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Sample records for proton structure functions

  1. Proton structure functions at HERA

    NASA Astrophysics Data System (ADS)

    Abt, Iris

    2014-05-01

    The "proton structure" is a wide field. Discussed are predominantly the precision measurements of the proton structure functions at HERA and some of their implications for the LHC measurements. In addition, a discussion of what a proton structure function represents is provided. Finally, a connection to nuclear physics is attempted. This contribution is an updated reprint of a contribution to "Deep Inelastic Scattering 2012".1

  2. Proton structure functions at small x

    DOE PAGES

    Hentschinski, Martin

    2015-11-03

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recentmore » result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA data.« less

  3. Proton structure functions at small x

    SciTech Connect

    Hentschinski, Martin

    2015-11-03

    Proton structure functions are measured in electron-proton collision through inelastic scattering of virtual photons with virtuality Q on protons; x denotes the momentum fraction carried by the struck parton. Proton structure functions are currently described with excellent accuracy in terms of scale dependent parton distribution functions, defined in terms of collinear factorization and DGLAP evolution in Q. With decreasing x however, parton densities increase and are ultimately expected to saturate. In this regime DGLAP evolution will finally break down and non-linear evolution equations w.r.t x are expected to take over. In the first part of the talk we present recent result on an implementation of physical DGLAP evolution. Unlike the conventional description in terms of parton distribution functions, the former describes directly the Q dependence of the measured structure functions. It is therefore physical insensitive to factorization scheme and scale ambiguities. It therefore provides a more stringent test of DGLAP evolution and eases the manifestation of (non-linear) small x effects. It however requires a precise measurement of both structure functions F2 and FL, which will be only possible at future facilities, such as an Electron Ion Collider. In the second part we present a recent analysis of the small x region of the combined HERA data on the structure function F2. We demonstrate that (linear) next-to-leading order BFKL evolution describes the effective Pomeron intercept, determined from the combined HERA data, once a resummation of collinear enhanced terms is included and the renormalization scale is fixed using the BLM optimal scale setting procedure. We also provide a detailed description of the Q and x dependence of the full structure functions F2 in the small x region, as measured at HERA. As a result, predictions for the structure function FL are found to be in agreement with the existing HERA

  4. Spin structure functions: Proton / deuteron measurements in the resonance region

    SciTech Connect

    Mark Jones; RSS Collaboration

    2006-02-01

    The RSS experiment ran in Hall C at Jefferson Lab and measured the proton and deuteron beam-target asymmetries for parallel and perpendicular target fields over a W range from pion threshold to 1.9 GeV at Q{sup 2} {approx} 1.3 GeV{sup 2}. Preliminary results for the proton spin structure functions g{sub 1} and g{sub 2} are presented.

  5. Spin Structure Functions of the Proton - SANE experiment

    NASA Astrophysics Data System (ADS)

    Baghdasaryan, Hovhannes

    2012-03-01

    The Spin Asymmetries of the Nucleon Experiment (SANE) is a measurement of inclusive electron scattering parallel and near perpendicular double spin asymmetries from a proton target. The main goal of the experiment was to measure A and A80 and to extract the spin asymmetries of the proton A1^p, A2^p and the spin structure functions g1^p and g2^p. Using the Thomas Jefferson National Accelerator Facility's polarized electron beam and the University of Virginia's polarized frozen ammonia (^14NH3) target in Hall C, the experiment ran in 2009, collecting data in a Q^2 region from 2.5 to 6.5 GeV^2 and between Bjorken x of 0.3 and 0.8. Particle detection was accomplished using the Big Electron Telescope Array (BETA), a novel non-magnetic detector. The physics motivation for the experiment and a brief overview of the polarized target and the detector will be presented along with the analysis developed in order to extract the proton spin asymmetries and structure functions. Results will be presented.

  6. Proton structure and parton distribution functions from HERA

    NASA Astrophysics Data System (ADS)

    Chekelian, Vladimir

    2016-11-01

    The H1 and ZEUS collaborations at the electron-proton collider HERA collected e± p scattering data corresponding to an integrated luminosity of about 1 fb-1. The data were taken at proton beam energies of 920, 820, 575 and 460 GeV and an electron beam energy of 27.5 GeV, with different electric charges and longitudinal polarisation of the electron beam. Using these data inclusive neutral and charged current deep inelastic cross sections were measured over six orders of magnitude in negative four-momentum-transfer squared, Q2, and Bjorken x. A combination of all inclusive cross sections, published by the H1 and ZEUS collaborations at HERA, was performed. Using these combined HERA data and the individual H1 and ZEUS data taken using the polarised electron beams, the proton structure functions F2, FγZ2, xFγZ3 and FL were obtained, and scaling violations, electroweak unification, and polarisation effects in the charged current process were demonstrated. The combined cross sections were used as a sole input to QCD analyses at leading, next-to-leading and next-to-next-to-leading orders, providing a new set of parton distribution functions, denoted as HERAPDF2.0. An extension of the analysis by including HERA data on charm and jet production allowed a simultaneous determination of parton distributions and the strong coupling.

  7. Considering protonation as a posttranslational modification regulating protein structure and function.

    PubMed

    Schönichen, André; Webb, Bradley A; Jacobson, Matthew P; Barber, Diane L

    2013-01-01

    Posttranslational modification is an evolutionarily conserved mechanism for regulating protein activity, binding affinity, and stability. Compared with established posttranslational modifications such as phosphorylation or ubiquitination, posttranslational modification by protons within physiological pH ranges is a less recognized mechanism for regulating protein function. By changing the charge of amino acid side chains, posttranslational modification by protons can drive dynamic changes in protein conformation and function. Addition and removal of a proton is rapid and reversible and, in contrast to most other posttranslational modifications, does not require an enzyme. Signaling specificity is achieved by only a minority of sites in proteins titrating within the physiological pH range. Here, we examine the structural mechanisms and functional consequences of proton posttranslational modification of pH-sensing proteins regulating different cellular processes.

  8. Measurement of the Proton and Deuteron Spin Structure Functions G1 and G2

    SciTech Connect

    Tobias, Al

    2003-04-02

    The SLAC experiment E155 was a deep-inelastic scattering experiment that scattered polarized electrons off polarized proton and deuteron targets in the effort to measure precisely the proton and deuteron spin structure functions. The nucleon structure functions g{sub 1} and g{sub 2} are important quantities that help test our present models of nucleon structure. Such information can help quantify the constituent contributions to the nucleon spin. The structure functions g{sub 1}{sup p} and G{sub 1}{sup d} have been measured over the kinematic range 0.01 {le} x {le} 0.9 and 1 {le} Q{sup 2} {le} 40 GeV{sup 2} by scattering 48.4 GeV longitudinally polarized electrons off longitudinally polarized protons and deuterons. In addition, the structure functions g{sub 2}{sup p} and g{sub 2}{sup d} have been measured over the kinematic range 0.01 {le} x {le} 0.7 and 1 {le} Q{sup 2} {le} 17 GeV{sup 2} by scattering 38.8 GeV longitudinally polarized electrons off transversely polarized protons and deuterons. The measurements of g{sub 1} confirm the Bjorken sum rule and find the net quark polarization to be {Delta}{Sigma} = 0.23 {+-} 0.04 {+-} 0.6 while g{sub 2} is found to be consistent with the g{sub 2}{sup WW} model.

  9. Measurement of the proton structure function F 2 from the 1993 HERA data

    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.; 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.; 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.; Schneider, J.-L.; 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.; Gialas, I.; 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.; Jeleń, K.; Kisielewska, D.; Kowalski, T.; Rulikowska-Zarębska, E.; Suszycki, L.; Zając, J.; Kędzierski, 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.; Hagge, L.; Hain, W.; Hasell, D.; Heßling, 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.; Mainusch, J.; 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.; Voß, 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.; Lohrmann, E.; 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.; 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.; Mitchell, J. W.; Patel, P. M.; Sinclair, L. E.; Stairs, D. G.; St. Laurent, M.; Ullmann, R.; 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.; Gasparini, F.; 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.; 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.; 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.; 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.

    1995-09-01

    The ZEUS detector has been used to measure the proton structure function F 2. During 1993 HERA collided 26.7 GeV electrons on 820 GeV protons. The data sample corresponds to an integrated luminosity of 0.54 pb-1, representing a twenty fold increase in statistics compared to that of 1992. Results are presented for 7< Q 2<104 GeV2 and x values as low as 3×10-4. The rapid rise in F 2 as x decreases observed previously is now studied in greater detail and persists for Q 2 values up to 500 GeV2.

  10. Measurement of inclusive proton double-spin asymmetries and polarized structure functions

    NASA Astrophysics Data System (ADS)

    Fersch, Robert G., Jr.

    2008-10-01

    The scattering of polarized electrons from a polarized proton target provides a means for studying the internal spin structure of the proton. The CLAS (CEBAF Large Acceptance Spectrometer) EG1b experiment in Hall-B at Jefferson Laboratory measured double-spin inclusive and exclusive electron-nucleon scattering asymmetries using longitudinally polarized frozen NH3 and ND3 targets and a longitudinally polarized electron beam at 4 different energies (1.6, 2.5, 4.2, 5.6 GeV). Extraction of the virtual photon asymmetry Ap1 (for 0.05 GeV2 < Q2 < 5.0 GeV2) provides precision measurements of the polarized proton spin-structure function gp1 in and above the resonance region. Linear regression of data between the varying energies yields new constraints on the virtual photon asymmetry Ap2 (and thus the structure function gp2 ) in the resonance region (for 0.3 GeV2 < Q2 < 1.0 GeV2). Measurements of these structure functions and their moments allows testing of perturbative Quantum Chromodynamics (pQCD) models and evaluation of moments of the structure functions in the Operator Product Expansion. Testing of Chiral Perturbation Theory (chiPT) at Q2 < 0.2 GeV 2 is enabled by the new data. Other applications of polarized structure functions include measurement of foward-spin polarizability, evaluation of high-order corrections in 1H hyperfine splitting, and testing of quark-hadron duality.

  11. 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.

  12. Leading and higher twists in proton, neutron and deuteron unpolarized structure functions F2

    SciTech Connect

    S. Simula

    2007-03-01

    We summarize the results of a recent global analysis of proton and deuteron F2 structure function world data performed over a large range of kinematics, including recent measurements done at JLab with the CLAS detector. From these data the lowest moments (n≤10) of the unpolarized structure functions are determined with good statistics and systematics. The Q2 evolution of the extracted moments is analyzed in terms of an OPE-based twist expansion, taking into account soft-gluon effects at large x. A clean separation among the leading- and higher-twist terms is achieved. By combining proton and deuteron measurements the lowest moments of the neutron F2 structure function are determined and its leading-twist term is extracted. Particular attention is paid to nuclear effects in the deuteron, which become increasingly important for the higher moments. Our results for the non-singlet, isovector (p-n) combination of the leading-twist moments are used to test recent lattice simulations. We also determine the lowest few moments of the higher-twist contributions, and find these to be approximately isospin independent, suggesting the possible dominance of ud correlations over uu and dd in the nucleon.

  13. Proton and deuteron spin structure function measurements in the resonance region

    SciTech Connect

    F.R. Wesselmann

    2003-07-01

    The RSS collaboration has measured the spin structure functions of the proton and the deuteron at Jefferson Lab using the Hall C HMS spectrometer, a polarized electron beam and a polarized solid target. The asymmetries A and A were measured in the region of the nucleon resonances (0.82 GeV < W < 1.98 GeV) at an average four momentum transfer of Q2 = 1.3 GeV2. The extracted spin structure functions and their kinematic dependence will make a significant contribution in the study of higher-twist effects and polarized duality tests. A description of the experiment and the latest findings of the analysis will be presented.

  14. Proton and deuteron structure functions in muon scattering at 470 GeV

    SciTech Connect

    Kotwal, A.V.; E665 Collaboration

    1995-05-01

    The proton and deuteron structure functions F{sub 2}{sup p} and F{sub 2}{sup d} measured in inelastic muon scattering with an average beam energy of 470 GeV. The data were taken at Fermilab experiment 665 during 1991-1992 using liquid hydrogen and deuterium targets. The F{sub 2} measurements are reported in the range 0.0008 < x < 0.6 and 0.2 < Q{sup 2} < 75 GeV{sup 2}. These are the first precise measurements of F{sub 2} in the low x and Q{sub 2} range of the data. The E665 data overlap in x with the HERA data, and there is a smooth connection in Q{sup 2} between the two data sets. At high Q{sup 2} the E665 measurements are consistent with QCD-evolved leading twist structure function models. The data are qualitatively described by structure function models incorporating the hadronic nature of the photon at low Q{sup 2}. The Q{sup 2} and the W dependence of the data measure the transition in the nature of the photon between a point-probe at high Q{sup 2} and a hadronic object at low Q{sup 2}.

  15. Longitudinal Structure Function F L of Proton from Regge Like Behaviour of Structure Function at Small-x

    NASA Astrophysics Data System (ADS)

    Baruah, Nomita; Das, Mrinal Kumar; Sarma, Jayanta Kumar

    2014-08-01

    The evolutions of longitudinal structure function F L from quantum chromodynamics (QCD) evolution equation in next-to-leading order at small-x is presented using the Regge like behaviour of the structure function. The proposed simple analytical expression for F L structure function provides the t- and x-evolution equations to study the behaviour of F L structure function at small-x. The calculated results are compared with the data of H1, ZEUS collaborations and results of Block model, Donnachie-Landshoff model. Our calculated results can be described within the framework of perturbative QCD.

  16. 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.

  17. Structural Basis for the Function and Inhibition of an Influenze Virus Proton Channel

    SciTech Connect

    Stouffer,A.; Acharya, R.; Salom, D.; Levine, A.; Di Costanzo, L.; Soto, C.; Tershko, V.; Nanda, V.; Stayrook, S.; DeGrado, W.

    2008-01-01

    The M2 protein from influenza A virus is a pH-activated proton channel that mediates acidification of the interior of viral particles entrapped in endosomes. M2 is the target of the anti-influenza drugs amantadine and rimantadine; recently, resistance to these drugs in humans, birds and pigs has reached more than 90% (ref. 1). Here we describe the crystal structure of the transmembrane-spanning region of the homotetrameric protein in the presence and absence of the channel-blocking drug amantadine. pH-dependent structural changes occur near a set of conserved His and Trp residues that are involved in proton gating2. The drug-binding site is lined by residues that are mutated in amantadine-resistant viruses3, 4. Binding of amantadine physically occludes the pore, and might also perturb the pKa of the critical His residue. The structure provides a starting point for solving the problem of resistance to M2-channel blockers.

  18. Proton and deuteron F2 structure function at low Q2

    SciTech Connect

    Tvaskis, Vladas; Asaturyan, Razmik; Baker, Oliver; Blok, Henk; Bosted, Peter; Boswell, Melissa; Bruell, Antje; Christy, Michael; Cochran, Anthony; Ent, Rolf; Filippone, Bradley; Gasparian, Ashot; Keppel, Cynthia; Kinney, Edward; Lapikas, L; Lorenzon, Wolfgang; Mammei, Juliette; Martin, J W; Mkrtchyan, Hamlet; Niculescu, Maria-Ioana; Piercey, Rodney; Potterveld, David; Smith, Gregory; Spurlock, Kurt; Van der Steenhoven, Gerard; Stepanyan, Stepan; Tadevosyan, Vardan; Wood, Stephen

    2010-06-01

    Measurements of the proton and deuteron F2 structure functions are presented. The data, taken at Jefferson Lab Hall C, span the four-momentum transfer range 0.062<2.8GeV2 and Bjorken x values from 0.009 to 0.45, thus extending the knowledge of F2 to low values of Q2 at low x. Next-to-next-to-leading-order calculations using recent parton distribution functions start to deviate from the data for Q2<2 GeV2 at the low and high x values. Down to the lowest value of Q2, the structure function is in good agreement with a parametrization of F2 based on data that have been taken at much higher values of Q2 or much lower values of x, and which are constrained by data at the photon point. The ratio of the deuteron and proton structure functions at low x remains well described by a logarithmic dependence on Q2 at low Q2.

  19. Measurement of the deep-inelastic spin-dependent structure functions of the proton and neutron at HERA

    SciTech Connect

    Beck, D.H.; Filippone, B.W.; Jourdan, J.; McKeown, R.D.; Milner, R.G.; Woodward, C.E.; Freedman, S.J.; Geesaman, D.F.; Holt, R.J.; Jackson, H.E.

    1988-01-01

    It is possible to measure the deep-inelastic spin-dependent structure functions g/sub 1//sup p/(x) and g/sub 1//sup n/(x) for the proton and neutron using internal polarized hydrogen, deuterium, and /sup 3/He targets of polarization 50% and thickness 10/sup 14/ to 10/sup 15/ cm/sup -2/ and the 60 mA longitudinally polarized 30 GeV electron beam in the HERA electron storage ring. The measurement of the deep-inelastic spin-structure of both isospin states of the nucleon at the same kinematics and using the same apparatus allows the Bjorken sum rule to be experimentally checked. In addition, it uniquely constrains the spin distribution of the u and d quarks as a function of x in any model of the nucleon. Possible target and detector configurations are described and an estimate of the accuracy of such a measurement is presented.

  20. The Gdh Sum Rule with Nearly Real Photons and the G1 Proton Structure Function at Low Momentum Transfer

    NASA Astrophysics Data System (ADS)

    de Vita, R.

    2005-02-01

    A measurement of the proton structure function g1 for momentum transfer Q2 in the range 0.01-0.5 GeV2/c2 is planned in Hall B at Jefferson Lab using the CEBAF Large Acceptance Spectrometer (CLAS). The CEBAF polarized electron beam with energy between 1 and 3.2 GeV will scatter off a polarized solid state target. The outgoing electrons will be detected down to a minimum angle of ~5 degrees in CLAS thanks to a new gas Cherenkoy counter designed to optimize the detection efficiency and pion rejection in the operating conditions of this experiment. The proton spin structure function g1 will be measured from the threshold region to the resonance region and beyond. The expected results will add high precision information on the nucleon spin response in kinematics where tests of Chiral Perturbation Theory are possible, and provide the data for an improved understanding of hadronic spin processes in the confinement regime.

  1. Proposal to measure spin-structure functions and semi-exclusive asymmetries for the proton and neutron at HERA

    SciTech Connect

    Jackson, H.E.; Hansen, J.O.; Jones, C.E.

    1995-08-01

    Nucleon spin physics will be studied in the HERMES experiment, that will use polarized internal targets of essentially pure atomic H, D, and {sup 3}He in the HERA electron storage ring at DESY. A series of measurements of spin-dependent properties of the nucleon and few-body nuclei will be made; the spin structure function g{sub 1}(x) of the proton and neutron will be measured to test the Bjorken sum rule and study the fraction of the nucleon spin carried by quarks; the spin structure function g{sub 2}W, sensitive to quark-gluon correlations, and the structure functions b{sub 1}(x), and {Delta}(x), sensitive to nuclear binding effects, will be measured; and, using the particle identification capability of the HERMES detector, pions will be detected in coincidence with the scattered electrons. The coincident hadron measurements represent the most important extension that can be made at this time to the existing measurements on the nucleon spin structure functions because they provide information about the flavor-dependence of the quark spin distribution in the nucleon. Argonne is providing the Cerenkov counter to be used for particle identification and developing the drifilm coating technique for the ultrathin target cell required for this experiment. The HERMES collaboration intends to use polarized targets with the highest available figures of merit, and the Argonne laser-driven source offers the most promise for a significant advance in present-day targets.

  2. Proton-Proton Elastic Scattering Excitation Functions at Intermediate Energies

    SciTech Connect

    Bisplinghoff, J.; Daniel, R.; Diehl, O.; Engelhardt, H.; Ernst, J.; Eversheim, P.; Gro-Hardt, R.; Heider, S.; Heine, A.; Hinterberger, F.; Jahn, R.; Jeske, M.; Lahr, U.; Maschuw, R.; Mayer-Kuckuk, T.; Mosel, F.; Rohdje, H.; Rosendaal, D.; Ro, U.; Scheid, H.; Schulz-Rojahn, M.; Schwandt, F.; Schwarz, V.; Trelle, H.; Wiedmann, W.; Ziegler, R.; Albers, D.; Bollmann, R.; Bueer, K.; Dohrmann, F.; Gasthuber, M.; Greiff, J.; Gro, A.; Igelbrink, M.; Langkau, R.; Lindlein, J.; Mueller, M.; Muenstermann, M.; Schirm, N.; Scobel, W.; Wellinghausen, A.; Woller, K.; Cloth, P.; Gebel, R.; Maier, R.; Prasuhn, D.; von Rossen, P.; Sterzenbach, G.

    1997-03-01

    Excitation functions of proton-proton elastic scattering cross sections have been measured in narrow steps for projectile momenta p{sub p} (energies T{sub p}) from 1100 to 3300MeV/c (500 to 2500MeV) in the angular range 35{degree}{le}{Theta}{sub c.m.}{le}90{degree} with a detector providing {Delta}{Theta}{sub c.m.}{approx}1.4{degree} resolution. Measurements have been performed continuously during projectile acceleration in the cooler synchrotron COSY with an internal CH{sub 2} fiber target, taking particular care to monitor luminosity as a function of T{sub p}. The advantages of this experimental technique are demonstrated, and the excitation functions obtained are compared to existing cross section data. No evidence for narrow structures was found. {copyright} {ital 1997} {ital The American Physical Society}

  3. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: γ-rays and protons in action.

    PubMed

    Ježková, Lucie; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, Alla; Krasavin, Evgeny; Kozubek, Stanislav

    2014-01-01

    According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure-the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams.

  4. A Kinematically Complete Measurement of the Proton Structure Function F2 in the Resonance Region and Evaluation of Its Moments

    SciTech Connect

    Mikhail Osipenko; Et. Al.

    2003-05-01

    We measured the inclusive electron-proton cross section in the nucleon resonance region (W<2.5 GeV) at momentum transfers Q2 below 4.5 (GeV/c)2 with the CLAS detector. The large acceptance of CLAS allowed the measurement of the cross section in a large, contiguous two-dimensional range of Q2 and x, making it possible to perform an integration of the data at fixed Q2 over the significant x interval. >From these data we extracted the structure function F2 and, by including other world data, we studied the Q2 evolution of its moments, Mn(Q2), in order to estimate higher twist contributions. The small statistical and systematic uncertainties of the CLAS data allow a precise extraction of the higher twists and will require significant improvements in theoretical predictions if a meaningful comparison with these new experimental results is to be made.

  5. Kinematically complete measurement of the proton structure function F2 in the resonance region and evaluation of its moments

    NASA Astrophysics Data System (ADS)

    Osipenko, M.; Ricco, G.; Taiuti, M.; Ripani, M.; Simula, S.; Adams, G.; Anciant, E.; Anghinolfi, M.; Asavapibhop, B.; Audit, G.; Auger, T.; Avakian, H.; Bagdasaryan, H.; Ball, J. P.; Barrow, S.; Battaglieri, M.; Beard, K.; Bektasoglu, M.; Bianchi, N.; Biselli, A. S.; Boiarinov, S.; Bosted, P.; Bouchigny, S.; Bradford, R.; Branford, D.; Briscoe, W. J.; Brooks, W. K.; Burkert, V. D.; Calarco, J. R.; Carman, D. S.; Carnahan, B.; Cazes, A.; Cetina, C.; Ciciani, L.; Clark, R.; Cole, P. L.; Coleman, A.; Cords, D.; Corvisiero, P.; Crabb, D.; Crannell, H.; Cummings, J. P.; de Sanctis, E.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; de Vita, R.; Dharmawardane, K. V.; Djalali, C.; Dodge, G. E.; Domingo, J. J.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dytman, S.; Eckhause, M.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Empl, A.; Fatemi, R.; Fedotov, G.; Feuerbach, R. J.; Ficenec, J.; Forest, T. A.; Funsten, H.; Gaff, S. J.; Gai, M.; Gavalian, G.; Gilad, S.; Gilfoyle, G. P.; Giovanetti, K. L.; Girard, P.; Griffioen, K.; Golovatch, E.; Gordon, C. I.; Guidal, M.; Guillo, M.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hardie, J.; Heddle, D.; Hersman, F. W.; Hicks, K.; Hicks, R. S.; Holtrop, M.; Hu, J.; Hyde-Wright, C. E.; Ishkhanov, B. S.; Ito, M. M.; Jenkins, D.; Joo, K.; Kelley, J. H.; Kellie, J. D.; Khandaker, M.; Kim, D. H.; Kim, K. Y.; Kim, K.; Kim, M. S.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Klusman, M.; Kossov, M.; Kramer, L. H.; Kuang, Y.; Kuhn, S. E.; Kuhn, J.; Lachniet, J.; Laget, J. M.; Lawrence, D.; Li, Ji; Livingston, K.; Lukashin, K.; Manak, J. J.; Marchand, C.; McAleer, S.; McCarthy, J.; McNabb, J. W.; Mecking, B. A.; Mehrabyan, S.; Mestayer, M. D.; Meyer, C. A.; Mikhailov, K.; Minehart, R.; Mirazita, M.; Miskimen, R.; Mokeev, V.; Morand, L.; Morrow, S. A.; Muccifora, V.; Mueller, J.; Murphy, L. Y.; Mutchler, G. S.; Napolitano, J.; Nasseripour, R.; Nelson, S. O.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; O'Rielly, G. V.; Opper, A. K.; Park, K.; Paschke, K.; Pasyuk, E.; Peterson, G.; Philips, S. A.; 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.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Sabourov, K.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Sargsyan, M.; Schumacher, R. A.; Serov, V. S.; Sharabian, Y. G.; Shaw, J.; Simionatto, S.; Skabelin, A. V.; Smith, E. S.; Smith, L. C.; Sober, D. I.; Spraker, M.; Stavinsky, A.; Stepanyan, S.; Stoler, P.; Taylor, S.; Tedeschi, D. J.; Thoma, U.; Thompson, R.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Wang, K.; Weinstein, L. B.; Weller, H.; Weygand, D. P.; Whisnant, C. S.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zhang, B.; Zhao, J.; Zhou, Z.

    2003-05-01

    We measured the inclusive electron-proton cross section in the nucleon resonance region (W<2.5 GeV) at momentum transfers Q2 below 4.5 (GeV/c)2 with the CLAS detector. The large acceptance of CLAS allowed the measurement of the cross section in a large, contiguous two-dimensional range of Q2 and x, making it possible to perform an integration of the data at fixed Q2 over the significant x interval. From these data we extracted the structure function F2 and, by including other world data, we studied the Q2 evolution of its moments, Mn(Q2), in order to estimate higher twist contributions. The small statistical and systematic uncertainties of the CLAS data allow a precise extraction of the higher twists and will require significant improvements in theoretical predictions if a meaningful comparison with these new experimental results is to be made.

  6. Precision Measurement of the Proton and Deuteron Spin Structure Functions g2

    SciTech Connect

    Rock, Stephen E.

    2003-02-27

    We measured the spin structure functions g{sub 2}{sup p} and g{sub 2}{sup d} in the range 0.02 {le} x {le} 0.8 and 0.7 {le} Q{sup 2} {le} 20 GeV{sup 2} by scattering 29.1 and 32.3 GeV longitudinally polarized electrons from transversely polarized NH{sub 3} and {sup 6}LiD targets. g{sub 2} approximately follows the twist-2 Wandzura-Wilczek calculation. The twist-3 reduced matrix elements d{sub 2}{sup p} and d{sub 2}{sup m} are less than two standard deviations from zero. The data are inconsistent with the Burkhardt-Cottingham sum rule if there is no pathological behavior as x {yields} 0. The Efremov-Leader-Teryaev integral is consistent with zero.

  7. Precision measurement of the proton and deuteron spin structure functions g2 and asymmetries A2

    NASA Astrophysics Data System (ADS)

    E155 Collaboration; Anthony, P. L.; Arnold, R. G.; Averett, T.; Band, H. R.; Benmouna, N.; Boeglin, W.; Borel, H.; Bosted, P. E.; Bültmann, S. L.; Court, G. R.; Crabb, D.; Day, D.; Decowski, P.; Depietro, P.; Egiyan, H.; Erbacher, R.; Erickson, R.; Fatemi, R.; Frlez, E.; Griffioen, K. A.; Harris, C.; Hughes, E. W.; Hyde-Wright, C.; Igo, G.; Johnson, J.; King, P.; Kramer, K.; Kuhn, S. E.; Lawrence, D.; Liang, Y.; Lindgren, R.; Lombard-Nelsen, R. M.; McKee, P.; McNulty, D. E.; Meyer, W.; Mitchell, G. S.; Mitchell, J.; Olson, M.; Penttila, S.; Peterson, G. A.; Pitthan, R.; Pocanic, D.; Prepost, R.; Prescott, C.; Raue, B. A.; Reyna, D.; Ryan, P.; Rochester, L. S.; Rock, S.; Rondon-Aramayo, O.; Sabatie, F.; Smith, T.; Sorrell, L.; Lorant, S. St.; Szalata, Z.; Terrien, Y.; Tobias, A.; Toole, T.; Trentalange, S.; Wesselmann, F. R.; Wright, T. R.; Zeier, M.; Zhu, H.; Zihlmann, B.

    2003-01-01

    We have measured the spin structure functions g2p and g2d and the virtual photon asymmetries A2p and A2d over the kinematic range /0.02<=x<=0.8 and 0.7<=Q2<=20GeV2 by scattering 29.1 and 32.3 GeV longitudinally polarized electrons from transversely polarized NH3 and 6LiD targets. Our measured g2 approximately follows the twist-2 Wandzura-Wilczek calculation. The twist-3 reduced matrix elements d2p and d2n are less than two standard deviations from zero. The data are inconsistent with the Burkhardt-Cottingham sum rule if there is no pathological behavior as /x-->0. The Efremov-Leader-Teryaev integral is consistent with zero within our measured kinematic range. The absolute value of A2 is significantly smaller than the A2<√R(1+A1)/2 limit.

  8. Global Analysis of Data on the Proton Structure Function g{sub 1} and Extraction of its Moments

    SciTech Connect

    Mikhail Osipenko; Silvano Simula; Wolodymyr Melnitchouk; Peter Bosted; Volker Burkert; Eric Christy; Keith Griffioen; Cynthia Keppel; Sebastian Kuhn; Giovani Ricco

    2005-01-01

    Inspired by recent measurements with the CLAS detector at Jefferson Lab, we perform a self-consistent analysis of world data on the proton structure function g{sub 1} in the range 0.17 < Q{sup 2} < 30 (GeV/c){sup 2}. We compute low-order moments g{sub 1} and study their evolution from small to large values of Q{sup 2}. The analysis takes includes the latest data on the unpolarized inclusive cross sections, the recent results for the ratio R = {sigma}{sub L}/{sigma}{sub T}, and a new model for the transverse asymmetry A{sub 2} in the resonance region. The contributions of both leading and higher twists are extracted, taking into account effects from radiative corrections beyond the next-to-leading order by means of soft-gluon resummation techniques. The contribution of higher twists to the g{sub 1} moments is found to be significantly larger than in the case of the unpolarized structure function F{sub 2}.

  9. The proton-linked monocarboxylate transporter (MCT) family: structure, function and regulation.

    PubMed Central

    Halestrap, A P; Price, N T

    1999-01-01

    Monocarboxylates such as lactate and pyruvate play a central role in cellular metabolism and metabolic communication between tissues. Essential to these roles is their rapid transport across the plasma membrane, which is catalysed by a recently identified family of proton-linked monocarboxylate transporters (MCTs). Nine MCT-related sequences have so far been identified in mammals, each having a different tissue distribution, whereas six related proteins can be recognized in Caenorhabditis elegans and 4 in Saccharomyces cerevisiae. Direct demonstration of proton-linked lactate and pyruvate transport has been demonstrated for mammalian MCT1-MCT4, but only for MCT1 and MCT2 have detailed analyses of substrate and inhibitor kinetics been described following heterologous expression in Xenopus oocytes. MCT1 is ubiquitously expressed, but is especially prominent in heart and red muscle, where it is up-regulated in response to increased work, suggesting a special role in lactic acid oxidation. By contrast, MCT4 is most evident in white muscle and other cells with a high glycolytic rate, such as tumour cells and white blood cells, suggesting it is expressed where lactic acid efflux predominates. MCT2 has a ten-fold higher affinity for substrates than MCT1 and MCT4 and is found in cells where rapid uptake at low substrate concentrations may be required, including the proximal kidney tubules, neurons and sperm tails. MCT3 is uniquely expressed in the retinal pigment epithelium. The mechanisms involved in regulating the expression of different MCT isoforms remain to be established. However, there is evidence for alternative splicing of the 5'- and 3'-untranslated regions and the use of alternative promoters for some isoforms. In addition, MCT1 and MCT4 have been shown to interact specifically with OX-47 (CD147), a member of the immunoglobulin superfamily with a single transmembrane helix. This interaction appears to assist MCT expression at the cell surface. There is still

  10. Two-Jet Differential Cross-Section and Structure Functions in Proton-Antiproton Collisions at SQRT.S = 1.8 Tev

    NASA Astrophysics Data System (ADS)

    Harris, Robert M.

    Data from the 1987 run of the Collider Detector at Fermilab has been used to measure the two jet differential cross section d^3sigma/dE_ t deta_1 deta_2 in proton antiproton collisions at sqrt{s} = 1.8 TeV. For this measurement, one jet was restricted to the central region |eta_1 | < 0.6, where eta_1 and eta_2 are the pseudorapidity of the two jets with largest transverse energy in the event, and E_ t is the transverse energy of the centrally produced jet. Leading order QCD and the similarity of subprocess scattering angular distributions in a modified "single effective subprocess" approximation have been used to extract the "proton effective structure function" in parametric form. Using lowest order QCD, and quark and anti-quark structure functions evolved from deep inelastic scattering measurements, the gluon structure function of the proton has been estimated from the measured two jet differential cross section. The two jet differential cross section, effective structure function, and gluon structure function from CDF are all in agreement with the predictions of lowest order QCD and structure functions evolved from deep inelastic scattering measurements.

  11. Functional polymers for anhydrous proton transport

    NASA Astrophysics Data System (ADS)

    Chikkannagari, Nagamani

    Anhydrous proton conducting polymers are highly sought after for applications in high temperature polymer electrolyte membrane fuel cells (PEMFCs). N-heterocycles (eg. imidazole, triazole, and benzimidazole), owing to their amphoteric nature, have been widely studied to develop efficient anhydrous proton transporting polymers. The proton conductivity of N-heterocyclic polymers is influenced by several factors and the design and development of polymers with a delicate balance among various synergistic and competing factors to provide appreciable proton conductivities has been a challenging task. In this thesis, the proton transport (PT) characteristics of polymers functionalized with two diverse classes of functional groups--- N-heterocycles and phenols have been investigated and efforts have been made to develop the molecular design criteria for the design and development of efficient proton transporting functional groups and polymers. The proton conduction pathway in 1H-1,2,3-triazole polymers is probed by employing structurally analogous N-heterocyclic (triazole, imidazole, and pyrazole) and benz-N-heterocyclic (benzotriazole, benzimidazole, and benzopyrazole) polymers. Imidazole-like pathway was found to dominate the proton conductivity of triazole and pyrazole-like pathway makes only a negligible contribution, if any. Polymers containing benz-N-heterocycles exhibited higher proton conductivity than those with the corresponding N-heterocycles. Pyrazole-like functional groups, i.e. the molecules with two nitrogen atoms adjacent to each other, were found not to be good candidates for PT applications. A new class of proton transporting functional groups, phenols, has been introduced for anhydrous PT. One of the highlighting features of phenols over N-heterocycles is that the hydrogen bond donor/acceptor reorientation can happen on a single -OH site, allowing for facile reorientational dynamics in Grotthuss PT and enhanced proton conductivities in phenolic polymers

  12. Measurement of inclusive cross sections at high at and 252 GeV and of the longitudinal proton structure function at HERA

    NASA Astrophysics Data System (ADS)

    Andreev, V.; Baghdasaryan, A.; Baghdasaryan, S.; Begzsuren, K.; Belousov, A.; Belov, P.; Boudry, V.; Bradt, G.; Brinkmann, M.; Brisson, V.; Britzger, D.; Buniatyan, A.; Bylinkin, A.; Bystritskaya, L.; Campbell, A. J.; Cantun Avila, K. B.; Ceccopieri, F.; Cerny, K.; Chekelian, V.; Contreras, J. G.; Dainton, J. B.; Daum, K.; De Wolf, E. A.; Diaconu, C.; Dobre, M.; Dodonov, V.; Dossanov, A.; Dubak, A.; Eckerlin, G.; Egli, S.; Elsen, E.; Favart, L.; Fedotov, A.; Feltesse, J.; Ferencei, J.; Fleischer, M.; Fomenko, A.; Gabathuler, E.; Gayler, J.; Ghazaryan, S.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Gouzevitch, M.; Grab, C.; Grebenyuk, A.; Greenshaw, T.; Grindhammer, G.; Habib, S.; Haidt, D.; Henderson, R. C. W.; Herbst, M.; Hildebrandt, M.; Hladkỳ, J.; Hoffmann, D.; Horisberger, R.; Hreus, T.; Huber, F.; Jacquet, M.; Janssen, X.; Jung, A. W.; Jung, H.; Kapichine, M.; Kiesling, C.; Klein, M.; Kleinwort, C.; Kogler, R.; Kostka, P.; Kretzschmar, J.; Krüger, K.; Landon, M. P. J.; Lange, W.; Laycock, P.; Lebedev, A.; Levonian, S.; Lipka, K.; List, B.; List, J.; Lobodzinski, B.; Lubimov, V.; Malinovski, E.; Martyn, H.-U.; Maxfield, S. J.; Mehta, A.; Meyer, A. B.; Meyer, H.; Meyer, J.; Mikocki, S.; Morozov, A.; Müller, K.; Naumann, Th.; Newman, P. R.; Niebuhr, C.; Nowak, G.; Nowak, K.; Olivier, B.; Olsson, J. E.; Ozerov, D.; Pahl, P.; Pascaud, C.; Patel, G. D.; Perez, E.; Petrukhin, A.; Picuric, I.; Pirumov, H.; Pitzl, D.; Plačakytė, R.; Pokorny, B.; Polifka, R.; Radescu, V.; Raicevic, N.; Raspereza, A.; Ravdandorj, T.; Reimer, P.; Rizvi, E.; Robmann, P.; Roosen, R.; Rostovtsev, A.; Rotaru, M.; Rusakov, S.; Šálek, D.; Sankey, D. P. C.; Sauter, M.; Sauvan, E.; Schmitt, S.; Schoeffel, L.; Schöning, A.; Schultz-Coulon, H.-C.; Sefkow, F.; Shushkevich, S.; Soloviev, Y.; Sopicki, P.; South, D.; Spaskov, V.; Specka, A.; Steder, M.; Stella, B.; Straumann, U.; Sykora, T.; Thompson, P. D.; Traynor, D.; Truöl, P.; Tsakov, I.; Tseepeldorj, B.; Turnau, J.; Valkárová, A.; Vallée, C.; Van Mechelen, P.; Vazdik, Y.; Wegener, D.; Wünsch, E.; Žáček, J.; Zhang, Z.; Žlebčík, R.; Zohrabyan, H.; Zomer, F.

    2014-04-01

    Inclusive double differential cross sections for neutral current deep inelastic scattering are measured with the H1 detector at HERA. The data were taken with a lepton beam energy of GeV and two proton beam energies of and 575 GeV corresponding to centre-of-mass energies of 225 and 252 GeV, respectively. The measurements cover the region of for GeV up to . The measurements are used together with previously published H1 data at GeV and lower data at , and GeV to extract the longitudinal proton structure function in the region GeV.

  13. Chemistry as a function of the fine-structure constant and the electron-proton mass ratio

    SciTech Connect

    King, Rollin A.; Siddiqi, Ali; Allen, Wesley D.; Schaefer, Henry F. III

    2010-04-15

    In standard computations in theoretical quantum chemistry the accepted values of the fundamental physical constants are assumed. Alternatively, the tools of computational quantum chemistry can be used to investigate hypothetical chemistry that would result from different values of these constants, given the same physical laws. In this work, the dependence of a variety of basic chemical quantities on the values of the fine-structure constant and the electron-proton mass ratio is explored. In chemistry, the accepted values of both constants may be considered small, in the sense that their increase must be substantial to seriously impact bond energies. It is found that if the fine-structure constant were larger, covalent bonds between light atoms would be weaker, and the dipole moment and hydrogen-bonding ability of water would be reduced. Conversely, an increase in the value of the electron-proton mass ratio increases dissociation energies in molecules such as H{sub 2}, O{sub 2}, and CO{sub 2}. Specifically, a sevenfold increase in the fine-structure constant decreases the strength of the O-H bond in the water molecule by 7 kcal mol{sup -1} while reducing its dipole moment by at least 10%, whereas a 100-fold increase in the electron-proton mass ratio increases the same bond energy by 11 kcal mol{sup -1}.

  14. Anatomy of the differential gluon structure function of the proton from the experimental data on F2p(x,Q2)

    NASA Astrophysics Data System (ADS)

    Ivanov, I. P.; Nikolaev, N. N.

    2002-03-01

    The differential gluon structure function of the proton F(x,Q2) introduced by Fadin, Kuraev, and Lipatov in 1975 is used in many applications of small-x QCD. We report here ready-to-use parametrizations of F(x,Q2) from the κ-factorization phenomenology of the experimental data on the small-x proton structure function F2p(x,Q2). These parametrizations are based partly on the available Dokshitzer-Gribov-Lipatov-Altarelli-Parisi (DGLAP) evolution fits [Glück-Reya-Vogt, Coordinated Theoretical/Experimental Project on QCD Phenomenology (CTEQ), and Martin-Roberts-Stirling] to parton distribution functions and on realistic extrapolations into a soft region. We discuss the impact of soft gluons on various observables. The x dependence of the F(x,Q2) so determined varies strongly with Q2 and does not exhibit simple Regge properties. Nonetheless, the hard-to-soft diffusion is found to give rise to a viable approximation of the proton structure function F2p(x,Q2) by the soft and hard Regge components with intercepts Δsoft=0 and Δhard~0.4.

  15. Measurement of the Proton Structure Function F{sub L}(x, Q{sup 2}) with the H1 Experiment

    SciTech Connect

    Raicevic, Natasa

    2010-01-21

    A preliminary measurement is reported of the longitudinal proton structure function F{sub L}(x, Q{sup 2}) obtained from the H1 experiment at the ep collider HERA. This is the first measurement of the longitudinal structure function in a range of squared four-momentum transfer 2.5<=Q{sup 2}<=800 GeV{sup 2}. Employing the energy dependence of the cross section, the measurement is based on inclusive deep inelastic e{sup +}p scattering cross section measurements with a positron beam energy of 27.5 GeV and proton beam energies of 920, 575 and 460 GeV. The measure F{sub L} values are compared with higher order QCD calculations based on parton densities obtained using cross section data previously measured at HERA.

  16. (1)JCH NMR Profile: Identification of Key Structural Features and Functionalities by Visual Observation and Direct Measurement of One-Bond Proton-Carbon Coupling Constants.

    PubMed

    Marcó, Núria; Souza, Alexandre A; Nolis, Pau; Cobas, Carlos; Gil, Roberto R; Parella, Teodor

    2017-02-17

    A user-friendly NMR interface for the visual and accurate determination of experimental one-bond proton-carbon coupling constants ((1)JCH) in small molecules is presented. This intuitive (1)JCH profile correlates directly to δ((1)H), and (1)JCH facilitates the rapid identification and assignment of (1)H signals belonging to key structural elements and functional groups. Illustrative examples are provided for some target molecules, including terminal alkynes, strained rings, electronegative substituents, or lone-pair-bearing heteronuclei.

  17. 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

  18. 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.

  19. Local structure investigation of oxide ion and proton defects in Ge-apatites by pair distribution function analysis.

    PubMed

    Malavasi, Lorenzo; Orera, Alodia; Slater, Peter R; Panchmatia, Pooja M; Islam, M Saiful; Siewenie, Joan

    2011-01-07

    In this communication we provide a direct insight into the local structure and defects of oxygen excess Ge-apatites, in both dry and deuterated states, by means of pair distribution function analysis.

  20. Spin structure of the proton

    SciTech Connect

    Nathan Isgur

    1995-08-01

    In these lectures the author argues that their response to the spin crisis should not be to abandon the naive quark model baby, but rather to allow it to mature. He begin by recalling what a beautiful baby the quark model is via an overview of its successes in spectroscopy, dynamics, and valence spin structure. He also introduces the conservative hypothesis that dynamical q{anti q} pairs are its key missing ingredient. He then discusses dressing the baby. He first shows that it can be clothed in glue without changing its spectroscopic successes. In the process, several dynamical mysteries associated with quark model spectroscopy are potentially explained. Next, he dresses the baby in q{anti q} pairs, first showing that this can be done without compromising the naive quark model's success with either spectroscopy or the OZI rule. Finally, he shows that despite their near invisibility elsewhere, pairs do play an important role in the proton's spin structure by creating an antipolarized q{anti q} sea. In the context of an explicit calculation he demonstrate that it is plausible that the entire ''spin crisis'' arises from this effect.

  1. 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

  2. Proton Spin Structure in the Resonance Region

    SciTech Connect

    F. R. Wesselmann; K. Slifer; S. Tajima; A. Aghalaryan; A. Ahmidouch; R. Asaturyan; F. Bloch; W. Boeglin; P. Bosted; C. Carasco; R. Carlini; J. Cha; J. P. Chen; M. E. Christy; L. Cole; L. Coman; D. Crabb; S. Danagoulian; D. Day; J. Dunne; M. Elaasar; R. Ent; H. Fenker; E. Frlez; L. Gan; D. Gaskell; J. Gomez; B. Hu; M. K. Jones; J. Jourdan; C. Keith; C. E. Keppel; M. Khandaker; A. Klein; L. Kramer; Y. Liang; J. Lichtenstadt; R. Lindgren; D. Mack; P. McKee; D. McNulty; D. Meekins; H. Mkrtchyan; R. Nasseripour; I. Niculescu; K. Normand; B. Norum; D. Pocanic; Y. Prok; B. Raue; J. Reinhold; J. Roche; D. Rohe; O. A. Rondon; N. Savvinov; B. Sawatzky; M. Seely; I. Sick; C. Smith; G. Smith; S. Stepanyan; L. Tang; G. Testa; W. Vulcan; K. Wang; G. Warren; S. Wood; C. Yan; L. Yuan; Junho Yun; Markus Zeier; Hong Guo Zhu

    2006-10-11

    The RSS collaboration has measured the spin structure functions g{sub 1} and g{sub 2} of the proton at Jefferson Lab using the lab's polarized electron beam, the Hall C HMS spectrometer and the UVa polarized solid target. The asymmetries A{sub parallel} and A{sub perp} were measured at the elastic peak and in the region of the nucleon resonances (1.085 GeV < W < 1.910 GeV) at an average four momentum transfer of Q{sup 2} = 1.3 GeV{sup 2}. The extracted spin structure functions and their kinematic dependence make a significant contribution in the study of higher-twist effects and polarized duality tests.

  3. Understanding the proton's spin structure

    SciTech Connect

    Fred Myhrer; Thomas, Anthony W.

    2010-02-01

    We discuss the tremendous progress that has been towards an understanding of how the spin of the proton is distributed on its quark and gluon constituents. This is a problem that began in earnest twenty years ago with the discovery of the proton "spin crisis" by the European Muon Collaboration. The discoveries prompted by that original work have given us unprecedented insight into the amount of spin carried by polarized gluons and the orbital angular momentum of the quarks.

  4. Spin Structure Moments of the Proton and Deuteron

    SciTech Connect

    Slifer, Karl; Rondon-Aramayo, Oscar; Aghalaryan, Aram; Ahmidouch, Abdellah; Asaturyan, Razmik; Bloch, Frederic; Boeglin, Werner; Bosted, Peter; Carasco, Cedric; Carlini, Roger; Cha, Jinseok; Chen, Jian-Ping; Christy, Michael; Cole, Leon; Coman, Luminita; Crabb, Donald; Danagoulian, Samuel; Day, Donal; Dunne, James; Elaasar, Mostafa; Ent, Rolf; Fenker, Howard; Frlez, Emil; Gaskell, David; Gan, Liping; Gomez, Javier; Hu, Bitao; Jourdan, Juerg; Jones, Mark; Keith, Christopher; Keppel, Cynthia; Khandaker, Mahbubul; Klein, Andreas; Kramer, Laird; Liang, Yongguang; Lichtenstadt, Jechiel; Lindgren, Richard; Mack, David; McKee, Paul; McNulty, Dustin; Meekins, David; Mkrtchyan, Hamlet; Nasseripour, Rakhsha; Niculescu, Maria-Ioana; Normand, Kristoff; Norum, Blaine; Pocanic, Dinko; Prok, Yelena; Raue, Brian; Reinhold, Joerg; Roche, Julie; Rohe, Daniela; Savvinov, Nikolai; Sawatzky, Bradley; Seely, Mikell; Sick, Ingo; Smith, C.; Smith, G.; Stepanyan, Samuel; Tang, Liguang; Tajima, Shigeyuki; Testa, Giuseppe; Vulcan, William; Wang, Kebin; Warren, G.; Wesselmann, Frank; Wood, Stephen; Yan, Chen; Yuan, Lulin; Yun, Junho; Zeier, Markus; Guo Zhu, Hong

    2009-01-01

    Moments of the spin structure functions g1 and g2 of the proton and deuteron have been measured in the resonance region at intermediate four momentum transfer. We perform a Nachtmann moment analysis of this data, along with isovector and isoscalar combinations, in order to rigorously account for target mass effects. This analysis provides the first definitive evidence for dynamic higher twists.

  5. Structure in the Proton and the Neutron

    DOE R&D Accomplishments Database

    Hofstadter, R.

    1958-06-01

    A survey of the recent work on the structures of the proton and the neutron carried out by high-energy electron-scattering methods is presented. Early work established finite size effects in the proton and led to information about the charge and magnetic density distributions in the proton. The rms size was established to be close to (0.77 plus or minus 0.10) x 10{sup -13} cm, and the density distributions of charge and anomalous magnetic moment were shown to be approximately of the same shape. The form factors could be described in terms of several alternative models given, for example, by an exponential, gaussian, hollow exponential, hollow gaussian, etc., distribution of densities. Many other shapes were excluded by the experimental data. Recent work by Bumiller and Hofstadter now fixes one among these models that is appropriate to the proton and provides an extremely good fit at all angles between energies of 200 and 650 Mev. The new evidence clearly favors the exponential model with rms radius (0.80 plus or minus 0.04) 10{sup -13} cm. Recent studies of the proton have attempted to answer the question: how closely similar are the charge and magnetic form factors? This work now shows that the distributions have the same sizes and shapes to within 10 per cent, and each distribution is given very closely by the exponential model described above with radius (0.80 plus or minus 0.04) x 10{sup -13}. Certain other similar models will be discussed. Early work on the inelastic continuum in the deuteron established that the neutron's magnetic structure was extended and not a point. It was further shown that the neutron's size was approximately the same as that of the proton. This work has recently been extended by Yearian and Hofstadter to a determination of the variation of the neutron's magnetic form factor over the range where the proton's form factor is known. The new results show: (1) the neutron is not a point, (2) the neutron's magnetic structure has a size lying

  6. Analytic functions fit to proton transfer potentials

    NASA Astrophysics Data System (ADS)

    Duan, Xiaofeng; Scheiner, Steve

    1992-07-01

    Proton transfer potentials are traced out in (H 2OH 2OH +OH 2OH 2) and (H 3NH 3NH +NH 3NH 3) by ab initio computations for a series of different H-bond lengths. Attempts are then made to fit these quantum mechanical results by various forms of analytic functions. Best results are achieved by a pair of Morse functions with correlation coefficients in excess of 0.997. The numerical values of the Morse parameters are fairly insensitive to H-bond length, allowing their use in more general situations. The Φ 4 function and its related fourth-order polynomial also fit well, but the parameters are much more sensitive to H-bond length. Gaussian-type functions or a Lippincott—Schroeder potential do not fit as well and a sinusoidal function gives rather poor agreement with the quantum mechanical results.

  7. A Precision Measurement of the Spin Structure Function g{sub 1}(x,Q{sup 2}) for the Proton and Deuteron

    SciTech Connect

    Mitchell, Gregory

    1999-06-28

    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}, 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.

  8. Tests of proton structure functions using leptons at CDF and DØ: W charge asymmetry and Drell-Yan production

    NASA Astrophysics Data System (ADS)

    Barbaro, Pawel de

    1996-02-01

    High statistics W charge asymmetry measurements at the Tevatron p¯p collider significantly constrain the u and d quark distributions, and specifically the slope of the d(x)/u(x) in the x range 0.007 to 0.27. We present measurements of the lepton charge asymmetry as a function of lepton rapidity, A(yl) at √s=1.8 TeV for ‖yl‖<2.0, for W decays to electrons and muons recorded by the CDF detector during the 1992-93 run (≊20 pb-1), and the first ≊50 pb-1 of data from the 1994-95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992-93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994-95 run. W charge asymmetry results from DO/ based on ≊6.5 pb-1 of data from the 1992-93 run and ≊29.7 pb-1 of data from the 1994-1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, we present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993-94 run (≊20 pb-1) and a high mass dimuon sample from the combined 1993-94 and 1994-95 runs (≊70 pb-1). The measurement is in good agreement with predictions using the most recent parton density functions in a dilepton mass range between 11 and 350 GeV/c2.

  9. Tests of proton structure functions using leptons at CDF and DO/: {ital W} charge asymmetry and Drell-Yan production

    SciTech Connect

    Barbaro, P.d.

    1996-02-01

    High statistics {ital W} charge asymmetry measurements at the Tevatron {bar {ital p}}{ital p} collider significantly constrain the {ital u} and {ital d} quark distributions, and specifically the slope of the {ital d}({ital x})/{ital u}({ital x}) in the {ital x} range 0.007 to 0.27. We present measurements of the lepton charge asymmetry as a function of lepton rapidity, {ital A}({ital y}{sub {ital l}}) at {radical}{ital s}=1.8 TeV for {parallel}{ital y}{sub {ital l}}{parallel}{lt}2.0, for {ital W} decays to electrons and muons recorded by the CDF detector during the 1992{endash}93 run ({approx_equal}20 {ital pb}{sup {minus}1}), and the first {approx_equal}50 {ital pb}{sup {minus}1} of data from the 1994{endash}95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992{endash}93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994{endash}95 run. {ital W} charge asymmetry results from DO/ based on {approx_equal}6.5 {ital pb}{sup {minus}1} of data from the 1992{endash}93 run and {approx_equal}29.7 {ital pb}{sup {minus}1} of data from the 1994{endash}1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, we present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993{endash}94 run ({approx_equal}20 {ital pb}{sup {minus}1}) and a high mass dimuon sample from the combined 1993{endash}94 and 1994{endash}95 runs ({approx_equal}70 {ital pb}{sup {minus}1}). The measurement is in good agreement with predictions using the most recent parton density functions in a dilepton mass range between 11 and 350 GeV/{ital c}{sup 2}. {copyright} {ital 1996 American Institute of Physics.}

  10. Simulating the function of sodium/proton antiporters

    PubMed Central

    Alhadeff, Raphael; Warshel, Arieh

    2015-01-01

    The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level. PMID:26392528

  11. Conductivity and structure of DBSA-protonated polyaniline

    NASA Astrophysics Data System (ADS)

    Taka, T.; Laakso, J.; Levon, K.

    1994-11-01

    The discovery of a processable and conducting polyaniline complexes including functionalized sulphonic acids is an important discovery in the field of conjugated polymers. The conductivity, electronic and crystalline structure properties of polyaniline protonated with dodecylbenzenesulphonic acid are proportional to the molar concentration of the acid. The protonation leads to a layer structure evident in X-ray diffraction patterns and the crystallinity follows a growth as a function of the acid concentration similar to the conductivity increase. The electronic structure measured by UV-VIS spectroscopy shows an increase in the polaron concentration up to an acid concentration of 0.35 after which a broadening of the peak indicates the formation of a polaron band.

  12. Proton-neutron interaction and nuclear structure

    SciTech Connect

    Casten, R.F.

    1986-01-01

    The pervasive role of the proton-neutron interaction in nuclear structure is discussed. Particular emphasis is given to its influence on the onset of collectivity and deformation, on intruder states, and on the evolution of subshell structure. The N/sub p/N/sub n/ scheme is outlined and some applications of it to collective model calculations and to nuclei far off stability are described. The concept of N/sub p/N/sub n/ multiplets is introduced. 32 refs., 20 figs.

  13. Controlling Proton Delivery through Catalyst Structural Dynamics

    SciTech Connect

    Cardenas, Allan Jay P.; Ginovska, Bojana; Kumar, Neeraj; Hou, Jianbo; Raugei, Simone; Helm, Monte L.; Appel, Aaron M.; Bullock, R. Morris; O'Hagan, Molly

    2016-09-27

    The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates of electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of

  14. Controlling Proton Delivery through Catalyst Structural Dynamics.

    PubMed

    Cardenas, Allan Jay P; Ginovska, Bojana; Kumar, Neeraj; Hou, Jianbo; Raugei, Simone; Helm, Monte L; Appel, Aaron M; Bullock, R Morris; O'Hagan, Molly

    2016-10-17

    The fastest synthetic molecular catalysts for H2 production and oxidation emulate components of the active site of hydrogenases. The critical role of controlled structural dynamics is recognized for many enzymes, including hydrogenases, but is largely neglected in designing synthetic catalysts. Our results demonstrate the impact of controlling structural dynamics on H2 production rates for [Ni(P(Ph)2 N(C6H4R)2 )2 ](2+) catalysts (R=n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl). The turnover frequencies correlate inversely with the rates of chair-boat ring inversion of the ligand, since this dynamic process governs protonation at either catalytically productive or non-productive sites. These results demonstrate that the dynamic processes involved in proton delivery can be controlled through modification of the outer coordination sphere, in a manner similar to the role of the protein architecture in many enzymes. As a design parameter, controlling structural dynamics can increase H2 production rates by three orders of magnitude with a minimal increase in overpotential.

  15. Structure and Decay at Rapid Proton Capture Waiting Points

    NASA Astrophysics Data System (ADS)

    Hove, D.; Garrido, E.; Jensen, A. S.; Fynbo, H. O. U.; Fedorov, D. V.; Zinner, N. T.

    2017-01-01

    We investigate the region of the nuclear chart around A ˜eq 70 from a three-body perspective, where we compute reaction rates for the radiative capture of two protons. One key quantity is here the photon dissociation cross section for the inverse process where two protons are liberated from the borromean nucleus by photon bombardment. We find a number of peaks at low photon energy in this cross section where each peak is located at the energy corresponding to population of a three-body resonance. Thus, for these energies the decay or capture processes proceed through these resonances. However, the next step in the dissociation process still has the option of following several paths, that is either sequential decay by emission of one proton at a time with an intermediate two-body resonance as stepping stone, or direct decay into the continuum of both protons simultaneously. The astrophysical reaction rate is obtained by folding of the cross section as function of energy with the occupation probability for a Maxwell-Boltzmann temperature distribution. The reaction rate is then a function of temperature, and of course depending on the underlying three-body bound state and resonance structures. We show that a very simple formula at low temperature reproduces the elaborate numerically computed reaction rate.

  16. Fast Proton-Coupled Electron Transfer Observed for a High-Fidelity Structural and Functional [2Fe–2S] Rieske Model

    PubMed Central

    2015-01-01

    Rieske cofactors have a [2Fe–2S] cluster with unique {His2Cys2} ligation and distinct Fe subsites. The histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (PCET) during quinol oxidation in respiratory and photosynthetic ET chains. Here we present the highest fidelity synthetic analogue for the Rieske [2Fe–2S] cluster reported so far. This synthetic analogue 5x– emulates the heteroleptic {His2Cys2} ligation of the [2Fe–2S] core, and it also serves as a functional model that undergoes fast concerted proton and electron transfer (CPET) upon reaction of the mixed-valent (ferrous/ferric) protonated 5H2– with TEMPO. The thermodynamics of the PCET square scheme for 5x– have been determined, and three species (diferric 52–, protonated diferric 5H–, and mixed-valent 53–) have been characterized by X-ray diffraction. pKa values for 5H– and 5H2– differ by about 4 units, and the reduction potential of 5H– is shifted anodically by about +230 mV compared to that of 52–. While the N–H bond dissociation free energy of 5H2– (60.2 ± 0.5 kcal mol–1) and the free energy, ΔG°CPET, of its reaction with TEMPO (−6.3 kcal mol–1) are similar to values recently reported for a homoleptic {N2/N2}-coordinated [2Fe–2S] cluster, CPET is significantly faster for 5H2– with biomimetic {N2/S2} ligation (k = (9.5 ± 1.2) × 104 M–1 s–1, ΔH‡ = 8.7 ± 1.0 kJ mol–1, ΔS‡ = −120 ± 40 J mol–1 K–1, and ΔG‡ = 43.8 ± 0.3 kJ mol–1 at 293 K). These parameters, and the comparison with homoleptic analogues, provide important information and new perspectives for the mechanistic understanding of the biological Rieske cofactor. PMID:24506804

  17. Strange magnetism and the anapole structure of the proton.

    SciTech Connect

    Hasty, R.; Hawthorne-Allen, A. M.; Averett, T.; Barkhuff, D.; Beck, D. H.; Mueller, B.; SAMPLE Collaboration; Physics; Univ. of Illinois; Virginia Polytechnic Inst. and State Univ.; Coll. of William and Mary; Lab. for Nuclear Science and Department of Physics

    2000-12-15

    The violation of mirror symmetry in the weak force provides a powerful tool to study the internal structure of the proton. Experimental results have been obtained that address the role of strange quarks in generating nuclear magnetism. The measurement reported here provides an unambiguous constraint on strange quark contributions to the proton's magnetic moment through the electron-proton weak interaction. We also report evidence for the existence of a parity-violating electromagnetic effect known as the anapole moment of the proton. The proton's anapole moment is not yet well understood theoretically, but it could have important implications for precision weak interaction studies in atomic systems such as cesium.

  18. Structural and energetic determinants of proton transfer in bacteriorhodopsin

    SciTech Connect

    Bondar, A.N.; Smith, Jeremy C; Fischer, S.

    2006-05-01

    In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.

  19. 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 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

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

    SciTech Connect

    Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas; Schrader, Tobias; Evans, Gary B.; Kovalevskyi, Andrii Y.; Ronning, Donald R.

    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 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), 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.

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

    SciTech Connect

    Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas; Schrader, Tobias; Evans, Gary B.; Kovalevskyi, Andrii Y.; Ronning, Donald R.

    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 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), 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.

  2. Proton pump inhibitors for functional dyspepsia.

    PubMed

    Pinto-Sanchez, Maria Ines; Yuan, Yuhong; Bercik, Premysl; Moayyedi, Paul

    2017-03-08

    Functional dyspepsia (FD or non-ulcer dyspepsia) is defined as continuous or frequently recurring epigastric pain or discomfort for which no organic cause can be found. Acid suppressive therapy, including proton pump inhibitors (PPIs), has been proposed as a therapeutic option in FD, but its efficacy remains controversial. While PPIs are generally considered safe and well tolerated, they have been associated with adverse events, especially in the long term. For this reason, decisions on whether to initiate or continue PPI therapy should be made based on an appropriate clinical indication. Therefore, we conducted a systematic review to evaluate whether PPI therapy provides symptomatic relief in FD. To determine the efficacy of proton pump inhibitors in the improvement of global symptoms of dyspepsia and quality of life compared to placebo, H2 receptor antagonists or prokinetics, in people with functional dyspepsia. We searched in the following electronic databases: the Cochrane Library (to January 2016), MEDLINE (OvidSP; to February 2016), Embase (OvidSP; to February 2016), and SIGLE grey literature (up to February 2016) and clinical trial registries; we handsearched abstracts from conferences up to February 2016. We screened non-systematic reviews, systematic reviews and guidelines to identify any additional trials. We contacted trialists to obtain missing information. All randomized controlled trials (RCTs) comparing any PPI with placebo, H2 receptor antagonists (H2RAs) or prokinetics for the treatment of FD. Participants were adults (aged 16 years or greater) with an adequate diagnosis of FD (any validated criteria such as Rome I, II, III or Lancet Working Group). Two review authors independently assessed eligibility, trial quality and extracted data. We collected data on dyspeptic symptoms, quality of life and number of overall adverse events. Specific adverse events were beyond the scope of this review. We identified 23 RCTs from 22 papers (with 8759

  3. Proton Conductivity of Proton Exchange Membrane Synergistically Promoted by Different Functionalized Metal-Organic Frameworks.

    PubMed

    Rao, Zhuang; Tang, Beibei; Wu, Peiyi

    2017-07-12

    In this study, two functionalized metal-organic frameworks (MOFs), UiO-66-SO3H and UiO-66-NH2, were synthesized. Then, different composite proton exchange membranes (PEMs) were prepared by single doping and codoping of these two MOFs, respectively. It was found that codoping of these two MOFs with suitable sizes was more conducive to the proton conductivity enhancement of the composite PEM. A synergistic effect between these two MOFs led to the the formation of more consecutive hydration channels in the composite PEM. It further greatly promoted the proton conductivity of the composite PEM. The proton conductivity of the codoped PEM reached up to 0.256 S/cm under 90 °C, 95% RH, which was ∼1.17 times higher than that of the recast Nafion (0.118 S/cm). Besides, the methanol permeability of the codoped PEM was prominently decreased owing to the methanol trapping effect of the pores of these two MOFs. Meanwhile, the high water and thermal stabilities of these two MOFs were beneficial to the high proton conductivity stability of the codoped PEM under high humidity and high temperature. The proton conductivity of the codoped PEM was almost unchanged throughout 3000 min of testing under 90 °C, 95% RH. This work provides a valuable reference for designing different functionalized MOFs to synergistically promote the proton conductivities of PEMs.

  4. Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane

    NASA Astrophysics Data System (ADS)

    Bagusetty, Abhishek; Choudhury, Pabitra; Saidi, Wisssam A.; Derksen, Bridget; Gatto, Elizabeth; Johnson, J. Karl

    2017-05-01

    Graphane functionalized with hydroxyl groups is shown to rapidly conduct protons under anhydrous conditions through a contiguous network of hydrogen bonds. Density functional theory calculations predict remarkably low barriers to diffusion of protons along a 1D chain of surface hydroxyls. Diffusion is controlled by the local rotation of hydroxyl groups, a mechanism that is very different from that found in 1D water wires in confined nanopores or in bulk water. The proton mean square displacement in the 1D chain was observed to follow Fickian diffusion rather than the expected single-file mobility. A charge analysis reveals that the charge on the proton is essentially equally shared by all hydrogens bound to oxygens, effectively delocalizing the proton.

  5. Facile Anhydrous Proton Transport on Hydroxyl Functionalized Graphane.

    PubMed

    Bagusetty, Abhishek; Choudhury, Pabitra; Saidi, Wisssam A; Derksen, Bridget; Gatto, Elizabeth; Johnson, J Karl

    2017-05-05

    Graphane functionalized with hydroxyl groups is shown to rapidly conduct protons under anhydrous conditions through a contiguous network of hydrogen bonds. Density functional theory calculations predict remarkably low barriers to diffusion of protons along a 1D chain of surface hydroxyls. Diffusion is controlled by the local rotation of hydroxyl groups, a mechanism that is very different from that found in 1D water wires in confined nanopores or in bulk water. The proton mean square displacement in the 1D chain was observed to follow Fickian diffusion rather than the expected single-file mobility. A charge analysis reveals that the charge on the proton is essentially equally shared by all hydrogens bound to oxygens, effectively delocalizing the proton.

  6. Proton pump inhibitors drastically modify triosephosphate isomerase from Giardia lamblia at functional and structural levels, providing molecular leads in the design of new antigiardiasic drugs.

    PubMed

    García-Torres, Itzhel; de la Mora-de la Mora, Ignacio; Marcial-Quino, Jaime; Gómez-Manzo, Saúl; Vanoye-Carlo, América; Navarrete-Vázquez, Gabriel; Colín-Lozano, Blanca; Gutiérrez-Castrellón, Pedro; Sierra-Palacios, Edgar; López-Velázquez, Gabriel; Enríquez-Flores, Sergio

    2016-01-01

    Proton pump inhibitors (PPIs) are extensively used in clinical practice because of their effectiveness and safety. Omeprazole is one of the best-selling drugs worldwide and, with other PPIs, has been proposed to be potential drugs for the treatment of several diseases. We demonstrated that omeprazole shows cytotoxic effects in Giardia and concomitantly inactivates giardial triosephosphate isomerase (GlTIM). Therefore, we evaluated the efficiency of commercially available PPIs to inactivate this enzyme. We assayed the effect of PPIs on the GlTIM WT, single Cys mutants, and the human counterpart, following enzyme activity, thermal stability, exposure of hydrophobic regions, and susceptibility to limited proteolysis. PPIs efficiently inactivated GlTIM; however, rabeprazole was the best inactivating drug and was nearly ten times more effective. The mechanism of inactivation by PPIs was through the modification of the Cys 222 residue. Moreover, there are important changes at the structural level, the thermal stability of inactivated-GlTIM was drastically diminished and the structural rigidity was lost, as observed by the exposure of hydrophobic regions and their susceptibility to limited proteolysis. Our results demonstrate that rabeprazole is the most potent PPI for GlTIM inactivation and that all PPIs tested have substantial abilities to alter GITIM at the structural level, causing serious damage. This is the first report demonstrating the effectiveness of commercial PPIs on a glycolytic parasitic enzyme, with structural features well known. This study is a step forward in the use and understanding the implicated mechanisms of new antigiardiasic drugs safe in humans. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Optimized enzymatic dual functions of PaPrx protein by proton irradiation

    PubMed Central

    Park, Chul-Hong; Lee, Seung Sik; Kim, Kye Ryung; Jung, Myung Hwan; Lee, Sang Yeol; Cho, Eun Ju; Singh, Sudhir; Chung, Byung Yeoup

    2014-01-01

    We investigated the effects of proton irradiation on the function and structure of the Pseudomonas aeruginosa peroxiredoxin (PaPrx). Polyacrylamide gel demonstrated that PaPrx proteins exposed to proton irradiation at several doses exhibited simultaneous formation of high molecular weight (HMW) complexes and fragmentation. Size-exclusion chromatography (SEC) analysis revealed that the number of fragments and very low molecular weight (LMW) structures increased as the proton irradiation dose increased. The peroxidase activity of irradiated PaPrx was preserved, and its chaperone activity was significantly increased by increasing the proton irradiation dose. The chaperone activity increased about 3–4 fold after 2.5 kGy proton irradiation, compared with that of non-irradiated PaPrx, and increased to almost the maximum activity after 10 kGy proton irradiation. We previously obtained functional switching in PaPrx proteins, by using gamma rays and electron beams as radiation sources, and found that the proteins exhibited increased chaperone activity but decreased peroxidase activity. Interestingly, in this study we newly found that proton irradiation could enhance both peroxidase and chaperone activities. Therefore, we can suggest proton irradiation as a novel protocol for conserved 2-Cys protein engineering. PMID:23753570

  8. Structure-function studies on bacteriorhodopsin. X. Individual substitutions of arginine residues by glutamine affect chromophore formation, photocycle, and proton translocation

    SciTech Connect

    Stern, L.J.; Khorana, H.G. )

    1989-08-25

    We have individually replaced all 7 of the arginine residues in bacteriorhodopsin by glutamine. The mutants with substitutions at positions 7, 164, 175, and 225 showed essentially the wild-type phenotype in regard to chromophore regeneration, chromophore lambda max, and proton pumping, although the mutant Arg-175----Gln showed decreased rate of chromophore regeneration. Glutamine substitutions of Arg-82, -134, and -227 affected proton pumping ability, and caused specific alterations in the bacteriorhodopsin photocycle. Finally, electrostatic interactions are proposed between Arg-82 and -227, and specific carboxylic acid residues in helices C and G, which regulate the purple to blue transition and proton transfers during the photocycle.

  9. Probing the Spin Structure of the Proton Using Polarized Proton-Proton Collisions and the Production of W Bosons

    SciTech Connect

    Beaumier, Michael J.

    2016-08-01

    This thesis discusses the process of extracting the longitudinal asymmetry, A$W±\\atop{L}$ describing W → μ production in forward kinematic regimes. This asymmetry is used to constrain our understanding of the polarized parton distribution functions characterizing $\\bar{u}$ and $\\bar{d}$ sea quarks in the proton. This asymmetry will be used to constrain the overall contribution of the sea-quarks to the total proton spin. The asymmetry is evaluated over the pseudorapidity range of the PHENIX Muon Arms, 2.1 < |η| 2.6, for longitudinally polarized proton-proton collisions at 510 GeV √s. In particular, I will discuss the statistical methods used to characterize real muonic W decays and the various background processes is presented, including a discussion of likelihood event selection and the Extended Unbinned Maximum Likelihood t. These statistical methods serve estimate the yields of W muonic decays, which are used to calculate the longitudinal asymmetry.

  10. A broken-symmetry density functional study of structures, energies, and protonation states along the catalytic O-O bond cleavage pathway in ba3 cytochrome c oxidase from Thermus thermophilus.

    PubMed

    Han Du, Wen-Ge; Götz, Andreas W; Yang, Longhua; Walker, Ross C; Noodleman, Louis

    2016-08-21

    Broken-symmetry density functional calculations have been performed on the [Fea3, CuB] dinuclear center (DNC) of ba3 cytochrome c oxidase from Thermus thermophilus in the states of [Fea3(3+)-(HO2)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], using both PW91-D3 and OLYP-D3 functionals. Tyr237 is a special tyrosine cross-linked to His233, a ligand of CuB. The calculations have shown that the DNC in these states strongly favors the protonation of His376, which is above propionate-A, but not of the carboxylate group of propionate-A. The energies of the structures obtained by constrained geometry optimizations along the O-O bond cleavage pathway between [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] and [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] have also been calculated. The transition of [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] → [Fea3(4+)[double bond, length as m-dash]O(2-)HO(-)-CuB(2+), Tyr237˙] shows a very small barrier, which is less than 3.0/2.0 kcal mol(-1) in PW91-D3/OLYP-D3 calculations. The protonation state of His376 does not affect this O-O cleavage barrier. The rate limiting step of the transition from state A (in which O2 binds to Fea3(2+)) to state PM ([Fea3(4+)[double bond, length as m-dash]O(2-), OH(-)-CuB(2+), Tyr237˙], where the O-O bond is cleaved) in the catalytic cycle is, therefore, the proton transfer originating from Tyr237 to O-O to form the hydroperoxo [Fea3(3+)-(O-OH)(-)-CuB(2+), Tyr237(-)] state. The importance of His376 in proton uptake and the function of propionate-A/neutral-Asp372 as a gate to prevent the proton from back-flowing to the DNC are also shown.

  11. Proton NMR studies of functionalized nanoparticles in aqueous environments

    NASA Astrophysics Data System (ADS)

    Tataurova, Yulia Nikolaevna

    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.

  12. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.

    PubMed

    Andreas, Loren B; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-08-16

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of (1)H-(1)H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.

  13. Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

    PubMed Central

    Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Le Marchand, Tanguy; Cala-De Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido

    2016-01-01

    Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of 1H-1H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins. PMID:27489348

  14. Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

    Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation (epc) functionals that produce even qualitatively accurate proton densities. Herein an electron-proton correlation functional, epc17, is derived analogously to the Colle-Salvetti formalism for electron correlation and is implemented within the nuclear-electronic orbital (NEO) framework. The NEO-DFT/epc17 method produces accurate proton densities efficiently and is promising for diverse applications.

  15. Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities.

    PubMed

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

    2017-09-21

    Multicomponent density functional theory (DFT) enables the consistent quantum mechanical treatment of both electrons and protons. A major challenge has been the design of electron-proton correlation (epc) functionals that produce even qualitatively accurate proton densities. Herein an electron-proton correlation functional, epc17, is derived analogously to the Colle-Salvetti formalism for electron correlation and is implemented within the nuclear-electronic orbital (NEO) framework. The NEO-DFT/epc17 method produces accurate proton densities efficiently and is promising for diverse applications.

  16. Strangeness production as a function of charged particle multiplicity in proton-proton collisions

    NASA Astrophysics Data System (ADS)

    Bianchi, Livio

    2016-12-01

    Recent measurements performed in high-multiplicity proton-proton (pp) and proton-lead (p-Pb) collisions have shown features that are reminiscent of those observed in lead-lead (Pb-Pb) collisions. These observations warrant a comprehensive measurement of the production of identified particles. We report on the production of KS0, Λ, Λ ‾, Ξ± and Ω± at mid-rapidity measured as a function of multiplicity in pp collisions at √{ s} = 7 TeV with the ALICE experiment. Spectral shapes studied both for individual particles and via particle ratios such as (Λ / KS0) as a function of pT exhibit an evolution with event multiplicity and the production rates of hyperons are observed to increase more strongly than those of non-strange hadrons. These phenomena are qualitatively similar to the ones observed in p-Pb and Pb-Pb collisions.

  17. 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.

  18. Mesomorphic structures of protonated surfactant-encapsulated polyoxometalate complexes.

    PubMed

    Yin, Shengyan; Li, Wen; Wang, Jinfeng; Wu, Lixin

    2008-04-03

    Keggin-type heteropolyanions, H(3)PW(12)O(40) (HPW), Na(3)PW(12)O(40) (NaPW), H(4)SiW(12)O(40) (HSiW) and K(4)SiW(12)O(40) (KSiW), were encapsulated by a cationic surfactant, di[12-(4'-octyloxy-4-azophenyl)dodecyloxy]dimethylam monium bromide (L), through the replacement of counterions. The resulting surfactant-encapsulated polyoxometalate complexes were characterized by UV-vis, Raman, and NMR spectra in detail. The measurement results indicated that some azobenzene groups of the surfactant were protonated in the complexes HL/HPW (HL is the abbreviation of the protonated surfactant), HL/NaPW, and HL/HSiW during the process of encapsulation, whereas the protonation was not observed in L/KSiW. The thermotropic liquid crystal properties of these complexes were investigated by differential scanning calorimetry, polarized optical microscopy and variable-temperature X-ray diffraction. Interestingly, different smectic mesophases were observed between the protonated HL/HSiW and the non-protonated L/KSiW, which suggests that the protonation of azobenzene groups in HL/HSiW plays a key role in the liquid crystalline organization. However, protonated HL/HPW and HL/NaPW exhibit a similar smectic B phase to that of the de-protonated one, L/HPW. A competitive balance between the phase separation and the volume minimization of surfactants was proposed to explain the self-organized liquid crystal structures of these protonated and non-protonated complexes. To the best of our knowledge, the present investigation provides a specific example for protonated hybrid materials with stable liquid crystal properties.

  19. Structures and spectral signatures of protonated water networks in bacteriorhodopsin.

    PubMed

    Mathias, Gerald; Marx, Dominik

    2007-04-24

    Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.

  20. Structural and functional analysis of aa3-type and cbb3-type cytochrome c oxidases of Paracoccus denitrificans reveals significant differences in proton-pump design.

    PubMed

    de Gier, J W; Schepper, M; Reijnders, W N; van Dyck, S J; Slotboom, D J; Warne, A; Saraste, M; Krab, K; Finel, M; Stouthamer, A H; van Spanning, R J; van der Oost, J

    1996-06-01

    In Paracoccus denitrificans the aa3-type cytochrome c oxidase and the bb3-type quinol oxidase have previously been characterized in detail, both biochemically and genetically. Here we report on the isolation of a genomic locus that harbours the gene cluster ccoNOOP, and demonstrate that it encodes an alternative cbb3-type cytochrome c oxidase. This oxidase has previously been shown to be specifically induced at low oxygen tensions, suggesting that its expression is controlled by an oxygen-sensing mechanism. This view is corroborated by the observation that the ccoNOOP gene cluster is preceded by a gene that encodes an FNR homologue and that its promoter region contains an FNR-binding motif. Biochemical and physiological analyses of a set of oxidase mutants revealed that, at least under the conditions tested, cytochromes aa3, bb3 and cbb3 make up the complete set of terminal oxidases in P. denitrificans. Proton-translocation measurements of these oxidase mutants indicate that all three oxidase types have the capacity to pump protons. Previously, however, we have reported decreased H+/e- coupling efficiencies of the cbb3-type oxidase under certain conditions. Sequence alignment suggests that many residues that have been proposed to constitute the chemical and pumped proton channels in cytochrome aa3 (and probably also in cytochrome bb3) are not conserved in cytochrome cbb3. It is concluded that the design of the proton pump in cytochrome cbb3 differs significantly from that in the other oxidase types.

  1. 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...

  2. A Proton-Cyclotron Wave Storm Generated by Unstable Proton Distribution Functions in the Solar Wind

    NASA Technical Reports Server (NTRS)

    Wicks, R. T.; Alexander, R. L.; Stevens, M.; Wilson, L. B., III; Moya, P. S.; Vinas, A.; Jian, L. K.; Roberts, D. A.; O’Modhrain, S.; Gilbert, J. A.; Zurbuchen, T. H.

    2016-01-01

    We use audification of 0.092 seconds cadence magnetometer data from the Wind spacecraft to identify waves with amplitudes greater than 0.1 nanoteslas near the ion gyrofrequency (approximately 0.1 hertz) with duration longer than 1 hour during 2008. We present one of the most common types of event for a case study and find it to be a proton-cyclotron wave storm, coinciding with highly radial magnetic field and a suprathermal proton beam close in density to the core distribution itself. Using linear Vlasov analysis, we conclude that the long-duration, large-amplitude waves are generated by the instability of the proton distribution function. The origin of the beam is unknown, but the radial field period is found in the trailing edge of a fast solar wind stream and resembles other events thought to be caused by magnetic field footpoint motion or interchange reconnection between coronal holes and closed field lines in the corona.

  3. A Proton-Cyclotron Wave Storm Generated by Unstable Proton Distribution Functions in the Solar Wind

    NASA Technical Reports Server (NTRS)

    Wicks, R. T.; Alexander, R. L.; Stevens, M.; Wilson, L. B., III; Moya, P. S.; Vinas, A.; Jian, L. K.; Roberts, D. A.; O’Modhrain, S.; Gilbert, J. A.; hide

    2016-01-01

    We use audification of 0.092 seconds cadence magnetometer data from the Wind spacecraft to identify waves with amplitudes greater than 0.1 nanoteslas near the ion gyrofrequency (approximately 0.1 hertz) with duration longer than 1 hour during 2008. We present one of the most common types of event for a case study and find it to be a proton-cyclotron wave storm, coinciding with highly radial magnetic field and a suprathermal proton beam close in density to the core distribution itself. Using linear Vlasov analysis, we conclude that the long-duration, large-amplitude waves are generated by the instability of the proton distribution function. The origin of the beam is unknown, but the radial field period is found in the trailing edge of a fast solar wind stream and resembles other events thought to be caused by magnetic field footpoint motion or interchange reconnection between coronal holes and closed field lines in the corona.

  4. Structures of protonated methanol clusters and temperature effects

    NASA Astrophysics Data System (ADS)

    Fifen, Jean Jules; Nsangou, Mama; Dhaouadi, Zoubeida; Motapon, Ousmanou; Jaidane, Nejm-Eddine

    2013-05-01

    The accurate evaluation of pKa's, or solvation energies of the proton in methanol at a given temperature is subject to the determination of the most favored structures of various isomers of protonated (H+(MeOH)n) and neutral ((MeOH)n) methanol clusters in the gas phase and in methanol at that temperature. Solvation energies of the proton in a given medium, at a given temperature may help in the determination of proton affinities and proton dissociation energies related to the deprotonation process in that medium and at that temperature. pKa's are related to numerous properties of drugs. In this work, we were interested in the determination of the most favored structures of various isomers of protonated methanol clusters in the gas phase and in methanol, at a given temperature. For this aim, the M062X/6-31++G(d,p) and B3LYP/6-31++G(d,p) levels of theory were used to perform geometries optimizations and frequency calculations on various isomers of (H+(MeOH)n) in both phases. Thermal effects were retrieved using our homemade FORTRAN code. Thus, we accessed the relative populations of various isomers of protonated methanol clusters, in both phases for temperatures ranging from 0 to 400 K. As results, in the gas phase, linear structures are entropically more favorable at high temperatures, while more compact ones are energetically more favorable at lower temperatures. The trend is somewhat different when bulk effects are taken into account. At high temperatures, the linear structure only dominates the population for n ⩽ 6, while it is dominated by the cyclic structure for larger cluster sizes. At lower temperatures, compact structures still dominate the population, but with an order different from the one established in the gas phase. Hence, temperature effects dominate solvent effects in small cluster sizes (n ⩽ 6), while the reverse trend is noted for larger cluster sizes.

  5. Excitation functions of proton-proton elastic scattering at intermediate energies

    NASA Astrophysics Data System (ADS)

    Scobel, W.; Dohrmann, F.; Bisplinghoff, J.; Hinterberger, F.; Scobel, W.; Altmeier, M.; Bauer, F.; Bisplinghoff, J.; Bissel, T.; Bollmann, R.; Busch, M.; Büßer, K.; Cloth, P.; Danie, R.; Diehl, O.; Dohrmann, F.; Engelhardt, H. P.; Ernst, J.; Eversheim, P. D.; Felden, O.; Flammer, J.; Gasthuber, M.; Gebel, R.; Greiff, J.; Groß, A.; Groß-Hardt, R.; Hebbel, K.; Hinterberger, F.; Hüskes, T.; Jahn, R.; Koch, I.; Langkau, R.; Lindemann, T.; Lindlein, J.; Maier, R.; Maschuw, R.; Mayer-Kuckuk, T.; Pfuff, M.; Prasuhn, D.; Rohdjeß, H.; Rosendaal, D.; von Rossen, P.; Schirm, N.; Schulz-Rojahn, M.; Schwarz, V.; Scobel, W.; Steinbeck, S.; Sterzenbach, G.; Thomas, S.; Trelle, H. J.; Walker, M.; Weise, E.; Wellinghausen, A.; Woller, K.; Ziegler, R.; EDDA Collaboration at COSY; EDDA Collaboration

    1998-03-01

    Excitation functions of proton-proton elastic cross sections have been measured in narrow momentum steps Δp = 28 MeV/c in the kinetic energy range from 0.5 to 2.5 GeV and the angular range 35° ≤ Θcm ≤ 90° with a detector providing ΔΘcm ≈ 1.4° resolution and 82% solid angle coverage. Measurements have been performed continuously during projectile acceleration in the Cooler Synchrotron COSY with an internal CH 2 fiber target; background corrections were derived from measurements with a carbon fiber target and from Monte Carlo simulations of inelastic pp contributions. Particular care was taken to monitor the luminosity as a function of beam energy. The results provide excitation functions and angular distributions of unprecedented precision and internal consistency. The measured cross sections are compared to recent phase shift analyses, and their impact on the present solution SM97 [1] is discussed.

  6. ``PROTON Sponges": a Rigid Organic Scaffold to Reveal the Quantum Structure of the Intramolecular Proton Bond

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Johnson, Mark A.; Scerba, Michael T.; Bloom, Steven; Lectka, Thomas; Dudding, Travis

    2012-06-01

    Spectroscopic analysis of systems containing charged hydrogen bonds (e.g. the Zundel ion, {H}5{O}2+) in a vibrationally cold regime is useful in decongesting numerous anharmonic features common to room temperature measurements.[Roscioli, J. R.; et. al. Science 2007] This approach has been extended to conjugate acids of the ``Proton Sponge" family of organic compounds, which contain strong intramolecular hydrogen bonds between proton donor (D) and acceptor (A) groups at the 1- and 8-positions. By performing {H}_2/{D}_2 vibrational predissociation spectroscopy on cryogenically cooled ions, we explore how the proximity and spatial orientation of D and A moieties relates to the spectroscopic signature of the shared proton. In the cases studied ({D = Me2N-H+; A = OH, O(C=O)Ph}), we observe strong anharmonic couplings between the shared proton and dark states that persist at these cryogenic temperatures. This leads to intense NH stretching features throughout the nominal CH stretching region (2800-3000 {cm}-1). Isotopic substitution has verified that the oscillator strength of these broad features is driven by NH stretching. Furthermore, the study of A = O(C=O)Ph has provided a spectroscopic snapshot of the shared proton at work as an active catalytic moiety fostering ester hydrolysis by first order acylium fission ({AAC1}). This is apparent by the high frequency carbonyl stretch at 1792 {cm}-1, which is a consequence of the strong hydrogen bond to the ether-ester oxygen atom. Thus, these ``Proton Sponges" are useful model systems that unearth the quantum structure and reactivity of shared proton interactions in organic compounds.

  7. Proton spin structure from lattice QCD

    SciTech Connect

    Fukugita, M.; Kuramashi, Y.; Okawa, M.; Ukawa, A. ||

    1995-09-11

    A lattice QCD calculation of the proton matrix element of the flavor singlet axial-vector current is reported. Both the connected and disconnected contributions are calculated, for the latter employing the variant method of wall source without gauge fixing. From simulations in quenched QCD with the Wilson quark action on a 16{sup 3}{times}20 lattice at {beta}=5.7 (the lattice spacing {ital a}{approx}0.14 fm), we find {Delta}{Sigma}={Delta}{ital u}+{Delta}{ital d}+{Delta}{ital s}=+0.638(54){minus}0.347(46){minus}0.109(30)=+0.18(10) with the disconnected contribution to {Delta}{ital u} and {Delta}{ital d} equal to {minus}0.119(44), which is reasonably consistent with the experiment.

  8. Proton fragmentation functions considering finite-mass corrections

    NASA Astrophysics Data System (ADS)

    Moosavi Nejad, S. M.; Soleymaninia, M.; Maktoubian, A.

    2016-10-01

    We present new sets of proton fragmentation functions (FFs) describing the production of protons from the gluon and each of the quarks, obtained by the NLO QCD fits to all relevant data sets of single-inclusive electron-positron annihilation. Specifically, we determine their uncertainties using the Gaussian method for error estimation. Our analysis is in good agreement with the e + e - annihilation data. We also include finite-mass effects of the proton in our calculations, a topic to which very little attention is paid in the literature. Proton mass effects turn out to be appreciable for gluon and light quark FFs. The inclusion of finite-mass effects tends to improve the overall description of the data by reducing the minimized χ2 values significantly. As an application, we apply the extracted FFs to make predictions for the scaled-energy distribution of protons inclusively produced in top quark decays at next-to-leading order, relying on the universality and scaling violations of FFs.

  9. How Bright is the Proton? A Precise Determination of the Photon Parton Distribution Function

    NASA Astrophysics Data System (ADS)

    Manohar, Aneesh; Nason, Paolo; Salam, Gavin P.; Zanderighi, Giulia

    2016-12-01

    It has become apparent in recent years that it is important, notably for a range of physics studies at the Large Hadron Collider, to have accurate knowledge on the distribution of photons in the proton. We show how the photon parton distribution function (PDF) can be determined in a model-independent manner, using electron-proton (e p ) scattering data, in effect viewing the e p →e +X process as an electron scattering off the photon field of the proton. To this end, we consider an imaginary, beyond the Standard Model process with a flavor changing photon-lepton vertex. We write its cross section in two ways: one in terms of proton structure functions, the other in terms of a photon distribution. Requiring their equivalence yields the photon distribution as an integral over proton structure functions. As a result of the good precision of e p data, we constrain the photon PDF at the level of 1%-2% over a wide range of momentum fractions.

  10. Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures.

    PubMed

    Pinotsi, Dorothea; Grisanti, Luca; Mahou, Pierre; Gebauer, Ralph; Kaminski, Clemens F; Hassanali, Ali; Kaminski Schierle, Gabriele S

    2016-03-09

    Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.

  11. Measurements of the Q{sup 2}-Dependence of the Proton and Neutron SpinStructure Functions g{sub 1}{sup p} and g{sub 1}{sup n}

    SciTech Connect

    Bosted, Peter

    2000-07-24

    The structure functions g{sub 1}{sup p} and g{sub 1}{sup n} have been measured over the range 0.014 < x < 0.9 and 1 < Q{sup 2} < 40 GeV{sup 2} using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. The authors find that the Q{sup 2} dependence of g{sub 1}{sup p}(g{sub 1}{sup n}) at fixed x is very similar to that of the spin-averaged structure function F{sub 1}{sup p} (F{sub 1}{sup n}). From an NLO QCD fit to all available data they find Gamma{sub 1}{sup p}-Gamma{sub 1}{sup p} = 0.176 {+-} 0.003 {+-} 0.007 at Q{sup 2} = 5 GeV{sub 2}, in agreement with the Bjorken sum rule prediction of 0.182 {+-} 0.005.

  12. Measurements of the Q{sup 2}-Dependence of the Proton and Neutron Spin Structure Functions g{sub 1}{sup p} and g{sub 1}{sup n}

    SciTech Connect

    Perry Anthony; R.G. Arnold; Todd Averett; H.R. Band; M.C. Berisso; H. Borel; Peter Bosted; Stephen Bueltmann; M. Buenerd; T. Chupp; Steve Churchwell; G.R. Court; Donald Crabb; Donal Day; Piotr Decowski; P. DePietro; Robin D. Erbacher; R. Erickson; A. Feltham; Helene Fonvieille; Emil Frlez; R. Gearhart; V. Ghazikhanian; Javier Gomez; Keith Griffioen; C. Harris; M.A. Houlden; Emlyn Hughes; Charles Hyde-wright; G. Igo; Sebastien Incerti; John Jensen; J.R. Johnson; Paul King; Yu.G. Kolomensky; Sebastian Kuhn; Richard Lindgren; R.M. Lombard-Nelsen; Jacques Marroncle; James Mccarthy; Paul Mckee; Werner Meyer; Gregory Mitchell; Joseph Mitchell; Michael Olson; Seppo Penttila; Gerald Peterson; Gerassimos Petratos; R. Pitthan; Dinko Pocanic; R. Prepost; C. Prescott; Liming Qin; Brian Raue; D. Reyna; L.S. Rochester; Stephen Rock; Oscar Rondon-aramayo; Franck Sabatie; Ingo Sick; Tim Smith; Lee Sorrell; F. Staley; S. St. Lorant; L.M. Stuart; Z. Szalata; Y. Terrien; William Tobias; Luminita Todor; T. Toole; S. Trentalange; D. Walz; Robert Welsh; Frank Wesselmann; T.R. Wright; C.C. Young; Markus Zeier; Hong Guo Zhu; Benedikt Zihlmann

    2000-11-09

    The structure functions g{sub 1}{sup p} and g{sub 1}{sup n} have been measured over the range 0.014 < x < 0.9 and 1 < Q{sup 2} < 40 GeV{sup 2} using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. We find that the Q{sup 2} dependence of g{sub 1}{sup p} (g{sub 1}{sup n}) at fixed x is very similar to that of the spin-averaged structure function F{sub 1}{sup p} (F{sub 1}{sup n}). From a NLO QCD fit to all available data we find {Gamma}{sub 1}{sup p} - {Gamma}{sub 1}{sup n} = 0.176 {+-} 0.003 {+-} 0.007 at Q{sup 2} = 5 GeV{sup 2}, in agreement with the Bjorken sum rule prediction of 0.182 {+-} 0.005.

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

    SciTech Connect

    Banco, Michael T.; Mishra, Vidhi; Ostermann, Andreas; Schrader, Tobias E.; Evans, Gary B.; Kovalevsky, Andrey; Ronning, Donald R.

    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), 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.

  14. Pulse structure dependence of proton spin polarization rate

    NASA Astrophysics Data System (ADS)

    Kawahara, Tomomi; Uesaka, Tomohiro; Shimizu, Youhei; Sakaguchi, Satoshi; Wakui, Takashi

    2009-10-01

    A polarized proton solid target for RI beam experiments has been developed at Center for Nuclear Study, University of Tokyo [1]. The proton is polarized by transferring population difference in photo-excited triplet states of aromatic molecule. Through this method proton polarization of about 20% have been obtained at 0.1 T and in 100 K. Although this target has been successfully applied to RI beam experiments [2,3], further improvement in the polarization is desirable for future applications. To pursuit possible improvement in photo-excitation power, we have examined pulse-structure dependence of proton polarization rate. The excitation light is provided by a cw Ar-ion laser and pulsed by an optical chopper. We have found that proton polarization depends strongly on the pulse structure and the optimum condition is found to be a duty factor of 50% and a repetition frequency of 10 kHz. At this condition, the polarization rate can be increased by a factor 2.5 or more compared with the old settings, where a duty factor and a repetition frequency were 5% and 2.5 kHz, respectively. [1] T. Wakui et al., Nucl. Instrum. Methods A 550 (2005) 521. [2] M. Hatano et al., Eur. Phys. J. A 25 (2005) 255. [3] S. Sakaguchi et al., CNS Annual Report 2006 (2007).

  15. 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.

  16. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  17. Impact of proton transfer phenomena on the electronic structure of model Schiff bases: An AIM/NBO/ELF study

    NASA Astrophysics Data System (ADS)

    Panek, Jarosław J.; Filarowski, Aleksander; Jezierska-Mazzarello, Aneta

    2013-10-01

    Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor/acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

  18. Proton Transfer in Molten Lithium Carbonate: Mechanism and Kinetics by Density Functional Theory Calculations.

    PubMed

    Lei, Xueling; Huang, Kevin; Qin, Changyong

    2017-08-07

    Using static and dynamic density functional theory (DFT) methods with a cluster model of [(Li2CO3)8H](+), the mechanism and kinetics of proton transfer in lithium molten carbonate (MC) were investigated. The migration of proton prefers an inter-carbonate pathway with an energy barrier of 8.0 kcal/mol at the B3LYP/6-31 G(d,p) level, which is in good agreement with the value of 7.6 kcal/mol and 7.5 kcal/mol from experiment and FPMD simulation, respectively. At transition state (TS), a linkage of O-H-O involving O 2p and H 1 s orbitals is formed between two carbonate ions. The calculated trajectory of H indicates that proton has a good mobility in MC, oxygen can rotate around carbon to facilitate the proton migration, while the movement of carbon is very limited. Small variations on geometry and atomic charge were detected on the carbonate ions, implying that the proton migration is a synergetic process and the whole carbonate structure is actively involved. Overall, the calculated results indicate that MC exhibits a low energy barrier for proton conduction in IT-SOFCs.

  19. Measurements of the proton and neutron spin structure at SLAC

    SciTech Connect

    Rondon, O.A.

    1994-10-26

    The deep inelastic polarized structure fimctions g{sub 1}{sup p,d} and g{sub 2}{sup g,d} have been recently measured at the Stanford Linear Accelerator Center (SLAC) End Station A facility by the E143 Collaboration using 29.1 GeV, 16.2 and 9.7 GeV longitudinally polarized electrons incident on longitudinally and transversally polarized ammonia (NH{sub 3}) and deuterated ammonia (ND{sub 3}) targets. Polarized electrons were produced by photemission from a strained GaAs cathode that produced beam polarizations of 85%, measured using a Moller spectrometer with coincidence and single arm detectors. The polarized target operated in a 5 T magnetic field at 1 K. Average dynamic nuclear target polarizations (at 80 nA average beam current) of 60% for protons and 30% for deuterons have been attained. The scattered electrons were detected in two spectrometers placed at 4.5{degrees} and -7{degrees} with respect to the incident beam.The range of the kinematic scaling variables x{sub Bjorken} and momentum transfer Q{sup 2} covered at 29.1 GeV is 0.03 to 0.76 for X{sub B} and 1.25 GeV{sup 2} to 9.7 GeV{sup 2} for Q{sup 2}, for invariant masses W > 2 GeV/c{sup 2} in the deep inelastic region. The 29.1 GeV longitudinal data has been analyzed`for protons and deuterons, and combined to extract the neutron structure. The results indicate that the extrapolated integrals of the structure functions {Gamma}{sub 1}{sup p} and{Gamma}{sub 1}{sup d} evaluated at the fixed Q{sup 2} = 3 GeV{sup 2} are not in agreement with the theoretical predictions by Ellis and Jaffe. The combined integral {Gamma}{sub 1}{sup p} - {Gamma}{sub 1}{sup n} agrees with the Bjorken Sum Rule prediction when 3rd. order I QCD corrections are included. The methods used to evaluate the structure fimctions at a common Q{sup 2} are being filrther investigated.

  20. Interstellar pickup protons at pressure-balanced structures

    NASA Astrophysics Data System (ADS)

    Isenberg, Philip A.

    1991-01-01

    An improved version is presented of a recent investigation that attempted to measure the presence of interstellar pickup protons in the distant solar wind through their effects on the variations within pressure-balanced structures. The previous study's conclusion that the pickup protons, expected to be correlated with the solar wind density through the charge exchange ionization process, had become smeared in the radial direction is confirmed. It is proposed that quasi-linear diffusion of these energetic particles will produce the spatial uniformity inferred from the observations.

  1. Proton-structure corrections to hyperfine splitting in muonic hydrogen

    SciTech Connect

    Carlson, Carl E.; Nazaryan, Vahagn; Griffioen, Keith

    2011-04-15

    We present the derivation of the formulas for the proton structure-dependent terms in the hyperfine splitting of muonic hydrogen. We use compatible conventions throughout the calculations to derive a consistent set of formulas that reconcile differences between our results and some specific terms in earlier work. Convention conversion corrections are explicitly presented, which reduce the calculated hyperfine splitting by about 46 ppm. We also note that using only modern fits to the proton elastic form factors gives a smaller than historical spread of Zemach radii and leads to a reduced uncertainty in the hyperfine splitting. Additionally, hyperfine splittings have an impact on the muonic hydrogen Lamb shift and proton radius measurement, however the correction we advocate has a small effect there.

  2. 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.

  3. Structures, fragmentation, and protonation of trideoxynucleotide CCC mono- and dianions.

    PubMed

    Anichina, Janna; Feil, Stefan; Uggerud, Einar; Bohme, Diethard K

    2008-07-01

    Both quantum chemical calculations and ESI mass spectrometry are used here to explore the gas-phase structures, energies, and stabilities against collision-induced dissociation of a relatively small model DNA molecule--a trideoxynucleotide with the sequence CCC, in its singly and doubly deprotonated forms, (CCC-H)(-) and (CCC-2H)(2-), respectively. Also, the gas-phase reactivity of these two anions was measured with HBr, a potential proton donor, using an ESI/SIFT/QqQ instrument. The computational results provide insight into the gas-phase structures of the electrosprayed (CCC-2H)(2-) and (CCC-H)(-) anions and the neutral CCC, as well as the proton affinities of the di- and monoanions. The dianion (CCC-2H)(2-) was found to dissociate upon CID by charge separation via two competing channels: separation into deprotonated cytosine (C-H)(-) and (CCC-(C-H)-2H)(-), and by w(1)(-)/a(2)(-) cleavage of the backbone. The monoanion (CCC-H)(-) loses a neutral cytosine upon CID, and an H/D-exchangeable proton, presumably residing on one of the phosphate groups, is transferred to the partially liberated (C-H)(-) before dissociation. This was confirmed by MS/MS experiments with the deuterated analog. The reaction of (CCC-2H)(2-) with HBr was observed to be rapid, k=(1.4+/-0.4) x 10(-9) cm(3) molecule(-1) s(-1), and to proceed both by addition (78%) and by proton transfer (22%) while (CCC-H)(-) reacts only by HBr addition, k=(7.1+/-2.1) x 10(-10) cm(3) molecule(-1) s(-1). This is in accord with the computed proton affinities of (CCC-2H)(2-) and (CCC-H)(-) anions that bracket the known proton affinity of Br(-).

  4. Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

    SciTech Connect

    Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K.

    2009-05-19

    Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-{angstrom} resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK{sub a} of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as {approx}45%, and the 46{sup o} angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.

  5. Gas-phase Structure and Fragmentation Pathways of Singly Protonated Peptides with N-terminal Arginine

    PubMed Central

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

    2010-01-01

    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 b2 ions or facilely rearrange to form anhydrides from which both b2 and b2+H2O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b2 and b2+H2O 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 b1 ion, neutral loss (H2O, NH3, guanidine) fragment ions and the d3 ion. PMID:20973555

  6. Vibrational and structural relaxation of hydrated protons in Nafion membranes

    NASA Astrophysics Data System (ADS)

    Liu, Liyuan; Lotze, Stephan; Bakker, Huib J.

    2017-02-01

    We study the vibrational dynamics of the bending mode at 1730 cm-1 of proton hydration structures in Nafion membranes with polarization-resolved infrared (IR) pump-probe spectroscopy. The bending mode relaxes to an intermediate state with a time constant T1 of 170 ± 30 fs. Subsequently, the dissipated energy equilibrates with Teq of 1.5 ± 0.2 ps. The transient absorption signals show a long-living anisotropy, which indicates that for part of the excited proton hydration clusters the vibrational energy dissipation results in a local structural change, e.g. the breaking of a local hydrogen bond. This structural relaxation relaxes with a time constant of 38 ± 4 ps.

  7. New results on proton structure from HERA

    NASA Astrophysics Data System (ADS)

    Raičević, Nataša

    2016-03-01

    In this paper we show the new set of parton distribution functions (PDFs) determined using new combined H1 and ZEUS data on neutral and charged current inclusive cross sections from all running periods (1994-2007). The combined data are used as the sole input to NLO and NNLO QCD analyses. The new set of PDFs is termed as HERAPDF2.0. Also we show an extended QCD analysis at NLO including the combined data on jet and charm production which enables the simultaneous determination of PDFs (HERAPDF2.0Jets) and the strong coupling constant from HERA data alone.

  8. New results on proton structure from HERA

    SciTech Connect

    Raičević, Nataša

    2016-03-25

    In this paper we show the new set of parton distribution functions (PDFs) determined using new combined H1 and ZEUS data on neutral and charged current inclusive cross sections from all running periods (1994-2007). The combined data are used as the sole input to NLO and NNLO QCD analyses. The new set of PDFs is termed as HERAPDF2.0. Also we show an extended QCD analysis at NLO including the combined data on jet and charm production which enables the simultaneous determination of PDFs (HERAPDF2.0Jets) and the strong coupling constant from HERA data alone.

  9. The 3D Structure of the Proton

    NASA Astrophysics Data System (ADS)

    Kaiser, Ralf

    2012-09-01

    When Rutherford, Geiger and Marsden discovered the atomic nucleus in 1909 in Manchester, they at the same time also laid the foundations for the most successful method to study the structure of nuclei and nucleons. They found a point-like scattering centre inside the atom and identified it with the atomic nucleus and the theoretical description of this process has been known as Rutherford scattering ever since. The deviation between the theoretical description for a point-like scattering centre and experimental data has since been used to reveal information about the structure of the nucleus as well as the nucleon. There has been a continuous development from Hofstadters experiments in the 1950s, over the SLAC experiments in the 60s and 70s to the the HERA experiments at DESY and the experimental programme at Jeffersonlab. In this paper I am presenting the most recent results in Deeply Virtual Compton Scattering from the Hermes experiment at DESY, taken with a high density unpolarised target and a recoil detector in 2006/7.

  10. The QCD Analysis Of The World Data On Structure Functions g{sub 1}{sup p,d,n} For Proton, Deuteron And Neutron

    SciTech Connect

    Savin, I. A.

    2007-06-13

    The fits of all published data on g1, including the new COMPASS measurements of g{sub 1}{sup d}(x,Q{sup 2}), have been performed by using two different QCD evolution formalisms in the next-to-leading-order (NLO) approximation. In both methods we obtain two solutions for fitted parameters of the parton distribution functions (PDFs), one with {delta}G>0 and the other - with {delta}G<0, where {delta}G is the first moment of the polarized gluon distribution in nucleon.

  11. 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.

  12. Photon structure function - theory

    SciTech Connect

    Bardeen, W.A.

    1984-12-01

    The theoretical status of the photon structure function is reviewed. Particular attention is paid to the hadronic mixing problem and the ability of perturbative QCD to make definitive predictions for the photon structure function. 11 references.

  13. 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

  14. Surface, structural and tensile properties of proton beam irradiated zirconium

    NASA Astrophysics Data System (ADS)

    Rafique, Mohsin; Chae, San; Kim, Yong-Soo

    2016-02-01

    This paper reports the surface, structural and tensile properties of proton beam irradiated pure zirconium (99.8%). The Zr samples were irradiated by 3.5 MeV protons using MC-50 cyclotron accelerator at different doses ranging from 1 × 1013 to 1 × 1016 protons/cm2. Both un-irradiated and irradiated samples were characterized using Field Emission Scanning Electron Microscope (FESEM), X-ray Diffraction (XRD) and Universal Testing Machine (UTM). The average surface roughness of the specimens was determined by using Nanotech WSxM 5.0 develop 7.0 software. The FESEM results revealed the formation of bubbles, cracks and black spots on the samples' surface at different doses whereas the XRD results indicated the presence of residual stresses in the irradiated specimens. Williamson-Hall analysis of the diffraction peaks was carried out to investigate changes in crystallite size and lattice strain in the irradiated specimens. The tensile properties such as the yield stress, ultimate tensile stress and percentage elongation exhibited a decreasing trend after irradiation in general, however, an inconsistent behavior was observed in their dependence on proton dose. The changes in tensile properties of Zr were associated with the production of radiation-induced defects including bubbles, cracks, precipitates and simultaneous recovery by the thermal energy generated with the increase of irradiation dose.

  15. Tests of proton structure functions using leptons at CDF and D0: W charge asymmetry and Drell-Yan production. Version 1.0

    SciTech Connect

    Barbaro, P. de

    1995-06-13

    High statistics W charge asymmetry measurements at the Tevatron {bar p}p collider significantly constrain the u and d quark distributions, and specifically the slope of the d(x)/u(x) in the x range 0.007 to 0.27. The authors present measurements of lepton charge asymmetry as a function of lepton rapidity, A(y{sub l}) at {radical}s = 1.8 TeV for {vert_bar}y{sub l}{vert_bar} < 2.0, for the W decays to electrons and muons recorded by the CDF detector during the 1992-93 run ({approx} 20 pb{sup {minus}1}), and the first {approx} 50 pb{sup {minus}1} of data from the 1994-95 run. These precise data make possible further discrimination between sets of modern parton distributions. In particular it is found that the most recent parton distributions, which included the CDF 1992-93 W asymmetry data in their fits (MRSA, CTEQ3M and GRV94) are still in good agreement with the more precise data from the 1994-95 run. W charge asymmetry results from D0 based on {approx} 6.5 pb{sup {minus}1} data from 1992-1993 run and {approx} 29.7 pb{sup {minus}1} data from 1994-1995 run, using the W decays to muons, are also presented and are found to be consistent with CDF results. In addition, the authors present preliminary measurement of the Drell-Yan cross-section by CDF using a dielectron sample collected during the 1993-94 run ({approx} 20 pb{sup {minus}1}) and a high mass dimuon sample from the combined 1993-94 and 1994-95 runs ({approx} 70 pb{sup {minus}1}). The measurement is in good agreement with predictions using the most recent PDFs in a dilepton mass range between 11 and 350 GeV/c{sup 2}.

  16. Di/mono-nuclear iron(I)/(II) complexes as functional models for the 2Fe2S subunit and distal Fe moiety of the active site of [FeFe] hydrogenases: protonations, molecular structures and electrochemical properties.

    PubMed

    Gao, Shang; Fan, Jiangli; Sun, Shiguo; Song, Fengling; Peng, Xiaojun; Duan, Qian; Jiang, Dayong; Liang, Qingcheng

    2012-10-21

    Di/mono-nuclear iron(I)/(II) complexes containing conjugated and electron-withdrawing S-to-S linkers, [{(μ-S)(2)(C(4)N(2)H(2))}Fe(2)(CO)(6)] (1), [{(μ-S)(2)(C(4)N(2)H(2))}Fe(2)(CO)(5)(PMe(3))] (1P), and [{(μ-S)(2)(C(4)N(2)H(2))}Fe(CO)(2)(PMe(3))(2)] (2) were prepared as biomimetic models for the 2Fe2S subunit and distal Fe moiety of the active site of [FeFe] hydrogenases. The N atoms in the heterocyclic pyrazines of 1 and 2 were protonated in the presence of proton acid to generate one and two hydrides, [1(NH)](+) CF(3)SO(3)(-), [2(NH)](+) CF(3)SO(3)(-), and [2(NH)(2)](2+) (CF(3)SO(3)(-))(2), respectively. The protonation processes were evidenced by in situ IR and NMR spectroscopy. The molecular structures of the protonated species [1(NH)](+) CF(3)SO(3)(-) and [2(NH)(2)](2+) (CF(3)SO(3)(-))(2) together with their originating complexes and , and the mono-PMe(3) substituted diiron complex were identified by X-ray crystallography. The IR and single-crystal analysis data all suggested that the electron-withdrawing bridge, pyrazine, led to decreased electron density at the Fe centers of the model complexes, which was consistent with the electrochemical studies. The cyclic voltammograms indicated that complex exhibited a low primary reduction potential at -1.17 V vs. Fc-Fc(+) with a 270 mV positive shift compared with that of the benzene-1,2-dithiolate (bdt) bridged analogue [(μ-bdt)Fe(2)(CO)(6)]. Under the weak acid conditions, complexes 1 and 2 could electrochemically catalyze the proton reduction. More interestingly, the mononuclear ferrous complex 2 showed two catalytic peaks during the formation of hydrogen, confirming its potential as a catalyst for hydrogen production.

  17. Structural and Electrochemical Consequences of [Cp*] Ligand Protonation.

    PubMed

    Peng, Yun; Ramos-Garcés, Mario V; Lionetti, Davide; Blakemore, James D

    2017-09-05

    There are few examples of the isolation of analogous metal complexes bearing [η(5)-Cp*] and [η(4)-Cp*H] (Cp* = pentamethylcyclopentadienyl) complexes within the same metal/ligand framework, despite the relevance of such structures to catalytic applications. Recently, protonation of Cp*Rh(bpy) (bpy = 2,2'-bipyridyl) has been shown to yield a complex bearing the uncommon [η(4)-Cp*H] ligand, rather than generating a [Rh(III)-H] complex. We now report the purification and isolation of this protonated species, as well as characterization of analogous complexes of 1,10-phenanthroline (phen). Specifically, reaction of Cp*Rh(bpy) or Cp*Rh(phen) with 1 equiv of Et3NH(+)Br(-) affords rhodium compounds bearing endo-η(4)-pentamethylcyclopentadiene (η(4)-Cp*H) as a ligand. NMR spectroscopy and single-crystal X-ray diffraction studies confirm protonation of the Cp* ligand, rather than formation of metal hydride complexes. Analysis of new structural data and electronic spectra suggests that phen is significantly reduced in Cp*Rh(phen), similar to the case of Cp*Rh(bpy). Backbonding interactions with olefinic motifs are activated by formation of [η(4)-Cp*H]; protonation of [Cp*] stabilizes the low-valent metal center and results in loss of reduced character on the diimine ligands. In accord with these changes in electronic structure, electrochemical studies reveal a distinct manifold of redox processes that are accessible in the [Cp*H] complexes in comparison with their [Cp*] analogues; these processes suggest new applications in catalysis for the complexes bearing endo-η(4)-Cp*H.

  18. First measurement of the deep-inelastic structure of proton diffraction

    NASA Astrophysics Data System (ADS)

    Ahmed, T.; Aid, S.; Andreev, V.; Andrieu, B.; Appuhn, R.-D.; Arpagaus, M.; Babaev, A.; Baehr, J.; Bán, J.; Ban, Y.; Baranov, P.; Barrelet, E.; 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.; 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.; 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, 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.; 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.; 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.; Kolva, 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.; 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.; 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.; 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.; 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.; 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.; 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

    A measurement is presented, using data taken with the H1 detector at HERA, of the contribution of diffractive interactions to deep-inelastic electron-proton ( ep) scattering in the kinematic range 8.5 < Q2 < 50GeV 2, 2.4 × 10 -4 < Bjorken- x < 0.0133, and 3.7 × 10 -4 < χp < 0.043. The diffractive contribution to the proton structure function F2( x, Q2) is evaluated as a function of the appropriate deep-inelastic scattering variables χp, Q2, β (= {χ}/{χ p}) using a class of deep-inelastic ep scattering events with no hadronic energy flow in an interval of pseudo-rapidity adjacent to the proton beam direction. the dependence of this contribution on χp is measured to be χp- n with n = 1.19 ± 0.06 (stat.) ± 0.07 (syst.) independent of β and Q2, which is consistent with both a diffractive interpretation and a factorisable ep diffractive cross section. A first measurement of the deep-inelastic structure of the pomeron in the form of the Q2 and β dependences of a factorised structure function is presented. For all measured β, this structure function is observed to be consistent with scale invariance.

  19. 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

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

    SciTech Connect

    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 are 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.

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

    SciTech Connect

    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 are 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.

  2. Outcomes of Proton Therapy for Patients With Functional Pituitary Adenomas

    SciTech Connect

    Wattson, Daniel A.; Tanguturi, Shyam K.; Spiegel, Daphna Y.; Niemierko, Andrzej; Biller, Beverly M.K.; Nachtigall, Lisa B.; Bussière, Marc R.; Swearingen, Brooke; Chapman, Paul H.; Loeffler, Jay S.; Shih, Helen A.

    2014-11-01

    Purpose/Objective(s): This study evaluated the efficacy and toxicity of proton therapy for functional pituitary adenomas (FPAs). Methods and Materials: We analyzed 165 patients with FPAs who were treated at a single institution with proton therapy between 1992 and 2012 and had at least 6 months of follow-up. All but 3 patients underwent prior resection, and 14 received prior photon irradiation. Proton stereotactic radiosurgery was used for 92% of patients, with a median dose of 20 Gy(RBE). The remainder received fractionated stereotactic proton therapy. Time to biochemical complete response (CR, defined as ≥3 months of normal laboratory values with no medical treatment), local control, and adverse effects are reported. Results: With a median follow-up time of 4.3 years (range, 0.5-20.6 years) for 144 evaluable patients, the actuarial 3-year CR rate and the median time to CR were 54% and 32 months among 74 patients with Cushing disease (CD), 63% and 27 months among 8 patients with Nelson syndrome (NS), 26% and 62 months among 50 patients with acromegaly, and 22% and 60 months among 9 patients with prolactinomas, respectively. One of 3 patients with thyroid stimulating hormone—secreting tumors achieved CR. Actuarial time to CR was significantly shorter for corticotroph FPAs (CD/NS) compared with other subtypes (P=.001). At a median imaging follow-up time of 43 months, tumor control was 98% among 140 patients. The actuarial 3-year and 5-year rates of development of new hypopituitarism were 45% and 62%, and the median time to deficiency was 40 months. Larger radiosurgery target volume as a continuous variable was a significant predictor of hypopituitarism (adjusted hazard ratio 1.3, P=.004). Four patients had new-onset postradiosurgery seizures suspected to be related to generously defined target volumes. There were no radiation-induced tumors. Conclusions: Proton irradiation is an effective treatment for FPAs, and hypopituitarism remains the primary

  3. Molecular Simulations of Hydrated Proton Exchange Membranes: the Structure

    NASA Astrophysics Data System (ADS)

    Marchand, Gabriel; Bopp, Philippe A.; Spohr, Eckhard

    2013-02-01

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion® (Dupont) and Hyflon® (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms.

  4. Infrared Structural Biology: Detect Functionally Important Structural Motions of Proteins

    NASA Astrophysics Data System (ADS)

    Xie, Aihua

    Proteins are dynamic. Lack of dynamic structures of proteins hampers our understanding of protein functions. Infrared structural biology (IRSB) is an emerging technology. There are several advantages of IRSB for mechanistic studies of proteins: (1) its excellent dynamic range (detecting structural motions from picoseconds to >= seconds); (2) its high structural sensitivity (detect tiny but functionally important structural motions such as proton transfer and changes in hydrogen bonding interaction); (3) its ability to detect different structural motions simultaneously. Successful development of infrared structural biology demands not only new experimental techniques (from infrared technologies to chemical synthesis and cell biology), but also new data processing (how to translate infrared signals into quantitative structural information of proteins). These topics will be discussed as well as examples of how to use IRSB to study structure-function relationship of proteins. This work was supported by NSF DBI1338097 and OCAST HR10-078.

  5. Proton Transport in Imidazoles: Unraveling the Role of Supramolecular Structure

    DOE PAGES

    Cosby, James T.; Holt, Adam P.; Griffin, Phillip; ...

    2015-09-18

    The impact of supramolecular hydrogen bonded networks on dynamics and charge transport in 2-ethyl-4-methylimidazole (2E4MIm), a model proton-conducting system, is investigated by broadband dielectric spectroscopy, depolarized dynamic light scattering, viscometry, and calorimetry. It is observed that the slow, Debye-like relaxation reflecting the supramolecular structure in neat 2E4MIm is eliminated upon the addition of minute amounts of levulinic acid. This is attributed to the dissociation of imidazole molecules and the breaking down of hydrogen-bonded chains, which leads to a 10-fold enhancement of ionic conductivity.

  6. Functional Dissection of the Proton Pumping Modules of Mitochondrial Complex I

    PubMed Central

    Sokolova, Lucie; Zwicker, Klaus; Barth, Hans-Dieter; Morgner, Nina; Heide, Heinrich; Steger, Mirco; Nübel, Esther; Zickermann, Volker; Kerscher, Stefan; Brutschy, Bernhard; Radermacher, Michael; Brandt, Ulrich

    2011-01-01

    Mitochondrial complex I, the largest and most complicated proton pump of the respiratory chain, links the electron transfer from NADH to ubiquinone to the pumping of four protons from the matrix into the intermembrane space. In humans, defects in complex I are involved in a wide range of degenerative disorders. Recent progress in the X-ray structural analysis of prokaryotic and eukaryotic complex I confirmed that the redox reactions are confined entirely to the hydrophilic peripheral arm of the L-shaped molecule and take place at a remarkable distance from the membrane domain. While this clearly implies that the proton pumping within the membrane arm of complex I is driven indirectly via long-range conformational coupling, the molecular mechanism and the number, identity, and localization of the pump-sites remains unclear. Here, we report that upon deletion of the gene for a small accessory subunit of the Yarrowia complex I, a stable subcomplex (nb8mΔ) is formed that lacks the distal part of the membrane domain as revealed by single particle analysis. The analysis of the subunit composition of holo and subcomplex by three complementary proteomic approaches revealed that two (ND4 and ND5) of the three subunits with homology to bacterial Mrp-type Na+/H+ antiporters that have been discussed as prime candidates for harbouring the proton pumps were missing in nb8mΔ. Nevertheless, nb8mΔ still pumps protons at half the stoichiometry of the complete enzyme. Our results provide evidence that the membrane arm of complex I harbours two functionally distinct pump modules that are connected in series by the long helical transmission element recently identified by X-ray structural analysis. PMID:21886480

  7. Structure and Dynamics Investigations of Sr/Ca-Doped LaPO4 Proton Conductors

    DOE PAGES

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

    2017-05-15

    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 LaPO4 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 LaPO4 can exist as self-supported structures at high temperatures during solid oxide fuel cell operation. Thermal stability, surface topography, size distribution aremore » 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

  8. 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

  9. Disruption of SLX4-MUS81 Function Increases the Relative Biological Effectiveness of Proton Radiation

    PubMed Central

    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

    2016-01-01

    Purpose/Objective(s) Clinical proton beam therapy has been based on the use of a generic relative biological effectiveness (RBE) of ~1.1. However, emerging data suggest that Fanconi Anemia (FA) and homologous recombination pathway defects may lead to a variable RBE, at least in-vitro. Here, 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) or with 250 kVp X-rays, and clonogenic survival fractions (SF) were determined. To estimate the RBE of 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 employed to monitor damage responses, and cell cycle distributions were assessed by flow cytometry. The PARP inhibitor olaparib was used for comparison. Results Loss of SLX4 function resulted in an enhanced proton RBE(Co60Eq) of 1.42 compared to 1.11 for wild-type cells (at SF=0.1, p<0.05) which correlated with increased persistent DNA double-strand breaks in cells in 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. 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 damages. In-vivo and clinical studies are needed to confirm these findings in human cancers. PMID:27084631

  10. Chromosome structure and function

    SciTech Connect

    Risley, M.S.

    1986-01-01

    This book presents topics in chromosome structure and function. Topics covered include: the structure of interphase chromatin; chromatin structure, gene expression and differentiation; organization of mitotic chromosomes; organization of meiotic chromosomes and synaptonimal complexes; the lampbrush chromsome of animal oocytes; dosage compensation in mammals: x chromosome inactivation; and polytene chromosomes.

  11. Static and dynamic aspect of covariant density functional theory in proton rich nuclei

    SciTech Connect

    Ring, P.; Lalazissis, G. A.; Paar, N.; Vretenar, D.

    2007-11-30

    Proton rich nuclei are investigated in the framework of Covariant Density Functional Theory (CDFT). The Relativistic Hartree Bogoliubov (RHB) model is used to study the proton drip line in the region of heavy and superheavy nuclei. The dynamical behavior of nuclei with a large proton excess is studied within the Relativistic Quasiparticle Random Phase Approximation (RQRPA). Low lying El-strength is observed and it is shown that it corresponds to an oscillation of the proton skin against the isospin saturated neutron-proton core. This mode is in full analogy to the neutron pygmy resonances found in many nuclei with neutron excess.

  12. Monte Carlo simulation of proton track structure in biological matter

    DOE PAGES

    Quinto, Michele A.; Monti, Juan M.; Weck, Philippe F.; ...

    2017-05-25

    Here, understanding the radiation-induced effects at the cellular and subcellular levels remains crucial for predicting the evolution of irradiated biological matter. In this context, Monte Carlo track-structure simulations have rapidly emerged among the most suitable and powerful tools. However, most existing Monte Carlo track-structure codes rely heavily on the use of semi-empirical cross sections as well as water as a surrogate for biological matter. In the current work, we report on the up-to-date version of our homemade Monte Carlo code TILDA-V – devoted to the modeling of the slowing-down of 10 keV–100 MeV protons in both water and DNA –more » where the main collisional processes are described by means of an extensive set of ab initio differential and total cross sections.« less

  13. The Neutron Structure Function

    NASA Astrophysics Data System (ADS)

    Holt, Roy

    2013-10-01

    Knowledge of the neutron structure function is important for testing models of the nucleon, for a complete understanding of deep inelastic scattering (DIS) from nuclei, and for high energy experiments. As there exist no free neutron targets, neutron structure functions have been determined from deep inelastic scattering from the deuteron. Unfortunately, the short-range part of the deuteron wave function becomes important in extracting the neutron structure function at very high Bjorken x. New methods have been devised for Jefferson Lab experiments to mitigate this problem. The BONUS experiment involves tagging spectator neutrons in the deuteron, while the MARATHON experiment minimizes nuclear structure effects by a comparison of DIS from 3H and 3He. A summary of the status and future plans will be presented. This work supported by the U. S. Department of Energy, Office of Nuclear Physics, under contract DE-AC02-06CH11357.

  14. Protonation-deprotonation and structural dynamics of antidiabetic drug metformin.

    PubMed

    Hernández, Belén; Pflüger, Fernando; Kruglik, Sergei G; Cohen, Régis; Ghomi, Mahmoud

    2015-10-10

    Since the late 1950s, metformin is the worldwide first-line pharmacologic treatment for type 2 diabetes. Beyond the fact that the mode of action of this drug has always been very difficult to elucidate, little is known about its physicochemical properties in aqueous solution. Herein, we focus on the protonation-deprotonation features of metformin by using jointly Raman scattering and theoretical calculations. Vibrational markers evidence the fact that within a wide pH interval extended at either side of the physiological one, i.e. ∼7 ± 4, metformin is mainly monoprotonated. Although the biprotonated form appears as major population at very low pH values (<1.5), Raman markers of neutral species do not dominate even at very high pH values (>13), presumably because of the extreme basicity of metformin as described by recent NMR measurements. Density functional theory calculations using both explicit and implicit hydration models, have led to presume a possible coexistence of two possible monoprotonated forms in aqueous environment. In conclusion, the biophysical features of this molecule and the amount used in clinical practice might certainly explain the pleiotropic actions toward several targets where metformin could be a permanent cationic partner, a proton donor/acceptor, as well as a good candidate for stabilizing the so-called π→π interactions. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Structure function monitor

    DOEpatents

    McGraw, John T [Placitas, NM; Zimmer, Peter C [Albuquerque, NM; Ackermann, Mark R [Albuquerque, NM

    2012-01-24

    Methods and apparatus for a structure function monitor provide for generation of parameters characterizing a refractive medium. In an embodiment, a structure function monitor acquires images of a pupil plane and an image plane and, from these images, retrieves the phase over an aperture, unwraps the retrieved phase, and analyzes the unwrapped retrieved phase. In an embodiment, analysis yields atmospheric parameters measured at spatial scales from zero to the diameter of a telescope used to collect light from a source.

  16. Dynamic versus Static Hadronic Structure Functions

    SciTech Connect

    Brodsky, Stanley J.; /SLAC

    2009-01-09

    'Static' structure functions are the probabilistic distributions computed from the square of the light-front wavefunctions of the target hadron. In contrast, the 'dynamic' structure functions measured in deep inelastic lepton-hadron scattering include the effects of rescattering associated with the Wilson line. Initial- and final-state rescattering, neglected in the parton model, can have a profound effect in QCD hard-scattering reactions, producing single-spin asymmetries, diffractive deep inelastic scattering, diffractive hard hadronic reactions, the breakdown of the Lam-Tung relation in Drell-Yan reactions, nuclear shadowing, and non-universal nuclear antishadowing|novel leading-twist physics not incorporated in the light-front wavefunctions of the target computed in isolation. I also review how 'direct' higher-twist processes--where a proton is produced in the hard subprocess itself--can explain the anomalous proton-to-pion ratio seen in high centrality heavy ion collisions.

  17. Two-Proton Radioactivity as a Tool for Nuclear Structure

    NASA Astrophysics Data System (ADS)

    Blank, B.; Ascher, P.; Audirac, L.; Giovinazzo, J.; Adimi, N.; Canchel, G.; Delalee, F.; Demonchy, C. E.; Dossat, C.; Grévy, S.; Hay, L.; Huikari, J.; Kurtukian-Nieto, T.; Leblanc, S.; Matea, I.; Pedroza, J.-L.; Pibernat, J.; Serani, L.; de Oliveira Santos, F.; Perrot, L.; Srivastava, P. C.; Stodel, C.; Thomas, J.-C.; Borcea, C.; Companis, I.; Brown, B. A.; Grigorenko, L. V.

    2013-09-01

    The decay of the ground-state two-proton emitters 45Fe and 54Zn was studied with a time-projection chamber and the emission of two protons was unambiguously identified. The total decay energy and the half-life measured agree with the results from previous experiments. The energy sharing between the two protons and their relative emission angle was determined with a time projection chamber and is compared to model predictions. In parallel, we observed directly β-delayed two- and three-proton emission from 43Cr, a known β-delayed two-proton emitter.

  18. Influence of microhydration on the structures and proton-induced charge transfer in RNA intermediates.

    PubMed

    Bacchus-Montabonel, M C; Calvo, F

    2016-11-01

    Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets. Uracil has been widely investigated both experimentally and theoretically in this context, and 2-aminooxazole was recently shown to be a potentially important intermediate in prebiotic chemistry. Focusing here on doubly hydrated biomolecules, stable structures and infrared spectra were obtained by combining the results of molecular dynamics simulations with those of quantum chemistry calculations performed at the density-functional theory level with the double hybrid M06-2X functional. The charge-transfer cross-sections upon proton impact were obtained from ab initio molecular calculations and after applying a semi-classical approach to investigate the collision. Our results suggest a significant relationship between the detailed hydration structure and the efficacy of proton-induced charge transfer, highlighting the competing roles of inter- and intramolecular hydrogen bonding.

  19. A Proton Wire and Water Channel Revealed in the Crystal Structure of Isatin Hydrolase

    PubMed Central

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

    2014-01-01

    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. PMID:24917679

  20. Electronic band structure effects in the stopping of protons in copper

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

    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 -10 a .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 are 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 -0.3 a .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.

  1. Dimers of formic acid: Structures, stability, and double proton transfer

    NASA Astrophysics Data System (ADS)

    Farfán, Paola; Echeverri, Andrea; Diaz, Estefanía; Tapia, Juan David; Gómez, Sara; Restrepo, Albeiro

    2017-07-01

    A stochastic search of the potential energy surface for the formic acid dimers results in 21 well-defined minima. A number of structures are reported here for the first time, others have already been experimentally detected or computationally predicted. Four types of different hydrogen bonds (HBs) are at play stabilizing the clusters: primary C=O⋯ H—O and H—O⋯ H—O and secondary C=O⋯ H—C and H—O⋯ H—C HBs corresponding to well-characterized bonding paths are identified. A novel C=O⋯ C stabilizing interaction is also reported. The double proton transfer reaction is calculated to occur in a synchronous fashion, with an energy barrier smaller than the energy needed to break up the dimers.

  2. Dimers of formic acid: Structures, stability, and double proton transfer.

    PubMed

    Farfán, Paola; Echeverri, Andrea; Diaz, Estefanía; Tapia, Juan David; Gómez, Sara; Restrepo, Albeiro

    2017-07-28

    A stochastic search of the potential energy surface for the formic acid dimers results in 21 well-defined minima. A number of structures are reported here for the first time, others have already been experimentally detected or computationally predicted. Four types of different hydrogen bonds (HBs) are at play stabilizing the clusters: primary C=O⋯ H-O and H-O⋯ H-O and secondary C=O⋯ H-C and H-O⋯ H-C HBs corresponding to well-characterized bonding paths are identified. A novel C=O⋯ C stabilizing interaction is also reported. The double proton transfer reaction is calculated to occur in a synchronous fashion, with an energy barrier smaller than the energy needed to break up the dimers.

  3. Controlled multiple functionalization of mesoporous silica nanoparticles: homogeneous implementation of pairs of functionalities communicating through energy or proton transfers.

    PubMed

    Noureddine, Achraf; Lichon, Laure; Maynadier, Marie; Garcia, Marcel; Gary-Bobo, Magali; Zink, Jeffrey I; Cattoën, Xavier; Wong Chi Man, Michel

    2015-07-14

    The synthesis of mesoporous silica nanoparticles bearing organic functionalities is strained by the careful adjustment of the reaction parameters, as the incorporation of functional and/or voluminous organosilanes during the sol-gel synthesis strongly affects the final structure of the nanoparticles. In this paper we describe the design of new clickable mesoporous silica nanoparticles as spheres or rods, synthesized by the co-condensation of TEOS with two clickable organosilanes (bearing alkyne and azide groups) and readily multi-functionalizable by CuAAC click chemistry. We show that controlled loadings of clickable functions can be homogeneously distributed within the MSN, allowing us to efficiently click-graft various pairs of functionalities while preserving the texture and morphology of the particles. The homogeneous distribution of the grafted functionalities was probed by FRET experiments between two anchored fluorophores. Moreover, a communication by proton transfer between two functions was demonstrated by constructing a light-actuated nanomachine that works through a proton transfer between a photoacid generator and a pH-sensitive supramolecular nanogate. The activation of the nanomachine enabled the successful release of rhodamine B in buffered solutions and the delivery of doxorubicin in breast cancer cells (MCF-7) upon blue irradiation.

  4. Visualizing proton antenna in a high-resolution green fluorescent protein structure.

    PubMed

    Shinobu, Ai; Palm, Gottfried J; Schierbeek, Abraham J; Agmon, Noam

    2010-08-18

    "Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.9 A). It allows the identification of some pivotal hydrogen atoms pertinent to uncertainties concerning the protonation state of the chromophore. Applying a computer algorithm for mapping proton wires in proteins reveals the previously observed "active site wire" connecting Glu222 with the surface carboxylate Glu5. In addition, it is now possible to identify what appears to be a proton-collecting apparatus of GFP. It consists of a negative surface patch containing carboxylates, threonines, and water molecules, connected by a HB network to Glu5. Furthermore, we detect exit points via Asn146 and His148 to a hydrophobic surface region. The more extensive HB network of the present structure, as compared with earlier GFP structures, is not accidental. A systematic investigation of over 100 mutants shows a clear correlation between the observed water content of GFP X-ray structures and their resolution. With increasing water content, the proton wires become progressively larger. These findings corroborate the scenario in which the photodissociated proton from wild-type GFP can leak outside, whereafter another proton is recruited via the proton-collecting apparatus reported herein.

  5. Electron correlated and density functional studies on hydrogen-bonded proton transfer in adenine thymine base pair of DNA

    NASA Astrophysics Data System (ADS)

    Shimizu, Naoto; Kawano, Satoyuki; Tachikawa, Masanori

    2005-02-01

    The potential energy surface along the hydrogen-bonded proton transfer between the Watson-Crick (WC) adenine-thymine (A-T) base pair of deoxyribonucleic acid (DNA) and its tautomeric structures is calculated with 6-31G(d,p) basis set in Hartree-Fock (HF), density functional theory with Becke's three-parameter hybrid Lee-Yang-Parr exchange-correlation functional (B3LYP), second order Møller-Plesset perturbation (MP2), and coupled cluster singles and doubles (CCSD) levels. The tautomeric structure, where both two hydrogen-bonded protons in the A-T base pair have transferred each other, is found at all level of calculations. Though the optimized structure in which only one hydrogen-bonded proton in adenine has migrated to thymine is found at HF level, we could not obtain such optimized structure at both MP2 and B3LYP levels. Including electron correlations, the energy differences between the canonical A-T and the two hydrogen-bonded protons transferred tautomeric structure become smaller. Aside from this, potential energy surface from the WC A-T to the Hoogsteen type A-T gives almost the same among each level of calculation.

  6. Preexisting domain motions underlie protonation-dependent structural transitions of the P-type Ca(2+)-ATPase.

    PubMed

    Fernández-de Gortari, Eli; Espinoza-Fonseca, L Michel

    2017-04-12

    We have performed microsecond molecular dynamics (MD) simulations to determine the mechanism for protonation-dependent structural transitions of the sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA), one of the most prominent members of the large P-type ATPase superfamily that transports ions across biological membranes. The release of two H(+) from the transport sites activates SERCA by inducing a structural transition between low (E2) and high (E1) Ca(2+)-affinity states (E2-to-E1 transition), but the structural mechanism by which transport site deprotonation facilitates this transition is unknown. We performed microsecond all-atom MD simulations to determine the effects of transport site protonation on the structural dynamics of the E2 state in solution. We found that the protonated E2 state has structural characteristics that are similar to those observed in crystal structures of E2. Upon deprotonation, a single Na(+) ion rapidly (<10 ns) binds to the transmembrane transport sites and induces a kink in M5, disrupts the M3-M5 interface, and increases the mobility of the M3/A-M3 linker. Principal component analysis showed that counter-rotation of the cytosolic N-A domains about the membrane normal axis, which is the primary motion driving the E2-to-E1 transition, is present in both protonated and deprotonated E2 states; however, protonation-dependent structural changes in the transmembrane domain control the hierarchical organization and amplitude of this motion. We propose that preexisting rigid-body domain motions underlie structural transitions of SERCA, where the functionally important directionality is preserved while transport site protonation controls the dominance and amplitude of motion to shift the equilibrium between the E1 and E2 states. We conclude that ligand-induced modulation of preexisting domain motions is likely a common theme in structural transitions of the P-type ATPase superfamily.

  7. Proton conductive Pt-Co nanoparticles anchoring on citric acid functionalized graphene for efficient oxygen reduction reaction

    NASA Astrophysics Data System (ADS)

    Zhao, Yige; Liu, Jingjun; Wu, Yijun; Wang, Feng

    2017-08-01

    Designing highly efficient electro-catalysts for the oxygen reduction reaction (ORR) has been regarded as a demanding task in the development of renewable energy sources. However, little attention has been paid on improving Pt-based catalysts by promoting proton transfer from the electrolyte solutions to the catalyst layer at the cathode. Herein, we design proton conductive Pt-Co alloy nanoparticles anchoring on citric acid functionalized graphene (Pt-Co/CA-G) catalysts for efficient ORR. The facile modification approach for graphene can introduce oxygenated functional groups on the graphene surface to promote proton transfer as well as keeping the high electron conductivity without destroying the graphene original structure. The electrochemical results show that the Pt-Co/CA-G catalyst exhibits more excellent ORR activity and stability than the commercial Pt/C catalyst, which can be attributed to its improved proton transfer ability. The fast proton transfer comes from the hydrogen-bonding networks formed by the interaction between the oxygenated functional groups and water molecules. This work provides not only a novel and simple approach to modify graphene but also an effective strategy to improve Pt-based catalysts for the ORR.

  8. Enhanced proton conductivity of sulfonated poly(p-phenylene-co-aryl ether ketone) proton exchange membranes with controlled microblock structure

    NASA Astrophysics Data System (ADS)

    He, Qingyi; Xu, Tong; Qian, Huidong; Zheng, Jifu; Shi, Ce; Li, Yunqi; Zhang, Suobo

    2015-03-01

    A new series of sulfonated poly(p-phenylene-co-aryl ether ketone)s (s, m, l-SPP-co-PAEKs) microblock polymers containing different hydrophobic units with precisely defined lengths have been prepared via the nickel (0) catalyzed coupling copolymerization and characterized to act as proton exchange membranes. By controlling the length and chemical structure of the hydrophobic units in the copolymers, these novel microblock polymers can exhibit well-developed nanophase morphologies and large length-scale of the ionic channels, resulting in the improvement of the proton conductivity in both the wet and dry state. Moreover, the membrane l-SPP-co-PAEK 1.80 with the largest hydrophobic micro-block length shows high proton conductivity, excellent dimensional stability, low glass-transition temperature (Tg), good oxidative stability and superior cell performance.

  9. Neutron spin structure with polarized deuterons and spectator proton tagging at EIC

    SciTech Connect

    Cosyn, W.; Guzey, V.; Higinbotham, D. W.; Hyde, C.; Kuhn, S.; Nadel-Turonski, P.; Park, K.; Sargsian, M.; Strikman, M.; Weiss, C.

    2014-10-27

    The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Thus, traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x << 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < pR << several 100 MeV in the nucleus rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.

  10. Neutron spin structure with polarized deuterons and spectator proton tagging at EIC

    DOE PAGES

    Cosyn, W.; Guzey, V.; Higinbotham, D. W.; ...

    2014-10-27

    The neutron's deep-inelastic structure functions provide essential information for the flavor separation of the nucleon parton densities, the nucleon spin decomposition, and precision studies of QCD phenomena in the flavor-singlet and nonsinglet sectors. Thus, traditional inclusive measurements on nuclear targets are limited by dilution from scattering on protons, Fermi motion and binding effects, final-state interactions, and nuclear shadowing at x << 0.1. An Electron-Ion Collider (EIC) would enable next-generation measurements of neutron structure with polarized deuteron beams and detection of forward-moving spectator protons over a wide range of recoil momenta (0 < pR << several 100 MeV in the nucleusmore » rest frame). The free neutron structure functions could be obtained by extrapolating the measured recoil momentum distributions to the on-shell point. The method eliminates nuclear modifications and can be applied to polarized scattering, as well as to semi-inclusive and exclusive final states. We review the prospects for neutron structure measurements with spectator tagging at EIC, the status of R&D efforts, and the accelerator and detector requirements.« less

  11. Identifying the proton transfer reaction mechanism via a proton-bound dimeric intermediate for esomeprazoles by a kinetic method combined with density functional theory calculations.

    PubMed

    Cao, Xiaoji; Zhang, Feifei; Zhu, Kundan; Ye, Xuemin; Shen, Lingxiao; Chen, Jiaoyu; Mo, Weimin

    2014-05-15

    Esomeprazole analogs are a class of important proton pump inhibitors for the treatment of gastro-esophageal reflux diseases. Understanding the fragmentation reaction mechanism of the protonated esomeprazole analogs will facilitate the characterization of their complex metabolic fate in humans. In this paper, the kinetic method and theoretical calculations were applied to evaluate the fragmentation of protonated esomeprazole analogs. All collision-induced dissociation (CID) mass spectrometry experiments were carried out using electrospray ionization (ESI) ion trap mass spectrometry in positive ion mode. Also the accurate masses of fragments were measured on by ESI quadrupole time-of-flight (QTOF) MS in positive ion mode. Theoretical calculations were carried out by the density functional theory (DFT) method with the 6-31G(d) basis set in the Gaussian 03 program. In the fragmentation of the protonated esomeprazole analogs, C-S bond breakage is observed, which gives rise to protonated 2-(sulfinylmethylene)pyridines and protonated benzimidazoles. DFT calculations demonstrate that the nitrogen atom of the pyridine part is the thermodynamically most favorable protonation site, and the C-S bond cleavage is triggered by the transfer of this ionizing proton from the nitrogen atom of the pyridine part to the carbon atom of the benzimidazole part to which the sulfinyl is attached. Moreover, with the kinetic plot, the intensity ratios of two protonated product ions yield a linear relationship with the differences in proton affinities of the corresponding neutral molecules, which provides strong experimental evidence that the reaction proceeds via proton-bound 2-(sulfinylmethylene)pyridine/benzimidazole complex intermediates. The kinetic method combined with theoretical calculations was successfully applied to probe the proton transfer reaction by proton-bound 2-(sulfinylmethylene)pyridine/benzimidazole complexes in the fragmentation of protonated esomeprazole analogs by ESI

  12. Caveolae structure and function

    PubMed Central

    Thomas, Candice M; Smart, Eric J

    2008-01-01

    Abstract Studies on the structure and function of caveolae have revealed how this versatile subcellular organelle can influence numerous signalling pathways. This brief review will discuss a few of the key features of caveolae as it relates to signalling and disease processes. PMID:18315571

  13. Proton currents constrain structural models of voltage sensor activation

    PubMed Central

    Randolph, Aaron L; Mokrab, Younes; Bennett, Ashley L; Sansom, Mark SP; Ramsey, Ian Scott

    2016-01-01

    The Hv1 proton channel is evidently unique among voltage sensor domain proteins in mediating an intrinsic ‘aqueous’ H+ conductance (GAQ). Mutation of a highly conserved ‘gating charge’ residue in the S4 helix (R1H) confers a resting-state H+ ‘shuttle’ conductance (GSH) in VGCs and Ci VSP, and we now report that R1H is sufficient to reconstitute GSH in Hv1 without abrogating GAQ. Second-site mutations in S3 (D185A/H) and S4 (N4R) experimentally separate GSH and GAQ gating, which report thermodynamically distinct initial and final steps, respectively, in the Hv1 activation pathway. The effects of Hv1 mutations on GSH and GAQ are used to constrain the positions of key side chains in resting- and activated-state VS model structures, providing new insights into the structural basis of VS activation and H+ transfer mechanisms in Hv1. DOI: http://dx.doi.org/10.7554/eLife.18017.001 PMID:27572256

  14. Monte Carlo simulation of proton track structure in biological matter

    NASA Astrophysics Data System (ADS)

    Quinto, Michele A.; Monti, Juan M.; Weck, Philippe F.; Fojón, Omar A.; Hanssen, Jocelyn; Rivarola, Roberto D.; Senot, Philippe; Champion, Christophe

    2017-05-01

    Understanding the radiation-induced effects at the cellular and subcellular levels remains crucial for predicting the evolution of irradiated biological matter. In this context, Monte Carlo track-structure simulations have rapidly emerged among the most suitable and powerful tools. However, most existing Monte Carlo track-structure codes rely heavily on the use of semi-empirical cross sections as well as water as a surrogate for biological matter. In the current work, we report on the up-to-date version of our homemade Monte Carlo code TILDA-V - devoted to the modeling of the slowing-down of 10 keV-100 MeV protons in both water and DNA - where the main collisional processes are described by means of an extensive set of ab initio differential and total cross sections. Contribution to the Topical Issue "Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces", edited by A.N. Grum-Grzhimailo, E.V. Gryzlova, Yu V. Popov, and A.V. Solov'yov.

  15. 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.

  16. Higher-order proton structure corrections to the Lamb shift in muonic hydrogen

    SciTech Connect

    Carlson, Carl E.; Vanderhaeghen, Marc

    2011-08-15

    The recent conundrum with the proton charge radius inspires reconsideration of the corrections that enter into determinations of the proton size. We study the two-photon proton-structure corrections, with special consideration of the nonpole subtraction term in the dispersion relation and using fits to modern data to evaluate the energy contributions. We find that individual contributions change more than the total and present results with error estimates.

  17. Guest molecule-responsive functional calcium phosphonate frameworks for tuned proton conductivity.

    PubMed

    Bazaga-García, Montse; Colodrero, Rosario M P; Papadaki, Maria; Garczarek, Piotr; Zoń, Jerzy; Olivera-Pastor, Pascual; Losilla, Enrique R; León-Reina, Laura; Aranda, Miguel A G; Choquesillo-Lazarte, Duane; Demadis, Konstantinos D; Cabeza, Aurelio

    2014-04-16

    We report the synthesis, structural characterization, and functionality (framework interconversions together with proton conductivity) of an open-framework hybrid that combines Ca(2+) ions and the rigid polyfunctional ligand 5-(dihydroxyphosphoryl)isophthalic acid (PiPhtA). Ca2[(HO3PC6H3COOH)2]2[(HO3PC6H3(COO)2H)(H2O)2]·5H2O (Ca-PiPhtA-I) is obtained by slow crystallization at ambient conditions from acidic (pH ≈ 3) aqueous solutions. It possesses a high water content (both Ca coordinated and in the lattice), and importantly, it exhibits water-filled 1D channels. At 75 °C, Ca-PiPhtA-I is partially dehydrated and exhibits a crystalline diffraction pattern that can be indexed in a monoclinic cell with parameters close to the pristine phase. Rietveld refinement was carried out for the sample heated at 75 °C, Ca-PiPhtA-II, using synchrotron powder X-ray diffraction data, which revealed the molecular formula Ca2[(HO3PC6H3COOH)2]2[(HO3PC6H3(COO)2H)(H2O)2]. All connectivity modes of the "parent" Ca-PiPhtA-I framework are retained in Ca-PiPhtA-II. Upon Ca-PiPhtA-I exposure to ammonia vapors (28% aqueous NH3) a new derivative is obtained (Ca-PiPhtA-NH3) containing 7 NH3 and 16 H2O molecules according to elemental and thermal analyses. Ca-PiPhtA-NH3 exhibits a complex X-ray diffraction pattern with peaks at 15.3 and 13.0 Å that suggest partial breaking and transformation of the parent pillared structure. Although detailed structural identification of Ca-PiPhtA-NH3 was not possible, due in part to nonequilibrium adsorption conditions and the lack of crystallinity, FT-IR spectra and DTA-TG analysis indicate profound structural changes compared to the pristine Ca-PiPhtA-I. At 98% RH and T = 24 °C, proton conductivity, σ, for Ca-PiPhtA-I is 5.7 × 10(-4) S·cm(-1). It increases to 1.3 × 10(-3) S·cm(-1) upon activation by preheating the sample at 40 °C for 2 h followed by water equilibration at room temperature under controlled conditions. Ca-PiPhtA-NH3 exhibits the

  18. 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, pKa's, optimized geometries, and reaction paths.

  19. 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

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

    PubMed

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

    2017-01-06

    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.

  1. Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments.

    PubMed

    Czodrowski, Paul; Sotriffer, Christoph A; Klebe, Gerhard

    2007-04-13

    The protonation states of a protein and a ligand can be altered upon complex formation. Such changes can be detected experimentally by isothermal titration calorimetry (ITC). For a series of ligands binding to the serine proteases trypsin and thrombin, we previously performed an extensive ITC and crystallographic study and were able to identify protonation changes for four complexes. However, since ITC measures only the overall proton exchange, it does not provide structural insights into the functional groups involved in the proton transfer. Using Poisson-Boltzmann calculations based on our recently developed PEOE_PB charges, we compute pK(a) values for all complexes of our former study in order to reveal the residues with altered protonation states. The results indicate that His57, a member of the catalytic triad, is responsible for the most relevant pK(a) shifts leading to the experimentally detected protonation changes. This finding is in contrast to our previous assumption that the observed protonation changes occur at the carboxylic group of the ligands. The newly detected proton acceptor is used for a revised factorization of the ITC data, which is necessary whenever the protonation inventory changes upon complexation. The pK(a) values of complexes showing no protonation change in the ITC experiment are reliably predicted in most cases, whereas predictions of strongly coupled systems remain problematic.

  2. ARTEMIS observations of the solar wind proton scattering function from lunar crustal magnetic anomalies

    NASA Astrophysics Data System (ADS)

    Poppe, A. R.; Halekas, J. S.; Lue, C.; Fatemi, S.

    2017-04-01

    Despite their small scales, lunar crustal magnetic fields are routinely associated with observations of reflected and/or backstreaming populations of solar wind protons. Solar wind proton reflection locally reduces the rate of space weathering of the lunar regolith, depresses local sputtering rates of neutrals into the lunar exosphere, and can trigger electromagnetic waves and small-scale collisionless shocks in the near-lunar space plasma environment. Thus, knowledge of both the magnitude and scattering function of solar wind protons from magnetic anomalies is crucial in understanding a wide variety of planetary phenomena at the Moon. We have compiled 5.5 years of ARTEMIS (Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon's Interaction with the Sun) observations of reflected protons at the Moon and used a Liouville tracing method to ascertain each proton's reflection location and scattering angles. We find that solar wind proton reflection is largely correlated with crustal magnetic field strength, with anomalies such as South Pole/Aitken Basin (SPA), Mare Marginis, and Gerasimovich reflecting on average 5-12% of the solar wind flux while the unmagnetized surface reflects between 0.1 and 1% in charged form. We present the scattering function of solar wind protons off of the SPA anomaly, showing that the scattering transitions from isotropic at low solar zenith angles to strongly forward scattering at solar zenith angles near 90°. Such scattering is consistent with simulations that have suggested electrostatic fields as the primary mechanism for solar wind proton reflection from crustal magnetic anomalies.

  3. Structure and Proton Conductivity in Mixtures of Poly(acrylic acid) and Imidazole

    NASA Astrophysics Data System (ADS)

    Yang, Han-Chang; Griffin, Philip J.; Winey, Karen I.; University of Pennsylvania Team

    2015-03-01

    Proton conductivity in polymer electrolyte membranes (PEMs) typically involves water, which requires that during operation the humidity of the PEM be carefully controlled. In contrast, anhydrous protic polymer membranes promote proton transport by incorporating heterocyclic molecules, such as imidazole and its derivatives, into acid-containing polymers. In this work, we explore the interplay between nanoscale-structure and proton conduction of poly(acrylic acid) (PAA) blended at varying compositions with 2-ethyl-4-methylimidazole (EMI). We present the glass transition temperature from differential scanning calorimetry, morphology characterization from X-ray scattering, and proton conductivity from electrical impedance spectroscopy.

  4. Microdosimetry of the full slowing down of protons using Monte Carlo track structure simulations.

    PubMed

    Liamsuwan, T; Uehara, S; Nikjoo, H

    2015-09-01

    The article investigates two approaches in microdosimetric calculations based on Monte Carlo track structure (MCTS) simulations of a 160-MeV proton beam. In the first approach, microdosimetric parameters of the proton beam were obtained using the weighted sum of proton energy distributions and microdosimetric parameters of proton track segments (TSMs). In the second approach, phase spaces of energy depositions obtained using MCTS simulations in the full slowing down (FSD) mode were used for the microdosimetric calculations. Targets of interest were water cylinders of 2.3-100 nm in diameters and heights. Frequency-averaged lineal energies ([Formula: see text]) obtained using both approaches agreed within the statistical uncertainties. Discrepancies beyond this level were observed for dose-averaged lineal energies ([Formula: see text]) towards the Bragg peak region due to the small number of proton energies used in the TSM approach and different energy deposition patterns in the TSM and FSD of protons.

  5. Effective Hyperfine-structure Functions of Ammonia

    NASA Astrophysics Data System (ADS)

    Augustovičová, L.; Soldán, P.; Špirko, V.

    2016-06-01

    The hyperfine structure of the rotation-inversion (v 2 = 0+, 0-, 1+, 1-) states of the 14NH3 and 15NH3 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. 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.

  6. Hydrophobic plug functions as a gate in voltage-gated proton channels.

    PubMed

    Chamberlin, Adam; Qiu, Feng; Rebolledo, Santiago; Wang, Yibo; Noskov, Sergei Y; Larsson, H Peter

    2014-01-14

    Voltage-gated proton (Hv1) channels play important roles in the respiratory burst, in pH regulation, in spermatozoa, in apoptosis, and in cancer metastasis. Unlike other voltage-gated cation channels, the Hv1 channel lacks a centrally located pore formed by the assembly of subunits. Instead, the proton permeation pathway in the Hv1 channel is within the voltage-sensing domain of each subunit. The gating mechanism of this pathway is still unclear. Mutagenic and fluorescence studies suggest that the fourth transmembrane (TM) segment (S4) functions as a voltage sensor and that there is an outward movement of S4 during channel activation. Using thermodynamic mutant cycle analysis, we find that the conserved positively charged residues in S4 are stabilized by countercharges in the other TM segments both in the closed and open states. We constructed models of both the closed and open states of Hv1 channels that are consistent with the mutant cycle analysis. These structural models suggest that electrostatic interactions between TM segments in the closed state pull hydrophobic residues together to form a hydrophobic plug in the center of the voltage-sensing domain. Outward S4 movement during channel activation induces conformational changes that remove this hydrophobic plug and instead insert protonatable residues in the center of the channel that, together with water molecules, can form a hydrogen bond chain across the channel for proton permeation. This suggests that salt bridge networks and the hydrophobic plug function as the gate in Hv1 channels and that outward movement of S4 leads to the opening of this gate.

  7. Protonic charge defect structures in floating water bridges observed as Zundel and Eigen solvation arrangements

    NASA Astrophysics Data System (ADS)

    Teschke, Omar; de Castro, Jose Roberto; Valente Filho, Juracyr Ferraz; Soares, David Mendez

    2017-10-01

    Protonic arrangements were detected in water bridge structures using confocal Raman microscopy, and the spectra show two formed structures. The measured Raman spectra were modified using the voltage applied to the bridge structure, which changed the proportion of these two species. Initially, for a 6.3 kV applied voltage, there was a measurable increase in the bridge current above the Ohmic contribution and the observed Raman spectrum of this new injected specie corresponded to the computed spectrum for the Zundel protonic arrangement. As the voltage further increases a contribution from the Eigen proton solvation specie is added to the measured spectrum.

  8. Proton imaging of an electrostatic field structure formed in laser-produced counter-streaming plasmas

    NASA Astrophysics Data System (ADS)

    Morita, T.; Kugland, N. L.; Wan, W.; Crowston, R.; Drake, R. P.; Fiuza, F.; Gregori, G.; Huntington, C.; Ishikawa, T.; Koenig, M.; Kuranz, C.; Levy, M. C.; Martinez, D.; Meinecke, J.; Miniati, F.; Murphy, C. D.; Pelka, A.; Plechaty, C.; Presura, R.; Quirós, N.; Remington, B. A.; Reville, B.; Ross, J. S.; Ryutov, D. D.; Sakawa, Y.; Steele, L.; Takabe, H.; Yamaura, Y.; Woolsey, N.; Park, H.-S.

    2016-03-01

    We report the measurements of electrostatic field structures associated with an electrostatic shock formed in laser-produced counter-streaming plasmas with proton imaging. The thickness of the electrostatic structure is estimated from proton images with different proton kinetic energies from 4.7 MeV to 10.7 MeV. The width of the transition region is characterized by electron scale length in the laser-produced plasma, suggesting that the field structure is formed due to a collisionless electrostatic shock.

  9. Hybrid Functional Calculations of Acceptor Doping in Protonic Conductor SrZrO3

    NASA Astrophysics Data System (ADS)

    Weston, Leigh; Janotti, Anderson; Cui, Xiangyuan; Stampfl, Catherine; van de Walle, Chris

    2015-03-01

    Perovskite oxides such as SrZrO3 (SZO), which exhibit high temperature proton conductivity, are promising electrolyte materials for use in solid oxide fuel cells (SOFCs). Proton conductivity in SZO is typically achieved via acceptor doping with trivalent cations substituting at the Zr site, where the formation of charge compensating oxygen vacancies facilitates proton solvation. We present a detailed study of Sc and Y dopants in SZO based on first-principles, hybrid density functional calculations. When substituting at the Zr site, both dopants form deep acceptors, where the neutral charge state forms a localized hole polaron state. Under certain growth conditions Sc and Y will form auto-compensating donor species by substituting at the Sr site, which would inhibit proton solubility. Moreover, the proton - dopant association was found to be strong, with proton binding energies of -0.41 eV and -0.31 eV for Sc Zr- and Y Zr- respectively, indicating that proton transport is limited by trapping. These new results will be useful in the development of zirconate based proton conducting electrolyte materials for solid oxide fuel cells.

  10. Parkin structure and function.

    PubMed

    Seirafi, Marjan; Kozlov, Guennadi; Gehring, Kalle

    2015-06-01

    Mutations in the parkin or PINK1 genes are the leading cause of the autosomal recessive form of Parkinson's disease. The gene products, the E3 ubiquitin ligase parkin and the serine/threonine kinase PINK1, are neuroprotective proteins, which act together in a mitochondrial quality control pathway. Here, we review the structure of parkin and mechanisms of its autoinhibition and function as a ubiquitin ligase. We present a model for the recruitment and activation of parkin as a key regulatory step in the clearance of depolarized or damaged mitochondria by autophagy (mitophagy). We conclude with a brief overview of other functions of parkin and considerations for drug discovery in the mitochondrial quality control pathway. © 2015 The Authors. FEBS Journal published by John Wiley & Sons Ltd on behalf of FEBS.

  11. Structure changes upon deprotonation of the proton release group in the bacteriorhodopsin photocycle.

    PubMed

    Morgan, Joel E; Vakkasoglu, Ahmet S; Lanyi, Janos K; Lugtenburg, Johan; Gennis, Robert B; Maeda, Akio

    2012-08-08

    In the photocycle of bacteriorhodopsin at pH 7, a proton is ejected to the extracellular medium during the protonation of Asp-85 upon formation of the M intermediate. The group that releases the ejected proton does not become reprotonated until the prephotolysis state is restored from the N and O intermediates. In contrast, at acidic pH, this proton release group remains protonated to the end of the cycle. Time-resolved Fourier transform infrared measurements obtained at pH 5 and 7 were fitted to obtain spectra of kinetic intermediates, from which the spectra of M and N/O versus unphotolyzed state were calculated. Vibrational features that appear in both M and N/O spectra at pH 7, but not at pH 5, are attributable to deprotonation from the proton release group and resulting structural alterations. Our results agree with the earlier conclusion that this group is a protonated internal water cluster, and provide a stronger experimental basis for this assignment. A decrease in local polarity at the N-C bond of the side chain of Lys-216 resulting from deprotonation of this water cluster may be responsible for the increase in the proton affinity of Asp-85 through M and N/O, which is crucial for maintaining the directionality of proton pumping. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Using AN Organic Scaffold to Modulate the Quantum Structure of AN Intramolecular Proton Bond: Cryogenic Vibrational Predissociation Spectroscopy of H2 on Protonated 8-NAPHTHALENE-1-AMINE

    NASA Astrophysics Data System (ADS)

    Deblase, Andrew F.; Guasco, Timothy L.; Leavitt, Christopher M.; Johnson, Mark A.; Lectka, Thomas

    2011-06-01

    The quantum structure of the intermolecular proton bond is a key aspect in understanding proton transfer events that govern the efficiency of fuel cells and various biological membranes. Previously, we have constructed a soft binding motif, that consists of a "point contact" between the lone pairs of two small molecules (combinations of ethers, alcohols, ammonia, and water) that are linked by a shared proton [Science 2007, 613, 249]. Although the frequency of the shared proton vibration has been correlated with effects of acid and base structure, such as proton affinities and dipole moments, the spatial arrangement of the proton donor and acceptor remains unexplored. Towards this aim, we have obtained a molecule of rigid topology that contains a proton donor and acceptor capable of intramolecular proton-bonding (protonated 8-flouronaphthalene-1-amine). Using electrospray ionization coupled with a novel cryogenic mass spectrometry scheme, we employ vibrational predissociation spectroscopy of H2 tagged ions to elucidate how a forced spatial configuration of the acid and base perturbs the energetics of the proton bond.

  13. Protonated arginine and protonated lysine: hydration and its effect on the stability of salt-bridge structures.

    PubMed

    Gao, Bing; Wyttenbach, Thomas; Bowers, Michael T

    2009-07-23

    Using a mass spectrometer equipped with a drift cell, water binding energies of protonated arginine (ArgH+) and protonated lysine (LysH+) were determined in equilibrium experiments and supplementary calculations at the B3LYP/6-311++G** level of theory. The binding energy of the first water molecule was measured to be 10.3 and 10.9 kcal/mol for ArgH+ and LysH+, respectively. Water binding energies decrease with increasing degree of hydration reaching values of 6-7 kcal/mol for the fourth and fifth water molecule. Theory reproduces this trend of decreasing binding energies correctly and theoretical water binding energies agree with experiment quantitatively within 2 kcal/mol. Lowest-energy theoretical structures of ArgH+ and LysH+ are characterized by protonated side chains and neutral alpha-amino and carboxyl groups which form intramolecular hydrogen bonds to the ionic group (charge solvation or CS structures). The salt bridge (SB) structures with two cationic groups (side chain and alpha-amine) and one anionic group (carboxyl) are 13.1 and 9.3 kcal/mol higher in energy for ArgH+ and LysH+, respectively. Theory indicated that the first water molecule binds to the ionic group of the CS structures of ArgH+ and LysH+. With increasing degree of hydration intramolecular interactions are replaced one by one with water bridges with water inserted into the intramolecular hydrogen bonds. Whereas the global minima of ArgH+.(H2O)n and LysH+.(H2O)n, n<7, were calculated to represent CS structures, 7-fold hydrated CS and SB structures, ArgH+.(H2O)7 and LysH+.(H2O)7, are nearly isoenergetic (within <1 kcal/mol).

  14. Density Functional Reactivity Theory Characterizes Charge Separation Propensity in Proton-Coupled Electron Transfer Reactions

    SciTech Connect

    Liu, Shubin; Ess, Daniel H.; Schauer, Cynthia

    2011-04-20

    Proton-coupled electron transfer (PCET) reactions occur in many biological and artificial solar energy conversion processes. In these reactions the electron is often transferred to a site distant to the proton acceptor site. In this work, we employ the dual descriptor and the electrophilic Fukui function from density functional reactivity theory (DFRT) to characterize the propensity for an electron to be transferred to a site other than the proton acceptor site. The electrophilic regions of hydrogen bond or van der Waal reactant complexes were examined using these DFRT descriptors to determine the region of space to which the electron is most likely to be transferred. This analysis shows that in PCET reactions the electrophilic region of the reactant complex does not include the proton acceptor site.

  15. The Spin Structure of the Proton in the Resonance Region

    SciTech Connect

    Fatemi, Renee H.

    2002-01-01

    Inclusive double spin asymmetries have been measured for $\\vec{p}$($\\vec{e}$,e') using the CLAS detector and a polarized 15NH3 target at Jefferson Lab in 1998. The virtual photon asymmetry A1, the longitudinal spin structure function, g1 (x, Q2), and the first moment Γ$1\\atop{p}$, have been extracted for a Q2 range of 0.15-2.0 GeV2. These results provide insight into the low Q2 evolution of spin dependent asymmetries and structure functions as well as the transition of Γ$1\\atop{p}$ from the photon point, where the Gerasimov, Drell and Hearn Sum Rule is expected to be satisfied, to the deep inelastic region.

  16. A functional model for the Rieske center: full characterization of a biomimetic N-ligated [2Fe-2S] cluster in different protonation states.

    PubMed

    Albers, Antonia; Bayer, Thomas; Demeshko, Serhiy; Dechert, Sebastian; Meyer, Franc

    2013-07-29

    Give and take both: A bis(benzimidazolate)-capped biomimetic [2Fe-2S] cluster has been characterized in different protonation states, both in the diferric and mixed-valent forms. Protonation does not lead to structural changes of the [2Fe-2S] core, but facilitates its reduction and causes pronounced valence localization in the mixed-valent state. Concerted proton and electron transfer back to the diferric cluster emulates a key step in the function of mitochondrial Rieske proteins (see scheme). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Spin-rotation functions for 500-MeV protons scattered by UCa nuclei

    SciTech Connect

    Berezhnoi, Y.A.; Molev, A.S.; Pilipenko, V.V.; Soznik, A.P.

    1985-06-01

    The polarization characteristics in the elastic and inelastic scattering of 500-MeV protons by UCa nuclei are analyzed, using the theory of multiple diffraction scattering. The investigated proton-spin-rotation functions are very sensitive to the NN-amplitude parameters. A set of NN-amplitude parameters is found that correctly describes the set of measured observables. The analysis yields valuable information on the NN amplitude, especially on its spin-orbit part.

  18. A Precision Measurement of the Spin Structure of the Proton at SLAC

    SciTech Connect

    Erbacher, Robin D

    1999-09-22

    E143 at SLAC Endstation A performed deep-inelastic scattering measurements of polarized electrons from polarized protons and deuterons within cryogenic {sup 15}NH{sub 3} and {sup 15}ND{sub 3}, respectively. Data were taken at incident energies of 29.1, 16.2 and 9.7 GeV, and covered the kinematical range x > 0:03 and 0:3 < Q{sup 2} < 12 (GeV/c){sup 2}. The scattered electrons were detected by two spectrometers at angles of 4.5{sup o} and 7.0{sup o}. From these data, the spin-dependent structure functions g{sub 1}{sup p}(x; Q{sup 2}) and g{sub 1}{sup d}(x; Q{sup 2}) were determined. This dissertation describes the experiment, with emphasis on the results on the proton spin structure. The integral of g{sub 1} over the range 0 < x < 1 was found to be {Gamma}{sub 1}{sup p} = 0.130 {+-} 0.003 {+-} 0.008 for the proton and {Gamma}{sub 1}{sup d} = 0.044 {+-} 0.003 {+-} 0.004 for the deuteron. Both values are in agreement with world data, and violate the Ellis-Jaffe sum rule by more than 3 standard deviations. The neutron structure function was obtained by combining proton and deuteron results, giving {Gamma}{sub 1}{sup n} = [0.035 {+-} 0.007 {+-} 0.010]. From this the integral {Gamma}{sub 1}{sup p}-{Gamma}{sub 1}{sup n} followed, yielding 0.165 {+-} 0.009 {+-} 0.016 at Q{sup 2} = 3 (GeV/c){sup 2}, in agreement with the Bjorken sum rule to within one standard deviation. The Q{sup 2}-dependence of the ratio g{sub 1}/F{sub 1} was determined to be small for Q{sup 2} > 1 (GeV/c){sup 2}, validating the assumption of no Q{sup 2}-dependence used in obtaining the integrals. A small rise with increasing Q{sup 2} was seen in the ratio for Q{sup 2} < 1 (GeV/c){sup 2}, however. The total quark contribution to the spin was found to be {Delta}q = 0.28 {+-} 0.09 for the proton, and {Delta}q = 0.32 {+-} 0.05 for the deuteron. Furthermore, a large negative spin contribution from the strange sea quarks was measured for both nucleons, giving {Delta}s = 0.10 {+-} 0.03 and {Delta}s = -0

  19. 2-Naphthol: A simple example of proton transfer effected by water structure

    NASA Astrophysics Data System (ADS)

    Lee, J.; Griffin, R. D.; Robinson, G. W.

    1985-06-01

    Using picosecond spectroscopic techniques, the proton transfer process of 2-naphthol in its first excited singlet state is investigated in water/methanol mixtures at different temperatures. The proton transfer rate is found to increase as the temperature increases, and to decrease as the methanol concentration increases. A Markov random walk theory previously used to electron transfer kinetics is employed to analyze the data. By this method, a water cluster containing 4±1 members is shown to be the proton acceptor. Suggestively, a ``four-cluster'' structure (H9O4)+ has been hypothesized as the most probable hydrating unit for the proton in acid-base equilibria, charge transfer, and other chemical systems. The observed activation energy of 3.45 kcal/mol in pure water is attributed to the energy required for rearrangement of the hydrogen bonding in the normal water structure to form the proton accepting cluster. Proton transfer kinetics thus exactly parallels electron transfer kinetics in aqueous media. The critical size of 4±1 molecules and a specific structure of the water cluster apparently determine the controlling rates for both electron and proton charge transfer processes in aqueous media.

  20. Crystal structure of the sodium–proton antiporter NhaA dimer and new mechanistic insights

    PubMed Central

    Lee, Chiara; Yashiro, Shoko; Dotson, David L.; Uzdavinys, Povilas; Iwata, So; Sansom, Mark S.P.; von Ballmoos, Christoph

    2014-01-01

    Sodium–proton antiporters rapidly exchange protons and sodium ions across the membrane to regulate intracellular pH, cell volume, and sodium concentration. How ion binding and release is coupled to the conformational changes associated with transport is not clear. Here, we report a crystal form of the prototypical sodium–proton antiporter NhaA from Escherichia coli in which the protein is seen as a dimer. In this new structure, we observe a salt bridge between an essential aspartic acid (Asp163) and a conserved lysine (Lys300). An equivalent salt bridge is present in the homologous transporter NapA, but not in the only other known crystal structure of NhaA, which provides the foundation of most existing structural models of electrogenic sodium–proton antiport. Molecular dynamics simulations show that the stability of the salt bridge is weakened by sodium ions binding to Asp164 and the neighboring Asp163. This suggests that the transport mechanism involves Asp163 switching between forming a salt bridge with Lys300 and interacting with the sodium ion. pKa calculations suggest that Asp163 is highly unlikely to be protonated when involved in the salt bridge. As it has been previously suggested that Asp163 is one of the two residues through which proton transport occurs, these results have clear implications to the current mechanistic models of sodium–proton antiport in NhaA. PMID:25422503

  1. ELECTROMAGNETIC SIMULATIONS OF LINEAR PROTON ACCELERATOR STRUCTURES USING DIELECTRIC WALL ACCELERATORS

    SciTech Connect

    Nelson, S; Poole, B; Caporaso, G

    2007-06-15

    Proton accelerator structures for medical applications using Dielectric Wall Accelerator (DWA) technology allow for the utilization of high electric field gradients on the order of 100 MV/m to accelerate the proton bunch. Medical applications involving cancer therapy treatment usually desire short bunch lengths on the order of hundreds of picoseconds in order to limit the extent of the energy deposited in the tumor site (in 3D space, time, and deposited proton charge). Electromagnetic simulations of the DWA structure, in combination with injections of proton bunches have been performed using 3D finite difference codes in combination with particle pushing codes. Electromagnetic simulations of DWA structures includes these effects and also include the details of the switch configuration and how that switch time affects the electric field pulse which accelerates the particle beam.

  2. DNA structure and function.

    PubMed

    Travers, Andrew; Muskhelishvili, Georgi

    2015-06-01

    The proposal of a double-helical structure for DNA over 60 years ago provided an eminently satisfying explanation for the heritability of genetic information. But why is DNA, and not RNA, now the dominant biological information store? We argue that, in addition to its coding function, the ability of DNA, unlike RNA, to adopt a B-DNA structure confers advantages both for information accessibility and for packaging. The information encoded by DNA is both digital - the precise base specifying, for example, amino acid sequences - and analogue. The latter determines the sequence-dependent physicochemical properties of DNA, for example, its stiffness and susceptibility to strand separation. Most importantly, DNA chirality enables the formation of supercoiling under torsional stress. We review recent evidence suggesting that DNA supercoiling, particularly that generated by DNA translocases, is a major driver of gene regulation and patterns of chromosomal gene organization, and in its guise as a promoter of DNA packaging enables DNA to act as an energy store to facilitate the passage of translocating enzymes such as RNA polymerase.

  3. Structures of heterogeneous proton-bond dimers with a high dipole moment monomer: covalent vs electrostatic interactions.

    PubMed

    Fridgen, Travis D

    2006-05-11

    A number of calculated structures of heterogeneous proton-bound dimers containing monomers such as acetonitrile, cyanamide, vinylene carbonate, and propiolactone, which have high dipole moments, are presented. These proton-bound dimers are predicted to have a structural anomaly pertaining to the bond distances between the central proton and the basic sites on each of the monomers. The monomers with the high dipole moments also have the larger proton affinity and, on the basis of difference in proton affinities, it would be expected that the proton would be closer to this monomer than the one with the lower proton affinity. However, the proton is found to lie substantially closer to the monomer with the lower proton affinity in most cases, unless the difference in proton affinity is too large. Simply stated, the difference in proton affinities is smaller than the difference in the affinity to form an ion-dipole complex for the two monomers and it is the larger affinity for the high dipole moment monomer (which also has the higher proton affinity) to form an ion-dipole complex that is responsible for the proton lying closer to the low proton affinity monomer. The bond distances between the central proton and the monomers are found to be related to the difference in proton affinity. It is found, though, that the proton-bound dimers can be grouped into two separate groups, one where the proton-bound dimer contains a high dipole moment monomer and one group where the proton-bound dimer does not contain a high dipole moment monomer. From these plots it has been determined that a high dipole moment monomer is one that has a dipole moment greater than 2.9 D.

  4. Toward proton MR spectroscopic imaging of stimulated brain function

    SciTech Connect

    Singh, M. . Dept. of Radiology)

    1992-08-01

    With the objective of complementing local cerebral metabolic studies of PET, and as a prelude to spectroscopic imaging, the authors have performed the first localized proton spectroscopic study of the stimulated human auditory cortex. Water suppressed localized spectroscopy (voxel size 3cm [times] 3cm [times] 3cm enclosing the auditory cortex, Te = 272ms, Tr = 3s) was performed on a 1.5T MRI/MRS system and spectra were acquired during stimulation with a 1kHz tone presented at 2Hz. Measurements were conducted for 30-40 min with a temporal resolution of 3.2 min (64 averages per time block). Results included in this paper from six subjects show a lactate peak which increases during stimulation compared to baseline values. These results suggest an increase in anaerobic glycolysis during stimulation and provide unique and valuable information that should complement glucose metabolism and flood flow studies of PET.

  5. A pKa calculation of residues in a proton pump, bacteriorhodopsin, from structures determined by electron crystallography.

    PubMed

    Mitsuoka, Kaoru

    2014-11-01

    Bacteriorhodopsin (bR) is a light-driven proton pump, which is a membrane protein found in halophilic archeae like Halobacterium salinarum and in eubacteria [1]. When the covalently bound retinal chromophore absorbs the light energy, it changes the conformation from all-trans to 13-cis. This configuration change initiates ion translocation across the cell membrane and a proton moves from inside to outside of the cell. The bR molecules are forming two-dimensional crystals on the membranes of halophilic archeae, and therefore the atomic model of bR was first determined by electron crystallography. The determined structure can be used to determine the pKa values, through which the charge states of ionizable residues in bR determine their pH-dependent properties. The pH-dependent properties are crucial for proton translocation from ionizable residues or to ionizable residues. Detection of the intermediate states of the reaction cycle (photocycle) produced spectroscopic information, which can predict the ionization state of the ionozable residues. In the transition from the L intermediate to the M intermediate, it is known that a proton moves from the Shiff base on the retinal chromophore to Asp85, while a proton is released to the extracellar side from proton-releasing groups including Glu194 and Glu204. Experimentally the pKa value of the proton release is determined to be about 9.7, while the pKa value of Asp85 was measured to change from 2.6 to 7.5 by the proton release from the proton-releasing groups [2]. Here we used the PROPKA program [3] to calculate the pKa values of Asp85 and the proton-releasing groups from the structures at pH 5.5 and at pH 10.0 determined by electron crystallography. The calculation showed that the pKa value of Asp85 changes from 5.3 to 6.1, which qualitatively show the similar changes with the measured difference. The largest change between the structures is the shift of Arg82 by the proton release from the proton-releasing groups

  6. Enhanced proton acceleration by an ultrashort laser interaction with structured dynamic plasma targets.

    PubMed

    Zigler, A; Eisenman, S; Botton, M; Nahum, E; Schleifer, E; Baspaly, A; Pomerantz, I; Abicht, F; Branzel, J; Priebe, G; Steinke, S; Andreev, A; Schnuerer, M; Sandner, W; Gordon, D; Sprangle, P; Ledingham, K W D

    2013-05-24

    We experimentally demonstrate a notably enhanced acceleration of protons to high energy by relatively modest ultrashort laser pulses and structured dynamical plasma targets. Realized by special deposition of snow targets on sapphire substrates and using carefully planned prepulses, high proton yields emitted in a narrow solid angle with energy above 21 MeV were detected from a 5 TW laser. Our simulations predict that using the proposed scheme protons can be accelerated to energies above 150 MeV by 100 TW laser systems.

  7. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2010-04-27

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  8. Multi-functional composite structures

    DOEpatents

    Mulligan, Anthony C.; Halloran, John; Popovich, Dragan; Rigali, Mark J.; Sutaria, Manish P.; Vaidyanathan, K. Ranji; Fulcher, Michael L.; Knittel, Kenneth L.

    2004-10-19

    Fibrous monolith processing techniques to fabricate multifunctional structures capable of performing more than one discrete function such as structures capable of bearing structural loads and mechanical stresses in service and also capable of performing at least one additional non-structural function.

  9. Empirical Proton-Neutron Interactions and Nuclear Density Functional Theory: Global, Regional, and Local Comparisons

    SciTech Connect

    Stoitsov, Mario; Cakirli, R. B.; Casten, R. F.; Nazarewicz, Witold; Satula, W.

    2007-01-01

    Calculations of nuclear masses, using nuclear density functional theory, are presented for even-even nuclei spanning the nuclear chart. The resulting binding energy differences can be interpreted in terms of valence proton-neutron interactions. These are compared globally, regionally, and locally with empirical values. Overall, excellent agreement is obtained. Discrepancies highlight neglected degrees of freedom and can point to improved density functionals.

  10. Empirical Proton-Neutron Interactions and Nuclear Density Functional Theory: Global, Regional, and Local Comparisons

    SciTech Connect

    Stoitsov, M.; Cakirli, R. B.; Casten, R. F.; Nazarewicz, W.; Satula, W.

    2007-03-30

    Calculations of nuclear masses, using nuclear density functional theory, are presented for even-even nuclei spanning the nuclear chart. The resulting binding energy differences can be interpreted in terms of valence proton-neutron interactions. These are compared globally, regionally, and locally with empirical values. Overall, excellent agreement is obtained. Discrepancies highlight neglected degrees of freedom and can point to improved density functionals.

  11. Empirical proton-neutron interactions and nuclear density functional theory: global, regional, and local comparisons.

    PubMed

    Stoitsov, M; Cakirli, R B; Casten, R F; Nazarewicz, W; Satuła, W

    2007-03-30

    Calculations of nuclear masses, using nuclear density functional theory, are presented for even-even nuclei spanning the nuclear chart. The resulting binding energy differences can be interpreted in terms of valence proton-neutron interactions. These are compared globally, regionally, and locally with empirical values. Overall, excellent agreement is obtained. Discrepancies highlight neglected degrees of freedom and can point to improved density functionals.

  12. Determination of the neutron spin-structure function

    SciTech Connect

    Petratos, G.G.; SLAC E-142 Collaboration

    1993-10-01

    The neutron spin-structure function g{sub 1}{sup n} has been determined by measuring the asymmetry in deep inelastic scattering of polarized electrons off a polarized {sup 3}He target. The results are interpreted in the quark-parton model and used, in conjuction with earlier proton results, to test the Bjorken sum rule.

  13. Structure and dynamics of proton transfer in liquid imidazole. A molecular dynamics simulation.

    PubMed

    Li, Ailin; Cao, Zhen; Li, Yao; Yan, Tianying; Shen, Panwen

    2012-10-25

    Proton transfer (PT) via the Grotthuss mechanism in liquid imidazole (im) at 393 K is studied with molecular dynamics simulation using a reactive multistate empirical valence bond (MS-EVB) model. It is found that the proton is tightly binded to an imidazole to form an imidazolium (imH(+)), which is solvated in a distorted Eigen-like complex (im-imH(+)-im), whereas the Zundel-like complex (im-H(+)-im) is rare. PT occurs via an Eigen-Zundel-Eigen scenario for switching the identity of imH(+) from an Eigen-like complex to another, intermediated by a Zundel-like complex. Structural and dynamical analyses demonstrate that PT in imidazole can be considered as a local event with very short spatial/temporal correlation, characterized by a few "rattling" or recurrent PT events. At long time scale, the trend of the PT correlation function may be recast with the diffusion model of reversible geminate recombination toward the power-law decay. The formation of the hydrogen bonds (HBs) for the imidazole molecules between the first and second solvation shell of imH(+) is crucial to pave the PT pathway. The above features may be understood by the flexibility of the HBs in liquid imidazole, as a stable HB network is essential for the Grotthuss mechanism.

  14. Measurement of the longitudinal spin structure of the proton by COMPASS

    NASA Astrophysics Data System (ADS)

    Korzenev, A.; Compass Collaboration

    2010-01-01

    The inclusive A and hadron double-spin asymmetries Apπ+, Apπ-, ApK+, ApK- measured at COMPASS (CERN SPS) in deep-inelastic scattering of a polarized muon beam off a polarized NH 3 solid target are presented. The results have been obtained with the full statistics collected in 2007 for the longitudinal target polarization. Proton asymmetries have been combined with published deuteron ones. An evaluation of the non-singlet spin-dependent structure function g1NS(x,Q) and its first moment, which confirms the validity of the Bjorken sum-rule, is presented. A LO evaluation of polarized quark densities is also presented. The use of the proton data allows to perform a full flavor separation and to extract individual helicity densities of u, d, u¯, d¯ and s quarks. All sea quark densities are found to be compatible with zero in the full range of the measurements.

  15. Proton-functionalized two-dimensional graphitic carbon nitride nanosheet: an excellent metal-/label-free biosensing platform.

    PubMed

    Ma, Tian Yi; Tang, Youhong; Dai, Sheng; Qiao, Shi Zhang

    2014-06-25

    Ultrathin graphitic carbon nitride (g-C3N4) nanosheets, due to their interesting two-dimensional graphene-like structure and unique physicochemical properties, have attracted great research attention recently. Here, a new approach is developed to prepare, for the first time, proton-functionalized ultrathin g-C3N4 nanosheets by sonication-exfoliation of bulk g-C3N4 under an acid condition. This method not only reduces the exfoliation time from more than 10 h to 2 h, but also endows the nanosheets with positive charges. Besides retaining the properties of g-C3N4, the obtained nanosheets with the thickness of 2-4 nm (i.e., 6-12 atomic monolayers) also exhibit large specific surface area of 305 m(2) g(-1), enhanced fluorescence intensity, and excellent water dispersion stability due to their surface protonation and ultrathin morphology. The well-dispersed protonated g-C3N4 nanosheets are able to interact with negatively charged heparin, which results in the quenching of g-C3N4 fluorescence. A highly sensitive and highly selective heparin sensing platform based on protonated g-C3N4 nanosheets is established. This metal-free and fluorophore label-free system can reach the lowest heparin detection limit of 18 ng mL(-1). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. TURBULENCE-GENERATED PROTON-SCALE STRUCTURES IN THE TERRESTRIAL MAGNETOSHEATH

    SciTech Connect

    Vörös, Zoltán; Narita, Yasuhito; Yordanova, Emiliya; Echim, Marius M.; Consolini, Giuseppe

    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. During the analyzed one-hour time interval, about a hundred strong discontinuities, possibly proton-scale current sheets, were observed.

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

    PubMed

    Ke, Meng; Yuan, Yafei; Jiang, Xin; Yan, Nieng; Gong, Haipeng

    2017-06-01

    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.

  18. Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy.

    PubMed

    Garczarek, Florian; Gerwert, Klaus

    2006-01-05

    Much progress has been made in our understanding of water molecule reactions on surfaces, proton solvation in gas-phase water clusters and proton transfer through liquids. Compared with our advanced understanding of these physico-chemical systems, much less is known about individual water molecules and their cooperative behaviour in heterogeneous proteins during enzymatic reactions. Here we use time-resolved Fourier transform infrared spectroscopy (trFTIR) and in situ H2(18)O/H2(16)O exchange FTIR to determine how the membrane protein bacteriorhodopsin uses the interplay among strongly hydrogen-bonded water molecules, a water molecule with a dangling hydroxyl group and a protonated water cluster to transfer protons. The precise arrangement of water molecules in the protein matrix results in a controlled Grotthuss proton transfer, in contrast to the random proton migration that occurs in liquid water. Our findings support the emerging paradigm that intraprotein water molecules are as essential for biological functions as amino acids.

  19. Studying the spin structure of the proton using the solenoidal tracker at RHIC

    SciTech Connect

    Hallman, T.J.; STAR Collaboration

    1998-05-01

    The primary goal of RHIC is to produce nuclear matter under extremes of temperature and density sufficient to excite the QCD vacuum, resulting in the creation of a deconfined plasma of quarks and gluons. A second goal central to the RHIC scientific program is to advance the study of the spin structure of the proton significantly beyond what has been learned from deep inelastic scattering (DIS) measurements by studying spin asymmetries in strong processes involving the partonic constituents of polarized protons. After decades of being regarded as an inessential complication to the strong interaction at high energy, spin has again become a topic of considerable experimental and theoretical interest. This is largely due to the observation from DIS that the net contribution to the proton spin from the quark constituents ({approximately} 30%) is smaller than expected relative to the momentum carried in this sector. The RHIC accelerator will provide an unprecedented opportunity to fully explore the spin structure of the proton with high precision studies focused on measuring the spin-dependent parton distributions (valence quark, sea quark, gluon) of the proton. It is designed to operate both with high luminosity (10{sup 31}--10{sup 32} cm{sup {minus}2} sec{sup {minus}1}) and high polarization ({approximately} 70%). In addition, the energy range at RHIC ({radical}s = 200--500 GeV) is sufficiently high that spin effects in polarized proton interactions should be calculable once the spin structure of the proton is sufficiently understood. The experimental results will therefore provide a rigorous test of QCD. A further focus of the RHIC spin physics program will be to search for physics beyond the standard model. The increased sensitivity afforded by using polarized protons to study parity violation in inclusive jet production at high p{sub t} makes this exploration competitive with respect to ongoing searches using unpolarized beams.

  20. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH−(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH−(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH−(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  1. Encapsulating Mobile Proton Carriers into Structural Defects in Coordination Polymer Crystals: High Anhydrous Proton Conduction and Fuel Cell Application.

    PubMed

    Inukai, Munehiro; Horike, Satoshi; Itakura, Tomoya; Shinozaki, Ryota; Ogiwara, Naoki; Umeyama, Daiki; Nagarkar, Sanjog; Nishiyama, Yusuke; Malon, Michal; Hayashi, Akari; Ohhara, Takashi; Kiyanagi, Ryoji; Kitagawa, Susumu

    2016-07-13

    We describe the encapsulation of mobile proton carriers into defect sites in nonporous coordination polymers (CPs). The proton carriers were encapsulated with high mobility and provided high proton conductivity at 150 °C under anhydrous conditions. The high proton conductivity and nonporous nature of the CP allowed its application as an electrolyte in a fuel cell. The defects and mobile proton carriers were investigated using solid-state NMR, XAFS, XRD, and ICP-AES/EA. On the basis of these analyses, we concluded that the defect sites provide space for mobile uncoordinated H3PO4, H2PO4(-), and H2O. These mobile carriers play a key role in expanding the proton-hopping path and promoting the mobility of protons in the coordination framework, leading to high proton conductivity and fuel cell power generation.

  2. 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.

  3. Test report: Shock test of the electron/proton spectrometer structural test unit

    NASA Technical Reports Server (NTRS)

    Vincent, D. L.

    1972-01-01

    A shock test of the electron-proton spectrometer structural test unit was conducted. The purpose of the shock test was to verify the structural integrity of the electron-spectrometer design and to obtain data on the shock response of the electronics and electronic housing. The test equipment is described and typical shock response data are provided.

  4. USING KAPPA FUNCTIONS TO CHARACTERIZE OUTER HELIOSPHERE PROTON DISTRIBUTIONS IN THE PRESENCE OF CHARGE-EXCHANGE

    SciTech Connect

    Zirnstein, E. J.; McComas, D. J. E-mail: dmccomas@swri.edu

    2015-12-10

    Kappa functions have long been used in the analysis and modeling of suprathermal particles in various space plasmas. In situ observations of the supersonic solar wind show its distribution contains a cold ion core and power-law tail, which is well-represented by a kappa function. In situ plasma observations by Voyager, as well as observations of energetic neutral atom (ENA) spectra by the Interstellar Boundary Explorer (IBEX), showed that the compressed and heated inner heliosheath (IHS) plasma beyond the termination shock can also be represented by a kappa function. IBEX exposes the IHS plasma properties through the detection of ENAs generated by charge-exchange in the IHS. However, charge-exchange modifies the plasma as it flows through the IHS, and makes it difficult to ascertain the parent proton distribution. In this paper we investigate the evolution of proton distributions, initially represented by a kappa function, that experience losses due to charge-exchange in the IHS. In the absence of other processes, it is no longer representable by a single kappa function due to the energy-dependent, charge-exchange process. While one can still fit a kappa function to the evolving proton distribution over limited energy ranges, this yields fitting parameters (pseudo-density, pseudo-temperature, pseudo-kappa index) that depend on the energy range of the fit. We discuss the effects of fitting a kappa function to the IHS proton distribution over limited energy ranges, its dependence on the initial proton distribution properties at the termination shock, and implications for understanding the observations.

  5. Proton channel models

    PubMed Central

    Pupo, Amaury; Baez-Nieto, David; Martínez, Agustín; Latorre, Ramón; González, Carlos

    2014-01-01

    Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins. PMID:24755912

  6. Effect of 120 keV proton irradiation on mass loss and chemical structure of AG-80 epoxy resin

    NASA Astrophysics Data System (ADS)

    Gao, Yu; Jiang, Sheng-Ling; Dong, Shang-Li; Yang, De-Zhuang

    2010-11-01

    The AG-80 resin is a new type of thermosetting matrix for advanced carbon/epoxy composites. Mass loss effect and the related outgassing are major concerns for its application in space. The changes in mass loss, outgassing and chemical structure under 120 keV proton exposure were investigated for the AG-80 epoxy resin. The variation in chemistry was characterised by X-ray photoelectron spectroscopy. Experimental results show that by increasing the proton fluence, the surface colour of specimens becomes darker. Mass loss ratios ascend remarkably until the fluence of approximately 6.3×1015 cm-2 and then tend to level off. The surface roughness of specimens exhibits an increasing trend followed by a decreasing trend as a function of proton fluence. Under the exposure, the C‒C, C‒H, C‒N and C‒O bonds are broken, a variety of molecule ions with smaller molecular weight are formed and carbon is enriched in the surface layer of the specimens. The changes in mass loss and surface roughness of the AG-80 epoxy resin could be attributed to the formation of the molecule ions and the enrichment of carbon content in the surface layer due to proton radiation.

  7. Survey of the high resolution frequency structure of the fast magnetosonic mode and proton energy diffusion associated with these waves

    NASA Astrophysics Data System (ADS)

    Boardsen, S. A.; Hospodarsky, G. B.; Kletzing, C.; Santolik, O.; Wygant, J. R.; MacDonald, E.; Pfaff, R. F., Jr.; Kurth, W. S.; Khazanov, G. V.

    2015-12-01

    The fast magnetosonic mode, also referred to as equatorial noise, occurs at frequencies mainly between the proton cyclotron frequency (fcp) and the lower hybrid frequency. The wave properties of this mode are characterized by a strong magnetic compressional component. These waves are observed around the magnetic equator in the Earth's inner magnetosphere. Case studies of the spectra of these waves have found the emissions to be composed of 1) harmonics, usually with spacing near the local fcp, 2) broad band hiss-like structure, or 3) a superposition of the two spectral types. No statistical studies of the frequency structure of these waves have been made. Using ~600,000 burst mode wave captures from the EMFISIS Wave Form Receiver and the EFW instrument on the Van Allen Probes spacecraft this mode will be identified in the high resolution frequency spectra and its frequency structure will be characterized. The variation of the frequency structure will be investigated as a function of normalized frequency, location, and geomagnetic conditions, and with spacecraft separation. The frequency structure will be compared with path integrated gain using proton ring distributions as the wave source. Recently the modulation of the fast magnetosonic mode has been reported, with modulation periods in the range of 30s to 240s. It has been proposed that frequency drift observed during each modulation is due to strong inward diffusion in energy of the proton ring distributions that generate these waves. As the inner edge of the ring distribution diffuses towards lower energies the band of unstable harmonics increases in frequency. If in the source region, for modulations with periods greater than say 100s, the inward energy diffusion should be observable in the HOPE proton data which has a cycle time of 24s.

  8. Non-Sedated Rapid Volumetric Proton Density MRI Predicts Neonatal Brachial Plexus Birth Palsy Functional Outcome.

    PubMed

    Shen, Peter Y; Nidecker, Anna E; Neufeld, Ethan A; Lee, Paul S; James, Michelle A; Bauer, Andrea S

    2017-03-01

    The current prognostic biomarker of functional outcome in brachial plexus birth palsy is serial clinical examination throughout the first 6 months of age. This can delay surgical treatment and prolong parental anxiety in neonates who will recover spontaneously. A potentially superior biomarker is a volumetric proton density MRI performed at clinical presentation and within the first 12 weeks of life, providing a high spatial and contrast resolution examination in 4 minutes. Nine neonates ranging in age from 4 to 9 weeks who presented with brachial plexus birth palsy were enrolled. All subjects underwent non-sedated 3 Tesla MRI with Cube Proton Density MRI sequence at the same time as their initial clinical visit. Serial clinical examinations were conducted at routine 4 week intervals and the functional performance scores were recorded. MRI findings were divided into pre-ganglionic and post-ganglionic injuries and a radiological scoring system (Shriners Radiological Score) was developed for this study. Proton Density MRI was able to differentiate between pre-ganglionic and post-ganglionic injuries. Radiological scores (Shriners Radiological Score) correlated better with functional performance at 6 months of age (P = .022) than the initial clinical examinations (Active Movement Scale P = .213 and Toronto P = .320). Rapid non-sedated volumetric Cube Proton Density MRI protocol performed at initial clinical presentation can accurately grade severity of brachial plexus birth palsy injury and predict functional performance at 6 months of age. Copyright © 2016 by the American Society of Neuroimaging.

  9. The histidine phosphatase superfamily: structure and function.

    PubMed

    Rigden, Daniel J

    2008-01-15

    The histidine phosphatase superfamily is a large functionally diverse group of proteins. They share a conserved catalytic core centred on a histidine which becomes phosphorylated during the course of the reaction. Although the superfamily is overwhelmingly composed of phosphatases, the earliest known and arguably best-studied member is dPGM (cofactor-dependent phosphoglycerate mutase). The superfamily contains two branches sharing very limited sequence similarity: the first containing dPGM, fructose-2,6-bisphosphatase, PhoE, SixA, TIGAR [TP53 (tumour protein 53)-induced glycolysis and apoptosis regulator], Sts-1 and many other activities, and the second, smaller, branch composed mainly of acid phosphatases and phytases. Human representatives of both branches are of considerable medical interest, and various parasites contain superfamily members whose inhibition might have therapeutic value. Additionally, several phosphatases, notably the phytases, have current or potential applications in agriculture. The present review aims to draw together what is known about structure and function in the superfamily. With the benefit of an expanding set of histidine phosphatase superfamily structures, a clearer picture of the conserved elements is obtained, along with, conversely, a view of the sometimes surprising variation in substrate-binding and proton donor residues across the superfamily. This analysis should contribute to correcting a history of over- and mis-annotation in the superfamily, but also suggests that structural knowledge, from models or experimental structures, in conjunction with experimental assays, will prove vital for the future description of function in the superfamily.

  10. Structure functions for the three-nucleon system

    NASA Astrophysics Data System (ADS)

    Bissey, F.; Thomas, A. W.; Afnan, I. R.

    2001-08-01

    The spectral functions and light-cone momentum distributions of protons and neutrons in 3He and 3H are given in terms of the three-nucleon wave function for realistic nucleon-nucleon interactions. To reduce computational complexity, separable expansions are employed for the nucleon-nucleon potentials. The results for the light-cone momentum distributions suggest that they are not very sensitive to the details of the two-body interaction, as long as it has reasonable short-range repulsion. The unpolarized and polarized structure functions are examined for both 3He and 3H in order to test the usefulness of 3He as a neutron target. It is found that the measurement of the spin structure function of polarized 3H would provide a very clear test of the predicted change in the polarized parton distributions of a bound proton.

  11. Reversible proton-switchable fluorescence controlled by conjugation effect in an organically-functionalized polyoxometalate.

    PubMed

    Lv, Chunlin; Chen, Kun; Hu, Junjie; Zhang, Jin; Khan, Rao Naumaan Nasim; Wei, Yongge

    2016-06-20

    A novel monosubstituted organoimido hexamolybdate containing 6-nitroquinoline moiety has been successfully synthesized. This organically-functionalized polyoxometalate exhibits proton-induced switchable fluorescence property in aqueous acetonitrile solution at room temperature. Experimental and theoretical investigations of this reversible "on" and "off" switching mechanism have been carried out, and it is found that the protonation and deprotonation at the heterocyclic nitrogen atom within quinoline fragment leads to the breaking and reformation of the conjugation through strong d-π interaction between the hexamolybdate anionic cluster and the quinoline moiety, resulting in "on" and "off" luminescence signal.

  12. Reversible proton-switchable fluorescence controlled by conjugation effect in an organically-functionalized polyoxometalate

    PubMed Central

    Lv, Chunlin; Chen, Kun; Hu, Junjie; Zhang, Jin; Khan, Rao Naumaan Nasim; Wei, Yongge

    2016-01-01

    A novel monosubstituted organoimido hexamolybdate containing 6-nitroquinoline moiety has been successfully synthesized. This organically-functionalized polyoxometalate exhibits proton-induced switchable fluorescence property in aqueous acetonitrile solution at room temperature. Experimental and theoretical investigations of this reversible “on” and “off” switching mechanism have been carried out, and it is found that the protonation and deprotonation at the heterocyclic nitrogen atom within quinoline fragment leads to the breaking and reformation of the conjugation through strong d-π interaction between the hexamolybdate anionic cluster and the quinoline moiety, resulting in “on” and “off” luminescence signal. PMID:27321576

  13. Reversible proton-switchable fluorescence controlled by conjugation effect in an organically-functionalized polyoxometalate

    NASA Astrophysics Data System (ADS)

    Lv, Chunlin; Chen, Kun; Hu, Junjie; Zhang, Jin; Khan, Rao Naumaan Nasim; Wei, Yongge

    2016-06-01

    A novel monosubstituted organoimido hexamolybdate containing 6-nitroquinoline moiety has been successfully synthesized. This organically-functionalized polyoxometalate exhibits proton-induced switchable fluorescence property in aqueous acetonitrile solution at room temperature. Experimental and theoretical investigations of this reversible “on” and “off” switching mechanism have been carried out, and it is found that the protonation and deprotonation at the heterocyclic nitrogen atom within quinoline fragment leads to the breaking and reformation of the conjugation through strong d-π interaction between the hexamolybdate anionic cluster and the quinoline moiety, resulting in “on” and “off” luminescence signal.

  14. Protonation of naphthalene proton sponges containing higher N-alkyl groups. Structural consequences on proton accepting properties and intramolecular hydrogen bonding

    NASA Astrophysics Data System (ADS)

    Ozeryanskii, V. A.; Shevchuk, D. A.; Pozharskii, A. F.; Kazheva, O. N.; Chekhlov, A. N.; Dyachenko, O. A.

    2008-12-01

    1,8-Bis(dipropylamino)naphthalene and 1,8-di(pyrrolydin-1-yl)naphthalene as well as monoprotonated forms of the latter and of 1,8-di(piperidin-1-yl)naphthalene were structurally analyzed and compared with known data for 1,8-bis(dimethylamino)naphthalene and its protonated form. The N-alkyl groups enlarging the N …N distance (up to ˜2.9 Å) and changing the degree of conjugation between the NAlk 2 and naphthalene moieties modify in a complex way the basicity (p Ka values of conjugated acids) as well as the properties of intramolecular hydrogen bonds both in the solid state and in solution for a set of 1,8-bis(dialkylamino)naphthalenes.

  15. Measurement of the proton spin structure function g1(x,Q2) for Q2 from 0.15 to 1.6 GeV2 with CLAS.

    PubMed

    Fatemi, R; Skabelin, A V; Burkert, V D; Crabb, D; De Vita, R; Kuhn, S E; Minehart, R; Adams, G; Anciant, E; Anghinolfi, M; Asavapibhop, B; Audit, G; Auger, T; Avakian, H; Bagdasaryan, H; Ball, J P; Barrow, S; Battaglieri, M; Beard, K; Bektasoglu, M; Bellis, M; Bertozzi, W; Bianchi, N; Biselli, A S; Boiarinov, S; Bonner, B E; Bosted, P E; Bouchigny, S; Bradford, R; Branford, D; Brooks, W K; Butuceanu, C; Calarco, J R; Carman, D S; Carnahan, B; Cetina, C; Ciciani, L; Clark, R; Cole, P L; Coleman, A; Connelly, J; Cords, D; Corvisiero, P; Crannell, H; Cummings, J P; De Sanctis, E; Degtyarenko, P V; Denizli, H; Dennis, L; Dharmawardane, K V; Dhuga, K S; Djalali, C; Dodge, G E; Doughty, D; Dragovitsch, P; Dugger, M; Dytman, S; Eckhause, M; Egiyan, H; Egiyan, K S; Elouadrhiri, L; Empl, A; Eugenio, P; Farhi, L; Feuerbach, R J; Freyberger, A; Ficenec, J; Forest, T A; Frolov, V; Funsten, H; Gaff, S J; Garçon, M; Gavalian, G; Gilad, S; Gilfoyle, G P; Giovanetti, K L; Girard, P; Gordon, C I O; Griffioen, K A; Guidal, M; Guillo, M; Guo, L; Gyurjyan, V; Hadjidakis, C; Hancock, D; Hardie, J; Heddle, D; Heimberg, P; Hersman, F W; Hicks, K; Hicks, R S; Holtrop, M; Hu, J; Hyde-Wright, C E; Ilieva, Y; Ito, M M; Jenkins, D; Joo, K; Keith, C; Kelley, J H; Kellie, J D; Khandaker, M; Kim, K Y; Kim, K; Kim, W; Klein, A; Klein, F J; Klimenko, A V; Klusman, M; Kossov, M; Koubarovski, V; Kramer, L H; Kuang, Y; Kuhn, J; Lachniet, J; Laget, J M; Lawrence, D; Li, Ji; Livingston, K; Longhi, A; Lukashin, K; Major, W; Manak, J J; Marchand, C; McAleer, S; McNabb, J W C; Mecking, B A; Mehrabyan, S; Mestayer, M D; Meyer, C A; Mikhailov, K; Mirazita, M; Miskimen, R; Morand, L; Morrow, S A; Muccifora, V; Mueller, J; Mutchler, G S; Napolitano, J; Nasseripour, R; Nelson, S O; Niccolai, S; Niculescu, G; Niculescu, I; Niczyporuk, B B; Niyazov, R A; Nozar, M; O'Brien, J T; O'Rielly, G V; Osipenko, M; Park, K; Pasyuk, E; Peterson, G; 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; Ricco, G; Ripani, M; Ritchie, B G; Rock, S E; Ronchetti, F; Rossi, P; Rowntree, D; Rubin, P D; Sabatié, F; Sabourov, K; Salgado, C; Santoro, J P; Sapunenko, V; Sargsyan, M; Schumacher, R A; Seely, M; Serov, V S; Sharabian, Y G; Shaw, J; Simionatto, S; Smith, E S; Smith, T; Smith, L C; Sober, D I; Sorrel, L; Spraker, M; Stavinsky, A; Stepanyan, S; Stoler, P; Strauch, S; Taiuti, M; Taylor, S; Tedeschi, D J; Thoma, U; Thompson, R; Todor, L; Tur, C; Ungaro, M; Vineyard, M F; Vlassov, A V; Wang, K; Weinstein, L B; Weller, H; Weygand, D P; Whisnant, C S; Wolin, E; Wood, M H; Yegneswaran, A; Yun, J; Zhang, B; Zhao, J; Zhou, Z

    2003-11-28

    Double-polarization asymmetries for inclusive ep scattering were measured at Jefferson Lab using 2.6 and 4.3 GeV longitudinally polarized electrons incident on a longitudinally polarized NH3 target in the CLAS detector. The polarized structure function g(1)(x,Q2) was extracted throughout the nucleon resonance region and into the deep inelastic regime, for Q(2)=0.15-1.64 GeV2. The contributions to the first moment Gamma(1)(Q2)= integral g(1)(x,Q2) dx were determined up to Q(2)=1.2 GeV2. Using a parametrization for g(1) in the unmeasured low x regions, the complete first moment was estimated over this Q2 region. A rapid change in Gamma(1) is observed for Q2<1 GeV2, with a sign change near Q(2)=0.3 GeV2, indicating dominant contributions from the resonance region. At Q(2)=1.2 GeV2 our data are below the perturbative QCD evolved scaling value.

  16. Measurement of the Proton Spin Structure Function g1(x,Q2) for Q2 from 0.15 to 1.6 GeV2 with CLAS

    NASA Astrophysics Data System (ADS)

    Fatemi, R.; Skabelin, A. V.; Burkert, V. D.; Crabb, D.; Vita, R. De; Kuhn, S. E.; Minehart, R.; Adams, G.; Anciant, E.; Anghinolfi, M.; Asavapibhop, B.; Audit, G.; Auger, T.; Avakian, H.; Bagdasaryan, H.; Ball, J. P.; Barrow, S.; Battaglieri, M.; Beard, K.; Bektasoglu, M.; Bellis, M.; Bertozzi, W.; Bianchi, N.; Biselli, A. S.; Boiarinov, S.; Bonner, B. E.; Bosted, P. E.; Bouchigny, S.; Bradford, R.; Branford, D.; Brooks, W. K.; Butuceanu, C.; Calarco, J. R.; Carman, D. S.; Carnahan, B.; Cetina, C.; Ciciani, L.; Clark, R.; Cole, P. L.; Coleman, A.; Connelly, J.; Cords, D.; Corvisiero, P.; Crannell, H.; Cummings, J. P.; de Sanctis, E.; Degtyarenko, P. V.; Denizli, H.; Dennis, L.; Dharmawardane, K. V.; Dhuga, K. S.; Djalali, C.; Dodge, G. E.; Doughty, D.; Dragovitsch, P.; Dugger, M.; Dytman, S.; Eckhause, M.; Egiyan, H.; Egiyan, K. S.; Elouadrhiri, L.; Empl, A.; Eugenio, P.; Farhi, L.; Feuerbach, R. J.; Freyberger, A.; Ficenec, J.; Forest, T. A.; Frolov, V.; Funsten, H.; Gaff, S. J.; Garçon, M.; Gavalian, G.; Gilad, S.; Gilfoyle, G. P.; Giovanetti, K. L.; Girard, P.; Gordon, C. I.; Griffioen, K. A.; Guidal, M.; Guillo, M.; Guo, L.; Gyurjyan, V.; Hadjidakis, C.; Hancock, D.; Hardie, J.; Heddle, D.; Heimberg, P.; Hersman, F. W.; Hicks, K.; Hicks, R. S.; Holtrop, M.; Hu, J.; Hyde-Wright, C. E.; Ilieva, Y.; Ito, M. M.; Jenkins, D.; Joo, K.; Keith, C.; Kelley, J. H.; Kellie, J. D.; Khandaker, M.; Kim, K. Y.; Kim, K.; Kim, W.; Klein, A.; Klein, F. J.; Klimenko, A. V.; Klusman, M.; Kossov, M.; Koubarovski, V.; Kramer, L. H.; Kuang, Y.; Kuhn, J.; Lachniet, J.; Laget, J. M.; Lawrence, D.; Li, Ji; Livingston, K.; Longhi, A.; Lukashin, K.; Major, W.; Manak, J. J.; Marchand, C.; McAleer, S.; McNabb, J. W.; Mecking, B. A.; Mehrabyan, S.; Mestayer, M. D.; Meyer, C. A.; Mikhailov, K.; Mirazita, M.; Miskimen, R.; Morand, L.; Morrow, S. A.; Muccifora, V.; Mueller, J.; Mutchler, G. S.; Napolitano, J.; Nasseripour, R.; Nelson, S. O.; Niccolai, S.; Niculescu, G.; Niculescu, I.; Niczyporuk, B. B.; Niyazov, R. A.; Nozar, M.; O'Brien, J. T.; O'Rielly, G. V.; Osipenko, M.; Park, K.; Pasyuk, E.; Peterson, G.; 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.; Ricco, G.; Ripani, M.; Ritchie, B. G.; Rock, S. E.; Ronchetti, F.; Rossi, P.; Rowntree, D.; Rubin, P. D.; Sabatié, F.; Sabourov, K.; Salgado, C.; Santoro, J. P.; Sapunenko, V.; Sargsyan, M.; Schumacher, R. A.; Seely, M.; Serov, V. S.; Sharabian, Y. G.; Shaw, J.; Simionatto, S.; Smith, E. S.; Smith, T.; Smith, L. C.; Sober, D. I.; Sorrel, L.; Spraker, M.; Stavinsky, A.; Stepanyan, S.; Stoler, P.; Strauch, S.; Taiuti, M.; Taylor, S.; Tedeschi, D. J.; Thoma, U.; Thompson, R.; Todor, L.; Tur, C.; Ungaro, M.; Vineyard, M. F.; Vlassov, A. V.; Wang, K.; Weinstein, L. B.; Weller, H.; Weygand, D. P.; Whisnant, C. S.; Wolin, E.; Wood, M. H.; Yegneswaran, A.; Yun, J.; Zhang, B.; Zhao, J.; Zhou, Z.

    2003-11-01

    Double-polarization asymmetries for inclusive ep scattering were measured at Jefferson Lab using 2.6 and 4.3GeV longitudinally polarized electrons incident on a longitudinally polarized NH3 target in the CLAS detector. The polarized structure function g1(x,Q2) was extracted throughout the nucleon resonance region and into the deep inelastic regime, for Q2=0.15 1.64 GeV2. The contributions to the first moment Γ1(Q2)=∫g1(x,Q2) dx were determined up to Q2=1.2 GeV2. Using a parametrization for g1 in the unmeasured low x regions, the complete first moment was estimated over this Q2 region. A rapid change in Γ1 is observed for Q2<1 GeV2, with a sign change near Q2=0.3 GeV2, indicating dominant contributions from the resonance region. At Q2=1.2 GeV2 our data are below the perturbative QCD evolved scaling value.

  17. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents.

  18. High velocity proton collision with liquid lithium: a time dependent density functional theory study.

    PubMed

    Bi, Gang; Kang, Jun; Wang, Lin-Wang

    2017-03-29

    Liquid lithium is often used as a coating material in fusion reaction chambers, where it is under constant bombardment from high speed neutrons and protons. However, numerous fundamental questions are unanswered, for example whether a single proton impact can cause Li atom sputtering, and what is the electron excitation energy profile after a collision particularly for extremely high energy projectiles. Herein, we use a real-time dependent density functional method to study these questions for proton energies in the range of 30 eV to 1 MeV. The calculated stopping power agrees well with experiment, and it is found that the stopping power cannot be described by the single electron exciting spectrum based on the adiabatic eigen energies, and Li atom sputtering is not observed within our simulation time.

  19. Ab initio molecular dynamics simulations investigating proton transfer in perfluorosulfonic acid functionalized carbon nanotubes.

    PubMed

    Habenicht, Bradley F; Paddison, Stephen J; Tuckerman, Mark E

    2010-08-21

    Proton dissociation and transfer were examined with ab initio molecular dynamics (AIMD) simulations of carbon nanotubes (CNT) functionalized with perfluorosulfonic acid (-CF(2)SO(3)H) groups with 1-3 H(2)O/SO(3)H. The CNT systems were constructed both with and without fluorine atoms covalently bound to the walls to elucidate the effects of the presence of a strongly hydrophobic environment, the fluorine, on proton dissociation, hydration, and stabilization. The simulations revealed that the dissociated proton was preferentially stabilized as a hydrated hydronium cation (i.e., Eigen like) in the fluorinated CNTs but as a Zundel (H(5)O(2)(+)) cation in the nonfluorinated CNTs. This feature is attributed to the fluorine atoms forming hydrogen bonds with the water molecules coordinated to the central hydronium ion.

  20. Protons stabilize the closed conformation of gain-of-function mutants of the TRPV1 channel.

    PubMed

    Boukalova, Stepana; Teisinger, Jan; Vlachova, Viktorie

    2013-03-01

    The vanilloid transient receptor potential channel TRPV1 is a molecular integrator of noxious stimuli, including capsaicin, heat and protons. Despite clear similarities between the overall architecture of TRPV1 and voltage-dependent potassium (Kv) channels, the extent of conservation in the molecular logic for gating is unknown. In Kv channels, a small contact surface between S1 and the pore-helix is required for channel functioning. To explore the function of S1 in TRPV1, we used tryptophan-scanning mutagenesis and characterized the responses to capsaicin and protons. Wild-type-like currents were generated in 9 out of 17 mutants; three mutants (M445W, A452W, R455W) were non-functional. The conservative mutation R455K in the extracellular extent of S1 slowed down capsaicin-induced activation and prevented normal channel closure. This mutant was neither activated nor potentiated by protons, on the contrary, protons promoted a rapid deactivation of its currents. Similar phenotypes were found in two other gain-of-function mutants and also in the pore-helix mutant T633A, known to uncouple proton activation. We propose that the S1 domain contains a functionally important region that may be specifically involved in TRPV1 channel gating, and thus be important for the energetic coupling between S1-S4 sensor activation and gate opening. Analogous to Kv channels, the S1-pore interface might serve to stabilize conformations associated with TRPV1 channel gating. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Structural origins of efficient proton abstraction from carbon by a catalytic antibody

    PubMed Central

    Debler, Erik W.; Ito, Shuichiro; Seebeck, Florian P.; Heine, Andreas; Hilvert, Donald; Wilson, Ian A.

    2005-01-01

    Antibody 34E4 catalyzes the conversion of benzisoxazoles to salicylonitriles with high rates and multiple turnovers. The crystal structure of its complex with the benzimidazolium hapten at 2.5-Å resolution shows that a combination of hydrogen bonding, π stacking, and van der Waals interactions is exploited to position both the base, GluH50, and the substrate for efficient proton transfer. Suboptimal placement of the catalytic carboxylate, as observed in the 2.8-Å structure of the GluH50Asp variant, results in substantially reduced catalytic efficiency. In addition to imposing high positional order on the transition state, the antibody pocket provides a highly structured microenvironment for the reaction in which the carboxylate base is activated through partial desolvation, and the highly polarizable transition state is stabilized by dispersion interactions with the aromatic residue TrpL91 and solvation of the leaving group oxygen by external water. The enzyme-like efficiency of general base catalysis in this system directly reflects the original hapten design, in which a charged guanidinium moiety was strategically used to elicit an accurately positioned functional group in an appropriate reaction environment and suggests that even larger catalytic effects may be achievable by extending this approach to the induction of acid-base pairs capable of bifunctional catalysis. PMID:15788533

  2. Invited Article: Relation between electric and magnetic field structures and their proton-beam images

    SciTech Connect

    Kugland, N. L.; Ryutov, D. D.; Plechaty, C.; Ross, J. S.; Park, H.-S.

    2012-10-15

    Proton imaging is commonly used to reveal the electric and magnetic fields that are found in high energy density plasmas. Presented here is an analysis of this technique that is directed towards developing additional insight into the underlying physics. This approach considers: formation of images in the limits of weak and strong intensity variations; caustic formation and structure; image inversion to obtain line-integrated field characteristics; direct relations between images and electric or magnetic field structures in a plasma; imaging of sharp features such as Debye sheaths and shocks. Limitations on spatial and temporal resolution are assessed, and similarities with optical shadowgraphy are noted. Synthetic proton images are presented to illustrate the analysis. These results will be useful for quantitatively analyzing experimental proton imaging data and verifying numerical codes.

  3. Invited article: Relation between electric and magnetic field structures and their proton-beam images.

    PubMed

    Kugland, N L; Ryutov, D D; Plechaty, C; Ross, J S; Park, H-S

    2012-10-01

    Proton imaging is commonly used to reveal the electric and magnetic fields that are found in high energy density plasmas. Presented here is an analysis of this technique that is directed towards developing additional insight into the underlying physics. This approach considers: formation of images in the limits of weak and strong intensity variations; caustic formation and structure; image inversion to obtain line-integrated field characteristics; direct relations between images and electric or magnetic field structures in a plasma; imaging of sharp features such as Debye sheaths and shocks. Limitations on spatial and temporal resolution are assessed, and similarities with optical shadowgraphy are noted. Synthetic proton images are presented to illustrate the analysis. These results will be useful for quantitatively analyzing experimental proton imaging data and verifying numerical codes.

  4. {sup 12}O resonant structure evaluated by the two-proton emission process

    SciTech Connect

    Leite, T. N.; Teruya, N.; Dimarco, A.; Duarte, S. B.; Tavares, O. A. P.

    2009-07-15

    The characteristics of the {sup 12}O resonant ground state are investigated through the analysis of the experimental data for the two-proton decay process. The sequential and simultaneous two-proton emission decay modes have been considered in a statistical calculation of the decay energy distribution. The resonant structures of {sup 11}N have been employed as intermediate states for the sequential mode, having their parameters determined by considering the structure of single particle resonance in quantum scattering problem. The width of the {sup 12}O resonant ground state has been extracted from a best fit to the experimental data. The contributions from the different channels to the decay energy distribution have been evaluated, and width and peak location parameters of the {sup 12}O resonant ground state are compared with results of other works for the sequential and simultaneous two-proton decay modes.

  5. Theoretical study of the structures of flavin in different oxidation and protonation states

    SciTech Connect

    Zheng, Y.J.; Ornstein, R.L.

    1996-10-02

    Ab initio molecular orbital theory was used to investigate the structure of flavin in different oxidation and protonation states using lumiflavin as a model compound. According to our study. oxidized flavin is planar no matter what its protonation state or whether it participates in hydrogen bonding. The structures of flavin semiquinone radicals are planar or very close to planar, but the reduced flavin H{sub 3}Fl{sub red} (9) is bent with a ring puckering angle of 27.3{degree} along the N5 and N10 axis. The calculations indicate that N1 is the site of protonation for oxidized flavin, which is in agreement with several crystallographic studies. The calculated spin density distribution for flavin semiquinone radicals is also consistent with experimental results. Electrostatic potential derived charges at the RHF/6-31G{sup *} level of theory are also provided for both oxidized and reduced flavins. 34 refs., 4 figs., 5 tabs.

  6. Spliceosome structure and function.

    PubMed

    Will, Cindy L; Lührmann, Reinhard

    2011-07-01

    Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton ribonucleoprotein (RNP) complex comprised of five snRNPs and numerous proteins. Intricate RNA-RNA and RNP networks, which serve to align the reactive groups of the pre-mRNA for catalysis, are formed and repeatedly rearranged during spliceosome assembly and catalysis. Both the conformation and composition of the spliceosome are highly dynamic, affording the splicing machinery its accuracy and flexibility, and these remarkable dynamics are largely conserved between yeast and metazoans. Because of its dynamic and complex nature, obtaining structural information about the spliceosome represents a major challenge. Electron microscopy has revealed the general morphology of several spliceosomal complexes and their snRNP subunits, and also the spatial arrangement of some of their components. X-ray and NMR studies have provided high resolution structure information about spliceosomal proteins alone or complexed with one or more binding partners. The extensive interplay of RNA and proteins in aligning the pre-mRNA's reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme. However, elucidation of the precise nature of the spliceosome's active site, awaits the generation of a high-resolution structure of its RNP core.

  7. Spliceosome Structure and Function

    PubMed Central

    Will, Cindy L.; Lührmann, Reinhard

    2011-01-01

    SUMMARY Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton ribonucleoprotein (RNP) complex comprised of five snRNPs and numerous proteins. Intricate RNA-RNA and RNP networks, which serve to align the reactive groups of the pre-mRNA for catalysis, are formed and repeatedly rearranged during spliceosome assembly and catalysis. Both the conformation and composition of the spliceosome are highly dynamic, affording the splicing machinery its accuracy and flexibility, and these remarkable dynamics are largely conserved between yeast and metazoans. Because of its dynamic and complex nature, obtaining structural information about the spliceosome represents a major challenge. Electron microscopy has revealed the general morphology of several spliceosomal complexes and their snRNP subunits, and also the spatial arrangement of some of their components. X-ray and NMR studies have provided high resolution structure information about spliceosomal proteins alone or complexed with one or more binding partners. The extensive interplay of RNA and proteins in aligning the pre-mRNA's reactive groups, and the presence of both RNA and protein at the core of the splicing machinery, suggest that the spliceosome is an RNP enzyme. However, elucidation of the precise nature of the spliceosome's active site, awaits the generation of a high-resolution structure of its RNP core. PMID:21441581

  8. Molecular models of the structural arrangement of subunits and the mechanism of proton translocation in the membrane domain of F(1)F(0) ATP synthase.

    PubMed

    Groth, G

    2000-05-31

    Subunit c of the proton-transporting ATP synthase of Escherichia coli forms an oligomeric complex in the membrane domain that functions in transmembrane proton conduction. The arrangement of subunit c monomers in this oligomeric complex was studied by scanning mutagenesis. On the basis of these studies and structural information on subunit c, different molecular models for the potential arrangement of monomers in the c-oligomer are discussed. Intersubunit contacts in the F(0) domain that have been analysed in the past by chemical modification and mutagenesis studies are summarised. Transient contacts of the c-oligomer with subunit a might play a crucial role in the mechanism of proton translocation. Schematic models presented by several authors that interpret proton transport in the F(0) domain by a relative rotation of the c-subunit oligomer against subunit a are reviewed against the background of the molecular models of the oligomer.

  9. Nonperturbative Strange Sea in Proton Using Wave Functions Inspired by Light Front Holography

    NASA Astrophysics Data System (ADS)

    Vega, Alfredo; Schmidt, Ivan; Gutsche, Thomas; Lyubovitskij, Valery E.

    2017-03-01

    We use different light-front wave functions (two inspired by the AdS/QCD formalism), together with a model of the nucleon in terms of meson-baryon fluctuations to calculate the nonperturbative (intrinsic) contribution to the s(x) - bar{s}(x) asymmetry of the proton sea. The holographic wave functions for an arbitrary number of constituents, recently derived by us, give results quite close to known parametrizations that appear in the literature.

  10. Nano and micro structured targets to modulate the spatial profile of laser driven proton beams

    NASA Astrophysics Data System (ADS)

    Giuffrida, L.; Svensson, K.; Psikal, J.; Margarone, D.; Lutoslawski, P.; Scuderi, V.; Milluzzo, G.; Kaufman, J.; Wiste, T.; Dalui, M.; Ekerfelt, H.; Gallardo Gonzalez, I.; Lundh, O.; Persson, A.; Picciotto, A.; Crivellari, M.; Bagolini, A.; Bellutti, P.; Magnusson, J.; Gonoskov, A.; Klimsa, L.; Kopecek, J.; Lastovicka, T.; Cirrone, G. A. P.; Wahlström, C.-G.; Korn, G.

    2017-03-01

    Nano and micro structured thin (μ m-scale) foils were designed, fabricated and irradiated with the high intensity laser system operating at LLC (Lund Laser Centre, Sweden) in order to systematically study and improve the main proton beam parameters. Nano-spheres deposited on the front (laser irradiated) surface of a flat Mylar foil enabled a small enhancement of the maximum energy and number of the accelerated protons. Nano-spheres on the rear side allowed to modify the proton beam spatial profile. In particular, with nanospheres deposited on the rear of the target, the proton beam spatial homogeneity was clearly enhanced. Silicon nitride thin foils having micro grating structures (with different step dimensions) on the rear surface were also used as targets to influence the divergence of the proton beam and drastically change its shape through a sort of stretching effect. The target fabrication process used for the different target types is described, and representative experimental results are shown and discussed along with supporting 3D particle-in-cell simulations.

  11. Voltage-gated proton currents in microglia of distinct morphology and functional state.

    PubMed

    Klee, R; Heinemann, U; Eder, C

    1999-01-01

    Whole-cell patch-clamp measurements were performed to investigate voltage-gated proton currents (I(PR)) in cultured murine microglia of distinct morphology and functional state. We studied I(PR) in ameboid microglia of untreated cultures, in ameboid microglia which had been activated by lipopolysaccharide, and in ramified microglia which had been exposed to astrocyte-conditioned medium. Proton currents of these three microglia populations did not differ regarding their activation threshold or the voltage dependence of steady-state activation. Moreover, pharmacological properties of I(PR) were similar: proton currents were sensitive to extracellularly applied Zn2+ or La3+, and could be abolished by each of those at a concentration of 100 microM. In the presence of extracellular Na+, I(PR) was decreased to a similar small extent due to activity of the Na+/H+ exchanger in all microglial populations. In contrast, proton currents of microglia differed between the three cell populations with respect to their current density and their time-course of activation: in comparison with untreated microglia, the current density of I(PR) was reduced by about 50% in microglia after their treatment with either lipopolysaccharide or astrocyte-conditioned medium. Moreover, I(PR) activated significantly more slowly in cells exposed to lipopolysaccharide or astrocyte-conditioned medium than in untreated cells. It can be concluded that the distinct H+ current characteristics of the three microglial populations do not correlate with the functional state of the cells.

  12. Nonvolatile memory functionality of ZnO nanowire transistors controlled by mobile protons.

    PubMed

    Yoon, Jongwon; Hong, Woong-Ki; Jo, Minseok; Jo, Gunho; Choe, Minhyeok; Park, Woojin; Sohn, Jung Inn; Nedic, Stanko; Hwang, Hyungsang; Welland, Mark E; Lee, Takhee

    2011-01-25

    We demonstrated the nonvolatile memory functionality of ZnO nanowire field effect transistors (FETs) using mobile protons that are generated by high-pressure hydrogen annealing (HPHA) at relatively low temperature (400 °C). These ZnO nanowire devices exhibited reproducible hysteresis, reversible switching, and nonvolatile memory behaviors in comparison with those of the conventional FET devices. We show that the memory characteristics are attributed to the movement of protons between the Si/SiO(2) interface and the SiO(2)/ZnO nanowire interface by the applied gate electric field. The memory mechanism is explained in terms of the tuning of interface properties, such as effective electric field, surface charge density, and surface barrier potential due to the movement of protons in the SiO(2) layer, consistent with the UV photoresponse characteristics of nanowire memory devices. Our study will further provide a useful route of creating memory functionality and incorporating proton-based storage elements onto a modified CMOS platform for FET memory devices using nanomaterials.

  13. Protonation of Trimethylamine N-Oxide (TMAO) is required for stabilization of RNA tertiary structure

    PubMed Central

    Denning, Elizabeth J.; Thirumalai, D.; MacKerell, Alexander D.

    2013-01-01

    The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQl riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQl. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQl ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent. PMID:24012912

  14. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

    PubMed

    Denning, Elizabeth J; Thirumalai, D; MacKerell, Alexander D

    2013-12-31

    The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.

  15. Understanding the proton radius puzzle: Nuclear structure effects in light muonic atoms

    NASA Astrophysics Data System (ADS)

    Ji, Chen; Hernandez, Oscar Javier; Nevo Dinur, Nir; Bacca, Sonia; Barnea, Nir

    2016-03-01

    We present calculations of nuclear structure effects to the Lamb shift in light muonic atoms. We adopt a modern ab-initio approach by combining state-of-the-art nuclear potentials with the hyperspherical harmonics method. Our calculations are instrumental to the determination of nuclear charge radii in the Lamb shift measurements, which will shed light on the proton radius puzzle.

  16. Spectroscopy, Structure and Proton Dynamics of 2-Hydroxypyridine and Its Clusters with Water and Ammonia

    DTIC Science & Technology

    1988-07-12

    Proton Dvnamics of 2-hydroxypyridine and its Clusters with Water and Ammonia" 12. ffPAONtL AIITHO(C’ -.X. ’Imlos, .. Kelley, E.R. Bernstein 13a. TYPE OF...8217’!j’vN \\.. J.b"#~ *.’ * vrv-~:v .’ Spectroscopy, Structure and Proton Dynamics of 2-hydroxypyridlne and its Clusters With Water and...spectrum. The mixing is removed in the disolvate water cluster but not in monosolvate clusters of ammonia or water . The lactam is shown to be nonplanar

  17. A Structural Element that Facilitates Proton-Coupled Electron Transfer in Oxalate Decarboxylase†,††

    PubMed Central

    Saylor, Benjamin T.; Reinhardt, Laurie A.; Lu, Zhibing; Shukla, Mithila S.; Nguyen, Linda; Cleland, W. Wallace; Angerhofer, Alexander; Allen, Karen N.; Richards, Nigel G. J.

    2012-01-01

    The conformational properties of an active-site loop segment, defined by residues Ser161-Glu162-Asn163-Ser164, have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments (Imaram et al., 2011, Free Rad. Biol. Med. 50, 1009–1015). This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center. PMID:22404040

  18. The structures of proton-bound dimers of glycine with phenylalanine and pentafluorophenylalanine

    NASA Astrophysics Data System (ADS)

    Fu, Weiqiang; Xiong, Jeffrey; Lecours, Michael J.; Carr, Patrick J. J.; Marta, Rick A.; Fillion, Eric; McMahon, Terry; Steinmetz, Vincent; Hopkins, W. Scott

    2016-12-01

    Infrared multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H+·Gly) and pentafluorophenylalanine/glycine (F5-Phe·H+·Gly) have been acquired in the 975-1975 cm-1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F5-Phe·H+·Gly is assigned predominantly to isomers exhibiting a Nsbnd H+⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F5-Phe. In contrast, the spectrum Phe·H+·Gly is found to consist of a mixture of isomers exhibiting the Nsbnd H+⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a Nsbnd H+⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H+·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

  19. 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

  20. Color transparency and the structure of the proton in quantum chromodynamics

    SciTech Connect

    Brodsky, S.J.

    1989-06-01

    Many anomalies suggest that the proton itself is a much more complex object than suggested by simple non-relativistic quark models. Recent analyses of the proton distribution amplitude using QCD sum rules points to highly-nontrivial proton structure. Solutions to QCD in one-space and one-time dimension suggest that the momentum distributions of non-valence quarks in the hadrons have a non-trivial oscillatory structure. The data seems also to be suggesting that the intrinsic'' bound state structure of the proton has a non-negligible strange and charm quark content, in addition to the extrinsic'' sources of heavy quarks created in the collision itself. As we shall see in this lecture, the apparent discrepancies with experiment are not so much a failure of QCD, but rather symptoms of the complexity and richness of the theory. An important tool for analyzing this complexity is the light-cone Fock state representation of hadron wavefunctions, which provides a consistent but convenient framework for encoding the features of relativistic many-body systems in quantum field theory. 121 refs., 44 figs., 1 tab.

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

    SciTech Connect

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

    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 start 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.

  2. 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

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

    PubMed

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

    2015-12-25

    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.

  4. Two-parameter Fermi function fits to experimental charge and point-proton densities for 208Pb

    NASA Astrophysics Data System (ADS)

    Jones, Adam B.; Brown, B. Alex

    2014-12-01

    We use the model-independent experimental charge density for 208Pb to determine a model-independent point-proton density. An improved two-parameter Fermi function representation for the this point-proton density provides input for the analysis of experiments for the neutron density interpreted in terms of neutron skin and halo properties of 208Pb.

  5. Quasi-particle structure of proton-hole cobalt isotopes

    NASA Astrophysics Data System (ADS)

    Gupta, Anuradha; Verma, Preeti; Singh, Suram; Bharti, Arun; Khosa, S. K.; Bhat, G. H.; Sheikh, J. A.

    2015-09-01

    Projected Shell Model calculations have been employed for the description of the ground band in odd mass 57-67Co isotopes. In the present work, quadrupole and monopole pairing interactions as well as quadrupole-quadrupole interactions are effectively included in the Hamiltonian for obtaining various nuclear structure properties using the angular momentum projection technique. The yrast spectra of these isotopes are described as interplay between the angular momentum projected states around the Fermi level. The quasi-particle structure of these nuclei is found to be comprised of different intrinsic K-quantum numbers. Rotational alignments in terms of kinetic moment of inertia (ℑ (1)) have also been discussed. The electromagnetic transition probabilities [ B (E2) and B (M1)] are also obtained in the present work and are found to be in good agreement with the available experimental as well as the other theoretical data, which tests the consistency of the applied projected shell model. The present PSM calculations also report the existence of low lying deformed structure along with the spherical structure at N = 40.

  6. The proton FL dipole approximation in the KMR and the MRW unintegrated parton distribution functions frameworks

    NASA Astrophysics Data System (ADS)

    Modarres, M.; Masouminia, M. R.; Hosseinkhani, H.; Olanj, N.

    2016-01-01

    In the spirit of performing a complete phenomenological investigation of the merits of Kimber-Martin-Ryskin (KMR) and Martin-Ryskin-Watt (MRW) unintegrated parton distribution functions (UPDF), we have computed the longitudinal structure function of the proton, FL (x ,Q2), from the so-called dipole approximation, using the LO and the NLO-UPDF, prepared in the respective frameworks. The preparation process utilizes the PDF of Martin et al., MSTW2008-LO and MSTW2008-NLO, as the inputs. Afterwards, the numerical results are undergone a series of comparisons against the exact kt-factorization and the kt-approximate results, derived from the work of Golec-Biernat and Stasto, against each other and the experimental data from ZEUS and H1 Collaborations at HERA. Interestingly, our results show a much better agreement with the exact kt-factorization, compared to the kt-approximate outcome. In addition, our results are completely consistent with those prepared from embedding the KMR and MRW UPDF directly into the kt-factorization framework. One may point out that the FL, prepared from the KMR UPDF shows a better agreement with the exact kt-factorization. This is despite the fact that the MRW formalism employs a better theoretical description of the DGLAP evolution equation and has an NLO expansion. Such unexpected consequence appears, due to the different implementation of the angular ordering constraint in the KMR approach, which automatically includes the resummation of ln ⁡ (1 / x), BFKL logarithms, in the LO-DGLAP evolution equation.

  7. Technique for sparing previously irradiated critical normal structures in salvage proton craniospinal irradiation

    PubMed Central

    2013-01-01

    Background Cranial reirradiation is clinically appropriate in some cases but cumulative radiation dose to critical normal structures remains a practical concern. The authors developed a simple technique in 3D conformal proton craniospinal irradiation (CSI) to block organs at risk (OAR) while minimizing underdosing of adjacent target brain tissue. Methods Two clinical cases illustrate the use of proton therapy to provide salvage CSI when a previously irradiated OAR required sparing from additional radiation dose. The prior radiation plan was coregistered to the treatment planning CT to create a planning organ at risk volume (PRV) around the OAR. Right and left lateral cranial whole brain proton apertures were created with a small block over the PRV. Then right and left lateral “inverse apertures” were generated, creating an aperture opening in the shape of the area previously blocked and blocking the area previously open. The inverse aperture opening was made one millimeter smaller than the original block to minimize the risk of dose overlap. The inverse apertures were used to irradiate the target volume lateral to the PRV, selecting a proton beam range to abut the 50% isodose line against either lateral edge of the PRV. Together, the 4 cranial proton fields created a region of complete dose avoidance around the OAR. Comparative photon treatment plans were generated with opposed lateral X-ray fields with custom blocks and coplanar intensity modulated radiation therapy optimized to avoid the PRV. Cumulative dose volume histograms were evaluated. Results Treatment plans were developed and successfully implemented to provide sparing of previously irradiated critical normal structures while treating target brain lateral to these structures. The absence of dose overlapping during irradiation through the inverse apertures was confirmed by film. Compared to the lateral X-ray and IMRT treatment plans, the proton CSI technique improved coverage of target brain tissue

  8. Proton-insertion-enhanced pseudocapacitance based on the assembly structure of tungsten oxide.

    PubMed

    Zhu, Minshen; Meng, Wenjun; Huang, Yan; Huang, Yang; Zhi, Chunyi

    2014-11-12

    The capacitances of supercapacitors with carbon and metal oxides as electrodes are usually associated with the available surface areas of the electrode materials. However, in this paper, we report that proton insertion, an unusual capacitive mechanism, may effectively enhance the capacitance of metal oxides with low surface area but specific structures. Tungsten trioxide (WO3) as the electrode material for supercapacitors has always suffered from low capacitance. Nevertheless, enhanced by the proton insertion mechanism, we demonstrate that electrodes fabricated by an assembly structure of hexagonal-phase WO3 (h-WO3) nanopillars achieve a high capacitance of up to 421.8 F g(-1) under the current density of 0.5 A g(-1), which is the highest capacitance achieved with pure WO3 as the electrodes so far, to the best of our knowledge. Detailed analyses indicate that proton insertion dominates the electrochemical behavior of h-WO3 and plays the key role in reaching high capacitance by excluding other mechanisms. In addition, a thorough investigation on the temperature-dependent electrochemical performance reveals excellent performance stability at different temperatures. This study provides a new approach to achieving high capacitance by effective proton insertion into ordered tunnels in crystallized metal oxides, which is primarily important for the fabrication of compact high-performance energy storage devices.

  9. Structure of the c14 Rotor Ring of the Proton Translocating Chloroplast ATP Synthase*

    PubMed Central

    Vollmar, Melanie; Schlieper, Daniel; Winn, Martyn; Büchner, Claudia; Groth, Georg

    2009-01-01

    The structure of the membrane integral rotor ring of the proton translocating F1F0 ATP synthase from spinach chloroplasts was determined to 3.8 Å resolution by x-ray crystallography. The rotor ring consists of 14 identical protomers that are symmetrically arranged around a central pore. Comparisons with the c11 rotor ring of the sodium translocating ATPase from Ilyobacter tartaricus show that the conserved carboxylates involved in proton or sodium transport, respectively, are 10.6–10.8 Å apart in both c ring rotors. This finding suggests that both ATPases have the same gear distance despite their different stoichiometries. The putative proton-binding site at the conserved carboxylate Glu61 in the chloroplast ATP synthase differs from the sodium-binding site in Ilyobacter. Residues adjacent to the conserved carboxylate show increased hydrophobicity and reduced hydrogen bonding. The crystal structure reflects the protonated form of the chloroplast c ring rotor. We propose that upon deprotonation, the conformation of Glu61 is changed to another rotamer and becomes fully exposed to the periphery of the ring. Reprotonation of Glu61 by a conserved arginine in the adjacent a subunit returns the carboxylate to its initial conformation. PMID:19423706

  10. Structured Functional Principal Component Analysis

    PubMed Central

    Shou, Haochang; Zipunnikov, Vadim; Crainiceanu, Ciprian M.; Greven, Sonja

    2015-01-01

    Summary Motivated by modern observational studies, we introduce a class of functional models that expand nested and crossed designs. These models account for the natural inheritance of the correlation structures from sampling designs in studies where the fundamental unit is a function or image. Inference is based on functional quadratics and their relationship with the underlying covariance structure of the latent processes. A computationally fast and scalable estimation procedure is developed for high-dimensional data. Methods are used in applications including high-frequency accelerometer data for daily activity, pitch linguistic data for phonetic analysis, and EEG data for studying electrical brain activity during sleep. PMID:25327216

  11. Challenging nuclear structure models through a microscopic description of proton inelastic scattering off 208Pb

    NASA Astrophysics Data System (ADS)

    Dupuis, M.; Karataglidis, S.; Bauge, E.; Delaroche, J.-P.; Gogny, D.

    2008-07-01

    Differential cross sections from fully microscopic calculations of inelastic proton scattering off 208Pb are compared to experimental scattering data for incident proton energies between 65 and 201 MeV. The required nucleon-nucleus interactions were formed by folding nuclear structure information with a reliable nucleon-nucleon effective interaction that has no adjustable parameter. The absence of phenomenological normalisation in our approach offers the possibility to interpret with confidence the calculated results in terms of the quality of the underlying nuclear structure description: a feature that had been reserved, until recently, to the electron probe. We have used this method to investigate the effect of long range correlations embedded in excited states on calculated inelastic observables and demonstrate the sensitivity of nucleon scattering predictions to details of the nuclear structure.

  12. Structural changes in bacteriorhodopsin during proton translocation revealed by neutron diffraction

    SciTech Connect

    Dencher, N.A.; Dresselhaus, D.; Zaccai, G.; Bueldt, G. )

    1989-10-01

    A neutron diffraction study of spectroscopic states for the light-energized proton pump bacteriorhodopsin (BR) is presented. The photocycle states BR-568 and M were generated at temperatures above 4 degrees C and were measured after trapping at--180{degree}C. In the BR-568 to M-state transition, which is known to be a key step in transmembrane proton pumping, reversible structural changes of the protein were detected. These structural alterations occur in the neighborhood of the cyclohexene ring and at the Schiff's base end of the chromophore retinal. They are interpreted as a 1-2 degree tilt of three or four of the transmembrane alpha-helices or as positional changes of four or five amino acids. The structural changes observed are inherent in the transport mechanism of bacteriorhodopsin.

  13. Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools

    PubMed Central

    Chang, Chia-En A.; Huang, Yu-Ming M.; Mueller, Leonard J.; You, Wanli

    2016-01-01

    This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations. PMID:27885336

  14. Structure of brain functional networks.

    PubMed

    Kuchaiev, Oleksii; Wang, Po T; Nenadic, Zoran; Przulj, Natasa

    2009-01-01

    Brain is a complex network optimized both for segregated and distributed information processing. To perform cognitive tasks, different areas of the brain must "cooperate," thereby forming complex networks of interactions also known as brain functional networks. Previous studies have shown that these networks exhibit "small-world" characteristics. Small-world topology, however, is a general property of all brain functional networks and does not capture structural changes in these networks in response to different stimuli or cognitive tasks. Here we show how novel graph theoretic techniques can be utilized for precise analysis of brain functional networks. These techniques allow us to detect structural changes in brain functional networks in response to different stimuli or cognitive tasks. For certain types of cognitive tasks we have found that these networks exhibit geometric structure in addition to the small-world topology. The method has been applied to the electrocorticographic signals of six epileptic patients.

  15. Protonation of Glu135 Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter

    PubMed Central

    Liu, Yufeng; Ke, Meng; Gong, Haipeng

    2015-01-01

    Major facilitator superfamily (MFS) transporters typically need to alternatingly sample the outward-facing and inward-facing conformations, in order to transport the substrate across membrane. To understand the mechanism, in this work, we focused on one MFS member, the L-fucose/H+ symporter (FucP), whose crystal structure exhibits an outward-open conformation. Previous experiments imply several residues critical to the substrate/proton binding and structural transition of FucP, among which Glu135, located in the periplasm-accessible vestibule, is supposed as being involved in both proton translocation and conformational change of the protein. Here, the structural transition of FucP in presence of substrate was investigated using molecular-dynamics simulations. By combining the equilibrium and accelerated simulations as well as thermodynamic calculations, not only was the large-scale conformational change from the outward-facing to inward-facing state directly observed, but also the free energy change during the structural transition was calculated. The simulations confirm the critical role of Glu135, whose protonation facilitates the outward-to-inward structural transition both by energetically favoring the inward-facing conformation in thermodynamics and by reducing the free energy barrier along the reaction pathway in kinetics. Our results may help the mechanistic studies of both FucP and other MFS transporters. PMID:26244736

  16. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    PubMed Central

    Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H.

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

  17. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

    PubMed

    Christensen, Anders S; Linnet, Troels E; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3)J(NC')) spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  18. Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus.

    PubMed

    Fee, James A; Case, David A; Noodleman, Louis

    2008-11-12

    A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O 2 to the Fe-Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)- (-)O-O (-)-Cu(II) to form water and the active oxidized enzyme, Fe(III)- (-)OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba 3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O 2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O 2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with Cu B. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421-437) and shows how the chemistry of O 2 reduction in the heme a 3 -Cu B dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.

  19. Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: Application of Density Functional Theory to cytochrome ba3 of Thermus thermophilus

    PubMed Central

    Fee, James A.; Case, David A.; Noodleman, Louis

    2009-01-01

    A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly-exergonic, two-electron reduction of Fe-bound O2 to the Fe-Cu bridging peroxodianion, and three protons are pumped in conjunction with the highly-exergonic, two-electron reduction of Fe(III)-−O-O−-Cu(II) to form water and the active oxidized enzyme, Fe(III)-−OH, Cu(II). The scheme is based on the active site structure of cytochrome ba3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from DFT geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O2. Each proton pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with CuB. Density functional theory (DFT) of four types was applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model [P. E. M. Siegbahn & M. A. R. Blomberg (2000) 100 421 - 437] and, shows how the chemistry of O2-reduction in the heme a3-CuB dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer. PMID:18928258

  20. Synthetic Models for the [FeFe]-Hydrogenase: Catalytic Proton Reduction and the Structure of the Doubly Protonated Intermediate

    PubMed Central

    Carroll, Maria E.; Barton, Bryan E.; Rauchfuss, Thomas B.; Carroll, Patrick J.

    2012-01-01

    This report compares biomimetic HER catalysts with and without the amine cofactor (adtNH): Fe2(adtNH)(CO)2(dppv)2 (1NH) and Fe2(pdt)(CO)2(dppv)2 (2; (adtNH)2− = (HN(CH2S)22−, pdt2− = 1,3-(CH2)3S22−). These compounds are spectroscopically, structurally, and stereodynamically very similar but exhibit very different catalytic properties. Protonation of 1NH and 2 each give three isomeric hydrides beginning with the kinetically favored terminal hydride, which converts sequentially to sym and unsym isomers of the bridging hydrides. In the case of the amine, the corresponding ammonium-hydrides are also observed. In the case of the terminal amine hydride [t-H1NH]BF4, the ammonium/amine-hydride equilibrium is sensitive to counteranions and solvent. The species [t-H1NH2](BF4)2 represents the first example of a crystallographically characterized terminal hydride produced by protonation. The NH--HFe distance of 1.88(7) Å indicates dihydrogen bonding. The bridging hydrides [µ-H1NH]+ and [µ-H2]+ reduce near −1.8 V, about 150 mV more negative than the reductions of the terminal hydride [t-H1NH]+ and [t-H2]+ at −1.65 V. Reductions of the amine hydrides [t-H1NH]+ and [t-H1NH2]2+ are irreversible. For the pdt analog, the [t-H2]+/0 couple is unaffected by weak acids (pKaMeCN 15.3) but exhibits catalysis with HBF4•Et2O, albeit with a TOF around 4 s−1 and an overpotential greater than 1 V. The voltammetry of [t-H1NH]+ is strongly affected by relatively weak acids and proceeds at 5000 s−1 with an overpotential of 0.7 V. The ammonium-hydride [t-H1NH2]2+ is a faster catalyst with an estimated TOF of 58,000 s−1 and an overpotential of 0.5 V. PMID:23126330

  1. Functional Generalized Structured Component Analysis.

    PubMed

    Suk, Hye Won; Hwang, Heungsun

    2016-12-01

    An extension of Generalized Structured Component Analysis (GSCA), called Functional GSCA, is proposed to analyze functional data that are considered to arise from an underlying smooth curve varying over time or other continua. GSCA has been geared for the analysis of multivariate data. Accordingly, it cannot deal with functional data that often involve different measurement occasions across participants and a large number of measurement occasions that exceed the number of participants. Functional GSCA addresses these issues by integrating GSCA with spline basis function expansions that represent infinite-dimensional curves onto a finite-dimensional space. For parameter estimation, functional GSCA minimizes a penalized least squares criterion by using an alternating penalized least squares estimation algorithm. The usefulness of functional GSCA is illustrated with gait data.

  2. A proton current associated with sour taste: distribution and functional properties

    PubMed Central

    Bushman, Jeremy D.; Ye, Wenlei; Liman, Emily R.

    2015-01-01

    Sour taste is detected by taste receptor cells that respond to acids through yet poorly understood mechanisms. The cells that detect sour express the protein PKD2L1, which is not the sour receptor but nonetheless serves as a useful marker for sour cells. By use of mice in which the PKD2L1 promoter drives expression of yellow fluorescent protein, we previously reported that sour taste cells from circumvallate papillae in the posterior tongue express a proton current. To establish a correlation between this current and sour transduction, we examined its distribution by patch-clamp recording. We find that the current is present in PKD2L1-expressing taste cells from mouse circumvallate, foliate, and fungiform papillae but not in a variety of other cells, including spinal cord neurons that express PKD2L1. We describe biophysical properties of the current, including pH-dependent Zn2+ inhibition, lack of voltage-dependent gating, and activation at modest pH values (6.5) that elicit action potentials in isolated cells. Consistent with a channel that is constitutively open, the cytosol of sour taste cells is acidified. These data define a functional signature for the taste cell proton current and indicate that its expression is mostly restricted to the subset of taste cells that detect sour.—Bushman, J. D., Ye, W., Liman, E. R. A proton current associated with sour taste: distribution and functional properties. PMID:25857556

  3. Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR.

    PubMed

    Ohori, Yuka; Okazaki, Honoka; Watanabe, Satoru; Tochio, Naoya; Arai, Munehito; Kigawa, Takanori; Nishimura, Chiaki

    2014-03-01

    The HIV-1 p17 matrix protein is a multifunctional protein that interacts with other molecules including proteins and membranes. The dynamic structure between its folded and partially unfolded states can be critical for the recognition of interacting molecules. One of the most important roles of the p17 matrix protein is its localization to the plasma membrane with the Gag polyprotein. The myristyl group attached to the N-terminus on the p17 matrix protein functions as an anchor for binding to the plasma membrane. Biochemical studies revealed that two regions are important for its function: D14-L31 and V84-V88. Here, the dynamic structures of the p17 matrix protein were studied using NMR for relaxation and amide proton exchange experiments at the physiological pH of 7.0. The results revealed that the α12-loop, which includes the 14-31 region, was relatively flexible, and that helix 4, including the 84-88 region, was the most protected helix in this protein. However, the residues in the α34-loop near helix 4 had a low order parameter and high exchange rate of amide protons, indicating high flexibility. This region is probably flexible because this loop functions as a hinge for optimizing the interactions between helices 3 and 4. The C-terminal long region of K113-Y132 adopted a disordered structure. Furthermore, the C-terminal helix 5 appeared to be slightly destabilized due to the flexible C-terminal tail based on the order parameters. Thus, the dynamic structure of the p17 matrix protein may be related to its multiple functions.

  4. Ecosystem structure and function modeling

    USGS Publications Warehouse

    Humphries, H.C.; Baron, J.S.; Jensen, M.E.; Bourgeron, P.

    2001-01-01

    An important component of ecological assessments is the ability to predict and display changes in ecosystem structure and function over a variety of spatial and temporal scales. These changes can occur over short (less than 1 year) or long time frames (over 100 years). Models may emphasize structural responses (changes in species composition, growth forms, canopy height, amount of old growth, etc.) or functional responses (cycling of carbon, nutrients, and water). Both are needed to display changes in ecosystem components for use in robust ecological assessments. Structure and function models vary in the ecosystem components included, algorithms employed, level of detail, and spatial and temporal scales incorporated. They range from models that track individual organisms to models of broad-scale landscape changes. This chapter describes models appropriate for ecological assessments. The models selected for inclusion can be implemented in a spatial framework and for the most part have been run in more than one system.

  5. Selective CO2 Capture and High Proton Conductivity of a Functional Star-of-David Catenane Metal-Organic Framework.

    PubMed

    Huang, You-Gui; Wu, Shu-Qi; Deng, Wei-Hua; Xu, Gang; Hu, Fa-Lu; Hill, Jonathan P; Wei, Wei; Su, Sheng-Qun; Shrestha, Lok Kumar; Sato, Osamu; Wu, Ming-Yan; Hong, Mao-Chun; Ariga, Katsuhiko

    2017-09-28

    Network structures based on Star-of-David catenanes with multiple superior functionalities have been so far elusive, although numerous topologically interesting networks are synthesized. Here, a metal-organic framework featuring fused Star-of-David catenanes is reported. Two triangular metallacycles with opposite handedness are triply intertwined forming a Star-of-David catenane. Each catenane fuses with its six neighbors to generate a porous twofold intercatenated gyroid framework. The compound possesses exceptional stability and exhibits multiple functionalities including highly selective CO2 capture, high proton conductivity, and coexistence of slow magnetic relaxation and long-range ordering. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Investigation of the structure of light exotic nuclei by proton elastic scattering in inverse kinematics

    SciTech Connect

    Alkhazov, G. D.; Vorobyov, A. A.; Dobrovolsky, A. V. Inglessi, A. G.; Korolev, G. A.; Khanzadeev, A. V.

    2015-05-15

    In order to study the spatial structure of exotic nuclei, it was proposed at the Petersburg Nuclear Physics Institute (PNPI) to measure the differential cross section for small-angle proton elastic scattering in inverse kinematics. Several experiments in beams of 0.7-GeV/nucleon exotic nuclei were performed at the heavy-ion accelerator facility of GSI (Gesellschaft für Schwerionenforschung, Darmstadt, Germany) by using the IKAR ionization spectrometer developed at PNPI. The IKAR ionization chamber filled with hydrogen at a pressure of 10 bar served simultaneously as a target and as a recoil-proton detector, which measured the recoil-proton energy. The beam-particle scattering angle was also measured. The results obtained for the cross sections in question were analyzed on the basis of the Glauber-Sitenko theory using phenomenological nuclear-density distributions with two free parameters. Nuclear-matter distributions and root-mean-square radii were found for the nuclei under investigation. The size of the halo in the {sup 6}He, {sup 8}He, {sup 11}Li, and {sup 14}Be nuclei was determined among other things. Information about neutron distributions in nuclei was deduced by combining the data obtained here with the known values of the radii of proton distributions. A sizable neutron skin was revealed in the {sup 8}Li, {sup 9}Li, and {sup 12}Be nuclei.

  7. Changes in the hydration structure of imidazole upon protonation: Neutron scattering and molecular simulations

    NASA Astrophysics Data System (ADS)

    Duboué-Dijon, Elise; Mason, Philip E.; Fischer, Henry E.; Jungwirth, Pavel

    2017-05-01

    The imidazole motif is widely encountered in biomolecules, and its biological role, for instance, as a proton relay, is often linked to its ability to form hydrogen bonds with water molecules. The detailed characterization of the hydration pattern of imidazole and of its changes upon protonation is thus of high interest. Here, we combine neutron scattering experiments with force field simulations to provide an unprecedented characterization of the neutral and protonated imidazole solvation at the atomistic level. We show that neutron diffraction data can be used to assess the quality of the imidazole force field in molecular simulations. Simulations using the CHARMM general force field for imidazole are in excellent agreement with the experimental neutron scattering data and we use them to provide an atomic scale interpretation of the neutron scattering patterns. Upon protonation, we clearly identify the signature of the reorganization in the hydration pattern caused by the change from one H-bond donor and one H-bond acceptor group for imidazole to two H-bond donor groups for imidazolium. We also point the limits of the experiment, which are rather insensitive to details of the H-bond geometry at the deprotonated nitrogen of imidazole and further complement the description of the hydration structure with ab initio molecular dynamics simulations.

  8. Investigation of the structure of light exotic nuclei by proton elastic scattering in inverse kinematics

    NASA Astrophysics Data System (ADS)

    Alkhazov, G. D.; Vorobyov, A. A.; Dobrovolsky, A. V.; Inglessi, A. G.; Korolev, G. A.; Khanzadeev, A. V.

    2015-05-01

    In order to study the spatial structure of exotic nuclei, it was proposed at the Petersburg Nuclear Physics Institute (PNPI) to measure the differential cross section for small-angle proton elastic scattering in inverse kinematics. Several experiments in beams of 0.7-GeV/nucleon exotic nuclei were performed at the heavy-ion accelerator facility of GSI (Gesellschaft für Schwerionenforschung, Darmstadt, Germany) by using the IKAR ionization spectrometer developed at PNPI. The IKAR ionization chamber filled with hydrogen at a pressure of 10 bar served simultaneously as a target and as a recoil-proton detector, which measured the recoil-proton energy. The beam-particle scattering angle was also measured. The results obtained for the cross sections in question were analyzed on the basis of the Glauber-Sitenko theory using phenomenological nuclear-density distributions with two free parameters. Nuclear-matter distributions and root-mean-square radii were found for the nuclei under investigation. The size of the halo in the 6He, 8He, 11Li, and 14Be nuclei was determined among other things. Information about neutron distributions in nuclei was deduced by combining the data obtained here with the known values of the radii of proton distributions. A sizable neutron skin was revealed in the 8Li, 9Li, and 12Be nuclei.

  9. Excitation energies of a water-bridged twisted retinal structure in the bacteriorhodopsin proton pump: a theoretical investigation.

    PubMed

    Wolter, Tino; Welke, Kai; Phatak, Prasad; Bondar, Ana-Nicoleta; Elstner, Marcus

    2013-08-14

    The first proton transfer in the bacteriorhodopsin photocycle takes place during the L → M transition. Structural details of the pre proton transfer L intermediate have been investigated using experiments and computations. Here, we assess L-state structural models by performing hybrid quantum mechanical/molecular mechanical molecular dynamics and excitation energy calculations. The computations suggest that a water-bridged twisted retinal structure gives the closest agreement with the experimental L/bR shift in the excitation energy.

  10. The structure of rigid functions

    NASA Astrophysics Data System (ADS)

    Balka, Richárd; Elekes, Márton

    2008-09-01

    A function is called vertically rigid if graph(cf) is isometric to graph(f) for all c[not equal to]0. We prove Jankovic's conjecture by showing that a continuous function is vertically rigid if and only if it is of the form a+bx or a+bekx (). We answer the question of Cain, Clark and Rose by showing that there exists a Borel measurable vertically rigid function which is not of the above form. We discuss the Lebesgue and Baire measurable case, consider functions bounded on some interval and functions with at least one point of continuity. We also introduce horizontally rigid functions, and show that a certain structure theorem can be proved without assuming any regularity.

  11. Role of the bound-state wave function in capture-loss rates: Slow proton in an electron gas

    SciTech Connect

    Alducin, M.; Nagy, I.

    2003-07-01

    Capture and loss rates for protons moving in an electron gas are calculated using many-body perturbation theory. The role of the form of the bound-state wave function for weakly bound states around the proton is analyzed. We find significant differences (up to a factor of 2 higher) in the values of Auger capture and loss rates when using Hulthen-type instead of hydrogenic wave functions. Its relevance in stopping power is briefly discussed.

  12. Structure functions and parton distributions

    SciTech Connect

    Martin, A.D.; Stirling, W.J.; Roberts, R.G.

    1995-07-01

    The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed.

  13. Design summary of the magnet support structures for the proton storage ring injection line upgrade

    SciTech Connect

    Bernardin, J.D.; Ledford, J.E.; Smith, B.G.

    1997-05-01

    This report summarizes the technical engineering and design issues associated with the Proton Storage Ring (PSR) Injection Line upgrade of the Los Alamos Neutron Science Center (LANSCE). The main focus is on the engineering design calculations of several magnet support structures. The general procedure based upon a set number of design criteria is outlined, followed by a case-by-case summary of the engineering design analyses, reutilization or fabrication callouts and design safety factors.

  14. Test report: Vibration testing of the electron/proton spectrometer structural test unit

    NASA Technical Reports Server (NTRS)

    Vincent, D. L.

    1972-01-01

    The structural test unit of the electron-proton spectrometer was tested to a random vibration spectra and to a sinusoidal resonant search to comply with the requirements of a verification plan for the spectrometer. The test item consisted of mass simulated electronic and printed circuit boards mounted in a flight type electronic housing. The arrangement, center of gravity, and weight were as proposed for flight units.

  15. Transport properties of proton-exchange membranes: Effect of supercritical-fluid processing and chemical functionality

    NASA Astrophysics Data System (ADS)

    Pulido Ayazo

    conductivity, even with blends of these and blends with Nafion membranes. Other alternative studied was the functionalization of the membranes SIBS with metallic cations, which decreased the methanol permeability in the membranes containing the cations Mg2+, Zn2+ and Al 3+, while the proton conductivity was maintained more or less constant. The permeation of methanol vapor was investigated and the behavior through the membranes studied followed a pattern of Fick's Law, while the pattern shown by the permeation in liquid phase was non-Fickian.

  16. 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.

  17. 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

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

    SciTech Connect

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

    2008-11-01

    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 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 {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

  19. Investigating Proton Spin Structure: A Measurement of g2p at Low Q2

    NASA Astrophysics Data System (ADS)

    Cummings, Melissa A.

    The g2p collaboration performed the first measurement of the reaction vec{p}(vec{ e},e')X in the kinematic range 0.02 < Q2 < 0.2 GeV2 in the resonance region. Experiment E08-027 took place in Hall A at the Thomas Jefferson National Accelerator Facility from March-May of 2012. Data was taken with a longitudinally polarized electron beam, using an NH3 target polarized in both parallel and perpendicular configurations. Very preliminary results for g1p and g2p are shown in this thesis. To extract the spin structure functions, asymmetries are calculated from data taken with a 2.2 GeV electron beam and a 5 T target field, and combined with the Bosted model proton cross section. Preliminary dilution factors and preliminary radiative corrections are included in the asymmetry analysis. Sum rules and chiPT allow us to test the Burkhardtt-Cottingham (BC) sum rule and obtain the spin polarizability quantities gamma0 and deltaLT. The BC sum rule, valid for all values of Q2 says that the integral of g 2 over all Bjorken x vanishes. The very preliminary result presented here shows the contribution to the integral from the measured kinematic region. Although the contribution from the resonance region is not consistent with the expected result of zero, an extrapolation to high and low x must be included to test whether the BC sum rule is satisfied. The difficulty in chiPT calculations of gamma0 and deltaLT is how to include the resonance contributions, particularly the Delta-resonance, which dominates. Recent developments have found better agreement with neutron experimental results, however this is little proton data to compare with the calculations, particularly at low Q 2. The very preliminary results shown here do not show agreement with any of the current chiPT predictions. However, as this is only the contribution from the measured kinematic region, it is necessary to include the extrapolation outside the resonance region to draw a stronger conclusion. Further analysis is

  20. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    NASA Astrophysics Data System (ADS)

    Masson, Antoine; Williams, Evan R.; Rizzo, Thomas R.

    2015-09-01

    The effects of tagging protonated glycine with either He or between 1 and 14 H2 molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H2 molecule attached indicate that even a single H2 molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H2 molecules, but evidence for H2 attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H2 molecules. This results in a 55 cm-1 red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H2 molecules attached to this site are observed. These results are supported by theory, which indicates that H2 molecules can effectively break this weak hydrogen bond with three or more H2 molecules. These results indicate that large spectral shifts as a result of H2 molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H2 molecules can change the structure of the ion itself.

  1. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine.

    PubMed

    Masson, Antoine; Williams, Evan R; Rizzo, Thomas R

    2015-09-14

    The effects of tagging protonated glycine with either He or between 1 and 14 H2 molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H2 molecule attached indicate that even a single H2 molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H2 molecules, but evidence for H2 attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H2 molecules. This results in a 55 cm(-1) red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H2 molecules attached to this site are observed. These results are supported by theory, which indicates that H2 molecules can effectively break this weak hydrogen bond with three or more H2 molecules. These results indicate that large spectral shifts as a result of H2 molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H2 molecules can change the structure of the ion itself.

  2. Neutron structure of human carbonic anhydrase II: implications for proton transfer.

    PubMed

    Fisher, S Zoë; Kovalevsky, Andrey Y; Domsic, John F; Mustyakimov, Marat; McKenna, Robert; Silverman, David N; Langan, Paul A

    2010-01-26

    Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H-D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 A resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D(2)O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented.

  3. Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer†

    PubMed Central

    Fisher, S. Zoë; Kovalevsky, Andrey Y.; Domsic, John F.; Mustyakimov, Marat; McKenna, Robert; Silverman, David N.; Langan, Paul A.

    2010-01-01

    Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H–D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 Å resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D2O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented. PMID:20025241

  4. Functionality of the voltage-gated proton channel truncated in S4

    PubMed Central

    Sakata, Souhei; Kurokawa, Tatsuki; Nørholm, Morten H. H.; Takagi, Masahiro; Okochi, Yoshifumi; von Heijne, Gunnar; Okamura, Yasushi

    2010-01-01

    The voltage sensor domain (VSD) is the key module for voltage sensing in voltage-gated ion channels and voltage-sensing phosphatases. Structurally, both the VSD and the recently discovered voltage-gated proton channels (Hv channels) voltage sensor only protein (VSOP) and Hv1 contain four transmembrane segments. The fourth transmembrane segment (S4) of Hv channels contains three periodically aligned arginines (R1, R2, R3). It remains unknown where protons permeate or how voltage sensing is coupled to ion permeation in Hv channels. Here we report that Hv channels truncated just downstream of R2 in the S4 segment retain most channel properties. Two assays, site-directed cysteine-scanning using accessibility of maleimide-reagent as detected by Western blotting and insertion into dog pancreas microsomes, both showed that S4 inserts into the membrane, even if it is truncated between the R2 and R3 positions. These findings provide important clues to the molecular mechanism underlying voltage sensing and proton permeation in Hv channels. PMID:20018719

  5. Functionality of the voltage-gated proton channel truncated in S4.

    PubMed

    Sakata, Souhei; Kurokawa, Tatsuki; Nørholm, Morten H H; Takagi, Masahiro; Okochi, Yoshifumi; von Heijne, Gunnar; Okamura, Yasushi

    2010-02-02

    The voltage sensor domain (VSD) is the key module for voltage sensing in voltage-gated ion channels and voltage-sensing phosphatases. Structurally, both the VSD and the recently discovered voltage-gated proton channels (Hv channels) voltage sensor only protein (VSOP) and Hv1 contain four transmembrane segments. The fourth transmembrane segment (S4) of Hv channels contains three periodically aligned arginines (R1, R2, R3). It remains unknown where protons permeate or how voltage sensing is coupled to ion permeation in Hv channels. Here we report that Hv channels truncated just downstream of R2 in the S4 segment retain most channel properties. Two assays, site-directed cysteine-scanning using accessibility of maleimide-reagent as detected by Western blotting and insertion into dog pancreas microsomes, both showed that S4 inserts into the membrane, even if it is truncated between the R2 and R3 positions. These findings provide important clues to the molecular mechanism underlying voltage sensing and proton permeation in Hv channels.

  6. Measuring Form Factors and Structure Functions with CLAS

    SciTech Connect

    G.P. Gilfoyle

    2007-09-10

    The physics program at the Thomas Jefferson National Accelerator Facility includes a strong effort to measure form factors and structure functions to probe the structure of hadronic matter, reveal the nature of confinement, and develop an understanding of atomic nuclei using quark-gluon degrees of freedom. The CLAS detector is a large acceptance device occupying one of the end stations. We discuss here two programs that use CLAS; measuring the magnetic form factor of the neutron and the virtual photon asymmetry of the proton. The form factor has been measured with unprecedented kinematic coverage and precision up to Q2=4.7 GeV2 and is consistent within 5%-10% of the dipole parameterization. The proton virtual photon asymmetry has been measured across a wide range in Bjorken x. The data exceed the SU(6)-symmetric quark prediction and show evidence of a smooth approach to the scaling limit prescribed by perturbative QCD.

  7. Understanding structure, function, and mutations in the mitochondrial ATP synthase

    PubMed Central

    Xu, Ting; Pagadala, Vijayakanth; Mueller, David M.

    2015-01-01

    The mitochondrial ATP synthase is a multimeric enzyme complex with an overall molecular weight of about 600,000 Da. The ATP synthase is a molecular motor composed of two separable parts: F1 and Fo. The F1 portion contains the catalytic sites for ATP synthesis and protrudes into the mitochondrial matrix. Fo forms a proton turbine that is embedded in the inner membrane and connected to the rotor of F1. The flux of protons flowing down a potential gradient powers the rotation of the rotor driving the synthesis of ATP. Thus, the flow of protons though Fo is coupled to the synthesis of ATP. This review will discuss the structure/function relationship in the ATP synthase as determined by biochemical, crystallographic, and genetic studies. An emphasis will be placed on linking the structure/function relationship with understanding how disease causing mutations or putative single nucleotide polymorphisms (SNPs) in genes encoding the subunits of the ATP synthase, will affect the function of the enzyme and the health of the individual. The review will start by summarizing the current understanding of the subunit composition of the enzyme and the role of the subunits followed by a discussion on known mutations and their effect on the activity of the ATP synthase. The review will conclude with a summary of mutations in genes encoding subunits of the ATP synthase that are known to be responsible for human disease, and a brief discussion on SNPs. PMID:25938092

  8. Fourth dimension of the nucleon structure: Spacetime analysis of the timelike electromagnetic proton form factors

    NASA Astrophysics Data System (ADS)

    Bianconi, Andrea; Tomasi-Gustafsson, Egle

    2017-01-01

    As is well known, spacelike proton form factors expressed in the Breit frame may be interpreted as the Fourier transform of static space distributions of electric charge and current. In particular, the electric form factor is simply the Fourier transform of the charge distribution F (q ) =∫ei q ⃗.r ⃗ρ (r ) d3r . We do not have an intuitive interpretation of the same level of simplicity for the proton timelike form factor appearing in the reactions e+e-↔p ¯p . However, one may suggest that, in the center-of-mass frame, where qμxμ=q t , a timelike electric form factor is the Fourier transform F (q ) =∫ei q tR (t ) d t of a function R (t ) expressing how the electric properties of the forming (or annihilating) proton-antiproton pair evolve in time. Here we analyze in depth this idea and show that the functions ρ (r ) and R (t ) can be formally written as the time and space integrals of a unique correlation function depending on both time and space coordinates.

  9. Structural Plasticity and Hippocampal Function

    PubMed Central

    Leuner, Benedetta; Gould, Elizabeth

    2010-01-01

    The hippocampus is a region of the mammalian brain that shows an impressive capacity for structural reorganization. Preexisting neural circuits undergo modifications in dendritic complexity and synapse number, and entirely novel neural connections are formed through the process of neurogenesis. These types of structural change were once thought to be restricted to development. However, it is now generally accepted that the hippocampus remains structurally plastic throughout life. This article reviews structural plasticity in the hippocampus over the lifespan, including how it is investigated experimentally. The modulation of structural plasticity by various experiential factors as well as the possible role it may have in hippocampal functions such as learning and memory, anxiety, and stress regulation are also considered. Although significant progress has been made in many of these areas, we highlight some of the outstanding issues that remain. PMID:19575621

  10. Evaluation of ion mobility spectroscopy for determining charge-solvated versus salt-bridge structures of protonated trimers.

    PubMed

    Wong, Richard L; Williams, Evan R; Counterman, Anne E; Clemmer, David E

    2005-07-01

    The cross sections of five different protonated trimers consisting of two base molecules and trifluoroacetic acid were measured by using ion mobility spectrometry. The gas-phase basicities of these five base molecules span an 8-kcal/mol range. These cross sections are compared with those determined from candidate low-energy salt-bridge and charge-solvated structures identified by using molecular mechanics calculations using three different force fields: AMBER*, MMFF, and CHARMm. With AMBER*, the charge-solvated structures are all globular and the salt-bridge structures are all linear, whereas with CHARMm, these two forms of the protonated trimers can adopt either shape. Globular structures have smaller cross sections than linear structures. Conclusions about the structure of these protonated trimers are highly dependent on the force field used to generate low-energy candidate structures. With AMBER*, all of the trimers are consistent with salt-bridge structures, whereas with MMFF the measured cross sections are more consistent with charge-solvated structures, although the assignments are ambiguous for two of the protonated trimers. Conclusions based on structures generated by using CHARMm suggest a change in structure from charge-solvated to salt-bridge structures with increasing gas-phase basicity of the constituent bases, a result that is most consistent with structural conclusions based on blackbody infrared radiative dissociation experiments for these protonated trimers and theoretical calculations on the uncharged base-acid pairs.

  11. Functional analysis of amino acids of the Na+/H+ exchanger that are important for proton translocation.

    PubMed

    Wiebe, Christine A; Rieder, Carmen; Young, Paul G; Dibrov, Pavel; Fliegel, Larry

    2003-12-01

    The Na+/H+ exchanger is an integral membrane protein found in the plasma membrane of eukaryotic and prokaryotic cells. In eukaryotes it functions to exchange one proton for a sodium ion. In mammals it removes intracellular protons while in plants and fungal cells the plasma membrane form removes intracellular sodium in exchange for extracellular protons. In this study we used the Na+/H+ exchanger of Schizosaccharomyces pombe (Sod2) as a model system to study amino acids critical for activity of the protein. Twelve mutant forms of the Na+/H+ exchanger were examined for their ability to translocate protons as assessed by a Cytosensor microphysiometer. Mutation of the amino acid Histidine 367 resulted in defective proton translocation. The acidic residues Asp145, Asp178, Asp266 and Asp267 were important in the proton translocation activity of the Na+/H+ exchanger. Mutation of amino acids His98, His233 and Asp241 did not significantly impair proton translocation by the Na+/H+ exchanger. These results confirm that polar amino acids are important in proton flux activity of Na+/H+ exchangers.

  12. Structure and Function of Wood

    Treesearch

    Alex C. Wiedenhoeft

    2012-01-01

    Wood is a complex biological structure, a composite of many cell types and chemistries acting together to serve the needs of living plant. Attempting to understand wood inthe context of wood technology, we have often overlooked the basic fact that wood evolved over the course of millions of years to serve three main functions in plants-conduction of water from the...

  13. Constructing Ionic Liquid-Filled Proton Transfer Channels within Nanocomposite Membrane by Using Functionalized Graphene Oxide.

    PubMed

    Wu, Wenjia; Li, Yifan; Chen, Pingping; Liu, Jindun; Wang, Jingtao; Zhang, Haoqin

    2016-01-13

    Herein, nanocomposite membranes are fabricated based on functionalized graphene oxides (FGOs) and sulfonated poly(ether ether ketone) (SPEEK), followed by being impregnated with imidazole-type ionic liquid (IL). The functional groups (acidic group or basic group) on FGOs generate strong interfacial interactions with SPEEK chains and then adjust their motion and stacking. As a result, the nanocomposite membranes possess tunable interfacial domains as determined by its free volume characteristic, which provides regulated location for IL storage. The stored ILs act as hopping sites for water-free proton conduction along the FGO-constructed interfacial channels. The microstructure at SPEEK-FGO interface governs the IL uptake and distribution in nanocomposite membrane. Different from GO and vinyl imidazole functionalized GO (VGO), the presence of acidic (-SO3H) groups confers the p-styrenesulfonic acid functionalized GO (SGO) incorporated nanocomposite membrane loose interface and strong electrostatic attraction with imidazole-type IL, imparting an enhanced IL uptake and anhydrous proton conductivity. Nanocomposite membrane containing 7.5% SGO attains the maximum IL uptake of 73.7% and hence the anhydrous conductivity of 21.9 mS cm(-1) at 150 °C, more than 30 times that of SPEEK control membrane (0.69 mS cm(-1)). In addition, SGOs generate electrostatic attractions to the ILs confined within SGO-SPEEK interface, affording the nanocomposite membrane enhanced IL retention ability.

  14. Spectroscopic and structural study of proton and halide ion cooperative binding to gfp.

    PubMed

    Arosio, Daniele; Garau, Gianpiero; Ricci, Fernanda; Marchetti, Laura; Bizzarri, Ranieri; Nifosì, Riccardo; Beltram, Fabio

    2007-07-01

    This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E(2)GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5-10, of a single fully protonated E(2)GFP.halogen complex. To resolve the structural determinants of E(2)GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I(-), Br(-), and Cl(-) bound E(2)GFP. Remarkably the first high-resolution (1.4 A) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 A) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E(2)GFP.halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed.

  15. Spectroscopic and Structural Study of Proton and Halide Ion Cooperative Binding to GFP

    PubMed Central

    Arosio, Daniele; Garau, Gianpiero; Ricci, Fernanda; Marchetti, Laura; Bizzarri, Ranieri; Nifosì, Riccardo; Beltram, Fabio

    2007-01-01

    This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E2GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E2GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5–10, of a single fully protonated E2GFP·halogen complex. To resolve the structural determinants of E2GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I−, Br−, and Cl− bound E2GFP. Remarkably the first high-resolution (1.4 Å) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 Å) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E2GFP·halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed. PMID:17434942

  16. XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.

    PubMed

    Thomaston, Jessica L; Woldeyes, Rahel A; Nakane, Takanori; Yamashita, Ayumi; Tanaka, Tomoyuki; Koiwai, Kotaro; Brewster, Aaron S; Barad, Benjamin A; Chen, Yujie; Lemmin, Thomas; Uervirojnangkoorn, Monarin; Arima, Toshi; Kobayashi, Jun; Masuda, Tetsuya; Suzuki, Mamoru; Sugahara, Michihiro; Sauter, Nicholas K; Tanaka, Rie; Nureki, Osamu; Tono, Kensuke; Joti, Yasumasa; Nango, Eriko; Iwata, So; Yumoto, Fumiaki; Fraser, James S; DeGrado, William F

    2017-08-23

    The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 Å using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

  17. Measurement of Proton Structure and Parton Density Functions from HERA

    SciTech Connect

    Raicevic, Natasa

    2010-01-21

    A preliminary result is reported of the charged current and neutral current inclusive cross sections from e{sup +}p and e{sup -}p scattering obtained from a combination of published measurements from H1 and ZEUS. Taking into account the systematic error correlations in a coherent approach, a reduction of experimental uncertainties for combined results is achieved compared to the separate results of the H1 and ZEUS experiments. The combined results are used as input for a next-to-leading order (NLO) QCD parton distribution determination.

  18. The Neutron Structure of Urate Oxidase Resolves a Long-Standing Mechanistic Conundrum and Reveals Unexpected Changes in Protonation

    PubMed Central

    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. PMID:24466188

  19. X-ray crystal structure of voltage-gated proton channel.

    PubMed

    Takeshita, Kohei; Sakata, Souhei; Yamashita, Eiki; Fujiwara, Yuichiro; Kawanabe, Akira; Kurokawa, Tatsuki; Okochi, Yoshifumi; Matsuda, Makoto; Narita, Hirotaka; Okamura, Yasushi; Nakagawa, Atsushi

    2014-04-01

    The voltage-gated proton channel Hv1 (or VSOP) has a voltage-sensor domain (VSD) with dual roles of voltage sensing and proton permeation. Its gating is sensitive to pH and Zn(2+). Here we present a crystal structure of mouse Hv1 in the resting state at 3.45-Å resolution. The structure showed a 'closed umbrella' shape with a long helix consisting of the cytoplasmic coiled coil and the voltage-sensing helix, S4, and featured a wide inner-accessible vestibule. Two out of three arginines in S4 were located below the phenylalanine constituting the gating charge-transfer center. The extracellular region of each protomer coordinated a Zn(2+), thus suggesting that Zn(2+) stabilizes the resting state of Hv1 by competing for acidic residues that otherwise form salt bridges with voltage-sensing positive charges on S4. These findings provide a platform for understanding the general principles of voltage sensing and proton permeation.

  20. 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.

  1. Excitation Functions and Yields for RE-186G Production by Proton Cyclotron

    NASA Astrophysics Data System (ADS)

    Persico, E.; Bonardi, M. L.; Groppi, F.; Zona, C.; Canella, L.; Manenti, S.; Marchetti, M.; Abbas, K.; Holzwarth, U.; Simonelli, F.

    2008-06-01

    Excitation functions and yields for the 181-186Re radionuclides were measured by the activation method on natural tungsten foils for the proton energies up to 17 MeV. A new data sets have been given for the investigated radionuclides. These results are compared both with the experimental literature values and the ones calculated by EMPIRE II code (version 2.19). In particular, the attention is focused on Re-186g due to its remarkable applications in Nuclear Medicine for metabolic radiotherapy of tumours.

  2. Spherical proton-neutron structure of isomeric states in {sup 128}Cd

    SciTech Connect

    Caceres, L.; Gorska, M.; Grawe, H.; Sieja, K.; Geissel, H.; Gerl, J.; Kojouharov, I.; Kurz, N.; Montes, F.; Martinez-Pinedo, G.; Prokopowicz, W.; Schaffner, H.; Tashenov, S.; Wollersheim, H. J.; Jungclaus, A.; Pfuetzner, M.; Werner-Malento, E.; Nowacki, F.

    2009-01-15

    The {gamma}-ray decay of isomeric states in the even-even nucleus {sup 128}Cd has been observed. The nucleus of interest was produced both by the fragmentation of {sup 136}Xe and the fission of {sup 238}U primary beams. The level scheme was unambiguously constructed based on {gamma}{gamma} coincidence relations in conjunction with detailed lifetime analysis employed for the first time on this nucleus. Large-scale shell-model calculations, without consideration of excitations across the N=82 shell closure, were performed and provide a consistent description of the experimental level scheme. The structure of the isomeric states and their decays exhibit coexistence of proton, neutron, and strongly mixed configurations due to {pi}{nu} interaction in overlapping orbitals for both proton and neutron holes.

  3. Spherical proton-neutron structure of isomeric states in Cd128

    NASA Astrophysics Data System (ADS)

    Cáceres, L.; Górska, M.; Jungclaus, A.; Pfützner, M.; Grawe, H.; Nowacki, F.; Sieja, K.; Pietri, S.; Rudolph, D.; Podolyák, Zs.; Regan, P. H.; Werner-Malento, E.; Detistov, P.; Lalkovski, S.; Modamio, V.; Walker, J.; Andgren, K.; Bednarczyk, P.; Benlliure, J.; Benzoni, G.; Bruce, A. M.; Casarejos, E.; Cederwall, B.; Crespi, F. C. L.; Doornenbal, P.; Geissel, H.; Gerl, J.; Grebosz, J.; Hadinia, B.; Hellström, M.; Hoischen, R.; Ilie, G.; Khaplanov, A.; Kmiecik, M.; Kojouharov, I.; Kumar, R.; Kurz, N.; Maj, A.; Mandal, S.; Montes, F.; Martínez-Pinedo, G.; Myalski, S.; Prokopowicz, W.; Schaffner, H.; Simpson, G. S.; Steer, S. J.; Tashenov, S.; Wieland, O.; Wollersheim, H. J.

    2009-01-01

    The γ-ray decay of isomeric states in the even-even nucleus Cd128 has been observed. The nucleus of interest was produced both by the fragmentation of Xe136 and the fission of U238 primary beams. The level scheme was unambiguously constructed based on γγ coincidence relations in conjunction with detailed lifetime analysis employed for the first time on this nucleus. Large-scale shell-model calculations, without consideration of excitations across the N=82 shell closure, were performed and provide a consistent description of the experimental level scheme. The structure of the isomeric states and their decays exhibit coexistence of proton, neutron, and strongly mixed configurations due to πν interaction in overlapping orbitals for both proton and neutron holes.

  4. Optimization of current modulation function for proton spread-out Bragg peak fields

    SciTech Connect

    Lu, H.-M.; Kooy, Hanne

    2006-05-15

    Proton treatments with spread-out Bragg peak (SOBP) fields often use a rotating modulation wheel of varying thickness to modulate the pristine Bragg peak in depth and intensity. The technique of modulating also the beam current independently over the wheel rotation provides an additional control over the intensities of the pulled-back Bragg peaks. As a result, a single wheel can be used over a large range of energies and SOBP parameters and field-specific wheels are no longer necessary. An essential task in commissioning a particular treatment depth is the determination of this current modulation function. We have developed a method for the optimization of the current modulation function. The basic idea is to treat the entire beam nozzle, housing the various beam scattering and modulating components, as a whole and to characterize its effect as a transformation from a modulating beam current to a depth-dose distribution. While this transformation is difficult to calculate theoretically due to the complex scattering paths in the nozzle and the phantom, it can, however, be determined by time-resolved dose measurements. Using this transformation, we can calculate SOBP depth-dose distributions for any current modulation function and optimize it by a simple numerical optimization. We have applied the new method to a number of proton beams with satisfactory results.

  5. Structure and Function of AApeptides

    PubMed Central

    Bolarinwa, Olapeju; Nimmagadda, Alekhya; Su, Ma; Cai, Jianfeng

    2017-01-01

    The intrinsic drawbacks encountered in bioactive peptides in chemical biology and biomedical sciences have diverted research efforts to the development of sequence-specific peptidomimetics that are capable of mimicking the structure and function of peptides and proteins. Modifications in the backbone and/or the side chain of peptides have been explored to develop biomimetic molecular probes or drug leads for biologically important targets. To expand the family of oligomeric peptidomimetics to facilitate their further application, we recently developed a new class of peptidomimetics, AApeptides based on a chiral peptide nucleic acid backbone. AApeptides are resistant to proteolytic degradation and amenable to enormous chemical diversification. Moreover, they could mimic the primary structure of peptides and also fold into discrete secondary structure such as helices and turn-like structures. Furthermore, they have started to show promise in applications in material and biomedical sciences. Herein, we highlight the structural design and some function of AApeptides and present our perspective on their future development. PMID:28029249

  6. Density functional investigation of photo induced Intramolecular Proton Transfer (IPT) in Indole-7-carboxaldehyde and its experimental verification

    NASA Astrophysics Data System (ADS)

    Singla, Nidhi; Chowdhury, Papia

    2013-08-01

    A detail theoretical study has been performed using Density functional theory (DFT) and Time dependent DFT (TDDFT) to investigate the Intramolecular Proton Transfer (IPT) mechanism in Indole-7-carboxaldehyde (I7C) from its normal (I*) to zwitterion (II*) form. B3LYP/6-311++G (d, p) basis set has been used to obtain structural parameters and relative energies in the ground state (S0) and excited state (S1). Atoms in Molecules (AIMs), Mulliken and Natural bond orbitals (NBOs) analysis proves the existence of intramolecular hydrogen bonding (IHB). The electron density (ρ) at Bond critical points (BCPs) on a hydrogen bridge (N15sbnd H12⋯O18) certify IHB and possibility of IPT from acidic (N15sbnd H12) to basic (lbond2 C16dbnd O18) group and creation of II*. Transition state (TS) with dual minima in the Potential energy surface (PES) confirms the I* → TS → II* transition due to excited state Intramolecular Proton Transfer (ESIPT). Photo-physical pathway from I* → II* agrees well with computed/experimental emission peaks.

  7. Spectroscopic study on the structural isomers of 7-azaindole(ethanol)n (n=1-3) and multiple-proton transfer reactions in the gas phase

    NASA Astrophysics Data System (ADS)

    Sakota, Kenji; Komure, Noriyuki; Ishikawa, Wataru; Sekiya, Hiroshi

    2009-06-01

    The resonance-enhanced two-photon ionization (RE2PI) and laser-induced fluorescence excitation spectra were recorded for the S1-S0(ππ ∗) region of the 7-azaindole(ethanol)n (n =1-3) [7AI(EtOH)n (n =1-3)] clusters in the gas phase to investigate the geometrical structures and the multiple-proton/hydrogen atom transfer reaction dynamics. Four and two structural isomers were identified for 7AI(EtOH)2 and 7AI(EtOH)3, respectively. Density functional theory calculations at the B3LYP/6-31++G∗∗/6-31G∗ level predicted four different conformations of the ethyl group for 7AI(EtOH)2, in good agreement with the observation of the four structural isomers in the RE2PI spectra. Visible fluorescence from the tautomeric forms was observed in the S1 states for all isomers of 7AI(EtOH)2, but no sign of double-proton/hydrogen atom transfer and quadruple-proton/hydrogen atom transfer has been obtained in the electronic spectra of 7AI(EtOH)1 and 7AI(EtOH)3, respectively. These results suggest that the multiple-proton transfer reaction is cluster-size selective, and the triple-proton/hydrogen atom transfer potential is dominated by the cyclic hydrogen-bonded network in 7AI(EtOH)2. The excitation of the in-phase intermolecular stretching vibration prominently enhances the excited-state triple-proton/hydrogen atom transfer reaction.

  8. Structural/Functional Role of Chloride in Photosystem II

    PubMed Central

    Rivalta, Ivan; Amin, Muhamed; Luber, Sandra; Vassiliev, Serguei; Pokhrel, Ravi; Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren; Kamiya, Nobuo; Bruce, Doug; Brudvig, Gary W.; Gunner, M. R.; Batista, Victor S.

    2011-01-01

    Chloride binding in photosystem II (PSII) is essential for photosynthetic water oxidation. However, the functional roles of chloride and possible binding sites, during oxygen evolution, remain controversial. This paper examines the functions of chloride based on its binding site revealed in the X-ray crystal structure of PSII at 1.9 Å resolution. We find that chloride depletion induces formation of a salt-bridge between D2-K317 and D1-D61 that could suppress proton transfer to the lumen. PMID:21678923

  9. [Protein phosphatases: structure and function].

    PubMed

    Bulanova, E G; Budagian, V M

    1994-01-01

    The process of protein and enzyme systems phosphorylation is necessary for cell growth, differentiation and preparation for division and mitosis. The conformation changes of protein as a result of phosphorylation lead to increased enzyme activity and enhanced affinity to substrates. A large group of enzymes--protein kinases--is responsible for phosphorylation process in cell, which are divided into tyrosine- and serine-threonine-kinases depending on their ability to phosphorylate appropriate amino acid residues. In this review has been considered the functional importance and structure of protein phosphatases--enzymes, which are functional antagonists of protein kinases.

  10. Unprecedented χ isomers of single-side triol-functionalized Anderson polyoxometalates and their proton-controlled isomer transformation.

    PubMed

    Zhang, Jiangwei; Liu, Zhenhua; Huang, Yichao; zhang, Jin; Hao, Jian; Wei, Yongge

    2015-06-04

    The μ2-O atom in Anderson polyoxometalates was regioselectively activated by the introduction of protons, which, upon functionalization with triol ligands, could afford a series of unique χ isomers of the organically-derived Anderson cluster {[RCC(CH2O)3]MMo6O18(OH)3}(3-). Herein proton-controlled isomer transformation between the δ and χ isomer was observed by using the fingerprint region in the IR spectra and (13)C NMR spectra.

  11. 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

  12. A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

    SciTech Connect

    He, Bo; Dai, Jing; Zherebetskyy, Danylo; Chen, Teresa L.; Zhang, Benjamin A.; Teat, Simon J.; Zhang, Qichun; Wang, Linwang; Liu, Yi

    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, 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.

  13. Structure and functions of angiotensinogen

    PubMed Central

    Lu, Hong; Cassis, Lisa A; Kooi, Craig W Vander; Daugherty, Alan

    2016-01-01

    Angiotensinogen (AGT) is the sole precursor of all angiotensin peptides. Although AGT is generally considered as a passive substrate of the renin–angiotensin system, there is accumulating evidence that the regulation and functions of AGT are intricate. Understanding the diversity of AGT properties has been enhanced by protein structural analysis and animal studies. In addition to whole-body genetic deletion, AGT can be regulated in vivo by cell-specific procedures, adeno-associated viral approaches and antisense oligonucleotides. Indeed, the availability of these multiple manipulations of AGT in vivo has provided new insights into the multifaceted roles of AGT. In this review, the combination of structural and functional studies is highlighted to focus on the increasing recognition that AGT exerts effects beyond being a sole provider of angiotensin peptides. PMID:26888118

  14. Structural insights into Elongator function.

    PubMed

    Glatt, Sebastian; Müller, Christoph W

    2013-04-01

    The eukaryotic Elongator complex was initially identified in yeast as a RNA polymerase II (Pol II) associated transcription elongation factor, although there is accumulating evidence that its main cellular function is the specific modification of uridines at the wobble base position of tRNAs. Elongator complex is built up by six highly conserved subunits and was shown to be involved in a variety of different cellular activities. Here, we summarize structural and functional information on individual Elongator subunits or subcomplexes. On the basis of homology models of the Elp1, Elp2 and Elp3 subunits and the crystal structure of the Elp456 subcomplex, the role of each subunit in Elongator complex assembly and catalytic activity is discussed. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Structure and function of wood

    Treesearch

    Alex Wiedenhoeft

    2010-01-01

    Wood is a complex biological structure, a composite of many chemistries and cell types acting together to serve the needs of a living plant. Attempting to understand wood in the context of wood technology, we have often overlooked the key and basic fact that wood evolved over the course of millions of years to serve three main functions in plants― conduction of water...

  16. Structure and Function of Glucansucrases

    NASA Astrophysics Data System (ADS)

    Dijkstra, B. W.; Vujičić-Žagar, A.

    2008-03-01

    Glucansucrases are relatively large (~160 kDa) extracellular enzymes produced by lactic acid bacteria. Using sucrose as a substrate they synthesize high molecular mass glucose polymers, called α-glucans, which allow the bacteria to adhere to surfaces and create a biofilm. The glucan polymers are of importance for the food and dairy industry as thickening and jellying agents. An overview is given of the current insights into the structure and functioning of these and related enzymes.

  17. Functional and mechanistic roles of the human proton-coupled folate transporter transmembrane domain 6–7 linker

    PubMed Central

    Wilson, Mike R.; Hou, Zhanjun; Wilson, Lucas J.; Ye, Jun; Matherly, Larry H.

    2016-01-01

    The proton-coupled folate transporter (PCFT; SLC46A1) is a folate–proton symporter expressed in solid tumors and is used for tumor-targeted delivery of cytotoxic antifolates. Topology modeling suggests that the PCFT secondary structure includes 12 transmembrane domains (TMDs) with TMDs 6 and 7 linked by an intracellular loop (positions 236–265) including His247, implicated as functionally important. Single-cysteine (Cys) mutants were inserted from positions 241 to 251 in Cys-less PCFT and mutant proteins were expressed in PCFT-null (R1–11) HeLa cells; none were reactive with 2-aminoethyl methanethiosulfonate biotin, suggesting that the TMD6–7 loop is intracellular. Twenty-nine single alanine mutants spanning the entire TMD6–7 loop were expressed in R1–11 cells; activity was generally preserved, with the exception of the 247, 250, and 251 mutants, partly due to decreased surface expression. Coexpression of PCFT TMD1–6 and TMD7–12 half-molecules in R1–11 cells partially restored transport activity, although removal of residues 252–265 from TMD7–12 abolished transport. Chimeric proteins, including a nonhomologous sequence from a thiamine transporter (ThTr1) inserted into the PCFT TMD6–7 loop (positions 236–250 or 251–265), were active, although replacement of the entire loop with the ThTr1 sequence resulted in substantial loss of activity. Amino acid replacements (Ala, Arg, His, Gln, and Glu) or deletions at position 247 in wild-type and PCFT–ThTr1 chimeras resulted in differential effects on transport. Collectively, our findings suggest that the PCFT TMD6–7 connecting loop confers protein stability and may serve a unique functional role that depends on secondary structure rather than particular sequence elements. PMID:27514717

  18. How well do we know the neutron structure function?

    SciTech Connect

    J. Arrington, J. G. Rubin, W. Melnitchouk

    2012-06-01

    We present a detailed analysis of the uncertainty in the neutron F{sub 2}n structure function extracted from inclusive deuteron and proton deep-inelastic scattering data. The analysis includes experimental uncertainties as well as uncertainties associated with the deuteron wave function, nuclear smearing, and nucleon off-shell corrections. Consistently accounting for the Q{sup 2} dependence of the data and calculations, and restricting the nuclear corrections to microscopic models of the deuteron, we find significantly smaller uncertainty in the extracted F{sub 2}n/F{sub 2}p ratio than in previous analyses. In addition to yielding an improved extraction of the neutron structure function, this analysis also provides an important baseline that will allow future, model-independent extractions of neutron structure to be used to examine nuclear medium effects in the the deuteron.

  19. Characteristics of velocity distribution functions and entry mechanisms of protons in the near-lunar wake from SWIM/SARA on Chandrayaan-1

    NASA Astrophysics Data System (ADS)

    Dhanya, M. B.; Barabash, Stas; Wieser, Martin; Holmström, Mats; Bhardwaj, Anil; Wurz, Peter; Alok, Abhinaw; Futaana, Yoshifumi

    2016-07-01

    Moon is an airless body with no global magnetic field, although regions of crustal magnetic fields known as magnetic anomalies exist on Moon. Solar wind, the magnetized plasma flow from the Sun, continuously impinges on Moon. Due to the high absorption of solar wind plasma on the lunar dayside, a large scale wake structure is formed downstream of the Moon. However, recent in-situ observations have revealed the presence of protons in the near-lunar wake (100 km to 200 km from the surface). The source of these protons have been found to be the solar wind that enter the wake either directly or after interaction with the lunar surface or with the magnetic anomalies. Using the entire data from the SWIM sensor, which was an ion-mass analyzer, of the SARA experiment onboard Chandrayaan-1, the characteristics of velocity distribution of these protons were investigated to understand the entry mechanisms to near lunar wake. The velocity distribution functions were computed in the two dimensional velocity space, namely in the directions parallel and perpendicular to the IMF (v_allel and v_perp) in the solar wind rest frame. Several proton populations were identified from the velocity distribution and their possible entry mechanism were inferred based on the characteristics of the velocity distribution. These entry mechanisms include (i) diffusion of solar wind protons into the wake along IMF, (ii) the solar wind protons with finite gyro-radii that are aided by the wake boundary electric field, (iii) solar wind protons with gyro-radii larger than lunar radii from the tail of the solar wind velocity distribution, and (iv) scattering of solar wind protons from the dayside lunar surface or from magnetic anomalies. In order to gain more insight into the entry mechanisms associated with different populations, the trajectories of the protons were computed backward in time (backtracing) for each of these populations. For most of the populations, the source mechanism obtained from

  20. A counterintuitive structural effect of metal-metal bond protonation and its electronic underpinnings.

    PubMed

    Phillips, Andrew D; Ienco, Andrea; Reinhold, Joachim; Böttcher, Hans-Christian; Mealli, Carlo

    2006-06-02

    Protonation across the metal-metal bond in the complexes [(CO)(2)M(mu-dppm)(mu-PtBu(2))(mu-H)M(CO)(2)] (M=Fe or Ru, dppm=Ph(2)PCH(2)PPh(2)) induces M-M bond shortening of up to about 0.05 A. DFT calculations on simplified iron models reproduce this trend well. Conversely, the computations show that the M-M distance in the dimer [{Cp*Ir(CO)}(2)] lengthens with two consecutive protonations, but there are no crystal structure determinations to highlight the effects on the Ir-Ir bond. DFT calculations and the analogous cobalt system confirm that the transformation of a two-electron, two-center (2e-2c) bond into a 2e-3c bond is accompanied by the predicted elongation. An MO analysis indicated similar nature and evolution of the M-M bonding these cases. In particular, the HOMOs of the mono-hydrido cations [Cp(CO)M(mu-H)M(CO)Cp](+) (M=Ir, Co) have evident M-M bent-bond character, and hence subsequent protonation invariably causes a decrease in the bond index. The Fe(2) and Co(2) systems have also been analyzed with the quantum theory of atoms in molecules (QTAIM) method, but in no case was an M-M bond critical point located unless an artificially shorter M-M distance was imposed. However, the trends for the atoms-in-molecules (AIM) bond delocalization indexes delta(M-M) confirm the overall M-M bond weakening on protonation. In conclusion, all the computational results for the iron system indicate that the paradigm of a direct correlation between bond strength and distance is not always applicable. This is attributable to a very flat potential energy surface and various competing effects imposed by the bridging ligands.

  1. The potential utility of predicted one bond carbon-proton coupling constants in the structure elucidation of small organic molecules by NMR spectroscopy.

    PubMed

    Venkata, Chandrasekhar; Forster, Mark J; Howe, Peter W A; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation.

  2. The Potential Utility of Predicted One Bond Carbon-Proton Coupling Constants in the Structure Elucidation of Small Organic Molecules by NMR Spectroscopy

    PubMed Central

    Venkata, Chandrasekhar; Forster, Mark J.; Howe, Peter W. A.; Steinbeck, Christoph

    2014-01-01

    NMR spectroscopy is the most popular technique used for structure elucidation of small organic molecules in solution, but incorrect structures are regularly reported. One-bond proton-carbon J-couplings provide additional information about chemical structure because they are determined by different features of molecular structure than are proton and carbon chemical shifts. However, these couplings are not routinely used to validate proposed structures because few software tools exist to predict them. This study assesses the accuracy of Density Functional Theory for predicting them using 396 published experimental observations from a diverse range of small organic molecules. With the B3LYP functional and the TZVP basis set, Density Functional Theory calculations using the open-source software package NWChem can predict one-bond CH J-couplings with good accuracy for most classes of small organic molecule. The root-mean-square deviation after correction is 1.5 Hz for most sp3 CH pairs and 1.9 Hz for sp2 pairs; larger errors are observed for sp3 pairs with multiple electronegative substituents and for sp pairs. These results suggest that prediction of one-bond CH J-couplings by Density Functional Theory is sufficiently accurate for structure validation. This will be of particular use in strained ring systems and heterocycles which have characteristic couplings and which pose challenges for structure elucidation. PMID:25365289

  3. Molecular-Level Modeling of the Structure and Proton Transport within the Membrane Electrode Assembly of Hydrogen Proton Exchange Membrane Fuel Cells

    NASA Astrophysics Data System (ADS)

    Selvan, Myvizhi Esai; Keffer, David J.

    The creation of proton exchange membrane fuel cells (PEMFCs) in the early 1960's attracted great interest with the prospect of serving as a highly efficient and eco-friendly power source. This nascent technology found a broad range of applications spanning from spacecrafts to automobiles and electronic devices. The PEMFC in its simplest form consists of an anode, where the hydrogen fuel is catalytically electro-oxidized (dissociated into protons and electrons), a cathode, where oxygen is catalytically electro-reduced (combined with protons to form water) and a polymer electrolyte membrane, which serves as the structural framework of the cell and transports protons from anode to cathode, while the electrons are forced through the external circuit generating electricity. Today, fuel cell remains one of the most promising means of generating energy from alternative fuels, with tremendous potential to reduce oil dependence and carbon emissions. However, current PEMFCs have a relatively narrow operational range and a high cost of production, thus requiring significant experimental and theoretical research to develop a thorough understanding of this technology (at both the molecular and macroscopic scale), which will ultimately render the fuel cell as an economically viable option.

  4. Mitochondria: isolation, structure and function.

    PubMed

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-09-15

    Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work.

  5. Mitochondria: isolation, structure and function

    PubMed Central

    Picard, Martin; Taivassalo, Tanja; Gouspillou, Gilles; Hepple, Russell T

    2011-01-01

    Abstract Mitochondria are complex organelles constantly undergoing processes of fusion and fission, processes that not only modulate their morphology, but also their function. Yet the assessment of mitochondrial function in skeletal muscle often involves mechanical isolation of the mitochondria, a process which disrupts their normally heterogeneous branching structure and yields relatively homogeneous spherical organelles. Alternatively, methods have been used where the sarcolemma is permeabilized and mitochondrial morphology is preserved, but both methods face the downside that they remove potential influences of the intracellular milieu on mitochondrial function. Importantly, recent evidence shows that the fragmented mitochondrial morphology resulting from routine mitochondrial isolation procedures used with skeletal muscle alters key indices of function in a manner qualitatively similar to mitochondria undergoing fission in vivo. Although these results warrant caution when interpreting data obtained with mitochondria isolated from skeletal muscle, they also suggest that isolated mitochondrial preparations might present a useful way of interrogating the stress resistance of mitochondria. More importantly, these new findings underscore the empirical value of studying mitochondrial function in minimally disruptive experimental preparations. In this review, we briefly discuss several considerations and hypotheses emerging from this work. PMID:21708903

  6. Quark structure of the nucleon and angular asymmetry of proton-neutron hard elastic scattering.

    PubMed

    Granados, Carlos G; Sargsian, Misak M

    2009-11-20

    We investigate an asymmetry in the angular distribution of hard elastic proton-neutron scattering with respect to the 90 degrees center of mass scattering angle and demonstrate that it's magnitude is related to the helicity-isospin symmetry of the quark wave function of the nucleon. Our estimate of the asymmetry within the quark-interchange model of hard scattering demonstrates that the quark wave function of a nucleon based on the exact SU(6) symmetry predicts an angular asymmetry opposite to that of experimental observations. We found that the quark wave function based on the diquark picture of the nucleon produces a correct asymmetry. Comparison with the data allowed us to show that the vector diquarks contribute around 10% in the nucleon wave function and they are in negative phase relative to the scalar diquarks. These observations are essential in constraining QCD models of a nucleon.

  7. Molecular hydrogen messengers can lead to structural infidelity: A cautionary tale of protonated glycine

    SciTech Connect

    Masson, Antoine Rizzo, Thomas R. E-mail: thomas.rizzo@epfl.ch; Williams, Evan R. E-mail: thomas.rizzo@epfl.ch

    2015-09-14

    The effects of tagging protonated glycine with either He or between 1 and 14 H{sub 2} molecules on the infrared photodissociation spectra and the ion structure were investigated. Differences in the IR spectra with either a single He atom or H{sub 2} molecule attached indicate that even a single H{sub 2} molecule can affect the frequencies of some vibrational bands of this simple ion. The protonation site is the preferred location of the tag with He and with up to two H{sub 2} molecules, but evidence for H{sub 2} attachment to the hydrogen atom of the uncharged carboxylic acid is observed for ions tagged with three or more H{sub 2} molecules. This results in a 55 cm{sup −1} red shift in the carboxylic acid OH stretch, and evidence for some structural isomers where the hydrogen bond between the protonated nitrogen and the carbonyl oxygen is partially broken; as a result H{sub 2} molecules attached to this site are observed. These results are supported by theory, which indicates that H{sub 2} molecules can effectively break this weak hydrogen bond with three or more H{sub 2} molecules. These results indicate that large spectral shifts as a result of H{sub 2} molecules attaching to sites remote from the charge can occur and affect stretching frequencies as a result of charge transfer, and that tagging with multiple H{sub 2} molecules can change the structure of the ion itself.

  8. The structure and function of fungal cells

    NASA Technical Reports Server (NTRS)

    Nozawa, Y.

    1984-01-01

    The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

  9. Molecular and functional characterization of the voltage-gated proton channel in zebrafish neutrophils.

    PubMed

    Ratanayotha, Adisorn; Kawai, Takafumi; Higashijima, Shin-Ichi; Okamura, Yasushi

    2017-08-01

    Voltage-gated proton channels (Hv1/VSOP) are expressed in various cells types, including phagocytes, and are involved in diverse physiological processes. Although hvcn1, the gene encoding Hv1, has been identified across a wide range of species, most of the knowledge about its physiological function and expression profile is limited to mammals. In this study, we investigated the basic properties of DrHv1, the Hv1 ortholog in zebrafish (Danio rerio) which is an excellent animal model owing to the transparency, as well as its functional expression in native cells. Electrophysiological analysis using a heterologous expression system confirmed the properties of a voltage-gated proton channel are conserved in DrHv1 with differences in threshold and activation kinetics as compared to mouse (Mus musculus) Hv1 (mHv1). RT-PCR analysis revealed that hvcn1 is expressed in zebrafish neutrophils, as is the case in mammals. Subsequent electrophysiological analysis confirmed the functional expression of DrHv1 in zebrafish neutrophils, which suggests Hv1 function in phagocytes is conserved among vertebrates. We also found that DrHv1 is comparatively resistant to extracellular Zn(2+), which is a potent inhibitor of mammalian Hv1, and this phenomenon appears to reflect variation in the Zn(2+)-coordinating residue (histidine) within the extracellular linker region in mammalian Hv1. Notably, the serum Zn(2+) concentration is much higher in zebrafish than in mouse, raising the possibility that Zn(2+) sensitivity was acquired in accordance with a change in the serum Zn(2+) concentration. This study highlights the biological variation and importance of Hv1 in different animal species. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

  10. Proton nuclear magnetic resonance study of hirudin: resonance assignment and secondary structure

    SciTech Connect

    Sukumaran, D.K.; Clore, G.M.; Preuss, A.; Zarbock, J.; Gronenbron, A.M.

    1987-01-27

    The /sup 1/H NMR spectrum of the 65-residue protein hirudin is assigned in a sequential manner by using a combination of two-dimensional nuclear magnetic resonance techniques to demonstrate through-bond and through space (<5-A) connectives. The secondary structure of hirudin is deduced from a qualitative interpretation of the nuclear Overhauser effects involving the backbone NH, C/sup ..cap alpha../H, and C/sup ..beta../H protons. It is shown that hirudin has two ..beta..-sheets and no ..cap alpha..-helices.

  11. Structure of proton centers and associated nonthermal bursts at microwave frequencies

    NASA Technical Reports Server (NTRS)

    Enome, S.; Tanaka, H.

    1973-01-01

    A very broad band of electromagnetic radiation is emitted during solar flares, especially at the explosive phase. The existence of a large variety of plasmas with various densities and a wide range of temperatures or energies is proposed as the initiating agent. The manner in which the plasmas are heated and accelerated to subrelativistic and relativistic energies is discussed. Observational evidence on the characteristics of active regions which produced proton flares and on the structure of the associated nonthermal microwave bursts of the sun is presented. The behavior of subrelativistic electrons on the sun is described.

  12. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states

    PubMed Central

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-01-01

    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 O2 to 2H2O 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 O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an F o − F c map for Glu451a O∊2 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 O2-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. PMID:26627648

  13. X-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and O2-reduction states.

    PubMed

    Serrano-Posada, Hugo; Centeno-Leija, Sara; Rojas-Trejo, Sonia Patricia; Rodríguez-Almazán, Claudia; Stojanoff, Vivian; Rudiño-Piñera, Enrique

    2015-12-01

    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 O2 to 2H2O 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 O2 reduction was found in a double conformation: Glu451a (∼7 Å from the TNC) and Glu451b (∼4.5 Å from the TNC). A positive peak of electron density above 3.5σ in an Fo - Fc map for Glu451a O(ℇ2) 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 O2-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.

  14. Desmosome structure, composition and function.

    PubMed

    Garrod, David; Chidgey, Martyn

    2008-03-01

    Desmosomes are intercellular junctions of epithelia and cardiac muscle. They resist mechanical stress because they adopt a strongly adhesive state in which they are said to be hyper-adhesive and which distinguishes them from other intercellular junctions; desmosomes are specialised for strong adhesion and their failure can result in diseases of the skin and heart. They are also dynamic structures whose adhesiveness can switch between high and low affinity adhesive states during processes such as embryonic development and wound healing, the switching being signalled by protein kinase C. Desmosomes may also act as signalling centres, regulating the availability of signalling molecules and thereby participating in fundamental processes such as cell proliferation, differentiation and morphogenesis. Here we consider the structure, composition and function of desmosomes, and their role in embryonic development and disease.

  15. Microwave measurements of proton tunneling and structural parameters for the propiolic acid-formic acid dimer.

    PubMed

    Daly, Adam M; Douglass, Kevin O; Sarkozy, Laszlo C; Neill, Justin L; Muckle, Matt T; Zaleski, Daniel P; Pate, Brooks H; Kukolich, Stephen G

    2011-10-21

    initial rotational constants for the complex, structural parameters, and some details of the proton tunneling potential energy surface. A least squares fit to the isotopic data reveals a planar structure that is slightly asymmetric in the OH distances. The formic OH···O propiolic hydrogen bond length is 1.8 Å and the propiolic OH···O formic hydrogen bond length is 1.6 Å, for the equilibrium configuration. The magnitude of the dipole moment was experimentally determined to be 1.95(3) × 10(-30) C m (0.584(8) D) for the 0(+) states and 1.92(5) × 10(-30) C m (0.576(14) D) for the 0(-) states. © 2011 American Institute of Physics

  16. Microwave measurements of proton tunneling and structural parameters for the propiolic acid-formic acid dimer

    NASA Astrophysics Data System (ADS)

    Daly, Adam M.; Douglass, Kevin O.; Sarkozy, Laszlo C.; Neill, Justin L.; Muckle, Matt T.; Zaleski, Daniel P.; Pate, Brooks H.; Kukolich, Stephen G.

    2011-10-01

    Microwave spectra of the propiolic acid-formic acid doubly hydrogen bonded complex were measured in the 1 GHz to 21 GHz range using four different Fourier transform spectrometers. Rotational spectra for seven isotopologues were obtained. For the parent isotopologue, a total of 138 a-dipole transitions and 28 b-dipole transitions were measured for which the a-dipole transitions exhibited splittings of a few MHz into pairs of lines and the b-type dipole transitions were split by ˜580 MHz. The transitions assigned to this complex were fit to obtain rotational and distortion constants for both tunneling levels: A0+ = 6005.289(8), B0+ = 930.553(8), C0+ = 803.9948(6) MHz, Δ0+J = 0.075(1), Δ0+JK = 0.71(1), and δ0+j = -0.010(1) kHz and A0- = 6005.275(8), B0- = 930.546(8), C0- = 803.9907(5) MHz, Δ0-J = 0.076(1), Δ0-JK = 0.70(2), and δ0-j = -0.008(1) kHz. Double resonance experiments were used on some transitions to verify assignments and to obtain splittings for cases when the b-dipole transitions were difficult to measure. The experimental difference in energy between the two tunneling states is 291.428(5) MHz for proton-proton exchange and 3.35(2) MHz for the deuterium-deuterium exchange. The vibration-rotation coupling constant between the two levels, Fab, is 120.7(2) MHz for the proton-proton exchange. With one deuterium atom substituted in either of the hydrogen-bonding protons, the tunneling splittings were not observed for a-dipole transitions, supporting the assignment of the splitting to the concerted proton tunneling motion. The spectra were obtained using three Flygare-Balle type spectrometers and one chirped-pulse machine at the University of Virginia. Rotational constants and centrifugal distortion constants were obtained for HCOOH...HOOCCCH, H13COOH...HOOCCCH, HCOOD...HOOCCCH, HCOOH...DOOCCCH, HCOOD...DOOCCCH, DCOOH...HOOCCCH, and DCOOD...HOOCCCH. High-level ab initio calculations provided initial rotational constants for the complex, structural

  17. A proton current associated with sour taste: distribution and functional properties.

    PubMed

    Bushman, Jeremy D; Ye, Wenlei; Liman, Emily R

    2015-07-01

    Sour taste is detected by taste receptor cells that respond to acids through yet poorly understood mechanisms. The cells that detect sour express the protein PKD2L1, which is not the sour receptor but nonetheless serves as a useful marker for sour cells. By use of mice in which the PKD2L1 promoter drives expression of yellow fluorescent protein, we previously reported that sour taste cells from circumvallate papillae in the posterior tongue express a proton current. To establish a correlation between this current and sour transduction, we examined its distribution by patch-clamp recording. We find that the current is present in PKD2L1-expressing taste cells from mouse circumvallate, foliate, and fungiform papillae but not in a variety of other cells, including spinal cord neurons that express PKD2L1. We describe biophysical properties of the current, including pH-dependent Zn(2+) inhibition, lack of voltage-dependent gating, and activation at modest pH values (6.5) that elicit action potentials in isolated cells. Consistent with a channel that is constitutively open, the cytosol of sour taste cells is acidified. These data define a functional signature for the taste cell proton current and indicate that its expression is mostly restricted to the subset of taste cells that detect sour.

  18. Next-to leading order analysis of target mass corrections to structure functions and asymmetries

    SciTech Connect

    L. T. Brady, A. Accardi, T. J. Hobbs, W. Melnitchouk

    2011-10-01

    We perform a comprehensive analysis of target mass corrections (TMCs) to spin-averaged structure functions and asymmetries at next-to-leading order. Several different prescriptions for TMCs are considered, including the operator product expansion, and various approximations to it, collinear factorization, and xi-scaling. We assess the impact of each of these on a number of observables, such as the neutron to proton F{sub 2} structure function ratio, and parity-violating electron scattering asymmetries for protons and deuterons which are sensitive to gamma-Z interference effects. The corrections from higher order radiative and nuclear effects on the parity-violating deuteron asymmetry are also quantified.

  19. Structure and functions of arrestins.

    PubMed Central

    Palczewski, K.

    1994-01-01

    Transmembrane signal transductions in a variety of cell types that mediate signals as diverse as those carried by neurotransmitters, hormones, and sensory signals share basic biochemical mechanisms that include: (1) an extracellular perturbation (neurotransmitter, hormone, odor, light); (2) specific receptors; (3) coupling proteins, such as G proteins; and (4) effector enzymes or ion channels. Parallel to these amplification reactions, receptors are precisely inactivated by mechanisms that involve protein kinases and regulatory proteins called arrestins. The structure and functions of arrestins are the focus of this review. PMID:7833798

  20. The g2 Structure Function

    SciTech Connect

    Matthias Burkardt

    2009-07-01

    Polarized structure functions at low $Q^2$ have the physical interpretation of (generalized) spin polarizabilities. At high $Q^2$, the polarized parton distribution $g_2(x)$ provides access to quark-gluon correlations in the nucleon. We discuss the interpretation of the $x^2$ moment of $\\bar{g}_2(x)$ as an average transverse force on quarks in deep-inelastic scattering from a transversely polarized target. Qualitative connections with generalized parton distributions are emphasized. The $x^2$ moment of the chirally-odd twist-3 parton distribution $e(x)$ provides information on the dependence of the average transverse force on the transversity of the quark.

  1. Molecular Mechanism of Biological Proton Transport

    SciTech Connect

    Pomes, R.

    1998-09-01

    Proton transport across lipid membranes is a fundamental aspect of biological energy transduction (metabolism). This function is mediated by a Grotthuss mechanism involving proton hopping along hydrogen-bonded networks embedded in membrane-spanning proteins. Using molecular simulations, the authors have explored the structural, dynamic, and thermodynamic properties giving rise to long-range proton translocation in hydrogen-bonded networks involving water molecules, or water wires, which are emerging as ubiquitous H{sup +}-transport devices in biological systems.

  2. Functional nanometer-scale structures

    NASA Astrophysics Data System (ADS)

    Chan, Tsz On Mario

    Nanometer-scale structures have properties that are fundamentally different from their bulk counterparts. Much research effort has been devoted in the past decades to explore new fabrication techniques, model the physical properties of these structures, and construct functional devices. The ability to manipulate and control the structure of matter at the nanoscale has made many new classes of materials available for the study of fundamental physical processes and potential applications. The interplay between fabrication techniques and physical understanding of the nanostructures and processes has revolutionized the physical and material sciences, providing far superior properties in materials for novel applications that benefit society. This thesis consists of two major aspects of my graduate research in nano-scale materials. In the first part (Chapters 3--6), a comprehensive study on the nanostructures based on electrospinning and thermal treatment is presented. Electrospinning is a well-established method for producing high-aspect-ratio fibrous structures, with fiber diameter ranging from 1 nm--1 microm. A polymeric solution is typically used as a precursor in electrospinning. In our study, the functionality of the nanostructure relies on both the nanostructure and material constituents. Metallic ions containing precursors were added to the polymeric precursor following a sol-gel process to prepare the solution suitable for electrospinning. A typical electrospinning process produces as-spun fibers containing both polymer and metallic salt precursors. Subsequent thermal treatments of the as-spun fibers were carried out in various conditions to produce desired structures. In most cases, polymer in the solution and the as-spun fibers acted as a backbone for the structure formation during the subsequent heat treatment, and were thermally removed in the final stage. Polymers were also designed to react with the metallic ion precursors during heat treatment in some

  3. 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.

  4. 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.

  5. Structural features of the protophorphyrin-apomyoglobin complex. A proton NMR spectroscopy study

    SciTech Connect

    Lecomte, J.T.J.; Cocco, M.J. )

    1990-12-01

    The structural properties of the complex formed by apomyoglobin and protoporphyrin IX (des-iron myoglobin) were studied to probe the influence of iron-to-histidine coordination on the native myoglobin fold and the heme binding site geometry. Standard two-dimensional proton nuclear magnetic resonance spectroscopy methods were applied to identify porphyrin and protein signals. A pronounced spectral resemblance between carbonmonoxymyoglobin and des-iron myogobin was noticed that could be exploited to assign a number of resonances by nuclear Overhauser spectroscopy. Protoporphyrin IX was determined to bind in the same orientation as the heme. Most residues in contact with the prosthetic group were found in the holomyoglobin conformation. Several tertiary structure features were also characterized near the protein termini. It was concluded that the protoporphyrin-apomyoglobin interactions are capable of organizing the binding site and the unfolded region of the apoprotein into the native holoprotein structure.

  6. Ab Initio Thermodynamics and the Relationship between Octahedral Distortion, Lattice Structure, and Proton Substitution Defects in Malachite/Rosasite Group Endmember Pokrovskite Mg2CO3(OH)2.

    PubMed

    Chaka, Anne M

    2016-12-29

    Divalent metal hydroxycarbonates with M2CO3(OH)2 stoichiometry are widely used in industry and are abundant in nature as the malachite/rosasite group of minerals. Essential to their performance as catalytic precursors and in nanoelectronics, these materials and minerals exhibit a high degree of cation ordering in mixed metal systems due to differences in distortion of the octahedral metal sites. Density-functional theory (DFT) calculations on pokrovskite Mg2CO3(OH)2 in the rosasite structure and Mg analogues of monoclinic and orthorhombic forms of malachite determine that the octahedral sites are innately distorted, and that d(9) Cu(II) Jahn-Teller distortion accommodates this distortion rather than causes it, leading to the significant preference of Cu for the type I octahedral sites. This distortion also leads to a high propensity for formation of cation vacancies charge balanced by proton substitution. Ab initio thermodynamics is used to determine that there are conditions under which proton substitution defects are slightly more stable than the stoichiometric structure, consistent with the widespread observation of such defects in pokrovskite in nature. Pokrovskite itself is most likely to form under CO2-rich/low water conditions, particularly those utilizing supercritical CO2 for carbon sequestration and is sufficiently thermodynamically stable to trap CO2 under geological conditions. Low temperature and high water concentration promotes the formation of proton substitution defects, which has implications for synthesis of any material where octahedral strain may be relieved by proton substitution defects.

  7. Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer

    PubMed Central

    2010-01-01

    Background Laccases are enzymes that couple the oxidation of substrates with the reduction of dioxygen to water. They are the simplest members of the multi-copper oxidases and contain at least two types of copper centres; a mononuclear T1 and a trinuclear that includes two T3 and one T2 copper ions. Substrate oxidation takes place at the mononuclear centre whereas reduction of oxygen to water occurs at the trinuclear centre. Results In this study, the CotA laccase from Bacillus subtilis was used as a model to understand the mechanisms taking place at the molecular level, with a focus in the trinuclear centre. The structures of the holo-protein and of the oxidised form of the apo-protein, which has previously been reconstituted in vitro with Cu(I), have been determined. The former has a dioxygen moiety between the T3 coppers, while the latter has a monoatomic oxygen, here interpreted as a hydroxyl ion. The UV/visible spectra of these two forms have been analysed in the crystals and compared with the data obtained in solution. Theoretical calculations on these and other structures of CotA were used to identify groups that may be responsible for channelling the protons that are needed for reduction of dioxygen to water. Conclusions These results present evidence that Glu 498 is the only proton-active group in the vicinity of the trinuclear centre. This strongly suggests that this residue may be responsible for channelling the protons needed for the reduction. These results are compared with other data available for these enzymes, highlighting similarities and differences within laccases and multicopper oxidases. PMID:20822511

  8. Proton transport by halorhodopsin

    SciTech Connect

    Varo, G.; Brown, L.S.; Needleman, R.

    1996-05-28

    In halorhodopsin from Natronobacterium pharaonis, a light-driven chloride pump, the chloride binding site also binds azide. When azide is bound at this location the retinal Schiff base transiently deprotonates after photoexcitation with light >530 nm, like in the light-driven proton pump bacteriorhodopsin. As in the photocycle of bacteriorhodopsin, pyranine detects the release of protons to the bulk. The subsequent reprotonation of the Schiff base is also dependent on azide, but with different kinetics that suggest a shuttling of protons from the surface as described earlier for halorhodopsin from Halobacterium salinarium. The azide-dependent, bacteriorhodopsin-like photocycle results in active electrogenic proton transport in the cytoplasmic to extracellular direction, detected in cell envelope vesicle suspensions both with a potential-sensitive electrode and by measuring light-dependent pH change. We conclude that in halorhodopsin an azide bound to the extracellular side of the Schiff base, and another azide shuttling between the Schiff base and the cytoplasmic surface, fulfill the functions of Asp-85 and Asp-96, respectively, in bacteriorhodopsin. Thus, although halorhodopsin is normally a chloride ion pump, it evidently contains all structural requirements, except an internal proton acceptor and a donor, of a proton pump. This observation complements our earlier finding that when a chloride binding site was created in bacteriorhodopsin through replacement of Asp-85 with a threonine, that protein became a chloride ion pump. 52 refs., 9 figs.

  9. Response functions of Fuji imaging plates to monoenergetic protons in the energy range 0.6-3.2 MeV

    SciTech Connect

    Bonnet, T.; Denis-Petit, D.; Gobet, F.; Hannachi, F.; Tarisien, M.; Versteegen, M.; Aleonard, M. M.

    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, a 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.

  10. Evidence for a spin-aligned neutron-proton paired phase from the level structure of (92)Pd.

    PubMed

    Cederwall, B; Moradi, F Ghazi; Bäck, T; Johnson, A; Blomqvist, J; Clément, E; de France, G; Wadsworth, R; Andgren, K; Lagergren, K; Dijon, A; Jaworski, G; Liotta, R; Qi, C; Nyakó, B M; Nyberg, J; Palacz, M; Al-Azri, H; Algora, A; de Angelis, G; Ataç, A; Bhattacharyya, S; Brock, T; Brown, J R; Davies, P; Di Nitto, A; Dombrádi, Zs; Gadea, A; Gál, J; Hadinia, B; Johnston-Theasby, F; Joshi, P; Juhász, K; Julin, R; Jungclaus, A; Kalinka, G; Kara, S O; Khaplanov, A; Kownacki, J; La Rana, G; Lenzi, S M; Molnár, J; Moro, R; Napoli, D R; Singh, B S Nara; Persson, A; Recchia, F; Sandzelius, M; Scheurer, J-N; Sletten, G; Sohler, D; Söderström, P-A; Taylor, M J; Timár, J; Valiente-Dobón, J J; Vardaci, E; Williams, S

    2011-01-06

    Shell structure and magic numbers in atomic nuclei were generally explained by pioneering work that introduced a strong spin-orbit interaction to the nuclear shell model potential. However, knowledge of nuclear forces and the mechanisms governing the structure of nuclei, in particular far from stability, is still incomplete. In nuclei with equal neutron and proton numbers (N = Z), enhanced correlations arise between neutrons and protons (two distinct types of fermions) that occupy orbitals with the same quantum numbers. Such correlations have been predicted to favour an unusual type of nuclear superfluidity, termed isoscalar neutron-proton pairing, in addition to normal isovector pairing. Despite many experimental efforts, these predictions have not been confirmed. Here we report the experimental observation of excited states in the N = Z = 46 nucleus (92)Pd. Gamma rays emitted following the (58)Ni((36)Ar,2n)(92)Pd fusion-evaporation reaction were identified using a combination of state-of-the-art high-resolution γ-ray, charged-particle and neutron detector systems. Our results reveal evidence for a spin-aligned, isoscalar neutron-proton coupling scheme, different from the previous prediction. We suggest that this coupling scheme replaces normal superfluidity (characterized by seniority coupling) in the ground and low-lying excited states of the heaviest N = Z nuclei. Such strong, isoscalar neutron-proton correlations would have a considerable impact on the nuclear level structure and possibly influence the dynamics of rapid proton capture in stellar nucleosynthesis.

  11. A-dependence of weak nuclear structure functions

    SciTech Connect

    Haider, H.; Athar, M. Sajjad; Simo, I. Ruiz

    2015-05-15

    Effect of nuclear medium on the weak structure functions F{sub 2}{sup A}(x, Q{sup 2}) and F{sub 3}{sup A}(x, Q{sup 2}) have been studied using charged current (anti)neutrino deep inelastic scattering on various nuclear targets. Relativistic nuclear spectral function which incorporate Fermi motion, binding and nucleon correlations are used for the calculations. We also consider the pion and rho meson cloud contributions calculated from a microscopic model for meson-nucleus self-energies. Using these structure functions, F{sub i}{sup A}/F{sub i}{sup proton} and F{sub i}{sup A}/F{sub i}{sup deuteron}(i=2,3, A={sup 12}C, {sup 16}O, CH and H{sub 2}O) are obtained.

  12. Color dipole cross section and inelastic structure function

    NASA Astrophysics Data System (ADS)

    Jeong, Yu Seon; Kim, C. S.; Luu, Minh Vu; Reno, Mary Hall

    2014-11-01

    Instead of starting from a theoretically motivated form of the color dipole cross section in the dipole picture of deep inelastic scattering, we start with a parametrization of the deep inelastic structure function for electromagnetic scattering with protons, and then extract the color dipole cross section. Using the parametrizations of F 2(ξ = x or W 2 , Q 2) by Donnachie-Landshoff and Block et al., we find the dipole cross section from an approximate form of the presumed dipole cross section convoluted with the perturbative photon wave function for virtual photon splitting into a color dipole with massless quarks. The color dipole cross section determined this way reproduces the original structure function within about 10% for 0 .1 GeV2 ≤ Q 2 ≤10 GeV2. We discuss the dipole cross section at large and small dipole sizes and compare our results with other parametrizations.

  13. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution

    SciTech Connect

    Fang, Yiling; Jayaram, Hariharan; Shane, Tania; Kolmakova-Partensky, Ludmila; Wu, Fang; Williams, Carole; Xiong, Yong; Miller, Christopher

    2009-09-15

    To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic {beta}-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 {angstrom} resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.

  14. Structure of a Prokaryotic Virtual Proton Pump at 3.2 Astroms Resolution

    SciTech Connect

    Fang, Y.; Jayaram, H; Shane, T; Partensky, L; Wu, F; williams, C; Xiong, Y; Miller, C

    2009-01-01

    To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5-4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a 'virtual proton pump' in the inner membrane, called AdiC, that imports L-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis, facilitation of insulin release from pancreatic beta-cells, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 A resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.

  15. Proton NMR assignments and secondary structure of the snake venom protein echistatin

    SciTech Connect

    Yuan Chen; Baum, J. ); Pitzenberger, S.M.; Garsky, V.M.; Lumma, P.K.; Sanyal, G. )

    1991-12-17

    The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic resonance assignments are presented for the proton resonances of echistatin in water. The single-chain protein contains 49 amino acids and 4 cystine bridges. All of the backbone amide, C{sub alpha}H, and side-chain resonances, except for the {eta}-NH of the arginines, have been assigned. The secondary structure of the protein was characterized from the pattern of nuclear Overhauser enhancements, from the identification of slowly exchanging amide protons, from {sup 3}J{sub c{alpha}H-NH} coupling constants, and from circular dichroism studies. The data suggest that the secondary structure consists of a type I {beta}-turn, a short {beta}-hairpin, and a short-, irregular, antiparallel {beta}-sheet and that the Arg-Gly-Asp sequence is in a flexible loop connecting two strands of the distorted antiparallel {beta}-sheet.

  16. Structure and dynamics of cationic van-der-Waals clusters. II. Dynamics of protonated argon clusters

    NASA Astrophysics Data System (ADS)

    Ritschel, T.; Zuhrt, Ch.; Zülicke, L.; Kuntz, P. J.

    2007-01-01

    A diatomics-in-molecules (DIM) model with ab-initio input data, which in part I successfully described the structure and bonding properties of protonated argon clusters ArnH+, is used here to investigate some aspects of the dynamics of such aggregates for n up to 30. The simple triatomic ionic fragment, Ar2H+, is studied in some detail with respect to normal vibrations, characteristics of classical intramolecular dynamics as reflected in the Fourier spectra of dynamical variables, and accurate quantum states of the vibrational motion. For larger clusters ArnH+ (n ≤30), the normal vibrational frequencies (and displacement eigenvectors) are calculated and related to the cluster structure. In addition, the Fourier spectra are analyzed with respect to their variation with changing internal energy and cluster size. As expected, the clusters show some floppy character. Even a little vibrational excitation can lead to internal rearrangement and to Ar-atom evaporation from the clusters; this is studied in more detail for one small complex (n = 3). Electronic excitation to one of the low-lying excited states, which are all globally repulsive, leads to complete fragmentation (atomization) of the clusters. A variety of conceivable elementary collision processes involving protonated argon clusters are discussed. Some of these may play a role in the gas-phase formation of medium-sized ArnH+ aggregates.

  17. Proton and deuteron induced reactions on natGa: Experimental and calculated excitation functions

    NASA Astrophysics Data System (ADS)

    Hermanne, A.; Adam-Rebeles, R.; Tárkányi, F.; Takács, S.; Ditrói, F.

    2015-09-01

    Cross-sections for reactions on natGa, induced by protons (up to 65 MeV) and deuterons (up to 50 MeV), producing γ-emitting radionuclides with half-lives longer than 1 h were measured in a stacked-foil irradiation using thin Ga-Ni alloy (70-30%) targets electroplated on Cu or Au backings. Excitation functions for generation of 68,69Ge, 66,67,68,72Ga and 65,69mZn on natGa are discussed, relative to the monitor reactions natAl(d,x)24,22Na, natAl(p,x)24,22Na, natCu(p,x)62Zn and natNi(p,x)57Ni. The results are compared to our earlier measurements, the scarce literature values and to the results of the code TALYS 1.6 (online database TENDL-2014).

  18. Gamma Strength Functions and Level Densities from 300 MeV Proton Scatttering at 0°

    NASA Astrophysics Data System (ADS)

    von Neumann-Cosel, Peter; Bassauer, Sergej; Martin, Dirk

    The gamma strength function (GSF) as well as total level densities (LDs) in 208Pb and 96Mo were extracted from high-resolution forward angle inelastic proton scattering data taken at RCNP, Osaka, Japan, and compared to experimental results obtained with the Oslo method in order to test the validity of the Brink-Axel (BA) hypothesis in the energy region of the pygmy dipole resonance. The case of 208Pb is inconclusive because of strong fluctuations of the GSF due to the small level density in a doubly closed-shell nucleus. In 96Mo the data are consistent with the BA hypothesis. The good agreement of LDs provides an independent confirmation of the approach underlying the decomposition of GSF and LDs in Oslo-type experiments.

  19. Influence of 5-HALOGENATION on the Structure of Protonated Uridine: Irmpd Action Spectroscopy and Theoretical Studies of the Protonated 5-HALOURIDINES

    NASA Astrophysics Data System (ADS)

    Roy, Harrison; Hamlow, Lucas; Lee, Justin; Rodgers, M. T.; Berden, Giel; Oomens, Jos

    2016-06-01

    The chemical and structural diversity and the extent of post-transcriptional modification of RNA is remarkable! Presently, there are 142 different naturally-occurring and many more synthetically modified nucleosides known. Uridine (Urd) is the most commonly modified nucleoside among those that occur naturally, but has also been an important target for synthesis and development of modified nucleosides for pharmaceutical applications. Indeed, modified nucleosides are of pharmaceutical interest due to their bioactivities. In particular, 5-bromouridine (br5Urd) has been shown to exhibit antiviral activity to human immunodeficiency virus and has been used in RNA labeling studies. Halogenation is a common modification employed in pharmaceutical studies that enables systematic variation is the electronic properties of the molecule of interest due to the availability of halogen substituents that vary in size, dipole moment, polarizability, and electron withdrawing properties. In order to elucidate the influence of 5-halogenation on the intrinsic gas-phase structure and stability on the protonated form of Urd, synergistic spectroscopic and theoretical studies of the protonated forms of the 5-halouridines are performed here, where x5Urd = 5-fluorouridine (f5Urd), 5-chlorouridine (cl5Urd), br5Urd, and 5-iodouridine (i5Urd). Infrared multiple photon dissociation (IRMPD) action spectra of the protonated forms of the 5-halouridines, [x5Urd+H]+, are measured over the IR fingerprint region using the FELIX free electron laser and the hydrogen stretching region using an OPO/OPA laser from 3300-3800 wn. Complementary electronic structure calculations are performed to determine the stable low-energy conformations available to these species and to predict their IR spectra. Comparative analyses of the measured IRMPD spectra and predicted IR spectra are performed to elucidate the preferred sites of protonation, and the low-energy tautomeric conformations that are populated by

  20. Proton Transport

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    channel is large enough to contain water molecules. and is normally filled with water. In analogy to the mechanism of proton transfer in some other channels, it has been postulated that protons are translocated along the network of water molecules filling the pore of the channel. This mechanism, however, must involve an additional important step because the channel contains four histidine amino acid residues, one from each of the helices, which are sufficiently large to occlude the pore and interrupt the water network. The histidine residues ensure channel selectivity by blocking transport of small ions, such as sodium or potassium. They have been also implicated in gating protons due to the ability of each histidine to become positively charged by accepting an additional proton. Two mechanisms of gating have been proposed. In one mechanism, all four histidines acquire an additional proton and, due to repulsion between their positive charges, move away from one another, thus opening the channel. The alternative mechanism relies of the ability of protons to move between different atoms in a molecule (tautomerization). Thus, a proton is captured on one side of the gate while another proton is released from the opposite side, and the molecule returns to the initial state through tautomerization. The simulations were designed to test these two mechanisms. Large-scale, atomic-level molecular dynamics simulations of the channel with the histidine residues in different protonation states revealed that all intermediate states of the system involved in the tautomerization mechanism are structurally stable and the arrangement of water molecules in the channel is conducive to the proton transport. In contrast, in the four-protonated state, postulated to exist in the gate-opening mechanism, the electrostatic repulsion between the histidine residues appears to be so large that the channel loses its structural integrity and one helix moves away from the remaining three. Additional

  1. Three dimensional structure prediction and proton nuclear magnetic resonance analysis of toxic pesticides in human blood plasma.

    PubMed

    Sharma, Amit Kumar; Tiwari, Rajeev Kumar; Gaur, Mulayam Singh

    2012-05-01

    The purpose of this study was to investigate the nuclear magnetic resonance (NMR) assignments of hydrolyzed products extracted from human blood plasma. The correlations between chemical, functional and structural properties of highly toxic pesticides were investigated using the PreADME analysis. We observed that toxic pesticides possessed higher molecular weight and, more hydrogen bond donors and acceptors when compared with less toxic pesticides. The occurrence of functional groups and structural properties was analyzed using (1)H-NMR. The (1)H-NMR spectra of the phosphomethoxy class of pesticides were characterized by methyl resonances at 3.7-3.9 ppm (δ) with the coupling constants of 11-16 Hz (JP-CH3 ). In phosphoethoxy pesticides, the methyl resonance was about 1.4 ppm (δ) with the coupling constant of 10 Hz (JP-CH2 ) and the methylene resonances was 4.2-4.4 ppm (δ) with the coupling constant of 0.8 Hz (JP-CH3 ), respectively. Our study shows that the values of four parameters such as chemical shift, coupling constant, integration and relaxation time correlated with the concentration of toxic pesticides, and can be used to characterise the proton groups in the molecular structures of toxic pesticides.

  2. 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

  3. Crystal structure, spectroscopy, DFT studies and thermal characterization of Cobalt(II) complex with 2-protonated aminopyridinium cation as ligand

    NASA Astrophysics Data System (ADS)

    Mhadhbi, Noureddine; Saïd, Salem; Elleuch, Slim; Naïli, Houcine

    2016-03-01

    Single crystals of a new organic-inorganic hybrid compound (2-HAMP)2[CoBr4], (2-HAMP = 2-protonated aminopyridinium cation) was synthesized and characterized by X-Ray diffraction at room temperature, DTA-TG measurement, FT-IR and FT-Raman spectroscopies and optical absorption. Its crystal structure is a packing of alternated organic and inorganic layers parallel to (a, b) plane. The different components are connected by a network of N/C-H⋯Br hydrogen bonds and halogen⋯halogen interactions. These hydrogen bonds give notable vibrational effects. Theoretical calculations were performed using density functional theory (DFT) for studying the molecular structure, vibrational spectra and optical properties of the investigated molecule in the ground state. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) results complements with the experimental findings. The simulated spectra satisfactorily coincide with the experimental UV-Visible spectrum. The results show good consistent with the experiment and confirm the contribution of metal orbital to the HOMO-LUMO boundary. Thermal analysis studies indicate the presence of three phase transitions at 68, 125 and 172 °C, which are confirmed by X-ray powder diffraction as a function of temperature.

  4. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving.

    PubMed

    Pauli, Guido F; Niemitz, Matthias; Bisson, Jonathan; Lodewyk, Michael W; Soldi, Cristian; Shaw, Jared T; Tantillo, Dean J; Saya, Jordy M; Vos, Klaas; Kleinnijenhuis, Roel A; Hiemstra, Henk; Chen, Shao-Nong; McAlpine, James B; Lankin, David C; Friesen, J Brent

    2016-02-05

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of "structural correctness" depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D (1)H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D (1)H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by (1)H iterative full spin analysis (HiFSA). Fully characterized 1D (1)H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication.

  5. Toward Structural Correctness: Aquatolide and the Importance of 1D Proton NMR FID Archiving

    PubMed Central

    2016-01-01

    The revision of the structure of the sesquiterpene aquatolide from a bicyclo[2.2.0]hexane to a bicyclo[2.1.1]hexane structure using compelling NMR data, X-ray crystallography, and the recent confirmation via full synthesis exemplify that the achievement of “structural correctness” depends on the completeness of the experimental evidence. Archived FIDs and newly acquired aquatolide spectra demonstrate that archiving and rigorous interpretation of 1D 1H NMR data may enhance the reproducibility of (bio)chemical research and curb the growing trend of structural misassignments. Despite being the most accessible NMR experiment, 1D 1H spectra encode a wealth of information about bonds and molecular geometry that may be fully mined by 1H iterative full spin analysis (HiFSA). Fully characterized 1D 1H spectra are unideterminant for a given structure. The corresponding FIDs may be readily submitted with publications and collected in databases. Proton NMR spectra are indispensable for structural characterization even in conjunction with 2D data. Quantum interaction and linkage tables (QuILTs) are introduced for a more intuitive visualization of 1D J-coupling relationships, NOESY correlations, and heteronuclear experiments. Overall, this study represents a significant contribution to best practices in NMR-based structural analysis and dereplication. PMID:26812443

  6. Low energy proton bidirectional anisotropies and their relation to transient interplanetary magnetic structures: ISEE-3 observations

    NASA Technical Reports Server (NTRS)

    Marsden, R. G.; Sanderson, T. R.; Wenzel, K. P.; Smith, E. J.

    1985-01-01

    It is known that the interplanetary medium in the period approaching solar maximum is characterized by an enhancement in the occurrence of transient solar wind streams and shocks and that such systems are often associated with looplike magnetic structures or clouds. There is observational evidence that bidirectional, field aligned flows of low energy particles could be a signature of such looplike structures, although detailed models for the magnetic field configuration and injection mechanisms do not exist at the current time. Preliminary results of a survey of low energy proton bidirectional anisotropies measured on ISEE-3 in the interplanetary medium between August 1978 and May 1982, together with magnetic field data from the same spacecraft are presented.

  7. Differential Velocity between Solar Wind Protons and Alpha Particles in Pressure Balance Structures

    NASA Technical Reports Server (NTRS)

    Yamauchi, Yohei; Suess, Steven T.; Steinberg, John T.; Sakurai, Takashi

    2004-01-01

    Pressure balance structures (PBSs) are a common high-plasma beta feature in high-latitude, high-speed solar wind. They have been proposed as remnants of coronal plumes. If true, they should reflect the observation that plumes are rooted in unipolar magnetic flux concentrations in the photosphere and are heated as oppositely directed flux is advected into and reconnects with the flux concentration. A minimum variance analysis (MVA) of magnetic discontinuities in PBSs showed there is a larger proportion of tangential discontinuities than in the surrounding high-speed wind, supporting the hypothesis that plasmoids or extended current sheets are formed during reconnection at the base of plumes. To further evaluate the character of magnetic field discontinuities in PBSs, differential streaming between alpha particles and protons is analyzed here for the same sample of PBSs used in the MVA. Alpha particles in high-speed wind generally have a higher radial flow speed than protons. However, if the magnetic field is folded back on itself, as in a large-amplitude Alfven wave, alpha particles will locally have a radial flow speed less than protons. This characteristic is used here to distinguish between folded back magnetic fields (which would contain rotational discontinuities) and tangential discontinuities using Ulysses high-latitude, high-speed solar wind data. The analysis indicates that almost all reversals in the radial magnetic field in PBSs are folded back field lines. This is found to also be true outside PBSs, supporting existing results for typical high-speed, high-latitude wind. There remains a small number of cases that appear not to be folds in the magnetic field and which may be flux tubes with both ends rooted in the Sun. The distinct difference in MVA results inside and outside PBSs remains unexplained.

  8. Measurement of the strange quark contribution to the vector structure of the proton

    SciTech Connect

    Phillips, Sarah

    2007-11-30

    The goal of the G0 experiment is to determine the contribution of the strange quarks in the quark-antiquark sea to the structure of the nucleon. To this end, the experiment measured parityviolating asymmetries from elastic electron-proton scattering from 0.12 ≤ Q2 ≤ 1.0 (GeV/c)2 at Thomas Jefferson National Accelerator Facility. These asymmetries come from the interference of the electromagnetic and neutral weak interactions, and are sensitive to the strange quark contributions in the proton. The results from the forward-angle measurement, the linear combination of the strange electric and magnetic form factors GsE +ηGsM, suggest possible non-zero, Q2 dependent, strange quark contributions and provide new information to understand the magnitude of the contributions. This dissertation presents the analysis and results of the forward-angle measurement. In addition, the G0 experiment measured the beam-normal single-spin asymmetry in the elastic scattering of transversely polarized 3 GeV electrons from unpolarized protons at Q2 = 0.15, 0.25 (GeV/c)2 as part of the forward-angle measurement. The transverse asymmetry provides a direct probe of the imaginary component of the two-photon exchange amplitude, the complete description of which is important in the interpretation of data from precision electron-scattering experiments. The results of the measurement indicate that calculations using solely the elastic nucleon intermediate state are insufficient and generally agree with calculations that include significant inelastic hadronic intermediate state contributions. This dissertation presents the analysis and results of this measurement.

  9. Structures and Functions of Oligosaccharins

    SciTech Connect

    Albersheim, Peter

    1995-12-01

    We have made considerable progress during the 2.5 year funding period just ending in our studies of the structures and functions of oligosaccharide signal molecules (oligosaccharins). We have emphasized studies of the enzymes that solubilize, process, and degrade oligosaccharins and of the proteins that inhibit those enzymes. We have been especially interested in elucidating how oligosaccharins and their processing enzymes participate in determining the outcome of challenges to plants by pathogenic microbes. We have studied, to a lesser extent, the roles of oligosaccharins in plant growth and development. Abstracts of papers describing results acquired with support from this grant that have been published, submitted, or in preparation are presented to summarize the progress made during the last two and one half years. The report highlights the most important contributions made in our oiigosaccharin research during this time period, and the corresponding abstract is referenced. Results of work in progress are described primarily in conjunction with our application for continued support.

  10. Functional evolution of nuclear structure

    PubMed Central

    Dawson, Scott C.

    2011-01-01

    The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis. PMID:22006947

  11. Heliolatitude structure of the solar wind proton speed and density at 1 AU for heliospheric modeling

    NASA Astrophysics Data System (ADS)

    Sokol, Justyna Maria; Swaczyna, Pawel; Bzowski, Maciej; Tokumaru, Munetoshi

    2014-05-01

    The heliolatitudinal structure of solar wind proton speed and density varies with solar activity. A model of its variation with time is needed for heliospheric studies and modeling. It is important for the global heliospheric structure, allows for an assessment of ionization rates of neutral species in the heliosphere and interpretation of observations of the energetic neutral atoms and neutral interstellar atoms. Sokół et al. 2013 presented a model of the heliolatitudinal and time variations of solar wind structure based on results of the computer assisted tomography analysis of the solar wind speed enabled by remote-sensing observations of interplanetary scintillations, in-situ measurements from Ulysses, and in-ecliptic measurements from various missions gathered in the OMNI2 database. They determined the 3D structure of solar wind on a yearly time grid from 1990 to 2011. Now we increase the time resolution of the grid used in the model. Because of the weather conditions in Japan, where the interplanetary scintillation observations are carried out, the solar wind data sets contain systematic gaps. For the purposes of the increase of the time resolution of the model for heliospheric studies the method of filling of these gap is needed. We present a comparison of various methods of gap filling. We present results of the investigation of the procedures of reconstruction of the solar wind density with the use of the solar wind invariants published in the literature. Additionally we study various algorithms of extrapolation of the heliolatitudinal time series of the solar wind proton speed and number density in time.

  12. Rotavirus gene structure and function.

    PubMed Central

    Estes, M K; Cohen, J

    1989-01-01

    Knowledge of the structure and function of the genes and proteins of the rotaviruses has expanded rapidly. Information obtained in the last 5 years has revealed unexpected and unique molecular properties of rotavirus proteins of general interest to virologists, biochemists, and cell biologists. Rotaviruses share some features of replication with reoviruses, yet antigenic and molecular properties of the outer capsid proteins, VP4 (a protein whose cleavage is required for infectivity, possibly by mediating fusion with the cell membrane) and VP7 (a glycoprotein), show more similarities with those of other viruses such as the orthomyxoviruses, paramyxoviruses, and alphaviruses. Rotavirus morphogenesis is a unique process, during which immature subviral particles bud through the membrane of the endoplasmic reticulum (ER). During this process, transiently enveloped particles form, the outer capsid proteins are assembled onto particles, and mature particles accumulate in the lumen of the ER. Two ER-specific viral glycoproteins are involved in virus maturation, and these glycoproteins have been shown to be useful models for studying protein targeting and retention in the ER and for studying mechanisms of virus budding. New ideas and approaches to understanding how each gene functions to replicate and assemble the segmented viral genome have emerged from knowledge of the primary structure of rotavirus genes and their proteins and from knowledge of the properties of domains on individual proteins. Localization of type-specific and cross-reactive neutralizing epitopes on the outer capsid proteins is becoming increasingly useful in dissecting the protective immune response, including evaluation of vaccine trials, with the practical possibility of enhancing the production of new, more effective vaccines. Finally, future analyses with recently characterized immunologic and gene probes and new animal models can be expected to provide a basic understanding of what regulates the

  13. Structure and Mechanism of Proton Transport Through the Transmembrane Tetrameric M2 Protein Bundle of the Influenza A Virus

    SciTech Connect

    R Acharya; V Carnevale; G Fiorin; B Levine; A Polishchuk; V Balannick; I Samish; R Lamb; L Pinto; et al.

    2011-12-31

    The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2{sup +} and 3{sup +} with a pK{sub a} near 6. A 1.65 {angstrom} resolution X-ray structure of the transmembrane protein (residues 25-46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models.

  14. Electromagnetic structure of the proton within the CP-violation hypothesis

    SciTech Connect

    Krutov, A. F. Kudinov, M. Yu.

    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.

  15. Structures and spectroscopy of medium size protonated ammonia clusters at different temperatures, H+(NH3)10-16

    NASA Astrophysics Data System (ADS)

    Malloum, Alhadji; Fifen, Jean Jules; Dhaouadi, Zoubeida; Nana Engo, Serge Guy; Jaidane, Nejm-Eddine

    2017-01-01

    Structures of protonated ammonia clusters ( H + ( NH3 ) n ) are very important for the determination of pKa's and solvation energies of the proton in ammonia. In this work, their structures were investigated at M06-2X/6-31++g(d,p) level of theory, for n = 10 - 16 and for temperatures ranging from 0 to 400 K. In the cluster community, this is the first theoretical study on the protonated ammonia clusters larger than the nonamer. We noted that the population of the investigated clusters is reproduced by branched cage or cage like structures at low temperatures, while branched linear and branched cyclic or branched double cyclic isomers are the only isomers responsible for the population at higher temperatures. In these isomers, the proton is highly and entirely solvated at the center of the cluster. In addition, protonated ammonia clusters are all Eigen structures and the first solvation shell of the related ammonium ion core is saturated by four ammonia molecules. Moreover, infrared (IR) spectra of all isomers have been investigated and these spectra show good agreement with the experiment. This allowed us to assign experimental peaks and to provide the constitution of the populations of the various clusters.

  16. Reactions of acids with naphthyridine-functionalized ferrocenes: protonation and metal extrusion.

    PubMed

    Sadhukhan, Nabanita; Sarkar, Mithun; Ghatak, Tapas; Rahaman, S M Wahidur; Barbour, Leonard J; Bera, Jitendra K

    2013-02-04

    Reaction of 1,8-naphthyrid-2-yl-ferrocene (FcNP) with a variety of acids affords protonated salts at first, whereas longer reaction time leads to partial demetalation of FcNP resulting in a series of Fe complexes. The corresponding salts [FcNP·H][X] (X = BF(4) or CF(3)SO(3) (1)) are isolated for HBF(4) and CF(3)SO(3)H. Reaction of FcNP with equimolar amount of CF(3)CO(2)H for 12 h affords a neutral complex [Fe(FcNP)(2)(O(2)CCF(3))(2)(OH(2))(2)] (2). Use of excess acid gave a trinuclear Fe(II) complex [Fe(3)(H(2)O)(2)(O(2)CCF(3))(8)(FcNP·H)(2)] (3). Three linear iron atoms are held together by four bridging trifluoroacetates and two aqua ligands in a symmetric fashion. Reaction with ethereal solution of HCl afforded [(FcNP·H)(3)(Cl)][FeCl(4)](2) (4) irrespective of the amount of the acid used. Even the picric acid (HPic) led to metal extrusion giving rise to [Fe(2)(Cl)(2)(FcNP)(2)(Pic)(2)] (5) when crystallized from dichloromethane. Metal extrusion was also observed for CF(3)SO(3)H, but an analytically pure compound could not be isolated. The demetalation reaction proceeds with an initial proton attack to the distal nitrogen of the NP unit. Subsequently, coordination of the conjugate base to the electrophilic Fe facilitates the release of Cp rings from metal. The conjugate base plays an important role in the demetalation process and favors the isolation of the Fe complex as well. The 1,1'-bis(1,8-naphthyrid-2-yl)ferrocene (FcNP(2)) does not undergo demetalation under identical conditions. Two NP units share one positive charge causing the Fe-Cp bonds weakened to an extent that is not sufficient for demetalation. X-ray structure of the monoprotonated FcNP(2) reveals a discrete dimer [(FcNP(2)·H)](2)[OTf](2) (6) supported by two N-H···N hydrogen bonds. Crystal packing and dispersive forces associated with intra- and intermolecular π-π stacking interactions (NP···NP and Cp···NP) allow the formation of the dimer in the solid-state. The protonation and

  17. Energy dependent track structure parametrisations for protons and carbon ions based on nanometric simulations

    NASA Astrophysics Data System (ADS)

    Alexander, Frauke; Villagrasa, Carmen; Rabus, Hans; Wilkens, Jan J.

    2015-09-01

    The BioQuaRT project within the European Metrology Research Programme aims at correlating ion track structure characteristics with the biological effects of radiation and develops measurement and simulation techniques for determining ion track structure on different length scales from about 2 nm to about 10 μm. Within this framework, we investigate methods to translate track-structure quantities derived on a nanometre scale to macroscopic dimensions. Input data sets were generated by simulations of ion tracks of protons and carbon ions in liquid water using the Geant 4 Monte Carlo toolkit with the Geant4-DNA processes. Based on the energy transfer points - recorded with nanometre resolution - we investigated parametrisations of overall properties of ion track structure. Three different track structure parametrisations have been developed using the distances to the 10 next neighbouring ionisations, the radial energy distribution and ionisation cluster size distributions. These parametrisations of nanometric track structure build a basis for deriving biologically relevant mean values which are essential in the clinical situation where each voxel is exposed to a mixed radiation field. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey Solov'yov, Nigel Mason, Gustavo García, Eugene Surdutovich.

  18. 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.

  19. Structure of olefin-imidacloprid and gas-phase fragmentation chemistry of its protonated form.

    PubMed

    Fusetto, Roberto; White, Jonathan M; Hutton, Craig A; O'Hair, Richard A J

    2016-02-07

    One of the major insect metabolites of the widely used neonicotinoid insecticide imidacloprid, 1 (1-[(6-chloro-3-pyridinyl)methyl]-N-nitro-1H-imidazol-2-amine), is the olefin 2. To better understand how the structure of olefin 2 relates to the gas-phase fragmentation of its protonated form, 2H(+), X-ray crystallography, tandem mass spectrometry experiments and DFT calculations were carried out. Olefin 2 was found to be in a tautomeric form where the proton is on the N(1) position of the imidazole ring and forms a hydrogen bond to one of the oxygen atoms of the coplanar nitroamine group. Under conditions of low-energy collision-induced dissociation (CID) in a linear ion trap, 2H(+), formed via electrospray ionization (ESI), fragments via a major loss of water, together with minor competing losses of HNO2 and NO2•.This contrasts with 1H+, which mainly undergoes bond homolysis via NO2• loss. Thus, installation of the double bond in 2 plays a key role in facilitating the loss of water. DFT calculations, carried out using the B3LYP/6-311G++(d,p) level of theory, revealed that loss of water was energetically more favourable compared to HNO2 and NO2• loss. Three multistep, energetically accessible mechanisms were identified for loss of water from 2H(+), and these have the following barriers: (I) direct proton transfer from N(5) of the pyridine to O(1) on the NO2 group (119 kJ mol(-1)); (II) rotation of the N(2)-N(4) bond (117 kJ mol(-1)); (III) 1,3-intramolecular proton transfer between the two oxygen atoms of the NO2 group (145 kJ mol(-1)). Given that the lowest barrier for the losses of HNO2 and NO2• is 156 kJ mol(-1), it is likely that all three water loss mechanisms occur concurrently.

  20. The proton collecting function of the inner surface of cytochrome c oxidase from Rhodobacter sphaeroides.

    PubMed

    Marantz, Y; Nachliel, E; Aagaard, A; Brzezinski, P; Gutman, M

    1998-07-21

    The experiments presented in this study address the problem of how the cytoplasmic surface (proton-input side) of cytochrome c oxidase interacts with protons in the bulk. For this purpose, the cytoplasmic surface of the enzyme was labeled with a fluorescein (Flu) molecule covalently bound to Cys223 of subunit III. Using the Flu as a proton-sensitive marker on the surface and phiOH as a soluble excited-state proton emitter, the dynamics of the acid-base equilibration between the surface and the bulk was measured in the time-resolved domain. The results were analyzed by using a rigorous kinetic analysis that is based on numeric integration of coupled nonliner differential rate equations in which the rate constants are used as adjustable parameters. The analysis of 11 independent measurements, carried out under various initial conditions, indicated that the protonation of the Flu proceeds through multiple pathways involving diffusion-controlled reactions and proton exchange among surface groups. The surface of the protein carries an efficient system made of carboxylate and histidine moieties that are sufficiently close to each other as to form a proton-collecting antenna. It is the passage of protons among these sites that endows cytochrome c oxidase with the capacity to pick up protons from the buffered cytoplasmic matrix within a time frame compatible with the physiological turnover of the enzyme.

  1. Structural water cluster as a possible proton acceptor in the adduct decay reaction of oat phototropin 1 LOV2 domain.

    PubMed

    Chan, Ruby H; Bogomolni, Roberto A

    2012-09-06

    LOV domains (Light, Oxygen, Voltage) are the light-sensory modules of phototropins, the blue-light photoreceptor kinases in plants, and of a wide variety of flavoproteins found in all three domains of life. These 12 kDa modules bind a flavin chromophore (FMN or FAD) noncovalently and undergo a photochemical activation in which the sulfur atom of a conserved cysteine forms an adduct to the C(4a) carbon of the flavin. The adduct breaks spontaneously in a base-catalyzed reaction involving a rate-limiting proton-transfer step, regenerating the dark state in seconds. This photocycle involves chromophore and protein structural changes that activate the C-terminal serine/threonine kinase. Previous studies (Biochemistry 2007, 46, 7016-7021) showed that decreased hydration obtained at high glycerol concentrations stabilizes the adduct state in a manner similar to that attained at low temperatures, resulting in much longer adduct decay times. This kinetic effect was attributed to an increased protein rigidity that hindered structural fluctuations necessary for the decay reaction. In this work, we studied the adduct decay kinetics of oat phototropin 1 (phot1) LOV2 at varying hydration using a specially designed chamber that allowed for measurement of UV-visible and FTIR spectra of the same samples. Therefore, we obtained LOV protein concentrations, adduct decay kinetics, and the different populations of bound water by deconvolution of the broad water absorption peak around 3500 cm(-1). A linear dependence of the adduct decay rate constant on the concentration of double and triple hydrogen-bonded waters strongly suggests that the adduct decay is a pseudo-first-order reaction in which both the adduct and the strongly bound waters are reactants. We suggest that a cluster of strongly bound water functions as the proton acceptor in the rate-limiting step of adduct decay.

  2. Endocrine function following high dose proton therapy for tumors of the upper clivus

    SciTech Connect

    Slater, J.D.; Austin-Seymour, M.; Munzenrider, J.; Birnbaum, S.; Carroll, R.; Klibanski, A.; Riskind, P.; Urie, M.; Verhey, L.; Goitein, M.

    1988-09-01

    The endocrine status of patients receiving proton radiation for tumors of the upper clivus was reviewed to evaluate the effect of high dose treatment on the pituitary gland. The fourteen patients had chordomas or low grade chondrosarcomas and were all treated by the same techniques. The median tumor dose was 69.7 Cobalt Gray Equivalent (CGE) with a range from 66.6 to 74.4 CGE. (CGE is used because modulated protons have an RBE of 1.1 compared to 60Co). The daily fraction size was 1.8-2.1 CGE. The median follow-up time is 48 months, ranging from 30 to 68 months. All treatments were planned using a computerized multi-dimensional system with the position of the pituitary outlined on the planning CT scan. Review of the dose distribution indicated that the dose to the pituitary ranged from 60.5 to 72.3 CGE, with a median of 67.6 CGE. One female patient had decreased thyroid and gonadotropin function at the time of diagnosis and has been on hormone replacement since that time. The other three females were all pre-menopausal at the time of radiotherapy. At this time four patients (3 males and 1 female) have developed endocrine abnormalities 14 to 45 months after irradiation. All four had evidence of hypothyroidism and two have also developed corticotropin deficiency. The three males had decreased testosterone levels; the female patient developed amenorrhea and hyperprolactinemia. All four are asymptomatic with ongoing hormone replacement.

  3. Observations of defect structure evolution in proton and Ni ion irradiated Ni-Cr binary alloys

    NASA Astrophysics Data System (ADS)

    Briggs, Samuel A.; Barr, Christopher M.; Pakarinen, Janne; Mamivand, Mahmood; Hattar, Khalid; Morgan, Dane D.; Taheri, Mitra; Sridharan, Kumar

    2016-10-01

    Two binary Ni-Cr model alloys with 5 wt% Cr and 18 wt% Cr were irradiated using 2 MeV protons at 400 and 500 °C and 20 MeV Ni4+ ions at 500 °C to investigate microstructural evolution as a function of composition, irradiation temperature, and irradiating ion species. Transmission electron microscopy (TEM) was applied to study irradiation-induced void and faulted Frank loops microstructures. Irradiations at 500 °C were shown to generate decreased densities of larger defects, likely due to increased barriers to defect nucleation as compared to 400 °C irradiations. Heavy ion irradiation resulted in a larger density of smaller voids when compared to proton irradiations, indicating in-cascade clustering of point defects. Cluster dynamics simulations were in good agreement with the experimental findings, suggesting that increases in Cr content lead to an increase in interstitial binding energy, leading to higher densities of smaller dislocation loops in the Ni-18Cr alloy as compared to the Ni-5Cr alloy.

  4. Interaction of ring current and radiation belt protons with ducted plasmaspheric hiss. 2. Time evolution of the distribution function

    NASA Astrophysics Data System (ADS)

    Kozyra, J. U.; Rasmussen, C. E.; Miller, R. H.; Villalon, E.

    1995-11-01

    The evolution of the bounce-averaged ring current/radiation belt proton distribution is simulated during resonant interactions with ducted plasmaspheric hiss. The plasmaspheric hiss is assumed to be generated by ring current electrons and to be damped by the energetic protons. Thus energy is transferred between energetic electrons and protons using the plasmaspheric hiss as a mediary. The problem is not solved self-consistently. During the simulation period, interactions with ring current electrons (not represented in the model) are assumed to maintain the wave amplitudes in the presence of damping by the energetic protons, allowing the wave spectrum to be held fixed. Diffusion coefficients in pitch angle, cross pitch angle/energy, and energy were previously calculated by Kozyra et al. (1994) and are adopted for the present study. The simulation treats the energy range, E>=80 keV, within which the wave diffusion operates on a shorter timescale than other proton loss processes (i.e., Coulomb drag and charge exchange). These other loss processes are not included in the simulation. An interesting result of the simulation is that energy diffusion maximizes at moderate pitch angles near the edge of the atmospheric loss cone. Over the simulation period, diffusion in energy creates an order of magnitude enhancement in the bounce-averaged proton distribution function at moderate pitch angles. The loss cone is nearly empty because scattering of particles at small pitch angles is weak. The bounce-averaged flux distribution, mapped to ionospheric heights, results in elevated locally mirroring proton fluxes. OGO 5 observed order of magnitude enhancements in locally mirroring energetic protons at altitudes between 350 and 1300 km and invariant latitudes between 50° and 60° (Lundblad and Soraas, 1978). The proton distributions were highly anisotropic in pitch angle with nearly empty loss cones. The similarity between the observed distributions and those resulting from this

  5. Comparison of γZ-structure function models

    SciTech Connect

    Rislow, Benjamin C.

    2013-11-07

    The γZ-box is an important contribution to the proton's weak charge. The γZ-box is calculated dispersively and depends on γZ-structure functions, F{sub 1,2,3}{sup γZ}(x,Q{sup 2}). At present there is no data for these structure functions and they must be modeled by modifying existing fits to electromagnetic data. Each group that has studied the γZ-box used different modifications. The results of the PVDIS experiment at Jefferson Lab may provide a first test of the validity of each group's models. I present details of the different models and their predictions for the PVDIS result.

  6. Comparison of {gamma}Z-structure function models

    SciTech Connect

    Rislow, Benjamin C.

    2013-11-01

    The {gamma}Z-box is an important contribution to the proton's weak charge. The {gamma}Z-box is calculated dispersively and depends on {gamma}Z-structure functions, F{sub {gamma}Z1,2,3}(x,Q{sup 2}) . At present there is no data for these structure functions and they must be modeled by modifying existing fits to electromagnetic data. Each group that has studied the {gamma}Z-box used different modifications. The results of the PVDIS experiment at Jefferson Lab may provide a first test of the validity of each group's models. I present details of the different models and their predictions for the PVDIS result.

  7. Jet and underlying event properties as a function of charged-particle multiplicity in proton-proton collisions at sqrt(s) = 7 TeV

    SciTech Connect

    Chatrchyan, Serguei; et al.,

    2013-12-17

    Characteristics of multi-particle production in proton-proton collisions at sqrt(s) = 7 TeV are studied as a function of the charged-particle multiplicity, N[ch]. The produced particles are separated into two classes: those belonging to jets and those belonging to the underlying event. Charged particles are measured with pseudorapidity abs(eta) < 2.4 and transverse momentum pt > 0.25 GeV. Jets are reconstructed from charged-particles only and required to have pt > 5 GeV. The distributions of jet pt, average pt of charged particles belonging to the underlying event or to jets, jet rates, and jet shapes are presented as functions of N[ch] and compared to the predictions of the PYTHIA and HERWIG event generators. Predictions without multi-parton interactions fail completely to describe the N[ch]-dependence observed in the data. For increasing N[ch], PYTHIA systematically predicts higher jet rates and harder pt spectra than seen in the data, whereas HERWIG shows the opposite trends. At the highest multiplicity, the data-model agreement is worse for most observables, indicating the need for further tuning and/or new model ingredients.

  8. Jet and underlying event properties as a function of charged-particle multiplicity in proton-proton collisions at [Formula: see text].

    PubMed

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Rohe, T; Bachmair, F; Bäni, L; Bianchini, L; Bortignon, P; Buchmann, M A; Casal, B; Chanon, N; Deisher, A; Dissertori, G; Dittmar, M; Donegà, M; Dünser, M; Eller, P; Freudenreich, K; Grab, C; Hits, D; Lecomte, P; Lustermann, W; Mangano, B; Marini, A C; Martinez Ruiz Del Arbol, P; Meister, D; Mohr, N; Moortgat, F; Nägeli, C; Nef, P; Nessi-Tedaldi, F; Pandolfi, F; Pape, L; Pauss, F; Peruzzi, M; Quittnat, M; Ronga, F J; Rossini, M; Sala, L; Sanchez, A K; Starodumov, A; Stieger, B; Takahashi, M; Tauscher, L; Thea, A; Theofilatos, K; Treille, D; Urscheler, C; Wallny, R; Weber, H A; Amsler, C; Chiochia, V; Favaro, C; Ivova Rikova, M; Kilminster, B; Millan Mejias, B; Robmann, P; Snoek, H; Taroni, S; Verzetti, M; Yang, Y; Cardaci, M; Chen, K H; Ferro, C; Kuo, C M; Li, S W; Lin, W; Lu, Y J; Volpe, R; Yu, S S; Bartalini, P; Chang, P; Chang, Y H; Chang, Y W; Chao, Y; Chen, K F; Dietz, C; Grundler, U; Hou, W-S; Hsiung, Y; Kao, K Y; Lei, Y J; Lu, R-S; Majumder, D; Petrakou, E; Shi, X; Shiu, J G; Tzeng, Y M; 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Sun, W; Teo, W D; Thom, J; Thompson, J; Tucker, J; Weng, Y; Winstrom, L; Wittich, P; Winn, D; Abdullin, S; Albrow, M; Anderson, J; Apollinari, G; Bauerdick, L A T; Beretvas, A; Berryhill, J; Bhat, P C; Burkett, K; Butler, J N; Chetluru, V; Cheung, H W K; Chlebana, F; Cihangir, S; Elvira, V D; Fisk, I; Freeman, J; Gao, Y; Gottschalk, E; Gray, L; Green, D; Gutsche, O; Hare, D; Harris, R M; Hirschauer, J; Hooberman, B; Jindariani, S; Johnson, M; Joshi, U; Kaadze, K; Klima, B; Kunori, S; Kwan, S; Linacre, J; Lincoln, D; Lipton, R; Lykken, J; Maeshima, K; Marraffino, J M; Martinez Outschoorn, V I; Maruyama, S; Mason, D; McBride, P; Mishra, K; Mrenna, S; Musienko, Y; Newman-Holmes, C; O'Dell, V; Prokofyev, O; Ratnikova, N; Sexton-Kennedy, E; Sharma, S; Spalding, W J; Spiegel, L; Taylor, L; Tkaczyk, S; Tran, N V; Uplegger, L; Vaandering, E W; Vidal, R; Whitmore, J; Wu, W; Yang, F; Yun, J C; Acosta, D; Avery, P; Bourilkov, D; Chen, M; Cheng, T; Das, S; De Gruttola, M; Di Giovanni, G P; Dobur, D; Drozdetskiy, A; Field, R D; Fisher, M; Fu, Y; Furic, I K; Hugon, J; Kim, B; Konigsberg, J; Korytov, A; Kropivnitskaya, A; Kypreos, T; Low, J F; Matchev, K; Milenovic, P; Mitselmakher, G; Muniz, L; Remington, R; Rinkevicius, A; Skhirtladze, N; Snowball, M; Yelton, J; Zakaria, M; Gaultney, V; Hewamanage, S; Linn, S; Markowitz, P; Martinez, G; Rodriguez, J L; Adams, T; Askew, A; Bochenek, J; Chen, J; Diamond, B; Haas, J; Hagopian, S; Hagopian, V; Johnson, K F; Prosper, H; Veeraraghavan, V; Weinberg, M; Baarmand, M M; Dorney, B; Hohlmann, M; Kalakhety, H; Yumiceva, F; Adams, M R; Apanasevich, L; Bazterra, V E; Betts, R R; Bucinskaite, I; Callner, J; Cavanaugh, R; Evdokimov, O; Gauthier, L; Gerber, C E; Hofman, D J; Khalatyan, S; Kurt, P; Lacroix, F; Moon, D H; O'Brien, C; Silkworth, C; Strom, D; Turner, P; Varelas, N; Akgun, U; Albayrak, E A; Bilki, B; Clarida, W; Dilsiz, K; Duru, F; Griffiths, S; Merlo, J-P; Mermerkaya, H; Mestvirishvili, A; Moeller, A; Nachtman, J; Newsom, C R; Ogul, H; 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Zhukova, V; Dahmes, B; De Benedetti, A; Gude, A; Haupt, J; Kao, S C; Klapoetke, K; Kubota, Y; Mans, J; Pastika, N; Rusack, R; Sasseville, M; Singovsky, A; Tambe, N; Turkewitz, J; Acosta, J G; Cremaldi, L M; Kroeger, R; Oliveros, S; Perera, L; Rahmat, R; Sanders, D A; Summers, D; Avdeeva, E; Bloom, K; Bose, S; Claes, D R; Dominguez, A; Eads, M; Gonzalez Suarez, R; Keller, J; Kravchenko, I; Lazo-Flores, J; Malik, S; Meier, F; Snow, G R; Dolen, J; Godshalk, A; Iashvili, I; Jain, S; Kharchilava, A; Kumar, A; Rappoccio, S; Wan, Z; Alverson, G; Barberis, E; Baumgartel, D; Chasco, M; Haley, J; Massironi, A; Nash, D; Orimoto, T; Trocino, D; Wood, D; Zhang, J; Anastassov, A; Hahn, K A; Kubik, A; Lusito, L; Mucia, N; Odell, N; Pollack, B; Pozdnyakov, A; Schmitt, M; Stoynev, S; Sung, K; Velasco, M; Won, S; Berry, D; Brinkerhoff, A; Chan, K M; Hildreth, M; Jessop, C; Karmgard, D J; Kolb, J; Lannon, K; Luo, W; Lynch, S; Marinelli, N; Morse, D M; Pearson, T; Planer, M; Ruchti, R; Slaunwhite, J; Valls, N; Wayne, M; Wolf, M; Antonelli, L; Bylsma, B; Durkin, L S; Hill, C; Hughes, R; Kotov, K; Ling, T Y; Puigh, D; Rodenburg, M; Smith, G; Vuosalo, C; Winer, B L; Wolfe, H; Berry, E; Elmer, P; Halyo, V; Hebda, P; Hegeman, J; Hunt, A; Jindal, P; Koay, S A; Lujan, P; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Piroué, P; Quan, X; Raval, A; Saka, H; Stickland, D; Tully, C; Werner, J S; Zenz, S C; Zuranski, A; Brownson, E; Lopez, A; Mendez, H; Ramirez Vargas, J E; Alagoz, E; Benedetti, D; Bolla, G; Bortoletto, D; De Mattia, M; Everett, A; Hu, Z; Jones, M; Jung, K; Koybasi, O; Kress, M; Leonardo, N; Lopes Pegna, D; Maroussov, V; Merkel, P; Miller, D H; Neumeister, N; Shipsey, I; Silvers, D; Svyatkovskiy, A; Wang, F; Xie, W; Xu, L; Yoo, H D; Zablocki, J; Zheng, Y; Parashar, N; Adair, A; Akgun, B; Ecklund, K M; Geurts, F J M; Li, W; Michlin, B; Padley, B P; Redjimi, R; Roberts, J; Zabel, J; Betchart, B; Bodek, A; Covarelli, R; de Barbaro, P; Demina, R; Eshaq, Y; Ferbel, T; Garcia-Bellido, A; Goldenzweig, P; Han, J; Harel, A; Miner, D C; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Ciesielski, R; Demortier, L; Goulianos, K; Lungu, G; Malik, S; Mesropian, C; Arora, S; Barker, A; Chou, J P; Contreras-Campana, C; Contreras-Campana, E; Duggan, D; Ferencek, D; Gershtein, Y; Gray, R; Halkiadakis, E; Hidas, D; Lath, A; Panwalkar, S; Park, M; Patel, R; Rekovic, V; Robles, J; Salur, S; Schnetzer, S; Seitz, C; Somalwar, S; Stone, R; Thomas, S; Thomassen, P; Walker, M; Cerizza, G; Hollingsworth, M; Rose, K; Spanier, S; Yang, Z C; York, A; Bouhali, O; Eusebi, R; Flanagan, W; Gilmore, J; Kamon, T; Khotilovich, V; Montalvo, R; Osipenkov, I; Pakhotin, Y; Perloff, A; Roe, J; Safonov, A; Sakuma, T; Suarez, I; Tatarinov, A; Toback, D; Akchurin, N; Cowden, C; Damgov, J; Dragoiu, C; Dudero, P R; Kovitanggoon, K; Lee, S W; Libeiro, T; Volobouev, I; Appelt, E; Delannoy, A G; Greene, S; Gurrola, A; Johns, W; Maguire, C; Mao, Y; Melo, A; Sharma, M; Sheldon, P; Snook, B; Tuo, S; Velkovska, J; Arenton, M W; Boutle, S; Cox, B; Francis, B; Goodell, J; Hirosky, R; Ledovskoy, A; Lin, C; Neu, C; Wood, J; Gollapinni, S; Harr, R; Karchin, P E; Kottachchi Kankanamge Don, C; Lamichhane, P; Sakharov, A; Belknap, D A; Borrello, L; Carlsmith, D; Cepeda, M; Dasu, S; Duric, S; Friis, E; Grothe, M; Hall-Wilton, R; Herndon, M; Hervé, A; Klabbers, P; Klukas, J; Lanaro, A; Loveless, R; Mohapatra, A; Ojalvo, I; Perry, T; Pierro, G A; Polese, G; Ross, I; Sarangi, T; Savin, A; Smith, W H; Swanson, J

    Characteristics of multi-particle production in proton-proton collisions at [Formula: see text] are studied as a function of the charged-particle multiplicity, Nch. The produced particles are separated into two classes: those belonging to jets and those belonging to the underlying event. Charged particles are measured with pseudorapidity |η|<2.4 and transverse momentum pT>0.25 GeV/c. Jets are reconstructed from charged-particles only and required to have pT>5 GeV/c. The distributions of jet pT, average pT of charged particles belonging to the underlying event or to jets, jet rates, and jet shapes are presented as functions of Nch and compared to the predictions of the pythia and herwig event generators. Predictions without multi-parton interactions fail completely to describe the Nch-dependence observed in the data. For increasing Nch, pythia systematically predicts higher jet rates and harder pT spectra than seen in the data, whereas herwig shows the opposite trends. At the highest multiplicity, the data-model agreement is worse for most observables, indicating the need for further tuning and/or new model ingredients.

  9. Structure and functions of fungal cell surfaces

    NASA Technical Reports Server (NTRS)

    Nozawa, Y.

    1984-01-01

    A review with 24 references on the biochemistry, molecular structure, and function of cell surfaces of fungi, especially dermatophytes: the chemistry and structure of the cell wall, the effect of polyene antibiotics on the morphology and function of cytoplasmic membranes, and the chemical structure and function of pigments produced by various fungi are discussed.

  10. Excitation Functions and Production Rates of Radionuclides Produced in the Proton Bombardment of natPr and natLa

    SciTech Connect

    Vermeulen, C.; Steyn, G.F.; Walt, T.N. van der; Nortier, F.M.; Szelecsenyi, F.; Kovacs, Z.

    2005-05-24

    Excitation functions and production rates are presented for various radionuclides formed in the bombardment of natPr and natLa with protons. Comparisons are made with theoretical predictions based on the geometry dependent hybrid model. Alternative production routes for 139Pr and 139Ce are investigated.

  11. Structure functions at large Bjorken x and the Transition between perturbative and non-perturbative QCD

    SciTech Connect

    Liuti, S.; Bianchi, N.; Fantoni, A.

    2005-10-06

    We study both polarized and unpolarized proton structure functions in the kinematical region of large Bjorken x and four-momentum tranfer of few GeV2, characterized by the phenomenon of parton-hadron duality between the smooth continuation of the deep inelastic scattering curve and the average of the nucleon resonances which dominate this region. We present results on a perturbative-QCD analysis using recent accurate data aimed at extracting the infrared behavior of the nucleon structure functions.

  12. Pion structure function from leading neutron electroproduction and SU(2) flavor asymmetry

    NASA Astrophysics Data System (ADS)

    McKenney, J. R.; Sato, Nobuo; Melnitchouk, W.; Ji, Chueng-Ryong

    2016-03-01

    We examine the efficacy of pion exchange models to simultaneously describe leading neutron electroproduction at HERA and the d ¯ -u ¯ flavor asymmetry in the proton. A detailed χ2 analysis of the ZEUS and H1 cross sections, when combined with constraints on the pion flux from Drell-Yan data, allows regions of applicability of one-pion exchange to be delineated. The analysis disfavors several models of the pion flux used in the literature and yields an improved extraction of the pion structure function and its uncertainties at parton momentum fractions in the pion of 4 ×10-4≲xπ≲0.05 at a scale of Q2=10 GeV2 . Based on the fit results, we provide estimates for leading proton structure functions in upcoming tagged deep-inelastic scattering experiments at Jefferson Lab on the deuteron with forward protons.

  13. Pion structure function from leading neutron electroproduction and SU(2) flavor asymmetry

    SciTech Connect

    McKenney, Joshua R.; Sato Gonzalez, Nobuo; Melnitchouk, Wally; Ji, Chueng-Ryong

    2016-03-01

    We examine the efficacy of pion exchange models to simultaneously describe leading neutron electroproduction at HERA and the $\\bar{d}-\\bar{u}$ flavor asymmetry in the proton. A detailed $\\chi^2$ analysis of the ZEUS and H1 cross sections, when combined with constraints on the pion flux from Drell-Yan data, allows regions of applicability of one-pion exchange to be delineated. The analysis disfavors several models of the pion flux used in the literature, and yields an improved extraction of the pion structure function and its uncertainties at parton momentum fractions in the pion of $4 \\times 10^{-4} \\lesssim x_\\pi \\lesssim 0.05$ at a scale of $Q^2$=10 GeV$^2$. Based on the fit results, we provide estimates for leading proton structure functions in upcoming tagged deep-inelastic scattering experiments at Jefferson Lab on the deuteron with forward protons.

  14. Pion structure function from leading neutron electroproduction and SU(2) flavor asymmetry

    SciTech Connect

    McKenney, Joshua R.; Sato, Nobuo; Melnitchouk, Wally; Ji, Chueng-Ryong

    2016-03-07

    In this paper, we examine the efficacy of pion exchange models to simultaneously describe leading neutron electroproduction at HERA and the $\\bar{d}-\\bar{u}$ flavor asymmetry in the proton. A detailed $\\chi^2$ analysis of the ZEUS and H1 cross sections, when combined with constraints on the pion flux from Drell-Yan data, allows regions of applicability of one-pion exchange to be delineated. The analysis disfavors several models of the pion flux used in the literature, and yields an improved extraction of the pion structure function and its uncertainties at parton momentum fractions in the pion of $4 \\times 10^{-4} \\lesssim x_\\pi \\lesssim 0.05$ at a scale of $Q^2$=10 GeV$^2$. Also, we provide estimates for leading proton structure functions in upcoming tagged deep-inelastic scattering experiments on the deuteron with forward protons, based on the fit results, at Jefferson Lab.

  15. Proton beam writing of long, arbitrary structures for micro/nano photonics and fluidics applications

    NASA Astrophysics Data System (ADS)

    Udalagama, Chammika; Teo, E. J.; Chan, S. F.; Kumar, V. S.; Bettiol, A. A.; Watt, F.

    2011-10-01

    The last decade has seen proton beam writing maturing into a versatile lithographic technique able to produce sub-100 nm, high aspect ratio structures with smooth side walls. However, many applications in the fields of photonics and fluidics require the fabrication of structures with high spatial resolution that extends over several centimetres. This cannot be achieved by purely magnetic or electrostatic beam scanning due to the large off-axis beam aberrations in high demagnification systems. As a result, this has limited us to producing long straight structures using a combination of beam and stage scanning. In this work we have: (1) developed an algorithm to include any arbitrary pattern into the writing process by using a more versatile combination of beam and stage scanning while (2) incorporating the use of the ubiquitous AutoCAD DXF (drawing exchange format) into the design process. We demonstrate the capability of this approach in fabricating structures such as Y-splitters, Mach-Zehnder modulators and microfluidic channels that are over several centimetres in length, in polymer. We also present optimisation of such parameters as scanning speed and scanning loops to improve on the surface roughness of the structures. This work opens up new possibilities of using CAD software in PBW for microphotonics and fluidics device fabrication.

  16. Improved transport property of proton-conducting solid oxide fuel cell with multi-layered electrolyte structure

    NASA Astrophysics Data System (ADS)

    Shimada, Hiroyuki; Yamaguchi, Toshiaki; Sumi, Hirofumi; Nomura, Katsuhiro; Yamaguchi, Yuki; Fujishiro, Yoshinobu

    2017-10-01

    A multi-layered electrolyte structure is proposed for proton-conducting solid oxide fuel cells (SOFCs) to achieve higher power density and higher open-circuit voltage (OCV). Although recent proton-conducting SOFCs have demonstrated high power density, their OCVs have been lower than that of conventional SOFCs with stabilized zirconia because proton-conducting oxides intrinsically have electron-hole conduction. The proposed electrolyte structure has a porous BaZr0.1Ce0.7Y0.1Yb0.1O3-δ (BZCYYb) layer deposited on a dense BZCYYb layer. This structure effectively improves both cathode polarization and ionic transport property, resulting in higher power density with higher OCV. Also, discussion based on an equivalent circuit model of proton-conducting SOFCs clearly reveals a mechanism that determines OCV, namely, higher ohmic resistance and lower electrode polarization resistance lead to higher OCV. Our results suggest that higher electrode performance is essential for proton-conducting SOFCs to achieve higher OCV, particularly in the case of anode-supported configurations with thin electrolyte.

  17. The energy spectra of solar energetic protons in the large energy range: their functional form and parameters.

    NASA Astrophysics Data System (ADS)

    Nymmik, Rikho; Pervaia, Taisia

    2016-07-01

    Experimental data on the fluxes of protons of solar energetic particles (SEP) are analyzed. It is known that above energies of 2-45 MeV (averaging 27-30 MeV), the proton spectra are a power-law function of the energy (at relativistic energies - from the momentum) of the particles. At lower energies, the spectra become harder, with the high-energy part of the spectra forming the "knee". This report is devoted to the determination of the parameters of the SEP spectra, having the form of a "double power-law shape", to ascertain the reliability of the parameters of the approximations of the experimental data.

  18. Molecular mechanisms for proton transport in membranes.

    PubMed Central

    Nagle, J F; Morowitz, H J

    1978-01-01

    Likely mechanisms for proton transport through biomembranes are explored. The fundamental structural element is assumed to be continuous chains of hydrogen bonds formed from the protein side groups, and a molecular example is presented. From studies in ice, such chains are predicted to have low impedance and can function as proton wires. In addition, conformational changes in the protein may be linked to the proton conduction. If this possibility is allowed, a simple proton pump can be described that can be reversed into a molecular motor driven by an electrochemical potential across the membrane. PMID:272644

  19. Structure and function of vanadium compounds in living organisms.

    PubMed

    Rehder, D

    1992-01-01

    Vanadium has been recognized as a metal of biological importance only recently. In this mini-review, its main functions uncovered during the past few years are addressed. These encompass (i) the regulation of phosphate metabolizing enzymes (which is exemplified for the inhibition of ribonucleases by vanadate), (ii) the halogenation of organic compounds by vanadate-dependent non-heme peroxidases from seaweeds, (iii) the reductive protonation of nitrogen (nitrogen fixation) by alternative, i.e. vanadium-containing, nitrogenases from N2-fixing bacteria, (iv) vanadium sequestering by sea squirts (ascidians), and (v) amavadine, a low molecular weight complex of V(IV) accumulated in the fly agaric and related toadstools. The function of vanadium, while still illusive in ascidians and toadstools, begins to be understood in vanadium-enzyme interaction. Investigations into the structure and function of model compounds play an increasingly important role in elucidating the biological significance of vanadium.

  20. M2 protein from influenza A: from multiple structures to biophysical and functional insights.

    PubMed

    Cross, Timothy A; Dong, Hao; Sharma, Mukesh; Busath, David D; Zhou, Huan-Xiang

    2012-04-01

    The M2 protein from influenza A is a proton channel as a tetramer, with a single transmembrane helix from each monomer lining the pore. Val27 and Trp41 form gates at either end of the pore and His37 mediates the shuttling of protons across a central barrier between the N-terminal and C-terminal aqueous pore regions. Numerous structures of this transmembrane domain and of a longer construct that includes an amphipathic helix are now in the Protein Data Bank. Many structural differences are apparent from samples obtained in a variety of membrane mimetic environments. High-resolution structural results in lipid bilayers have provided novel insights into the functional mechanism of the unique HxxxW cluster in the M2 proton channel.

  1. Rotational structure of the odd-proton nuclide 171Tm: A projected shell model study

    NASA Astrophysics Data System (ADS)

    Liu, YanXin; Chen, FangQi; Yu, ShaoYing; Sun, Yang

    2015-05-01

    Deformed odd-mass nuclei are ideal examples where the interplay between single-particle and collective degrees of freedom can be studied. Inspired by the recent experimental high-spin data in the odd-proton nuclide 171Tm, we perform projected shell model (PSM) calculations to investigate structure of the ground band and other bands based on isomeric states. In addition to the usual quadrupole-quadrupole force in the Hamiltonian, we employ the hexadecapole-hexadecapole ( HH) interaction, in a self-consistent way with the hexadecapole deformation of the deformed basis. It is found that the known experimental data can be well described by the PSM calculation. The effect of the HH force on the quasiparticle isomeric states is discussed.

  2. Predicting the axial structure of the proton using a quark-diquark model

    NASA Astrophysics Data System (ADS)

    Oxholm, Trevor M.; Hobbs, Timothy J.; Miller, Gerald A.

    2017-01-01

    The form factors of the proton typically measured via elastic electroweak scattering have long been a rich testing ground for models of nucleon structure. We explore the ability of a model based in a quark/spectator diquark picture to describe form factors in the electromagnetic sector, as well as to predict the form of the nucleon's axial current. Making use of a realistic spin decomposition and phenomenological vertex factors, we choose model parameters so as to fit experimental data on the electric and magnetic Sachs form factors, as well as the low-momentum isovector axial form factor. With the model we then predict the pseudoscalar form factor and extend axial form factor predictions to higher momenta, comparing our predictions to those of other frameworks and techniques. DOE Grant DE-FG02-97ER-41014, NSF REU program.

  3. Temperature and density structure of thermal proton flows. [in magnetosphere and ionosphere

    NASA Technical Reports Server (NTRS)

    Banks, P. M.; Schunk, R. W.; Raitt, W. J.

    1974-01-01

    Thermal proton flows along magnetic field lines are an important feature of magnetosphere-ionosphere coupling. In this paper we report the results of a theoretical study of the thermal structure of such flows. The adopted steady state model is based upon O+, H+, and electrons with self-consistent solutions for the separate O+, H+, and electron temperatures, the O+ and H+ densities and the H+ drift velocity. Through investigation of a number of parameters affecting the model, it is shown that Joule heating arising from the flow of H+ through O+ preferentially heats H+, so that the H+ temperature is substantially greater than the O+ temperature. Low O+ densities characteristic of the trough region appear to give high H+/O+ temperature ratios. Typical O+ densities characteristic of polar wind flow regions give moderate H+/O3 temperature ratios. The Mach number of H+ outflow is substantially reduced in the present models in comparison with the older fixed temperature calculations.

  4. Enterobactin Protonation and Iron Release: Structural Characterization of the Salicylate Coordination Shift in Ferric Enterobactin

    PubMed Central

    Abergel, Rebecca J.; Warner, Jeffrey A.; Shuh, David K.; Raymond, Kenneth N.

    2011-01-01

    The siderophore enterobactin (Ent) is produced by many species of enteric bacteria to mediate iron uptake. This iron scavenger can be reincorporated by the bacteria as the ferric complex [FeIII(Ent)]3- and is subsequently hydrolyzed by an esterase to facilitate intracellular iron release. Recent literature reports on altered protein recognition and binding of modified enterobactin increase the significance of understanding the structural features and solution chemistry of ferric enterobactin. The structure of the neutral protonated ferric enterobactin complex [FeIII(H3Ent)]0 has been the source of some controversy and confusion in the literature. To demonstrate the proposed change of coordination from the tris-catecholate [FeIII(Ent)]3- to the tris-salicylate [FeIII(H3Ent)]0 upon protonation, the coordination chemistry of two new model compounds N,N’,N”-tris[2-(hydroxybenzoyl)carbonyl]cyclotriseryl trilactone (SERSAM) and N,N’,N”-tris[2-hydroxy,3-methoxy(benzoyl)carbonyl]cyclotriseryl trilactone (SER(3M)SAM) was examined in solution and solid state. Both SERSAM and SER(3M)SAM form tris-salicylate ferric complexes with spectroscopic and solution thermodynamic properties (with log β110 values of 39 and 38 respectively) similar to those of [FeIII(H3Ent)]0. The fits of EXAFS spectra of the model ferric complexes and the two forms of ferric enterobactin provided bond distances and disorder factors in the metal coordination sphere for both coordination modes. The protonated [FeIII(H3Ent)]0 complex (dFe-O = 1.98 Å, σ2stat(O) = 0.00351(10) Å2) exhibits a shorter average Fe-O bond length but a much higher static Debye-Waller factor for the first oxygen-shell than the catecholate [FeIII(Ent)]3- complex (dFe-O = 2.00 Å, σ2stat(O) = 0.00067(14) Å2). 1H NMR spectroscopy was used to monitor the amide bond rotation between the catecholate and salicylate geometries using the gallic complexes of enterobactin; [GaIII(Ent)]3- and [GaIII(H3Ent)]0. The ferric salicylate

  5. Nuclear Structure of {sup 8}B Studied by Proton Resonance Scatterings on {sup 7}Be

    SciTech Connect

    Yamaguchi, H.; Wakabayashi, Y.; Hayakawa, S.; Amadio, G.; Kubono, S.; Fujikawa, H.; Niikura, M.; Binh, D. N.; Saito, A.; He, J. J.; Teranishi, T.; Kwon, Y. K.; Nishimura, S.; Togano, Y.; Iwasa, N.; Inafuku, K.; Khiem, L. H.

    2008-05-21

    A new measurement of the proton resonance scattering on {sup 7}Be was performed up to the excitation energy of 6.8 MeV using the low-energy RI beam facility CRIB (CNS Radioactive Ion Beam separator) at the Center for Nuclear Study (CNS) of the University of Tokyo. The excitation function of {sup 8}B above 3.5 MeV was successfully measured for the first time, providing important information about the reaction rate of {sup 7}Be(p,{gamma}){sup 8}B, which is the key reaction in the solar {sup 8}B neutrino production. For more intensive experimental studies with RI beams, the development of a cryogenic gas target system is ongoing at CNS. In this paper a preliminary result of the {sup 7}Be experiment and the present status of the development of the target system are presented.

  6. Structure-Derived Proton-Transfer Mechanism of Action Human Pyruvate Dehydrogenase

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Dominiak, Paulina

    2003-01-01

    The derivative of vitamin B1 thiamin pyrophosphate (TPP) is a cofactor of pyruvate dehydrogenase (E1p) that is involved in decarboxylation of pyruvate followed by reductive acetylation of lipoic acid covalently bound to a lysine residue of dihydrolipoamide acetyltransferase. The structure of E1p recently determined in our laboratory revealed patterns of association of foul subunits and specifics of two TPP binding sites. The mechanism of action in part includes a conserved hydrogen bond between the N1' atom of the aminopyrimidine ring of the cofactor and the carboxylate group of Glu59 from the beta subunits, and a V-conformation of the cofactor that brings the N4' atom of the aminopyrimidine ring to the distance of the intramolecular hydrogen bond formed with the C2-atom of the thiazolium moiety. The carboxylate group of Glu59 is the local proton acceptor that enables proton translocation within the aminopyrimidine ring and stabilization of the rare N4' - iminopyrimidine tautomer. Based on the analysis of E1p structure, we postulate that the protein environment drives N4' - amino/N4' - imino dynamics resulting in a concerted shuttle-like movement of the subunits. We also propose that this movement of the subunits is strictly coordinated with the two enzymatic reactions carried out in E1p by each of the two cofactor sites. It is proposed that these reactions are in alternating phases such that when one active site is involved in decarboxylation, the other is involved in acetylation of lipoyl noiety.

  7. Structure-Derived Proton-Transfer Mechanism of Action Human Pyruvate Dehydrogenase

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Dominiak, Paulina

    2003-01-01

    The derivative of vitamin B1 thiamin pyrophosphate (TPP) is a cofactor of pyruvate dehydrogenase (E1p) that is involved in decarboxylation of pyruvate followed by reductive acetylation of lipoic acid covalently bound to a lysine residue of dihydrolipoamide acetyltransferase. The structure of E1p recently determined in our laboratory revealed patterns of association of foul subunits and specifics of two TPP binding sites. The mechanism of action in part includes a conserved hydrogen bond between the N1' atom of the aminopyrimidine ring of the cofactor and the carboxylate group of Glu59 from the beta subunits, and a V-conformation of the cofactor that brings the N4' atom of the aminopyrimidine ring to the distance of the intramolecular hydrogen bond formed with the C2-atom of the thiazolium moiety. The carboxylate group of Glu59 is the local proton acceptor that enables proton translocation within the aminopyrimidine ring and stabilization of the rare N4' - iminopyrimidine tautomer. Based on the analysis of E1p structure, we postulate that the protein environment drives N4' - amino/N4' - imino dynamics resulting in a concerted shuttle-like movement of the subunits. We also propose that this movement of the subunits is strictly coordinated with the two enzymatic reactions carried out in E1p by each of the two cofactor sites. It is proposed that these reactions are in alternating phases such that when one active site is involved in decarboxylation, the other is involved in acetylation of lipoyl noiety.

  8. Slowing of proton transport processes in the structure of bacterial reaction centers and bacteriorhodopsin in the presence of dipyridamole.

    PubMed

    Knox, P P; Lukashev, E P; Mamedov, M D; Semenov, A Y; Seifullina, N H; Zakharova, N I

    2000-02-01

    Dipyridamole, 2,6-bis(diethanolamino)-4,8-dipiperidinopyrimido(5, 4-d)pyrimidine, is employed in clinical practice as a vasodilator. It can also inhibit a specific membrane protein (glycoprotein P) which pumps anticancer drugs out of tumor cells. Dipyridamole (10-4 M) markedly slows down the kinetics of the electrogenic phase of the photoelectric response in Rhodobacter sphaeroides chromatophores. This phase is due to proton transfer from the external medium to the secondary quinone acceptor in the reaction center. In purple membranes of bacterium Halobacterium salinarium containing bacteriorhodopsin dipyridamole (in its charged state) significantly slowed the kinetics of proton transfer from the primary donor, Asp-96 (in membranes from bacteria of wild type), or from the external medium (in D96N mutant) to the Schiff base. It is suggested that dipyridamole can influence the structural-dynamic state of membrane proteins including modification of the structure of their hydrogen bonds involved in proton-transport processes.

  9. Oxide-ion and proton conducting electrolyte materials for clean energy applications: structural and mechanistic features.

    PubMed

    Malavasi, Lorenzo; Fisher, Craig A J; Islam, M Saiful

    2010-11-01

    This critical review presents an overview of the various classes of oxide materials exhibiting fast oxide-ion or proton conductivity for use as solid electrolytes in clean energy applications such as solid oxide fuel cells. Emphasis is placed on the relationship between structural and mechanistic features of the crystalline materials and their ion conduction properties. After describing well-established classes such as fluorite- and perovskite-based oxides, new materials and structure-types are presented. These include a variety of molybdate, gallate, apatite silicate/germanate and niobate systems, many of which contain flexible structural networks, and exhibit different defect properties and transport mechanisms to the conventional materials. It is concluded that the rich chemistry of these important systems provides diverse possibilities for developing superior ionic conductors for use as solid electrolytes in fuel cells and related applications. In most cases, a greater atomic-level understanding of the structures, defects and conduction mechanisms is achieved through a combination of experimental and computational techniques (217 references).

  10. Expression in Sf9 insect cells, purification and functional reconstitution of the human proton-coupled folate transporter (PCFT, SLC46A1).

    PubMed

    Date, Swapneeta S; Fiori, Mariana C; Altenberg, Guillermo A; Jansen, Michaela

    2017-01-01

    The proton-coupled folate transporter (PCFT) provides an essential uptake route for the vitamin folic acid (B9) in mammals. In addition, it is currently of high interest for targeting chemotherapeutic agents to tumors due to the increased folic acid requirement of rapidly dividing tumor cells as well as the upregulated PCFT expression in several tumors. To understand its function, determination of its atomic structure and molecular mechanism of transport are essential goals that require large amounts of functional PCFT. Here, we present a high-level heterologous expression system for human PCFT using a recombinant baculovirus and Spodoptera frugiperda (Sf9) insect cells. We demonstrate folate transport functionality along the PCFT expression, isolation, and purification process. Importantly, purified PCFT transports folic acid after reconstitution. We thus succeeded in overcoming heterologous expression as a major bottleneck of PCFT research. The availability of an overexpression system for human PCFT provides the basis for future biochemical, biophysical and structural studies.

  11. Disgust: Evolved Function and Structure

    ERIC Educational Resources Information Center

    Tybur, Joshua M.; Lieberman, Debra; Kurzban, Robert; DeScioli, Peter

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and that of information processing. Although there is…

  12. Vacancy-Induced Electronic Structure Variation of Acceptors and Correlation with Proton Conduction in Perovskite Oxides.

    PubMed

    Kim, Hye-Sung; Jang, Ahreum; Choi, Si-Young; Jung, WooChul; Chung, Sung-Yoon

    2016-10-17

    In most proton-conducing perovskite oxides, the electrostatic attraction between negatively charged acceptor dopants and protonic defects having a positive charge is known to be a major cause of retardation of proton conduction, a phenomenon that is generally referred to as proton trapping. We experimentally show that proton trapping can be suppressed by clustering of positively charged oxygen vacancies to acceptors in BaZrO3-δ and BaCeO3-δ . In particular, to ensure the vacancy-acceptor association is effective against proton trapping, the valence electron density of acceptors should not significantly vary when the oxygen vacancies cluster, based on the weak hybridization between the valence d or p orbitals of acceptors and the 2p orbitals of oxygen.

  13. The effects of the RHIC E-lenses magnetic structure layout on the proton beam trajectory

    SciTech Connect

    Gu, X.; Pikin, A.; Luo, Y.; Okamura, M.; Fischer, W.; Gupta, R.; Hock, J.; Raparia, D.

    2011-03-28

    We are designing two electron lenses (E-lens) to compensate for the large beam-beam tune spread from proton-proton interactions at IP6 and IP8 in the Relativistic Heavy Ion Collider (RHIC). They will be installed in RHIC IR10. First, the layout of these two E-lenses is introduced. Then the effects of e-lenses on proton beam are discussed. For example, the transverse fields of the e-lens bending solenoids and the fringe field of the main solenoids will shift the proton beam. For the effects of the e-lens on proton beam trajectory, we calculate the transverse kicks that the proton beam receives in the electron lens via Opera at first. Then, after incorporating the simplified E-lens lattice in the RHIC lattice, we obtain the closed orbit effect with the Simtrack Code.

  14. Evaluation of Liver Function After Proton Beam Therapy for Hepatocellular Carcinoma

    SciTech Connect

    Mizumoto, Masashi; Okumura, Toshiyuki; Hashimoto, Takayuki; Fukuda, Kuniaki; Oshiro, Yoshiko; Fukumitsu, Nobuyoshi; Abei, Masato; Kawaguchi, Atsushi; Hayashi, Yasutaka; Ohkawa, Ayako; Hashii, Haruko; Kanemoto, Ayae; Moritake, Takashi; Tohno, Eriko; Tsuboi, Koji; Sakae, Takeji; Sakurai, Hideyuki

    2012-03-01

    Purpose: Our previous results for treatment of hepatocellular carcinoma with proton beam therapy (PBT) revealed excellent local control. In this study, we focused on the impact of PBT on normal liver function. Methods and Materials: The subjects were 259 patients treated with PBT at University of Tsukuba between January 2001 and December 2007. We evaluated the Child-Pugh score pretreatment, on the final day of PBT, and 6, 12, and 24 months after treatment with PBT. Patients who had disease progression or who died with tumor progression at each evaluation point were excluded from the analysis to rule out an effect of tumor progression. An increase in the Child-Pugh score of 1 or more was defined as an adverse event. Results: Of the 259 patients, 241 had no disease progression on the final day of PBT, and 91 had no progression within 12 months after PBT. In univariate analysis, the percentage volumes of normal liver receiving at least 0, 10, 20, and 30 GyE in PBT (V0, 10, 20, and 30) were significantly associated with an increase of Child-Pugh score at 12 months after PBT. Of the 91 patients evaluated at 12 months, 66 had no increase of Child-Pugh score, 15 had a 1-point increase, and 10 had an increase of {>=}2 points. For the Youden index, the optimal cut-offs for V0, V10, V20, and V30 were 30%, 20%, 26%, and 18%, respectively. Conclusion: Our findings indicate that liver function after PBT is significantly related to the percentage volume of normal liver that is not irradiated. This suggests that further study of the relationship between liver function and PBT is required.

  15. The Perisperm-endosperm Envelope in Cucumis: Structure, Proton Diffusion and Cell Wall Hydrolysing Activity

    PubMed Central

    RAMAKRISHNA, P.; AMRITPHALE, DILIP

    2005-01-01

    • Background and Aims The envelope surrounding the embryo in cucurbit seed, which consists of a single layer of live endosperm cells covered by lipid- and callose-rich layers, is reported to show semi-permeability and also to act as the primary barrier to radicle emergence. Structure, development and permeability of the envelope and activity of cell wall hydrolases during germination of cucumber and muskmelon seeds were investigated. • Methods Sections of seeds were stained with aniline blue and Sudan III. Proton diffusion and endo-β-mannanase activity were detected by tissue printing. A gel-diffusion assay was performed to quantify endo-β-mannanase activity, while the activity of β-glucanase was determined with laminarin as the substrate and glucose formation measured using the GOD-POD method. • Key Results The lipid layer differentiated during seed development in cucumber in the epidermis of a multilayered nucellus, whereas the callose layer appeared to develop outside the endosperm cell layer. Accordingly, the envelope has been called the perisperm-endosperm (PE) envelope. Chloroform treatment of seeds, which resulted in a substantial reduction in Sudan staining of the lipid layer, also enhanced the permeability of the PE envelope to 2,3,5-triphenyltetrazolium chloride. Proton diffusion occurred when the PE envelopes from seeds had their inner surface in contact with bromocresol purple-containing agarose gels, but not when their outer surface was in contact. Substantial endo-β-mannanase activity was present in the caps of the PE envelopes, whereas a marked increase in β-glucanase activity was observed in radicles prior to germination. • Conclusions The lipid layer seems to contribute to the semi-permeability of the PE envelope. The diffusion of protons might create an acidic environment conducive to the activity of cell wall hydrolases, namely endo-β-mannanase (EC 3.2.1.78) and β-glucanase [β(1→3)glucanohydrolase; EC 3.2.1.6], which, in turn

  16. Mechanisms of proton pumping in bacteriorhodopsin

    SciTech Connect

    Ebrey, T.G.

    1991-01-01

    The purple membrane of Halobacterium halobium probably represents the simplest biological solar energy conversion system. Light absorbed by bacteriorhodopsin directly leads to the transport of protons across the cell membrane. The resulting chemosmotic potential can be used to make ATP. An additional feature of the purple membrane is its ability to pump protons over a wide variety of salt concentration including in extreme saline environments. This project investigates the relationship between the transport of protons across the membrane and structure and conformation of bacteriorhodospin. We have proposed experiments to study the pH dependence of proton pumping. Secondly, we are examining the role of divalent cations and the effect of the large surface potential of the purple membrane on the proton pumping function of this membrane using the photocurrents associated with the pumping process. Finally we are studying the role of proteinatable amino acids in proton transport. 16 refs.

  17. RHA Implications of Proton on Gold-Plated Package Structures in SEE Evaluations

    NASA Astrophysics Data System (ADS)

    Turflinger, T. L.; Clymer, D. A.; Mason, L. W.; Stone, S.; George, J. S.; Savage, M.; Koga, R.; Beach, E.; Huntington, K.

    2015-12-01

    Proton single event dielectric rupture was observed in Analog Devices OP470 devices only when the package included gold flashing facing the die on the inner surface of the metal lid. The supply voltage was also a factor. Analysis shows that proton on gold fission fragments have the linear energy transfer and range to cause this effect. The physics of proton on gold reactions and radiation hardness assurance implications are explored.

  18. Flagged uniform particle splitting for variance reduction in proton and carbon ion track-structure simulations

    NASA Astrophysics Data System (ADS)

    Ramos-Méndez, José; Schuemann, Jan; Incerti, Sebastien; Paganetti, Harald; Schulte, Reinhard; Faddegon, Bruce

    2017-08-01

    Flagged uniform particle splitting was implemented with two methods to improve the computational efficiency of Monte Carlo track structure simulations with TOPAS-nBio by enhancing the production of secondary electrons in ionization events. In method 1 the Geant4 kernel was modified. In method 2 Geant4 was not modified. In both methods a unique flag number assigned to each new split electron was inherited by its progeny, permitting reclassification of the split events as if produced by independent histories. Computational efficiency and accuracy were evaluated for simulations of 0.5-20 MeV protons and 1-20 MeV u-1 carbon ions for three endpoints: (1) mean of the ionization cluster size distribution, (2) mean number of DNA single-strand breaks (SSBs) and double-strand breaks (DSBs) classified with DBSCAN, and (3) mean number of SSBs and DSBs classified with a geometry-based algorithm. For endpoint (1), simulation efficiency was 3 times lower when splitting electrons generated by direct ionization events of primary particles than when splitting electrons generated by the first ionization events of secondary electrons. The latter technique was selected for further investigation. The following results are for method 2, with relative efficiencies about 4.5 times lower for method 1. For endpoint (1), relative efficiency at 128 split electrons approached maximum, increasing with energy from 47.2  ±  0.2 to 66.9  ±  0.2 for protons, decreasing with energy from 51.3  ±  0.4 to 41.7  ±  0.2 for carbon. For endpoint (2), relative efficiency increased with energy, from 20.7  ±  0.1 to 50.2  ±  0.3 for protons, 15.6  ±  0.1 to 20.2  ±  0.1 for carbon. For endpoint (3) relative efficiency increased with energy, from 31.0  ±  0.2 to 58.2  ±  0.4 for protons, 23.9  ±  0.1 to 26.2  ±  0.2 for carbon. Simulation results with and without splitting agreed within 1% (2 standard

  19. Textbook Error, 138: The Singly Protonated Structure of Thiamine: Basicity of the Heterocyclic Nitrogen versus NH2 Nitrogen.

    ERIC Educational Resources Information Center

    Panijpan, Bhinyo

    1979-01-01

    Spectroscopic studies on solutions and x-ray diffraction work on crystals lead to the conclusion that the Metrogen of the pyrimidine ring is preferentially protonated. The correct monoprotonated structures of thiamine and its 4-amino-pyrimidine synthetic precursor are presented. (BT)

  20. Textbook Error, 138: The Singly Protonated Structure of Thiamine: Basicity of the Heterocyclic Nitrogen versus NH2 Nitrogen.

    ERIC Educational Resources Information Center

    Panijpan, Bhinyo

    1979-01-01

    Spectroscopic studies on solutions and x-ray diffraction work on crystals lead to the conclusion that the Metrogen of the pyrimidine ring is preferentially protonated. The correct monoprotonated structures of thiamine and its 4-amino-pyrimidine synthetic precursor are presented. (BT)

  1. Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer

    PubMed Central

    Chreifi, Georges; Baxter, Elizabeth L.; Doukov, Tzanko; Cohen, Aina E.; McPhillips, Scott E.; Song, Jinhu; Meharenna, Yergalem T.; Soltis, S. Michael; Poulos, Thomas L.

    2016-01-01

    The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray–generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH. PMID:26787871

  2. Mapping GFP structure evolution during proton transfer with femtosecond Raman spectroscopy.

    PubMed

    Fang, Chong; Frontiera, Renee R; Tran, Rosalie; Mathies, Richard A

    2009-11-12

    Tracing the transient atomic motions that lie at the heart of chemical reactions requires high-resolution multidimensional structural information on the timescale of molecular vibrations, which commonly range from 10 fs to 1 ps. For simple chemical systems, it has been possible to map out in considerable detail the reactive potential-energy surfaces describing atomic motions and resultant reaction dynamics, but such studies remain challenging for complex chemical and biological transformations. A case in point is the green fluorescent protein (GFP) from the jellyfish Aequorea victoria, which is a widely used gene expression marker owing to its efficient bioluminescence. This feature is known to arise from excited-state proton transfer (ESPT), yet the atomistic details of the process are still not fully understood. Here we show that femtosecond stimulated Raman spectroscopy provides sufficiently detailed and time-resolved vibrational spectra of the electronically excited chromophore of GFP to reveal skeletal motions involved in the proton transfer that produces the fluorescent form of the protein. In particular, we observe that the frequencies and intensities of two marker bands, the C-O and C = N stretching modes at opposite ends of the conjugated chromophore, oscillate out of phase with a period of 280 fs; we attribute these oscillations to impulsively excited low-frequency phenoxyl-ring motions, which optimize the geometry of the chromophore for ESPT. Our findings illustrate that femtosecond simulated Raman spectroscopy is a powerful approach to revealing the real-time nuclear dynamics that make up a multidimensional polyatomic reaction coordinate.

  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.

  4. Biophysical and structural characterization of proton-translocating NADH-dehydrogenase (complex I) from the strictly aerobic yeast Yarrowia lipolytica.

    PubMed

    Djafarzadeh, R; Kerscher, S; Zwicker, K; Radermacher, M; Lindahl, M; Schägger, H; Brandt, U

    2000-07-20

    Mitochondrial proton-translocating NADH-dehydrogenase (complex I) is one of the largest and most complicated membrane bound protein complexes. Despite its central role in eukaryotic oxidative phosphorylation and its involvement in a broad range of human disorders, little is known about its structure and function. Therefore, we have started to use the powerful genetic tools available for the strictly aerobic yeast Yarrowia lipolytica to study this respiratory chain enzyme. To establish Y. lipolytica as a model system for complex I, we purified and characterized the multisubunit enzyme from Y lipolytica and sequenced the nuclear genes coding for the seven central subunits of its peripheral part. Complex I from Y lipolytica is quite stable and could be isolated in a highly pure and monodisperse state. One binuclear and four tetranuclear iron-sulfur clusters, including N5, which was previously known only from mammalian mitochondria, were detected by EPR spectroscopy. Initial structural analysis by single particle electron microscopy in negative stain and ice shows complex I from Y. lipolytica as an L-shaped particle that does not exhibit a thin stalk between the peripheral and the membrane parts that has been observed in other systems.

  5. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism.

    PubMed

    Dance, Ian

    2015-11-07

    Nitrogenase contains a well defined and conserved chain of water molecules leading to the FeMo cofactor (FeMo-co, an [Fe7MoCS9] cluster with bidentate chelation of Mo by homocitrate) that is the active site where N2 and other substrates are sequentially hydrogenated using multiple protons and electrons. The function of this chain is proposed to be a proton wire, serially translocating protons to triply-bridging S3B of FeMo-co, where, concomitant with electron transfer to FeMo-co, an H atom is generated on S3B. Density functional simulations of this proton translocation mechanism are reported here, using a large 269-atom model that includes all residues hydrogen bonded to and surrounding the water chain, and likely to influence proton transfer: three carboxylate O atoms of obligatory homocitrate are essential. The mechanism involves the standard two components of the Grotthuss mechanism, namely H atom slides that shift H3O(+) from one water site to the next, and HOH molecular rotations that convert backward (posterior) OH bonds in the water chain to forward (anterior) OH bonds. The topography of the potential energy surface for each of these steps has been mapped. H atom slides pass through very short (ca. 2.5 Å) O-H-O hydrogen bonds, while HOH rotations involve the breaking of O-HO hydrogen bonds, and the occurrence of long (up to 3.6 Å) separations between contiguous water molecules. Both steps involve low potential energy barriers, <7 kcal mol(-1). During operation of the Grotthuss mechanism in nitrogenase there are substantial displacements of water molecules along the chain, occurring as ripples. These characteristics of the 'Grotthuss two-step', coupled with a buffering ability of two carboxylate O atoms of homocitrate, and combined with density functional characterisation of the final proton slide from the ultimate water molecule to S3B (including electron addition), have been choreographed into a complete mechanism for serial hydrogenation of FeMo-co. The

  6. Stories: The Function of Structure.

    ERIC Educational Resources Information Center

    Mandler, Jean M.

    The differences between story grammar and story schema are outlined and discussed based on research on story understanding by children and adults. The contention of all story grammars is that stories have a relatively invariant structure despite great differences in story content. The importance of structure within folk tales, and the ways in…

  7. The Structural Response of Polyelectrolyte Dendrimer toward the Molecular Protonation: The Inconsistence Revealed by SANS and NMR

    SciTech Connect

    Chen, Wei-Ren; Herwig, Kenneth W; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Porcar, L.; Shew, Chwen-Yang; Smith, Gregory Scott; Wu, Bin; Liu, Dazhi; Gao, Carrie Y

    2012-01-01

    Polyamidoamine (PAMAM) dendrimers and their charged state in deuterium oxide have been investigated with diffusion NMR and small angle neutron scattering (SANS) techniques. NMR measurement suggests that, upon increasing the molecular protonation by progressive acidification of solutions, significant variation of hydrodynamic radius, calculated by the Stokes-Einstein relation with given surface condition, is observed upon increasing the molecular protonation. However, comparative SANS experiment indicates little dependence of dendrimer global size, in terms of radius of gyration, on molecular protonation. This observed inconsistence indicates the necessity of incorporating the effect of molecular interface modification by dressed counterion, when dynamical measurements are used for determination the structural characteristics of ionic soft colloids even in a dilute enough suspension.

  8. Modelling proton bunches focussed to submicrometre scales: low-LET radiation damage in high-LET-like spatial structure.

    PubMed

    Friedland, W; Kundrát, P; Schmitt, E

    2015-09-01

    Microbeam experiments approximating high-LET tracks by bunches of lower-LET particles focussed to submicrometre scales (Schmid et al. 2012, Phys. Med. Biol. 57, 5889) provide an unprecedented benchmark for models of biological effects of radiation. PARTRAC track structure-based Monte Carlo simulations have verified that focussed 20 MeV proton bunches resemble the radial dose distributions of single 55 MeV carbon ions as used in the experiments. However, the predicted yields of double-strand break and short (<1 kbp) DNA fragments by focussed protons correspond to homogeneous proton irradiation and are much smaller than for carbon tracks. The calculated yields of dicentrics overestimate the effect of focussing but reproduce the fourfold difference between carbon ions and homogeneously distributed protons. The extent to which focussed low-LET particles approximate high-LET radiation is limited by the achievable focussing: submicrometre focussing of proton bunches cannot reproduce local nanometre clustering, i.e. DNA damage complexity characteristic of high-LET radiation.

  9. Differential protonation and dynamic structure of doxylamine succinate in solution using 1H and 13C NMR.

    PubMed

    Somashekar, B S; Nagana Gowda, G A; Ramesha, A R; Khetrapal, C L

    2004-07-01

    A protonation and dynamic structural study of doxylamine succinate, a 1:1 salt of succinic acid with dimethyl-[2-(1-phenyl-1-pyridin-2-yl-ethoxy)ethyl]amine, in solution using one- and two-dimensional 1H and 13C NMR experiments at variable temperature and concentration is presented. The two acidic protons of the salt doxylamine succinate are in 'intermediate' exchange at room temperature, as evidenced by the appearance of a broad signal. This signal evolves into two distinct signals below about -30 degrees C. A two-dimensional 1H-1H double quantum filtered correlation experiment carried out at -55 degrees C shows protonation of one of the acidic protons to the dimethylamine nitrogen. A two-dimensional rotating frame 1H-1H NOE experiment at the same temperature reveals that the other proton remains with the succinate moiety. Comparison of the 1H and 13C chemical shifts and the 13C T1 relaxation times of the salt with those of the free base further substantiate the findings.

  10. [Proton bomb inhibitors: a study of the prescription in a functional recovery unit].

    PubMed

    López-Dóriga Bonnardeaux, Pedro; Neira Álvarez, Marta; Mansilla Laguía, Sara

    2013-01-01

    The use of proton pump inhibitors (PPI) has increased exponentially since they were introduced. However concerns have been raised regarding the appropriateness of these prescriptions, and the potential side effects, particularly in frail elderly people, as well as the cost of this treatment. The aim of this study was to assess the extent and appropriateness of PPI prescribing in a group of patients over 65 years old admitted to the functional recovery unit of a medium-stay hospital. A retrospective review of inpatient prescribing of PPI was carried out in a functional recovery unit in Hospital de la Fuenfría, selecting those older than 65 years, who were admitted during 2011. Data obtained from medical records included, prescription of a PPI before admission and at the time of discharge from hospital (both acute care hospital and Hospital de la Fuenfría), type of PPI, and indications for their prescription. Inclusion criteria were met by 296 patients (mean age 78.8 years, 70.6% females). A total of 45.3, 79.1 and 75.5% of patients were on PPIs before admission, and at the time of being discharge from acute care hospital, and Hospital de la Fuenfría, respectively. A valid indication for therapy was not apparent in 62.7, 30.8 and 54.2% of them. Omeprazole was the most widely prescribed PPI. There appears to be a widespread and inappropriate use of PPIs in hospital practice. Interventions are needed to curtail this inappropriate prescribing practice, avoiding side effects and drug interactions. Copyright © 2013 SEGG. Published by Elsevier Espana. All rights reserved.

  11. Functional keratin as structural platforms

    USDA-ARS?s Scientific Manuscript database

    Wool with up to 95% keratin by weight is a rich and pure source of proteinous biomaterial. As polymeric polyamide it exhibits high functionality through amide, carboxyl, sulfoxide, sulfide, and thiosulfide functions. Solubilized wool was transformed into keratin morphologies with the unique characte...

  12. Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin.

    PubMed

    Hagiwara, Yoshinori; Wada, Kei; Irikawa, Teppei; Sato, Hideaki; Unno, Masaki; Yamamoto, Ken; Fukuyama, Keiichi; Sugishima, Masakazu

    2016-10-01

    Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH(+) ) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH(+) . To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH(+) complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH(+) structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA. © 2016 Federation of European Biochemical Societies.

  13. 3-dimensional free standing micro-structures by proton beam writing of Su 8-silver nanoParticle polymeric composite

    NASA Astrophysics Data System (ADS)

    Igbenehi, H.; Jiguet, S.

    2012-09-01

    Proton beam lithography a maskless direct-write lithographic technique (well suited for producing 3-Dimensional microstructures in a range of resist and semiconductor materials) is demonstrated as an effective tool in the creation of electrically conductive freestanding micro-structures in an Su 8 + Nano Silver polymer composite. The structures produced show non-ohmic conductivity and fit the percolation theory conduction model of tunneling of separated nanoparticles. Measurements show threshold switching and a change in conductivity of at least 4 orders of magnitude. The predictable range of protons in materials at a given energy is exploited in the creation of high aspect ratio, free standing micro-structures, made from a commercially available SU8 Silver nano-composite (GMC3060 form Gersteltec Inc. a negative tone photo-epoxy with added metallic nano-particles(Silver)) to create films with enhanced electrical properties when exposed and cured. Nano-composite films are directly written on with a finely focused MeV accelerated Proton particle beam. The energy loss of the incident proton beams in the target polymer nano- composite film is concentrated at the end of its range, where damage occurs; changing the chemistry of the nano-composite film via an acid initiated polymerization - creating conduction paths. Changing the energy of the incident beams provide exposed regions with different penetration and damage depth - exploited in the demonstrated cantilever microstructure.

  14. Polarized DIS Structure Functions from Neural Networks

    SciTech Connect

    Del Debbio, L.; Guffanti, A.; Piccione, A.

    2007-06-13

    We present a parametrization of polarized Deep-Inelastic-Scattering (DIS) structure functions based on Neural Networks. The parametrization provides a bias-free determination of the probability measure in the space of structure functions, which retains information on experimental errors and correlations. As an example we discuss the application of this method to the study of the structure function g{sub 1}{sup p}(x,Q{sup 2})

  15. Structure and Function of Your Skin

    MedlinePlus

    ... Name: Category: Share: Yes No, Keep Private Structure & Function of Your Skin Share | What It Looks Like . . . ... in the dermis. What It Does . . . The major function of skin is to provide a barrier between ...

  16. Structure of high spin state in proton-rich 74,76,78Kr isotopes: A projected shell model description

    NASA Astrophysics Data System (ADS)

    Liu, YanXin; Yu, ShaoYing; Shen, CaiWan

    2015-01-01

    The N≈ Z nuclei in the mass A˜80 region has been researched because of an abundance of nuclear structure phenomena. The projected shell model (PSM) was adopted to investigate the structure of high spin state in proton-rich 74,76,78Kr isotopes including yrast spectra, moment of inertia, electric quadrupole transitions and the behavior of single particle. The calculated results are in good agreement with available data and the shape coexistence in low-spin is also discussed.

  17. Site selectivity in the protonation of a phosphinito bridged Pt(I)-Pt(I) complex: a combined NMR and density-functional theory mechanistic study.

    PubMed

    Latronico, Mario; Polini, Flavia; Gallo, Vito; Mastrorilli, Piero; Calmuschi-Cula, Beatrice; Englert, Ulli; Re, Nazzareno; Repo, Timo; Räisänen, Minna

    2008-11-03

    The protonation of the dinuclear phosphinito bridged complex [(PHCy2)Pt(mu-PCy2){kappa(2)P,O-mu-P(O)Cy2}Pt(PHCy2)] (Pt-Pt) (1) by Brønsted acids affords hydrido bridged Pt-Pt species the structure of which depends on the nature and on the amount of the acid used. The addition of 1 equiv of HX (X = Cl, Br, I) gives products of formal protonation of the Pt-Pt bond of formula syn-[(PHCy2)(X)Pt(mu-PCy2)(mu-H)Pt(PHCy2){kappaP-P(O)Cy2}] (Pt-Pt) (5, X = Cl; 6, X = Br; 8, X = I), containing a Pt-X bond and a dangling kappa P-P(O)Cy2 ligand. Uptake of a second equivalent of HX results in the protonation of the P(O)Cy2 ligand with formation of the complexes [(PHCy2)(X)Pt(mu-PCy2)(mu-H)Pt(PHCy2){kappaP-P(OH)Cy2}]X (Pt-Pt) (3, X = Cl; 4, X = Br; 9, X = I). Each step of protonation is reversible, thus reactions of 3, 4, with NaOH give, first, the corresponding neutral complexes 5, 6, and then the parent compound 1. While the complexes 3 and 4 are indefinitely stable, the iodine analogue 9 transforms into anti-[(PHCy2)(I)Pt(mu-PCy2)(mu-H)Pt(PHCy2)(I)] (Pt-Pt) (7) deriving from substitution of an iodo group for the P(OH)Cy2 ligand. Complexes 3 and 4 are isomorphous crystallizing in the triclinic space group P1 and show an intramolecular hydrogen bond and an interaction between the halide counteranion and the POH hydrogen. The occurrence of such an interaction also in solution was ascertained for 3 by (35)Cl NMR. Multinuclear NMR spectroscopy (including (31)P-(1)H HOESY) and density-functional theory calculations indicate that the mechanism of the reaction starts with a prior protonation of the oxygen with formation of an intermediate (12) endowed with a six membered Pt(1)-X...H-O-P-Pt(2) ring that evolves into thermodynamically stable products featuring the hydride ligand bridging the Pt atoms. Energy profiles calculated for the various steps of the reaction between 1 and HCl showed very low barriers for the proton transfer and the subsequent rearrangement to 12, while a barrier

  18. Structural and functional comparison of polysaccharide-degrading enzymes.

    PubMed

    Jedrzejas, M J

    2000-01-01

    Sugar molecules as well as enzymes degrading them are ubiquitously present in physiological systems, especially for vertebrates. Polysaccharides have at least two aspects to their function, one due to their mechanical properties and the second one involves multiple regulatory processes or interactions between molecules, cells, or extracellular space. Various bacteria exert exogenous pressures on their host organism to diversity glycans and their structures in order for the host organism to evade the destructive function of such microbes. Many bacterial organism produce glycan-degrading enzymes in order to facilitate their invasion of host tissues. Such polysaccharide degrading enzymes utilize mainly two modes of polysaccharide-degradation, a hydrolysis and a beta-elimination process. The three-dimensional structures of several of these enzymes have been elucidated recently using X-ray crystallography. There are many common structural motifs among these enzymes, mainly the presence of an elongated cleft transversing these molecules which functions as a polysaccharide substrate binding site as well as the catalytic site for these enzymes. The detailed structural information obtained about these enzymes allowed formulation of proposed mechanisms of their action. The polysaccharide lyases utilize a proton acceptance and donation mechanism (PAD), whereas polysaccharide hydrolases use a direct double displacement (DD) mechanism to degrade their substrates.

  19. Deuteron Spin Structure function g1 at low Q^2

    NASA Astrophysics Data System (ADS)

    Adhikari, Krishna; Kuhn, Sebastian

    2012-10-01

    The spin structure function g1(x,Q^2) and its moments provide crucial information on the internal structure of the nucleon. At low momentum transfer Q^2, one can study the transition from partonic (quark-gluon) to hadronic (nucleonic) degrees of freedom and test effective theories based on QCD, for instance Chiral Perturbation Theory (ChPT). As Q^2 goes to zero, the first moment of g1 is constrained by the GDH sum rule and its ChPT extensions, which makes measurements of g1 in this region uniquely interesting. As part of the large program of spin structure function measurements with CLAS at Jefferson Lab, the EG4 experiment measured the cross section difference between electron beam and proton/deuteron target spins parallel and antiparallel to each other (and the beam direction) down to small scattering angles (approx. 7 degrees). From these differences, g1 can be extracted, with minimal model uncertainties, down to Q^2 as low as 0.01 GeV^2. We will give a brief overview of the experiment and its analysis, and present first preliminary results on the deuteron spin structure function g1d(x,Q^2).

  20. Protonation effect on the electronic structure of small PAHs: Acenaphthylene and Acenaphthene

    NASA Astrophysics Data System (ADS)

    Omidyan, Reza

    2011-12-01

    The low lying singlet and triplet electronic excited states of neutral and protonated Acenaphthylene (C12H8, ACYN) and Acenaphthene (C12H10, ACN) have been investigated extensively by RI-MP2 and RI-CC2 methods. The first and second electronic excited tates (S1, S2) of protonated ACYN and ACN have ππ∗ nature and lie in the visible or UV region. Similar to naphthalene, anthracene, and other linear PAHs, the protonation of ACYN and ACN leads to a strong red shift of the electronic transition as compared to the neutral molecule. The calculations indicate a charged transfer character of S1-S0 transition in protonated ACYN and ACN as well as protonated naphthalene.

  1. Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps.

    PubMed

    Muroda, Kosuke; Nakashima, Keisuke; Shibata, Mikihiro; Demura, Makoto; Kandori, Hideki

    2012-06-12

    Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.

  2. From structure to function, via dynamics

    NASA Astrophysics Data System (ADS)

    Stetter, O.; Soriano, J.; Geisel, T.; Battaglia, D.

    2013-01-01

    Neurons in the brain are wired into a synaptic network that spans multiple scales, from local circuits within cortical columns to fiber tracts interconnecting distant areas. However, brain function require the dynamic control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, strength and direction of causal influences between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such directed functional influences can be quantified resorting to causal analysis of time-series based on tools like Granger Causality or Transfer Entropy. The ability to quickly reorganize inter-areal interactions is a chief requirement for performance in a changing natural environment. But how can manifold functional networks stem "on demand" from an essentially fixed structure? We explore the hypothesis that the self-organization of neuronal synchronous activity underlies the control of brain functional connectivity. Based on simulated and real recordings of critical neuronal cultures in vitro, as well as on mean-field and spiking network models of interacting brain areas, we have found that "function follows dynamics", rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different functional digraphs (functional multiplicity). We also highlight the crucial role of dynamics in establishing a structure-to-function link, by showing that whenever different structural topologies lead to similar dynamical states, than the associated functional connectivities are also very similar (structural degeneracy).

  3. Structure and function of wood

    Treesearch

    Alex C. Wiedenhoeft; Regis B. Miller

    2005-01-01

    Despite the many human uses to which various woods are suited, at a fundamental level wood is a complex biological structure, itself a composite of many chemistries and cell types acting together to serve the needs of the plant. Although humans have striven to understand wood in the context of wood technology, we have often overlooked the key and basic fact that wood...

  4. An Infrared Spectroscopic Study on the Formation of the Hydrogen Bonded Inclusion-Structures in the Protonated Metnanol Water Clusters

    NASA Astrophysics Data System (ADS)

    Katada, Marusu; Hsu, Po-Jen; Fujii, Asuka; Kuo, Jer-Lai

    2016-06-01

    We measured IR spectra of the protonated methanol-water mixed clusters (H+(CH3OH)n(H2O)1, n =6 - 10) in the OH stretching vibrational region. Spectra of their Ar tagged clusters were also measured to explore hydrogen-bonded structure changes by the vibrational cooling. The temperature dependence of the isomer distribution was also examined by the harmonic superposition approximation (HSA) simulation. No essential change of the structures with the Ar tagging (lowering of temperature) was concluded in the size range of n = 8 - 10, indicating the remarkable stability of the inclusion structures in this size range. On the other hand, at n = 7, the large isomer distribution change with the Ar tagging is suggested. Moreover, at n = 6, the IR spectrum showed dramatic changes upon the Ar tagging. The protonated site switching from water to methanol well explained these observed changes.

  5. Beta-alanine-oxalic acid (1:1) hemihydrate crystal: structure, 13C NMR and vibrational properties, protonation character.

    PubMed

    Godzisz, D; Ilczyszyn, M; Ilczyszyn, M M

    2003-03-01

    The crystal structure of beta-alanine-oxalic acid (1:1) hemihydrate complex has been reinvestigated by X-ray diffraction method at 293 K. Formation of monoclinic crystal system belonging to C2/c space group and consisting of semi-oxalate chains, diprotonated beta-alanine dimers and water molecules bonded to both these units is confirmed. New results are obtained for distances in the carboxylic groups and hydrogen bonds. These structural observations are used for protonation degree monitoring on the carboxylic oxygen atoms. They are in accordance with our vibrational study. The 13C NMR spectra provide insights into the solid structure of this complex, character of its hydrogen bonds and the beta-alanine protonation.

  6. Structure, function, and wavelength selection in blue-absorbing proteorhodopsin.

    PubMed

    Hillebrecht, Jason R; Galan, Jhenny; Rangarajan, Rekha; Ramos, Lavoisier; McCleary, Kristina; Ward, Donald E; Stuart, Jeffrey A; Birge, Robert R

    2006-02-14

    The absorption maximum of blue proteorhodopsin (BPR) is the most blue-shifted of all retinal proteins found in archaea or bacteria, with the exception of sensory rhodopsin II (SRII). The absorption spectrum also exhibits a pH dependence larger than any other retinal protein. We examine the structural origins of these two properties of BPR by using optical spectroscopy, homology modeling, and molecular orbital theory. Bacteriorhodopsin (BR) and SRII are used as homology parents for comparative purposes. We find that the tertiary structure of BPR based on SRII is more realistic with respect to free energy, dynamic stability, and spectroscopic properties. Molecular orbital calculations including full single- and double-configuration interaction within the chromophore pi-electron system provide perspectives on the wavelength regulation in this protein and indicate that Arg-95, Gln-106, Glu-143, and Asp-229 play important, and in some cases pH-dependent roles. A possible model for the 0.22 eV red shift of BPR at low pH is examined, in which Glu-143 becomes protonated and releases Arg-95 to rotate up into the binding site, altering the electrostatic environment of the chromophore. At high pH, BPR has spectroscopic properties similar to SRII, but at low pH, BPR has spectroscopic properties more similar to BR. Nevertheless, SRII is a significantly better homology model for BPR and opens up the question of whether this protein serves as a proton pump, as commonly believed, or is a light sensor with structure-function properties more comparable to those of SRII. The function of BPR in the native organism is discussed with reference to the results of the homology model.

  7. Investigation of structure in Al23 via resonant proton scattering of Mg22+p and the 22Mg(p,γ) Al23 astrophysical reaction rate

    NASA Astrophysics Data System (ADS)

    He, J. J.; Kubono, S.; Teranishi, T.; Notani, M.; Baba, H.; Nishimura, S.; Moon, J. Y.; Nishimura, M.; Iwasaki, H.; Yanagisawa, Y.; Hokoiwa, N.; Kibe, M.; Lee, J. H.; Kato, S.; Gono, Y.; Lee, C. S.

    2007-11-01

    Proton resonant states in Al23 have been investigated for the first time by the resonant elastic and inelastic scattering of Mg22+p with a Mg22 beam at 4.38 MeV/nucleon bombarding a thick (CH2)n target. The low-energy Mg22 beam was separated by the CNS radioactive ion beam separator (CRIB). The energy spectra of recoiled protons were measured at average scattering angles of θlab≈4°,17° and 23°. A new state has been observed at Ex=3.00 MeV with a spin-parity assignment of (3/2+). In addition, resonant inelastic scattering has populated three more states at excitation energies of 3.14, 3.26, and 3.95 MeV, with proton decay to the first excited state in Mg22 being observed. The new state at 3.95 MeV has been assigned a spin-parity of Jπ=(7/2+). The resonant parameters were determined by an R-matrix analysis of the excitation functions with a SAMMY-M6-BETA code. The core-excited structure of Al23 is discussed within a shell-model picture. The stellar reaction rate of the Mg22(p,γ)Al23 reaction has been reevaluated, and the revised total reaction rate is about 40% greater than the previous result for temperatures beyond T9=0.3.

  8. The HERA Proton

    NASA Astrophysics Data System (ADS)

    Habib, Shiraz

    2014-04-01

    The almost 1 fb-1 of ep data collected by the H1 and ZEUS collider experiments at HERA allows for a precise determination of the proton's parton distribution functions (PDFs). Measurements used to constrain the PDFs—inclusive and jet cross sections, charm contribution to the F2 proton structure function, F_2cbar c — are presented herein. The measurement process itself includes cataloguing the sensitivity of the cross sections to the various sources of correlated systematic uncertainties. In the jet measurement, correlations of a statistical nature are also quantified and catalogued. These correlations provide a basis to combine measurements of the same physical observable across different time periods, experiments and measurement methodology. The subsequent PDF fitting procedure also takes into account such correlations. The resulting HERAPDF1.5 set based on inclusive data as well as PDF sets derived from inclusive plus charm data are presented togeteher with their predictions for pp cross sections at the LHC.

  9. Micro-structuring of epoxy resists containing nanoparticles by proton beam writing

    NASA Astrophysics Data System (ADS)

    Sano, Ryo; Hayakawa, Simon; Hayashi, Hidetaka; Ishii, Yasuyuki; Nishikawa, Hiroyuki

    2017-08-01

    Proton beam writing (PBW) on SU-8 composites with nanoparticles (size: 14-750 nm) of silver, silica, alumina, and carbon with concentration of 5.0 wt% was studied aiming for high-aspect-ratio micro-structuring. Results of SRIM simulation suggest that deep micromachining of more than 100 μm is possible by 3.0 MeV PBW with increase in lateral straggling of less than 5.0%. Sensitivity loss of 150% was observed by introduction of 5.0 wt% nanoparticles to SU-8. There is a correlation between the sensitivity loss and volume concentration of nanoparticles. We fabricated pillar arrays of SU-8/silver nanocomposites with 10 μm in diameter and 80 μm in height by PBW at 3.0 MeV. Cross-sectional observation of the SU-8/silver pillar arrays shows that silver nanoparticles are homogeneously dispersed in SU-8, while aggregation was observed at the side surface.

  10. Study of proton resonance structure in {sup 27}P via resonant elastic scattering of {sup 26}Si+p

    SciTech Connect

    Jung, H. S.; Lee, C. S.; Kwon, Y. K.; Moon, J. Y.; Lee, J. H.; Yun, C. C.; Kubono, S.; Yamaguchi, H.; Hashimoto, T.; Kahl, D.; Hayakawa, S.; Choi, Seonho; Kim, M. J.; Kim, Y. H.; Kim, Y. K.; Park, J. S.; Kim, E. J.; Moon, C.-B.; Teranishi, T.; Wakabayashi, Y.; and others

    2012-11-12

    A measurement of resonant elastic scattering of {sup 26}Si+p was performed with a thick target using a {sup 26}Si radioactive ion beam at the CRIB (CNS Radioactive Ion Beam separator) of the Center for Nuclear Study (CNS), the University of Tokyo. The excitation function of {sup 27}P was measured successfully with the inverse kinematics method through a covered the range of excitation energies from E{sub x}{approx} 2.3 to 3.8 MeV, providing information about the resonance structure of this nucleus. The properties of these resonances are important to better determine the production rates of {sup 26}Si(p,g){sup 27}P reaction, which is one of the astrophysically important nuclear reactions to understand the production of the {sup 26}Al. Some new resonant states have been investigated, and determined their resonance parameters, such as excitation energies, proton partial widths, and spin-parities by R-matrix calculation.

  11. Understanding the gas diffusion layer in proton exchange membrane fuel cells. I. How its structural characteristics affect diffusion and performance

    NASA Astrophysics Data System (ADS)

    Morgan, Jason M.; Datta, Ravindra

    2014-04-01

    The proton exchange membrane fuel cell (PEMFC) has a significant potential in transportation, backup, and portable power applications, although there still are remaining technical and cost challenges. A key current goal is improving the performance while reducing the cost of the gas diffusion layer (GDL). Designing a commercial GDL, however, is far more complex than simply making a porous, sturdy, conductive layer, because of the trade-offs among performance, manufacturability, and cost. An improved understanding of its multifarious functions in the fuel cell can help attain this goal. Here, we identify 11 key characteristic parameters of the GDL and their significance to its performance. We begin a discussion of some of these parameters in this paper, specifically those related to the structure of the GDL substrate and the microporous layer (MPL), how these are measured experimentally ex-situ, how they influence fuel cell performance, and how they can be altered via the manufacturing process. In particular, we investigate the correlation between ex-situ measured effective diffusivity of water vapor and in-situ performance and limiting current density in a PEM fuel cell. Further, we examine the effect of adding multiple MPLs, MPL loading, and MPL particle size on cell performance under both wet and dry operating conditions.

  12. Structure and Function of Immunoglobulins

    PubMed Central

    Schroeder, Harry W; Cavacini, Lisa

    2013-01-01

    Immunoglobulins are heterodimeric proteins composed of two heavy (H) and two light (L) chains. They can be separated functionally into variable (V) domains that binds antigens and constant (C) domains that specify effector functions such as activation of complement or binding to Fc receptors. The variable domains are created by means of a complex series of gene rearrangement events, and can then be subjected to somatic hypermutation after exposure to antigen to allow affinity maturation. Each V domain can be split into three regions of sequence variability, termed the complementarity determining regions, or CDRs, and four regions of relatively constant sequence termed the framework regions, or FRs. The three CDRs of the H chain are paired with the three CDRs of the L chain to form the antigen binding site, as classically defined. There are five main classes of heavy chain C domains. Each class defines the IgM, IgG, IgA, IgD, and IgE isotypes. IgG can be split into four subclasses, IgG1, IgG2, IgG3, and IgG4, each with its own biologic properties; and IgA can similarly be split into IgA1 and IgA2. The constant domains of the H chain can be switched to allow altered effector function while maintaining antigen specificity. PMID:20176268

  13. Structure and function of immunoglobulins.

    PubMed

    Schroeder, Harry W; Cavacini, Lisa

    2010-02-01

    Immunoglobulins are heterodimeric proteins composed of 2 heavy and 2 light chains. They can be separated functionally into variable domains that bind antigens and constant domains that specify effector functions, such as activation of complement or binding to Fc receptors. The variable domains are created by means of a complex series of gene rearrangement events and can then be subjected to somatic hypermutation after exposure to antigen to allow affinity maturation. Each variable domain can be split into 3 regions of sequence variability termed the complementarity-determining regions (CDRs) and 4 regions of relatively constant sequence termed the framework regions. The 3 CDRs of the heavy chain are paired with the 3 CDRs of the light chain to form the antigen-binding site, as classically defined. The constant domains of the heavy chain can be switched to allow altered effector function while maintaining antigen specificity. There are 5 main classes of heavy chain constant domains. Each class defines the IgM, IgG, IgA, IgD, and IgE isotypes. IgG can be split into 4 subclasses, IgG1, IgG2, IgG3, and IgG4, each with its own biologic properties, and IgA can similarly be split into IgA1 and IgA2.

  14. Fabrication and evaluation of flexible Mach-Zehnder waveguide structure embedded in a poly(dimethylsiloxane) thin film using a proton microbeam

    NASA Astrophysics Data System (ADS)

    Parajuli, Raj Kumar; Saruya, Ryota; Akutzu, Naoki; Miura, Satoshi; Kada, Wataru; Kawabata, Shunsuke; Matsubara, Yoshinori; Satoh, Takahiro; Koka, Masashi; Yamada, Naoto; Kamiya, Tomihiro; Miura, Kenta; Hanaizumi, Osamu

    2016-06-01

    A flexible Mach-Zehnder (MZ) optical waveguide was fabricated in a poly(dimethylsiloxane) (PDMS) film by proton beam writing (PBW). A focused 750 keV proton microbeam was used to fabricate a 40 × 20 mm2 MZ optical waveguide structure with a width of 8 µm embedded in a PDMS film for the single-mode light propagation of infrared (IR) laser light. The structure was measured by ion-beam-induced luminescence (IBIL) analysis and the beam fluence was optimized according to the IBIL intensity obtained from the waveguide structure. The entire structure of the MZ waveguide functioned well, confirmed by observing the near-field pattern (NFP) with a tunable IR laser (1.55 µm) for different PDMS film conditions. The optical throughput measurements for different sample configurations were obtained under continuous mechanical stress and a relatively low optical loss was observed at an inclination angle of 16°. Our results suggest that the MZ waveguide can be used for optical interlink connections under continuous mechanical stress.

  15. Voltage Gated Ion Channel Function: Gating, Conduction, and the Role of Water and Protons

    PubMed Central

    Kariev, Alisher M.; Green, Michael E.

    2012-01-01

    Ion channels, which are found in every biological cell, regulate the concentration of electrolytes, and are responsible for multiple biological functions, including in particular the propagation of nerve impulses. The channels with the latter function are gated (opened) by a voltage signal, which allows Na+ into the cell and K+ out. These channels have several positively charged amino acids on a transmembrane domain of their voltage sensor, and it is generally considered, based primarily on two lines of experimental evidence, that these charges move with respect to the membrane to open the channel. At least three forms of motion, with greatly differing extents and mechanisms of motion, have been proposed. There is a “gating current”, a capacitative current preceding the channel opening, that corresponds to several charges (for one class of channel typically 12–13) crossing the membrane field, which may not require protein physically crossing a large fraction of the membrane. The coupling to the opening of the channel would in these models depend on the motion. The conduction itself is usually assumed to require the “gate” of the channel to be pulled apart to allow ions to enter as a section of the protein partially crosses the membrane, and a selectivity filter at the opposite end of the channel determines the ion which is allowed to pass through. We will here primarily consider K+ channels, although Na+ channels are similar. We propose that the mechanism of gating differs from that which is generally accepted, in that the positively charged residues need not move (there may be some motion, but not as gating current). Instead, protons may constitute the gating current, causing the gate to open; opening consists of only increasing the diameter at the gate from approximately 6 Å to approximately 12 Å. We propose in addition that the gate oscillates rather than simply opens, and the ion experiences a barrier to its motion across the channel that is tuned

  16. Structure and function of cytochrome bc complexes

    SciTech Connect

    Berry, E.A.; Guergova-Kuras, M.; Huang, Li-Shar; Crofts, A.R.

    2000-05-01

    The cytochrome bc complexes represent a phylogenetically diverse group of electron-transfer membrane protein complexes, most familiarly represented by the mitochondrial and bacterial bc1 complexes and the chloroplast and cyanobacterial b6f complex. All these complexes couple electron transfer to protein translocation across a closed lipid bilayer membrane, conserving the free energy released by the oxidation-reduction process in the form of an electrochemical proton gradient across the membrane. Recent exciting developments include the application of site-directed mutagenesis to define the role of conserved residues, and the emergence over the past 5 years of x-ray structures for several mitochondrial complexes, and for two important domains of the b6f complex.

  17. Functionalized Nano and Micro Structured Composite Coatings

    DTIC Science & Technology

    2011-06-01

    AFRL-RX-TY-TR-2011-0069 FUNCTIONALIZED NANO AND MICRO STRUCTURED COMPOSITE COATINGS (FINAL REPORT) Igor Luzinov and Konstantin Kornev...Technical Report 21-MAY-2009 -- 31-MAY-2011 Functional Polymeric Materials - from Research Labs to Field Applications: Functionalized Nano and Micro ...work was to conduct research on development of effective nano and micro structured composite coatings capable to collect and decontaminate the

  18. Structural Health Monitoring Using Transmittance Functions

    NASA Astrophysics Data System (ADS)

    Zhang, H.; Schulz, M. J.; Naser, A.; Ferguson, F.; Pai, P. F.

    1999-09-01

    A technique for structural health monitoring that can detect damage away from a sensor location and during operation of a structure is presented. The technique, Transmittance Function Monitoring, uses vibration measurements to detect damage, but without measuring the excitation force or using a model of the structure. Accelerometers or piezoceramic patches are attached to the structure for sensing, and piezoceramic patches or inertial actuators are used for exciting the structure. The sensor-actuator system actively interrogates the structure using broadband excitation, and transmittance functions between consecutive sensors from the healthy structure are stored as historical data. Changes in the functions are then used to detect, locate and assess damage to the structure. Transmittance functions can be computed from different types of measured structural responses. Here, structural translations and curvatures are used to detect damage on a composite beam. The sensitivity of the two different methods is compared, and the optimal frequency range to detect damage is experimentally determined. In addition, the wavelengths of the structural mode shapes are computed to estimate the highest frequency at which the structural response can be measured by a given length piezoceramic sensor.

  19. Optimized Structures and Proton Affinities of Fluorinated Dimethyl Ethers: An Ab Initio Study

    NASA Technical Reports Server (NTRS)

    Orgel, Victoria B.; Ball, David W.; Zehe, Michael J.

    1996-01-01

    Ab initio methods have been used to investigate the proton affinity and the geometry changes upon protonation for the molecules (CH3)2O, (CH2F)2O, (CHF2)2O, and (CF3)2O. Geometry optimizations were performed at the MP2/3-2 I G level, and the resulting geometries were used for single-point energy MP2/6-31G calculations. The proton affinity calculated for (CH3)2O was 7 Kjoule/mole from the experimental value, within the desired variance of +/- 8Kjoule/mole for G2 theory, suggesting that the methodology used in this study is adequate for energy difference considerations. For (CF3)20, the calculated proton affinity of 602 Kjoule/mole suggests that perfluorinated ether molecules do not act as Lewis bases under normal circumstances; e.g. degradation of commercial lubricants in tribological applications.

  20. Effect of a triaxial nuclear shape on proton tunneling: the decay and structure of 145Tm.

    PubMed

    Seweryniak, D; Blank, B; Carpenter, M P; Davids, C N; Davinson, T; Freeman, S J; Hammond, N; Hoteling, N; Janssens, R V F; Khoo, T L; Liu, Z; Mukherjee, G; Robinson, A; Scholey, C; Sinha, S; Shergur, J; Starosta, K; Walters, W B; Woehr, A; Woods, P J

    2007-08-24

    Gamma rays deexciting states in the proton emitter 145Tm were observed using the recoil-decay tagging method. The 145Tm ground-state rotational band was found to exhibit the properties expected for an h{11/2} proton decoupled band. In addition, coincidences between protons feeding the 2{+} state in 144Er and the 2{+}-->0{+} gamma-ray transition were detected, the first measurement of this kind, leading to a more precise value for the 2{+} excitation energy of 329(1) keV. Calculations with the particle-rotor model and the core quasiparticle coupling model indicate that the properties of the pi{11/2} band and the proton-decay rates in 145Tm are consistent with the presence of triaxiality with an asymmetry parameter gamma approximately 20 degrees .

  1. Structure and function of desmosomes.

    PubMed

    Holthöfer, Bastian; Windoffer, Reinhard; Troyanovsky, Sergey; Leube, Rudolf E

    2007-01-01

    Desmosomes are prominent adhesion sites that are tightly associated with the cytoplasmic intermediate filament cytoskeleton providing mechanical stability in epithelia and also in several nonepithelial tissues such as cardiac muscle and meninges. They are unique in terms of ultrastructural appearance and molecular composition with cell type-specific variations. The dynamic assembly properties of desmosomes are important prerequisites for the acquisition and maintenance of tissue homeostasis. Disturbance of this equilibrium therefore not only compromises mechanical resilience but also affects many other tissue functions as becomes evident in various experimental scenarios and multiple diseases.

  2. Orientation-dependent proton double-quantum NMR build-up function for soft materials with anisotropic mobility.

    PubMed

    Naumova, Anna; Tschierske, Carsten; Saalwächter, Kay

    In recent years, the analysis of proton double-quantum NMR build-up curves has become an important tool to quantify anisotropic mobility in different kinds of soft materials such as polymer networks or liquid crystals. In the former case, such data provides a measure of orientation-dependent residual (time-averaged) dipolar couplings arising from anisotropic segmental motions, informing about the length and the state of local stretching of the network chains. Previous studies of macroscopically ordered, i.e. stretched, networks were subject to the limitation that a detailed build-up curve analysis on the basis of a universal "Abragam-like" (A-l) build-up function valid for a proton multi-spin system was only possible for an isotropic orientation-averaged response. This situation is here remedied by introducing a generic orientation-dependent build-up function for an anisotropically mobile protonated molecular segment. We discuss an application to the modeling of data for a stretched network measured at different orientations with respect to the magnetic field, and present a validation by fitting data of different liquid-crystal molecules oriented in the magnetic field.

  3. Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

    PubMed Central

    Phatak, Prasad; Ghosh, Nilanjan; Yu, Haibo; Cui, Qiang; Elstner, Marcus

    2008-01-01

    The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally difficult to determine unambiguously. Using combined quantum mechanical/molecular mechanical computations, we demonstrate that a pair of conserved glutamate residues (Glu 194/204) bonded by a delocalized proton is the proton release group that has been long sought in the proton pump, bacteriorhodopsin. This model is consistent with all available experimental structural and infrared data for both the wild-type bacteriorhodopsin and several mutants. In particular, the continuum infrared band in the 1,800- to 2,000-cm−1 region is shown to arise due to the partially delocalized nature of the proton between the glutamates in the wild-type bacteriorhodopsin; alternations in the flexibility of the glutamates and electrostatic nature of nearby residues in various mutants modulate the degree of proton delocalization and therefore intensity of the continuum band. The strong hydrogen bond between Glu 194/204 also significantly shifts the carboxylate stretches of these residues well <1,700 cm−1, which explains why carboxylate spectral shift was not observed experimentally in the typical >1,700-cm−1 region upon proton release. By contrast, simulations with the proton restrained on the nearby water cluster, as proposed by several recent studies [see, for example, Garezarek K, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109], led to significant structural deviations from available X-ray structures. This study establishes a biological function for strong, low-barrier hydrogen bonds. PMID:19064907

  4. Track structure model for damage to mammalian cell cultures during solar proton events

    NASA Technical Reports Server (NTRS)

    Cucinotta, F. A.; Wilson, J. W.; Townsend, L. W.; Shinn, J. L.; Katz, R.

    1992-01-01

    Solar proton events (SPEs) occur infrequently and unpredictably, thus representing a potential hazard to interplanetary space missions. Biological damage from SPEs will be produced principally through secondary electron production in tissue, including important contributions due to delta rays from nuclear reaction products. We review methods for estimating the biological effectiveness of SPEs using a high energy proton model and the parametric cellular track model. Results of the model are presented for several of the historically largest flares using typical levels and body shielding.

  5. Tear Lipocalin: Structure and Function

    PubMed Central

    Dartt, Darlene A.

    2014-01-01

    Lipocalins are a family of diverse low molecular weight proteins that act extracellularly. They use multiple recognition properties that include: 1) ligand binding to small hydrophobic molecules, 2) macromolecular complexation with other soluble macromolecules, and 3) binding to specific cell surface receptors to deliver cargo. Tear lipocalin (TLC) is a major protein in tears and has a large ligand binding cavity that allows the lipocalin to bind an extensive and diverse set of lipophilic molecules. TLC can also bind to macromolecules including the tear proteins lactoferin and lysozyme. The receptor to which TLC binds is termed tear lipocalin interacting membrane receptor (LIMR). LIMR appears to work by endocytosis. TLC has a variety of suggested functions in tears including regulation of tear viscosity, binding and release of lipids, endonuclease inactivation of viral DNA, binding of microbial siderophores (iron chelators used to deliver essential iron to bacteria), use as a biomarker for dry eye, and possession of anti-inflammatory activity. Additional research is warranted to determine the actual functions of TLC in tears and the presence of its receptor on the ocular surface. PMID:21791187

  6. Effect of wave function on the proton induced L XRP cross sections for {sub 62}Sm and {sub 74}W

    SciTech Connect

    Shehla,; Kaur, Rajnish; Kumar, Anil; Puri, Sanjiv

    2015-08-28

    The L{sub k}(k= 1, α, β, γ) X-ray production cross sections have been calculated for {sub 74}W and {sub 62}Sm at different incident proton energies ranging 1-5 MeV using theoretical data sets of different physical parameters, namely, the Li(i=1-3) sub-shell X-ray emission rates based on the Dirac-Fork (DF) model, the fluorescence and Coster Kronig yields based on the Dirac- Hartree-Slater (DHS) model and two sets the proton ionization cross sections based on the DHS model and the ECPSSR in order to assess the influence of the wave function on the XRP cross sections. The calculated cross sections have been compared with the measured cross sections reported in the recent compilation to check the reliability of the calculated values.

  7. 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

  8. [Interferons: between structure and function].

    PubMed

    Bandurska, Katarzyna; Król, Izabela; Myga-Nowak, Magdalena

    2014-05-06

    Interferons are a family of proteins that are released by a variety of cells in response to infections caused by viruses. Currently, we distinguish three types of interferons. They are classified based on the nucleotide sequence, interaction with specific receptors, chromosomal location, structure and physicochemical properties. The following interferons are classified as type I: α, β, ω, κ, ε, ζ, τ, δ, ν. They are recognized and bound by a receptor formed by two peptides, IFN-αR1 and IFN-αR2. Representative of type II interferons is interferon-γ. It binds to a receptor composed of chains IFNGR-1 and IFNGR-2. The recently classified type III interferons comprise IFN-λ1, IFN-λ2, and IFN-λ3. They act on receptors formed by λR1 IFN-and IL-10R2 subunits. A high level of antiviral protection is achieved by IFN-α, IFN-β and IFN-λ. Antiviral activity of interferons is based on the induction and regulation of innate and acquired immune mechanisms. By binding to transmembrane receptors, IFN interacts with target cells mainly by activating the JAK/STAT, but also other signaling pathways. This leads to induction and activation of many antiviral agents, such as protein kinase RNA-activated (PKR), ribonuclease 2-5A pathway, and Mx proteins, as well as numerous apoptotic pathways. As a result of the protective effect of interferons, the virus binding to cells and viral particles penetration into cells is stopped, and the release of the nucleocapsid from an envelope is suppressed. Disruption of transcription and translation processes of the structural proteins prevents the formation of virions or budding of viruses, and as a result degradation of the viral mRNA; the started processes inhibit the chain synthesis of viral proteins and therefore further stimulate the immune system cells.

  9. Measurements of the g{sup p}{sub 1} spin structure function

    SciTech Connect

    Lichtenstadt, J.

    1994-10-26

    The spin structure function g{sub 1}{sup p} of the proton has been measured b deep inelastic scattering of polarized muons from polarized protons. The data were taken over the kinematic range 0.003 {le} x B{sub j} {le} 0.7 and 1 GeV{sup 2} {le} Q{sup 2} {le} 60 GeV{sup 2}. The first moment {Gamma}{sub 1}{sup p} = {integral}{sub 0}{sup 1}G{sub 1}{sup p}(x)dx was evaluated and compared to the I Ellis-Jaffe sum rule. The consistency of existing proton deuteron and neutron data is discussed. Combination of the data allows a test the fundamental Bjorken sum rule which is confirmed at the level of 10% of its theoretical value, when high QCD corrections are considered. The contribution of the quark spins to the nucleon spin is evaluated within the quark-parton model.

  10. High-spin structure of sup 189 Tl: Role of h sub 9/2 protons in the prolate minimum of light Hg isotopes

    SciTech Connect

    Porquet, M.; Kreiner, A.J.; Hannachi, F.; Vanin, V.; Bastin, G.; Bourgeois, C.; Davidson, J.; Debray, M.; Falcone, G.; Korichi, A.; Mosca, H.; Perrin, N.; Sergolle, H.; Beck, F.A.; Merdinger, J. Departamento de Fisica, Comision Nacional de Energia Atomica, 1429 Buenos Aires Centre de Recherches Nucleaires, 67037 Strasbourg Instituto de Fisica, Universidade de Sao Paulo, 1000 Sao Paulo Institut de Physique Nucleaire, 91406 Orsay )

    1991-12-01

    High-spin states in {sup 189}Tl have been populated through the {sup 165}Ho({sup 28}Si,4{ital n}) reaction and studied with in-beam {gamma}-ray spectroscopy techniques. Both oblate and prolate structures associated with the {ital i}13/2 proton orbit are confirmed and extended to higher spins (19/2 and 41/2, respectively). However, only the oblate structure related to the {pi}{ital h}9/2 has been observed meaning that the associated prolate structure is nonyrast contrary to expectation. This experimental result points clearly to a large amplitude of ({pi}{ital h}9/2){sup 2} in the wave function of the prolate minimum of {sup 188}Hg.

  11. DESIGN OF SUPERCONDUCTING COMBINED FUNCTION MAGNETS FOR THE 50 GEV PROTON BEAM LINE FOR THE J-PARC NEUTRINO EXPERIMENT.

    SciTech Connect

    WANDERER,P.; ET AL.

    2003-06-15

    Superconducting combined function magnets will be utilized for the 50GeV-750kW proton beam line for the J-PARC neutrino experiment and an R and D program has been launched at KEK. The magnet is designed to provide a combined function with a dipole field of 2.59 T and a quadrupole field of 18.7 T/m in a coil aperture of 173.4 mm. A single layer coil is proposed to reduce the fabrication cost and the coil arrangement in the 2-D cross-section results in left-right asymmetry. This paper reports the design study of the magnet.

  12. Possibilities of studying the structure of halo nuclei in reactions of quasifree proton scattering at low energies

    SciTech Connect

    Zuyev, S. V. Kasparov, A. A.; Konobeevski, E. S.

    2015-07-15

    The possibility of experimentally studying the structure of halo nuclei in reactions induced by quasifree proton scattering on clusters of these nuclei is considered. Quasifree proton scattering on {sup 6}He, {sup 4}He, {sup 4}n, {sup 2}n, and n clusters in inverse kinematics is considered for the example of the {sup 8}He nucleus. Angular and energy distributions of secondaries are obtained for various representations of the cluster structure of the {sup 8}He nucleus. It is clearly shown that, in the angular and energy distributions of secondaries, one can single out regions that receive dominant contributions from reactions on specific clusters and which correspond to concrete cluster configurations of halo nuclei. Possible relevant experiments are proposed.

  13. Beta-alanine-hydrochloride (2:1) crystal: structure, 13C NMR and vibrational properties, protonation character.

    PubMed

    Godzisz, D; Ilczyszyn, M; Ciunik, Z

    2003-01-15

    The crystal structure of beta-alanine-hydrochloride (2:1) complex (2A-HCl) has been determined by X-ray diffraction method at 298 and 100 K as monoclinic, space group C2/c, Z=4. The crystal comprises chloride anions and protonated beta-alanine dimers: two beta-alanine zwitterions are joined by strong, symmetric (Ci) hydrogen bond with the O...O distance of 2.473 A at room temperature. Powder FT-IR and FT-Raman as well as solid state 13C NMR spectra provide insights into the solid structure of this complex, character of its hydrogen bonds and the beta-alanine protonation.

  14. Development of embedded Mach-Zehnder optical waveguide structures in polydimethylsiloxane thin films by proton beam writing

    NASA Astrophysics Data System (ADS)

    Kada, W.; Miura, K.; Kato, H.; Saruya, R.; Kubota, A.; Satoh, T.; Koka, M.; Ishii, Y.; Kamiya, T.; Nishikawa, H.; Hanaizumi, O.

    2015-04-01

    A focused 750 keV proton microbeam was used to fabricate an embedded Mach-Zehnder (MZ) optical waveguide in a polydimethylsiloxane (PDMS) film for interferometer application. The sample position was precisely controlled by a mechanical stage together with scanning microbeam to form an embedded MZ waveguide structure within an area of 0.3 mm × 40 mm. The MZ waveguides with core size of 8 μm was successfully embedded in PDMS film at a depth of 18 μm by 750 keV proton microbeam with fluences from 10 to 100 nC/mm2. The MZ waveguides were coupled with an IR fiber-laser with a center wavelength of 1550 nm and evaluated by using the transmitted intensity images from an IR vidicon camera. The results indicate that the embedded MZ waveguide structure in PDMS achieved single spot light propagation, which is necessary for building optical switching circuits based on polymer MZ waveguides.

  15. Synthesis of an extra-large molecular sieve using proton sponges as organic structure-directing agents.

    PubMed

    Martínez-Franco, Raquel; Moliner, Manuel; Yun, Yifeng; Sun, Junliang; Wan, Wei; Zou, Xiaodong; Corma, Avelino

    2013-03-05

    The synthesis of crystalline microporous materials containing large pores is in high demand by industry, especially for the use of these materials as catalysts in chemical processes involving bulky molecules. An extra-large-pore silicoaluminophosphate with 16-ring openings, ITQ-51, has been synthesized by the use of bulky aromatic proton sponges as organic structure-directing agents. Proton sponges show exceptional properties for directing extra-large zeolites because of their unusually high basicity combined with their large size and rigidity. This extra-large-pore material is stable after calcination, being one of the very few examples of hydrothermally stable molecular sieves containing extra-large pores. The structure of ITQ-51 was solved from submicrometer-sized crystals using the rotation electron diffraction method. Finally, several hypothetical zeolites related to ITQ-51 have been proposed.

  16. Nitrogenase structure and function relationships by density functional theory.

    PubMed

    Harris, Travis V; Szilagyi, Robert K

    2011-01-01

    Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we pr