μ2 = 25 to 50 GeV 2. The gluon momentum fraction xg has been obtained from the measured kinematics of the scattered electron and the D ∗ meson in the final state. The results compare well with the gluon distribution obtained from the analysis of scaling violations of the proton structure function F2.

[Effects of exogenous spermidine on lipid peroxidation and membrane proton pump activity of cucumber seedling leaves under high temperature stress].

PubMed

Tian, Jing; Guo, Shi-Rong; Sun, Jin; Wang, Li-Ping; Yang, Yan-Juan; Li, Bin

2011-12-01

Taking a relatively heat-resistant cucumber (Cucumis sativus) cultivar 'Jinchun No. 4' as test material, a sand culture experiment was conducted in growth chamber to investigate the effects of foliar spraying spermidine (Spd) on the lipid peroxidation, membrane proton pump activity, and corresponding gene expression of cucumber seedling leaves under high temperature stress. Compared with the control, foliar spraying Spd increased the plant height, stem diameter, dry and fresh mass, and leaf area significantly, and inhibited the increase of leaf relative conductivity, malondialdehyde (MDA) content, and lipoxygenase (LOX) activity effectively. Foliar spraying Spd also helped to the increase of leaf plasma membrane- and tonoplast H(+)-ATPase activity, but no significant difference was observed in the gene expression levels. These results suggested that exogenous Spd could significantly decrease the leaf lipid peroxidation and increase the proton pump activity, and thus, stabilize the leaf membrane structure and function, alleviate the damage induced by high temperature stress, and enhance the heat tolerance of cucumber seedlings.

Infrared spectroscopy of protonated trimethylamine-(benzene)(n) (n = 1-4) as model clusters of the quaternary ammonium-aromatic ring interaction.

PubMed

Shishido, Ryunosuke; Kawai, Yuki; Fujii, Asuka

2014-09-04

The essence of the molecular recognition of the neurotransmitter acetylcholine has been attributed to the attractive interaction between a quaternary ammonium and aromatic rings. We employed protonated trimethylamine-(benzene)n clusters (n = 1-4) in the gas phase as a model to study the recognition mechanism of acetylcholine at the microscopic level. We applied size-selective infrared spectroscopy to the clusters and observed the NH and CH stretching vibrational regions. We also performed density functional theory calculations of stable structures, charge distributions, and infrared spectra of the clusters. It was shown that the methyl groups of protonated trimethylamine are solvated by benzene one at a time in the n > 1 clusters, and the validity of these clusters as a model system of the acetylcholine recognition was demonstrated. The nature of the interactions between a quaternary ammonium and aromatic rings is discussed on the basis of the observed infrared spectra and the theoretical calculations.

Structure and substrate ion binding in the sodium/proton antiporter PaNhaP

PubMed Central

Wöhlert, David; Kühlbrandt, Werner; Yildiz, Özkan

2014-01-01

Sodium/proton antiporters maintain intracellular pH and sodium levels. Detailed structures of antiporters with bound substrate ions are essential for understanding how they work. We have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter PaNhaP from Pyrococcus abyssi at 3.2 Å, and have determined its structure in two different conformations at pH 8 and pH 4. The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in the unwound stretch of trans-membrane helix 5 at the deepest point of a negatively charged cytoplasmic funnel. A second narrow polar channel may facilitate proton uptake from the cytoplasm. Transport activity of PaNhaP is cooperative at pH 6 but not at pH 5. Cooperativity is due to pH-dependent allosteric coupling of protomers through two histidines at the dimer interface. Combined with comprehensive transport studies, the structures of PaNhaP offer unique new insights into the transport mechanism of sodium/proton antiporters. DOI: http://dx.doi.org/10.7554/eLife.03579.001 PMID:25426802

Structural Characterization of Monomers and Oligomers of D-Amino Acid-Containing Peptides Using T-Wave Ion Mobility Mass Spectrometry

NASA Astrophysics Data System (ADS)

Pang, Xueqin; Jia, Chenxi; Chen, Zhengwei; Li, Lingjun

2017-01-01

The D-residues are crucial to biological function of D-amino acid containing peptides (DAACPs). Previous ion mobility mass spectrometry (IM-MS) studies revealing oligomerization patterns of amyloid cascade demonstrated conversion from native soluble unstructured assembly to fibril ß-sheet oligomers, which has been implicated in amyloid diseases, such as Alzheimer's disease and type 2 diabetes. Although neuropeptides are typically present at very low concentrations in circulation, their local concentrations could be much higher in large dense core vesicles, forming dimers or oligomers. We studied the oligomerization of protonated and metal-adducted achatin I and dermorphin peptide isomers with IM-MS. Our results suggested that dimerization, oligomerization, and metal adduction augment the structural differences between D/L peptide isomers compared to protonated monomers. Dimers and oligomers enhanced the structural differences between D/L peptide isomers in both aqueous and organic solvent system. Furthermore, some oligomer forms were only observed for either D- or L-isomers, indicating the importance of chiral center in oligomerization process. The oligomerization patterns of D/L isomers appear to be similar. Potassium adducts were detected to enlarge the structural differences between D/L isomers.

Conformational Analysis on structural perturbations of the zinc finger NEMO

NASA Astrophysics Data System (ADS)

Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

2014-03-01

The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

PubMed Central

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo

2017-01-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. PMID:28213527

Proton donor acidity controls selectivity in nonaromatic nitrogen heterocycle synthesis.

PubMed

Duttwyler, Simon; Chen, Shuming; Takase, Michael K; Wiberg, Kenneth B; Bergman, Robert G; Ellman, Jonathan A

2013-02-08

Piperidines are prevalent in natural products and pharmaceutical agents and are important synthetic targets for drug discovery and development. We report on a methodology that provides highly substituted piperidine derivatives with regiochemistry selectively tunable by varying the strength of acid used in the reaction. Readily available starting materials are first converted to dihydropyridines via a cascade reaction initiated by rhodium-catalyzed carbon-hydrogen bond activation. Subsequent divergent regio- and diastereoselective protonation of the dihydropyridines under either kinetic or thermodynamic control provides two distinct iminium ion intermediates that then undergo highly diastereoselective nucleophilic additions. X-ray structural characterization of both the kinetically and thermodynamically favored iminium ions along with density functional theory calculations provide a theoretical underpinning for the high selectivities achieved for the reaction sequences.

Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels.

PubMed

Tahat, Amani; Martí, Jordi

2016-07-01

Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 Å(-3) have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Three-Dimensional Magnetohydrodynamic Modeling of the Solar Wind Including Pickup Protons and Turbulence Transport

NASA Technical Reports Server (NTRS)

Usmanov, Arcadi V.; Goldstein, Melvyn L.; Matthaeus, William H.

2012-01-01

To study the effects of interstellar pickup protons and turbulence on the structure and dynamics of the solar wind, we have developed a fully three-dimensional magnetohydrodynamic solar wind model that treats interstellar pickup protons as a separate fluid and incorporates the transport of turbulence and turbulent heating. The governing system of equations combines the mean-field equations for the solar wind plasma, magnetic field, and pickup protons and the turbulence transport equations for the turbulent energy, normalized cross-helicity, and correlation length. The model equations account for photoionization of interstellar hydrogen atoms and their charge exchange with solar wind protons, energy transfer from pickup protons to solar wind protons, and plasma heating by turbulent dissipation. Separate mass and energy equations are used for the solar wind and pickup protons, though a single momentum equation is employed under the assumption that the pickup protons are comoving with the solar wind protons.We compute the global structure of the solar wind plasma, magnetic field, and turbulence in the region from 0.3 to 100 AU for a source magnetic dipole on the Sun tilted by 0 deg - .90 deg and compare our results with Voyager 2 observations. The results computed with and without pickup protons are superposed to evaluate quantitatively the deceleration and heating effects of pickup protons, the overall compression of the magnetic field in the outer heliosphere caused by deceleration, and the weakening of corotating interaction regions by the thermal pressure of pickup protons.

Well-Known Mediators of Selective Oxidation with Unknown Electronic Structure: Metal-Free Generation and EPR Study of Imide-N-oxyl Radicals.

PubMed

Krylov, Igor B; Kompanets, Mykhailo O; Novikova, Katerina V; Opeida, Iosip O; Kushch, Olga V; Shelimov, Boris N; Nikishin, Gennady I; Levitsky, Dmitri O; Terent'ev, Alexander O

2016-01-14

Nitroxyl radicals are widely used in chemistry, materials sciences, and biology. Imide-N-oxyl radicals are subclass of unique nitroxyl radicals that proved to be useful catalysts and mediators of selective oxidation and CH-functionalization. An efficient metal-free method was developed for the generation of imide-N-oxyl radicals from N-hydroxyimides at room temperature by the reaction with (diacetoxyiodo)benzene. The method allows for the production of high concentrations of free radicals and provides high resolution of their EPR spectra exhibiting the superhyperfine structure from benzene ring protons distant from the radical center. An analysis of the spectra shows that, regardless of the electronic effects of the substituents in the benzene ring, the superhyperfine coupling constant of an unpaired electron with the distant protons at positions 4 and 5 of the aromatic system is substantially greater than that with the protons at positions 3 and 6 that are closer to the N-oxyl radical center. This is indicative of an unusual character of the spin density distribution of the unpaired electron in substituted phthalimide-N-oxyl radicals. Understanding of the nature of the electron density distribution in imide-N-oxyl radicals may be useful for the development of commercial mediators of oxidation based on N-hydroxyimides.

Designing a protonic ceramic fuel cell with novel electrochemically active oxygen electrodes based on doped Nd0.5Ba0.5FeO3-δ.

PubMed

Lyagaeva, Julia; Danilov, Nilolay; Tarutin, Arthem; Vdovin, Gennady; Medvedev, Dmitry; Demin, Anatoly; Tsiakaras, Panagiotis

2018-06-19

The Fe-based perovskite-structured Nd0.5Ba0.5FeO3-δ (NBF) system represents the basis for developing promising electrode materials for solid oxide fuel cells with proton-conducting electrolytes. This study aims at investigating the strategy of slight doping of neodymium-barium ferrite with some transition metals (M = Ni, Cu, Co) and examining the effect of this doping on the functional characteristics, such as phase structure, thermal expansion, total and ionic conductivity as well as electrochemical behavior, of Nd0.5Ba0.5Fe0.9M0.1O3-δ (NBFM) under testing in symmetrical cell (SC) and fuel cell (FC) modes of operation. Among the investigated dopants, cobalt (Co) is found to be the optimal dopant, resulting in an enhancement of transport properties and avoiding an undesirable increase in the thermal expansion coefficient. As a result, the electrode material made of NBFCo exhibits highest ionic conductivity and lowest polarization resistance in the SC mode of operation. Electrochemical characterization of the NBFCo cathode material in a protonic ceramic fuel cell (PCFC) followed by comparison of the obtained results with literature data demonstrates that NBFCo is an attractive cathode candidate for PCFC applications.

Parton distributions with small- x resummation: evidence for BFKL dynamics in HERA data

NASA Astrophysics Data System (ADS)

Ball, Richard D.; Bertone, Valerio; Bonvini, Marco; Marzani, Simone; Rojo, Juan; Rottoli, Luca

2018-04-01

We present a determination of the parton distribution functions of the proton in which NLO and NNLO fixed-order calculations are supplemented by NLL x small- x resummation. Deep-inelastic structure functions are computed consistently at NLO+NLLx or NNLO+NLLx, while for hadronic processes small- x resummation is included only in the PDF evolution, with kinematic cuts introduced to ensure the fitted data lie in a region where the fixed-order calculation of the hard cross-sections is reliable. In all other respects, the fits use the same methodology and are based on the same global dataset as the recent NNPDF3.1 analysis. We demonstrate that the inclusion of small- x resummation leads to a quantitative improvement in the perturbative description of the HERA inclusive and charm-production reduced cross-sections in the small x region. The impact of the resummation in our fits is greater at NNLO than at NLO, because fixed-order calculations have a perturbative instability at small x due to large logarithms that can be cured by resummation. We explore the phenomenological implications of PDF sets with small- x resummation for the longitudinal structure function F_L at HERA, for parton luminosities and LHC benchmark cross-sections, for ultra-high-energy neutrino-nucleus cross-sections, and for future high-energy lepton-proton colliders such as the LHeC.

Membrane-Based Functions in the Origin of Cellular Life

NASA Technical Reports Server (NTRS)

Wilson, Michael A.

2003-01-01

How simple membrane peptides performed such essential proto-cellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we investigate how these peptides insert into membranes, self-assemble into higher-order structures and acquire functions. We have studied the insertion of an a-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)S into a model membrane. The transmembrane state is metastable, and approximately 15 kcal/mol is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)S and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self- assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to reengineering the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

A Vibrational Spectral Maker for Probing the Hydrogen-Bonding Status of Protonated Asp and Glu Residues

PubMed Central

Nie, Beining; Stutzman, Jerrod; Xie, Aihua

2005-01-01

Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen-bonding interactions of a COOH group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function theory. For hydrogen-bonding interactions with polar side-chain groups, our results show a strong correlation between the C=O stretching frequency and the hydrogen bond number of a COOH group: ∼1759–1776 cm−1 for zero, ∼1733–1749 cm−1 for one, and 1703–1710 cm−1 for two hydrogen bonds. Experimental evidence for this correlation will be discussed. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching versus O-H stretching, may be employed to identify the specific type of hydrogen-bonding interaction. This vibrational spectral marker for hydrogen-bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins. PMID:15653739

Memory device using movement of protons

DOEpatents

Warren, William L.; Vanheusden, Karel J. R.; Fleetwood, Daniel M.; Devine, Roderick A. B.; Archer, Leo B.; Brown, George A.; Wallace, Robert M.

2000-01-01

An enhancement of an electrically written memory element utilizing the motion of protons within a dielectric layer surrounded by layers on either side to confine the protons within the dielectric layer with electrode means attached to the surrounding layers to change the spatial position of the protons within the dielectric layer. The device is preferably constructed as a silicon-silicon dioxide-silicon layered structure with the protons being introduced to the structure during an anneal in an atmosphere containing hydrogen gas. Device operation is enhanced by concluding this anneal step with a sudden cooling. The device operates at low power, is preferably nonvolatile, is radiation tolerant, and is compatible with convention silicon MOS processing for integration with other microelectronics elements on the same silicon substrate.

Nonlinear Wave-Particle Interaction: Implications for Newborn Planetary and Backstreaming Proton Velocity Distribution Functions

NASA Astrophysics Data System (ADS)

Romanelli, N.; Mazelle, C.; Meziane, K.

2018-02-01

Seen from the solar wind (SW) reference frame, the presence of newborn planetary protons upstream from the Martian and Venusian bow shocks and SW protons reflected from each of them constitutes two sources of nonthermal proton populations. In both cases, the resulting proton velocity distribution function is highly unstable and capable of giving rise to ultralow frequency quasi-monochromatic electromagnetic plasma waves. When these instabilities take place, the resulting nonlinear waves are convected by the SW and interact with nonthermal protons located downstream from the wave generation region (upstream from the bow shock), playing a predominant role in their dynamics. To improve our understanding of these phenomena, we study the interaction between a charged particle and a large-amplitude monochromatic circularly polarized electromagnetic wave propagating parallel to a background magnetic field, from first principles. We determine the number of fix points in velocity space, their stability, and their dependence on different wave-particle parameters. Particularly, we determine the temporal evolution of a charged particle in the pitch angle-gyrophase velocity plane under nominal conditions expected for backstreaming protons in planetary foreshocks and for newborn planetary protons in the upstream regions of Venus and Mars. In addition, the inclusion of wave ellipticity effects provides an explanation for pitch angle distributions of suprathermal protons observed at the Earth's foreshock, reported in previous studies. These analyses constitute a mean to evaluate if nonthermal proton velocity distribution functions observed at these plasma environments present signatures that can be understood in terms of nonlinear wave-particle processes.

Electron Transfer Ion/Ion Reactions in a Three-Dimensional Quadrupole Ion Trap: Reactions of Doubly and Triply Protonated Peptides with SO2·−

PubMed Central

Pitteri, Sharon J.; Chrisman, Paul A.; Hogan, Jason M.; McLuckey, Scott A.

2005-01-01

Ion–ion reactions between a variety of peptide cations (doubly and triply charged) and SO2 anions have been studied in a 3-D quadrupole ion trap, resulting in proton and electron transfer. Electron transfer dissociation (ETD) gives many c- and z-type fragments, resulting in extensive sequence coverage in the case of triply protonated peptides with SO2·−. For triply charged neurotensin, in which a direct comparison can be made between 3-D and linear ion trap results, abundances of ETD fragments relative to one another appear to be similar. Reactions of doubly protonated peptides with SO2·− give much less structural information from ETD than triply protonated peptides. Collision-induced dissociation (CID) of singly charged ions formed in reactions with SO2·− shows a combination of proton and electron transfer products. CID of the singly charged species gives more structural information than ETD of the doubly protonated peptide, but not as much information as ETD of the triply protonated peptide. PMID:15762593

Neutral-current weak interactions at an EIC

DOE PAGES

Zhao, Y. X.; Deshpande, A.; Huang, J.; ...

2017-03-21

Here, a simulation study of measurements of neutral current structure functions of the nucleon at the future high-energy and high-luminosity polarized electron-ion collider (EIC) is presented. A new series of γ-Z interference structure functions, F γZ 1, F γZ 3, g γZ 1, g γZ 5 become accessible via parity-violating asymmetries in polarized electron-nucleon deep inelastic scattering (DIS). Within the context of the quark-parton model, they provide a unique and, in some cases, yet-unmeasured combination of unpolarized and polarized parton distribution functions. The uncertainty projections for these structure functions using electron-proton collisions are considered for various EIC beam energy configurations.more » Also presented are uncertainty projections for measurements of the weak mixing angle sin 2θ W using electron-deuteron collisions which cover a much higher Q 2 than that accessible in fixed target measurements. QED and QCD radiative corrections and effects of detector smearing are included with the calculations.« less

Proton movement and coupling in the POT family of peptide transporters

PubMed Central

Parker, Joanne L.; Li, Chenghan; Brinth, Allete; Wang, Zhi; Vogeley, Lutz; Solcan, Nicolae; Ledderboge-Vucinic, Gregory; Swanson, Jessica M. J.; Caffrey, Martin; Voth, Gregory A.

2017-01-01

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate. PMID:29180426

Proton movement and coupling in the POT family of peptide transporters.

PubMed

Parker, Joanne L; Li, Chenghan; Brinth, Allete; Wang, Zhi; Vogeley, Lutz; Solcan, Nicolae; Ledderboge-Vucinic, Gregory; Swanson, Jessica M J; Caffrey, Martin; Voth, Gregory A; Newstead, Simon

2017-12-12

POT transporters represent an evolutionarily well-conserved family of proton-coupled transport systems in biology. An unusual feature of the family is their ability to couple the transport of chemically diverse ligands to an inwardly directed proton electrochemical gradient. For example, in mammals, fungi, and bacteria they are predominantly peptide transporters, whereas in plants the family has diverged to recognize nitrate, plant defense compounds, and hormones. Although recent structural and biochemical studies have identified conserved sites of proton binding, the mechanism through which transport is coupled to proton movement remains enigmatic. Here we show that different POT transporters operate through distinct proton-coupled mechanisms through changes in the extracellular gate. A high-resolution crystal structure reveals the presence of ordered water molecules within the peptide binding site. Multiscale molecular dynamics simulations confirm proton transport occurs through these waters via Grotthuss shuttling and reveal that proton binding to the extracellular side of the transporter facilitates a reorientation from an inward- to outward-facing state. Together these results demonstrate that within the POT family multiple mechanisms of proton coupling have likely evolved in conjunction with variation of the extracellular gate. Copyright © 2017 the Author(s). Published by PNAS.

Exploring Nucleon Spin Structure Through Neutrino Neutral-Current Interactions in MicroBooNE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodruff, Katherine

2017-02-02

The net contribution of the strange quark spins to the proton spin,more » $$\\Delta s$$, can be determined from neutral current elastic neutrino-proton interactions at low momentum transfer combined with data from electron-proton scattering. The probability of neutrino-proton interactions depends in part on the axial form factor, which represents the spin structure of the proton and can be separated into its quark flavor contributions. Low momentum transfer neutrino neutral current interactions can be measured in MicroBooNE, a high-resolution liquid argon time projection chamber (LArTPC) in its first year of running in the Booster Neutrino Beamline at Fermilab. The signal for these interactions in MicroBooNE is a single short proton track. We present our work on the automated reconstruction and classification of proton tracks in LArTPCs, an important step in the determination of neutrino- nucleon cross sections and the measurement of $$\\Delta s$$.« less

Morphology and Proton Transport in Sulfonated Block Copolymer and Mesoporous Polymer Electrolyte Membranes

NASA Astrophysics Data System (ADS)

Chen, Chelsea; Wong, David; Beers, Keith; Balsara, Nitash

2013-03-01

In an effort to understand the fundamentals of proton transport in polymer electrolyte membranes (PEMs), we have developed a series of poly(styrene-b-ethylene-b-styrene) (SES) membranes. The SES membranes were subsequently sulfonated to yield proton conducting S-SES membranes. We examine the effects of sulfonation level, temperature and thermal history on the morphology of S-SES membranes in both dry and hydrated states. The effects of these parameters on water uptake and proton transport characteristics of the membranes are also examined. Furthermore, building upon the strategy we deployed in sulfonating the SES membranes, we fabricated mesoporous S-SES membranes, with pores lined up with the proton conducting channels. These membranes have three distinct phases: structural block, proton-conducting block, and void. We examine the effects of pore size, domain structure and sulfonation level on water uptake and proton conductivity of the mesoporous PEMs at different temperatures. This work is funded by Department of Energy.

Combining density functional theory (DFT) and collision cross-section (CCS) calculations to analyze the gas-phase behaviour of small molecules and their protonation site isomers.

PubMed

Boschmans, Jasper; Jacobs, Sam; Williams, Jonathan P; Palmer, Martin; Richardson, Keith; Giles, Kevin; Lapthorn, Cris; Herrebout, Wouter A; Lemière, Filip; Sobott, Frank

2016-06-20

Electrospray ion mobility-mass spectrometry (IM-MS) data show that for some small molecules, two (or even more) ions with identical sum formula and mass, but distinct drift times are observed. In spite of showing their own unique and characteristic fragmentation spectra in MS/MS, no configurational or constitutional isomers are found to be present in solution. Instead the observation and separation of such ions appears to be inherent to their gas-phase behaviour during ion mobility experiments. The origin of multiple drift times is thought to be the result of protonation site isomers ('protomers'). Although some important properties of protomers have been highlighted by other studies, correlating the experimental collision cross-sections (CCSs) with calculated values has proven to be a major difficulty. As a model, this study uses the pharmaceutical compound melphalan and a number of related molecules with alternative (gas-phase) protonation sites. Our study combines density functional theory (DFT) calculations with modified MobCal methods (e.g. nitrogen-based Trajectory Method algorithm) for the calculation of theoretical CCS values. Calculated structures can be linked to experimentally observed signals, and a strong correlation is found between the difference of the calculated dipole moments of the protomer pairs and their experimental CCS separation.

Dynamics of Proton Spin: Role of qqq Force

NASA Astrophysics Data System (ADS)

Mitra, A. N.

The analytic structure of the qqq wave function, obtained recently in the high momentum regime of QCD, is employed for the formulation of baryonic transition amplitudes via quark loops. A new aspect of this study is the role of a direct (Y -shaped, Mercedes-Benz type) qqq force in generating the qqq wave function The dynamics is that of a Salpeter-like equation (3D support for the kernel) formulated covariantly on the light front, a la Markov-Yukawa Transversality Principle (MYTP) which warrants a 2-way interconnection between the 3D and 4D Bethe-Salpeter (BSE) forms for 2 as well as 3 fermion quarks. The dynamics of this 3-body force shows up through a characteristic singularity in the hypergeometric differential equation for the 3D wave function ϕ, corresponding to a negative eigenvalue of the spin operator iσ1·σ2 × σ3 which is an integral part of the qqq force. As a first application of this wave function to the problem of the proton spin anomaly, the two-gluon contribution to the anomaly yields an estimate of the right sign, although somewhat smaller in magnitude.

Innovative polymer nanocomposite electrolytes: nanoscale manipulation of ion channels by functionalized graphenes.

PubMed

Choi, Bong Gill; Hong, Jinkee; Park, Young Chul; Jung, Doo Hwan; Hong, Won Hi; Hammond, Paula T; Park, Hoseok

2011-06-28

The chemistry and structure of ion channels within the polymer electrolytes are of prime importance for studying the transport properties of electrolytes as well as for developing high-performance electrochemical devices. Despite intensive efforts on the synthesis of polymer electrolytes, few studies have demonstrated enhanced target ion conduction while suppressing unfavorable ion or mass transport because the undesirable transport occurs through an identical pathway. Herein, we report an innovative, chemical strategy for the synthesis of polymer electrolytes whose ion-conducting channels are physically and chemically modulated by the ionic (not electronic) conductive, functionalized graphenes and for a fundamental understanding of ion and mass transport occurring in nanoscale ionic clusters. The functionalized graphenes controlled the state of water by means of nanoscale manipulation of the physical geometry and chemical functionality of ionic channels. Furthermore, the confinement of bound water within the reorganized nanochannels of composite membranes was confirmed by the enhanced proton conductivity at high temperature and the low activation energy for ionic conduction through a Grotthus-type mechanism. The selectively facilitated transport behavior of composite membranes such as high proton conductivity and low methanol crossover was attributed to the confined bound water, resulting in high-performance fuel cells.

Conformational change during photocycle of bacteriorhodopsin and its proton-pumping mechanism.

PubMed

Chou, K C

1993-06-01

Based on the recent finding on the structural difference of seven helix bundles in the all-trans and 13-cis bacteriorhodopsins, the distances among the key groups performing the function of proton translocation as well as their microenvironments have been investigated. Consequently, a pore-gated model was proposed for the light-driven proton-pumping mechanism of bacteriorhodopsin. According to this model, the five double-bounded polyene chain in retinal chromophore can be phenomenologically likened to a molecular "lever," whose one end links to a "piston" (the beta-ionone ring) and the other end to a pump "relay station" (the Schiff base). During the photocycle of bacteriorhodopsin, the molecular "lever" is moving up and down as marked by the position change of the "piston," so as to trigger the gate of pore to open and close alternately. When the "piston" is up, the pore-controlled gate is open so that the water channel from Asp-96 to the Schiff base and that from the Schiff base to Asp-85 is established; when the "piston" is down, the pore-controlled gate is closed and the water channels for proton transportation in both the cytoplasmic half and extracellular half are blocked. The current model allows a consistent interpretation of a great deal of experimental data and also provides a useful basis for further investigating the mechanism of proton pumping by bacteriorhodopsin.

Mechanism of tyrosine D oxidation in Photosystem II.

PubMed

Saito, Keisuke; Rutherford, A William; Ishikita, Hiroshi

2013-05-07

Using quantum mechanics/molecular mechanics calculations and the 1.9-Å crystal structure of Photosystem II [Umena Y, Kawakami K, Shen J-R, Kamiya N (2011) Nature 473(7345):55-60], we investigated the H-bonding environment of the redox-active tyrosine D (TyrD) and obtained insights that help explain its slow redox kinetics and the stability of TyrD(•). The water molecule distal to TyrD, located ~4 Å away from the phenolic O of TyrD, corresponds to the presence of the tyrosyl radical state. The water molecule proximal to TyrD, in H-bonding distance to the phenolic O of TyrD, corresponds to the presence of the unoxidized tyrosine. The H(+) released on oxidation of TyrD is transferred to the proximal water, which shifts to the distal position, triggering a concerted proton transfer pathway involving D2-Arg180 and a series of waters, through which the proton reaches the aqueous phase at D2-His61. The water movement linked to the ejection of the proton from the hydrophobic environment near TyrD makes oxidation slow and quasiirreversible, explaining the great stability of the TyrD(•). A symmetry-related proton pathway associated with tyrosine Z is pointed out, and this is associated with one of the Cl(-) sites. This may represent a proton pathway functional in the water oxidation cycle.

Excitation functions of parameters extracted from three-source (net-)proton rapidity distributions in Au-Au and Pb-Pb collisions over an energy range from AGS to RHIC

NASA Astrophysics Data System (ADS)

Gao, Li-Na; Liu, Fu-Hu; Sun, Yan; Sun, Zhu; Lacey, Roy A.

2017-03-01

Experimental results of the rapidity spectra of protons and net-protons (protons minus antiprotons) emitted in gold-gold (Au-Au) and lead-lead (Pb-Pb) collisions, measured by a few collaborations at the alternating gradient synchrotron (AGS), super proton synchrotron (SPS), and relativistic heavy ion collider (RHIC), are described by a three-source distribution. The values of the distribution width σC and fraction kC of the central rapidity region, and the distribution width σF and rapidity shift Δ y of the forward/backward rapidity regions, are then obtained. The excitation function of σC increases generally with increase of the center-of-mass energy per nucleon pair √{s_{NN}}. The excitation function of σF shows a saturation at √{s_{NN}}=8.8 GeV. The excitation function of kC shows a minimum at √{s_{NN}}=8.8 GeV and a saturation at √{s_{NN}} ≈ 17 GeV. The excitation function of Δ y increases linearly with ln(√{s_{NN}}) in the considered energy range.

Protonated serotonin: Geometry, electronic structures and photophysical properties

NASA Astrophysics Data System (ADS)

Omidyan, Reza; Amanollahi, Zohreh; Azimi, Gholamhassan

2017-07-01

The geometry and electronic structures of protonated serotonin have been investigated by the aim of MP2 and CC2 methods. The relative stabilities, transition energies and geometry of sixteen different protonated isomers of serotonin have been presented. It has been predicted that protonation does not exhibit essential alteration on the S1 ← S0 electronic transition energy of serotonin. Instead, more complicated photophysical nature in respect to its neutral analogue is suggested for protonated system owing to radiative and non-radiative deactivation pathways. In addition to hydrogen detachment (HD), hydrogen/proton transfer (H/PT) processes from ammonium to indole ring along the NH+⋯ π hydrogen bond have been predicted as the most important photophysical consequences of SERH+ at S1 excited state. The PT processes is suggested to be responsible for fluorescence of SERH+ while the HD driving coordinate is proposed for elucidation of its nonradiative deactivation mechanism.

Octahydriodo diborane (B2H8) and its protonated cations containing five-, six-, and seven-coordinate boron atoms

PubMed Central

Olah, George A.; Surya Prakash, G. K.; Rasul, Golam

2012-01-01

Structures of octahydriodo diborane (B2H8) 1 and its protonated 3, diprotonated 5, triprotonated 6, and tetraprotonated 7 ions were found to be calculationally viable minima at the MP2/cc-pVTZ level of theory. Each structure contains two-electron three-center (2e-3c) bonds. The protonation of 1 to form 3 was found to be strongly exothermic by 176.0 kcal/mol. Subsequent protonation of 3 to form 5 was also found to be exothermic by 28.4 kcal/mol. Further protonation of 5 to form 6 was, however, computed to be endothermic by 122.0 kcal/mol whereas protonation of 6 to form 7 was again highly endothermic by 238.8 kcal/mol. Deprotonation barriers of the ions were also computed. PMID:22511715

Proton irradiation effects on beryllium – A macroscopic assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simos, Nikolaos; Elbakhshwan, Mohamed; Zhong, Zhong

Beryllium, due to its excellent neutron multiplication and moderation properties, in conjunction with its good thermal properties, is under consideration for use as plasma facing material in fusion reactors and as a very effective neutron reflector in fission reactors. While it is characterized by unique combination of structural, chemical, atomic number, and neutron absorption cross section it suffers, however, from irradiation generated transmutation gases such as helium and tritium which exhibit low solubility leading to supersaturation of the Be matrix and tend to precipitate into bubbles that coalesce and induce swelling and embrittlement thus degrading the metal and limiting itsmore » lifetime. Utilization of beryllium as a pion production low-Z target in high power proton accelerators has been sought both for its low Z and good thermal properties in an effort to mitigate thermos-mechanical shock that is expected to be induced under the multi-MW power demand. To assess irradiation-induced changes in the thermal and mechanical properties of Beryllium, a study focusing on proton irradiation damage effects has been undertaken using 200 MeV protons from the Brookhaven National Laboratory Linac and followed by a multi-faceted post-irradiation analysis that included the thermal and volumetric stability of irradiated beryllium, the stress-strain behavior and its ductility loss as a function of proton fluence and the effects of proton irradiation on the microstructure using synchrotron X-ray diffraction. The mimicking of high temperature irradiation of Beryllium via high temperature annealing schemes has been conducted as part of the post-irradiation study. This study focuses on the thermal stability and mechanical property changes of the proton irradiated beryllium and presents results of the macroscopic property changes of Beryllium deduced from thermal and mechanical tests.« less

Proton irradiation effects on beryllium – A macroscopic assessment

DOE PAGES

Simos, Nikolaos; Elbakhshwan, Mohamed; Zhong, Zhong; ...

2016-07-01

Beryllium, due to its excellent neutron multiplication and moderation properties, in conjunction with its good thermal properties, is under consideration for use as plasma facing material in fusion reactors and as a very effective neutron reflector in fission reactors. While it is characterized by unique combination of structural, chemical, atomic number, and neutron absorption cross section it suffers, however, from irradiation generated transmutation gases such as helium and tritium which exhibit low solubility leading to supersaturation of the Be matrix and tend to precipitate into bubbles that coalesce and induce swelling and embrittlement thus degrading the metal and limiting itsmore » lifetime. Utilization of beryllium as a pion production low-Z target in high power proton accelerators has been sought both for its low Z and good thermal properties in an effort to mitigate thermos-mechanical shock that is expected to be induced under the multi-MW power demand. To assess irradiation-induced changes in the thermal and mechanical properties of Beryllium, a study focusing on proton irradiation damage effects has been undertaken using 200 MeV protons from the Brookhaven National Laboratory Linac and followed by a multi-faceted post-irradiation analysis that included the thermal and volumetric stability of irradiated beryllium, the stress-strain behavior and its ductility loss as a function of proton fluence and the effects of proton irradiation on the microstructure using synchrotron X-ray diffraction. The mimicking of high temperature irradiation of Beryllium via high temperature annealing schemes has been conducted as part of the post-irradiation study. This study focuses on the thermal stability and mechanical property changes of the proton irradiated beryllium and presents results of the macroscopic property changes of Beryllium deduced from thermal and mechanical tests.« less

Proton irradiation effects on beryllium - A macroscopic assessment

NASA Astrophysics Data System (ADS)

Simos, Nikolaos; Elbakhshwan, Mohamed; Zhong, Zhong; Camino, Fernando

2016-10-01

Beryllium, due to its excellent neutron multiplication and moderation properties, in conjunction with its good thermal properties, is under consideration for use as plasma facing material in fusion reactors and as a very effective neutron reflector in fission reactors. While it is characterized by unique combination of structural, chemical, atomic number, and neutron absorption cross section it suffers, however, from irradiation generated transmutation gases such as helium and tritium which exhibit low solubility leading to supersaturation of the Be matrix and tend to precipitate into bubbles that coalesce and induce swelling and embrittlement thus degrading the metal and limiting its lifetime. Utilization of beryllium as a pion production low-Z target in high power proton accelerators has been sought both for its low Z and good thermal properties in an effort to mitigate thermos-mechanical shock that is expected to be induced under the multi-MW power demand. To assess irradiation-induced changes in the thermal and mechanical properties of Beryllium, a study focusing on proton irradiation damage effects has been undertaken using 200 MeV protons from the Brookhaven National Laboratory Linac and followed by a multi-faceted post-irradiation analysis that included the thermal and volumetric stability of irradiated beryllium, the stress-strain behavior and its ductility loss as a function of proton fluence and the effects of proton irradiation on the microstructure using synchrotron X-ray diffraction. The mimicking of high temperature irradiation of Beryllium via high temperature annealing schemes has been conducted as part of the post-irradiation study. This paper focuses on the thermal stability and mechanical property changes of the proton irradiated beryllium and presents results of the macroscopic property changes of Beryllium deduced from thermal and mechanical tests.

Novel target design for enhanced laser driven proton acceleration

NASA Astrophysics Data System (ADS)

Dalui, Malay; Kundu, M.; Tata, Sheroy; Lad, Amit D.; Jha, J.; Ray, Krishanu; Krishnamurthy, M.

2017-09-01

We demonstrate a simple method of preparing structured target for enhanced laser-driven proton acceleration under target-normal-sheath-acceleration scheme. A few layers of genetically modified, clinically grown micron sized E. Coli bacteria cell coated on a thin metal foil has resulted in an increase in the maximum proton energy by about 1.5 times and the total proton yield is enhanced by approximately 25 times compared to an unstructured reference foil at a laser intensity of 1019 W/cm2. Particle-in-cell simulations on the system shows that the structures on the target-foil facilitates anharmonic resonance, contributing to enhanced hot electron production which leads to stronger accelerating field. The effect is observed to grow as the number of structures is increased in the focal area of the laser pulse.

Proton transfer in liquid water confined inside graphene slabs

NASA Astrophysics Data System (ADS)

Tahat, Amani; Martí, Jordi

2015-09-01

The microscopic structure and dynamics of an excess proton in water constrained in narrow graphene slabs between 0.7 and 3.1 nm wide has been studied by means of a series of molecular dynamics simulations. Interaction of water and carbon with the proton species was modeled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of confinement on proton solvation structure and on its dynamical properties has been considered for varying densities. The system is organized in one interfacial and a bulk-like region, both of variable size. In the widest interplate separations, the lone proton shows a marked tendency to place itself in the bulk phase of the system, due to the repulsive interaction with the carbon atoms. However, as the system is compressed and the proton is forced to move to the vicinity of graphene walls it moves closer to the interface, producing a neat enhancement of the local structure. We found a marked slowdown of proton transfer when the separation of the two graphene plates is reduced. In the case of lowest distances between graphene plates (0.7 and 0.9 nm), only one or two water layers persist and the two-dimensional character of water structure becomes evident. By means of spectroscopical analysis, we observed the persistence of Zundel and Eigen structures in all cases, although at low interplate separations a signature frequency band around 2500 cm-1 suffers a blue shift and moves to characteristic values of asymmetric hydronium ion vibrations, indicating some unstability of the typical Zundel-Eigen moieties and their eventual conversion to a single hydronium species solvated by water.

Polybenzimidazole block copolymers for fuel cell: synthesis and studies of block length effects on nanophase separation, mechanical properties, and proton conductivity of PEM.

PubMed

Maity, Sudhangshu; Jana, Tushar

2014-05-14

A series of meta-polybenzimidazole-block-para-polybenzimidazole (m-PBI-b-p-PBI), segmented block copolymers of PBI, were synthesized with various structural motifs and block lengths by condensing the diamine terminated meta-PBI (m-PBI-Am) and acid terminated para-PBI (p-PBI-Ac) oligomers. NMR studies and existence of two distinct glass transition temperatures (Tg), obtained from dynamical mechanical analysis (DMA) results, unequivocally confirmed the formation of block copolymer structure through the current polymerization methodology. Appropriate and careful selection of oligomers chain length enabled us to tailor the block length of block copolymers and also to make varieties of structural motifs. Increasingly distinct Tg peaks with higher block length of segmented block structure attributed the decrease in phase mixing between the meta-PBI and para-PBI blocks, which in turn resulted into nanophase segregated domains. The proton conductivities of proton exchange membrane (PEM) developed from phosphoric acid (PA) doped block copolymer membranes were found to be increasing substantially with increasing block length of copolymers even though PA loading of these membranes did not alter appreciably with varying block length. For example when molecular weight (Mn) of blocks were increased from 1000 to 5500 then the proton conductivities at 160 °C of resulting copolymers increased from 0.05 to 0.11 S/cm. Higher block length induced nanophase separation between the blocks by creating less morphological barrier within the block which facilitated the movement of the proton in the block and hence resulting higher proton conductivity of the PEM. The structural varieties also influenced the phase separation and proton conductivity. In comparison to meta-para random copolymers reported earlier, the current meta-para segmented block copolymers were found to be more suitable for PBI-based PEM.

Effects of Surgery and Proton Therapy on Cerebral White Matter of Craniopharyngioma Patients

DOE Office of Scientific and Technical Information (OSTI.GOV)

Uh, Jinsoo, E-mail: jinsoo.uh@stjude.org; Merchant, Thomas E.; Li, Yimei

Purpose: The purpose of this study was to determine radiation dose effect on the structural integrity of cerebral white matter in craniopharyngioma patients receiving surgery and proton therapy. Methods and Materials: Fifty-one patients (2.1-19.3 years of age) with craniopharyngioma underwent surgery and proton therapy in a prospective therapeutic trial. Anatomical magnetic resonance images acquired after surgery but before proton therapy were inspected to identify white matter structures intersected by surgical corridors and catheter tracks. Longitudinal diffusion tensor imaging (DTI) was performed to measure microstructural integrity changes in cerebral white matter. Fractional anisotropy (FA) derived from DTI was statistically analyzed for 51more » atlas-based white matter structures of the brain to determine radiation dose effect. FA in surgery-affected regions in the corpus callosum was compared to that in its intact counterpart to determine whether surgical defects affect radiation dose effect. Results: Surgical defects were seen most frequently in the corpus callosum because of transcallosal resection of tumors and insertion of ventricular or cyst catheters. Longitudinal DTI data indicated reductions in FA 3 months after therapy, which was followed by a recovery in most white matter structures. A greater FA reduction was correlated with a higher radiation dose in 20 white matter structures, indicating a radiation dose effect. The average FA in the surgery-affected regions before proton therapy was smaller (P=.0001) than that in their non–surgery-affected counterparts with more intensified subsequent reduction of FA (P=.0083) after therapy, suggesting that surgery accentuated the radiation dose effect. Conclusions: DTI data suggest that mild radiation dose effects occur in patients with craniopharyngioma receiving surgery and proton therapy. Surgical defects present at the time of proton therapy appear to accentuate the radiation dose effect longitudinally. This study supports consideration of pre-existing surgical defects and their locations in proton therapy planning and studies of treatment effect.« less

Micro structure processing on plastics by accelerated hydrogen molecular ions

NASA Astrophysics Data System (ADS)

Hayashi, H.; Hayakawa, S.; Nishikawa, H.

2017-08-01

A proton has 1836 times the mass of an electron and is the lightest nucleus to be used for accelerator in material modification. We can setup accelerator with the lowest acceleration voltage. It is preferable characteristics of Proton Beam Writer (PBW) for industrial applications. On the contrary ;proton; has the lowest charge among all nuclei and the potential impact to material is lowest. The object of this research is to improve productivity of the PBW for industry application focusing on hydrogen molecular ions. These ions are generated in the same ion source by ionizing hydrogen molecule. There is no specific ion source requested and it is suitable for industrial use. We demonstrated three dimensional (3D) multilevel micro structures on polyester base FPC (Flexible Printed Circuits) using proton, H2+ and H3+. The reactivity of hydrogen molecular ions is much higher than that of proton and coincident with the level of expectation. We can apply this result to make micro devices of 3D multilevel structures on FPC.

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

PubMed

Gao, Juehan; Berden, Giel; Rodgers, M T; Oomens, Jos

2016-03-14

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Study of Proton Transfer in E. Coli Photolyase

NASA Astrophysics Data System (ADS)

Zhang, Meng; Liu, Zheyun; Li, Jiang; Wang, Lijuan; Zhong, Dongping

2013-06-01

Photolyase is a flavoprotein which utilizes blue-light energy to repair UV-light damaged DNA. The catalytic cofactor of photolyase, flavin adenine dinucleotide (FAD), has five redox states. Conversions between these redox states involve intraprotein electron transfer and proton transfer, which play important role in protein function. Here we systematically studied proton transfer in E. coli photolyase in vitro by site-directed mutagenesis and steady-state UV-vis spectroscopy, and proposed the proton channel in photolyase. We found that in the mutant N378C/E363L, proton channel was completely eliminated when DNA substrate was bound to the protein. Proton is suggested to be transported from protein surface to FAD by two pathways: the proton relay pathway through E363 and surface water to N378 and then to FAD; and the proton diffusion pathway through the substrate binding pocket. In addition, reaction kinetics of conversions between the redox states was then solved and redox potentials of the redox states were determined. These results described a complete picture of FAD redox changes, which are fundamental to the functions of all flavoenzymes.

Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism

PubMed Central

Boughlala, Zakaria; Fonseca Guerra, Célia

2016-01-01

Abstract We have analyzed the structure and bonding of gas‐phase Cl−X and [HCl−X]+ complexes for X+= H+, CH3 +, Li+, and Na+, using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl− and HCl for the various cations. The Cl−X bond becomes longer and weaker along X+ = H+, CH3 +, Li+, and Na+. Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn–Sham molecular orbital (KS‐MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities. PMID:27551660

Why Is It so? The [superscript 1]H-NMR CH[subscript 2] Splitting in Substituted Propanes

ERIC Educational Resources Information Center

Lim, Kieran F.; Dereani, Marino

2010-01-01

Nuclear magnetic resonance (NMR) spectroscopy is an important tool in the structural analysis of both organic and inorganic molecules. Proton NMR spectra can yield information about the chemical or bonding environment surrounding various protons, the number of protons in those environments, and the number of neighbouring protons around each…

Deformation of the proton emitter 113Cs from electromagnetic transition and proton-emission rates

NASA Astrophysics Data System (ADS)

Hodge, D.; Cullen, D. M.; Taylor, M. J.; Nara Singh, B. S.; Ferreira, L. S.; Maglione, E.; Smith, J. F.; Scholey, C.; Rahkila, P.; Grahn, T.; Braunroth, T.; Badran, H.; Capponi, L.; Girka, A.; Greenlees, P. T.; Julin, R.; Konki, J.; Mallaburn, M.; Nefodov, O.; O'Neill, G. G.; Pakarinen, J.; Papadakis, P.; Partanen, J.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Smolen, M.; Sorri, J.; Stolze, S.; Uusitalo, J.

2016-09-01

The lifetime of the (11 /2+ ) state in the band above the proton-emitting (3 /2+ ) state in 113Cs has been measured to be τ =24 (6 ) ps from a recoil-decay-tagged differential-plunger experiment. The measured lifetime was used to deduce the deformation of the states using wave functions from a nonadiabatic quasiparticle model to independently calculate both proton-emission and electromagnetic γ -ray transition rates as a function of deformation. The only quadrupole deformation, which was able to reproduce the experimental excitation energies of the states, the electromagnetic decay rate of the (11 /2+ ) state and the proton-emission rate of the (3 /2+ ) state, was found to be β2=0.22 (6 ) . This deformation is in agreement with the earlier proton emission studies which concluded that 113Cs was best described as a deformed proton emitter, however, it is now more firmly supported by the present measurement of the electromagnetic transition rate.

Theoretical studies for excited-state tautomerization in the 7-azaindole-(CH3OH)n (n = 1 and 2) complexes in the gas phase.

PubMed

Fang, Hua; Kim, Yongho

2011-12-01

The excited-state tautomerization of 7-azaindole (7AI) complexes bonded with either one or two methanol molecule(s) was studied by systematic quantum mechanical calculations in the gas phases. Electronic structures and energies for the reactant, transition state (TS), and product were computed at the complete active space self-consistent field (CASSCF) levels with the second-order multireference perturbation theory (MRPT2) to consider the dynamic electron correlation. The time-dependent density functional theory (TDDFT) was also used for comparison. The excited-state double proton transfer (ESDPT) in 7AI-CH(3)OH occurs in a concerted but asynchronous mechanism. Similarly, such paths are also found in the two transition states during the excited-state triple proton transfer (ESTPT) of the 7AI-(CH(3)OH)(2) complex. In the first TS, the pyrrole ring proton first migrated to methanol, while in the second the methanol proton moved first to the pyridine ring. The CASSCF level with the MRPT2 correction showed that the former path was much preferable to the latter, and the ESDPT is much slower than the ESTPT. Additionally, the vibrational-mode enhanced tautomerization in the 7AI-(CH(3)OH)(2) complex was also studied. We found that the excitation of the low-frequency mode shortens the reaction path to increase the tautomerization rate. Overall, most TDDFT methods used in this study predicted different TS structures and barriers from the CASSCF methods with MRPT2 corrections. © 2011 American Chemical Society

Structure-Function of α1-Adrenergic Receptors

PubMed Central

Perez, Dianne M.

2007-01-01

Summary The Easson-Stedman hypothesis provided the rationale for the first studies of drug design for the α1-adrenergic receptor. Through chemical modifications of the catecholamine core structure, the need was established for a protonated amine, a β-hydroxyl on a chiral center, and an aromatic ring with substitutions capable of hydrogen bonding. After the receptors were cloned and three α1-adrenergic receptor subtypes were discovered, drug design became focused on the analysis of receptor structure and new interactions were uncovered. It became clear that α1 and β-adrenergic receptors did not share stringent homology in the ligand-binding pocket but this difference has allowed for more selective drug design. Novel discoveries on allosterism and agonist trafficking may be used in the future design of therapeutics with fewer side effects. This review will explore past and current knowledge of the structure-function of the α1-adrenergic receptor subtypes. PMID:17052695

Electromagnetic structure of the proton within the CP-violation hypothesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krutov, A. F., E-mail: krutov@ssu.samara.ru; Kudinov, M. Yu., E-mail: kudinov@ssu.samara.ru

2013-11-15

The so-called non-Rosenbluth behavior of the proton electromagnetic form factors can be explained within the hypothesis of CP violation in electromagnetic processes involving composite systems of strongly interacting particles. It is shown that this hypothesis leads to the appearance of an additional, anapole, form factor of the proton. The proton electromagnetic form factors, including the anapole form factor, are estimated on the basis of experimental data on elastic electron-proton scattering.