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Sample records for 94ag isomeric states

  1. Spectroscopic characterization of isomerization transition states.

    PubMed

    Baraban, Joshua H; Changala, P Bryan; Mellau, Georg Ch; Stanton, John F; Merer, Anthony J; Field, Robert W

    2015-12-11

    Transition state theory is central to our understanding of chemical reaction dynamics. We demonstrate a method for extracting transition state energies and properties from a characteristic pattern found in frequency-domain spectra of isomerizing systems. This pattern-a dip in the spacings of certain barrier-proximal vibrational levels-can be understood using the concept of effective frequency, ω(eff). The method is applied to the cis-trans conformational change in the S1 state of C2H2 and the bond-breaking HCN-HNC isomerization. In both cases, the barrier heights derived from spectroscopic data agree extremely well with previous ab initio calculations. We also show that it is possible to distinguish between vibrational modes that are actively involved in the isomerization process and those that are passive bystanders. PMID:26659051

  2. Spectroscopic characterization of isomerization transition states

    NASA Astrophysics Data System (ADS)

    Baraban, Joshua H.; Changala, P. Bryan; Mellau, Georg Ch.; Stanton, John F.; Merer, Anthony J.; Field, Robert W.

    2015-12-01

    Transition state theory is central to our understanding of chemical reaction dynamics. We demonstrate a method for extracting transition state energies and properties from a characteristic pattern found in frequency-domain spectra of isomerizing systems. This pattern—a dip in the spacings of certain barrier-proximal vibrational levels—can be understood using the concept of effective frequency, ωeff. The method is applied to the cis-trans conformational change in the S1 state of C2H2 and the bond-breaking HCN-HNC isomerization. In both cases, the barrier heights derived from spectroscopic data agree extremely well with previous ab initio calculations. We also show that it is possible to distinguish between vibrational modes that are actively involved in the isomerization process and those that are passive bystanders.

  3. Nearly degenerate isomeric states of 75Cu

    NASA Astrophysics Data System (ADS)

    Petrone, C.; Daugas, J. M.; Simpson, G. S.; Stanoiu, M.; Plaisir, C.; Faul, T.; Borcea, C.; Borcea, R.; Cáceres, L.; Calinescu, S.; Chevrier, R.; Gaudefroy, L.; Georgiev, G.; Gey, G.; Kamalou, O.; Negoita, F.; Rotaru, F.; Sorlin, O.; Thomas, J. C.

    2016-08-01

    The decays of two isomeric states in the neutron-rich nucleus 75Cu have been studied via delayed γ -ray spectroscopy. These states were populated by the fragmentation of a 60.4 A MeV 86Kr primary beam, which impinged on a Be target at the LISE2k spectrometer of GANIL. Isomeric half-lives and branching ratios were measured, and a γ -γ coincidence analysis performed. These have allowed a revised level scheme of 75Cu to be proposed. A comparison with large-scale shell-model calculations using different effective interactions and valence spaces shows the importance of proton excitations across the Z =28 shell gap for reproducing the energy spacing between the isomeric states. The coexisting collective and single-particle properties of the (1 /2-) and (3 /2-) states, respectively, are similar to those of the same states in the neighboring 69,71,73Cu. The small energy spacings between the (1 /2-) , (3 /2-) , and 5 /2- states are responsible for the isomerism.

  4. Isomeric States and Collective Excitations of Heaviest Nuclei

    NASA Astrophysics Data System (ADS)

    Adamian, G. G.; Antonenko, N. V.; Jolos, R. V.; Kuzmina, A. N.; Malov, L. A.; Shirikova, N. Yu.; Sushkov, A. V.

    2013-03-01

    The isotopic dependence of two-quasiparticle isomeric states in Fm and No is treated. An α-decay chain through the isomeric states of super-heavy nuclei is demonstrated. The excitation energies and the structure of the low lying states with Kπ = 0‒ 1‒ 2‒ are calculated with the quasiparticle phonon model.

  5. Solid State Photochemical Isomerization: A Convenient Laboratory Experiment.

    ERIC Educational Resources Information Center

    Burton, W. B.

    1979-01-01

    Describes the use of benzophenone in the role of a solid state sensitizer in a photochemical isomerization and as an indicator in preparative layer chromatography for purification of the isomeride. (Author/SA)

  6. Excited state dynamics and isomerization in ruthenium sulfoxide complexes.

    PubMed

    King, Albert W; Wang, Lei; Rack, Jeffrey J

    2015-04-21

    Molecular photochromic compounds are those that interconvert between two isomeric forms with light. The two isomeric forms display distinct electronic and molecular structures and must not be in equilibrium with one another. These light-activated molecular switch compounds have found wide application in areas of study ranging from chemical biology to materials science, where conversion from one isomeric form to another by light prompts a response in the environment (e.g., protein or polymeric material). Certain ruthenium and osmium polypyridine sulfoxide complexes are photochromic. The mode of action is a phototriggered isomerization of the sulfoxide from S- to O-bonded. The change in ligation drastically alters both the spectroscopic and electrochemical properties of the metal complex. Our laboratory has pioneered the preparation and study of these complexes. In particular, we have applied femtosecond pump-probe spectroscopy to reveal excited state details of the isomerization mechanism. The data from numerous complexes allowed us to predict that the isomerization was nonadiabatic in nature, defined as occurring from a S-bonded triplet excited state (primarily metal-to-ligand charge transfer in character) to an O-bonded singlet ground state potential energy surface. This prediction was corroborated by high-level density functional theory calculations. An intriguing aspect of this reactivity is the coupling of nuclear motion to the electronic wave function and how this coupling affects motions productive for isomerization. In an effort to learn more about this coupling, we designed a project to examine phototriggered isomerization in bis-sulfoxide complexes. The goal of these studies was to determine whether certain complexes could be designed in which a single photon excitation event would prompt two sulfoxide isomerizations. We employed chelating sulfoxides in this study and found that both the nature of the chelate ring and the R group on the sulfoxide affect

  7. Excited State Isomerization of a Stilbene Analog: E / Z Phenylvinylacetylene

    NASA Astrophysics Data System (ADS)

    Newby, Josh J.; Müller, Christian W.; Liu, Ching-Ping; Lee, Hsiupu D.; Zwier, Timothy S.

    2009-06-01

    The excited state isomerization of the E and Z forms of phenylvinylacetylene (PVA, 1-phenyl-1-buten-3-yne) has been studied using ultraviolet population transfer spectroscopy (UVPT). UVPT is a pump-probe experiment, where single isomers are selectively excited and after a wait time, the induced change in population of reactant and product isomers is probed. In these experiments, after initial cooling, an isomer of PVA is selectively excited to vibrational levels in the S_{1} electronic state. If the energy supplied by the excitation is above the barrier to isomerization population can be transferred into a product well. Excited molecules are collisionally cooled via supersonic expansion and a new population distribution can be detected downstream via R2PI spectroscopy. From these experiments, product isomerization quantum yields have been determined for both E to Z and Z to E excited state pathways as a function of excess energy above the S_{1} origin.

  8. Further results in the search for the direct two-proton decay of ^94Ag^m (J^π= 21^+, 6.7 MeV)

    NASA Astrophysics Data System (ADS)

    Cerny, J.; Lee, D. W.; Perajarvi, K.; Moltz, D. M.; Barquest, B. R.; Grossman, L. E.; Jeong, W.; Jewett, C. C.

    2008-10-01

    Both direct one-proton decay and direct two-proton decay of ^94Ag^m from this 0.4 s isomeric state have been reported in experiments utilizing the GSI on-line mass separator [1]. In the latter decay, coincident events between silicon E detectors with a threshold energy of 0.4 MeV and a summed decay energy of 1.9±0.1 MeV were observed with a yield of 350±210 pb in coincidence with γ-decays in the ^92Rh daughter. We utilized our helium-jet system at the LBNL 88-inch cyclotron to repeat this experiment, again employing the ^58Ni(^40Ca,p3n) reaction at 197 MeV. Reaction products were transported via a capillary to a detection area and collected on a slowly rotating wheel in front of an assembly of 24 δEgas-δEgas-ESi detector telescopes with a threshold of 0.4 MeV for identifying protons. Five of these telescopes observe the 0.79 MeV single proton decay from ^94Ag^m at the reported yield of 1.3 nb. In the 240/276 identified proton detector combinations with low background, no proton-proton coincidences have been observed. Data from the remaining 36 detector combinations require a separate analysis, which is in progress. Monte Carlo analyses of our anticipated proton-proton coincidences for both sets of detector combinations will be presented. ^ 1Mukha et al., Nature 439, 298 (2006).

  9. g-factor measurements of isomeric states in 174W

    NASA Astrophysics Data System (ADS)

    Rocchini, M.; Nannini, A.; Benzoni, G.; Melon, B.; John, P. R.; Ur, C. A.; Avigo, R.; Bazzacco, D.; Blasi, N.; Bocchi, G.; Bottoni, S.; Bracco, A.; Camera, F.; Ceruti, S.; Crespi, F. C. L.; Georgiev, G.; Giaz, A.; Gottardo, A.; Leoni, S.; Menegazzo, R.; Mengoni, D.; Michelagnoli, C.; Million, B.; Modamio, V.; Morales, A. I.; Napoli, D. R.; Ottanelli, M.; Pellegri, L.; Perego, A.; Valiente-Dobon, J. J.; Wieland, O.

    2016-05-01

    The experimental setup GAMIPE used for gyro magnetic factor measurements at Laboratori Nazionali di Legnaro and a recent experimental work regarding K-isomers in 174W are described. Aim of the experiment is to study the detailed structure of the isomeric states wave functions, by the measurement of the magnetic dipole moments. This piece of information can provide interesting hints for theoretical models. Preliminary results concerning the population of the isomers of interest and half-lives are presented.

  10. Conversion coefficients of the isomeric state in {sup 72}Br

    SciTech Connect

    Briz, J. A.; Borge, M. J. G.; Maira, A.; Perea, A.; Tengblad, O.; Agramunt, J.; Algora, A.; Estevez, E.; Nacher, E.; Rubio, B.; Fraile, L. M.; Deo, A.; Farrelly, G.; Gelletly, W.; Podolyak, Z.

    2010-04-26

    In order to determine the Gamow-Teller strength distribution for the N Z nucleus {sup 72}Kr an experiment was performed with a Total Absorption Gamma Spectrometer. To fully accomplish this task it is crucial to determine the multipolarity of the low energy transitions as the spin-parity of the daughter ground state has been debated. This is done by experimental determination of the conversion coefficients. Preliminary results for the multipolarity and conversion coefficients of the transition connecting the isomeric state at 101 keV with the {sup 72}Br ground state are presented.

  11. Isomeric state in {sup 53}Co: A mean field analysis

    SciTech Connect

    Patra, S. K.; Bhat, F. H.; Panda, R. N.; Arumugam, P.; Gupta, Raj K.

    2009-04-15

    We study the ground and the first excited intrinsic states of {sup 53}Co and its mirror nucleus {sup 53}Fe, within the frameworks of the relativistic and nonrelativistic mean field formalisms. The analysis of the single-particle energy spectra of these nuclei show a competition of spins 1/2{sup -} and 3/2{sup -} in a low-lying excited state, which agrees well with the recent experimental observation [D. Rudolph et al., Eur. Phys. J. A 36, 131 (2008)] of spin and parity J{sup {pi}}=3/2{sup -} for the isomeric configuration in {sup 53}Co.

  12. High spin states and isomeric decays in doubly-odd 208Fr

    NASA Astrophysics Data System (ADS)

    Kanjilal, D.; Bhattacharya, S.; Goswami, A.; Kshetri, R.; Raut, R.; Saha, S.; Bhowmik, R. K.; Gehlot, J.; Muralithar, S.; Singh, R. P.; Jnaneswari, G.; Mukherjee, G.; Mukherjee, B.

    2010-10-01

    Neutron deficient isotopes of francium ( Z=87, N˜121-123) as excited nuclei were produced in the fusion-evaporation reaction: 197Au( 16O, xn) 213 - xFr at 100 MeV. The γ rays from the residues were observed through the high sensitivity Germanium Clover detector array INGA. The decay of the high spin states and the isomeric states of the doubly-odd 208Fr nuclei, identified from the known sequence of ground state transitions, were observed. The half-lives of the E=194(2) keV isomeric transition, known from earlier observations, was measured to be T=233(18) ns. A second isomeric transition at E=383(2) keV and T=33(7) ns was also found. The measured half-lives were compared with the corresponding single particle estimates, based on the level scheme obtained from the experiment.

  13. Method for detecting the isomeric state I =(3/2 ) + in 229Th with laser-induced fluorescence

    NASA Astrophysics Data System (ADS)

    Dembczyński, J.; Elantkowska, M.; Ruczkowski, J.

    2015-07-01

    There are different predictions regarding the position of the isomeric state of Thm229. There is some question as to whether it even exists. We propose simple experiments to provide the evidence of the existence of this isomeric state. If the metastable isomeric state exists, we should be able to observe the effects of mixing of the nuclear wave functions of the ground state I =5 /2 and the isomeric I =3 /2 state via electronic shells. It will be shown as the differences between the hyperfine A and B constants, which will be measured by means of the laser-induced fluorescence methods and those predicted by semiempirical calculations. The wave function for the atomic state |conf . S L J I F > contains contributions from both nuclear states I =5 /2 and 3 /2 , thus its effects on the hyperfine-structure patterns of spectral lines should be observed, confirming the existence of this isomeric state.

  14. Existence of long-lived isomeric states in naturally-occurring neutron-deficient Th isotopes

    SciTech Connect

    Marinov, A.; Kashiv, Y.; Rodushkin, I.; Halicz, L.; Segal, I.; Pape, A.; Miller, H. W.; Kolb, D.; Brandt, R.

    2007-08-15

    Four long-lived neutron-deficient Th isotopes with atomic mass numbers 211 to 218 and abundances of (1-10)x10{sup -11} relative to {sup 232}Th have been found in a study of naturally-occurring Th using inductively coupled plasma-sector field mass spectrometry. It is deduced that long-lived isomeric states exist in these isotopes. The hypothesis that they might belong to a new class of long-lived high spin super- and hyperdeformed isomeric states is discussed.

  15. No Evidence of Isomerism for the First Excited State of {sup 93}Rb

    SciTech Connect

    Miernik, K.; Gross, C.J.; Grzywacz, R.; Madurga, M.; Mendez, A.J.; Rykaczewski, K.P.; Stracener, D.W.; Zganjar, E.F.

    2014-06-15

    The 253.3–keV excited state located in {sup 93}Rb was studied at the Holifield Radioactive Ion Beam Facility in Oak Ridge. This state, described as isomeric in databases, was populated in the decay of {sup 93}Kr produced by proton–induced fission of {sup 238}U and isolated using the isotope separation on–line technique. We report that the 253.3–keV level does not reveal isomerism and the upper limit of the half-life from our measurement is 4 ns. Our findings are supported by previously reported results that were not taken into account in the latest nuclear databases.

  16. Mass Measurements and Implications for the Energy of the High-Spin Isomer in {sup 94}Ag

    SciTech Connect

    Kankainen, A.; Elomaa, V.-V.; Eronen, T.; Hager, U.; Hakala, J.; Jokinen, A.; Moore, I. D.; Penttilae, H.; Rahaman, S.; Rinta-Antila, S.; Rissanen, J.; Saastamoinen, A.; Sonoda, T.; Weber, C.; Aeystoe, J.; Batist, L.; Popov, A.; Seliverstov, D. M.; Eliseev, S.; Novikov, Yu. N.

    2008-10-03

    Nuclides in the vicinity of {sup 94}Ag have been studied with the Penning trap mass spectrometer JYFLTRAP at the Ion-Guide Isotope Separator On-Line. The masses of the two-proton-decay daughter {sup 92}Rh and the beta-decay daughter {sup 94}Pd of the high-spin isomer in {sup 94}Ag have been measured, and the masses of {sup 93}Pd and {sup 94}Ag have been deduced. When combined with the data from the one-proton- or two-proton-decay experiments, the results lead to contradictory mass excess values for the high-spin isomer in {sup 94}Ag, -46 370(170) or -44 970(100) keV, corresponding to excitation energies of 6960(400) or 8360(370) keV, respectively.

  17. Photo-Induced Population of the h11/2 Isomeric States in ({gamma}, n) Reactions

    SciTech Connect

    Angell, C. T.; Karwowski, H. J.; Kelley, J. H.; Tonchev, A. P.; Tornow, W.

    2006-03-13

    The mechanism of excitation of isomeric h11/2 states in nuclei around the closed shell at N=82 have been studied at the High-Intensity Gamma Source (HI{gamma}S). We have taken advantage of the monoenergetic ({delta}E/E=1.5%) and pulsed {gamma}-ray-beam from HI{gamma}S to perform in-beam spectroscopy measurements with an improved level of precision and sensitivity. The giant dipole resonances at 15 MeV in the N=82 target isotones 138Ba, 140Ce, and 142Nd have been excited, and following neutron emission the {gamma}-ray cascades leading to the isomeric h11/2 state and the ground state were observed in the N=81 isotones. For all three nuclei a very similar de-excitation scheme was found. The only level observed from which the isomeric state was populated was found to be J{pi} = 7/2-. The ground state is principally populated from the states with spin and parities J{pi} = 1/2+, 5/2+, and 7/2+. The structure of the N=81 isotones and the role of the gateway states in isomer population will be discussed. The results of the measurements will be compared with statistical model calculations.

  18. Discovery of a 10 {mu}s isomeric state in {sub 63}{sup 139}Eu

    SciTech Connect

    Cullen, D. M.; Mason, P. J. R; Kishada, A. M.; Procter, M. G.; Rigby, S. V.; Varley, B. J.; Scholey, C.; Eeckhaudt, S.; Grahn, T.; Greenlees, P. T.; Jakobsson, U.; Jones, P. M.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Leppaenen, A.-P.; Maentyniemi, K.; Nieminen, P.; Nyman, M.

    2011-01-15

    Recoil-isomer tagging with the {sup 54}Fe+{sup 92}Mo reaction was used to establish a 10(2)-{mu}s isomeric state in {sup 139}Eu. Prompt versus delayed {gamma}-ray coincidence data have revealed the presence of a prompt rotational band built upon the isomer. The alignment properties of the states in this band show that the isomer is based upon a proton g{sub 7/2} configuration. The decay of the isomer takes place through a single 26-keV E1 transition. The {gamma}-ray transition strength for this decay is consistent with those established in the neighboring isomeric gamma-soft nuclei. In these nuclei, isomers are expected to form as a consequence of differences in nuclear shapes or configurations, and the natural hindrance associated with configuration-changing E1 transitions. The isomeric nature of the state in {sup 139}Eu is reasoned to be because of difference in shape of the proton g{sub 7/2} state and the proton h{sub 11/2} ground state to which it decays.

  19. 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.

  20. Resolution of nuclear ground and isomeric states by a Penning trap mass spectrometer

    SciTech Connect

    Bollen, G.; Kluge, H.; Koenig, M.; Otto, T.; Savard, G.; Stolzenberg, H. ); Moore, R.B.; Rouleau, G. ); Audi, G. )

    1992-12-01

    Ground and isomeric states of a nucleus have been resolved for the first time by mass spectrometry. Measurements on [sup 78]Rb[sup [ital m],][ital g] and [sup 84]Rb[sup [ital m],][ital g] were performed using a tandem Penning trap mass spectrometer on-line with the isotope separator ISOLDE/CERN. The effects of ion-ion interaction were investigated for two ion species differing in mass and stored simultaneously in the trap.

  1. Isomerization, Perturbations, Calculations and the S_{1} State of C_{2}H_{2}

    NASA Astrophysics Data System (ADS)

    Baraban, J. H.; Changala, P. B.; Berk, J. R. P.; Field, R. W.; Stanton, J. F.; Merer, A. J.

    2013-06-01

    Preliminary analysis of the energy region of the cis-trans isomerization transition state on the S_{1} surface of C_{2}H_{2} has revealed novel patterns and surprising perturbations, including unusually large (and high-order) anharmonicities, as well as K-staggerings of several vibrational levels. These effects complicate the analysis considerably, and require new models and calculations to account for and predict features of the observed spectra. The ˜{A}-˜{X} spectrum of acetylene has been studied both experimentally and theoretically for almost a century, and this cycle of unexpected phenomena eliciting innovative responses is found throughout its history. Especially in the last ten years, progress in understanding the S_{1} state rovibrational level structure and cis-trans isomerization has been accelerated by combining the information available from both ab initio computation and spectroscopic observations. The resulting dialogue has then frequently suggested fruitful avenues for further experiments and calculations. Current challenges and recent results in understanding the cis-trans isomerization transition state region will be discussed in this context.

  2. Insights into excited-state and isomerization dynamics of bacteriorhodopsin from ultrafast transient UV absorption

    PubMed Central

    Schenkl, S.; van Mourik, F.; Friedman, N.; Sheves, M.; Schlesinger, R.; Haacke, S.; Chergui, M.

    2006-01-01

    A visible-pump/UV-probe transient absorption is used to characterize the ultrafast dynamics of bacteriorhodopsin with 80-fs time resolution. We identify three spectral components in the 265- to 310-nm region, related to the all-trans retinal, tryptophan (Trp)-86 and the isomerized photoproduct, allowing us to map the dynamics from reactants to products, along with the response of Trp amino acids. The signal of the photoproduct appears with a time delay of ≈250 fs and is characterized by a steep rise (≈150 fs), followed by additional rise and decay components, with time scales characteristic of the J intermediate. The delayed onset and the steep rise point to an impulsive formation of a transition state on the way to isomerization. We argue that this impulsive formation results from a splitting of a wave packet of torsional modes on the potential surface at the branching between the all-trans and the cis forms. Parallel to these dynamics, the signal caused by Trp response rises in ≈200 fs, because of the translocation of charge along the conjugate chain, and possible mechanisms are presented, which trigger isomerization. PMID:16537491

  3. Watching ultrafast barrierless excited-state isomerization of pseudocyanine in real time.

    PubMed

    Dietzek, Benjamin; Yartsev, Arkady; Tarnovsky, Alexander N

    2007-05-01

    The photoinduced excited-state processes in 1,1'-diethyl-2,2'-cyanine iodine are investigated using femtosecond time-resolved pump-probe spectroscopy. Using a broad range of probe wavelengths, the relaxation of the initially prepared excited-state wavepacket can be followed down to the sink region. The data directly visualize the directed downhill motion along the torsional reaction coordinate and suggest a barrierless excited-state isomerization in the short chain cyanine dye. Additionally, ultrafast ground-state hole and excited-state hole replica broadening is observed. While the narrow excited-state wavepacket broadens during pump-probe overlap, the ground-state hole burning dynamics takes place on a significantly longer time-scale. The experiment reported can be considered as a direct monitoring of the shape and the position of the photoprepared wavepacket on the excited-state potential energy surface. PMID:17417893

  4. A system to measure isomeric state half-lives in the 10 ns to 10 μs range

    NASA Astrophysics Data System (ADS)

    Toufen, D. L.; Allegro, P. R. P.; Medina, N. H.; Oliveira, J. R. B.; Cybulska, E. W.; Seale, W. A.; Linares, R.; Silveira, M. A. G.; Ribas, R. V.

    2014-07-01

    The Isomeric State Measurement System (SISMEI) was developed to search for isomeric nuclear states produced by fusion-evaporation reactions. The SISMEI consists of 10 plastic phoswich telescopes, two lead shields, one NaI(Tl) scintillation detector, two Compton suppressed HPGe γ-ray detectors, and a cone with a recoil product catcher. The new system was tested at the 8 UD Pelletron tandem accelerator of the University of São Paulo with the measurement of two known isomeric states: 54Fe, 10+ state (E = 6527.1 (11) keV, T1/2 = 364(7) ns) and the 5/2+ state of 19F (E = 197.143 (4) keV, T1/2 = 89.3 (10) ns). The results indicate that the system is capable of identifying delayed transitions, of measuring isomeric state lifetimes, and of identifying the feeding transitions of the isomeric state through the delayed γ-γ coincidence method. The measured half-life for the 10+ state was T1/2 = 365(14) ns and for the 5/2+ state, 100(36) ns.

  5. A system to measure isomeric state half-lives in the 10 ns to 10 μs range

    SciTech Connect

    Toufen, D. L.; Allegro, P. R. P.; Medina, N. H.; Oliveira, J. R. B.; Cybulska, E. W.; Seale, W. A.; Ribas, R. V.; Linares, R.; Silveira, M. A. G.

    2014-07-15

    The Isomeric State Measurement System (SISMEI) was developed to search for isomeric nuclear states produced by fusion-evaporation reactions. The SISMEI consists of 10 plastic phoswich telescopes, two lead shields, one NaI(Tl) scintillation detector, two Compton suppressed HPGe γ-ray detectors, and a cone with a recoil product catcher. The new system was tested at the 8 UD Pelletron tandem accelerator of the University of São Paulo with the measurement of two known isomeric states: {sup 54}Fe, 10{sup +} state (E = 6527.1 (11) keV, T{sub 1/2} = 364(7) ns) and the 5/2{sup +} state of {sup 19}F (E = 197.143 (4) keV, T{sub 1/2} = 89.3 (10) ns). The results indicate that the system is capable of identifying delayed transitions, of measuring isomeric state lifetimes, and of identifying the feeding transitions of the isomeric state through the delayed γ-γ coincidence method. The measured half-life for the 10{sup +} state was T{sub 1/2} = 365(14) ns and for the 5/2{sup +} state, 100(36) ns.

  6. Magnetic moment of the 13 /2 + isomeric state in 69Cu: Spin alignment in the one-nucleon removal reaction

    NASA Astrophysics Data System (ADS)

    Kusoglu, A.; Georgiev, G.; Sotty, C.; Balabanski, D. L.; Goasduff, A.; Ishii, Y.; Abe, Y.; Asahi, K.; Bostan, M.; Chevrier, R.; Chikamori, M.; Daugas, J. M.; Furukawa, T.; Nishibata, H.; Ichikawa, Y.; Ishibashi, Y.; Lozeva, R.; Miyatake, H.; Nagae, D.; Nanao, T.; Niikura, M.; Niwa, T.; Okada, S.; Ozawa, A.; Saito, Y.; Shirai, H.; Ueno, H.; Yordanov, D. T.; Yoshida, N.

    2016-05-01

    We report on a new measurement of the g factor of the (13 /2 + ) isomeric state in the neutron-rich nucleus 69Cu. This study demonstrates the possibility of obtaining considerable nuclear spin alignment for multi-quasiparticle states in single-nucleon removal reactions. The time-dependent perturbed angular distribution (TDPAD) method was used to extract the gyromagnetic factor of the (13 /2+ ) [T1 /2=351 (14 ) ns] isomeric state of 69Cu. Its g factor was obtained as g (13 /2+) =0.248 (9 ) . The experimentally observed spin alignment for the state of interest was deduced as A =-3.3 (9 )% .

  7. 20 {mu}s isomeric state in doubly odd {sub 61}{sup 134}Pm

    SciTech Connect

    Cullen, D. M.; Mason, P. J. R; Rigby, S. V.; Kishada, A. M.; Varley, B. J.; Scholey, C.; Eeckhaudt, S.; Grahn, T.; Greenlees, P. T.; Jakobsson, U.; Jones, P. M.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Leppaenen, A.-P.; Maentyniemi, K.; Nieminen, P.; Nyman, M.; Pakarinen, J.

    2009-08-15

    Recoil-isomer tagging at the Accelerator Laboratory of the University of Jyvaeskylae has been used to establish the isomeric nature of a known (7{sup -}) excited state in the doubly odd nucleus {sup 134}Pm. The isomeric state was determined to have a half-life of 20(1) {mu}s and was populated from the decay of a {pi}h{sub 11/2} x {nu}h{sub 11/2} band using the {sup 92}Mo({sup 54}Fe,2{alpha}3pn) reaction at 305 and 315 MeV. The isomer decays by a 71-keV transition that provides an intermediate step in linking the established {sup 134}Pm high-spin level scheme to the lower-spin states observed from the {beta} decay of {sup 134}Sm. Electron-conversion analysis for the 71-keV {gamma}-ray transition reveals that it is of E1 character and its small reduced-transition probability suggests that {sup 134}Pm may have a nuclear shape more rigid than that of the neighboring nuclei.

  8. Shape isomerism at N=40: Discovery of a proton intruder state in {sup 67}Co

    SciTech Connect

    Pauwels, D.; Ivanov, O.; Bree, N.; Buescher, J.; Cocolios, T. E.; Gentens, J.; Huyse, M.; Kudryavtsev, Yu.; Raabe, R.; Sawicka, M.; Walle, J. van de; Bergh, P. van den; Duppen, P. van; Korgul, A.; Stefanescu, I.; Walters, W. B.

    2008-10-15

    The nuclear structure of {sup 67}Co has been investigated through {sup 67}Fe {beta} decay. The {sup 67}Fe isotopes were produced at the LISOL facility in proton-induced fission of {sup 238}U and selected using resonant laser ionization combined with mass separation. The application of a new correlation technique unambiguously revealed a 496(33) ms isomeric state in {sup 67}Co at an unexpected low energy of 492 keV. A {sup 67}Co level scheme was deduced. Proposed spin and parities suggest a spherical (7/2{sup -}) {sup 67}Co ground state and a deformed first excited (1/2{sup -}) state at 492 keV, interpreted as a proton 1p-2h prolate intruder state.

  9. Rotational isomerism and physical properties of long-chain molecules in solid states

    NASA Astrophysics Data System (ADS)

    Kobayashi, M.

    1985-01-01

    Rotational isomerism occurring in solid state of organic long-chain compounds, including synthetic linear polymers, have been concerned in connection with the macroscopic physical properties of bulk materials. The conformational order in the non-crystalline part of polyethylene has been investigated by Raman spectra, and related to the elastic behaviors of bulk samples. In the solid-state phase transition induced by mechanical forces of poly(butylene terephthalate) the macroscopic strain has been related directly to the conformational conversion of the molecules. Concerning the piezoelectric and pyroelectric activities of poly(vinylidene fluoride), polymorphism, phase transition, and structural change on the poling process have been investigated. A ferroelectric-paraelectric phase transition has been found for a series of copolymers of vinylidene fluoride and trifluoroethylene. On the phase transition a great change in molecular conformation is accompanied with the scrambling of the dipolar orientation. This is the characteristic of polymer ferroelectrics in which the dipolar units are linked with each other by covalent bonds in a molecular chain. Spectroscopic evidences are presented indicating that the thermodynamic stability of polymorphs of n-fatty acids is closely related to the rotational isomerism occurring in the carboxyl groups.

  10. Theoretical studies of 2-quinolinol: Geometries, vibrational frequencies, isomerization, tautomerism, and excited states

    NASA Astrophysics Data System (ADS)

    Pan, Yi; Lau, Kai-Chung; Al-Mogren, Muneerah Mogren; Mahjoub, Ahmed; Hochlaf, Majdi

    2014-10-01

    We treat theoretically 2-quinolinol(lactam), an analog of carbostyril and DNA bases. We characterized the ground state structure of 2-quinolinol and its isomer(lactim) using density functional theory(DFT). The reaction profile and energetics for lactam-lactim tautomerization and cis-lactim to trans-lactim isomerization predicted with explicitly correlated methods. We explored the pattern of the lowest singlet and triplet manifolds of states and electronic S1 ← S0 transitions using multiconfigurational methodologies. The theoretical results are compared with available experimental data and used to interpret the on-going photoelectron study of 2-quinolinol. Our analysis should help to understand the effect of tautomerism and aromaticity on the DNA bases.

  11. Population of isomeric states in fusion and transfer reactions in beams of loosely bound nuclei near the Coulomb barrier

    SciTech Connect

    Skobelev, N. K.

    2015-07-15

    The influence of the mechanisms of nuclear reactions on the population of {sup 195m}Hg and {sup 197m}Hg(7/2{sup −}), {sup 198m}Tl and {sup 196m}Tl(7{sup +}), and {sup 196m}Au and {sub 198m}Au(12{sup −}) isomeric nuclear states obtained in reactions induced by beams of {sup 3}He, {sup 6}Li, and {sup 6}He weakly bound nuclei is studied. The behavior of excitation functions and high values of isomeric ratios (δ{sub m}/δ{sub g}) for products of nuclear reactions proceeding through a compound nucleus and involving neutron evaporation are explained within statistical models. Reactions in which the emission of charged particles occurs have various isomeric ratios depending on the reaction type. The isomeric ratio is lower in direct transfer reactions involving charged-particle emission than in reactions where the evaporation of charged particles occurs. Reactions accompanied by neutron transfer usually have a lower isomeric ratio, which behaves differently for different direct-reaction types (stripping versus pickup reactions)

  12. Experimental confirmation of ground state isotopic isomerization from OC⋯HI to OC⋯ID

    NASA Astrophysics Data System (ADS)

    Scott, Kevin W.; McElmurry, Blake A.; Leonov, Igor I.; Lucchese, Robert R.; Bevan, John W.

    2015-01-01

    The ν1 spectra of 16O12C-DI and 16O12C-ID, as well as ν2 of 16O12C-DI, 16O12C-ID have been recorded using a quantum cascade laser pulsed slit supersonic jet spectrometer. Intensity measurements made simultaneously in the same expansion for transitions in ν216O12C-HI: 16O12C-IH and ν116O12C-DI: 16O12C-ID isomers permit determination of the isomerization for the former pair to be +2.8(1.0) and the latter -6.0(1.0) cm-1. These results confirm prediction of ground state deuterium isotopic isomerization made using a generated morphed potential. Further analyses indicate OC.HI is a prototype for complexities associated with isomerization and isotopic effects in excited stretching vibrations.

  13. Isospin Symmetry at High Spin Studied via Nucleon Knockout from Isomeric States

    NASA Astrophysics Data System (ADS)

    Milne, S. A.; Bentley, M. A.; Simpson, E. C.; Baugher, T.; Bazin, D.; Berryman, J. S.; Bruce, A. M.; Davies, P. J.; Diget, C. Aa.; Gade, A.; Henry, T. W.; Iwasaki, H.; Lemasson, A.; Lenzi, S. M.; McDaniel, S.; Napoli, D. R.; Nichols, A. J.; Ratkiewicz, A.; Scruton, L.; Stroberg, S. R.; Tostevin, J. A.; Weisshaar, D.; Wimmer, K.; Winkler, R.

    2016-08-01

    One-neutron knockout reactions have been performed on a beam of radioactive 53Co in a high-spin isomeric state. The analysis is shown to yield a highly selective population of high-spin states in an exotic nucleus with a significant cross section, and hence represents a technique that is applicable to the planned new generation of fragmentation-based radioactive beam facilities. Additionally, the relative cross sections among the excited states can be predicted to a high level of accuracy when reliable shell-model input is available. The work has resulted in a new level scheme, up to the 1 1+ band-termination state, of the proton-rich nucleus 52Co (Z =27 , N =25 ). This has in turn enabled a study of mirror energy differences in the A =52 odd-odd mirror nuclei, interpreted in terms of isospin-nonconserving (INC) forces in nuclei. The analysis demonstrates the importance of using a full set of J -dependent INC terms to explain the experimental observations.

  14. Isospin Symmetry at High Spin Studied via Nucleon Knockout from Isomeric States.

    PubMed

    Milne, S A; Bentley, M A; Simpson, E C; Baugher, T; Bazin, D; Berryman, J S; Bruce, A M; Davies, P J; Diget, C Aa; Gade, A; Henry, T W; Iwasaki, H; Lemasson, A; Lenzi, S M; McDaniel, S; Napoli, D R; Nichols, A J; Ratkiewicz, A; Scruton, L; Stroberg, S R; Tostevin, J A; Weisshaar, D; Wimmer, K; Winkler, R

    2016-08-19

    One-neutron knockout reactions have been performed on a beam of radioactive ^{53}Co in a high-spin isomeric state. The analysis is shown to yield a highly selective population of high-spin states in an exotic nucleus with a significant cross section, and hence represents a technique that is applicable to the planned new generation of fragmentation-based radioactive beam facilities. Additionally, the relative cross sections among the excited states can be predicted to a high level of accuracy when reliable shell-model input is available. The work has resulted in a new level scheme, up to the 11^{+} band-termination state, of the proton-rich nucleus ^{52}Co (Z=27, N=25). This has in turn enabled a study of mirror energy differences in the A=52 odd-odd mirror nuclei, interpreted in terms of isospin-nonconserving (INC) forces in nuclei. The analysis demonstrates the importance of using a full set of J-dependent INC terms to explain the experimental observations. PMID:27588851

  15. Identification of a millisecond isomeric state in 129Cd81via the detection of internal conversion and Compton electrons

    SciTech Connect

    Taprogge, J.; Jungclaus, A.; Grawe, H.; Nishimura, S.; Xu, Z. Y.; Doornenbal, P.; Lorusso, G.; Nacher, E.; Simpson, G. S.; Soderstrom, P. A.; Sumikama, T.; Kondev, F. G.

    2014-11-10

    The decay of an isomeric state in the neutron-rich nucleus 129Cd has been observed via the detection of internal conversion and Compton electrons providing first experimental information on excited states in this nucleus. The isomer was populated in the projectile fission of a 238U beam at the Radioactive Isotope Beam Factory at RIKEN. From the measured yields of γ-rays and internal conversion electrons, a multipolarity of E 3 was tentatively assigned to the isomeric transition. A half-life of T1/2=3.6(2) msT1/2=3.6(2) ms was determined for the new state which was assigned a spin of (21/2+)(21/2+), based on a comparison to shell model calculations performed using state-of-the-art realistic effective interactions.

  16. Rotational isomeric state theory applied to the stiffness prediction of an anion polymer electrolyte membrane

    SciTech Connect

    Gao, Fei; Weiland, L.M.; Kitchin, J.R.

    2008-05-01

    While the acidic polymer electrolyte membrane (PEM) Nafion® has garnered considerable attention, the active response of basic PEMs offers another realm of potential applications. For instance, the basic PEM Selemion® is currently being considered in the development of a CO2 separation prototype device to be employed in coal power plant flue gas. The mechanical integrity of this material and subsequent effects in active response in this harsh environment will become important in prototype development. A multiscale modeling approach based on rotational isomeric state theory in combination with a Monte Carlo methodology may be employed to study mechanical integrity. The approach has the potential to be adapted to address property change of any PEM in the presence of foreign species (reinforcing or poisoning), as well as temperature and hydration variations. The conformational characteristics of the Selemion® polymer chain and the cluster morphology in the polymer matrix are considered in the prediction of the stiffness of Selemion® in specific states.

  17. Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide

    SciTech Connect

    Mantz, Yves A.; Branduardi, Davide; Bussi, Giovanni; Parrinello, Michele

    2009-09-17

    The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verified by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.

  18. Comment on ``Existence of long-lived isomeric states in naturally-occurring neutron-deficient Th isotopes''

    NASA Astrophysics Data System (ADS)

    Barber, R. C.; de Laeter, J. R.

    2009-04-01

    In their article “Existence of Long-Lived Isomeric States in Naturally-Occuring Neutron-Deficient Th Isotopes” [Phys. Rev. C 76, 021303 (2007)], Marinov fail to demonstrate that basic mass spectrometric protocols, such as abundance sensitivity, linearity, and freedom from possible interferences, have been met. In particular, the claim that four isomeric states of Th have been discovered, using an inductively coupled plasma-sector field mass spectrometer (ICP-SFMS), with abundances from (1-10)×10-11 relative to Th232, cannot be accepted, given the known abundance sensitivities of other sector field mass spectrometers. Accelerator mass spectrometry is the only mass spectrometric methodology capable of measuring relative abundances of the magnitude claimed by Marinov

  19. Identification of isomeric states in the N=73 neutron-deficient nuclei 132Pr and 130La

    NASA Astrophysics Data System (ADS)

    Taylor, M. J.; Alharshan, G. A.; Cullen, D. M.; Procter, M. G.; Lumley, N. M.; Grahn, T.; Greenlees, P. T.; Hauschild, K.; Herzan, A.; Jakobsson, U.; Jones, P.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Lopez-Martens, A.; Nieminen, P.; Partanen, J.; Peura, P.; Rahkila, P.; Rinta-Antila, S.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Sorri, J.; Stolze, S.; Uusitalo, J.; Xu, F. R.; Bai, Z. J.

    2012-10-01

    Decays from isomeric states in the neutron-deficient N=73 nuclei 132Pr and 130La have been observed for the first time. Half-lives of 486(70) ns and 2.46(4) μs were measured for two isomeric states in 132Pr. The decay from the 486 ns (8-) isomer has been interpreted as a hindered E1 transition from the bandhead state of the excited πh11/2⊗νg7/2 configuration. The decay from the 2.5 μs (8+) isomer is consistent with the Weisskopf estimate for a low-energy E2 transition. An analogous 0.74(3) μs decay from an (8+) isomer in the neighboring isotone 130La has also been observed which similarly can be explained if the transition has E2 character. The Weisskopf interpretation for the isomer hindrance is strengthened by the lack of evidence for shape or K isomerism due to the γ-soft shapes predicted by configuration-constrained potential-energy-surface calculations.

  20. Production and decay properties of the 1.9-s isomeric state in {sup 261}Rf

    SciTech Connect

    Haba, H.; Kaji, D.; Kikunaga, H.; Kudou, Y.; Morimoto, K.; Morita, K.; Ozeki, K.; Sumita, T.; Yoneda, A.; Kasamatsu, Y.; Komori, Y.; Ooe, K.; Shinohara, A.

    2011-03-15

    The 1.9-s isomeric state ({sup 261}Rf{sup b}) in {sup 261}Rf was directly populated in the {sup 248}Cm({sup 18}O,5n){sup 261}Rf{sup b} reaction. Alpha and spontaneous fission (SF) decays of {sup 261}Rf{sup b}, as well as the 68-s state {sup 261}Rf{sup a}, was investigated with a rotating wheel apparatus under low background conditions attained by a gas-jet transport system coupled to the RIKEN gas-filled recoil ion separator. An identification of {sup 261}Rf{sup b} was based on {alpha}-{alpha} correlations linking {alpha} decays of {sup 261}Rf{sup b} and its daughter {sup 257}No. The {alpha}-particle energy of {sup 261}Rf{sup b} was measured to be 8.52 {+-} 0.05 MeV. The half-life was determined to be 1.9 {+-} 0.4 s based on both 8.52-MeV {alpha} and SF decays. The {alpha} and SF branches are 0.27 {+-} 0.06 and 0.73 {+-} 0.06, respectively. The cross section for the {sup 248}Cm({sup 18}O,5n){sup 261}Rf{sup b} reaction is {sigma}({sup 261}Rf{sup b}) = 11 {+-} 2 nb at 95.1 MeV, which gives a cross-section ratio of {sigma}({sup 261}Rf{sup a})/{sigma}({sup 261}Rf{sup b}) = 1.1 {+-} 0.2.

  1. Spectroscopy of 201At including the observation of a shears band and the 29 /2+ isomeric state

    NASA Astrophysics Data System (ADS)

    Auranen, K.; Uusitalo, J.; Juutinen, S.; Jakobsson, U.; Grahn, T.; Greenlees, P. T.; Hauschild, K.; HerzáÅ, A.; Julin, R.; Konki, J.; Leino, M.; Pakarinen, J.; Partanen, J.; Peura, P.; Rahkila, P.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Sorri, J.; Stolze, S.

    2015-02-01

    The excited states of 201At were studied and an isomeric 29 /2+ state [T½=3.39 (9 ) μ s ] was identified by using a fusion-evaporation reaction, a gas-filled recoil separator, and recoil gating techniques. The 29 /2+ state is suggested to originate from the π (h9 /2) ⊗| 200Po ;11-> configuration, and it decays through the 269- and 339-keV E 2 - and E 3 -type transitions, respectively. Moreover, a cascade of magnetic dipole transitions that is suggested to originate from a shears band was observed by using recoil-gated γ -γ (-γ ) coincidence techniques.

  2. The role of dissociation channels of excited electronic states in quantum optimal control of ozone isomerization: A three-state dynamical model

    NASA Astrophysics Data System (ADS)

    Kurosaki, Yuzuru; Ho, Tak-San; Rabitz, Herschel

    2016-05-01

    The prospect of performing the open → cyclic ozone isomerization has attracted much research attention. Here we explore this consideration theoretically by performing quantum optimal control calculations to demonstrate the important role that excited-state dissociation channels could play in the isomerization transformation. In the calculations we use a three-state, one-dimensional dynamical model constructed from the lowest five 1A‧ potential energy curves obtained with high-level ab initio calculations. Besides the laser field-dipole couplings between all three states, this model also includes the diabatic coupling between the two excited states at an avoided crossing leading to competing dissociation channels that can further hinder the isomerization process. The present three-state optimal control simulations examine two possible control pathways previously considered in a two-state model, and reveal that only one of the pathways is viable, achieving a robust ∼95% yield to the cyclic target in the three-state model. This work represents a step towards an ultimate model for the open → cyclic ozone transformation capable of giving adequate guidance about the necessary experimental control field resources as well as an estimate of the ro-vibronic spectral character of cyclic ozone as a basis for an appropriate probe of its formation.

  3. Nuclear g-factor measurements of the (9/2){sup -} and (21/2){sup -} isomeric states in {sup 173}Ta

    SciTech Connect

    Thakur, P.; Kumar, V.; Bhati, A. K.; Bedi, S. C.; Singh, R. P.; Bhowmik, R. K.; Stuchbery, A. E.

    2006-09-15

    The nuclear g-factors of the one-quasiparticle isomeric state (9/2){sup -} at 165.8 keV and the three-quasiparticle isomeric state (21/2){sup -} at 1713.2 keV in {sup 173}Ta nuclei have been measured using the time differential perturbed angular distribution technique. The nuclear reaction {sup 165}Ho({sup 12}C, 4n{gamma}){sup 173}Ta was used to populate these isomeric states, and the recoiling {sup 173}Ta nuclei were implanted into a thick tantalum backing in the presence of a 7.04(4) kG external magnetic field. The measured value g((9/2){sup -}) = +0.591(18) shows that the (9/2){sup -} isomeric state is not a pure single-particle state but may have a collective contribution due to the octupole excitation of the core. Based on the measured value g((21/2){sup -}) = + 0.620(15) and multi-quasiparticle calculations, the (21/2){sup -} isomeric state is assigned a mixed configuration: {pi}{sup 3}((9/2){sup -}[514], (7/2){sup +}[404] (5/2){sup +}[402]) (39%) and {pi}{sup 1}((7/2){sup +}[404])(multiply-in-circle sign) {nu}{sup 2}((7/2){sup -}[514], (7/2){sup +}[633]) (61%)

  4. A VUV detection system for the direct photonic identification of the first excited isomeric state of 229Th

    NASA Astrophysics Data System (ADS)

    Seiferle, Benedict; von der Wense, Lars; Laatiaoui, Mustapha; Thirolf, Peter G.

    2016-03-01

    With an expected energy of 7.6(5) eV, 229Th possesses the lowest excited nuclear state in the landscape of all presently known nuclei. The energy corresponds to a wavelength of about 160 nm and would conceptually allow for an optical laser excitation of a nuclear transition. We report on a VUV optical detection system that was designed for the direct detection of the isomeric ground-state transition of 229Th. 229(m)Th ions originating from a 233U α-recoil source are collected on a micro electrode that is placed in the focus of an annular parabolic mirror. The latter is used to parallelize the UV fluorescence that may emerge from the isomeric ground-state transition of 229Th. The parallelized light is then focused by a second annular parabolic mirror onto a CsI-coated position-sensitive MCP detector behind the mirror exit. To achieve a high signal-to-background ratio, a small spot size on the MCP detector needs to be achieved. Besides extensive ray-tracing simulations of the optical setup, we present a procedure for its alignment, as well as test measurements using a D2 lamp, where a focal-spot size of ≈100 μm has been achieved. Assuming a purely photonic decay, a signal-to-background ratio of ≈7000:1 could be achieved.

  5. Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

    NASA Astrophysics Data System (ADS)

    Kurosaki, Yuzuru; Ho, Tak-San; Rabitz, Herschel

    2014-02-01

    We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O2 + O asymptote on the ground-state 1A' potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excited electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.

  6. Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

    SciTech Connect

    Kurosaki, Yuzuru; Ho, Tak-San Rabitz, Herschel

    2014-02-28

    We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excited electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.

  7. Isomeric character of the 41+ state in 44S: Mechanisms of breaking of the N = 28 shell

    NASA Astrophysics Data System (ADS)

    Parker, J., IV; Wiedenhover, I.; Baker, J.; Cottle, P.; McPherson, D.; Riley, M.; Santiago-Gonzalez, D.; Volya, A.; Bader, V.; Baugher, T.; Bazin, D.; Gade, A.; Ginter, T.; Iwasaki, H.; Loelius, C.; Morse, C.; Recchia, F.; Smalley, D.; Stroberg, R.; Weisshaar, D.; Whitmore, K.; Lemasson, A.; Crawford, H.; Macchiavelli, A.; Wimmer, K.

    2015-10-01

    The N = 28 nucleus 44S exhibits a rich structure of excitations which illustrates different mechanisms of breaking the N = 28 shell. A Coulomb excitation measurement and an implantation-decay experiment established the coexistence of 2p2h-deformed and 0p0h-spherical configurations. A two-proton knockout reaction indicated a 4+ state which shell model calculations suggest is likely isomeric, prolate-deformed and formed from a 1p1h configuration. A recent two-proton knockout experiment measured the lifetime of this 4+ state using the recoil distance method and the GRETINA array. Results for the lifetime of the 4+ state will be presented and its implication for the mechanisms of breaking the N = 28 shell will be discussed. Supported by the National Science Foundation.

  8. Isomeric states in neutron-rich 129In and the πg-19/2 vh-111/2 multiplet

    NASA Astrophysics Data System (ADS)

    Taprogge, J.; Jungclaus, A.; Simpson, G.

    2014-09-01

    Within the RISING stopped beam campaign the neutron-rich indium isotopes with masses A=125-130 have been studied using the method of isomer spectroscopy. The decays of several isomeric states have been observed and here we compare our results for 129In to previous measurements for this nucleus. The isomeric states were populated in the fragmentation of a 136Xe beam at 750 MeV/u and in the relativistic fission of a 238U beam at 650 MeV/u at the accelerator facility GSI (Darmstadt, Germany).

  9. Reduced dimension rovibrational variational calculations of the S(1) state of C2H2. II. The S(1) rovibrational manifold and the effects of isomerization.

    PubMed

    Changala, P Bryan; Baraban, Joshua H; Stanton, John F; Merer, Anthony J; Field, Robert W

    2014-01-14

    Reduced dimension variational calculations have been performed for the rovibrational level structure of the S1 state of acetylene. The state exhibits an unusually complicated level structure, for various reasons. First, the potential energy surface has two accessible conformers, trans and cis. The cis conformer lies about 2700 cm(-1) above the trans, and the barrier to cis-trans isomerization lies about 5000 cm(-1) above the trans minimum. The trans vibrations ν4 (torsion) and ν6 (asym. bend) interact very strongly by Darling-Dennison and Coriolis resonances, such that their combination levels and overtones form polyads with unexpected structures. Both conformers exhibit very large x36 cross-anharmonicity since the pathway to isomerization is a combination of ν6 and ν3 (sym. bend). Near the isomerization barrier, the vibrational levels show an even-odd K-staggering of their rotational levels as a result of quantum mechanical tunneling through the barrier. The present calculations address all of these complications, and reproduce the observed K-structures of the bending and C-C stretching levels with good qualitative accuracy. It is expected that they will assist with the assignment of the irregular patterns near the isomerization barrier. PMID:24437883

  10. Excited-state structure and isomerization dynamics of the retinal chromophore in rhodopsin from resonance Raman intensities.

    PubMed Central

    Loppnow, G R; Mathies, R A

    1988-01-01

    Resonance Raman excitation profiles have been measured for the bovine visual pigment rhodopsin using excitation wavelengths ranging from 457.9 to 647.1 nm. A complete Franck-Condon analysis of the absorption spectrum and resonance Raman excitation profiles has been performed using an excited-state, time-dependent wavepacket propagation technique. This has enabled us to determine the change in geometry upon electronic excitation of rhodopsin's 11-cis-retinal protonated Schiff base chromophore along 25 normal coordinates. Intense low-frequency Raman lines are observed at 98, 135, 249, 336, and 461 cm-1 whose intensities provide quantitative, mode-specific information about the excited-state torsional deformations that lead to isomerization. The dominant contribution to the width of the absorption band in rhodopsin results from Franck-Condon progressions in the 1,549 cm-1 ethylenic normal mode. The lack of vibronic structure in the absorption spectrum is shown to be caused by extensive progressions in low-frequency torsional modes and a large homogeneous linewidth (170 cm-1 half-width) together with thermal population of low-frequency modes and inhomogeneous site distribution effects. The resonance Raman cross-sections of rhodopsin are unusually weak because the excited-state wavepacket moves rapidly (approximately 35 fs) and permanently away from the Franck-Condon geometry along skeletal stretching and torsional coordinates. PMID:3416032

  11. Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States.

    PubMed

    Chan, Siu Kit; Kawaguchi, Haruki; Kubo, Hiroki; Murakami, Midori; Ihara, Kunio; Maki, Kosuke; Kouyama, Tsutomu

    2016-07-26

    Like other microbial rhodopsins, the light driven chloride pump halorhodopsin from Natronomonas pharaonis (pHR) contains a mixture of all-trans/15-anti and 13-cis/15-syn isomers in the dark adapted state. A recent crystallographic study of the reaction states of pHR has shown that reaction states with 13-cis/15-syn retinal occur in the anion pumping cycle that is initiated by excitation of the all-trans isomer. In this study, we investigated interconversions among different isomeric states of pHR in the absence of chloride ions. The illumination of chloride free pHR with red light caused a large blue shift in the absorption maximum of the retinal visible band. During this "red adaptation", the content of the 11-cis isomer increased significantly, while the molar ratio of the 13-cis isomer to the all-trans isomer remained unchanged. The results suggest that the thermally activated interconversion between the 13-cis and the all-trans isomers is very rapid. Diffraction data from red adapted crystals showed that accommodation of the retinal chromophore with the 11-cis/15-syn configuration was achieved without a large change in the retinal binding pocket. The measurement of absorption kinetics under illumination showed that the 11-cis isomer, with a λmax at 565 nm, was generated upon excitation of a red-shifted species (λmax = 625 nm) that was present as a minor component in the dark adapted state. It is possible that this red-shifted species mimics an O-like reaction state with 13-cis/15-syn retinal, which was hypothesized to occur at a late stage of the anion pumping cycle. PMID:27352034

  12. Application of a sealed tube neutron generator to the characterization of very short half-life isomeric states

    NASA Astrophysics Data System (ADS)

    Antonot, B.; Cluzeau, S.; Le Tourneur, P.; Bergamo, F.

    1995-05-01

    A SODERN sealed tube neutron generator producing 14 MeV neutrons has been used for detecting radionuclides with a half-life from about 20 μs to 1 s. An interesting feature of this kind of sealed tube neutron generator is the pulsed operation at adjustable pulse width from 5 μs to 10 ms or more, and at frequencies from continuous mode to 10 kHz. This capability allows the study of very short-lived isotopes down to a few microseconds with the cyclic activation method. A semiconductor γ ray detector Ge(HP) and ORTEC electronics were used for spectrometric measurements. The half-life measurement of short-lived activation products is performed with a fast multiscaler. Seven isomeric states have been successfully studied, characterized and their activation cross sections evaluated by the cyclic activation method: 114In ∗, 181Ta ∗, 181W ∗, 205Pb ∗, 206Pb ∗, 207Pb ∗, and 208Bi ∗.

  13. g-Factors of Isomeric States in the Neutron-Rich Nuclei

    SciTech Connect

    Georgiev, G.; Neyens, G.; Hass, M.; Balabanski, Dimiter Loukanov; Bingham, Carrol R; Borcea, C.; Coulier, N.; Coussenment, R.; Daugas, J. M.; De France, Gilles M; Gorska, M.; Grawe, Hubert H; Grzywacz, Robert Kazimierz; Lewitowicz, Marek; Mach, Henryk A; Matea, I.; de Oliveira Santos, F.; Page, R. D.; Pfutzner, Marek; Penionzhkevich, Yu. E.; Podolyak, Zsolt F; Regan, Patrick H; Rykaczewski, Krzysztof Piotr; Sawicka, M.; Smirnova, N. A.; Sobolev, Yu.; Stanoiu, M.; Teughels, S.; Vyvey, K.

    2004-02-01

    We report the results from the first experiment to measure gyromagnetic factors of {micro}s isomers in neutron-rich nuclei produced by intermediate-energy projectile-fragmentation reactions. The Time Dependent Perturbed Angular Distribution (TDPAD) method was applied in combination with the heavy-ion-gamma correlation technique. The nuclides in the vicinity of {sup 68}Ni were produced and spin-oriented following the fragmentation of a {sup 76}Ge, 61.4 MeV/ u beam at GANIL. The results obtained, |g|({sup 69 m}Cu) = 0.225(25) and |g|({sup 67 m}Ni) = 0.125(6) provide another indication of the importance of proton excitation across the Z = 28 shell gap for the description of these states.

  14. Manifestations of bodily isomerism.

    PubMed

    Loomba, Rohit S; Ahmed, Muhammad M; Spicer, Diane E; Backer, Carl L; Anderson, Robert H

    2016-01-01

    We report the findings present in 49 postmortem specimens from patients with so-called heterotaxy, concentrating on those found in the extracardiac systems of organs. Also known as bodily isomerism, we suggest that it is important to segregate the syndromes into their isomeric subtypes to be able to make inferences regarding likely extracardiac and intracardiac findings to allow for proper surveillance. We demonstrate that this is best done on the basis of the atrial appendages, which were isomeric in all the hearts obtained from the specimens available for our inspection. The abdominal organs do not demonstrate isomerism, and they show variable features when compared to the isomeric atrial appendages. PMID:26872066

  15. Magnetic moments of the isomeric states of /sup 141/Pr and /sup 143/Pm and the paramagnetism of promethium and praseodymium

    SciTech Connect

    Gorbachev, B.I.; Levon, A.I.; Nemets, O.F.; Fedotkin, S.N.; Stepanenko, V.A.

    1984-07-01

    The g-factors of the 11/2/sup -/ and 15/2/sup +/ isomeric states of the /sup 141/Pr and /sup 143/Pm nuclei (Tables I and II) have been measured by the method of differential and integrated perturbed angular distribution. The parametric corrections were determined for /sup 143/Pm from the measured temperature dependence g..beta..(T). The relaxation times have been measured for nuclear states aligned in beam reactions, metal targets, and targets made of La and Pr oxides. The results are analyzed in terms of the quasiparticle-phonon model with allowance for the spin-multipole interaction.

  16. Characterization of the Oxidation State of 229 Th Recoils Implanted in MgF2 for the Search of the Low-lying 229 Th Isomeric State

    NASA Astrophysics Data System (ADS)

    Barker, Beau; Meyer, Edmund; Schacht, Mike; Collins, Lee; Wilkerson, Marianne; Zhao, Xinxin

    2016-05-01

    The low-lying (7.8 eV) isomeric state in 229 Th has the potential to become a nuclear frequency standard. 229 Th recoils from 233 U decays have been collected in MgF2 for use in the direct search of the transition. Of interest is the oxidation state of the implanted 229 Th atoms as this can have an influence on the decay mechanisms and photon emission rate. Too determine the oxidation state of the implanted 229 Th recoils we have employed laser induced florescence (LIF), and plan-wave pseudopotential DFT calculations to search for emission from thorium ions in oxidation states less than + 4. Our search focused on detecting emission from Th3+ ions. The DFT calculations predicted the Th3+ state to be the most likely to be present in the crystal after Th4+. We also calculated the band structure for the Th3+ doped MgF2 crystal. For LIF spectra a number of excitation wavelengths were employed, emission spectra in the visible to near-IR were recorded along with time-resolved emission spectra. We have found no evidence for Th3+ in the MgF2 plates. We also analyzed the detection limit of our apprentice and found that the minimum number of Th3+ atoms that we could detect is quite small compared to the number of implanted 229 Th recoils. The number of implanted 229 Th recoils was derived from a γ-ray spectrum by monitoring emission from the daughters of 228 Th. These were present in the MgF2 plates due to a 232 U impurity, which decays to 228 Th, in the source. LA-UR-16-20442.

  17. Isomerization of sugars

    SciTech Connect

    Moliner-Marin, Manuel; Roman-Leshkov, Yuriy; Davis, Mark E; Nikolla, Eranda

    2014-05-20

    Disclosed are processes for isomerizing saccharides. Also disclosed are processes for converting saccharides to furan derivatives. Also disclosed are processes for converting starch to furan derivatives.

  18. Proposal for precision determination of 7.8 eV isomeric state in 229Th at heavy ion storage ring

    NASA Astrophysics Data System (ADS)

    Ma, X.; Wen, W. Q.; Huang, Z. K.; Wang, H. B.; Yuan, Y. J.; Wang, M.; Sun, Z. Y.; Mao, L. J.; Yang, J. C.; Xu, H. S.; Xiao, G. Q.; Zhan, W. L.

    2015-11-01

    The ultraviolet optical transition of the isomeric state in 229Th has attracted much attention recently due to its potential application to building an atomic/nuclear clock with ultra-high precision. However, the lowest nuclear excitation energy and the lifetime of the first excited state of 229Th were not measured directly and precisely until now, and how to precisely determine this isomer state of the 229Th is an urgent requirement. Here an experimental approach of using a technique similar to that of dielectronic recombination to measure the transition energy of the isomer state of 229Th at heavy ion storage rings is described. It is expected that the resonant transition can be found and determined with a precision better than several milli-eV.

  19. Least Squares Fitting of Perturbed Vibrational Polyads Near the Isomerization Barrier in the S_1 State of C_2H_2

    NASA Astrophysics Data System (ADS)

    Merer, A. J.; Baraban, J. H.; Changala, P. B.; Field, R. W.

    2013-06-01

    The S_1 electronic state of acetylene has recently been shown to have two potential minima, corresponding to cis- and trans-bent structures. The trans-bent isomer is the more stable, with the cis-bent isomer lying about 2670 cm^{-1} higher; the barrier to isomerization lies roughly 5000 cm^{-1} above the trans zero-point level. The ``isomerization coordinate'' (along which the molecule moves to get from the trans minimum to the barrier) is a combination of the ν_3 (trans bending) and ν_6 (cis bending) vibrational normal coordinates, but the spectrum is very confused because the ν_6 vibration interacts strongly with the ν_4 (torsion) vibration through Coriolis and Darling-Dennison resonances. Since the ν_4 and ν_6 fundamental frequencies are almost equal, the bending vibrational structure consists of polyads. At low vibrational energies the polyads where these three vibrations are excited can be fitted by least squares almost to experimental accuracy with a simple model of Coriolis and Darling-Dennison interactions, but at higher energies the huge x_{36} cross-anharmonicity, which is a symptom that the levels are approaching the isomerization barrier, progressively destroys the polyad structure; in addition the levels show an increasing even-odd staggering of their K-rotational structures, as predicted by group theory. It is not possible to fit the levels near the barrier with a simple model, though some success has been achieved with extended models. Progress with the fitting of the polyads near the barrier will be reviewed. A. L. Utz, J. D. Tobiason, E. Carrasquillo M., L. J. Sanders and F. F. Crim, J. Chem. Phys. {98}, 2742, 1993.

  20. Conceptual Difficulties with Isomerism.

    ERIC Educational Resources Information Center

    Schmidt, Hans-Jurgen

    1992-01-01

    Reports descriptive study concerning student understanding of isomers. Sample of 7,441 senior high school students completed tests which contained 12 questions on isomerism. Results indicate students are inclined to restrict their concept of isomerism to compounds belonging to the same class. There was no evidence students expected molecular…

  1. Variations of structures and solid-state conductivity of isomeric silver(I) coordination polymers having linear and V-shaped thiophene-centered ditriazole ligands

    SciTech Connect

    Hu, Bin; Geng, Jiao; Zhang, Lie; Huang, Wei

    2014-07-01

    A pair of new linear and V-shaped acceptor–donor–acceptor (A−D−A) thiophene-centered ditriazole structural isomers, i.e., 2,5-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 1}) and 3,4-di(1H-1,2,4-triazol-1-yl)thiophene (L{sup 2}), has been synthesized and characterized. They are used as μ{sub 2}-bridging ligands to prepare a pair of silver(I) coordination polymers formulated as [Ag(L{sup 1})(NO{sub 3})]{sub n} (1) and [Ag(L{sup 2})(NO{sub 3})]{sub n} (2), which are also structural isomers at the supramolecular level. X-ray single-crystal diffraction analyses for 1 and 2 reveal that they exhibit the same one-dimensional (1D) coordination polymers but different structural architectures because of the distinguishable shape and configuration of isomeric ligands (L{sup 1} and L{sup 2}) and the alterations of the coordination numbers. More interestingly, compared with the free ligands, 1D silver(I) polymeric isomers 1 and 2 show significant enhancement of solid-state conductivity to different extents (1.42×10{sup 4} and 2.17×10{sup 3} times), where 6.96 times' enhancement of solid-state conductivity from 1 to 2 has been observed. The formation of Ag–N coordinative bonds and the configurational discrepancy of L{sup 1} and L{sup 2} are believed to play important roles in facilitating the electron transport between molecules, which can also be supported by Density Function Theory calculations of their band gaps. - Graphical abstract: A pair of linear and V-shaped isomeric thiophene-centered ditriazole ligands (L{sup 1}) and L{sup 2} are used to prepare a pair of silver(I) polymeric isomers (1 and 2), where significant enhancement of solid-state conductivity to different extents are observed originating from the distinguishable shape and configuration of isomeric ligands. - Highlights: • A pair of linear and V-shaped thiophene-centered ditriazole structural isomers is prepared. • They are used as µ{sub 2}-bridging ligands to prepare a pair of silver

  2. Structural dynamics of nitrosylruthenium isomeric complexes studied with steady-state and transient pump-probe infrared spectroscopies.

    PubMed

    Zhao, Yan; Yang, Fan; Wang, Jianru; Yu, Pengyun; Pan, Huifen; Wang, Hongfei; Wang, Jianping

    2016-09-01

    The characteristic nitrosyl stretching (NO) in the region of 1800-1900cm(-1) was used to study the geometric and ligand effect on two nitrosylruthenium complexes, namely [Ru(OAc)(2QN)2NO] (QN=2-chloro-8-quinolinol (H2cqn) or QN=2-methyl-8-quinolinol (H2mqn)). The NO stretching frequency (νNO) was found in the following order: νcis-1 (2cqn)>νcis-2 (2cqn)>νcis-1 (2mqn)>νtrans (2mqn). The results exhibited a spectral sensitivity of the NO mode to both charge distribution and ligand arrangement, which was supported by ab initio computations and natural bond orbital (NBO) analyses. Further, the vibrational population of the vibrationally excited NO stretching mode was found to relax on the order of 7-10ps, showing less than 30% variation from one isomer to another, which were explained on the basis of NO local structures and solute-solvent interactions in these isomeric nitrosylruthenium complexes. PMID:27209490

  3. Structural dynamics of nitrosylruthenium isomeric complexes studied with steady-state and transient pump-probe infrared spectroscopies

    NASA Astrophysics Data System (ADS)

    Zhao, Yan; Yang, Fan; Wang, Jianru; Yu, Pengyun; Pan, Huifen; Wang, Hongfei; Wang, Jianping

    2016-09-01

    The characteristic nitrosyl stretching (NO) in the region of 1800-1900 cm- 1 was used to study the geometric and ligand effect on two nitrosylruthenium complexes, namely [Ru(OAc)(2QN)2NO] (QN = 2-chloro-8-quinolinol (H2cqn) or QN = 2-methyl-8-quinolinol (H2mqn)). The NO stretching frequency (νNO) was found in the following order: νcis-1 (2cqn) > νcis-2 (2cqn) > νcis-1 (2mqn) > νtrans (2mqn). The results exhibited a spectral sensitivity of the NO mode to both charge distribution and ligand arrangement, which was supported by ab initio computations and natural bond orbital (NBO) analyses. Further, the vibrational population of the vibrationally excited NO stretching mode was found to relax on the order of 7-10 ps, showing less than 30% variation from one isomer to another, which were explained on the basis of NO local structures and solute-solvent interactions in these isomeric nitrosylruthenium complexes.

  4. Isomeric ratio measurements with the ILL LOHENGRIN spectrometer

    NASA Astrophysics Data System (ADS)

    Chebboubi, A.; Kessedjian, G.; Litaize, O.; Serot, O.; Faust, H.; Bernard, D.; Blanc, A.; Köster, U.; Méplan, O.; Mutti, P.; Sage, C.

    2016-03-01

    The modelling of γ heating and neutron damage inside a nuclear reactor is essential to design the next generation of nuclear reactors. The determination of the fission fragment momentum is a key element to perform accurate calculations of the γ heating. One way to assess this information is to look at the isomeric ratio of different nuclei. According to the lifetime of the isomeric state, different experimental techniques were developed at the LOHENGRIN spectrometer. A focus on the measurement of isomeric ratios of 136I in neutron induced fission of 241Pu is presented. A discussion with the current assumptions used in the evaluation process for isomeric ratio is also shown.

  5. Reduced dimension rovibrational variational calculations of the S{sub 1} state of C{sub 2}H{sub 2}. II. The S{sub 1} rovibrational manifold and the effects of isomerization

    SciTech Connect

    Changala, P. Bryan Baraban, Joshua H.; Field, Robert W.; Stanton, John F.; Merer, Anthony J.

    2014-01-14

    Reduced dimension variational calculations have been performed for the rovibrational level structure of the S{sub 1} state of acetylene. The state exhibits an unusually complicated level structure, for various reasons. First, the potential energy surface has two accessible conformers, trans and cis. The cis conformer lies about 2700 cm{sup −1} above the trans, and the barrier to cis-trans isomerization lies about 5000 cm{sup −1} above the trans minimum. The trans vibrations ν{sub 4} (torsion) and ν{sub 6} (asym. bend) interact very strongly by Darling-Dennison and Coriolis resonances, such that their combination levels and overtones form polyads with unexpected structures. Both conformers exhibit very large x{sub 36} cross-anharmonicity since the pathway to isomerization is a combination of ν{sub 6} and ν{sub 3} (sym. bend). Near the isomerization barrier, the vibrational levels show an even-odd K-staggering of their rotational levels as a result of quantum mechanical tunneling through the barrier. The present calculations address all of these complications, and reproduce the observed K-structures of the bending and C–C stretching levels with good qualitative accuracy. It is expected that they will assist with the assignment of the irregular patterns near the isomerization barrier.

  6. Direct observation of an isomeric state in 98Rb and nuclear properties of exotic rubidium isotopes measured by laser spectroscopy

    NASA Astrophysics Data System (ADS)

    Procter, T. J.; Behr, J. A.; Billowes, J.; Buchinger, F.; Cheal, B.; Crawford, J. E.; Dilling, J.; Garnsworthy, A. B.; Leary, A.; Levy, C. D. P.; Mané, E.; Pearson, M. R.; Shelbaya, O.; Stolz, M.; Al Tamimi, W.; Voss, A.

    2015-02-01

    Fast-beam collinear laser spectroscopy experiments on rubidium have been performed at the ISAC radioactive ion beam facility at TRIUMF. Most recently, the neutron-rich 98Rb isotope has been studied for the investigation of shape coexistence. Two long-lived nuclear states in 98Rb have been clearly observed for the first time: a low-spin state, assigned a spin of I = 0, and a high-spin state. The high-spin state is tentatively assigned a spin of I = 3 based on this analysis in combination with gamma decay results. The measured nuclear properties of the two states are presented, alongside unpublished values of the neutron-deficient isotopes investigated previously. The mean-square charge radii of both states in 98Rb are observed to continue along the isodeformation line present after the N = 60 onset of deformation.

  7. Clinical implications of atrial isomerism.

    PubMed Central

    Chiu, I S; How, S W; Wang, J K; Wu, M H; Chu, S H; Lue, H C; Hung, C R

    1988-01-01

    Right atrial isomerism or left atrial isomerism is frequently diagnosed as situs ambiguous without further discrimination of the specific morbid anatomy. Thirty six cases of right atrial isomerism and seven cases of left atrial isomerism were collected from the records and pathological museum at the National Taiwan University Hospital. There was a necropsy report for 18 cases. In all patients one or more of the following conditions was met: (a) isomeric bronchial anatomy, (b) echocardiographic and angiocardiographic evidence of isomerism, and (c) surgical or necropsy evidence of abnormal atrial anatomy. An anomalous pulmonary venous connection was present in 55% of patients with right atrial isomerism; in left atrial isomerism one case (14%) had a partial anomalous pulmonary venous connection. Forty per cent of cases of anomalous pulmonary venous connection with right atrial isomerism had obstruction. Six (86%) of seven cases with left atrial isomerism had an ambiguous biventricular atrioventricular connection. In contrast, univentricular atrioventricular connection (26 of 36, 72%) was significantly more common in right atrial isomerism. A common atrioventricular valve was the most frequent mode of connection in both forms. Two discrete atrioventricular valves were significantly more common in left atrial isomerism. Atrioventricular valve regurgitation was detected in 14 cases. Double outlet right ventricle was the most common type of ventriculoarterial connection. The most commonly cited causes of death after either palliative or definitive operation were undetected anomalous pulmonary venous connection, pulmonary venous stricture, and uncorrected atrioventricular valve or aortic regurgitation complicated by abnormal coagulation. Although the prognosis is poor, successful operation depends on knowledge of the precise anatomical arrangement associated with atrial isomerism. Images Fig 1 Fig 2 Fig 3 PMID:3408620

  8. Conformational isomerism in the solid-state structures of tetracaine and tamoxifen with para-sulphonato-calix[4]arene

    NASA Astrophysics Data System (ADS)

    Danylyuk, Oksana; Monachino, Melany; Lazar, Adina N.; Suwinska, Kinga; Coleman, Anthony W.

    2010-02-01

    The solid-state complexes between para-sulphonato-calix[4]arene and the drugs tamoxifen and tetracaine show an unusual 4:1 guest-host stoichiometry with formation of hydrophobic layer of drug molecules held between bilayers of para-sulphonato-calix[4]arene. In both structures each of the four independent drug molecules adopts different conformation due to the different mode of interaction with the anionic host, the neighbouring drug cations and water molecules.

  9. Nuclear structure ''southeast'' of {sup 208}Pb: Isomeric states in {sup 208}Hg and {sup 209}Tl

    SciTech Connect

    Al-Dahan, N.; Podolyak, Zs.; Regan, P. H.; Alkhomashi, N.; Deo, A. Y.; Farrelly, G.; Steer, S. J.; Cullen, I. J.; Gelletly, W.; Swan, T.; Thomas, J. S.; Walker, P. M.; Gorska, M.; Grawe, H.; Gerl, J.; Pietri, S. B.; Wollersheim, H. J.; Boutachkov, P.; Domingo-Pardo, C.; Farinon, F.

    2009-12-15

    The nuclear structure of neutron-rich N>126 nuclei has been investigated following their production via relativistic projectile fragmentation of a E/A=1 GeV {sup 238}U beam. Metastable states in the N=128 isotones {sup 208}Hg and {sup 209}Tl have been identified. Delayed {gamma}-ray transitions are interpreted as arising from the decay of I{sup {pi}}=(8{sup +}) and (17/2{sup +}) isomers, respectively. The data allow for the so far most comprehensive verification of the shell-model approach in the region determined by magic numbers Z<82 and N>126.

  10. Effect of isomeric structures of branched cyclic hydrocarbons on densities and equation of state predictions at elevated temperatures and pressures.

    PubMed

    Wu, Yue; Bamgbade, Babatunde A; Burgess, Ward A; Tapriyal, Deepak; Baled, Hseen O; Enick, Robert M; McHugh, Mark A

    2013-07-25

    The cis and trans conformation of a branched cyclic hydrocarbon affects the packing and, hence, the density, exhibited by that compound. Reported here are density data for branched cyclohexane (C6) compounds including methylcyclohexane, ethylcyclohexane (ethylcC6), cis-1,2-dimethylcyclohexane (cis-1,2), cis-1,4-dimethylcyclohexane (cis-1,4), and trans-1,4-dimethylcyclohexane (trans-1,4) determined at temperatures up to 525 K and pressures up to 275 MPa. Of the four branched C6 isomers, cis-1,2 exhibits the largest densities and the smallest densities are exhibited by trans-1,4. The densities are modeled with the Peng-Robinson (PR) equation of state (EoS), the high-temperature, high-pressure, volume-translated (HTHP VT) PREoS, and the perturbed chain, statistical associating fluid theory (PC-SAFT) EoS. Model calculations highlight the capability of these equations to account for the different densities observed for the four isomers investigated in this study. The HTHP VT-PREoS provides modest improvements over the PREoS, but neither cubic EoS is capable of accounting for the effect of isomer structural differences on the observed densities. The PC-SAFT EoS, with pure component parameters from the literature or from a group contribution method, provides improved density predictions relative to those obtained with the PREoS or HTHP VT-PREoS. However, the PC-SAFT EoS, with either set of parameters, also cannot fully account for the effect of the C6 isomer structure on the resultant density. PMID:23815675

  11. Effect of Isomeric Structures of Branched Cyclic Hydrocarbons on Densities and Equation of State Predictions at Elevated Temperatures and Pressures

    SciTech Connect

    Wu, Yue; Bamgbade, Babatunde A; Burgess, Ward A; Tapriyal, Deepak; Baled, Hseen O; Enick, Robert M; McHugh, Mark

    2013-07-25

    The cis and trans conformation of a branched cyclic hydrocarbon affects the packing and, hence, the density, exhibited by that compound. Reported here are density data for branched cyclohexane (C6) compounds including methylcyclohexane, ethylcyclohexane (ethylcC6), cis-1,2-dimethylcyclohexane (cis-1,2), cis-1,4-dimethylcyclohexane (cis-1,4), and trans-1,4-dimethylcyclohexane (trans-1,4) determined at temperatures up to 525 K and pressures up to 275 MPa. Of the four branched C6 isomers, cis-1,2 exhibits the largest densities and the smallest densities are exhibited by trans-1,4. The densities are modeled with the Peng–Robinson (PR) equation of state (EoS), the high-temperature, high-pressure, volume-translated (HTHP VT) PREoS, and the perturbed chain, statistical associating fluid theory (PC-SAFT) EoS. Model calculations highlight the capability of these equations to account for the different densities observed for the four isomers investigated in this study. The HTHP VT-PREoS provides modest improvements over the PREoS, but neither cubic EoS is capable of accounting for the effect of isomer structural differences on the observed densities. The PC-SAFT EoS, with pure component parameters from the literature or from a group contribution method, provides improved density predictions relative to those obtained with the PREoS or HTHP VT-PREoS. However, the PC-SAFT EoS, with either set of parameters, also cannot fully account for the effect of the C6 isomer structure on the resultant density.

  12. Isomeric oxydiphthalic anhydride polyimides

    NASA Technical Reports Server (NTRS)

    Gerber, Margaret K.; Pratt, J. Richard; Stclair, Terry L.

    1988-01-01

    Much of the polyimide research at Langley Research Center has focused on isomeric modification of the diamine component; polyimides having considerably improved processability and adhesion have resulted. The present structure-property study was designed to investigate how isomeric attachment of the three oxydiphthalic anhydride (ODPA) polyimides affects their properties. Each dianhydride, 3,4,3',4'-oxydiphthalic anhydride (4,4'-OPDA,I), 2,3,2',3'-oxydiphthalic anhydride (3,3'-ODPA,II), and 2,3,3',4'-oxydiphthalic anhydride (3,4'-OPDA,III), was reacted with p-phenylenediamine, 4,4'-oxydianiline, 3,3'-diaminodiphenylsulfone, 3,3'-diaminobenzophenone, and 4,4'-bis(3-aminophenoxy)benzophenone in DMAc. The inherent viscosities of the resulting poly(amic acids) were determined. Thermally imidized films were studied for their creasability and solubility, as well as by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and wide angle X-ray scattering (WAXS). A comparison of these properties will be made.

  13. Probing cis-trans isomerization in the S{sub 1} state of C{sub 2}H{sub 2} via H-atom action and hot band-pumped IR-UV double resonance spectroscopies

    SciTech Connect

    Changala, P. Bryan; Baraban, Joshua H.; Field, Robert W.; Merer, Anthony J.

    2015-08-28

    We report novel experimental strategies that should prove instrumental in extending the vibrational and rotational assignments of the S{sub 1} state of acetylene, C{sub 2}H{sub 2}, in the region of the cis-trans isomerization barrier. At present, the assignments are essentially complete up to ∼500 cm{sup −1} below the barrier. Two difficulties arise when the assignments are continued to higher energies. One is that predissociation into C{sub 2}H + H sets in roughly 1100 cm{sup −1} below the barrier; the resulting quenching of laser-induced fluorescence (LIF) reduces its value for recording spectra in this region. The other difficulty is that tunneling through the barrier causes a staggering in the K-rotational structure of isomerizing vibrational levels. The assignment of these levels requires data for K values up to at least 3. Given the rotational selection rule K′ − ℓ{sup ′′} = ± 1, such data must be obtained via excited vibrational levels of the ground state with ℓ{sup ′′} > 0. In this paper, high resolution H-atom resonance-enhanced multiphoton ionization spectra are demonstrated to contain predissociated bands which are almost invisible in LIF spectra, while preliminary data using a hyperthermal pulsed nozzle show that ℓ{sup ′′} = 2 states can be selectively populated in a jet, giving access to K′ = 3 states in IR-UV double resonance.

  14. Probing cis-trans isomerization in the S1 state of C2H2 via H-atom action and hot band-pumped IR-UV double resonance spectroscopies

    NASA Astrophysics Data System (ADS)

    Changala, P. Bryan; Baraban, Joshua H.; Merer, Anthony J.; Field, Robert W.

    2015-08-01

    We report novel experimental strategies that should prove instrumental in extending the vibrational and rotational assignments of the S1 state of acetylene, C2H2, in the region of the cis-trans isomerization barrier. At present, the assignments are essentially complete up to ˜500 cm-1 below the barrier. Two difficulties arise when the assignments are continued to higher energies. One is that predissociation into C2H + H sets in roughly 1100 cm-1 below the barrier; the resulting quenching of laser-induced fluorescence (LIF) reduces its value for recording spectra in this region. The other difficulty is that tunneling through the barrier causes a staggering in the K-rotational structure of isomerizing vibrational levels. The assignment of these levels requires data for K values up to at least 3. Given the rotational selection rule K' - ℓ'' = ± 1, such data must be obtained via excited vibrational levels of the ground state with ℓ'' > 0. In this paper, high resolution H-atom resonance-enhanced multiphoton ionization spectra are demonstrated to contain predissociated bands which are almost invisible in LIF spectra, while preliminary data using a hyperthermal pulsed nozzle show that ℓ'' = 2 states can be selectively populated in a jet, giving access to K' = 3 states in IR-UV double resonance.

  15. Probing cis-trans isomerization in the S1 state of C2H2 via H-atom action and hot band-pumped IR-UV double resonance spectroscopies.

    PubMed

    Changala, P Bryan; Baraban, Joshua H; Merer, Anthony J; Field, Robert W

    2015-08-28

    We report novel experimental strategies that should prove instrumental in extending the vibrational and rotational assignments of the S1 state of acetylene, C2H2, in the region of the cis-trans isomerization barrier. At present, the assignments are essentially complete up to ∼500 cm(-1) below the barrier. Two difficulties arise when the assignments are continued to higher energies. One is that predissociation into C2H + H sets in roughly 1100 cm(-1) below the barrier; the resulting quenching of laser-induced fluorescence (LIF) reduces its value for recording spectra in this region. The other difficulty is that tunneling through the barrier causes a staggering in the K-rotational structure of isomerizing vibrational levels. The assignment of these levels requires data for K values up to at least 3. Given the rotational selection rule K' - ℓ('') = ± 1, such data must be obtained via excited vibrational levels of the ground state with ℓ('') > 0. In this paper, high resolution H-atom resonance-enhanced multiphoton ionization spectra are demonstrated to contain predissociated bands which are almost invisible in LIF spectra, while preliminary data using a hyperthermal pulsed nozzle show that ℓ('') = 2 states can be selectively populated in a jet, giving access to K' = 3 states in IR-UV double resonance. PMID:26328846

  16. Evidence of shell effects in the excitation function of 0.136-MeV isomeric state populated in the {sup 93}Nb(n,2n){sup 92}Nb{sup m} reaction

    SciTech Connect

    Gul, K.

    2004-09-01

    Calculation for the excitation function of 0.136-MeV (2{sup +}) isomeric state in {sup 92}Nb has been carried out using Hauser-Feshbach and pre-equilibrium nuclear reaction models in 10-20 MeV energy range. A satisfactory agreement between the calculation and measurements requires the suppression of contribution from the negative-parity doublet consisting of the 0.226-MeV (2{sup -}) and 0.390-MeV (3{sup -}) states in {sup 92}Nb. This can be explained on the basis of highly retarded gamma transitions of higher energy states to the negative-parity doublet on account of its different shell model configuration compared to the shell model configuration of positive-parity states.

  17. Ortho-para nuclear-spin isomerization energies for all bound vibrational states of ditritium (T2) from non-Born-Oppenheimer variational calculations performed with explicitly correlated all-particle Gaussian functions

    NASA Astrophysics Data System (ADS)

    Kirnosov, Nikita; Sharkey, Keeper L.; Adamowicz, Ludwik

    2015-11-01

    Direct variational calculations, where the Born-Oppenheimer (BO) approximation is not assumed, are performed for all 26 bound rovibrational states corresponding to the lowest rotational excitation (i.e. the N = 1 states) of the tritium molecule (T2). The non-BO energies are used to determine the ortho-para isomerization energies. All-particle explicitly correlated Gaussian basis functions are employed in the calculations and over 11 000 Gaussians independently generated for each state are used. The exponential parameters of the Gaussians are optimized with the aid of analytically calculated energy gradient determined with respect to these parameters. The non-BO wave functions are used to calculate expectation values of the inter-particle distances and the triton-triton correlation functions.

  18. Conformational isomerism in solid state of AMG 853--structure studies using solid-state nuclear magnetic resonance and X-ray diffraction.

    PubMed

    Kiang, Y-H; Nagapudi, Karthik; Wu, Tian; Peterson, Matthew L; Jona, Janan; Staples, Richard J; Stephens, Peter W

    2015-07-01

    Investigation of an additional resonance peak in the (19) F solid-state nuclear magnetic resonance (NMR) spectrum of AMG 853, a dual antagonist of DP and CRTH2 previously in clinical development for asthma, has led to the identification of two conformational isomers coexisting in the crystal lattice in a continuous composition range between 89.7%:10.3% and 96.5%:3.5%. These two isomers differ in the chloro-flurorophenyl moiety orientation-the aromatic ring is flipped by 180° in these two isomers. The level of the minor isomer is directly measured through integration of the two peaks in the (19) F solid-state NMR spectrum. The values obtained from the NMR data are in excellent agreement with the degree of disorder of the fluorine atom in the crystal structure, refined using both single-crystal and high-resolution powder X-ray diffraction data. PMID:25912152

  19. Isomerization Intermediates In Solution Phase Photochemistry Of Stilbenes

    NASA Astrophysics Data System (ADS)

    Doany, F. E.; Hochstrasser, R. M.; Greene, B. I.

    1985-04-01

    Picosecond and subpicosecond spectroscopic studies have revealed evidence for an isomerization intermediate between cis and trans in the photoinduced isomerism of both stilbene and biindanyledene ("stiff" stilbene). In stiff stilbene, a transient absorption at 351 nm displays time evolution and viscosity dependence consistent with absorption by a twisted intermediate ("phantom" state) with a lOps lifetime. An analagous bottleneck state with a life-time of 4ps is also consistent with the ground state recovery dynamics of t-stilbene following excitation of c-stilbene when monitored with 0.1ps resolution.

  20. A Comparative Account of the Kinetics of Light-Induced E-Z Isomerization of an Anthracene-Based Organogelator in Sol, Gel, Xerogel, and Powder States: Fiber to Crystal Transformation.

    PubMed

    Mondal, Sanjoy; Chakraborty, Priyadarshi; Das, Sujoy; Bairi, Partha; Nandi, Arun K

    2016-05-31

    The organogel of (E)-N'-(anthracene-10-ylmethylene)-3,4,5-tris(dodecyloxy)benzohydrazide (I) in methyl cyclohexane having a fibrillar network structure exhibits excellent fluorescence, which decreases sharply with time upon photoirradiation at λ = 365 nm. It has been attributed to the transformation of the E isomer of I to the Z isomer, and the kinetics of E-Z isomerization are compared for the sol, gel, xerogel, and powder states. The rate constants at different temperatures are measured from Avrami plots and its increase with an increase in temperature, indicating temperature acts as a promoter for photoirradiated E-Z isomeization along the imine (C═N) bond. In the powder form, the rate constant values are the lowest compared to those of other states for all temperatures and the xerogels exhibit the highest rate of E-Z isomerization. The rate constants of sol and gel states mostly lie between the two. The wide-angle X-ray scattering pattern changes after ultraviolet (UV) irradiation with the generation of new sharp peaks whose intensities increase with an increase in irradiation time. A polarized optical microscopic study indicates formation of small crystalline dots on the fibers in the gels, dendritic morphology on the xerogel fibers, and large needlelike morphology at the surface boundary of the solid. The dried I gel exhibits a melting peak at 96.7 °C, but upon irradiation, two peaks are observed at 98.5 and 152.7 °C; the latter has been attributed to the melting of crystals of Z isomers. Similar higher melting peaks are observed both for the xerogel and for powders after UV irradiation; the powders exhibit the highest meting peak at 159.4 °C. Possible reasons for the variation of rate constant values in the four different states and the difference in morphology and melting points of crystals of Z isomers of I are discussed. PMID:27159227

  1. Isomeric decay spectroscopy of the Bi217 isotope

    NASA Astrophysics Data System (ADS)

    Gottardo, A.; Valiente-Dobón, J. J.; Benzoni, G.; Lunardi, S.; Gadea, A.; Algora, A.; Al-Dahan, N.; de Angelis, G.; Ayyad, Y.; Bazzacco, D.; Benlliure, J.; Boutachkov, P.; Bowry, M.; Bracco, A.; Bruce, A. M.; Bunce, M.; Camera, F.; Casarejos, E.; Cortes, M. L.; Crespi, F. C. L.; Corsi, A.; Denis Bacelar, A. M.; Deo, A. Y.; Domingo-Pardo, C.; Doncel, M.; Engert, T.; Eppinger, K.; Farrelly, G. F.; Farinon, F.; Farnea, E.; Geissel, H.; Gerl, J.; Goel, N.; Górska, M.; Grebosz, J.; Gregor, E.; Habermann, T.; Hoischen, R.; Janik, R.; John, P. R.; Klupp, S.; Kojouharov, I.; Kurz, N.; Lenzi, S. M.; Leoni, S.; Mandal, S.; Menegazzo, R.; Mengoni, D.; Million, B.; Modamio, V.; Morales, A. I.; Napoli, D. R.; Naqvi, F.; Nicolini, R.; Nociforo, C.; Pfützner, M.; Pietri, S.; Podolyák, Zs.; Prochazka, A.; Prokopowicz, W.; Recchia, F.; Regan, P. H.; Reed, M. W.; Rudolph, D.; Sahin, E.; Schaffner, H.; Sharma, A.; Sitar, B.; Siwal, D.; Steiger, K.; Strmen, P.; Swan, T. P. D.; Szarka, I.; Ur, C. A.; Walker, P. M.; Weick, H.; Wieland, O.; Wollersheim, H.-J.

    2014-09-01

    The structure of the neutron-rich bismuth isotope Bi217 has been studied for the first time. The fragmentation of a primary U238 beam at the FRS-RISING setup at GSI was exploited to perform γ-decay spectroscopy, since μs isomeric states were expected in this nucleus. Gamma rays following the decay of a t1/2=3 μs isomer were observed, allowing one to establish the low-lying structure of Bi217. The level energies and the reduced electric quadrupole transition probability B (E2) from the isomeric state are compared to large-scale shell-model calculations.

  2. Retinal isomerization dynamics in dry bacteriorhodopsin films

    NASA Astrophysics Data System (ADS)

    Colonna, Anne; Groma, Géza I.; Vos, Marten H.

    2005-10-01

    The primary photoprocesses in neutral and acid forms of oriented dried bacteriorhodopsin films were investigated by femtosecond absorption spectroscopy. The excitation energy dependence of the signals was used to distinguish photochemistry from processes involving photophysics of photocycle intermediates. Both the kinetics and the quantum yield of all- trans excited state decay by retinal photoisomerization and subsequent J → K transition were found to be very similar as in hydrated environments. Therefore, unlike slower photocycle phases, communication of the retinal with the environment does not play a role in retinal isomerization. Our results are important for understanding recent nonlinear optical applications of such films.

  3. Homodimerization of the G Protein Srbeta in the Nucleotide-Free State Involves Proline cis/trans Isomerication in the Switch II Region

    SciTech Connect

    Schwartz,T.; Schmidt, D.; Brohawn, S.; Blobel, G.

    2006-01-01

    Protein translocation across and insertion into membranes is essential to all life forms. Signal peptide-bearing nascent polypeptide chains emerging from the ribosome are first sampled by the signal-recognition particle (SRP), then targeted to the membrane via the SRP receptor (SR), and, finally, transferred to the protein-conducting channel. In eukaryotes, this process is tightly controlled by the concerted action of three G proteins, the 54-kD subunit of SRP and the {alpha}- and {beta}-subunits of SR. We have determined the 2.2-Angstroms crystal structure of the nucleotide-free SR{beta} domain. Unexpectedly, the structure is a homodimer with a highly intertwined interface made up of residues from the switch regions of the G domain. The remodeling of the switch regions does not resemble any of the known G protein switch mechanisms. Biochemical analysis confirms homodimerization in vitro, which is incompatible with SR{alpha} binding. The switch mechanism involves cis/trans isomerization of a strictly conserved proline, potentially implying a new layer of regulation of cotranslational transport.

  4. Ultrafast excited state dynamics controlling photochemical isomerization of N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium coordinated to a {Re I(CO)3(2,2'-bipyridine)} chromophore.

    PubMed

    Busby, Michael; Hartl, Frantisek; Matousek, Pavel; Towrie, Mike; Vlcek, Antonín

    2008-01-01

    Two multifunctional photoactive complexes [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) and [Re(MeDpe(+))(CO)(3)(bpy)](2+) (MeDpe(+)=N-methyl-4-[trans-2-(4-pyridyl)ethenyl]pyridinium, bpy=2,2'-bipyridine) were synthesized, characterized, and their redox and photonic properties were investigated by cyclic voltammetry; ultraviolet-visible-infrared (UV/Vis/IR) spectroelectrochemistry, stationary UV/Vis and resonance Raman spectroscopy; photolysis; picosecond time-resolved absorption spectroscopy in the visible and infrared regions; and time-resolved resonance Raman spectroscopy. The first reduction step of either complex occurs at about -1.1 V versus Fc/Fc(+) and is localized at MeDpe(+). Reduction alone does not induce a trans-->cis isomerization of MeDpe(+). [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) is photostable, while [Re(MeDpe(+))(CO)(3)(bpy)](2+) and free MeDpe(+) isomerize under near-UV irradiation. The lowest excited state of [Re(Cl)(CO)(3)(MeDpe(+))(2)](2+) has been identified as the Re(Cl)(CO)(3)-->MeDpe(+ 3)MLCT (MLCT=metal-to-ligand charge transfer), decaying directly to the ground state with lifetimes of approximately 42 (73 %) and approximately 430 ps (27 %). Optical excitation of [Re(MeDpe(+))(CO)(3)(bpy)](2+) leads to population of Re(CO)(3)-->MeDpe(+) and Re(CO)(3)-->bpy (3)MLCT states, from which a MeDpe(+) localized intraligand (3)pipi* excited state ((3)IL) is populated with lifetimes of approximately 0.6 and approximately 10 ps, respectively. The (3)IL state undergoes a approximately 21 ps internal rotation, which eventually produces the cis isomer on a much longer timescale. The different excited-state behavior of the two complexes and the absence of thermodynamically favorable interligand electron transfer in excited [Re(MeDpe(+))(CO)(3)(bpy)](2+) reflect the fine energetic balance between excited states of different orbital origin, which can be tuned by subtle structural variations. The complex [Re(MeDpe(+))(CO)(3)(bpy)](2+) emerges as a prototypical

  5. Thermal isomerization of spiropyran to merocyanine in aqueous media and its application to colorimetric temperature indication.

    PubMed

    Shiraishi, Yasuhiro; Itoh, Masataka; Hirai, Takayuki

    2010-11-01

    Thermally-induced isomerization of spiropyran derivatives in aqueous media has been studied. The colorless spirocyclic (SP) forms of spiropyran derivatives are isomerized to colored merocyanine (MC) forms even in dark conditions at elevated temperature. Equilibrium, kinetic, and deuterium experiments reveal that the thermal SP → MC isomerization is due to the stabilization of MC form by a hydrogen bonding interaction with water molecules. This leads to the ground state energy of the MC form decreasing to lower than that of the SP form, resulting in SP → MC isomerization. The thermal isomerization property is applicable to a rough indication of solution temperature. The spiropyran derivatives, when dissolved in aqueous media under irradiation of visible light with an appropriate light intensity, demonstrate an increase in MC absorbance with a rise in temperature. The absorption response occurs reversibly regardless of the heating/cooling sequence. The spiropyran derivatives therefore have a potential for colorimetric temperature indication. PMID:20877830

  6. Elucidation of Isomerization Pathways of a Single Azobenzene Derivative Using an STM.

    PubMed

    Kazuma, Emiko; Han, Mina; Jung, Jaehoon; Oh, Junepyo; Seki, Takahiro; Kim, Yousoo

    2015-11-01

    The predominant pathway for the isomerization between cis- and trans-azobenzenes-either (i) inversion by the bending of an NNC bond or (ii) rotation by the torsion of two phenyl rings-continues to be a controversial topic. To elucidate each isomerization pathway, a strategically designed and synthesized azobenzene derivative was investigated on a Ag(111) surface. This was achieved by exciting the molecule with tunneling electrons from the tip of a scanning tunneling microscope (STM). Structural analyses of the molecularly resolved STM images reveal that both inversion and rotation pathways are available for isomerization on a metal surface and strongly depend on the initial adsorption structures of the molecule. On the basis of the potential energy diagrams for the isomerization, it is concluded that isomerization pathways on a metal surface are not simply related to the excited states. PMID:26722964

  7. Subnanosecond isomerization in an osmium-dimethyl sulfoxide complex.

    PubMed

    Mockus, Nicholas V; Petersen, Jeffrey L; Rack, Jeffrey J

    2006-01-01

    We report the structure, spectroscopy, and electrochemistry of cis-[Os(bpy)(2)(DMSO)(2)](OTf)(2), where bpy is 2,2'-bipyridine, DMSO is dimethyl sulfoxide, and OTf is trifluoromethanesulfonate. Electrochemical measurements are consistent with S-to-O isomerization following the oxidation of Os(2+) (1.8 V vs Ag/AgCl). Visible irradiation of the metal-to-ligand charge-transfer transition (355 nm) of [Os(bpy)(2)(DMSO)(2)](2+) in the solid state and solution yields an emissive S-bonded excited state and S-to-O excited-state isomerization on a subnanosecond time scale. These results and a comparison to the nonphotoactive [Os(bpy)(2)Cl(DMSO)](+) are discussed. PMID:16390034

  8. EXPLANATION FOR THE ISOMERIC COMPARTMENTALIZATION OF ENDOSULFAN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Endosulfan, an insecticide used on vegetables, fruits, cereals and cotton, exists as 7:3 isomeric mixture of alpha and beta when applied. However, this isomeric ratio is not conserved throughout the environmental compartments and the ratio is dependent on the compartment. Studies examining endosulf...

  9. Peptide Bond Isomerization in High-Temperature Simulations.

    PubMed

    Neale, Chris; Pomès, Régis; García, Angel E

    2016-04-12

    Force fields for molecular simulation are generally optimized to model macromolecules such as proteins at ambient temperature and pressure. Nevertheless, elevated temperatures are frequently used to enhance conformational sampling, either during system setup or as a component of an advanced sampling technique such as temperature replica exchange. Because macromolecular force fields are now put upon to simulate temperatures and time scales that greatly exceed their original design specifications, it is appropriate to re-evaluate whether these force fields are up to the task. Here, we quantify the rates of peptide bond isomerization in high-temperature simulations of three octameric peptides and a small fast-folding protein. We show that peptide octamers with and without proline residues undergo cis/trans isomerization every 1-5 ns at 800 K with three classical atomistic force fields (AMBER99SB-ILDN, CHARMM22/CMAP, and OPLS-AA/L). On the low microsecond time scale, these force fields permit isomerization of nonprolyl peptide bonds at temperatures ≥500 K, and the CHARMM22/CMAP force field permits isomerization of prolyl peptide bonds ≥400 K. Moreover, the OPLS-AA/L force field allows chiral inversion about the Cα atom at 800 K. Finally, we show that temperature replica exchange permits cis peptide bonds developed at 540 K to subsequently migrate back to the 300 K ensemble, where cis peptide bonds are present in 2 ± 1% of the population of Trp-cage TC5b, including up to 4% of its folded state. Further work is required to assess the accuracy of cis/trans isomerization in the current generation of protein force fields. PMID:26866899

  10. Deconstructing field-induced ketene isomerization through Lagrangian descriptors.

    PubMed

    Craven, Galen T; Hernandez, Rigoberto

    2016-02-01

    The time-dependent geometrical separatrices governing state transitions in field-induced ketene isomerization are constructed using the method of Lagrangian descriptors. We obtain the stable and unstable manifolds of time-varying transition states as dynamic phase space objects governing configurational changes when the ketene molecule is subjected to an oscillating electric field. The dynamics of the isomerization reaction are modeled through classical trajectory studies on the Gezelter-Miller potential energy surface and an approximate dipole moment model which is coupled to a time-dependent electric field. We obtain a representation of the reaction geometry, over varying field strengths and oscillation frequencies, by partitioning an initial phase space into basins labeled according to which product state is reached at a given time. The borders between these basins are in agreement with those obtained using Lagrangian descriptors, even in regimes exhibiting chaotic dynamics. Major outcomes of this work are: validation and extension of a transition state theory framework built from Lagrangian descriptors, elaboration of the applicability for this theory to periodically- and aperiodically-driven molecular systems, and prediction of regimes in which isomerization of ketene and its derivatives may be controlled using an external field. PMID:26778728

  11. Isomeric and ground-state properties of {sub 78}{sup 171}Pt, {sub 76}{sup 167}Os, and {sub 74}{sup 163}W

    SciTech Connect

    Scholey, C.; Eeckhaudt, S.; Grahn, T.; Greenlees, P. T.; Jones, P.; Julin, R.; Juutinen, S.; Ketelhut, S.; Leino, M.; Leppaenen, A.-P.; Nieminen, P.; Nyman, M.; Pakarinen, J.; Rahkila, P.; Saren, J.; Sorri, J.; Uusitalo, J.; Andgren, K.; Cederwall, B.; Hadinia, B.

    2010-01-15

    Decay paths, half-lives, and excitation energies of the i{sub 13/2} bandheads of the neutron-deficient nuclei {sup 171}Pt, {sup 167}Os, and {sup 163}W have been established for the first time. Gamma-ray transitions, X-rays, and internal conversion electrons have been observed, allowing internal-conversion coefficients to be measured and B(M2) reduced transition probabilities to be extracted. These results elucidate the low-lying single-quasiparticle structures and give the energy level spacings between the nuf{sub 7/2}, nuh{sub 9/2}, and nui{sub 13/2} quasineutron states for all three nuclei. Moreover, ground-state spin assignments have been made for the first time, along with the measurement of the {alpha}-decay branching ratio for {sup 171}Pt. The decay paths of the i{sub 13/2} bandheads were followed by favored {alpha} decays, indicating that all three nuclei have the same I{sup {pi}}=7/2{sup -} ground state.

  12. Incoherent Control of the Retinal Isomerization in Rhodopsin

    NASA Astrophysics Data System (ADS)

    Lucas, Felix; Hornberger, Klaus

    2014-08-01

    We propose to control the retinal photoisomerization yield through the backaction dynamics imparted by a nonselective optical measurement of the molecular electronic state. This incoherent effect is easier to implement than comparable coherent pulse shaping techniques, and is also robust to environmental noise. A numerical simulation of the quantum dynamics shows that the isomerization yield of this important biomolecule can be substantially increased above the natural limit.

  13. Isomerization controlled photopolymerization: effect of dye photophysics on photoinitiation efficiency.

    PubMed

    Ley, C; Ibrahim, A; Allonas, X

    2016-08-01

    The efficiency of free radical polymerization by photoinitiating systems based on two Astrazon orange cyanine dyes was shown to be directly related to the isomerization process of the dye in the excited states. The impact of resin viscosity on photopolymerization reactions was measured and related to the overall radical quantum yields. The quantum yields were calculated according to the photocyclic behaviour of the initiating systems based on the Astrazon orange dyes. These dyes are characterized by a viscosity dependent photophysics, which leads to an isomerization-diffusion-controlled photopolymerization. Besides this demonstration, Astrazon orange dyes appeared to be very good candidates for free radical photopolymerization in the visible, presenting high absorption coefficient, low cost and good sensitivity. PMID:27443964

  14. Ultrafast Extreme Ultraviolet Induced Isomerization of Acetylene Cations

    SciTech Connect

    Jiang, Y.; Rudenko, Artem; Herrwerth, O.; Foucar, L.; Kurka, M.; Kuhnel, K.; Lezius, M.; Kling, Matthias; van Tilborg, Jeroen; Belkacem, Ali; Ueda, K.; Dusterer, S.; Treusch, R.; Schroter, Claus-Dieter; Moshammer, Robbert; Ullrich, Joachim

    2011-06-17

    Ultrafast isomerization of acetylene cations ([HC = CH]{sup +}) in the low-lying excited A{sup 2}{Sigma}{sub g}{sup +} state, populated by the absorption of extreme ultraviolet (XUV) photons (38 eV), has been observed at the Free Electron Laser in Hamburg, (FLASH). Recording coincident fragments C{sup +} + CH{sub 2}{sup +} as a function of time between XUV-pump and -probe pulses, generated by a split-mirror device, we find an isomerization time of 52 {+-} 15 fs in a kinetic energy release (KER) window of 5.8 < KER < 8 eV, providing clear evidence for the existence of a fast, nonradiative decay channel.

  15. Ultrafast Extreme Ultraviolet Induced Isomerization of Acetylene Cations

    SciTech Connect

    Jiang, Y. H.; Kurka, M.; Kuehnel, K. U.; Schroeter, C. D.; Moshammer, R.; Rudenko, A.; Foucar, L.; Herrwerth, O.; Lezius, M.; Kling, M. F.; Tilborg, J. van; Belkacem, A.; Ueda, K.; Duesterer, S.; Treusch, R.; Ullrich, J.

    2010-12-31

    Ultrafast isomerization of acetylene cations ([HC=CH]{sup +}) in the low-lying excited A{sup 2}{Sigma}{sub g}{sup +} state, populated by the absorption of extreme ultraviolet (XUV) photons (38 eV), has been observed at the Free Electron Laser in Hamburg, (FLASH). Recording coincident fragments C{sup +}+CH{sub 2}{sup +} as a function of time between XUV-pump and -probe pulses, generated by a split-mirror device, we find an isomerization time of 52{+-}15 fs in a kinetic energy release (KER) window of 5.8

  16. Controlled subnanosecond isomerization of HCN to CNH in solution

    SciTech Connect

    Gong Jiangbin; Ma Ao; Rice, Stuart A.

    2005-05-22

    We report a study of control of the HCN{yields}CNH isomerization in a liquid Ar solution. We show, using molecular dynamics simulations, nearly complete conversion from HCN to CNH can be achieved in solution on the subnanosecond time scale without requiring laser pulse shaping or molecular alignment. The mechanism of the isomerization reaction involves multiphoton rovibrational excitation on the ground electronic state potential energy surface coupled with rapid rovibrational relaxation in solution. The results demonstrate the important role of rotation-vibration coupling in multiphoton excitation of small molecules and constitute the first realistic computational demonstration of fast, robust, and high-yield laser field manipulation of solution-phase molecular processes.

  17. Linkage isomerism in coordination polymers.

    PubMed

    Benmansour, Samia; Setifi, Fatima; Triki, Smail; Gómez-García, Carlos J

    2012-02-20

    The use of the recently prepared polynitrile ligand tcnopr3OH(-) ([(NC)(2)CC(OCH(2)CH(2)CH(2)OH)C(CN)(2)](-)) with different salts of Fe(II), Co(II), and Ni(II) has led to a very rare example of linkage isomerism in a coordination chain. These pairs of linkage isomers can be formulated as [M(tcnopr3OH-κN,κO)(2)(H(2)O)(2)]; M = Fe (1), Co (3), and Ni(5) and [M(tcnopr3OH-κN,κN')(2)(H(2)O)(2)]; M = Fe (2), Co (4), and Ni (6). Compounds 1-2, 3-4, and 5-6 are three pairs of linkage isomers since they present the same formula and chain structure and they only differ in the connectivity of the polynitrile ligand bridging the metal ions in the chain: through a N and an O atom (1κN:2κO-isomer) or through two N atoms (1κN:2κN'-isomer). The magnetic properties show, as expected, very similar behaviors for both isomers. PMID:22296602

  18. Isomerically Pure Tetramethylrhodamine Voltage Reporters.

    PubMed

    Deal, Parker E; Kulkarni, Rishikesh U; Al-Abdullatif, Sarah H; Miller, Evan W

    2016-07-27

    We present the design, synthesis, and application of a new family of fluorescent voltage indicators based on isomerically pure tetramethylrhodamines. These new Rhodamine Voltage Reporters, or RhoVRs, use photoinduced electron transfer (PeT) as a trigger for voltage sensing, display excitation and emission profiles in the green to orange region of the visible spectrum, demonstrate high sensitivity to membrane potential changes (up to 47% ΔF/F per 100 mV), and employ a tertiary amide derived from sarcosine, which aids in membrane localization and simultaneously simplifies the synthetic route to the voltage sensors. The most sensitive of the RhoVR dyes, RhoVR 1, features a methoxy-substituted diethylaniline donor and phenylenevinylene molecular wire at the 5'-position of the rhodamine aryl ring, exhibits the highest voltage sensitivity to date for red-shifted PeT-based voltage sensors, and is compatible with simultaneous imaging alongside green fluorescent protein-based indicators. The discoveries that sarcosine-based tertiary amides in the context of molecular-wire voltage indicators prevent dye internalization and 5'-substituted voltage indicators exhibit improved voltage sensitivity should be broadly applicable to other types of PeT-based voltage-sensitive fluorophores. PMID:27428174

  19. Conformational Isomerism Can Limit Antibody Catalysis

    SciTech Connect

    Debler, E.W.; Muller, R.; Hilvert, D.; Wilson, I.A.

    2009-05-14

    Ligand binding to enzymes and antibodies is often accompanied by protein conformational changes. Although such structural adjustments may be conducive to enzyme catalysis, much less is known about their effect on reactions promoted by engineered catalytic antibodies. Crystallographic and pre-steady state kinetic analyses of antibody 34E4, which efficiently promotes the conversion of benzisoxazoles to salicylonitriles, show that the resting catalyst adopts two interconverting active-site conformations, only one of which is competent to bind substrate. In the predominant isomer, the indole side chain of Trp{sup L91} occupies the binding site and blocks ligand access. Slow conformational isomerization of this residue, on the same time scale as catalytic turnover, creates a deep and narrow binding site that can accommodate substrate and promote proton transfer using Glu{sup H50} as a carboxylate base. Although 34E4 is among the best catalysts for the deprotonation of benzisoxazoles, its efficiency appears to be significantly limited by this conformational plasticity of its active site. Future efforts to improve this antibody might profitably focus on stabilizing the active conformation of the catalyst. Analogous strategies may also be relevant to other engineered proteins that are limited by an unfavorable conformational pre-equilibrium.

  20. Communication: An accurate calculation of the S1 C2H2 cis-trans isomerization barrier height

    NASA Astrophysics Data System (ADS)

    Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.

    2016-03-01

    A high level ab initio calculation of the cis-trans isomerization barrier height in the first excited singlet electronic state of acetylene is found to agree very well with a recent experimental determination.

  1. Special features of isomeric ratios in nuclear reactions induced by various projectile particles

    NASA Astrophysics Data System (ADS)

    Danagulyan, A. S.; Hovhannisyan, G. H.; Bakhshiyan, T. M.; Martirosyan, G. V.

    2016-05-01

    Calculations for ( p, n) and (α, p3 n) reactions were performed with the aid of the TALYS-1.4 code. Reactions in which the mass numbers of target and product nuclei were identical were examined in the range of A = 44-124. Excitation functions were obtained for product nuclei in ground and isomeric states, and isomeric ratios were calculated. The calculated data reflect well the dependence of the isomeric ratios on the projectile type. A comparison of the calculated and experimental data reveals, that, for some nuclei in a high-spin state, the calculated data fall greatly short of their experimental counterparts. These discrepancies may be due to the presence of high-spin yrast states and rotational bands in these nuclei. Calculations involving various level-density models included in the TALYS-1.4 code with allowance for the enhancement of collective effects do not remove the discrepancies in the majority of cases.

  2. Global reaction route mapping of isomerization pathways of exotic C{sub 6}H molecular species

    SciTech Connect

    Vikas, E-mail: qlabspu@yahoo.com; Kaur, Gurpreet

    2013-12-14

    C{sub 6}H radical is known to exist in the astrophysical environment in linear form; however, it may originate from nonlinear isomeric forms. Potential energy surface of C{sub 6}H is explored to search isomers of C{sub 6}H and transition states connecting them. This work reports first-ever identification of reaction pathways for isomerization of C{sub 6}H. The reaction route search is performed through global reaction route mapping method, which utilizes an uphill walking technique based on an anharmonic downward distortion following approach to search intermediates and transition states. The computations performed at the CASSCF/aug-cc-pVTZ, CCSD(T)/6-311++G(d,p)//DFT/B3LYP/6-311++G(d,p), and DFT/B3LYP/aug-cc-pVTZ levels of the theory identified 14 isomers (including 8 new isomeric forms of C{sub 6}H) and 28 transition states. Most of the identified isomers are found to have significant multireference character. The kinetic stability and natural bond orbital analysis of the identified isomers is also investigated. The isomeric forms are further characterized using spectral analysis involving rotational constants, vibrational frequencies, and Raman scattering activities as well as analyzing the effect of isotopic substitution of hydrogen on the spectral features. This study proposes that the linear-C{sub 6}H can readily isomerize to a six-member ring isomer.

  3. Low-lying isomeric levels in 75Cu

    SciTech Connect

    Daugas, J. M.; Faul, T.; Grawe, H.; Pfutzner, M.; Grzywacz, R.; Lewitowicz, M.; Achouri, N. L.; Bentida, R.; Beraud, R.; Borcea, C.; Bingham, C. R.; Catford, W.; Emsallem, A.; De France, G.; Grzywacz, K. L.; Lemmon, R.; Lopez Jimenez, M. J.; de Oliveira Santos, F.; Regan, P. H.; Rykaczewski, Krzysztof Piotr; Sauvestre, J. E.; Sawicka, M.; Stanoiu, M.; Sieja, K.; Nowacki, F.

    2010-01-01

    Isomeric low-lying states were identified and investigated in the 75Cu nucleus. Two states at 61.8(5)- and 128.3(7)-keV excitation energies with half-lives of 370(40)- and 170(15)-ns were assigned as 75m1Cu and 75m2Cu, respectively. The measured half-lives combined with the recent spin assignment of the ground state allow one to deduce tentatively spin and parity of the two isomers and the dominant multipolarities of the isomeric transitions with respect to the systematics of the Cu isotopes. Shell-model calculations using an up-to-date effective interaction reproduce the evolution of the 1/2 , 3/2 , and 5/2 states for the neutron-rich odd-mass Cu isotopes when filling the g9/2. The results indicate a significant change in the nuclear structure in this region, where a single-particle 5/2 state coexists with more and more collective 3/2 and 1/2 levels at low excitation energies.

  4. Low-lying isomeric levels in {sup 75}Cu

    SciTech Connect

    Daugas, J. M.; Faul, T.; Sauvestre, J. E.; Grawe, H.; Pfuetzner, M.; Sawicka, M.; Grzywacz, R.; Lewitowicz, M.; France, G. de; Lopez Jimenez, M. J.; Oliveira Santos, F. de; Baiborodin, D.; Bentida, R.; Beraud, R.; Emsallem, A.; Bingham, C. R.; Grzywacz, K. L.

    2010-03-15

    Isomeric low-lying states were identified and investigated in the {sup 75}Cu nucleus. Two states at 61.8(5)- and 128.3(7)-keV excitation energies with half-lives of 370(40)- and 170(15)-ns were assigned as {sup 75m1}Cu and {sup 75m2}Cu, respectively. The measured half-lives combined with the recent spin assignment of the ground state allow one to deduce tentatively spin and parity of the two isomers and the dominant multipolarities of the isomeric transitions with respect to the systematics of the Cu isotopes. Shell-model calculations using an up-to-date effective interaction reproduce the evolution of the 1/2{sup -}, 3/2{sup -}, and 5/2{sup -} states for the neutron-rich odd-mass Cu isotopes when filling the nug{sub 9/2}. The results indicate a significant change in the nuclear structure in this region, where a single-particle 5/2{sup -} state coexists with more and more collective 3/2{sup -} and 1/2{sup -} levels at low excitation energies.

  5. Ordering of azobenzenes by two-photon isomerization

    SciTech Connect

    Ishitobi, Hidekazu; Sekkat, Zouheir; Kawata, Satoshi

    2006-10-28

    We report on light induced orientation by two-photon isomerization of azobenzenes in films of polymer. The dynamics of isomerization and orientation by one-photon absorption and two-photon absorption (TPA) are similar, and TPA creates a degree of molecular orientation which is comparable to that achieved by single-photon isomerization, in agreement with the theoretical predictions of two-photon isomeric orientation.

  6. Ordering of azobenzenes by two-photon isomerization.

    PubMed

    Ishitobi, Hidekazu; Sekkat, Zouheir; Kawata, Satoshi

    2006-10-28

    We report on light induced orientation by two-photon isomerization of azobenzenes in films of polymer. The dynamics of isomerization and orientation by one-photon absorption and two-photon absorption (TPA) are similar, and TPA creates a degree of molecular orientation which is comparable to that achieved by single-photon isomerization, in agreement with the theoretical predictions of two-photon isomeric orientation. PMID:17092131

  7. Double well isomerization rate constants in solution

    NASA Astrophysics Data System (ADS)

    Zawadzki, Anthony G.; Hynes, James T.

    1985-02-01

    The rate constant k for a double well isomerization in solution is calculated over the entire friction range. The importance of frequency-dependent friction for both the vibrational energy transfer (VET) and barrier passage components of k is described. Rapid suppression of the VET transfer component with increasing degrees of freedom is discussed.

  8. Stability and isomerization reactions of phenyl cation C6H5+ isomers

    NASA Astrophysics Data System (ADS)

    Shi, Dandan; Yang, Xue; Zhang, Xiaomei; Shan, Shimin; Xu, Haifeng; Yan, Bing

    2016-03-01

    As a key polyatomic molecular cation that plays a pivotal role in growth of the polycyclic aromatic hydrocarbons, phenyl cation C6H5+ exhibits various isomers and isomerization reactions. Investigation on the structure and stability of the isomers as well as the isomerization is important for better understanding the chemical reactions involving C6H5+ cations. In this work, we have performed a theoretical study on the stability and isomerization reactions of C6H5+ isomers at density functional theory B3LYP/6-311G (d, p) level. We have obtained a total of 60 isomers of C6H5+ cations, most of which are reported for the first time. The geometries, vibrational frequencies, thermodynamic properties and stability of 28 out of 60 isomers have been summarized in detail. Different ring-to-ring and ring-to-chain isomerization pathways, which are connected via 28 transition states, have been investigated using the intrinsic reaction coordinate method. The results show that the isomerization reactions occur via hydrogen migration followed by bond-breaking and reconstruction.

  9. Ground-state and isomeric-state cross sections for 181Ta( n,2n )180Ta between 8 and 15 MeV

    SciTech Connect

    Bhatia, C.; Gooden, M. E.; Tornow, W.; Tonchev, A. P.

    2013-03-21

    Using the activation technique, the cross section for the reaction 181Ta(n,2n)180gTa was measured from 8 to 15 MeV in small energy steps to resolve inconsistencies in the existing database. The 93.4 keV γ ray from the decay of the 180gTa ground state was recorded with a high-purity germanium (HPGe) detector. The monitor reactions 27Al(n,α)24Na and 197Au(n,2n)196Au were used for neutron fluence determination. The ENDF VII.1 and TENDL 2011 evaluations are in considerable disagreement with the present data, which in turn agree very well with the majority of the existing data in the 14 MeV energy region. Furthermore, a detailed analysis using the code TALYS was performed to describe the present data and to predict the (n,2n) cross section to the isomeric state of 180Ta.

  10. Laser-driven isomerization of HCN → HNC: the importance of rotational excitation.

    PubMed

    Sun, Zhaopeng; Zheng, Yujun

    2015-03-26

    We report a time-dependent quantum wave packet theory, which is employed to interpret the isomerization dynamics of HCN molecules induced by an intense picosecond infrared laser field. Considering the molecular rotational degrees of the freedom, the wave functions are expanded in terms of molecular rotational bases. Our full-dimensional quantum model includes the full Coriolis coupling in the molecular kinetic energy Hamiltonian and dipole approximation in interaction terms. The numerical results show that the field-induced molecule rotational excitation plays an important role in the isomerization dynamical process. Some phenomena appear such as two-step two-photon absorption and highly oscillatory structure in rotational state distributions. The centrifugal sudden (CS) approximation calculation is also carried out and compared in this work; it is shown that the Coriolis couplings may lead to a significant decrease in the isomerization rate but highly enhanced molecular rotational excitation. PMID:25746130

  11. Vapor-controlled linkage isomerization of a vapochromic bis(thiocyanato)platinum(II) complex: new external stimuli to control isomerization behavior.

    PubMed

    Kobayashi, Atsushi; Fukuzawa, Yuki; Chang, Ho-Chol; Kato, Masako

    2012-07-16

    We synthesized a novel Pt(II)-diimine complex with a typical ambidentate thiocyanato ligand, [Pt(thiocyanato)(2)(H(2)dcbpy)] (1; H(2)dcbpy =4,4'-dicarboxy-2,2'-bipyridine), and found that the complex 1 exhibits unique linkage isomerizations with drastic color and luminescence changes driven by exposure to volatile organic chemical (VOC) vapors in the solid state. Reaction between [PtCl(2)(H(2)dcbpy)] and KSCN in aqueous solution at 0 °C enabled successful isolation of an isomer with the S-coordinated thiocyanato ligand, [Pt(SCN)(2)(H(2)dcbpy)] (1SS·H(2)O), as a nonluminescent orange solid. Interestingly, 1SS·H(2)O was isomerized completely to one isomer with the N-coordinated isothiocyanato ligand, [Pt(NCS)(2)(H(2)dcbpy)] (1NN·3DMF) by exposure to DMF vapor, and this isomerization was accompanied by significant color and luminescence changes from nonluminescent orange to luminescent red. IR spectroscopy and thermogravimetric analysis revealed that adsorption of the DMF vapor and transformation of the hydrogen-bonded structure both played important roles in this vapor-induced linkage isomerization. Another isomer containing both S- and N-coordinated thiocyanato ligands, [Pt(SCN)(NCS)(H(2)dcbpy)] (1SN), was obtained as a nonluminescent yellow solid simply by exposure of 1SS·H(2)O to acetone vapor at room temperature, and about 80% of 1SS·H(2)O was found to be converted to 1SN. In the solution state, each isomer changed gradually to an isomeric mixture, but pure 1SS was regenerated by UV light irradiation (λ(irr.) = 300 nm) of an MeOH solution of the mixture. In the crystal structure of 1SN, the complex molecules were hydrogen-bonded to each other through the carboxyl groups of the H(2)dcbpy ligand and the N site of the thiocyanato ligand, whereas the 1NN molecules in the 1NN·4DMF crystal were hydrogen-bonded to the solvated DMF molecules. Competition of the hydrogen-bonding ability among the carboxyl groups of the H(2)dcbpy ligand, N and S atoms of the

  12. Tungsta and platinum-tungsta supported on zirconia catalysts for alkane isomerization

    SciTech Connect

    Larsen, G.; Lotero, E.; Parra, R.D.

    1996-12-31

    Tungsta- and platinum-tungsta supported on zirconia catalysts (WZ and PtWZ) were tested for isomerization of n-butane with hydrogen at 573 K. The catalysts reduction kinetics and the chemical state of tungsten were studied by X-ray absorption near-edge spectroscopy (XANES) and conventional temperature-programmed (TPR) techniques. Platinum was found to catalyze the reduction of the support and the tungsta co-catalyst. An effective n-butane isomerization catalyst results from the combination of high-temperature calcination and low-temperature reduction. Pyridine adsorption, as monitored by diffuse reflectance infrared spectroscopy (DRIFTS), indicates that water of reduction generates Bronsted acid sites.

  13. CRIS: A new method in isomeric beam production

    NASA Astrophysics Data System (ADS)

    Lynch, K. M.; Billowes, J.; Bissell, M. L.; Budincevic, I.; Cocolios, T. E.; De Groote, R. P.; De Schepper, S.; Fedosseev, V. N.; Flanagan, K. T.; Franchoo, S.; Garcia Ruiz, R. F.; Heylen, H.; Marsh, B. A.; Mason, P. J. R.; Neyens, G.; Procter, T. J.; Rossel, R. E.; Rothe, S.; Simpson, G. S.; Smith, A. J.; Strashnov, I.; Stroke, H. H.; Walker, P. M.; Wendt, K. D. A.; Wood, R. T.

    2013-12-01

    The Collinear Resonance Ionization Spectroscopy (CRIS) experiment at ISOLDE, CERN, uses laser radiation to stepwise excite and ionize an atomic beam for the purpose of ultra-sensitive detection of rare isotopes, and hyperfine-structure measurements. The technique also offers the ability to purify an ion beam that is heavily contaminated with radioactive isobars, including the ground state of an isotope from its isomer, allowing decay spectroscopy on nuclear isomeric states to be performed. The isomeric ion beam is selected by resonantly exciting one of its hyperfine structure levels, and subsequently ionizing it. This selectively ionized beam is deflected to a decay spectroscopy station (DSS). This consists of a rotating wheel implantation system for alpha- and beta-decay spectroscopy, and up to three germanium detectors around the implantation site for gamma-ray detection. Resonance ionization spectroscopy and the new technique of laser assisted nuclear decay spectroscopy have recently been performed at the CRIS beam line on the neutron-deficient francium isotopes. Here an overview of the two techniques will be presented, alongside a description of the CRIS beam line and DSS.

  14. E/Z Isomers and Isomerization

    NASA Astrophysics Data System (ADS)

    Liaaen-Jensen, Synnøve; Lutnœes, Bjart Frode

    The natural occurrence of several carotenoid cis isomers and their biological significance were not anticipated in 1962, when the classical monograph on cis-trans isomeric carotenoids [1] was published. More recent research has demonstrated that various cis isomers occur naturally in bacteria plants, algae and invertebrate animals, and are present in human blood and tissues. The participation of cis isomers in the biosynthethic route to coloured carotenoids is well established (Volume 3, Chapter 2). Important biological functions of (15Z)-carotenoids in photosynthesis have been revealed [2]. In relation to health aspects of carotenoids, the bioavailability of cis isomers may be higher than that of the all-trans isomer [3], and accumulated evidence suggests that cis/trans isomerization may occur in biological tissues, particularly of lycopene (31) in human serum [4] (Volume 5, Chapter 7).

  15. Theoretical Study of Isomerization and Decomposition Reactions for Methyl-nitramine

    NASA Astrophysics Data System (ADS)

    Wei, Wen-mei; Zheng, Ren-hui; Tian, Yan; He, Tian-jing; He, Li; Chen, Dong-ming; Liu, Fan-chen

    2007-04-01

    The complex potential energy surface and reaction mechanisms for the unimolecular isomerization and decomposition of methyl-nitramine (CH3NHNO2) were theoretically probed at the QCISD(T)/6-311+Gast//B3LYP/6-311+Gast level of theory. The results demonstrated that there are four low-lying energy channels: (i) the N-N bond fission pathway; (ii) a sequence of isomerization reactions via CH3NN(OH)O; (IS2a); (iii) the HONO elimination pathway; (iv) the isomerization and the dissociation reactions via CH3NHONO (IS3). The rate constants of each initial step (rate-determining step) for these channels were calculated using the canonical transition state theory. The Arrhenius expressions of the channels over the temperature range 298-2000 K are k6(T)=1014.8e-46.0/RT, k7(T)=1013.7e-42.1/RT, k8(T)=1013.6e-51.8/RT and k9(T)=1015.6e-54.3/RT s-1, respectively. The calculated overall rate constants is 6.9×10-4 at 543 K, which is in good agreement with the experimental data. Based on the analysis of the rate constants, the dominant pathway is the isomerization reaction to form CH3NN(OH)O at low temperatures, while the N-N bond fission and the isomerization reaction to produce CH3NHONO are expected to be competitive with the isomerization reaction to form CH3NN(OH)O at high temperatures.

  16. Isomerization of one molecule observed through tip enhanced Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Yanxing; Lee, Joonhee; Apkarian, Vartkess A.; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Joonhee Lee, Vartkess A. Apkarian Team

    While exploring photoisomerization of azobenzyl thiols (ABT) adsorbed on Au(111), through joint scanning tunneling microscopy (STM) and tip-enhanced Raman scattering (TERS) studies, the reversible photoisomerization of one molecule is captured in TERS trajectories. The apparently heterogeneously photo-catalyzed reaction is assigned to cis-trans isomerization of an outlier, which is chemisorbed on the silver tip of the STM. In order to clarify the role of the silver tip of the STM, we perform systematic density functional theory (DFT) calculations. The results show that compared with the case on the flat Ag(111) surface, the energy difference between trans and cis states of ABT decrease as we add one silver atom or a tetrahedron silver cluster on Ag(111) surface which mimic the geometry of a silver tip. In particular, the trans stretches away from the surface on the tetrahedral silver cluster, and the energy difference between trans and cis decreases to 0.27 eV, from ~1 eV for ABT on the flat Ag(111) surface. This significantly increases the possibility of cis-trans isomerization, as observed in our experiments. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  17. Confirmed Assignments of Isomeric Dimethylbenzyl Radicals Generated by Corona Discharge

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Lee, Sang Kuk

    2012-06-01

    Polymethylbenzyl radicals, multi-methyl-substituted benzyl radicals, have been believed to be an ideal model for understanding the torsional effect of methyl group and substitution effect on electronic transition. These radicals are mainly generated from polymethylbenzenes by electric discharge for spectroscopic observation. However, the existence of several methyl groups on the benzene ring may produce several isomeric polymethylbenzyl radicals by removing one of the C-H bonds of each methyl group at different substitution position, which makes the assignment of spectrum ambiguous. In this work, the controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By using corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of precursors 1,2,3- and 1,2,4-trimethylbenzenes. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion using a pinhole-type glass nozzle, we revised previous assignments of the 2,6- and 2,3-dimethylbenzyl radicals as well as the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. In addition, spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of precursors.

  18. Connectivity matters - ultrafast isomerization dynamics of bisazobenzene photoswitches.

    PubMed

    Slavov, Chavdar; Yang, Chong; Schweighauser, Luca; Boumrifak, Chokri; Dreuw, Andreas; Wegner, Hermann A; Wachtveitl, Josef

    2016-06-01

    We have investigated the ultrafast dynamics of o-, m- and p-bisazobenzenes, which represent elementary building blocks for photoswitchable multiazobenzene nanostructures. The connectivity pattern within bisazobenzenes and the ensuing complex interactions between the individual azobenzene units determines the ultrafast dynamics of these compounds and their photochemical properties. While retaining a relatively high E → Z isomerization quantum yield, o-bisazobenzene exhibits a very high thermal relaxation rate (half-life of 1.6 ms). Our theoretical calculations reveal that the geometry allows intramolecular excitonic interaction between the azobenzene units, which is reflected in the femtosecond transient absorption data via the simultaneous bleaching of the two excitonic bands. In contrast, the properties of m-bisazobenzene are very similar to the monomeric azobenzene, with the two units acting nearly independently from each other. The highest degree of π conjugation extending over the two azobenzene units was observed for p-bisazobenzene, which results in strong planarity of the molecule, reduced excited state lifetime and relatively low isomerization quantum yield. Multiphotochromic systems bridge the gap between molecular photoswitches and macroscopic function and thus, understanding the properties of bisazobenzenes opens the way to the design and development of new structures with extensive and versatile applications. PMID:26996604

  19. Isomerization of C[sub 4] alkenes

    DOEpatents

    Smith, L.A. Jr.

    1984-11-13

    A method is described for isomerizing isobutene or n-butene to produce a mixture of isobutene and normal butene, and polymerizing at least a portion thereof to produce isobutene/n-butene co-dimer, which comprises feeding at least 80 weight % of either the isobutene or n-butene to a catalytic distillation reactor containing a fixed bed acidic cation exchange resin catalyst packing which provides both the catalyst sites and distillation sites for the reaction products, isomerizing a portion of the isobutene or n-butene to produce a mixture of isobutene and n-butene and reacting at least a portion of the isobutene and n-butene to form co-dimer of isobutene and n-butene, whereby an overhead fraction containing any unreacted isobutene and n-butene and a bottoms fraction containing co-dimer is produced. The result of the reaction is substantially the same regardless whether the feed is isobutene or n-butene. Other aspects of the invention, include combinations of procedures to produce high purity isobutene and n-butene. Either isobutene or n-butene product (depending on the desired product) can be recycled as feed, thus substantially carrying out the isomerization to extinction and total conversion to the desired product. 1 fig.

  20. Isomerization of C.sub.4 alkenes

    DOEpatents

    Smith, Jr., Lawrence A.

    1984-01-01

    A method for isomerizing isobutene or n-butene to produce a mixture of isobutene and normal butene, and polymerizing at least a portion thereof to produce isobutene/n-butene codimer, which comprieses feeding at least 80 weight % of either the isobutene or n-butene to a catalytic distillation reactor containing a fixed bed acidic cation exchange resin catalyst packing which provides both the catalyst sites and distillation sites for the reaction products, isomerizing a portion of the isobutene or n-butene to produce a mixture of isobutene and n-butene and reacting at least a portion of the isobutene and n-butene to form codimer of isobutene and n-butene, whereby an overhead fraction containing any unreacted isobutene and n-butene and a bottoms fraction containing codimer is produced. The result of the reaction is substantially the same regardless whether the feed is isobutene or n-butene. Other aspects of the invention, include combinations of procedures to produce high purity isobutene and n-butene. Either isobutene or n-butene product (depending on the desired product) can be recycled as feed, thus substantially carrying out the isomerization to extinction and total conversion to the desired product.

  1. Kinematic effects associated with molecular frames in structural isomerization dynamics of clusters

    NASA Astrophysics Data System (ADS)

    Yanao, Tomohiro; Takatsuka, Kazuo

    2004-05-01

    Kinematic effects associated with movements of molecular frames, which specify instantaneous orientation of molecules, is investigated in structural isomerization dynamics of a triatomic cluster whose total angular momentum is zero. The principal-axis frame is employed to introduce the so-called principal-axis hyperspherical coordinates, with which the mechanism of structural isomerization dynamics of the cluster is systematically analyzed. A force called "democratic centrifugal force" is extracted from the associated kinematics. This force arises from an intrinsic non-Euclidean metric in the internal space and has an effect of distorting the triatomic cluster to a collapsed shape and of trapping the system around collinear transition states. The latter effect is particularly important in that the kinematics effectively makes a basin at the saddle (transition state) on the potential surface. Based on this framework, we study the effect of the gauge field associated with the Eckart frame in internal space, which has not been carefully examined in the conventional reaction rate theories. Numerical comparison between the dynamics with and without the gauge field has revealed that this field has an effect to suppress the rate of isomerization reaction to a considerable amount. Thus a theory neglecting this effect will significantly overestimate the rate of isomerization. We show the physical origin of this suppressing effect.

  2. Photochromic ruthenium sulfoxide complexes: evidence for isomerization through a conical intersection.

    PubMed

    McClure, Beth Anne; Mockus, Nicholas V; Butcher, Dennis P; Lutterman, Daniel A; Turro, Claudia; Petersen, Jeffrey L; Rack, Jeffrey J

    2009-09-01

    The complexes [Ru(bpy)(2)(OS)](PF(6)) and [Ru(bpy)(2)(OSO)](PF(6)), where bpy is 2,2'-bipyridine, OS is 2-methylthiobenzoate, and OSO is 2-methylsulfinylbenzoate, have been studied. The electrochemical and photochemical reactivity of [Ru(bpy)(2)(OSO)](+) is consistent with an isomerization of the bound sulfoxide from S-bonded (S-) to O-bonded (O-) following irradiation or electrochemical oxidation. Charge transfer excitation of [Ru(bpy)(2)(OSO)](+) in MeOH results in the appearance of two new metal-to-ligand charge transfer (MLCT) maxima at 355 and 496 nm, while the peak at 396 nm diminishes in intensity. The isomerization is reversible at room temperature in alcohol or propylene carbonate solution. In the absence of light, solutions of O-[Ru(bpy)(2)(OSO)](+) revert to S-[Ru(bpy)(2)(OSO)](+). Kinetic analysis reveals a biexponential decay with rate constants of 5.66(3) x 10(-4) s(-1) and 3.1(1) x 10(-5) s(-1). Cyclic voltammograms of S-[Ru(bpy)(2)(OSO)](+) are consistent with electron-transfer-triggered isomerization of the sulfoxide. Analysis of these voltammograms reveal E(S)(o)' = 0.86 V and E(O)(o)' = 0.49 V versus Ag/Ag(+) for the S- and O-bonded Ru(3+/2+) couples, respectively, in propylene carbonate. We found k(S-->O) = 0.090(15) s(-1) in propylene carbonate and k(S-->O) = 0.11(3) s(-1) in acetonitrile on Ru(III), which is considerably slower than has been reported for other sulfoxide isomerizations on ruthenium polypyridyl complexes following oxidation. The photoisomerization quantum yield (Phi(S-->O) = 0.45, methanol) is quite large, indicating a rapid excited state isomerization rate constant. The kinetic trace at 500 nm is monoexponential with tau = 150 ps, which is assigned to the excited S-->O isomerization rate. There is no spectroscopic or kinetic evidence for an O-bonded (3)MLCT excited state in the spectral evolution of S-[Ru(bpy)(2)(OSO)](+) to O-[Ru(bpy)(2)(OSO)](+). Thus, isomerization occurs nonadiabatically from an S-bonded (or eta(2

  3. Chemical Kinetic Analysis of Thermal Decay of Rhodopsin Reveals Unusual Energetics of Thermal Isomerization and Hydrolysis of Schiff Base*

    PubMed Central

    Liu, Jian; Liu, Monica Yun; Fu, Li; Zhu, Gefei Alex; Yan, Elsa C. Y.

    2011-01-01

    The thermal properties of rhodopsin, which set the threshold of our vision, have long been investigated, but the chemical kinetics of the thermal decay of rhodopsin has not been revealed in detail. To understand thermal decay quantitatively, we propose a kinetic model consisting of two pathways: 1) thermal isomerization of 11-cis-retinal followed by hydrolysis of Schiff base (SB) and 2) hydrolysis of SB in dark state rhodopsin followed by opsin-catalyzed isomerization of free 11-cis-retinal. We solve the kinetic model mathematically and use it to analyze kinetic data from four experiments that we designed to assay thermal decay, isomerization, hydrolysis of SB using dark state rhodopsin, and hydrolysis of SB using photoactivated rhodopsin. We apply the model to WT rhodopsin and E181Q and S186A mutants at 55 °C, as well as WT rhodopsin in H2O and D2O at 59 °C. The results show that the hydrogen-bonding network strongly restrains thermal isomerization but is less important in opsin and activated rhodopsin. Furthermore, the ability to obtain individual rate constants allows comparison of thermal processes under various conditions. Our kinetic model and experiments reveal two unusual energetic properties: the steep temperature dependence of the rates of thermal isomerization and SB hydrolysis in the dark state and a strong deuterium isotope effect on dark state SB hydrolysis. These findings can be applied to study pathogenic rhodopsin mutants and other visual pigments. PMID:21921035

  4. Dynamics of radiation induced isomerization for HCN-CNH

    SciTech Connect

    Na, Kyungsun; Jung, Christof; Reichl, L. E.

    2006-07-21

    We have analyzed the dynamics underlying the use of sequential radiation pulses to control the isomerization between the HCN and the CNH molecules. The appearance of avoided crossings among Floquet eigenphases as the molecule interacts with the radiation pulses is the key to understanding the isomerization dynamics, both in the adiabatic and nonadiabatic regimes. We find that small detunings of the incident pulses can have a significant effect on the outcome of the isomerization process for the model we consider.

  5. Methods for suppressing isomerization of olefin metathesis products

    SciTech Connect

    Firth, Bruce E.; Kirk, Sharon E.; Gavaskar, Vasudeo S.

    2015-09-22

    A method for suppressing isomerization of an olefin metathesis product produced in a metathesis reaction includes adding an isomerization suppression agent to a mixture that includes the olefin metathesis product and residual metathesis catalyst from the metathesis reaction under conditions that are sufficient to passivate at least a portion of the residual metathesis catalyst. The isomerization suppression agent is phosphorous acid, a phosphorous acid ester, phosphinic acid, a phosphinic acid ester or combinations thereof. Methods of refining natural oils are described.

  6. Amine-Catalyzed Isomerization of Diethylmaleate to Diethylfumarate.

    ERIC Educational Resources Information Center

    Glover, Irving T.; And Others

    1978-01-01

    This reaction is used in an introductory organic chemistry course to illustrate principles of gas-liquid chromatography, geometrical isomerism, homogeneous catalysis, and activation energy determinations. (BB)

  7. Confirmed assignments of isomeric dimethylbenzyl radicals generated by corona discharge.

    PubMed

    Yoon, Young Wook; Lee, Sang Kuk

    2011-12-01

    The controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By employing corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of 1,2,4-trimethylbenzene. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion, we revised previous assignments of the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. Spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of 1,2,4-trimethylbenzene. PMID:22149790

  8. A comparison of tunneling transfer theories for asymmetric isomerization reactions

    NASA Astrophysics Data System (ADS)

    Cribb, Peter H.; Nordholm, Sture; Hush, N. S.

    1982-08-01

    In this paper, we discuss the basis of the transition state/trasmission coefficient theory of tunneling contributions to the rate of isomerization reactions. This theory, which is currently widely used, is found to deviate both quantitatively and qualitatively from an alternative theory, we have developed on the basis of a more rigorous interpretation of the reaction mechanism in accord with the original suggestion of Lindermann. We focus attention on the discrepancies which arise when there is asymmetry between the reactant and product potential wells. Comparative calculations are reported for a model potential advanced on the basis of spectroscopic measurements to represent the level spectrum associated with the ring- puckering motion in azetidine. Large differences are shown to exist between the predictions of the two types of theories.

  9. The gating isomerization of neuromuscular acetylcholine receptors

    PubMed Central

    Auerbach, Anthony

    2010-01-01

    Acetylcholine receptor-channels are allosteric proteins that isomerize (‘gate’) between conformations that have a low vs. high affinity for the transmitter and conductance for ions. In order to comprehend the mechanism by which the affinity and conductance changes are linked it is of value to know the magnitude, timing and distribution of energy flowing through the system. Knowing both the di- and unliganded gating equilibrium constants (E2 and E0) is a foundation for understanding the AChR gating mechanism and for engineering both the ligand and the protein to operate in predictable ways. In adult mouse neuromuscular receptors activated by acetylcholine, E2= 28 and E0≈ 6.5 × 10−7. At each (equivalent) transmitter binding site acetylcholine provides ∼5.2 kcal mol−1 to motivate the isomerization. The partial agonist choline provides ∼3.3 kcal mol−1. The relative time of a residue's gating energy change is revealed by the slope of its rate–equilibrium constant relationship. A map of this parameter suggests that energy propagates as a conformational cascade between the transmitter binding sites and the gate region. Although gating energy changes are widespread throughout the protein, some residues are particularly sensitive to perturbations. Several specific proposals for the structural events that comprise the gating conformational cascade are discussed. PMID:19933754

  10. Acid-Catalyzed Isomerization of Carvone to Carvacrol

    ERIC Educational Resources Information Center

    Kjonaas, Richard A.; Mattingly, Shawn P.

    2005-01-01

    The acid-catalyzed isomerization of carvone to carvacrol, first reported by Ritter and Ginsburg, is especially well suited with a permanent-magnet FT instrument. The acid-catalyzed isomerization of carvone to carvacrol produced a 61% yield after a three hour reflux with 30% aqueous sulfuric acid.

  11. Modification of isomerization activity and selectivity over sulfated zirconia catalysts

    SciTech Connect

    Soled, S.L.; Iglesia, E.; Kramer, G.M.; McVicker, G.B.

    1993-12-31

    The family of anion-modified oxide strong solid acid catalysts (oxides of Zr, Ti, Sn, or Fe, modified with sulfate) that have been recently reported in the literature were examined for the isomerization of C{sub 5}-C{sub 8} n-paraffins. Isomerization of C{sub 7+} feeds on conventional solid and liquid acids leads to extensive cracking; in particular, paraffins with seven or more carbon atoms are known to undergo acid cracking to undesirable light gases during isomerization over acid catalysts; thus, commercial isomerization practice is limited to C{sub 4}-C{sub 6} feeds. Cracking occurs because isobutane and propane are excellent leaving groups in carbonium ion rearrangements. Since both isomerization and cracking occur on strong acid sites it has been difficult to control one at the expense of the other. The authors have observed that low levels of that low levels of adamantane, a hydride transfer agent, added to a heptane or octain feed will double the isomerization rate while dramatically limiting cracking reactions. The adamantane enhances the rate determining hydride transfer step and limits the surface residence time of carbocation intermediates. This behavior contrasts with that of aromatic addition where poisoning of strong acid sites inhibits cracking but dramatically decreases the isomerization rate. This paper will suggest a mechanism that involves a nonfunctional acid catalyzed chain mechanism proceeding through intermolecular hydride transfer reactions. Finally we will discuss the remaining issues in obtaining a viable C{sub 7}+ isomerization process.

  12. Proton NMR characterization of isomeric sulfmyoglobins: preparation, interconversion, reactivity patterns, and structural features

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Kauten, R.J.

    1987-11-03

    The preparations of sulfmyoglobin (sulf-Mb) by standard procedures have been found heterogeneous by /sup 1/H NMR spectroscopy. Presented here are the results of a comprehensive study of the factors that influence the selection among the three dominant isomeric forms of sperm whale sulf-Mb and their resulting detailed optical and /sup 1/H NMR properties as related to their detectability and structural properties of the heme pocket. A single isomer is formed initially in the deoxy state; further treatment in any desired oxidation/ligation state can yield two other major isomers. Acid catalysis and chromatography facilitate formation of a second isomer, particularly in the high-spin state. At neutral pH, a third isomer is formed by a first-order process. The processes that alter oxidation/ligation state are found to be reversible and are judged to affect only the metal center, but the three isomeric sulf-Mbs are found to exhibit significantly different ligand affinity and chemical stability. The present results allow, for the first time, a rational approach for preparing a given isomeric sulf-Mb in an optimally pure state for subsequent characterization by other techniques. While optical spectroscopy can distinguish the alkaline forms, only /sup 1/H NMR clearly distinguishes all three ferric isomers. The hyperfine shift patterns in the various oxidation/spin states of sulf-Mbs indicate relatively small structural alteration, and the proximal and distal sides of the heme suggest that peripheral electronic effects are responsible for the differentially reduced ligand affinities for the three isomeric sulf-Mbs. The first /sup 1/H NMR spectra of sulfhemoglobins are presented, which indicate a structure similar to that of the initially formed sulf-Mb isomer but also suggest the presence of a similar molecular heterogeneity as found for sulf-Mb, albiet to a smaller extent.

  13. The mechanism for iron-catalyzed alkene isomerization in solution

    SciTech Connect

    Sawyer, Karma R.; Glascoe, Elizabeth A.; Cahoon, James F.; Schlegel, Jacob P.; Harris, Charles B.

    2008-05-27

    Here we report nano- through microsecond time-resolved IR experiments of iron-catalyzed alkene isomerization in room-temperature solution. We have monitored the photochemistry of a model system, Fe(CO){sub 4}({eta}{sup 2}-1-hexene), in neat 1-hexene solution. UV-photolysis of the starting material leads to the dissociation of a single CO to form Fe(CO){sub 3}({eta}{sup 2}-1-hexene), in a singlet spin state. This CO loss complex shows a dramatic selectivity to form an allyl hydride, HFe(CO){sub 3}({eta}{sup 3}-C{sub 6}H{sub 11}), via an internal C-H bond-cleavage reaction in 5-25 ns. We find no evidence for the coordination of an alkene molecule from the bath to the CO loss complex, but do observe coordination to the allyl hydride, indicating that it is the key intermediate in the isomerization mechanism. Coordination of the alkene ligand to the allyl hydride leads to the formation of the bis-alkene isomers, Fe(CO){sub 3}({eta}{sup 2}-1-hexene)({eta}{sup 2}-2-hexene) and Fe(CO){sub 3}({eta}{sup 2}-1-hexene){sub 2}. Because of the thermodynamic stability of Fe(CO){sub 3}({eta}{sup 2}-1-hexene)({eta}{sup 2}-2-hexene) over Fe(CO){sub 3}({eta}{sup 2}-1-hexene){sub 2} (ca. 12 kcal/mol), nearly 100% of the alkene population will be 2-alkene. The results presented herein provide the first direct evidence for this mechanism in solution and suggest modifications to the currently accepted mechanism.

  14. Cavity Ringdown Spectroscopy and Kinetics of Butoxy Isomerization: Detection of the {A}- {XCAVITY Ringdown Spectroscopy and Kinetics of Butoxy Isomerization: Detection of the {A}- {X

    NASA Astrophysics Data System (ADS)

    Sprague, Matthew K.; Okumura, Mitchio; Sander, Stanley P.

    2011-06-01

    Alkoxy radicals are atmospherically important species, playing a direct role in the HO_x and NO_x cycles that affect tropospheric air pollution. Alkoxy radicals that can form a six membered transition state can isomerize into a hydroxyalkyl radical. In the presence of O_2, a rapid association reaction occurs, forming a hydroxyalkylperoxy radical. The n-butoxy radical is the smallest alkoxy to undergo isomerization, forming the γ-hydroxybutylperoxy radical (HOC_4H_8OO). Direct detection of HOC_4H_8OO opens the door to measuring alkoxy reaction kinetics with higher precision than previous end product studies. In this talk, we report the first detection of the tilde{A}-tilde{X} electronic spectrum of the HOC_4H_8OO radical. The spectrum is similar in shape to the tilde{A}-tilde{X} spectrum of n-butyl peroxy: a broad spectroscopic band due to the multiple molecular conformers that are present. We also use the tilde{A}-tilde{X} band to measure the alkoxy isomerization kinetics relative to the alkoxy radical's reaction with O_2, similar to the previous kinetics studies. R. Atkinson, D. L. Baulch, R. A. Cox, J. N. Crowley, R. F. Hampson, R. G. Hynes, M. E. Jenkin, M. J. Rossi, and J. Troe J. Atmos. Chem. and Phys. 2006, 6, 3625. B. G. Glover and T. A. Miller. J. Phys. Chem. A 2005, 109, 11191.

  15. Ultrafast deactivation of bilirubin: dark intermediates and two-photon isomerization.

    PubMed

    Carreira-Blanco, Carlos; Singer, Patrick; Diller, Rolf; Luis Pérez Lustres, J

    2016-03-01

    Bilirubin is a neurotoxic product responsible for neonatal jaundice, which is generally treated by phototherapy. The photoreaction involves ultrafast internal conversion via an elusive intermediate and Z-E isomerization with minor yield (less than 3% in solution). The structure of the intermediate remains unclear. Here, the combination of UV-vis and mid-IR ultrafast transient absorption spectroscopy reports a comprehensive picture of the mechanism and provides essential structural information about the intermediate species. Thus, spectral dynamics during the earliest ps unveils a wavepacket travelling from the Franck-Condon region to the crossing point with a dark state. The latter shows a tighter molecular skeleton than the ground state and decays with 15 ps time constant. Remarkably, the relative contribution of a non-decaying component increases linearly with pump energy, suggesting that Z-E isomerization could also be triggered by two-photon excitation. Implications for the photochemistry of protein-bound open tetrapyrroles are discussed. PMID:26887629

  16. A comprehensive study of isomerization and protonation reactions in the photocycle of the photoactive yellow protein.

    PubMed

    Wei, Lili; Wang, Hongjuan; Chen, Xuebo; Fang, Weihai; Wang, Haobin

    2014-12-14

    The light-activated photoactive yellow protein (PYP) chromophore uses a series of reactions to trigger photo-motility and biological responses, and generate a wide range of structural signals. To provide a comprehensive mechanism of the overall process at the atomic level, we apply a CASPT2//CASSCF/AMBER QM/MM protocol to investigate the relaxation pathways for a variety of possible isomerization and proton transfer reactions upon photoexcitation of the wild-type PYP. The nonadiabatic relay through an S1/S0 conical intersection [CI(S1/S0)] is found to play a decisive major role in bifurcating the excited state relaxation into a complete and short photocycle. Two major and one minor deactivation channels were found starting from the CI(S1/S0)-like intermediate IT, producing the cis isomers pR1, ICP, and ICT through "hula twist", "bicycle pedal" and one-bond flip isomerization reactions. The overall photocycle can be achieved by competitive parallel/sequential reactions, in which the ground state recovery is controlled by a series of slow volume-conserving bicycle pedal/hula twist and one-bond flip isomerization reactions, as well as fast protonation-deprotonation processes and the hydrophobic-hydrophilic state transformation. PMID:25195953

  17. Roaming-mediated isomerization in the photodissociation of nitrobenzene

    NASA Astrophysics Data System (ADS)

    Hause, Michael L.; Herath, Nuradhika; Zhu, Rongshun; Lin, M. C.; Suits, Arthur G.

    2011-12-01

    Roaming reactions comprise a new class of reaction in which a molecule undergoes frustrated dissociation to radicals, followed by an intramolecular abstraction reaction. Nitro compounds have long been known to dissociate to give NO as a major product. However, rates based upon isomerization via calculated tight transition states are implausibly slow, so the key dissociation pathway for this important class of molecules remains obscure. Here, we present an imaging study of the photodissociation of nitrobenzene with state-specific detection of the resulting NO products. We observe a bimodal translational energy distribution in which the slow products are formed with low NO rotational excitation, and the fast component is associated with high rotational excitation. High-level ab initio calculations identified a ‘roaming-type’ saddle point on the ground state. Branching ratio calculations then show that thermal dissociation of nitrobenzene is dominated by ‘roaming-mediated isomerization’ to phenyl nitrite, which subsequently decomposes to give C6H5O + NO.

  18. Results of a direct search for the thorium-229 nuclear isomeric transition

    NASA Astrophysics Data System (ADS)

    Schneider, Christian; Jeet, Justin; Sullivan, Scott T.; Rellergert, Wade G.; Mirzadeh, Saed; Cassanho, A.; Jenssen, H. P.; Tkalya, Eugene V.; Hudson, Eric R.

    2015-05-01

    The nucleus of thorium-229 has an exceptionally low-energy isomeric transition in the vacuum-ultraviolet spectrum around 7 . 8 +/- 0 . 5 eV. The prospects of a laser-accessible nuclear transition are manifold but require spectroscopically resolving the transition. Our approach is a direct search using thorium-doped crystals as samples and exciting the isomeric state with vacuum-ultraviolet synchrotron radiation. In a recent experiment, we were able to search for the transition at the Advanced Light Source synchrotron, LBNL, between 7 . 3 eV and 8 . 8 eV. We found no evidence for the transition within a lifetime range of 1-2s to 2000-5600s. This result excludes large parts of the theoretically expected region. We conclude reporting on our efforts of a search using laser-generated vacuum-ultraviolet light.

  19. Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

    PubMed Central

    Florean, Andrei C.; Cardoza, David; White, James L.; Lanyi, J. K.; Sension, Roseanne J.; Bucksbaum, Philip H.

    2009-01-01

    A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 × 1016 photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration. PMID:19564608

  20. Theoretical study on the mechanism of iron carbonyls mediated isomerization of allylic alcohols to saturated carbonyls.

    PubMed

    Branchadell, Vicenç; Crévisy, Christophe; Grée, René

    2003-05-01

    The conversion of allylic alcohols to enols mediated by Fe(CO)(3) has been studied through density functional theoretical calculations. From the results obtained a complete catalytic cycle has been proposed in which the first intermediate is the [(allyl alcohol)Fe(CO)(3)] complex. This intermediate evolves to the [(enol)Fe(CO)(3)] complex through two consecutive 1,3-hydrogen shifts involving a pi-allyl hydride intermediate. The highest Gibbs energy transition state corresponds to the partial decoordination ot the enol ligand prior to the coordination of a new allyl alcohol molecule that regenerates the first intermediate. Alternative processes for the [(enol)Fe(CO)(3)] complex such as [Fe(CO)(3)]-mediated enol-aldehyde transformation and enol isomerization have also been considered. The results obtained show that the former process is unfavourable, whereas the enol isomerization may compete with the enol decoordination step of the catalytic cycle. PMID:12740854

  1. Photo-induced isomerization and chemical reaction dynamics in superfluid helium droplets

    NASA Astrophysics Data System (ADS)

    Merritt, Jeremy; Douberly, Gary; Miller, Roger

    2008-03-01

    Near threshold photo-induced isomerization and photo-induced chemical reactions have long been sough after as sensitive probes of the underlying potential energy surface. One of the most important questions asked is how the initially bright quantum state couples to the reaction coordinate, and thus relates to energy transfer in general. Helium droplets have now allowed us to stabilize entrance channel clusters behind very small reaction barriers such that vibrational excitation may result in reaction. Through two examples, namely the isomerization of the 2 binary complexes of HF-HCN Douberly et al. PCCP 2005, 7,463, and the induced reaction of the gallium-HCN complex Merritt et al. JPCA 2007, DOI:10.1021/jp074981e we will show how the branching ratios for reaction and predissociation can determined and the influence of the superfluid He solvent.

  2. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation

    SciTech Connect

    Schwartz, B.J.

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in {approximately}240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH{sub 2}I{sub 2} and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a {approximately}350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  3. Spectroscopic Identification of Isomeric Trimethylbenzyl Radicals Generated in Corona Discharge of Tetramethylbenzene

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Lee, Sang Kuk; Lee, Gi Woo

    2011-06-01

    The visible vibronic emission spectra were recorded from the corona discharge of precursor tetramethylbenzene with a large amount of inert carrier gas helium using a pinhole-type glass nozzle coupled with corona excited supersonic expansion (CESE) well developed in this laboratory. The spectra showed a series of vibronic bands in the D_1 → D_0 electronic transition of jet-cooled benzyl-type radicals formed from the precursor in a corona excitation. The analysis confirmed that two isomeric radicals, 2,3,4- and 2,3,6-trimethylbenzyl radicals and three isomeric radicals, 3,4,5-, 2,3,5- and 2,4,6-trimethylbenzyl radicals were produced, respectively, from 1,2,3,4- and 1,2,3,5-tetramethylbenzenes as a result of removal of a hydrogen atom from the methyl group at different substitution position. For each isomeric trimethylbenzyl radical generated in the corona discharge of precursor, the electronic transition and a few vibrational mode frequencies were determined in the ground electronic state by comparing with those from both ab initio calculations and the known vibrational data of the precursor. The substitution effect that states the shift of electronic transition depends on the nature, the number, and the position of substituents on the ring has been qualitatively proved for the case of benzyl-type radicals.

  4. Influence of the octupole mode on nuclear high-K isomeric properties

    NASA Astrophysics Data System (ADS)

    Minkov, Nikolay; Walker, Phil

    2014-05-01

    The influence of quadrupole-octupole deformations on the energy and magnetic properties of high-K isomeric states in even-even actinide (U, Pu, Cm, Fm, No), rare-earth (Nd, Sm and Gd), and superheavy (^{270}\\text{Ds}) nuclei is examined within a deformed shell model with pairing interaction. The neutron two-quasiparticle (2qp) isomeric energies and magnetic dipole moments are calculated over a wide range in the plane of quadrupole and octupole deformations. In most cases the magnetic moments exhibit a pronounced sensitivity to the octupole deformation. At the same time, the calculations outline three different groups of nuclei: with pronounced, shallow, and missing minima in the 2qp energy surfaces with respect to the octupole deformation. The result indicates regions of nuclei with octupole softness as well as with possible octupole deformation in the high-K isomeric states. These findings show the need for further theoretical analysis as well as of detailed experimental measurements of magnetic moments in heavy deformed nuclei.

  5. Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis.

    PubMed

    Yamamoto, Tsuyoshi; Tsunematsu, Yuta; Hara, Kodai; Suzuki, Tomohiro; Kishimoto, Shinji; Kawagishi, Hirokazu; Noguchi, Hiroshi; Hashimoto, Hiroshi; Tang, Yi; Hotta, Kinya; Watanabe, Kenji

    2016-05-17

    Geometric isomerization can expand the scope of biological activities of natural products. The observed chemical diversity among the pseurotin-type fungal secondary metabolites is in part generated by a trans to cis isomerization of an olefin. In vitro characterizations of pseurotin biosynthetic enzymes revealed that the glutathione S-transferase PsoE requires participation of the bifunctional C-methyltransferase/epoxidase PsoF to complete the trans to cis isomerization of the pathway intermediate presynerazol. The crystal structure of the PsoE/glutathione/presynerazol complex indicated stereospecific glutathione-presynerazol conjugate formation is the principal function of PsoE. Moreover, PsoF was identified to have an additional, unexpected oxidative isomerase activity, thus making it a trifunctional enzyme which is key to the complexity generation in pseurotin biosynthesis. Through the study, we identified a novel mechanism of accomplishing a seemingly simple trans to cis isomerization reaction. PMID:27072782

  6. Photochromism of isomeric diarylethenes with a methylpyridine substituent

    NASA Astrophysics Data System (ADS)

    Sun, Fengxia; Cui, Shiqiang; Liu, Gang; Zheng, Chunhong; Pu, Shouzhi

    2015-04-01

    Two new isomeric photochromic diarylethenes with a methylpyridine unit have been synthesized and their structures have been determined by single-crystal X-ray diffraction analysis. Both diarylethenes exhibited photochromism in both solution and PMMA films. In the single crystalline phase, the two isomeric compounds displayed different photochromism based on their various molecular conformations. In addition, their fluorescent properties are also diverse due to the distinct substitution position of the methyl group on the terminal pyridine.

  7. Methods for suppressing isomerization of olefin metathesis products

    SciTech Connect

    Firth, Bruce E.; Kirk, Sharon E.

    2015-10-27

    A method for suppressing isomerization of an olefin metathesis product produced in a metathesis reaction includes adding an isomerization suppression agent that includes nitric acid to a mixture that includes the olefin metathesis product and residual metathesis catalyst from the metathesis reaction under conditions that are sufficient to passivate at least a portion of the residual metathesis catalyst. Methods of refining a natural oil are described.

  8. Discussion of isomeric ratios in (p, n) and (d, 2 n) reaction

    NASA Astrophysics Data System (ADS)

    Bakhshiyan, T. M.

    2016-01-01

    Isomeric ratios (IR) in the (p, n) and (d, 2 n) reactions are considered. The dependence of IR values on the projectile type and energy, the target- and product-nucleus spin, the spin difference between the isomeric and ground states of products, and the product mass number is discussed. The isomeric ratios for 46 product nuclei (from 44m,gSc to 127m,gXe) obtained in reactions where target and product nuclei have identical mass numbers were calculated at energies from the reaction threshold to 50 MeV (with a step of Δ E = 1 MeV). The calculations in question were performed with the aid of the TALYS 1.4 code package. The calculated IR values were compared with their experimental counterparts available from the literature (EXFOR database). In the majority of cases, the calculated IR values agree well with the experimental data in question. It is noteworthy that the IR values obtained in (d, 2 n) reactions are substantially greater than those in (p, n) reactions.

  9. Understanding the isomerization of the HIV-1 dimerization initiation domain by the nucleocapsid protein

    PubMed Central

    Turner, Kevin B.; Hagan, Nathan A.

    2008-01-01

    The specific binding of HIV-1 nucleocapsid (NC) to the hinge region of the kissing-loop (KL) dimer formed by stemloop 1 (SL1) can have significant consequences on its ability to isomerize into the corresponding extended duplex (ED) form. The binding determinants and the effects on the isomerization process were investigated in vitro by a concerted strategy involving ad hoc RNA mutants and electrospray ionization-Fourier transform ion cyclotron resonance (ESI-FTICR) mass spectrometry, which enabled us to characterize the stoichiometry and conformational state of all possible protein-RNA and RNA-RNA assemblies present simultaneously in solution. For the first time, NC-hinge interactions were observed in constructs including at least one unpaired guanine at the 5′-end of the loop-loop duplex, whereas no interactions were detected when the unpaired guanine was placed at its 3′-end. This binding mode is supported by the presence of a grip-like motif described by recent crystal structures, which is formed by the 5′-purines of both hairpins held together by mutual stacking interactions. Using tandem mass spectrometry, hinge interactions were clearly shown to reduce the efficiency of KL/ED isomerization without inducing its complete block. This outcome is consistent with the partial stabilization of the extra-helical grip by the bound protein, which can hamper the purine components from parting ways and initiate the strand exchange process. These findings confirm that the broad binding and chaperone activities of NC induce unique effects that are clearly dependent on the structural context of the cognate nucleic acid substrate. For this reason, the presence of multiple binding sites on the different forms assumed by SL1 can produce seemingly contrasting effects that contribute to a fine modulation of the two-step process of RNA dimerization and isomerization. PMID:17466332

  10. Prolyl Isomerization as a Molecular Memory in the Allosteric Regulation of the Signal Adapter Protein c-CrkII

    PubMed Central

    Schmidpeter, Philipp A. M.; Schmid, Franz X.

    2015-01-01

    c-CrkII is a central signal adapter protein. A domain opening/closing reaction between its N- and C-terminal Src homology 3 domains (SH3N and SH3C, respectively) controls signal propagation from upstream tyrosine kinases to downstream targets. In chicken but not in human c-CrkII, opening/closing is coupled with cis/trans isomerization at Pro-238 in SH3C. Here, we used advanced double-mixing experiments and kinetic simulations to uncover dynamic domain interactions in c-CrkII and to elucidate how they are linked with cis/trans isomerization and how this regulates substrate binding to SH3N. Pro-238 trans → cis isomerization is not a simple on/off switch but converts chicken c-CrkII from a high affinity to a low affinity form. We present a double-box model that describes c-CrkII as an allosteric system consisting of an open, high affinity R state and a closed, low affinity T state. Coupling of the T-R transition with an intrinsically slow prolyl isomerization provides c-CrkII with a kinetic memory and possibly functions as a molecular attenuator during signal transduction. PMID:25488658

  11. Prolyl isomerization as a molecular memory in the allosteric regulation of the signal adapter protein c-CrkII.

    PubMed

    Schmidpeter, Philipp A M; Schmid, Franz X

    2015-01-30

    c-CrkII is a central signal adapter protein. A domain opening/closing reaction between its N- and C-terminal Src homology 3 domains (SH3N and SH3C, respectively) controls signal propagation from upstream tyrosine kinases to downstream targets. In chicken but not in human c-CrkII, opening/closing is coupled with cis/trans isomerization at Pro-238 in SH3C. Here, we used advanced double-mixing experiments and kinetic simulations to uncover dynamic domain interactions in c-CrkII and to elucidate how they are linked with cis/trans isomerization and how this regulates substrate binding to SH3N. Pro-238 trans → cis isomerization is not a simple on/off switch but converts chicken c-CrkII from a high affinity to a low affinity form. We present a double-box model that describes c-CrkII as an allosteric system consisting of an open, high affinity R state and a closed, low affinity T state. Coupling of the T-R transition with an intrinsically slow prolyl isomerization provides c-CrkII with a kinetic memory and possibly functions as a molecular attenuator during signal transduction. PMID:25488658

  12. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed. PMID:26529434

  13. Wavelength Dependent Cis-Trans Isomerization in Vision†

    PubMed Central

    Kim, Judy E.; Tauber, Michael J.; Mathies, Richard A.

    2005-01-01

    The primary event in vision is the light-driven cis-trans isomerization of the 11-cis-retinal chromophore in the G-protein coupled receptor rhodopsin. Early measurements showed that this photoisomerization has a reaction quantum yield Φ of ∼0.67 [Dartnall (1936) Proc. R. Soc. A 156, 158-170; Dartnall (1968) Vision Res. 8, 339-358] and suggested that the quantum yield was wavelength independent [Schneider (1939) Proc. Natl. Acad. Sci. U.S.A. 170, 102-112]. Here we more accurately determine Φ 500) = 0.65 ± 0.01 and reveal that Φ surprisingly depends on the wavelength of the incident light. Although there is no difference in the quantum yield between 450 and 480 nm, the quantum yield falls significantly as the photon energy is reduced below 20 000 cm-1 (500 nm). At the reddest wavelength measured (570 nm), the quantum yield is reduced by 5 ± 1% relative to the 500 nm value. These experiments correct the long-held presumption that the quantum yield in vision is wavelength independent, and support the hypothesis that the 200 fs photoisomerization reaction that initiates vision is dictated by nonstationary excited-state vibrational wave packet dynamics. PMID:11705366

  14. Wavelength dependent cis-trans isomerization in vision.

    PubMed

    Kim, J E; Tauber, M J; Mathies, R A

    2001-11-20

    The primary event in vision is the light-driven cis-trans isomerization of the 11-cis-retinal chromophore in the G-protein coupled receptor rhodopsin. Early measurements showed that this photoisomerization has a reaction quantum yield phi of approximately 0.67 [Dartnall (1936) Proc. R. Soc. A 156, 158-170; Dartnall (1968) Vision Res. 8, 339-358] and suggested that the quantum yield was wavelength independent [Schneider (1939) Proc. Natl. Acad. Sci. U.S.A. 170, 102-112]. Here we more accurately determine phi(500) = 0.65 +/- 0.01 and reveal that phi surprisingly depends on the wavelength of the incident light. Although there is no difference in the quantum yield between 450 and 480 nm, the quantum yield falls significantly as the photon energy is reduced below 20 000 cm(-1) (500 nm). At the reddest wavelength measured (570 nm), the quantum yield is reduced by 5 +/- 1% relative to the 500 nm value. These experiments correct the long-held presumption that the quantum yield in vision is wavelength independent, and support the hypothesis that the 200 fs photoisomerization reaction that initiates vision is dictated by nonstationary excited-state vibrational wave packet dynamics. PMID:11705366

  15. Iridium-Catalyzed Selective Isomerization of Primary Allylic Alcohols.

    PubMed

    Li, Houhua; Mazet, Clément

    2016-06-21

    This Account presents the development of the iridium-catalyzed isomerization of primary allylic alcohols in our laboratory over the past 8 years. Our initial interest was driven by the long-standing challenge associated with the development of a general catalyst even for the nonasymmetric version of this seemingly simple chemical transformation. The added value of the aldehyde products and the possibility to rapidly generate molecular complexity from readily accessible allylic alcohols upon a redox-economical isomerization reaction were additional sources of motivation. Certainly influenced by the success story of the related isomerization of allylic amines, most catalysts developed for the selective isomerization of allylic alcohols were focused on rhodium as a transition metal of choice. Our approach has been based on the commonly accepted precept that hydrogenation and isomerization are often competing processes, with the latter being usually suppressed in favor of the former. The cationic iridium complexes [(Cy3P)(pyridine)Ir(cod)]X developed by Crabtree (X = PF6) and Pfaltz (X = BArF) are usually considered as the most versatile catalysts for the hydrogenation of allylic alcohols. Using molecular hydrogen to generate controlled amounts of the active form of these complexes but performing the reaction in the absence of molecular hydrogen enabled deviation from the typical hydrogenation manifold and favored exclusively the isomerization of allylic alcohols into aldehydes. Isotopic labeling and crossover experiments revealed the intermolecular nature of the process. Systematic variation of the ligand on the iridium center allowed us to identify the structural features beneficial for catalytic activity. Subsequently, three generations of chiral catalysts have been investigated and enabled us to reach excellent levels of enantioselectivity for a wide range of 3,3-disubstituted aryl/alkyl and alkyl/alkyl primary allylic alcohols leading to β-chiral aldehydes. The

  16. Simulation of Photo-isomerization of Functionalized Azobenzene Derivatives

    NASA Astrophysics Data System (ADS)

    Tavazohi, Pedram; Herberger, Zachary; Lewis, James

    Photo-isomerization is the process of changing the isomer (cis , trans) of a molecule using light. In azobenzene this process can be utilized in a Metal Organic Framework (MOF) for adsorption of CO2. MOFs are created by two major components, metal ions, and organic molecules which are called linkers. The metal ions and linkers can be coordinated in a way that they form a porous material. In the cis isomer of azobenzene, the MOF's pore is available to be filled by CO2, but in the trans isomer the pore is filled with a benzene ring. The change from cis to trans will evacuate the pore if CO2 is present. The important considerations in using azobenzene photo-isomerization as a photo-switch in MOFs are, the quantum yield of the process, and the wavelength of the light which triggers photo-isomerization. By substitution of the functional groups of azobenzene and using the fewest switches surface-hopping algorithm in FIREBALL to simulate the photo-isomerization process we can tune the properties of the molecule as we desire and predict the best substitution sites for azobenzene functional groups. We studied the effects of functionalizing the molecule with OH, CH3, NH2, NO2 and COOH on isomerization quantum yield.

  17. A review of drug isomerism and its significance.

    PubMed

    Chhabra, Naveen; Aseri, Madan L; Padmanabhan, Deepak

    2013-01-01

    Isomerism finds its importance in the field of clinical pharmacology and pharmacotherapeutics, as isomers differ in their pharmacokinetic and pharmacodyanmic properties. Drug isomerism has opened a new era of drug development. Currently, knowledge of isomerism has helped us in introducing safer and more effective drug alternatives of the newer as well as existing drugs. Many existing drugs have gone chiral switch i.e., switching from racemic mixture to one of its isomers. Cetrizine to levocetrizine is one of such examples, where effective and safer drug has been made available. In this article, we have attempted to review the basic concepts of stereochemistry and chirality and their significance in pharmacotherapeutics. Various pharmacological aspects such as pharmacokinetic and pharmacodynamic variations resulting out of chirality has been discussed in detail in this article. PMID:23776834

  18. Nitric Oxide Catalysis of Diazene E/Z Isomerization.

    PubMed

    Bohle, D Scott; Rosadiuk, Kristopher A

    2015-08-01

    Nitric oxide is an efficient catalyst for the cis-trans (E/Z) isomerization of diazenes. We compare the effect of room temperature solutions bearing low concentrations of nitric oxide, nitrogen dioxide, or oxygen on the rate of cis-trans isomerization, CTI, of the alkene bond in stilbene and on the azo double bond in azobenzene, as well as in four azo derivatives as measured by UV-vis spectroscopy. These rate enhancements can be as large as 3 orders of magnitude for azobenzene in solution. A mechanism is proposed where catalysis is promoted by the interaction of the nitric oxide with the diazene nitrogen lone pairs. Density functional theory, B3LYP/6-311++g** suggests that the binding of NO to the diazene should be weak and reversible but that its NO adduct has an E/Z isomerization barrier of 7.5 kcal/mol. PMID:26200101

  19. A review of drug isomerism and its significance

    PubMed Central

    Chhabra, Naveen; Aseri, Madan L; Padmanabhan, Deepak

    2013-01-01

    Isomerism finds its importance in the field of clinical pharmacology and pharmacotherapeutics, as isomers differ in their pharmacokinetic and pharmacodyanmic properties. Drug isomerism has opened a new era of drug development. Currently, knowledge of isomerism has helped us in introducing safer and more effective drug alternatives of the newer as well as existing drugs. Many existing drugs have gone chiral switch i.e., switching from racemic mixture to one of its isomers. Cetrizine to levocetrizine is one of such examples, where effective and safer drug has been made available. In this article, we have attempted to review the basic concepts of stereochemistry and chirality and their significance in pharmacotherapeutics. Various pharmacological aspects such as pharmacokinetic and pharmacodynamic variations resulting out of chirality has been discussed in detail in this article. PMID:23776834

  20. Catalytic Isomerization of Biomass-Derived Aldoses: A Review.

    PubMed

    Delidovich, Irina; Palkovits, Regina

    2016-03-21

    Selected aldohexoses (d-glucose, d-mannose, and d-galactose) and aldopentoses (d-xylose, l-arabinose, and d-ribose) are readily available components of biopolymers. Isomerization reactions of these substances are very attractive as carbon-efficient processes to broaden the portfolio of abundant monosaccharides. This review focuses on the chemocatalytic isomerization of aldoses into the corresponding ketoses as well as epimerization of aldoses at C2. Recent advances in the fields of catalysis by bases and Lewis acids are considered. The emphasis is laid on newly uncovered catalytic systems and mechanisms of carbohydrate transformations. PMID:26948404

  1. Ethanol production from xylose by enzymic isomerization and yeast fermentation

    SciTech Connect

    Chiang, L.C.; Hsiao, H.Y.; Ueng, P.P.; Chen, L.F.; Tsao, G.T.

    1981-01-01

    Repetitive enzymic isomerization of xylose followed by yeast fermentation of xylulose, and simultaneous enzymic isomerization and yeast fermentation were proven to be methods capable of converting xylose to ethanol. The fermentation product, ethanol, xylitol, or glycerol, has little inhibitory or deactivation effect on the activity of isomerase. In a comparison of the ability of yeasts to ferment xylulose to ethanol, Schizosaccharomyces pombe was found to be superior to industrial bakers' yeast. Under optimal conditions (pH 6, temperature 30/sup 0/C), a final ethanol concentration of 6.3 wt.% was obtained from simulated hemicellulose hydrolysate using a simultaneous fermentation process. The ethanol yield was over 80% of the theoretical value.

  2. Excitation Localization/Delocalization Isomerism in a Strongly Coupled Covalent Dimer of 1,3-Diphenylisobenzofuran.

    PubMed

    Schrauben, Joel N; Akdag, Akin; Wen, Jin; Havlas, Zdenek; Ryerson, Joseph L; Smith, Millie B; Michl, Josef; Johnson, Justin C

    2016-05-26

    Two isomers of both the lowest excited singlet (S1) and triplet (T1) states of the directly para, para'-connected covalent dimer of the singlet-fission chromophore 1,3-diphenylisobenzofuran have been observed. In one isomer, excitation is delocalized over both halves of the dimer, and in the other, it is localized on one or the other half. For a covalent dimer in solution, such "excitation isomerism" is extremely rare. The vibrationally relaxed isomers do not interconvert, and their photophysical properties, including singlet fission, differ significantly. PMID:27158903

  3. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    SciTech Connect

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-12-28

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

  4. Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins

    PubMed Central

    Rinaldi, Silvia; Melaccio, Federico; Gozem, Samer; Fanelli, Francesca; Olivucci, Massimo

    2014-01-01

    Comparative modeling and ab initio multiconfigurational quantum chemistry are combined to investigate the reactivity of the human nonvisual photoreceptor melanopsin. It is found that both the thermal and photochemical isomerization of the melanopsin 11-cis retinal chromophore occur via a space-saving mechanism involving the unidirectional, counterclockwise twisting of the =C11H-C12H= moiety with respect to its Lys340-linked frame as proposed by Warshel for visual pigments [Warshel A (1976) Nature 260(5553):679–683]. A comparison with the mechanisms documented for vertebrate (bovine) and invertebrate (squid) visual photoreceptors shows that such a mechanism is not affected by the diversity of the three chromophore cavities. Despite such invariance, trajectory computations indicate that although all receptors display less than 100 fs excited state dynamics, human melanopsin decays from the excited state ∼40 fs earlier than bovine rhodopsin. Some diversity is also found in the energy barriers controlling thermal isomerization. Human melanopsin features the highest computed barrier which appears to be ∼2.5 kcal mol−1 higher than that of bovine rhodopsin. When assuming the validity of both the reaction speed/quantum yield correlation discussed by Warshel, Mathies and coworkers [Weiss RM, Warshel A (1979) J Am Chem Soc 101:6131–6133; Schoenlein RW, Peteanu LA, Mathies RA, Shank CV (1991) Science 254(5030):412–415] and of a relationship between thermal isomerization rate and thermal activation of the photocycle, melanopsin turns out to be a highly sensitive pigment consistent with the low number of melanopsin-containing cells found in the retina and with the extraretina location of melanopsin in nonmammalian vertebrates. PMID:24449866

  5. cis- and trans-Stilbenes: Chromatographic Separation and Photochemical Isomerization.

    ERIC Educational Resources Information Center

    Levine, Samuel G.; And Others

    1988-01-01

    Describes an experiment that is to be performed midway in the first semester of an undergraduate organic chemistry laboratory coinciding with the students' introduction to cis-trans isomerism in the study of alkenes. Discusses the apparatus, materials, experimental procedure, historical significance, and results. (CW)

  6. Conformational isomerization and collisional cooling dynamics of bis(2-hydroxyphenyl)methane.

    PubMed

    Pillsbury, Nathan R; Müller, Christian W; Zwier, Timothy S

    2009-04-30

    Stimulated emission pumping-population transfer spectroscopy (SEP-PTS) has been used to directly measure the energy threshold to isomerization between the two conformational isomers of bis(2-hydroxyphenyl)methane. These conformers have been shown in the preceding paper (DOI 10.1021/jp8098686) to be an OH...O H-bonded structure (conformer A) and a doubly OH() ...pi H-bonded conformer (conformer B). Lower and upper bounds on the energy threshold for A-->B isomerization are at 1344 and 1399 cm(-1), respectively, while the corresponding bounds on the B-->A isomerization are 1413 and 1467 cm(-1). The difference between these thresholds provides a measure of the relative energies of the two minima, with DeltaE(AB) = E(A) - E(B) = 14-123 cm(-1). The transition-state structure responsible for this energy threshold has been identified using DFT B3LYP, DFT M05-2X, and MP2 calculations, all with a 6-31+G* basis set. Only the DFT M05-2X calculations correctly reproduce both the energy ordering of the two minima and the magnitude of the barrier separating them. Below the energy threshold to isomerization, we have used the extensive Franck-Condon progressions present in the SEP spectrum of conformer A to undertake an SEP-PT study of its vibrational relaxation rate, as a function of internal energy over the 0-1200 cm(-1) region. The position of SEP excitation in the expansion was systematically varied in order to change the rate and number of cooling collisions that occur between SEP excitation and probe steps and the initial temperature at which SEP occurs. From this data set, three energy regimes were identified, each with a unique value of the average energy lost per collision with helium (region 1: 13 cm(-1)/collision for E = 300-1200 cm(-1), region 2: 0.6 cm(-1)/collision for E = 200-300 cm(-1), and region 3: 7 cm(-1)/collision for E < 200 cm(-1)). In region 1, the vibrational density of states is sufficient to support efficient loss of energy via Deltav = -1 collisions

  7. Femtosecond Dynamics of Fundamental Reaction Processes in Liquids: Proton Transfer, Geminate Recombination, Isomerization and Vibrational Relaxation.

    NASA Astrophysics Data System (ADS)

    Schwartz, Benjamin Joel

    Femtosecond and picosecond transient absorption spectroscopy are used to probe several fundamental aspects of chemical reactivity in the condensed phase including proton transfer, germinate recombination, isomerization and vibrational relaxation. The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured for the first time, and the effects of external hydrogen-bonding interactions on the proton transfer are studied in detail. The proton transfer takes place in ~240 fsec in non-polar environments, but becomes faster than the instrumental resolution of 110 fsec in methanol solutions. A simple model is proposed to explain these results. The dynamics following photodissociation of CH _2I_2 and other small molecules provide the first direct observations of germinate recombination. The recombination of many different photodissociating species occurs on a ~350 fsec time scale. Results also show that recombination yields but not rates depend on the molecular details of the solvent environment and suggest that recombination kinetics are dominated by a single collision with the surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. The data show no simple correlation between the hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes. This strongly implies that the isomerization of these systems does not provide a suitable testing ground for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in the photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial

  8. First spatial separation of a heavy ion isomeric beam with a multiple-reflection time-of-flight mass spectrometer

    NASA Astrophysics Data System (ADS)

    Dickel, T.; Plaß, W. R.; Ayet San Andres, S.; Ebert, J.; Geissel, H.; Haettner, E.; Hornung, C.; Miskun, I.; Pietri, S.; Purushothaman, S.; Reiter, M. P.; Rink, A.-K.; Scheidenberger, C.; Weick, H.; Dendooven, P.; Diwisch, M.; Greiner, F.; Heiße, F.; Knöbel, R.; Lippert, W.; Moore, I. D.; Pohjalainen, I.; Prochazka, A.; Ranjan, M.; Takechi, M.; Winfield, J. S.; Xu, X.

    2015-05-01

    211Po ions in the ground and isomeric states were produced via 238U projectile fragmentation at 1000 MeV/u. The 211Po ions were spatially separated in flight from the primary beam and other reaction products by the fragment separator FRS. The ions were energy-bunched, slowed-down and thermalized in a gas-filled cryogenic stopping cell (CSC). They were then extracted from the CSC and injected into a high-resolution multiple-reflection time-of-flight mass spectrometer (MR-TOF-MS). The excitation energy of the isomer and, for the first time, the isomeric-to-ground state ratio were determined from the measured mass spectrum. In the subsequent experimental step, the isomers were spatially separated from the ions in the ground state by an ion deflector and finally collected with a silicon detector for decay spectroscopy. This pioneering experimental result opens up unique perspectives for isomer-resolved studies. With this versatile experimental method new isomers with half-lives longer than a few milliseconds can be discovered and their decay properties can be measured with highest sensitivity and selectivity. These experiments can be extended to studies with isomeric beams in nuclear reactions.

  9. Lewis acid catalysis of photochemical reactions. 5. Selective isomerization of conjugated butenoic and dienoic esters

    SciTech Connect

    Lewis, F.D.; Howard, D.K.; Barancyk, S.V.; Oxman, J.D.

    1986-05-28

    The effects of Lewis and Broensted acids upon the photoisomerization reactions of several conjugated butenoic and dienoic esters have been investigated. Lewis acids inhibit the photochemical deconjugation of ..cap alpha..,..beta..- to ..beta..,..gamma..-unsaturated butenoic esters and shift the photoequilibrium between E and Z isomers toward the Z isomer. As such, irradiation of E ..cap alpha..,..beta..-unsaturated esters in the presence of EtAlCl/sub 2/ provides a convenient method for the preparation of the thermodynamically less stable Z isomer. Irradiation of methyl (E,E)-2,4-hexadienoate and methyl (E,E)-5-phenyl-2,4-pentadienoate in the absence of added catalysts results in nonselective E,Z isomerization to give mixtures of all four stereoisomers in roughly comparable yields. In the presence of the Broensted acid trifluoroacetic acid, quantitative conversion of methyl 2,4-hexadienoates to methyl 3,4-hexadienoate is observed. The acid serves as a catalyst for the thermal 1,3-hydrogen shift of an allenic enol ester formed via a photochemical 1,5-hydrogen shift of the conjugated esters. Irradiation of the ground-state complexes of the conjugated esters with the Lewis acids EtAlCl/sub 2/ or BF/sub 3/ results in selective E,Z isomerization about the ..cap alpha..,..beta..-double bond in methyl 2,4-hexadienoate and the ..gamma..,delta-double bond in methyl 5-phenyl-24-pentadienoate. The mechanistic bases for the observed effects of Lewis acids are selective excitation of the more strongly absorbing E complex and more efficient isomerization of the excited E vs. Z complex.

  10. Unveiling the mechanism of photoinduced isomerization of the photoactive yellow protein (PYP) chromophore

    SciTech Connect

    Gromov, Evgeniy V.

    2014-12-14

    A detailed theoretical analysis, based on extensive ab initio second-order approximate coupled cluster calculations, has been performed for the S{sub 1} potential energy surface (PES) of four photoactive yellow protein (PYP) chromophore derivatives that are hydrogen bonded with two water molecules and differ merely in the carbonyl substituent. The main focus is put on contrasting the isomerization properties of these four species in the S{sub 1} excited state, related to torsion around the chromophore's single and double carbon-carbon bonds. The analysis provides evidence of the different isomerization behavior of these four chromophore complexes, which relates to the difference in their carbonyl substituents. While a stable double-bond torsion pathway exists on the S{sub 1} PES of the chromophores bearing the –O–CH{sub 3} and –NH{sub 2} substituents, this is not the case for the –S–CH{sub 3} and –CH{sub 3} substituted species. The presence of the –S–CH{sub 3} group leads to a strong instability of the chromophore with respect to the single-bond twist, whereas in the case of the –CH{sub 3} substituent a crossing of the S{sub 1} and S{sub 2} PESs occurs, which perturbs the pathway. Based on this analysis, the key factors that support the double-bond torsion have been identified. These are (i) the hydrogen bonds at the phenolic oxygen of the chromophore, (ii) the weak electron-acceptor character of the carbonyl group, and (iii) the ethylene-like pattern of the torsion in the beginning of the process. Our results suggest that the interplay between these factors determines the chromophore's isomerization in the solvent environment and in the native PYP environment.

  11. A comprehensive mechanistic picture of the isomerizing alkoxycarbonylation of plant oils.

    PubMed

    Roesle, Philipp; Caporaso, Lucia; Schnitte, Manuel; Goldbach, Verena; Cavallo, Luigi; Mecking, Stefan

    2014-12-01

    Theoretical studies on the overall catalytic cycle of isomerizing alkoxycarbonylation reveal the steric congestion around the diphosphine coordinated Pd-center as decisive for selectivity and productivity. The energy profile of isomerization is flat with diphosphines of variable steric bulk, but the preference for the formation of the linear Pd-alkyl species is more pronounced with sterically demanding diphosphines. CO insertion is feasible and reversible for all Pd-alkyl species studied and only little affected by the diphosphine. The overall rate-limiting step associated with the highest energetic barrier is methanolysis of the Pd-acyl species. Considering methanolysis of the linear Pd-acyl species, whose energetic barrier is lowest within all the Pd-acyl species studied, the barrier is calculated to be lower for more congesting diphosphines. Calculations indicate that energy differences of methanolysis of the linear versus branched Pd-acyls are more pronounced for more bulky diphosphines, due to involvement of different numbers of methanol molecules in the transition state. Experimental studies under pressure reactor conditions showed a faster conversion of shorter chain olefin substrates, but virtually no effect of the double bond position within the substrate. Compared to higher olefins, ethylene carbonylation under identical conditions is much faster, likely due not just to the occurrence of reactive linear acyls exclusively but also to an intrinsically favorable insertion reactivity of the olefin. The alcoholysis reaction is slowed down for higher alcohols, evidenced by pressure reactor and NMR studies. Multiple unsaturated fatty acids were observed to form a terminal Pd-allyl species upon reaction with the catalytically active Pd-hydride species. This process and further carbonylation are slow compared to isomerizing methoxycarbonylation of monounsaturated fatty acids, but selective. PMID:25415929

  12. Combined CASSCF and MR-CI study on photoinduced dissociation and isomerization of acryloyl chloride.

    PubMed

    Cui, Gang-Long; Li, Qian-Song; Zhang, Feng; Fang, Wei-Hai; Yu, Jian-Guo

    2006-10-26

    The potential energy surfaces of isomerization and dissociation reactions for CH2CHCOCl in the S0, T1, T2, and S1 states have been mapped with DFT, CASSCF, MP2, and MR-CI calculations. Rate constants for adiabatic and nonadiabatic processes have been calculated with the RRKM rate theory, in conjugation with the vibronic interaction method. Mechanistic photochemistry of CH2CHCOCl at 230-310 nm has been characterized through the computed potential energy surfaces and rate constants. Upon photoexcitation of CH2CHCOCl at 310 nm, the S1-->T1 intersystem crossing is the dominant primary process, which is followed by the 1,3-Cl migration along the T1 pathway. Meanwhile, the S1-->S0 internal conversion occurs with considerable probability and the subsequent trans-cis isomerization proceeds in the ground state. The C-Cl bond cleavage is an exclusive primary channel upon photoexcitation of gaseous CH2CHCOCl at 230 nm. The direct C-Cl bond cleavage is partially blocked by effects of the matrix, and the internal conversion from S1 to S0 becomes an important process for the excited molecule to deactivate in the condensed phase. The present calculations not only provide a reasonable explanation of the experimental findings, but also give new insight into the mechanistic photochemistry of CH2CHCOCl. PMID:17048815

  13. Isomeric cross section of the {sup 197}Au(n,2n) reaction

    SciTech Connect

    Tsinganis, A.; Diakaki, M.; Kokkoris, M.; Mara, E.; Papadopoulos, C. T.; Vlastou, R.; Lagoyannis, A.

    2011-02-15

    In the present work, the {sup 197}Au(n,2n) reaction cross section is experimentally determined relative to the {sup 27}Al(n,{alpha}){sup 24}Na reaction at incident neutron energies of 9.0-10.5 MeV by means of the activation technique. The quasimonoenergetic fast neutron beam was produced via the {sup 2}H(d,n){sup 3}He reaction at the 5.5-MV Tandem Van de Graaff accelerator at the National Centre of Scientific Research (NCSR) ''Demokritos'' and was studied to determine the contribution of background 'parasitic' neutrons using the multiple foil activation technique and the SULSA unfolding code. The cross sections for the population of the second isomeric state (12{sup -}) of {sup 196}Au and the sum of the ground (2{sup -}) and first isomeric state (5{sup -}) population cross sections were independently determined. Auxiliary Monte Carlo simulations were performed with the MCNP code. Theoretical calculations of the above cross sections in the 8-25 MeV region were carried out with the use of the STAPRE-F, EMPIRE, and TALYS codes, which were also compared in their implementation of the generalized superfluid model. The theoretical results are compared with previous work in the same mass region, and the strong dependence on the level scheme of the nuclei involved was revealed.

  14. Taple-top imaging of the non-adiabatically driven isomerization in the acetylene cation

    NASA Astrophysics Data System (ADS)

    Beaulieu, Samuel; Ibrahim, Heide; Wales, Benji; Schmidt, Bruno E.; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T.; Wanie, Vincent; Giguere, Mathieu; Kieffer, Jean-Claude; Sanderson, Joe; Schuurman, Michael S.; Légaré, François

    2014-05-01

    One of the primary goals of modern ultrafast science is to follow nuclear and electronic evolution of molecules as they undergo a photo-chemical reaction. Most of the interesting dynamics phenomena in molecules occur when an electronically excited state is populated. When the energy difference between electronic ground and excited states is large, Free Electron Laser (FEL) and HHG-based VUV sources were, up to date, the only light sources able to efficiently initiate those non-adiabatic dynamics. We have developed a simple table-top approach to initiate those rich dynamics via multiphoton absorption. As a proof of principle, we studied the ultrafast isomerization of the acetylene cation. We have chosen this model system for isomerization since the internal conversion mechanism which leads to proton migration is still under debate since decades. Using 266 nm multiphoton absorption as a pump and 800 nm induced Coulomb Explosion as a probe, we have shoot the first high-resolution molecular movie of the non-adiabatically driven proton migration in the acetylene cation. The experimental results are in excellent agreement with high level ab initio trajectory simulations.

  15. Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study

    NASA Technical Reports Server (NTRS)

    Benjamin, Ilan; Pohorille, Andrew

    1993-01-01

    The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

  16. Performance of the major semiempirical, ab initio, and DFT methods for isomerization enthalpies of linear to branched heptanes.

    PubMed

    Rayne, Sierra; Forest, Kaya

    2016-06-01

    The gas phase standard state (298.15 K, 1 atm) isomerization enthalpy (ΔisomH°(g)) prediction performance of the major semiempirical, ab initio, and density functional levels of theory for environmentally relevant transformations was investigated using the linear to branched heptanes as a representative case study. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are well suited for investigating the thermodynamic properties of environmentally interesting isomerizations, although the M062X functional may not be appropriate for all systems. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise. PMID:26979512

  17. Femtosecond isomerization dynamics in the ethylene cation measured in an EUV-pump NIR-probe configuration

    SciTech Connect

    van Tilborg, Jeroen; Allison, Tom; Wright, Travis; Hertlein, Marc; Falcone, Roger; Liu, Yanwei; Merdji, Hamed; Belkacem, Ali

    2009-03-17

    Dynamics in the excited ethylene cation C{sub 2}H{sub 4}{sup +} lead to isomerization to the ethylidene configuration (HC-CH{sub 3}){sup +}, which is predicted to be a transient configuration for electronic relaxation. With an intense femtosecond EUV (extreme ultraviolet) pump pulse to populate the excited state, and an NIR (near infrared) probe pulse to produce the fragments CH{sup +} and CH{sub 3}{sup +} (which provides a direct signature of ethylidene), we measure optimum fragment yields at a probe delay of 80 fs. Also, an H{sub 2}-stretch transient configuration, yielding H{sub 2}{sup +} upon probing, is found to succeed the ethylidene configuration. We find that a simple single- or double-decay model does not match the data, and we present a modified model (introduction of an isomerization delay of 50 {+-} 25 fs) that does provide agreement.

  18. Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices.

    PubMed

    Justino, Licínia L G; Reva, Igor; Fausto, Rui

    2016-07-01

    Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated. PMID:27394105

  19. DFT study on the isomerization and tautomerism in vitamins B3 (niacin), B5 (pantothenic acid) and B7 (biotin)

    NASA Astrophysics Data System (ADS)

    Valadbeigi, Younes; Farrokhpour, Hossein; Tabrizchi, Mahmoud

    2014-05-01

    Isomerization and tautomerism of the three water soluble vitamins including B3, B5 and B7 were studied applying density functional theory using B3LYP method in gas and aqueous phases. Activation energies (Ea), Gibbs free energies of activation (ΔG#), and imaginary frequencies of the transition state structures were calculated for all the isomerization and tautomerism reactions. Activation energies of the neutral → zwitterion (amine-enamine) tautomerism in vitamin B3 were 310-360 kJ/mol where these values for the keto-enol tautomerism were 100-130 kJ/mol. It was found that water molecule catalyzes the tautomerism and decreases the activation energies about 90-160 kJ/mol.

  20. Tryptophan-47 rotational isomerization in variant-3 scorpion neurotoxin. A combination thermodynamic perturbation and umbrella sampling study.

    PubMed Central

    Haydock, C; Sharp, J C; Prendergast, F G

    1990-01-01

    A combination thermodynamic perturbation and umbrella sampling study predicts two free energy wells for the rotational isomerization of the variant-3 scorpion neurotoxin tryptophan-47 indole side chain. One well has the indole side chain in the crystallographic orientation; the other has the indole rotated approximately 220 degrees to form a new conformation with a relative free energy of 3 +/- 2 kcal/mol. The activation barrier is 8.5 kcal/mol from the crystallographic well, from which transition state theory predicts a rate of escape of 2 x 10(5) s-1. Correlations in the displacements of side chains neighboring tryptophan-47 and the isomerization reaction coordinate last up to 20 ps. Favorable conditions of experimental verification are discussed. PMID:2393708

  1. Thermally and vibrationally induced conformational isomerizations, infrared spectra, and photochemistry of gallic acid in low-temperature matrices

    NASA Astrophysics Data System (ADS)

    Justino, Licínia L. G.; Reva, Igor; Fausto, Rui

    2016-07-01

    Near-infrared (near-IR) narrowband selective vibrational excitation and annealing of gallic acid (3,4,5-trihydroxybenzoic acid) isolated in cryogenic matrices were used to induce interconversions between its most stable conformers. The isomerizations were probed by infrared spectroscopy. An extensive set of quantum chemical calculations, carried out at the DFT(B3LYP)/6-311++G(d,p) level of approximation, was used to undertake a detailed analysis of the ground state potential energy surface of the molecule. This investigation of the molecule conformational space allowed extracting mechanistic insights into the observed annealing- or near-IR-induced isomerization processes. The infrared spectra of the two most stable conformers of gallic acid in N2, Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.

  2. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation. [Spiropyrans

    SciTech Connect

    Schwartz, B.J.

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in [approximately]240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH[sub 2]I[sub 2] and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a [approximately]350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  3. Geometrical isomerization of fatty acids with sulfur as a catalyst

    SciTech Connect

    Grompone, M.A.; Tancredi, N.A. )

    1991-08-01

    This paper reports on the kinetics of the geometrical isomerization of oleic and palmitoleic acids, both contained in U.S.P. oleic acid that were studied. Sulfur powder was used as a catalyst. The methyl esters of fatty acids were analyzed by GLC with 15% OV-275 columns. The sulfur-catalyzed isomerization at 180 and 225{degrees} C proceeds via two consecutive mechanisms. The position of equilibrium is reached by the second mechanism. For this, at any particular initial concentration of sulfur, the pseudo- first-order rate dependence on substrate for a reversible reaction holds. The full rate has been shown to be proportional to the initial sulfur concentration taken to the 1.2 power. The rate constants at both temperatures and the activation energies were calculated.

  4. Resolving Isomeric Glycopeptide Glycoforms with Hydrophilic Interaction Chromatography (HILIC).

    PubMed

    Huang, Yining; Nie, Yongxin; Boyes, Barry; Orlando, Ron

    2016-09-01

    The ability to resolve glycans while attached to tryptic peptides would greatly facilitate glycoproteomics, as this would enable site-specific glycan characterization. Peptide/glycopeptide separations are typically performed using reversed-phase liquid chromatography (RPLC), where retention is driven by hydrophobic interaction. As the hydrophilic glycans do not interact significantly with the RPLC stationary phase, it is difficult to resolve glycopeptides that differ only in their glycan structure, even when these differences are large. Alternatively, glycans interact extensively with the stationary phases used in hydrophilic interaction chromatography (HILIC), and consequently, differences in glycan structure have profound chromatographic shifts in this chromatographic mode. Here, we evaluate HILIC for the separation of isomeric glycopeptide mixtures that have the same peptide backbone but isomeric glycans. Hydrophilic functional groups on both the peptide and the glycan interact with the HILIC stationary phase, and thus, changes to either of these moieties can alter the chromatographic behavior of a glycopeptide. The interactive processes permit glycopeptides to be resolved from each other based on differences in their amino acid sequences and/or their attached glycans. The separations of glycans in HILIC are sufficient to permit resolution of isomeric N-glycan structures, such as sialylated N-glycan isomers differing in α2-3 and α2-6 linkages, while these glycans remain attached to peptides. PMID:27582638

  5. Industrial application of catalytic systems for n-heptane isomerization.

    PubMed

    Alemán-Vázquez, Laura Olivia; Cano-Domínguez, José Luis; Torres-García, Enelio; Villagómez-Ibarra, José Roberto

    2011-01-01

    The ideal gasoline must have a high pump octane number, in the 86 to 94 range, and a low environmental impact. Alkanes, as a family, have much lower photochemical reactivities than aromatics or olefins, but only the highly branched alkanes have adequate octane numbers. The purpose of this work is to examine the possibilities of extending the technological alternative of paraffin isomerization to heavier feedstocks (i.e., n-heptane) using non-conventional catalytic systems which have been previously proposed in the literature: a Pt/sulfated zirconia catalyst and a molybdenum sub-oxide catalyst. Under the experimental conditions at which these catalysts have been evaluated, the molybdenum sub-oxide catalyst maintains a good activity and selectivity to isomerization after 24 h, while the Pt/sulfated zirconia catalyst shows a higher dimethylpentanes/methylhexanes ratio, probably due to a lower operating temperature, but also a high formation of cracking products, and presents signs of deactivation after 8 h. Though much remains to be done, the performance of these catalysts indicates that there are good perspectives for their industrial application in the isomerization of n-heptane and heavier alkanes. PMID:21760573

  6. Resolving Isomeric Glycopeptide Glycoforms with Hydrophilic Interaction Chromatography (HILIC)

    PubMed Central

    Huang, Yining; Nie, Yongxin; Boyes, Barry

    2016-01-01

    The ability to resolve glycans while attached to tryptic peptides would greatly facilitate glycoproteomics, as this would enable site-specific glycan characterization. Peptide/glycopeptide separations are typically performed using reversed-phase liquid chromatography (RPLC), where retention is driven by hydrophobic interaction. As the hydrophilic glycans do not interact significantly with the RPLC stationary phase, it is difficult to resolve glycopeptides that differ only in their glycan structure, even when these differences are large. Alternatively, glycans interact extensively with the stationary phases used in hydrophilic interaction chromatography (HILIC), and consequently, differences in glycan structure have profound chromatographic shifts in this chromatographic mode. Here, we evaluate HILIC for the separation of isomeric glycopeptide mixtures that have the same peptide backbone but isomeric glycans. Hydrophilic functional groups on both the peptide and the glycan interact with the HILIC stationary phase, and thus, changes to either of these moieties can alter the chromatographic behavior of a glycopeptide. The interactive processes permit glycopeptides to be resolved from each other based on differences in their amino acid sequences and/or their attached glycans. The separations of glycans in HILIC are sufficient to permit resolution of isomeric N-glycan structures, such as sialylated N-glycan isomers differing in α2-3 and α2-6 linkages, while these glycans remain attached to peptides. PMID:27582638

  7. Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

    NASA Astrophysics Data System (ADS)

    Jung, Yang Ouk; Lee, Jae Hyuk; Kim, Joonghan; Schmidt, Marius; Moffat, Keith; Šrajer, Vukica; Ihee, Hyotcherl

    2013-03-01

    Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (IT) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of IT bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.

  8. Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

    SciTech Connect

    Jung, Yang Ouk; Lee, Jae Hyuk; Kim, Joonghan; Schmidt, Marius; Moffat, Keith; Šrajer, Vukica; Ihee, Hyotcherl

    2013-02-03

    Trans-to-cis isomerization, the key reaction in photoactive proteins, usually cannot occur through the standard one-bond-flip mechanism. Owing to spatial constraints imposed by a protein environment, isomerization probably proceeds through a volume-conserving mechanism in which highly choreographed atomic motions are expected, the details of which have not yet been observed directly. Here we employ time-resolved X-ray crystallography to visualize structurally the isomerization of the p-coumaric acid chromophore in photoactive yellow protein with a time resolution of 100 ps and a spatial resolution of 1.6 Å. The structure of the earliest intermediate (IT) resembles a highly strained transition state in which the torsion angle is located halfway between the trans- and cis-isomers. The reaction trajectory of IT bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue through E46Q mutation, which switches off the bicycle-pedal pathway.

  9. Shape-Asymmetry Supramolecular Isomerism in Asymmetrical Ligand PCPs and the Expression Method of Three-Level Isomerism.

    PubMed

    Gao, Xiaonan; Fu, Ai-Yun; Wang, Yao-Yu

    2016-05-01

    We show here the supramolecular isomerism, with respect to shape-asymmetry of ligand and the new hierarchical classification for supramolecular isomerism, the three-level isomerism, which was advanced based on a thorough investigation for the four new Ni/dpt24 polymorphs [Hdpt24 = 3-(2-pyridyl)-5-(4-pyridyl)-1,2,4-triazole)]. Compounds 1, 2, and 3 are three-dimensional twofold interpenetrated porous coordination polymers with NbO topology, while 4 with two-dimensional grid structure is termed as the primary isomer of 1/2/3 due to the difference of dimensionality. Complex 3 possessing different shape-asymmetry of single networks from 1 and 2, is called as the secondary isomer of 1 and 2. Complexes 1 and 2 possess the same topology, single shape-asymmetry networks, but different interpenetration-orientation and interpenetration-asymmetry, and are defined as the tertiary isomers. Distinct differences in H2 and CO2 adsorption capacity were observed among each level of isomers. In addition, the hierarchical classification's relationship with characteristic classifications has been discussed. PMID:27058739

  10. The Photochemical Isomerization of Maleic to Fumaric Acid: An Undergraduate Organic Chemistry Experiment.

    ERIC Educational Resources Information Center

    Castro, Albert J.; And Others

    1983-01-01

    Describes an undergraduate organic chemistry experiment on the photochemical isomerization of maleic to fumaric acid. Background information, chemical reactions involved, and experimental procedures are included. (JN)

  11. Effects of PAH isomerizations on mutagenicity of combustion products

    SciTech Connect

    Howard, J.B.; Longwell, J.P.; Marr, J.A.; Pope, C.J.; Busby, W.F. Jr.; Lafleur, A.L.; Taghizadeh, K.

    1995-05-01

    Most of the mutagenicity of mixtures of polycyclic aromatic hydrocarbons (PAH) mixtures found in combustion exhaust gases is contributed by a relatively small number of the many PAH present. Since PAB mutagenicity is structure and hence isomer sensitive. changes in the distribution of isomers can change the mutagenicity of the mixture. Whether isomerization reactions in combustion play a significant role in determining the distributions of PAH isomers and the mutagenicity of product mixtures is assessed here for the following pairs of isomers: (1) fluoranthene-pyrene; (2) fluoranthene-acephenanthrylene; (3) cyclopental[cd]pyrene-benzol[ghi]fluoranthene; and (4) benzol[k]fluoranthene-benzo[a]pyrene. Concentration ratios of the isomer pairs were measured in ethylene combustion with naphthalene injection using a plug flow reactor at equivalence ratios of 1.2 and 2.2 and temperatures of 1520, 1620, and 1705 K, and compared with equilibrium ratios based on proper-ties computed from molecular mechanics and semiempirical quantum mechanical programs. Bacterial mutagenicity was measured by a forward mutation assay using Salmonella in the presence of rat liver supernatant, and found to vary significantly among the above compounds. The measured concentration ratios for isomer pairs (2) and (3) are near the equilibrium values and becoming more so as temperature increases, but the measured ratios for isomer pairs (1) and (4) are far from the equilibrium values at all the temperatures. From kinetics estimations, the characteristic isomerization time for isomer pairs (2) and (3) at 1705 K and perhaps at 1620 K is less than the experimental residence times, while the only isomerization mechanisms envisioned for isomer pairs (1) and (4) would not be kinetically viable at these temperatures.

  12. Trivalent nickel. The quinone oximate family: synthesis and redox regulation of isomerism and ligand redistribution

    SciTech Connect

    Ray, D.; Chakravorty, A.

    1988-09-21

    The synthesis of the tris chelates Ni/sup III/(RQ)/sub 3/ by electrooxidation of Ni/sup II/(RQ)/sub 3/- (HRQ = quinone monoximes) is reported. These complexes have afforded a unique opportunity for voltammetric and spectroscopic examination of geometric isomerism and isomer preferences of the two oxidation states of nickel in a N/sub 2/O/sub 3/ environment. A redox-driven ligand redistribution reaction that furnishes Ni(RQ)/sub 3/ following electrooxidation of Ni/sup II/(RQ)/sub 3/(N,N) to Ni/sup III/(RQ)/sub 2/(N,N)/sup +/, where N,N represents amine coordination is reported. The effects of geometric structure, substituents, and ligands on the Ni(III)-Ni(II) reduction potential in Ni(RQ)/sub 3/ and Ni(RQ)/sub 2/(N,N)/sup +/ are noted. 29 references, 5 figures, 4 tables.

  13. Carotene Degradation and Isomerization during Thermal Processing: A Review on the Kinetic Aspects.

    PubMed

    Colle, Ines J P; Lemmens, Lien; Knockaert, Griet; Van Loey, Ann; Hendrickx, Marc

    2016-08-17

    Kinetic models are important tools for process design and optimization to balance desired and undesired reactions taking place in complex food systems during food processing and preservation. This review covers the state of the art on kinetic models available to describe heat-induced conversion of carotenoids, in particular lycopene and β-carotene. First, relevant properties of these carotenoids are discussed. Second, some general aspects of kinetic modeling are introduced, including both empirical single-response modeling and mechanism-based multi-response modeling. The merits of multi-response modeling to simultaneously describe carotene degradation and isomerization are demonstrated. The future challenge in this research field lies in the extension of the current multi-response models to better approach the real reaction pathway and in the integration of kinetic models with mass transfer models in case of reaction in multi-phase food systems. PMID:25830560

  14. Kinetic barriers in the isomerization of substituted ureas: implications for computer-aided drug design.

    PubMed

    Loeffler, Johannes R; Ehmki, Emanuel S R; Fuchs, Julian E; Liedl, Klaus R

    2016-05-01

    Urea derivatives are ubiquitously found in many chemical disciplines. N,N'-substituted ureas may show different conformational preferences depending on their substitution pattern. The high energetic barrier for isomerization of the cis and trans state poses additional challenges on computational simulation techniques aiming at a reproduction of the biological properties of urea derivatives. Herein, we investigate energetics of urea conformations and their interconversion using a broad spectrum of methodologies ranging from data mining, via quantum chemistry to molecular dynamics simulation and free energy calculations. We find that the inversion of urea conformations is inherently slow and beyond the time scale of typical simulation protocols. Therefore, extra care needs to be taken by computational chemists to work with appropriate model systems. We find that both knowledge-driven approaches as well as physics-based methods may guide molecular modelers towards accurate starting structures for expensive calculations to ensure that conformations of urea derivatives are modeled as adequately as possible. PMID:27272323

  15. Slow and stored light by photo-isomerization induced transparency in dye doped chiral nematics.

    PubMed

    Wei, D; Bortolozzo, U; Huignard, J P; Residori, S

    2013-08-26

    Decelerating and stopping light is fundamental for optical processing, high performance sensor technologies and digital signal treatment, many of these applications relying on the ability of controlling the amplitude and phase of coherent light pulses. In this context, slow-light has been achieved by various methods, as coupling light into resonant media, Brillouin scattering in optical fibers, beam coupling in photorefractive and liquid crystal media or engineered dispersion in photonic crystals. Here, we present a different mechanism for slowing and storing light, which is based on photo-isomerization induced transparency of azo-dye molecules hosted in a chiral liquid crystal structure. Sharp spectral features of the medium absorption/dispersion, and the long population lifetime of the dye metastable state, enable the storage of light pulses with a significant retrieval after times much longer than the medium response time. PMID:24105502

  16. The trans-cis and the azide-tetrazole ring-chain isomerization of 2-azido-1,3-azoles: Quantum chemical study

    NASA Astrophysics Data System (ADS)

    Karakus, Nihat; Demirel, Merdan

    2015-08-01

    Quantum chemical calculations using Density Functional Theory (DFT) at the B3LYP/6-31++G(d,p) basis set level were performed to investigate the azide group rotation from the trans to the cis isomer and the azido-tetrazole ring-chain isomerism equilibrium of 2-azido-1,3-azoles in the gas phase, carbon tetrachloride (CCl4), acetonitrile (CH3CN) and water (H2O). The solvent effect on the relative stabilities of each species was analyzed within the self-consistent field theory using the Polarized Continuum Model (PCM). The transition states (TSs) of each step was identified and confirmed. The azido-tetrazole ring-chain isomerism equilibrium was investigated in detail. In addition, the electronic characteristics of each species were analyzed by means of Molecular Electrostatic Potential (MEP) and Natural Bond Orbital (NBO) analyses. The relative energies were increased with the increasing electronegativity of X atom in the 1,3-azole ring. The study confirmed that the relative stability of the tetrazole isomers could be maximized to a great extent by increasing the polarity of solvent, and vice versa for the azido isomers. The low rotational barrier of the azido group in the trans ⇋ cis isomerization and the significant increase of the dipole moment of the tetrazole isomers were determined factors in ring-chain isomerization. The results obtained in advance for 2-azido-1,3-thiazoles were found to be consistent with the experimental and theoretically data reported.

  17. Isomerization and increase in the antioxidant properties of lycopene from Momordica cochinchinensis (gac) by moderate heat treatment with UV-Vis spectra as a marker.

    PubMed

    Phan-Thi, Hanh; Waché, Yves

    2014-08-01

    Momordica cochinchinensis (gac) is a plant rich in lycopene. This pigment tends to solubilize in oil and get damaged during extraction. The impact of heating on cis-isomerization of oil-free lycopene in hexane was studied at 50 and 80°C during 240min with UV-Vis spectrometry, DAD-HPLC and TEAC test. The initial all-trans-form isomerized to the 13-cis isomer more rapidly at 80°C. After this treatment, 16% of the lycopene compounds were in the 9-cis-form. This isomer triggered an increase in the antioxidant properties which was detectable from concentrations above 9% and resulted in a change from 2.4 to 3.7μmol Trolox equivalent. It is thus possible to increase the bioactivity of lycopene samples by controlling heating. The evolution of ratios calculated from the global UV-Vis spectrum was representative of cis-isomerization and spectrometry can thus be a simple way to evaluate the state of isomerization of lycopene solutions. PMID:24629938

  18. Isomerization of Internal Alkynes to Iridium(III) Allene Complexes via C-H Bond Activation: Expanded Substrate Scope, and Progress towards a Catalytic Methodology.

    PubMed

    Phadke, Neha; Findlater, Michael

    2015-01-01

    The synthesis of a series of allene complexes (POCOP)Ir(η²-RC=(.)=CR') 1b-4b (POCOP = 2,6-bis(di-tert-butylphosphonito)benzene) via isomerization of internal alkynes is reported. We have demonstrated that the application of this methodology is viable for the isomerization of a wide variety of alkyne substrates. Deuterium labeling experiments support our proposed mechanism. The structures of the allene complexes 1b-4b were determined using spectroscopic data analysis. Additionally, the solid-state molecular structure of complex 2b was determined using single crystal X-ray diffraction studies and it confirmed the assignment of an iridium-bound allene isomerization product. The rates of isomerization were measured using NMR techniques over a range of temperatures to allow determination of thermodynamic parameters. Finally, we report a preliminary step towards developing a catalytic methodology; the allene may be liberated from the metal center by exposure of the complex to an atmosphere of carbon monoxide. PMID:26569203

  19. Isostructuralism among bridge-flipped' isomeric benzylideneanilines and phenylhydrazones.

    PubMed

    Ojala, William H; Smieja, Jonathan M; Spude, Jill M; Arola, Trina M; Kuspa, Marika K; Herrera, Nell; Ojala, Charles R

    2007-06-01

    Bridge-flipped' isomers may be defined as pairs of molecules related by a reversal of a bridge of atoms connecting two major parts of the individual molecules. This kind of isomerism is commonly found among benzylideneanilines and phenylhydrazones. Isostructural pairs might be suitable for co-crystallization and are thus useful in the preparation of new solid materials. Although most of the examples of bridge-flipped isomeric benzylideneanilines and phenylhydrazones in the crystallographic literature are not isostructural, a small number of isostructural pairs have been reported by previous workers. This paper describes the molecular and crystal structures of four pairs of bridge-flipped isomers: two isostructural phenylhydrazones, (E)-2-bromobenzaldehyde 4-cyanophenylhydrazone (I) and (E)-4-cyanobenzaldehyde 2-bromophenylhydrazone (II); two pairs of isostructural benzylideneanilines, N-(2-trifluoromethylbenzylidene)-2-methylaniline (III) and N-(2-methylbenzylidene)-2-trifluoromethylaniline (IV), and N-(2-bromobenzylidene)-2-methylaniline (V) and N-(2-methylbenzylidene)-2-bromoaniline (VI); and a pair of benzylideneanilines with closely similar unit-cell dimensions but different packing arrangements, N-(4-methylbenzylidene)-4-cyanoaniline (VII) and N-(4-cyanobenzylidene)-4-methylaniline (VIII). The structure of (V) is disordered. The packing arrangement of (VIII) resembles that of the chloro-/methyl-substituted benzylideneanilines MBZCLA/MBZCLB [N-(4-methylbenzylidene)-4-chloroaniline and N-(4-chlorobenzylidene)-4-methylaniline]. Although intermolecular hydrogen bonding plays a part in the isostructuralism of the two phenylhydrazones, the other examples of isostructuralism occur in the absence of similar, relatively strong intermolecular interactions. PMID:17507762

  20. mer and fac isomerism in tris chelate diimine metal complexes.

    PubMed

    Dabb, Serin L; Fletcher, Nicholas C

    2015-03-14

    In this perspective, we highlight the issue of meridional (mer) and facial (fac) orientation of asymmetrical diimines in tris-chelate transition metal complexes. Diimine ligands have long been the workhorse of coordination chemistry, and whilst there are now good strategies to isolate materials where the inherent metal centered chirality is under almost complete control, and systematic methodologies to isolate heteroleptic complexes, the conceptually simple geometrical isomerism has not been widely investigated. In systems where the two donor atoms are significantly different in terms of the σ-donor and π-accepting ability, the fac isomer is likely to be the thermodynamic product. For the diimine complexes with two trigonal planar nitrogen atoms there is much more subtlety to the system, and external factors such as the solvent, lattice packing and the various steric considerations play a delicate role in determining the observed and isolable product. In this article we discuss the possibilities to control the isomeric ratio in labile systems, consider the opportunities to separate inert complexes and discuss the observed differences in their spectroscopic properties. Finally we report on the ligand orientation in supramolecular systems where facial coordination leads to simple regular structures such as helicates and tetrahedra, but the ability of the ligand system to adopt a mer orientation enables self-assembled structures of considerable beauty and complexity. PMID:25600485

  1. On the isomerization of ent-kaurenic acid.

    PubMed

    Rojas, Julio; Aparicio, Rosa; Villasmil, Thayded; Peña, Alexis; Usubillaga, Alfredo

    2011-07-01

    Kaurenic acid (1a) is a tetracyclic diterpene that has an exocyclic double bond at delta16. Isokaurenic acid (2a) has an endocyclic delta15double bond. This compound has been isolated from Espeletia tenore (Espeletinae), a resinous plant from the Venezuelan Andes, but its occurrence is rare. In order to obtain a larger amount of 2a, the isomerization of la, which is easily obtained from other Espeletinae, was tried. Kaurenic acid methyl ester (1b) was treated with dil. HCl in CH3Cl/EtOH, after 6 h under reflux a yield of 41.5% isokaurenic acid methyl ester (2b) was obtained but 35.7% 16alpha-ethoxy-kauran-19-oic acid methyl ester (3b) had formed as a byproduct. Treating 1b with CF3COOH in refluxing CH2Cl2 permitted to obtain a yield of 66.6% of 2b in 4 h and only traces of 16alpha-hydroxy-kauran-19-oic acid methyl ester (3a) as a byproduct. Both isomers were separated on a silica gel column impregnated with 20% AgNO3. Treating 2b with KOH in refluxing DMSO yielded pure isokaurenic acid, no back isomerization was observed. PMID:21834227

  2. Quantum theory of rotational isomerism and Hill equation

    SciTech Connect

    Ugulava, A.; Toklikishvili, Z.; Chkhaidze, S.; Abramishvili, R.; Chotorlishvili, L.

    2012-06-15

    The process of rotational isomerism of linear triatomic molecules is described by the potential with two different-depth minima and one barrier between them. The corresponding quantum-mechanical equation is represented in the form that is a special case of the Hill equation. It is shown that the Hill-Schroedinger equation has a Klein's quadratic group symmetry which, in its turn, contains three invariant subgroups. The presence of these subgroups makes it possible to create a picture of energy spectrum which depends on a parameter and has many merging and branch points. The parameter-dependent energy spectrum of the Hill-Schroedinger equation, like Mathieu-characteristics, contains branch points from the left and from the right of the demarcation line. However, compared to the Mathieu-characteristics, in the Hill-Schroedinger equation spectrum the 'right' points are moved away even further for some distance that is the bigger, the bigger is the less deep well. The asymptotic wave functions of the Hill-Schroedinger equation for the energy values near the potential minimum contain two isolated sharp peaks indicating a possibility of the presence of two stable isomers. At high energy values near the potential maximum, the height of two peaks decreases, and between them there appear chaotic oscillations. This form of the wave functions corresponds to the process of isomerization.

  3. Communication: One-photon phase control of cis-trans isomerization in retinal

    SciTech Connect

    Arango, Carlos A.; Brumer, Paul

    2013-02-21

    We computationally demonstrate the one-photon phase control of retinal isomerization under conditions of low laser intensity. The calculations, utilizing the multiconfigurational time dependent Hartree method, include coupling between the two modes that are active in isomerization and the background molecular vibrational environment. Noting previously unsuccessful computations highlights the significance of this result.

  4. Using ruthenium-based isomerization to improve properties of bio-based materials

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new method that combines isomerization with other reactions has been shown to produce a family of isomeric materials. The chemistry involves the addition of a phosphorous-containing group to produce dibutyl-phosphono-octadecanoates. A low level of [Ru(CO)2(EtCO2)]n is first used for the isomerizat...

  5. Methods of refining and producing isomerized fatty acid esters and fatty acids from natural oil feedstocks

    DOEpatents

    Snead, Thomas E.; Cohen, Steven A.; Gildon, Demond L.; Beltran, Leslie V.; Kunz, Linda A.; Pals, Tessa M.; Quinn, Jordan R; Behrends, Jr., Raymond T.; Bernhardt, Randal J.

    2016-07-05

    Methods are provided for refining natural oil feedstocks and producing isomerized esters and acids. The methods comprise providing a C4-C18 unsaturated fatty ester or acid, and isomerizing the fatty acid ester or acid in the presence of heat or an isomerization catalyst to form an isomerized fatty ester or acid. In some embodiments, the methods comprise forming a dibasic ester or dibasic acid prior to the isomerizing step. In certain embodiments, the methods further comprise hydrolyzing the dibasic ester to form a dibasic acid. In certain embodiments, the olefin is formed by reacting the feedstock in the presence of a metathesis catalyst under conditions sufficient to form a metathesized product comprising olefins and esters, separating the olefins from the esters in the metathesized product, and transesterifying the esters in the presence of an alcohol to form a transesterified product having unsaturated esters.

  6. Regio- and stereoselective isomerization of hexabromocyclododecanes (HBCDs): kinetics and mechanism of beta-HBCD racemization.

    PubMed

    Heeb, Norbert V; Schweizer, W Bernd; Mattrel, Peter; Haag, Regula; Kohler, Martin; Schmid, Peter; Zennegg, Markus; Wolfensberger, Max

    2008-04-01

    Hexabromocyclododecanes (HBCDs) are high production volume chemicals currently produced in quantities exceeding 20000ty(-1). They are used as flame retardants for plastics and textiles. HBCDs are thermally labile compounds, rapidly decomposing at temperatures above 250 degrees C to form bromine radicals, which scavenge other radicals formed during pyrolysis. But certain HBCD stereoisomers must reach the environment without decomposition, because their levels in soils, sediments, and biota are increasing worldwide. The fate of individual HBCD stereoisomers during production, product use, disposal, and transformation in the environment remains unclear. Herein we report on the thermally induced, highly selective isomerization of (+) and (-)beta-HBCD. Regio- and stereoselective migration of only two of the six bromine atoms resulted in the racemization of both beta-HBCDs. First order rate constants (k(rac)) increased from 0.005, 0.011, 0.021, to 0.055min(-1) at 130, 140, 150, and 160 degrees C, corresponding to half life times tau(1/2) of 143, 63, 29, and 14min, respectively. From the deduced kinetic model, we conclude that any thermal treatment of enantiomerically enriched beta-HBCDs in the range of 100-160 degrees C will result in a loss of most optical activity within few hours. The simultaneous inversion of two asymmetric centers occurred with perfect stereocontrol. Selectively, vicinal dibromides with the RR- and the SS-configurations migrated at these temperatures. An intramolecular reaction mechanism with a four-center transition state is postulated, based on the obtained stereoisomer pattern and the observed reaction kinetics. Crystal structure analysis revealed that all vicinal dibromides in beta-HBCDs prefer synclinal (gauche) conformations. However, an antiperiplanar (staggered) conformation is assumed to facilitate the concerted 1.2-shifts of both bromine atoms, resulting in an inversion of both neighboring carbon atoms. First experiments with other HBCD

  7. cis-to-trans isomerization of azobenzene investigated by using thin films of metal-organic frameworks.

    PubMed

    Yu, Xiaojuan; Wang, Zhengbang; Buchholz, Maria; Füllgrabe, Nena; Grosjean, Sylvain; Bebensee, Fabian; Bräse, Stefan; Wöll, Christof; Heinke, Lars

    2015-09-21

    The activation barrier for cis-to-trans isomerization is a key parameter for governing the properties of photoswitchable molecules. This quantity can be computed by using theoretical methods, but experimental determination is not straightforward. Photoswitchable molecules typically do not change their conformation in the pure crystalline state. When the molecules are in solution, the switching is affected by the viscosity and polarity of the solvent and when embedded in polymers, the conformational change is affected by the polymer matrix. Here, we describe a novel approach where the photoswitchable group is integrated in a highly crystalline, porous molecular framework. Sufficiently large pore sizes in such metal-organic frameworks, MOFs, allow unhindered switching and the strictly periodic structure of the lattice eliminates virtually all contributions from inhomogeneities. Using IR spectroscopy to probe the conformational state of azobenzene, the energy barrier separating the cis and the trans state could be determined by an Arrhenius analysis of the data accumulated in a temperature regime between 314 K and 385 K. The result, 1.09 ± 0.09 eV, is in very good agreement with the activation energy reported for the thermal cis-to-trans isomerization of free azobenzene as computed by DFT calculations. PMID:26255748

  8. Ultrafast isomerization initiated by X-ray core ionization

    NASA Astrophysics Data System (ADS)

    Liekhus-Schmaltz, Chelsea E.; Tenney, Ian; Osipov, Timur; Sanchez-Gonzalez, Alvaro; Berrah, Nora; Boll, Rebecca; Bomme, Cedric; Bostedt, Christoph; Bozek, John D.; Carron, Sebastian; Coffee, Ryan; Devin, Julien; Erk, Benjamin; Ferguson, Ken R.; Field, Robert W.; Foucar, Lutz; Frasinski, Leszek J.; Glownia, James M.; Gühr, Markus; Kamalov, Andrei; Krzywinski, Jacek; Li, Heng; Marangos, Jonathan P.; Martinez, Todd J.; McFarland, Brian K.; Miyabe, Shungo; Murphy, Brendan; Natan, Adi; Rolles, Daniel; Rudenko, Artem; Siano, Marco; Simpson, Emma R.; Spector, Limor; Swiggers, Michele; Walke, Daniel; Wang, Song; Weber, Thorsten; Bucksbaum, Philip H.; Petrovic, Vladimir S.

    2015-09-01

    Rapid proton migration is a key process in hydrocarbon photochemistry. Charge migration and subsequent proton motion can mitigate radiation damage when heavier atoms absorb X-rays. If rapid enough, this can improve the fidelity of diffract-before-destroy measurements of biomolecular structure at X-ray-free electron lasers. Here we study X-ray-initiated isomerization of acetylene, a model for proton dynamics in hydrocarbons. Our time-resolved measurements capture the transient motion of protons following X-ray ionization of carbon K-shell electrons. We Coulomb-explode the molecule with a second precisely delayed X-ray pulse and then record all the fragment momenta. These snapshots at different delays are combined into a `molecular movie' of the evolving molecule, which shows substantial proton redistribution within the first 12 fs. We conclude that significant proton motion occurs on a timescale comparable to the Auger relaxation that refills the K-shell vacancy.

  9. Epoxidation of propylene dimers and isomerization of mixtures obtained

    SciTech Connect

    Dobrev, D.M.; Kurtev, K.S.

    1988-05-10

    Mixtures of hexenes are obtained in the dimerization of propylene on a Ziegler catalyst. By the epoxidation of this mixture by organic peroxides, followed by isomerization of the oxides, C/sub 6/ ketones, which are used as solvents, can be obtained. The hexenes were obtained by dimerization of propylene in the presence of a Ni(C/sub 5/H/sub 7/O/sub 2/)/sub 2/-P(C/sub 6/H/sub 5/)/sub 3/-(C/sub 3/H/sub 5/)/sub 2/AlCl catalytic system. The epoxidation was carried with technical grade isopropylbenzyl hydroperoxide (IPBHP). MoO/sub 2/(C/sub 5/H/sub 7/O/sub 2/)/sub 2/ was used as the catalyst. The relative rates of epoxidation of different isomers contained in the dimeric fraction, with respect to 2-methyl-1-pentene, was determined by means of competing reactions.

  10. Influence of isomerization on nonlinear optical properties of molecules.

    PubMed

    Kinnibrugh, T; Bhattacharjee, S; Sullivan, P; Isborn, C; Robinson, B H; Eichinger, B E

    2006-07-13

    The influence of rotational and geometrical isomerism on the nonlinear optical (NLO) properties, specifically the first-order hyperpolarizability beta, of chromophores of current interest has been investigated with density functional theory (DFT). In the first of this two-part study, the rotational isomerism of a linear chromophore was explored. Calculation of the torsion potentials about two of the rotatable and conformation-changing single bonds in a chromophore demonstrated the near equality of the molecular energies at 0 degrees and 180 degrees rotational angles. To explore the consequences of this near conformational energy degeneracy to NLO behavior, the eight low energy rotational isomers of FTC [Robinson, B. H.; et al. Chem. Phys. 1999, 245, 35] were investigated. This study provides the first-reported DFT-based calculation of the statistical mechanical average of beta over the conformational space of a molecule having substantial nonlinear optical behavior. The influence of the solvent reaction field on rotameric populations and on the beta tensor is reported. In the second part, two molecules having two donors and two acceptors bonded respectively in ortho and meta positions on a central benzene ring are shown to have substantially different beta tensors. These two so-called molecular Xs have different highest occupied molecular orbital to lowest unoccupied molecular orbital (HOMO-LUMO) distributions, and consistent with expectations, it is found that the larger beta(zzz) is associated with a large spatial asymmetry between the HOMOs and LUMOs. Large hyperpolarizability correlates with the HOMO concentrated on the donor groups and the LUMO on the acceptor groups. PMID:16821878

  11. Systematics of isomeric configurations in N=77 odd-Z isotones near the proton drip line

    SciTech Connect

    Tantawy, M.N.; Danchev, M.; Hartley, D.J.; Mazzocchi, C.; Bingham, C.R.; Grzywacz, R.; Rykaczewski, K.P.; Gross, C.J.; Shapira, D.; Yu, C.-H.; Batchelder, J.C.; Krolas, W.; Fong, D.; Hamilton, J. H.; Li, K.; Ramayya, A. V.; Ginter, T.N.; Stolz, A.; Hagino, K.; Karny, M.

    2006-02-15

    The systematics of the {pi}h{sub 11/2}x{nu}h{sub 11/2} and {pi}h{sub 11/2}x{nu}s{sub 1/2} isomeric configurations was studied for the odd-Z N=77 isotones near the proton drip line. The isomeric decays in {sup 140}Eu, {sup 142}Tb, {sup 144}Ho, and {sup 146}Tm were measured by means of x-ray, {gamma}-ray, and charged particle spectroscopy at the Recoil Mass Spectrometer at the Holifield Radioactive Ion Beam Facility (ORNL). The spin and parity of I{sup {pi}}=8{sup +} and 5{sup -} were deduced for the isomers in {sup 140}Eu and {sup 142}Tb. New decay schemes were established, and the half-lives of the 8{sup +} isomers were measured to be 302(4) ns for {sup 140m2}Eu and 25(1) {mu}s for {sup 142m2}Tb. No evidence for the expected 1{sup +} ground-state was found in the {sup 144}Ho decay data. The proton-emission from {sup 146}Tm was restudied. Five proton transitions were assigned to two proton-emitting states. The half-lives of 198(3) ms and 68(3) ms and the spin and parity values of I{sup {pi}}=10{sup +} and 5{sup -} were established for {sup 146m}Tm and {sup 146gs}Tm, respectively. For the first time for an odd-odd nucleus, the interpretation of the observed decay properties and structure of the proton-emitting states was made by accounting for deformation and proton and neutron coupling to the core excitations. A complex wave-function structure was obtained, with dominating components of {pi}h{sub 11/2}x{nu}h{sub 11/2} for the 10{sup +} isomer and {pi}h{sub 11/2}x{nu}s{sub 1/2} for the 5{sup -} ground state.

  12. Photochromism of halorhodopsin. cis/trans isomerization of the retinal around the 13-14 double bond.

    PubMed

    Lanyi, J K

    1986-10-25

    The isomeric composition of retinal in membrane-bound and in purified but detergent-free, dark-adapted halorhodopsin was found to be about 70% 13-cis and 30% all-trans. Any illumination increased the all-trans content relative to the dark-adapted state, but blue illumination shifted the isomeric composition more toward all-trans while red illumination of blue-adapted samples shifted it more toward 13-cis. In the presence of chloride this photoisomerization caused the kind of photochromic behavior reported earlier in Smith, S. O., Marvin, M. J., Bogomolni, R. A., and Mathies, R. A. (1984) J. Biol. Chem. 259, 12326-12329, i.e. blue light caused the absorption maximum to move toward longer wavelengths and red light reversed the shift. Only the all-trans chromophore exhibited the complete photocycle described earlier in detergent-solubilized halorhodopsin, and this was the form that could be associated with light-driven chloride transport activity in cell envelope vesicles. In the absence of chloride the spectroscopic changes caused by illumination were much smaller. Reconstitution of bleached preparations with 13-cis- and all-trans-retinal, in the presence and absence of chloride, confirmed that the difference between the absorption maxima of the two isomeric forms of the chromophore is affected by chloride: 13-cis-halorhodopsin absorbs at about 567-568 nm with and without chloride, and the all-trans pigment absorbs near 568 nm in the absence of chloride, but at 578 nm in its presence. The simplest explanation of this finding is that most of the red-shift which accompanies the 13-cis----all-trans transition originates from electrostatic interaction of the retinal with chloride bound in its vicinity. PMID:3771521

  13. Homogeneous hydrogenation and isomerization of 1-octene catalyzed by nickel(II) complexes with bidentate diarylphosphane ligands.

    PubMed

    Mooibroek, Tiddo J; Wenker, Erica C M; Smit, Wietse; Mutikainen, Ilpo; Lutz, Martin; Bouwman, Elisabeth

    2013-07-15

    A systematic library of 24 nickel(II) complexes with bidentate diphosphane ligands was synthesized, and the solid-state structures of five of them were determined with X-ray crystallography. The compounds C1-C3 are common P2Ni(II)X2-type complexes, while C4 contains a unique [P2Ni(II)(NH3)(OAc)](+) square-planar structure with a P2NO donor set and C5 constitutes a rare [(P2Ni(II))2(μ-OH)2](2+) dinuclear compound. The catalytic activity of all complexes was tested in the hydrogenation and/or isomerization of 1-octene in a CH2Cl2/CH3OH reaction medium. Catalyst precursors bearing ligands with o-alkoxy aryl rings selectively hydrogentate 1-octene to n-octane, while catalytic systems comprising ligands without the o-alkoxy functionality selectively isomerize the substrate to a mixture of internal alkenes, mostly cis- and trans-2-octene. The conversion is enhanced by equipping the ligand aryl rings with electron-donating alkoxy groups, by increasing the steric bulk of the backbone and/or the aryl rings, by employing relatively noncoordinating anions, and by adding a base as the cocatalyst. Using the compound [Ni(L3X)I2] as the catalyst precursor and upon application of standard hydrogenation conditions, full conversion of the substrate was achieved in 1 h to isomerization products only (TON = 1940). When a catalytic amount of the base is added, a similar result is obtained even in the absence of H2. A maximum TON of 4500 in 1 h with 96% selectivity for n-octane was achieved by employing [Ni(oMeO-L3X)(NH3)(OAc)]PF6 as the catalyst precursor. PMID:23822166

  14. Cross sections and isomeric cross-section ratios in the interactions of fast neutrons with isotopes of mercury

    SciTech Connect

    Al-Abyad, M.; Sudar, S.; Qaim, S. M.; Comsan, M.N.H.

    2006-06-15

    Excitation functions were measured for the reactions {sup 196}Hg(n, 2n){sup 195}Hg{sup m,g},{sup 198}Hg(n, 2n){sup 197}Hg{sup m,g},{sup 204}Hg(n, 2n){sup 203}Hg,{sup 198}Hg(n,p){sup 198}Au{sup g}, and {sup 199}Hg(n,p){sup 199}Au over the neutron energy range of 7.6-12.5 MeV. Quasimonoenergetic neutrons were produced via the {sup 2}H(d,n){sup 3}He reaction using a deuterium gas target at the Juelich variable energy compact cyclotron CV 28. Use was made of the activation technique in combination with high-resolution, high-purity Ge detector {gamma}-ray spectroscopy. All the data were measured for the first time over the investigated energy range. The transition from the present low-energy data to the literature data around 14 MeV is generally good. Nuclear model calculations using the codes STAPRE and EMPIRE-2.19, which employ the statistical and precompound model formalisms, were undertaken to describe the formation of both the isomeric and ground states of the products. The total reaction cross section of a particular channel is reproduced fairly well by the model calculations, with STAPRE giving slightly better results. Regarding the isomeric cross sections, the agreement between the experiment and theory is only in approximate terms. A description of the isomeric cross-section ratio by the model was possible only with a very low value of {eta}, i.e., the {theta}{sub eff}/{theta}{sub rig} ratio.

  15. Femtosecond spectroscopy of a 13-demethylrhodopsin visual pigment analogue: The role of nonbonded interactions in the isomerization process

    SciTech Connect

    Wang, Q.; Shank, C.V.; Kochendoerfer, G.G.; Mathies, R.A.; Schoenlein, R.W.; Verdegem, P.J.E.; Lugtenburg, J.

    1996-10-24

    The photoisomerization reaction of the visual pigment analogue 11-cis-13-demethylrhodopsin is investigated using femtosecond pump-probe techniques. Following excitation with a 40-fs pump pulse at 500 nm, differential trasnsient absorption spectra are measured from 470 to 560 nm using a 10-fs probe pulse centered at 500 nm and from 560 to 650 nm using a 10-fs probe pulse centered at 620 nm. The persistence of the excited-state absorption, the recovery kinetics of the ground-state bleach, and the formation time of the photoproduct absorption all indicate that this photoisomerization reaction is complete on the 400-fs time scale. Comparison of the reaction dynamics of 11-cis-rhodopsin with 11-cis-13-demethylrhodopsin suggests that the removal of the nonbonded steric intersection between the C{sub 13}-methyl group and the C{sub 10}-hydrogen atom slows down the initial torsional dynamics and that this in turn results in a lower isomerization quantum yield and a slower overall reaction time. Our results support the hypothesis that the quantum yield and the speed of the isomerization reaction are coupled according to a dynamic potential-sulfate crossing mechanism. 27 refs., 5 figs.

  16. Conversion of biomass to ethanol: Isomerization of xylose over HY zeolite

    SciTech Connect

    Lee, C.Y.; Wen, J.; Thomas, S.

    1995-12-31

    Xylose, a pentose indigestible to most yeasts, was converted to ethanol by a two-step isomerization and fermentation. HY zeolite was used to catalyze the isomerization of xylose, and the xylulose produced was directly used as the carbon source in ethanol fermentation. Zeolite catalysts offer pH compatibility with yeast fermentation and the ability to carry out isomerization at higher temperature where equilibrium xylulose concentration is higher. Initial rate studies indicate that xylose consumption follows pseudo-first-order kinetics, with a specific rate constant of 6.2 x 10{sup -4} L/solution/g zeolite/h.

  17. trans- cis Isomerism and acylimine formation in DsRed chromophore models: Intrinsic rotation barriers

    NASA Astrophysics Data System (ADS)

    Olsen, Seth; Smith, Sean C.

    2006-07-01

    The chromophore of the red fluorescent protein DsRed contains an acylimine substituent to a GFP-like chromophore structure. The acylimine is formed from the trans peptide linkage between residues F65 and Q66 in immature DsRed, but has a cis configuration in the mature protein. The relationship between acylimine formation and trans- cis isomerization is unresolved. We have calculated bond rotation profiles for models of mature and immature DsRed chromophores using B3LYP DFT. The isomerization barrier is substantially reduced in acylimine-substituted models, providing prima facie evidence that acylimine formation precedes trans- cis isomerization in DsRed chromophores.

  18. Exploitation of solar energy storage systems. Valence isomerization between norbornadiene and quadricyclane derivatives

    SciTech Connect

    Maruyama, K.; Teraka, K.; Yamamoto, Y.

    1981-01-01

    Use of copper(I)-nitrogen ligand catalysts such as Ph/sub 3/PCuCl.bpy, Ph/sub 3/PCuCl.phen, Ph/sub 3/PCuCl.phtha, and Ph/sub 3/PCuBr.py enables the photochemical isomerization of norbornadiene to quadricyclane to be performed at a longer wavelength than 350 nm, at which CuCl catalyst itself cannot induce such an isomerization. Among the norbornadiene derivatives bearing various chromophores, 3-(phenylcarbamoyl)norbornadiene-2-carboxylic acid undergoes a facile and quantitative isomerization into the corresponding quadricyclane derivative in sunlight. The back-isomerization of quadricyclane to 3-(phenylcarbamoyl)norbornadiene-2-carboxylic acid proceeds quantitatively by use of catalytic amounts of Rh/sub 2/(CO)/sub 4/Cl/sub 2/.

  19. Fuel properties of heptadecene isomers prepared via tandem isomerization-decarboxylation of oleic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heptadecene isomers were prepared via tandem isomerization-decarboxylation of oleic acid using catalytic triruthenium dodecacarbonyl [Ru3(CO)12]. Chromatographic and spectroscopic characterization of the isolated heptadecene mixture indicated that it consisted of 96% internal isomers and 4% aromatic...

  20. "W-X-M" transformations in isomerization of B39- borospherenes

    NASA Astrophysics Data System (ADS)

    Gao, Ting-Ting; Chen, Qiang; Mu, Yue-Wen; Lu, Haigang; Li, Si-Dian

    2016-06-01

    The Stone-Wales transformation plays an important role in the isomerization of fullerenes and graphenic systems. The continuous conversions between neighboring six- and seven-membered rings in the borospherene (all-boron fullerene) B40 had been discovered (Martínez-Guajardo et al. Sci. Rep. 5, 11287 (2015)). In the first axially chiral borospherenes C3 B39- and C2 B39-, we identify three active boron atoms which are located at the center of three alternative sites involving five boron atoms denoted as "W", "X", and "M", respectively. The concerted movements of these active boron atoms and their close neighbors between neighboring six- and seven-membered rings define the "W-X-M" transformation of borospherenes. Extensive first-principles molecular dynamics simulations and quadratic synchronous transit transition-state searches indicate that, via three transition states (TS1, TS2, and TS3) and two intermediate species (M1 and M2), the three-step "W-X-M" transformations convert the C3 B39- global minimum into its C2 isomer at room temperature (300 K) and vice versa. The maximum barriers are only 3.89 kcal/mol from C3 to C2 B39- and 2.1 kcal/mol from C2 to C3 B39-, rendering dynamic fluxionalities to these borospherenes. Therefore, the "W-X-M" transformation plays an important role in the borospherenes and borospherene-based nanostructures.

  1. Radiative lifetime and energy of the low-energy isomeric level in 229Th

    NASA Astrophysics Data System (ADS)

    Tkalya, E. V.; Schneider, Christian; Jeet, Justin; Hudson, Eric R.

    2015-11-01

    We estimate the range of the radiative lifetime and energy of the anomalous, low-energy 3 /2+(7.8 ±0.5 eV) state in the 229Th nucleus. Our phenomenological calculations are based on the available experimental data for the intensities of M 1 and E 2 transitions between excited levels of the 229Th nucleus in the Kπ[N nZΛ ] =5 /2+[633 ] and 3 /2+[631 ] rotational bands. We also discuss the influence of certain branching coefficients, which affect the currently accepted measured energy of the isomeric state. From this work, we establish a favored region, 0.66 ×106seV3/ω3≤τ ≤2.2 ×106seV3/ω3 , where the transition lifetime τ as a function of transition energy ω should lie at roughly the 95% confidence level. Together with the result of Beck et al. [LLNL-PROC-415170 (2009)], we establish a favored area where transition lifetime and energy should lie at roughly the 90% confidence level. We also suggest new nuclear physics measurements, which would significantly reduce the ambiguity in the present data.

  2. Vibrational predissociation and vibrationally induced isomerization of 3-aminophenol-ammonia.

    PubMed

    Heid, Cornelia G; Merrill, Wyatt G; Case, Amanda S; Crim, F Fleming

    2015-01-01

    We investigate the vibrational predissociation dynamics of the hydrogen-bonded 3-aminophenol-ammonia cluster (3-AP-NH3) in the OH and NH stretching regions. Vibrational excitation provides enough energy to dissociate the cluster into its constituent 3-AP and NH3 monomers, and we detect the 3-AP fragments via (1 + 1) resonance-enhanced multiphoton ionization (REMPI). The distribution of vibrational states of the 3-AP fragment suggests the presence of two distinct dissociation pathways. The first dissociation channel produces a broad, unstructured feature in the REMPI-action spectrum after excitation of any of the OH or NH stretching vibrations, pointing to a nearly statistical dissociation pathway with extensive coupling among the vibrations in the cluster during the vibrational predissociation. The second dissociation channel produces distinct, resolved features on top of the broad feature but only following excitation of the OH or symmetric NH3 stretch in the cluster. This striking mode-specificity is consistent with strong coupling of these two modes to the dissociation coordinate (the O-H⋯N bond). The presence of clearly resolved transitions to the electronic origin and to the 10a(2) + 10b(2) state of the cis-3-AP isomer shows that vibrational excitation is driving the isomerization of the trans-3-AP-NH3 isomer to the cis-3-AP-NH3 isomer in the course of the dissociation. PMID:25573564

  3. Vibrational predissociation and vibrationally induced isomerization of 3-aminophenol-ammonia

    SciTech Connect

    Heid, Cornelia G.; Merrill, Wyatt G.; Case, Amanda S. Crim, F. Fleming

    2015-01-07

    We investigate the vibrational predissociation dynamics of the hydrogen-bonded 3-aminophenol-ammonia cluster (3-AP-NH{sub 3}) in the OH and NH stretching regions. Vibrational excitation provides enough energy to dissociate the cluster into its constituent 3-AP and NH{sub 3} monomers, and we detect the 3-AP fragments via (1 + 1) resonance-enhanced multiphoton ionization (REMPI). The distribution of vibrational states of the 3-AP fragment suggests the presence of two distinct dissociation pathways. The first dissociation channel produces a broad, unstructured feature in the REMPI-action spectrum after excitation of any of the OH or NH stretching vibrations, pointing to a nearly statistical dissociation pathway with extensive coupling among the vibrations in the cluster during the vibrational predissociation. The second dissociation channel produces distinct, resolved features on top of the broad feature but only following excitation of the OH or symmetric NH{sub 3} stretch in the cluster. This striking mode-specificity is consistent with strong coupling of these two modes to the dissociation coordinate (the O–H⋯N bond). The presence of clearly resolved transitions to the electronic origin and to the 10a{sup 2} + 10b{sup 2} state of the cis-3-AP isomer shows that vibrational excitation is driving the isomerization of the trans-3-AP-NH{sub 3} isomer to the cis-3-AP-NH{sub 3} isomer in the course of the dissociation.

  4. Isomerization of alkanes on sulfated zirconia: Promotion by Pt and by adamantyl hydride transfer species

    SciTech Connect

    Iglesia, E.; Soled, S.L.; Kramer, G.M. )

    1993-11-01

    The work shows that hydride transfer species, such as adamantane, increase isomerization rates and inhibit C-C scission reactions. n-Heptane isomerization rates show positive hydrogen kinetic orders, suggesting that the reaction proceeds on Pt/ZrO[sub 2]-SO[sub 4] via chain transfer pathways, in which carbenium ions propagate, after a chain initiation step involvings loss of hydrogen from alkanes, by hydride transfer from neutral species to carbonations. These pathways contrast with those involved in the bifunctional (metal-acid) catalytic sequences usually required for alkane isomerization, in which metal sites catalyze alkane dehydrogenation and acid sites catalyze skeletal rearrangements of alkenes. Rate-limiting hydride transfer steps are consistent with the strong influence of molecular hydride transfer agents such as adamantane, which act as co-catalysts and increase isomerization rate and selectivity. The addition of small amounts of adamantane (0.1-0.8 wt%) to n-heptane increases isomerizations rates by a factor of 3 and inhibits undesirable cracking reactions. Adamantane increases hydride transfer and carbenium ion termination rates, thus reducing the surface residence time required for a catalytic turnover. As a result, desorption occurs before secondary cracking of isomerized carbenium ions. Less effective hydride transfer agents (n-alkanes, isoalkanes) also increase n-alkanes isomerization rate and selectivity, but require much higher concentrations than adamantane. Dihydrogen also acts as a hydride source in alkane isomerization catalysis, but it requires the additional presence of metals or reducible oxides, which catalyze H[sub 2] dissociation and the formation of hydridic and protonic forms of hydrogen. 40 refs., 10 figs., 4 tabs.

  5. Iridium complexes of new NCP pincer ligands: catalytic alkane dehydrogenation and alkene isomerization.

    PubMed

    Jia, Xiangqing; Zhang, Lei; Qin, Chuan; Leng, Xuebing; Huang, Zheng

    2014-09-28

    Iridium complexes of novel NCP pincer ligands containing pyridine and phosphinite arms have been synthesized. One Ir complex shows good catalytic activity for alkane dehydrogenation, and all complexes are highly active for olefin isomerization. A combination of the Ir complex and a (PNN)Fe pincer complex catalyzes the formation of linear alkylboronates selectively from internal olefins via sequential olefin isomerization-hydroboration. PMID:25101950

  6. Enzyme-like effect of metmyoglobin on the thermal cis-trans isomerization of stilbazolium betaine.

    PubMed

    Pastukhov, A V; Vogel, V R; Kotelnikov, A I

    2000-06-01

    A photochromic compound, stilbazolium betaine M, when associated with metmyoglobin undergoes an accelerated thermal cis-trans isomerization. A study of the pH and ionic strength dependence of the isomerization reaction rate of the photochrome associated with metmyoglobin was performed. A comparative investigation of the reaction carried out in the presence of three proteins, metmyoglobin, apomyoglobin, and human albumin, indicates a specific influence of the heme pocket environment on the reaction. Possible mechanisms of the reaction acceleration are considered. PMID:10907741

  7. Role of the protein cavity in phytochrome chromoprotein assembly and double-bond isomerization: a comparison with model compounds.

    PubMed

    Rohmer, Thierry; Lang, Christina; Gärtner, Wolfgang; Hughes, Jon; Matysik, Jörg

    2010-01-01

    Difference patterns of (13)C NMR chemicals shifts for the protonation of a free model compound in organic solution, as reported in the literature (M. Stanek, K. Grubmayr [1998] Chem. Eur. J.4, 1653-1659), were compared with changes in the protonation state occurring during holophytochrome assembly from phycocyanobilin (PCB) and the apoprotein. Both processes induce identical changes in the NMR signals, indicating that the assembly process is linked to protonation of the chromophore, yielding a cationic cofactor in a heterogeneous, quasi-liquid protein environment. The identity of both difference patterns implies that the protonation of a model compound in solution causes a partial stretching of the geometry of the macrocycle as found in the protein. In fact, the similarity of the difference pattern within the bilin family for identical chemical transformations represents a basis for future theoretical analysis. On the other hand, the change of the (13)C NMR chemical shift pattern upon the Pr --> Pfr photoisomerization is very different to that of the free model compound upon ZZZ --> ZZE photoisomerization. Hence, the character of the double-bond isomerization in phytochrome is essentially different from that of a classical photoinduced double-bond isomerization, emphasizing the role of the protein environment in the modulation of this light-induced process. PMID:20492561

  8. Influence of the steric effect of flexible isomeric phenylenediacetic acids on the resultant lead(II) coordination polymers

    SciTech Connect

    Wu, Yunlong; Zhao, Yanqing; Yang, Guo-Ping Guo, Yanjun; Wang, Yao-Yu Shi, Qi-Zhen

    2015-03-15

    To study the steric effect of the flexible dicarboxylate ligands on the resultant formations of coordination polymers (CPs), four new Pb{sup II} CPs [Pb(1,2-pda)(H{sub 2}O)]{sub n} (1), [Pb(1,3-pda)]{sub n}·nH{sub 2}O (2), [Pb{sub 2}(1,4-pda){sub 2}(H{sub 2}O)]{sub n}·2nH{sub 2}O (3a and 3b) have been produced by the isomeric phenylenediacetic acids (H{sub 2}pda). The X-ray crystallography study reveals that CP 1 is a two-dimensional (2D) 4-connected sql (4{sup 4}.6{sup 2}) network via the weak Pb···O interactions built on 1D chain-like structure. CP 2 crystallizes in orthorhombic system with chiral space group P2{sub 1}2{sub 1}2{sub 1}, showing a 4-connected sra (4{sup 2}.6{sup 3}.8) framework where a left-handed helical motif is formed by Pb{sup II} ions and trans-1,3-pda ligands. More interestingly, CPs 3a and 3b are two true 3D polymorphs and have the different morphology. Topologically, the framework of 3a exhibits a 4-connected lon 6{sup 6} motif, while that of 3b is a (4,6)-connected fsh (4{sup 3}.6{sup 3}){sub 2}(4{sup 6}.6{sup 6}.8{sup 3}) net. It is found that the three isomeric pda anions display the various coordination fashions in four CPs. The different structural arrangements show that the steric effect of the isomeric H{sub 2}pda tectons has a positive role in directing the final products of Pb{sup II} CPs. Also, the fluorescent properties of the CPs were studied in the solid state at room temperature. - Graphical abstract: Four new Pb{sup II}-based CPs have been produced by the isomeric phenylenediacetic acids (H{sub 2}pda). The different structural arrangements show that the steric effect of the isomeric H{sub 2}pda tectons has a positive role in directing the final products of Pb{sup II} CPs. Also, the fluorescent properties of the CPs were studied in the solid state at room temperature. - Highlights: • Four Pb{sup II}-based coordination polymers were produced by phenylenediacetic acids. • The crystal and topological structures of the

  9. Ion Mobility Mass Spectrometry Analysis of Isomeric Disaccharide Precursor, Product and Cluster Ions

    PubMed Central

    Li, Hongli; Bendiak, Brad; Siems, William F.; Gang, David R.; Hill, Herbert H.

    2015-01-01

    RATIONALE Carbohydrates are highly variable in structure owing to differences in their anomeric configurations, monomer stereochemistry, inter-residue linkage positions and general branching features. The separation of carbohydrate isomers poses a great challenge for current analytical techniques. METHODS The isomeric heterogeneity of disaccharide ions and monosaccharideglycolaldehyde product ions evaluated using electrospray traveling wave ion mobility mass spectrometry (Synapt G2 high definition mass spectrometer) in both positive and negative ion modes investigation. RESULTS The separation of isomeric disaccharide ions was observed but not fully achieved based on their mobility profiles. The mobilities of isomeric product ions, the monosaccharide-glycolaldehydes, derived from different disaccharide isomers were measured. Multiple mobility peaks were observed for both monosaccharide-glycolaldehyde cations and anions, indicating that there was more than one structural configuration in the gas phase as verified by NMR in solution. More importantly, the mobility patterns for isomeric monosaccharide-glycolaldehyde product ions were different, which enabled partial characterization of their respective disaccharide ions. Abundant disaccharide cluster ions were also observed. The Results showed that a majority of isomeric cluster ions had different drift times and, moreover, more than one mobility peak was detected for a number of specific cluster ions. CONCLUSIONS It is demonstrated that ion mobility mass spectrometry is an advantageous method to assess the isomeric heterogeneity of carbohydrate compounds. It is capable of differentiating different types of carbohydrate ions having identical m/z values as well as multiple structural configurations of single compounds. PMID:24591031

  10. Isomerization of 11-cis-retinol to all-trans-retinol in bovine rod outer segments.

    PubMed

    Shimizu, T; Ishiguro, S; Tamai, M

    1998-05-01

    It is known that exogenous 11-cis-retinol inhibits the recovery of photosensitivity of bleached rod outer segments (ROS) and 11-cis-retinol exists in the interphotorecepter matrix. We examined the conversion of 11-cis-retinol with bovine ROS. ROS was incubated with 11-cis-retinol under dim red light. Retinoids were extracted from the reaction mixture with hexane and analyzed by HPLC coupled with a fluorescence spectrophotometer. Isomerization of 11-cis-retinol to all-trans-retinol was observed in the presence of ROS. This isomerization was not suppressed by heat treatment and did not have stereospecificity. In addition, we incubated purified rhodopsin and phospholipids extracted from ROS with 11-cis-retinol. Rhodopsin was found to isomerize 11-cis-retinol to all-trans-retinol as well as ROS, but phospholipids did not. In contrast, the phospholipids inhibited the isomerization of 11-cis-retinol to all-trans-retinol by the purified rhodopsin. Commercially available phospholipids, especially phosphatidylserine, also inhibited the isomerization. Our results suggest that rhodopsin has activity for the isomerization of 11-cis-retinol to all-trans-retinol and may play an important role in the detoxification of 11-cis-retinol in the ROS. PMID:9562631

  11. Photochemical generation, isomerization, and oxygenation of stilbene cation radicals

    SciTech Connect

    Lewis, F.D.; Bedell, A.M.; Dykstra, R.E.; Elbert, J.E. ); Gould, I.R.; Farid, S. )

    1990-10-24

    The cation radicals of cis- and trans-stilbene and several of their ring-substituted derivatives have been generated in solution directly by means of pulsed-laser-induced electron transfer to singlet cyanoanthracenes or indirectly via electron transfer from biphenyl to the singlet cyanoanthracene followed by secondary electron transfer from the stilbenes to the biphenyl cation radical. Transient absorption spectra of the cis- and trans-stilbene cation radicals generated by secondary electron transfer are similar to those previously obtained in 77 K matrices. Quantum yields for radical ion-pair cage escape have been measured for direct electron transfer from the stilbenes to three neutral and one charged singlet acceptor. These values increase as the ion-pair energy increases due to decreased rate constants for radical ion-pair return electron transfer, in accord with the predictions of Marcus theory for highly exergonic electron transfer. Cage-escape efficiencies are larger for trans- vs cis-stilbene cation radicals, possibly due to the greater extent of charge delocalization in the planar trans vs nonpolar cis cation radicals. Cage-escape stilbene cation radicals can initiate a concentration-dependent one way cis- {yields} trans-stilbene isomerization reaction.

  12. Isomerization and fragmentation pathways of 1,2-azaborine.

    PubMed

    Edel, Klara; Fink, Reinhold F; Bettinger, Holger F

    2016-01-01

    The generation of 1,2-azaborine (4), the BN-analogue of ortho-benzyne, was recently achieved by elimination of tert-butyldimethylchlorosilane under the conditions of flash vacuum pyrolysis. The present investigation identifies by computational means pathways for the thermal isomerization and fragmentation of 1,2-azaborine. The computations were performed using single reference (hybrid/density functional, second order Møller-Plesset perturbation, and coupled cluster theories) as well as multiconfiguration methods (complete active space SCF based second order perturbation theory, multireference configuration interaction, and multiconfiguration coupled electron pair approximation) with basis sets up to polarized triple-ζ quality. The 1,2-azaborine is, despite the distortion of its molecular structure, the most stable C4H4BN isomer investigated. The formation of BN-endiyne isomers is highly unfavorable as the identified pathways involve barriers close to 80 kcal mol(-1). The concerted fragmentation to ethyne and 2-aza-3-bora-butadiyne even has a barrier close to 120 kcal mol(-1). The fragmentation of BN-enediynes has energetic requirements similar to enediynes. PMID:26418051

  13. Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism

    SciTech Connect

    Camilloni, Carlo; Sahakyan, Aleksander B.; Holliday, Michael; Isern, Nancy G.; Zhang, Fengli; Eisenmesser, Elan Z.; Vendruscolo, Michele

    2014-07-15

    Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions1-3. Different families of enzymes, known as peptidyl-prolyl isomerases (PPIases), catalyse this reaction, which involves the interconversion between the cis and trans isomers of the Nterminal amide bond of the amino acid proline2,3. A complete description of the mechanisms by which these enzymes function, however, has remained elusive. Here, we show that cyclophilin A, one of the most common PPIases4, provides a catalytic environment that acts on the substrate through an electrostatic lever mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carboxylic group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. This mechanism resulted from the analysis of an ensemble of conformations populated by cyclophilin A during the enzymatic reaction using a combination of NMR measurements, molecular dynamics simulations and density functional theory calculations. We anticipate that this approach will be helpful in elucidating whether the electrostatic lever mechanism that we describe is common to other PPIases, and more generally to characterise other enzymatic processes.

  14. Photochemical Isomerization and Topochemical Polymerization of the Programmed Asymmetric Amphiphiles.

    PubMed

    Kim, Dae-Yoon; Lee, Sang-A; Jung, Daseal; Jeong, Kwang-Un

    2016-01-01

    For the advancement in multi-stimuli responsive optical devices, we report the elaborate molecular engineering of the dual photo-functionalized amphiphile (abbreviated as AZ1DA) containing both a photo-isomerizable azobenzene and a photo-polymerizable diacetylene. To achieve the efficient photochemical reactions in thin solid films, the self-assembly of AZ1DA molecules into the ordered phases should be precisely controlled and efficiently utilized. First, the remote-controllable light shutter is successfully demonstrated based on the reversible trans-cis photo-isomerization of azobenzene group in the smectic A mesophase. Second, the self-organized monoclinic crystal phase allows us to validate the photo-polymerization of diacetylene moiety for the photo-patterned thin films and the thermo-responsible color switches. From the demonstrations of optically tunable thin films, it is realized that the construction of strong relationships between chemical structures, molecular packing structures and physical properties of the programmed molecules is the core research for the development of smart and multifunctional soft materials. PMID:27339163

  15. Thiocyanate linkage isomerism in a ruthenium polypyridyl complex.

    PubMed

    Brewster, Timothy P; Ding, Wendu; Schley, Nathan D; Hazari, Nilay; Batista, Victor S; Crabtree, Robert H

    2011-12-01

    Ruthenium polypyridyl complexes have seen extensive use in solar energy applications. One of the most efficient dye-sensitized solar cells produced to date employs the dye-sensitizer N719, a ruthenium polypyridyl thiocyanate complex. Thiocyanate complexes are typically present as an inseparable mixture of N-bound and S-bound linkage isomers. Here we report the synthesis of a new complex, [Ru(terpy)(tbbpy)SCN][SbF(6)] (terpy = 2,2';6',2''-terpyridine, tbbpy = 4,4'-di-tert-butyl-2,2'-bipyridine), as a mixture of N-bound and S-bound thiocyanate linkage isomers that can be separated based on their relative solubility in ethanol. Both isomers have been characterized spectroscopically and by X-ray crystallography. At elevated temperatures the isomers equilibrate, the product being significantly enriched in the more thermodynamically stable N-bound form. Density functional theory analysis supports our experimental observation that the N-bound isomer is thermodynamically preferred, and provides insight into the isomerization mechanism. PMID:22066656

  16. Photochemical Isomerization and Topochemical Polymerization of the Programmed Asymmetric Amphiphiles

    NASA Astrophysics Data System (ADS)

    Kim, Dae-Yoon; Lee, Sang-A.; Jung, Daseal; Jeong, Kwang-Un

    2016-06-01

    For the advancement in multi-stimuli responsive optical devices, we report the elaborate molecular engineering of the dual photo-functionalized amphiphile (abbreviated as AZ1DA) containing both a photo-isomerizable azobenzene and a photo-polymerizable diacetylene. To achieve the efficient photochemical reactions in thin solid films, the self-assembly of AZ1DA molecules into the ordered phases should be precisely controlled and efficiently utilized. First, the remote-controllable light shutter is successfully demonstrated based on the reversible trans-cis photo-isomerization of azobenzene group in the smectic A mesophase. Second, the self-organized monoclinic crystal phase allows us to validate the photo-polymerization of diacetylene moiety for the photo-patterned thin films and the thermo-responsible color switches. From the demonstrations of optically tunable thin films, it is realized that the construction of strong relationships between chemical structures, molecular packing structures and physical properties of the programmed molecules is the core research for the development of smart and multifunctional soft materials.

  17. Photochemical Isomerization and Topochemical Polymerization of the Programmed Asymmetric Amphiphiles

    PubMed Central

    Kim, Dae-Yoon; Lee, Sang-A; Jung, Daseal; Jeong, Kwang-Un

    2016-01-01

    For the advancement in multi-stimuli responsive optical devices, we report the elaborate molecular engineering of the dual photo-functionalized amphiphile (abbreviated as AZ1DA) containing both a photo-isomerizable azobenzene and a photo-polymerizable diacetylene. To achieve the efficient photochemical reactions in thin solid films, the self-assembly of AZ1DA molecules into the ordered phases should be precisely controlled and efficiently utilized. First, the remote-controllable light shutter is successfully demonstrated based on the reversible trans-cis photo-isomerization of azobenzene group in the smectic A mesophase. Second, the self-organized monoclinic crystal phase allows us to validate the photo-polymerization of diacetylene moiety for the photo-patterned thin films and the thermo-responsible color switches. From the demonstrations of optically tunable thin films, it is realized that the construction of strong relationships between chemical structures, molecular packing structures and physical properties of the programmed molecules is the core research for the development of smart and multifunctional soft materials. PMID:27339163

  18. Full-dimensional quantum dynamics study of vinylidene-acetylene isomerization: a scheme using the normal mode Hamiltonian.

    PubMed

    Ren, Yinghui; Li, Bin; Bian, Wensheng

    2011-02-14

    Full-dimensional quantum dynamics calculations of vinylidene-acetylene isomerization are performed and the state-specific resonance decay lifetimes of vinylidene(-d(2)) are computed. The theoretical scheme is a combination of several methods: normal coordinates are chosen to describe the nuclear motion of vinylidene, with both the parity and permutation symmetry exploited; phase space optimization in combination with physical considerations is used to generate an efficient discrete variable representation; the reaction coordinate is defined by us according to the three most relevant normal coordinates, along which a kind of optimal complex absorbing potential is imposed; the preconditioned inexact spectral transform method combined with an efficient preconditioner is employed to extract the energies and lifetimes of vinylidene. The overall computation is efficient. The computed energy levels generally agree with experiment well, and several state-specific lifetimes are reported for the first time. PMID:21186383

  19. Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). II. Velocity map imaging studies.

    PubMed

    Ryazanov, M; Rodrigo, C; Reisler, H

    2012-02-28

    The dissociation of the hydroxymethyl radical, CH(2)OH, and its isotopolog, CD(2)OH, following excitation in the 4ν(1) region (OH stretch overtone, near 13,600 cm(-1)) was studied using sliced velocity map imaging. A new vibrational band near 13,660 cm(-1) arising from interaction with the antisymmetric CH stretch was discovered for CH(2)OH. In CD(2)OH dissociation, D atom products (correlated with CHDO) were detected, providing the first experimental evidence of isomerization in the CH(2)OH ↔ CH(3)O (CD(2)OH ↔ CHD(2)O) system. Analysis of the H (D) fragment kinetic energy distributions shows that the rovibrational state distributions in the formaldehyde cofragments are different for the OH bond fission and isomerization pathways. Isomerization is responsible for 10%-30% of dissociation events in all studied cases, and its contribution depends on the excited vibrational level of the radical. Accurate dissociation energies were determined: D(0)(CH(2)OH → CH(2)O + H) = 10,160 ± 70 cm(-1), D(0)(CD(2)OH → CD(2)O + H) = 10,135 ± 70 cm(-1), D(0)(CD(2)OH → CHDO + D) = 10,760 ± 60 cm(-1). PMID:22380040

  20. A bacterial tyrosine aminomutase proceeds through retention or inversion of stereochemistry to catalyze its isomerization reaction.

    PubMed

    Wanninayake, Udayanga; Walker, Kevin D

    2013-07-31

    β-Amino acids are biologically active compounds of interest in medicinal chemistry. A class I lyase-like family of aminomutases isomerizes (S)-α-arylalanines to the corresponding β-amino acids by exchange of the NH2/H pair. This family uses a 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) group within the active site to initiate the reaction. The absolute stereochemistry of the product is known for an MIO-dependent tyrosine aminomutase from Chondromyces crocatus (CcTAM) that isomerizes (S)-α-tyrosine to (R)-β-tyrosine. To evaluate the cryptic stereochemistry of the CcTAM mechanism, (2S,3S)-[2,3-(2)H2]- and (2S,3R)-[3-(2)H]-α-tyrosine were stereoselectively synthesized from unlabeled (or [(2)H]-labeled) (4'-hydroxyphenyl)acrylic acids by reduction with D2 (or H2) gas and a chiral Rh-Prophos catalyst. GC/EIMS analysis of the [(2)H]-β-tyrosine biosynthesized by CcTAM revealed that the α-amino group was transferred to Cβ of the phenylpropanoid skeleton with retention of configuration. These labeled substrates also showed that the pro-(3S) proton exchanges with protons from the bulk media during its migration to Cα during catalysis. (1)H- and (2)H NMR analyses of the [(2)H]-β-tyrosine derived from (2S)-[3,3-(2)H2]-α-tyrosine by CcTAM catalysis showed that the migratory proton attached to Cα of the product also with retention of configuration. CcTAM is stereoselective for (R)-β-tyrosine (85%) yet also forms the (S)-β-tyrosine enantiomer (15%) through inversion of configuration at both migration termini, as described herein. The proportion of the (S)-β-isomer made by CcTAM during steady state interestingly increased with solvent pH, and this effect on the proposed reaction mechanism is also discussed. PMID:23800193

  1. Highly selective Lewis acid sites in desilicated MFI zeolites for dihydroxyacetone isomerization to lactic acid.

    PubMed

    Dapsens, Pierre Y; Mondelli, Cecilia; Pérez-Ramírez, Javier

    2013-05-01

    Desilication of commercial MFI-type (ZSM-5) zeolites in solutions of alkali metal hydroxides is demonstrated to generate highly selective heterogeneous catalysts for the aqueous-phase isomerization of biobased dihydroxyacetone (DHA) to lactic acid (LA). The best hierarchical ZSM-5 sample attains a LA selectivity exceeding 90 %, which is comparable to that of the state-of-the-art catalyst (i.e., the Sn-beta zeolite); this optimized hierarchical catalyst is recyclable over three runs. The Lewis acid sites, which are created through desilication along with the introduction of mesoporosity, are shown to play a crucial role in the formation of the desired product; these cannot be achieved by using other post-synthetic methods, such as steaming or impregnation of aluminum species. Desilication of other metallosilicates, such as Ga-MFI, also leads to high LA selectivity. In the presence of a soluble aluminum source, such as aluminum nitrate, alkaline-assisted alumination can introduce these unique Lewis acid centers in all-silica MFI zeolites. These findings highlight the potential of zeolites in the field of biomass-to-chemical conversion, and expand the applicability of desilication for the generation of selective catalytic centers. PMID:23554234

  2. Intramolecular interactions, isomerization and vibrational frequencies of two paracetamol analogues: A spectroscopic and a computational approach

    NASA Astrophysics Data System (ADS)

    Viana, Rommel B.; Ribeiro, Gabriela L. O.; Santos, Sinara F. F.; Quintero, David E.; Viana, Anderson B.; da Silva, Albérico B. F.; Moreno-Fuquen, Rodolfo

    2016-06-01

    The aim of this investigation was to determine the molecular properties and provide an interpretation of the vibrational mode couplings of these two paracetamol analogues: 2-bromo-2-methyl-N-(4-nitrophenyl)-propanamide and 2-bromo-2-methyl-N-p-tolyl-propanamide. E/Z isomers, keto/enol unimolecular rearrangement and prediction of the transition state structures in each mechanism were also assessed using the Density Functional Theory (DFT). The DFT estimates a high energy gap between E and Z isomers (9-11 kcal·mol- 1), with barrier heights ranging from 16 to 19 kcal·mol- 1. In contrast, the barrier energies on the keto/enol isomerization are almost 10 kcal·mol- 1 higher than those estimated for the E/Z rearrangement. The kinetic rate constant was also determined for each reaction mechanism. Natural bond orbital analysis and the quantum theory of atoms in molecules were used to interpret the intramolecular hydrogen bonds and to understand the most important interactions that govern the stabilization of each isomer. Furthermore, an analysis of the atomic charge distribution using different population methodologies was also performed.

  3. Intramolecular interactions, isomerization and vibrational frequencies of two paracetamol analogues: A spectroscopic and a computational approach.

    PubMed

    Viana, Rommel B; Ribeiro, Gabriela L O; Santos, Sinara F F; Quintero, David E; Viana, Anderson B; da Silva, Albérico B F; Moreno-Fuquen, Rodolfo

    2016-06-01

    The aim of this investigation was to determine the molecular properties and provide an interpretation of the vibrational mode couplings of these two paracetamol analogues: 2-bromo-2-methyl-N-(4-nitrophenyl)-propanamide and 2-bromo-2-methyl-N-p-tolyl-propanamide. E/Z isomers, keto/enol unimolecular rearrangement and prediction of the transition state structures in each mechanism were also assessed using the Density Functional Theory (DFT). The DFT estimates a high energy gap between E and Z isomers (9-11 kcal·mol(-1)), with barrier heights ranging from 16 to 19 kcal·mol(-1). In contrast, the barrier energies on the keto/enol isomerization are almost 10 kcal·mol(-1) higher than those estimated for the E/Z rearrangement. The kinetic rate constant was also determined for each reaction mechanism. Natural bond orbital analysis and the quantum theory of atoms in molecules were used to interpret the intramolecular hydrogen bonds and to understand the most important interactions that govern the stabilization of each isomer. Furthermore, an analysis of the atomic charge distribution using different population methodologies was also performed. PMID:26974474

  4. The mechanism of sugar phosphate isomerization by glucosamine 6-phosphate synthase.

    PubMed Central

    Teplyakov, A.; Obmolova, G.; Badet-Denisot, M. A.; Badet, B.

    1999-01-01

    Glucosamine 6-phosphate synthase converts fructose-6P into glucosamine-6P or glucose-6P depending on the presence or absence of glutamine. The isomerase activity is associated with a 40-kDa C-terminal domain, which has already been characterized crystallographically. Now the three-dimensional structures of the complexes with the reaction product glucose-6P and with the transition state analog 2-amino-2-deoxyglucitol-6P have been determined. Glucose-6P binds in a cyclic form whereas 2-amino-2-deoxyglucitol-6P is in an extended conformation. The information on ligand-protein interactions observed in the crystal structures together with the isotope exchange and site-directed mutagenesis data allow us to propose a mechanism of the isomerase activity of glucosamine-6P synthase. The sugar phosphate isomerization involves a ring opening step catalyzed by His504 and an enolization step with Glu488 catalyzing the hydrogen transfer from C1 to C2 of the substrate. The enediol intermediate is stabilized by a helix dipole and the epsilon-amino group of Lys603. Lys485 may play a role in deprotonating the hydroxyl O1 of the intermediate. PMID:10091662

  5. Ru-Zn heteropolynuclear complexes containing a dinucleating bridging ligand: synthesis, structure, and isomerism.

    PubMed

    Mognon, Lorenzo; Benet-Buchholz, Jordi; Rahaman, S M Wahidur; Bo, Carles; Llobet, Antoni

    2014-12-01

    Mononuclear complexes in- and out-[Ru(Cl)(trpy)(Hbpp)](+) (in-0, out-0; Hbpp is 2,2'-(1H-pyrazole-3,5-diyl)dipyridine and trpy is 2,2':6',2″-terpyridine) are used as starting materials for preparation of Ru-Zn heterodinuclear out-{[Ru(Cl)(trpy)][ZnCl2](μ-bpp)} (out-2) and heterotrinuclear in,in- and out,out-{[Ru(Cl)(trpy)]2(μ-[Zn(bpp)2])}(2+) (in-3, out-3) constitutional isomers. Further substitution of the Cl ligand from the former complexes leads to Ru-aqua out,out-{[Ru(trpy)(H2O)]2(μ-[Zn(bpp)2])}(4+) (out-4) and the oxo-bridged Ru-O-Ru complex in,in-{[Ru(III)(trpy)]2(μ-[Zn(bpp)2(H2O)]μ-(O)}(4+) (in-5). All complexes are thoroughly characterized by the usual analytical techniques as well as by spectroscopy by means of UV-vis, MS, and when diamagnetic NMR. CV and DPV are used to extract electrochemical information and monocrystal X-ray diffraction to characterize complexes out-2, in-3, out-3, and in-5 in the solid state. Complex out-3 photochemically isomerizes toward in-3, as can be observed by NMR spectroscopy and rationalized by density functional theory based calculations. PMID:25393055

  6. Tin-containing zeolites are highly active catalysts for the isomerization of glucose in water

    SciTech Connect

    Moliner, Manuel; Roman-Leshkov, Yuriy; Davis, Mark E.

    2010-04-06

    The isomerization of glucose into fructose is a large-scale reaction for the production of high-fructose corn syrup (HFCS; reaction performed by enzyme catalysts) and recently is being considered as an intermediate step in the possible route of biomass to fuels and chemicals. Here, it is shown that a large-pore zeolite that contains tin (Sn-Beta) is able to isomerize glucose to fructose in aqueous media with high activity and selectivity. Specifically, a 10% (wt/wt) glucose solution containing a catalytic amount of Sn-Beta (1:50 Sn:glucose molar ratio) gives product yields of approximately 46% (wt/wt) glucose, 31% (wt/wt) fructose, and 9% (wt/wt) mannose after 30 min and 12 min of reaction at 383 K and 413 K, respectively. This reactivity is achieved also when a 45 wt% glucose solution is used. The properties of the large-pore zeolite greatly influence the reaction behavior because the reaction does not proceed with a medium-pore zeolite, and the isomerization activity is considerably lower when the metal centers are incorporated in ordered mesoporous silica (MCM-41). The Sn-Beta catalyst can be used for multiple cycles, and the reaction stops when the solid is removed, clearly indicating that the catalysis is occurring heterogeneously. Most importantly, the Sn-Beta catalyst is able to perform the isomerization reaction in highly acidic, aqueous environments with equivalent activity and product distribution as in media without added acid. This enables Sn-Beta to couple isomerizations with other acid-catalyzed reactions, including hydrolysis/isomerization or isomerization/dehydration reaction sequences [starch to fructose and glucose to 5-hydroxymethylfurfural (HMF) demonstrated here].

  7. A Novel Technique that Enables Efficient Conduct of Simultaneous Isomerization and Fermentation (SIF) of Xylose

    NASA Astrophysics Data System (ADS)

    Rao, Kripa; Chelikani, Silpa; Relue, Patricia; Varanasi, Sasidhar

    Of the sugars recovered from lignocellulose, D-glucose can be readily converted into ethanol by baker's or brewer's yeast (Saccharomyces cerevisiae). However, xylose that is obtained by the hydrolysis of the hemicellulosic portion is not fermentable by the same species of yeasts. Xylose fermentation by native yeasts can be achieved via isomerization of xylose to its ketose isomer, xylulose. Isomerization with exogenous xylose isomerase (XI) occurs optimally at a pH of 7-8, whereas subsequent fermentation of xylulose to ethanol occurs at a pH of 4-5. We present a novel scheme for efficient isomerization of xylose to xylulose at conditions suitable for the fermentation by using an immobilized enzyme system capable of sustaining two different pH microenvironments in a single vessel. The proof-of-concept of the two-enzyme pellet is presented, showing conversion of xylose to xylulose even when the immobilized enzyme pellets are suspended in a bulk solution whose pH is sub-optimal for XI activity. The co-immobilized enzyme pellets may prove extremely valuable in effectively conducting "simultaneous isomerization and fermentation" (SIF) of xylose. To help further shift the equilibrium in favor of xylulose formation, sodium tetraborate (borax) was added to the isomerization solution. Binding of tetrahydroxyborate ions to xylulose effectively reduces the concentration of xylulose and leads to increased xylose isomerization. The formation of tetrahydroxyborate ions and the enhancement in xylulose production resulting from the complexation was studied at two different bulk pH values. The addition of 0.05 M borax to the isomerization solution containing our co-immobilized enzyme pellets resulted in xylose to xylulose conversion as high as 86% under pH conditions that are suboptimal for XI activity. These initial findings, which can be optimized for industrial conditions, have significant potential for increasing the yield of ethanol from xylose in an SIF approach.

  8. Intersubunit disulfide isomerization controls membrane fusion of human T-cell leukemia virus Env.

    PubMed

    Li, Kejun; Zhang, Shujing; Kronqvist, Malin; Wallin, Michael; Ekström, Maria; Derse, David; Garoff, Henrik

    2008-07-01

    Human T-cell leukemia virus (HTLV-1) Env carries a typical disulfide isomerization motif, C(225)XXC, in the C-terminal domain SU. Here we have tested whether this motif is used for isomerization of the intersubunit disulfide of Env and whether this rearrangement is required for membrane fusion. We introduced the C225A and C228A mutations into Env and found that the former but not the latter mutant matured into covalently linked SU-TM complexes in transfected cells. Next, we constructed a secreted Env ectodomain and showed that it underwent incubation-dependent intersubunit disulfide isomerization on target cells. However, the rearrangement was blocked by the C225A mutation, suggesting that C(225) carried the isomerization-active thiol. Still, it was possible to reduce the intersubunit disulfide of the native C225A ectodomain mutant with dithiothreitol (DTT). The importance of the CXXC-mediated disulfide isomerization for infection was studied using murine leukemia virus vectors pseudotyped with wild-type or C225A HTLV-1 Env. We found that the mutant Env blocked infection, but this could be rescued with DTT. The fusion activity was tested in a fusion-from-within assay using a coculture of rat XC target and transfected BHK-21 effector cells. We found that the mutation blocked polykaryon formation, but this could be reversed with DTT. Similar DTT-reversible inhibition of infection and fusion was observed when a membrane-impermeable alkylator was present during the infection/fusion incubation. We conclude that the fusion activity of HTLV-1 Env is controlled by an SU CXXC-mediated isomerization of the intersubunit disulfide. Thus, this extends the applicability of the isomerization model from gammaretroviruses to deltaretroviruses. PMID:18480461

  9. Thermal Dissociation and Roaming Isomerization of Nitromethane: Experiment and Theory.

    PubMed

    Annesley, Christopher J; Randazzo, John B; Klippenstein, Stephen J; Harding, Lawrence B; Jasper, Ahren W; Georgievskii, Yuri; Ruscic, Branko; Tranter, Robert S

    2015-07-16

    The thermal decomposition of nitromethane provides a classic example of the competition between roaming mediated isomerization and simple bond fission. A recent theoretical analysis suggests that as the pressure is increased from 2 to 200 Torr the product distribution undergoes a sharp transition from roaming dominated to bond-fission dominated. Laser schlieren densitometry is used to explore the variation in the effect of roaming on the density gradients for CH3NO2 decomposition in a shock tube for pressures of 30, 60, and 120 Torr at temperatures ranging from 1200 to 1860 K. A complementary theoretical analysis provides a novel exploration of the effects of roaming on the thermal decomposition kinetics. The analysis focuses on the roaming dynamics in a reduced dimensional space consisting of the rigid-body motions of the CH3 and NO2 radicals. A high-level reduced-dimensionality potential energy surface is developed from fits to large-scale multireference ab initio calculations. Rigid body trajectory simulations coupled with master equation kinetics calculations provide high-level a priori predictions for the thermal branching between roaming and dissociation. A statistical model provides a qualitative/semiquantitative interpretation of the results. Modeling efforts explore the relation between the predicted roaming branching and the observed gradients. Overall, the experiments are found to be fairly consistent with the theoretically proposed branching ratio, but they are also consistent with a no-roaming scenario and the underlying reasons are discussed. The theoretical predictions are also compared with prior theoretical predictions, with a related statistical model, and with the extant experimental data for the decomposition of CH3NO2, and for the reaction of CH3 with NO2. PMID:25886024

  10. Chronic Arrhythmias in the Setting of Heterotaxy: Differences between Right and Left Isomerism.

    PubMed

    Loomba, Rohit S; Willes, Richard J; Kovach, Joshua R; Anderson, Robert H

    2016-01-01

    So-called heterotaxy affects lateralization of the thoracic and abdominal organs. Congenital malformations may be present in one of several organ systems. Cardiac involvement includes both structural and conduction abnormalities. Data regarding arrhythmias in heterotaxy come from case reports and small case series. We pooled available data to further characterize arrhythmias in heterotaxy. A systematic review of the literature for manuscripts describing arrhythmias in heterotaxy patients was conducted. Databases including PubMed, EMBASE, and Ovid were searched. Studies describing arrhythmias in patients with heterotaxy were included if they were in English and presented characteristics of the arrhythmias. Arrhythmia characteristics were abstracted and are presented as pooled data. Freedom from arrhythmia by age was then analyzed using Kaplan-Meier analysis. A total of 19 studies with 121 patients were included in the pooled analysis. Those with right isomerism were found to be more likely to have atrial flutter, atrial tachycardia, junctional tachycardia, and ventricular tachycardia. Those with left isomerism were more likely to have atrioventricular block, intraventricular conduction delay, sick sinus syndrome, and atrioventricular nodal reentry tachycardia. Median age of onset for all arrhythmias was 4 years with no difference by specific arrhythmia or isomerism. Those with right and left isomerism are at risk for different arrhythmias but are likely to develop arrhythmias at the same age. Those with left isomerism are more likely to require pacemaker placement due to atrioventricular block. Understanding these differences allows for focused surveillance of development of these arrhythmias. PMID:26219620

  11. Identification of geometrical isomers and comparison of different isomeric samples of astaxanthin.

    PubMed

    Qiu, Dan; Wu, Yue-Chan; Zhu, Wen-Li; Yin, Hong; Yi, Long-Tao

    2012-09-01

    A high-performance liquid chromatographic (HPLC) analysis system for isomeric astaxanthin was developed. The separation system consisted of a C(30) column and an elution system of methanol/MTBE/water/dichloromethane (77:13:8:2, v/v/v/v). Using the combination of HPLC diode array detector and HPLC atmospheric pressure chemical ionization mass spectrometry, 11 geometrical isomers and 4 epoxides of astaxanthin were successfully identified. Referred to crystal, only isomerization with different degrees was found for solvent dissolving and iodine catalysis, while melting of astaxanthin caused isomerization, slight oxidation, and more noticeable polymerization confirmed by gel permeation chromatography. Chemical changes in isomeric samples all caused a decrease in UV content. The vibrational spectra (infrared and Raman) showed that epoxide was the only new functional group generated for melting. Changes of several key bands and formations of new bands were found in iodine catalysis and melting samples because of isomerization. Practical Application:  Eleven geometrical isomers and 4 epoxides, which were normally generated for solvent dissolving, iodine catalysis, and melting of astaxanthin, have been identified by C(30) -HPLC-MS technology. Furthermore, different samples were measured by gel permeation chromatography, UV, infrared, and Raman, based on the analysis of messages, the effect of each processing was well understood. PMID:22900833

  12. cis–trans-Amide isomerism of the 3,4-dehydroproline residue, the ‘unpuckered’ proline

    PubMed Central

    2016-01-01

    Summary Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis–trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state. PMID:27340450

  13. Interplay between metal binding and cis/trans isomerization in legume lectins: structural and thermodynamic study of P. angolensis lectin.

    PubMed

    Garcia-Pino, Abel; Buts, Lieven; Wyns, Lode; Loris, Remy

    2006-08-01

    The interplay between metal binding, carbohydrate binding activity, stability and structure of the lectin from Pterocarpus angolensis was investigated. Removal of the metals leads to a more flexible form of the protein with significantly less conformational stability. Crystal structures of this metal-free form show significant structural rearrangements, although some structural features that allow the binding of sugars are retained. We propose that substitution of an asparagine residue at the start of the C-terminal beta-strand of the legume lectin monomer hinders the trans-isomerization of the cis-peptide bond upon demetallization and constitutes an intramolecular switch governing the isomer state of the non-proline bond and ultimately the lectin phenotype. PMID:16824540

  14. Synthesis and spectral luminescent properties of certain pyridine and quinoline analogs of isomeric distyrylnaphthalenes and styryl- and distrylanthracenes

    SciTech Connect

    Vernigor, E.M.; Koz'menko, M.V; Lebedev, S.A.; Luk'yanets, E.A.; Savvina, L.P.; Shalaev, V.K.

    1987-12-01

    A series of pyridine and quinoline analogs of isomeric distyrylnaphthalenes and styryl- and distyrylanthracenes has been synthesized. Their spectral-luminescent properties were studied. Compounds whose structures are sterically hindered in the ground state have the highest Stokes' shift. The compounds synthesized have a trans-configuration; in their IR spectra there are absorption bands in the 970-990 cm/sup -1/ region, characteristic for trans-disubstituted alkenes. In the PMR spectrum of 9,10-di(..beta..-(4-pyridyl)vinyl)anthracene, two doublets of the AB spin system are observed with chemical shifts of 6.91 and 7.37 ppm, belonging to the vinyl protons. The SSCC (J = 16.5 Hz) indicates a trans-configuration of this compound.

  15. Visible-light-triggered molecular photoswitch based on reversible E/Z isomerization of a 1,2-dicyanoethene derivative.

    PubMed

    Guo, Xin; Zhou, Jiawang; Siegler, Maxime A; Bragg, Arthur E; Katz, Howard E

    2015-04-13

    A designed bis(dithienyl) dicyanoethene-based, strictly E/Z photoswitch (4TCE) operates through state-selective (E and Z isomer) photoactivation with visible light. The E and Z isomers of 4TCE exhibit remarkably different spectroscopic characteristics, including a large separation (70 nm) in their absorption maxima (λ(max)) and a 2.5-fold increase in molar extinction coefficient from cis to trans. The energetically stable trans form can be completely converted to the cis form within minutes when exposed to white light, whereas the reverse isomerization occurs readily upon irradiation by blue light (λ<480 nm) or completely by thermal conversion at elevated temperatures. These features together with excellent thermal stability and photostability of both isomers make this new E/Z photoswitch a promising building block for photoswitchable materials that operate without the need for UV light. PMID:25707025

  16. Crystal structure, matrix-isolation FTIR, and UV-induced conformational isomerization of 3-quinolinecarboxaldehyde.

    PubMed

    Kuş, Nihal; Henriques, Marta Sofia; Paixão, José António; Lapinski, Leszek; Fausto, Rui

    2014-09-25

    The crystal structure of 3-quinolinecarboxaldehyde (3QC) has been solved, and the compound has been shown to crystallize in the space group P21/c (monoclinic) with a = 6.306(4), b = 18.551(11), c = 6.999(4) Å, β = 106.111(13)°, and Z = 4. The crystals were found to exhibit pseudomerohedral twinning with a twin law corresponding to a two-fold rotation around the monoclinic (100) reciprocal lattice axis (or [4 0 1] in direct space). Individual molecules adopt the syn conformation in the crystal, with the oxygen atom of the aldehyde substituent directed toward the same side of the ring nitrogen atom. In the gas phase, the compound exists in two nearly isoenergetic conformers (syn and anti), which could be successfully trapped in solid argon at 10 K, and their infrared spectra are registered and interpreted. Upon in situ irradiation of matrix-isolated 3QC with UV light (λ > 315 nm), significant reduction of the population of the less stable anti conformer was observed, while that of the conformational ground state (syn conformer) increased, indicating occurrence of the anti → syn isomerization. Upon irradiation at higher energy (λ > 235 nm), the syn → anti reverse photoreaction was observed. Interpretation of the structural, spectroscopic, and photochemical experimental data received support from quantum chemical theoretical results obtained at both DFT/B3LYP (including TD-DFT investigation of excited states) and MP2 levels, using the 6-311++G(d,p) basis set. PMID:25144919

  17. Molecular polymorphism: microwave spectra, equilibrium structures, and an astronomical investigation of the HNCS isomeric family.

    PubMed

    McGuire, Brett A; Martin-Drumel, Marie-Aline; Thorwirth, Sven; Brünken, Sandra; Lattanzi, Valerio; Neill, Justin L; Spezzano, Silvia; Yu, Zhenhong; Zaleski, Daniel P; Remijan, Anthony J; Pate, Brooks H; McCarthy, Michael C

    2016-08-10

    The rotational spectra of thioisocyanic acid (HNCS), and its three energetic isomers (HSCN, HCNS, and HSNC) have been observed at high spectral resolution by a combination of chirped-pulse and Fabry-Pérot Fourier-transform microwave spectroscopy between 6 and 40 GHz in a pulsed-jet discharge expansion. Two isomers, thiofulminic acid (HCNS) and isothiofulminic acid (HSNC), calculated here to be 35-37 kcal mol(-1) less stable than the ground state isomer HNCS, have been detected for the first time. Precise rotational, centrifugal distortion, and nitrogen hyperfine coupling constants have been determined for the normal and rare isotopic species of both molecules; all are in good agreement with theoretical predictions obtained at the coupled cluster level of theory. On the basis of isotopic spectroscopy, precise molecular structures have been derived for all four isomers by correcting experimental rotational constants for the effects of rotation-vibration interaction calculated theoretically. Formation and isomerization pathways have also been investigated; the high abundance of HSCN relative to ground state HNCS, and the detection of strong lines of SH using CH3CN and H2S, suggest that HSCN is preferentially produced by the radical-radical reaction HS + CN. A radio astronomical search for HSCN and its isomers has been undertaken toward the high-mass star-forming region Sgr B2(N) in the Galactic Center with the 100 m Green Bank Telescope. While we find clear evidence for HSCN, only a tentative detection of HNCS is proposed, and there is no indication of HCNS or HSNC at the same rms noise level. HSCN, and tentatively HNCS, displays clear deviations from a single-excitation temperature model, suggesting weak masing may be occurring in some transitions in this source. PMID:27478937

  18. Domain catalyzed chemical reactions: A molecular dynamics simulation of isomerization kinetics

    NASA Astrophysics Data System (ADS)

    Toxvaerd, S.

    2004-04-01

    The model for domain catalyzed isomerization kinetics in condensed fluids [S. Toxvaerd, Phys. Rev. Lett. 85, 4747 (2000)] is applied for a diluted mixture of a chiral solute with a consolute temperature. The solution is quench to phase separation at temperatures below the consolute temperature. The droplet coalescence enhances the isomerization kinetics due to the substantial excess pressure inside the small droplets given by the Laplace equation. The domain catalyzed isomerization kinetics breaks the symmetry, and the droplets end with only one dominating species. We argue that D-Glyceraldehyde which is only moderately solvable in water and which has played a crucial role in the evolution is a candidate for the stereo specific ordering in bio-organic matter.

  19. Isomerization and optical bistability of DR1 doped organic-inorganic sol-gel thin film

    NASA Astrophysics Data System (ADS)

    Gao, Tianxi; Que, Wenxiu; Shao, Jinyou

    2015-10-01

    To investigate the isomerization process of the disperse red 1 (DR1) doped TiO2/ormosil thin film, both the photo-isomerization and the thermal isomerization of the thin films were observed as a change of the absorption spectrum. Under a real-time heat treatment, the change of the linear refractive index shows a thermal stable working temperature range below Tg. The optical bistability (OB) effect of the DR1 doped thin films based on different matrices was studied and measured at a wavelength of 532 nm. Results indicate that the TiO2/ormosils based thin film presents a better OB-gain than that of the poly (methyl methacrylate) (PMMA) based thin film due to its more rigid network structure. Moreover, it is also noted that higher titanium content is helpful for enhancing the OB-gain of the as-prepared hybrid thin films.

  20. Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

    NASA Astrophysics Data System (ADS)

    Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

    2015-09-01

    A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.

  1. Acinetobactin Isomerization Enables Adaptive Iron Acquisition in Acinetobacter baumannii through pH-Triggered Siderophore Swapping.

    PubMed

    Shapiro, Justin A; Wencewicz, Timothy A

    2016-02-12

    Pathogenic strains of Acinetobacter baumannii excrete multiple siderophores that enhance iron scavenging from host sources. The oxazoline siderophore pre-acinetobactin undergoes an unusual non-enzymatic isomerization, producing the isoxazolidinone acinetobactin. In this study, we explored the kinetics, mechanism, and biological consequence of this siderophore swapping. Pre-acinetobactin is excreted to the extracellular space where the isomerization to acinetobactin occurs with a pH-rate profile consistent with 5-exo-tet cyclization at C5' with clean stereochemical inversion. Pre-acinetobactin persists at pH <6, and acinetobactin is rapidly formed at pH >7, matching each siderophore's pH preference for iron(III) chelation and A. baumannii growth promotion. Acinetobactin isomerization provides two siderophores for the price of one, enabling A. baumannii to sequester iron over a broad pH range likely to be encountered during the course of an infection. PMID:27624967

  2. Kinetics and specificity of homogeneous protein disulphide-isomerase in protein disulphide isomerization and in thiol-protein-disulphide oxidoreduction.

    PubMed

    Lambert, N; Freedman, R B

    1983-07-01

    The protein disulphide-bond isomerization activity of highly active homogeneous protein disulphide-isomerase (measured by re-activation of 'scrambled' ribonuclease) is enhanced by EDTA and by phosphate buffers. As shown for previous less-active preparations, the enzyme has a narrow pH optimum around pH 7.8 and requires the presence of either a dithiol or a thiol. The dithiol dithiothreitol is effective at concentrations 100-fold lower than the monothiols reduced glutathione and cysteamine. The enzyme follows Michaelis-Menten kinetics with respect to these substrates; Km values are 4,620 and 380 microM respectively. The enzyme shows apparent inhibition by high concentrations of thiol or dithiol compounds (greater than 10 X Km), but the effect is mainly on the extent of reaction, not the initial rate. This is interpreted as indicating the formation of significant amounts of reduced ribonuclease in these more reducing conditions. The purified enzyme will also catalyse net reduction of insulin disulphide bonds by reduced glutathione (i.e. it has thiol:protein-disulphide oxidoreductase or glutathione:insulin transhydrogenase activity), but this requires considerably higher concentrations of enzyme and reduced glutathione than does the disulphide-isomerization activity. The Km for reduced glutathione in this reaction is an order of magnitude greater than that for the disulphide-isomerization activity, and the turnover number is considerably lower than that of other enzymes that can catalyse thiol-disulphide oxidoreduction. Conventional two-substrate steady-state analysis of the thiol:protein-disulphide oxidoreductase activity indicates that it follows a ternary-complex mechanism. The protein disulphide-isomerase and thiol:protein-disulphide oxidoreductase activities co-purify quantitatively through the final stages of purification, implying that a single protein species is responsible for both activities. It is concluded that previous preparations, from various sources

  3. Impacts of daily intakes on the isomeric profiles of perfluoroalkyl substances (PFASs) in human serum.

    PubMed

    Shan, Guoqiang; Wang, Zhi; Zhou, Lianqiu; Du, Pin; Luo, Xiaoxiao; Wu, Qiannian; Zhu, Lingyan

    2016-01-01

    Perfluoroalkyl substances (PFASs) have been well studied in human daily intake for assessment of potential health risks. However, little is known about the isomeric compositions of PFASs in daily intake and their impacts on isomeric profiles in humans. In this study, we investigated the occurrence of PFASs with isomeric analysis in various human exposure matrices including foodstuffs, tap water and indoor dust. Perfluorooctanesulfonate (PFOS) and/or perfluorooctanoate (PFOA) were predominant in these exposure matrices collected in Tianjin, China. In fish and meat, linear (n-) PFOA was enriched with a percentage of 92.2% and 99.6%, respectively. Although n-PFOS was higher in fish (84.8%) than in technical PFOS (ca. 70%), it was much lower in meat (63.1%) and vegetables (58.5%). Dietary intake contributed >99% of the estimated daily intake (EDI) for the general population. The isomeric profiles of PFOA and PFOS in human serum were predicted based on the EDI and a one-compartment, first-order pharmacokinetic model. The isomeric percentage of n-PFOA in the EDI (98.6%) was similar to that in human serum (predicted: 98.2%, previously measured: 99.7%) of Tianjin residents. The results suggest direct PFOA intake plays an important role in its isomeric compositions in humans. For PFOS, the predicted n-PFOS (69.3%) was much higher than the previously measured values (59.2%) in human serum. This implies that other factors, such as indirect exposure to PFOS precursors and multiple excretion pathways, may contribute to the lower percentage of n-PFOS in humans than of technical PFOS. PMID:26826363

  4. Irreversible H2-antagonism of the four isomeric butyl analogues of mifentidine.

    PubMed

    Bastiaans, H M; Donetti, A; Kramer, K; Bietti, G; Cereda, E; Dubini, D; Mondini, M; Bast, A; Timmerman, H

    1990-04-01

    It has been hypothesized that bidentate hydrogen bonding plays an important role in the interaction of imidazolylphenylformamidines with the H2-receptor. The present study, in which the degree of pseudo-irreversible H2-antagonism of the four isomeric butyl substituted mifentidine analogues was determined on the spontaneously beating right atrium of the male guinea-pig, lends further support to this hypothesis. In solution the EE/EZ ratio is different for the four isomeric butylated mifentidine analogues. The rank order of the percentage of E,E conformation, which favors a bidentate interaction, of the formamidine moiety parallels the rank order of pseudo-irreversible H2-antagonism. PMID:1973582

  5. Isomerization of Cyclooctadiene to Cyclooctyne with a Zinc/Zirconium Heterobimetallic Complex.

    PubMed

    Butler, Michael J; White, Andrew J P; Crimmin, Mark R

    2016-06-01

    Reaction of a zinc/zirconium heterobimetallic complex with 1,5-cyclooctadiene (1,5-COD) results in slow isomerization to 1,3-cyclooctadiene (1,3-COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5-COD to 1,3-COD, only in the case of the zinc species is the cyclooctyne adduct observed. PMID:27071992

  6. Mechanistic Aspects of the Palladium-Catalyzed Isomerization of Allenic Sulfones to 1-Arylsulfonyl 1,3-Dienes.

    PubMed

    Hampton, Carissa S; Harmata, Michael

    2016-06-01

    When an allenic sulfone is treated under palladium catalysis in the presence of a weak acid, isomerization to a 1-arylsulfonyl 1,3-diene occurs. Investigations of the mechanistic aspects of this isomerization were performed, leading to the mechanism proposed herein. Some further studies of reaction parameters are reported. PMID:27127922

  7. Solvent-induced and polyether-ligand-induced redox isomerization within an asymmetrically coordinated mixed-valence ion: trans-(py)(NH[sub 3])[sub 4]Ru(4-NCpy)Ru(2,2[prime]-bpy)[sub 2]Cl[sup 4+

    SciTech Connect

    Curtis, J.C.; Massum, M. ); Roberts, J.A.; Blackbourn, R.L.; Dong, Yuhua; Johnson, C.S.; Hupp, J.T. )

    1991-10-02

    Advantage is taken of oxidation-state-dependent ligand (ammine)/solvent interactions to shift redox potentials and effect redox isomerization in the title complex. In poorly basic solvents, the stable isomeric form is trans-(py)(NH[sub 3])[sub 4]Ru[sup II](NCpy)Ru[sup III](bpy)[sub 2]Cl[sup 4+] (py is pyridine; NCpy is 4-cyanopyridine; bpy is 2,2[prime]-bipyridine). In contrast, in stronger Lewis bases or in a mixture of strong and weak bases (dimethyl sulfoxide + nitromethane), the preferred isomer is trans-(py)(NH[sub 3])[sub 4]Ru[sup III](NCpy)Ru[sup II](bpy)Cl[sup 4+]. Evidence for redox isomerization was obtained, in part, from plots of formal potentials versus solvent Lewis basicity. Confirmatory evidence was obtained from a combination of electrochemical reaction entropy and resonance Raman spectroscopic experiments. UV-vis-near-IR absorption experiments, however, were not found to be useful in demonstrating isomerization. In a released series of experiments, redox isomerization was also demonstrated based on ammine binding by either a low molecular weight poly(ethylene glycol) species or by a macrocyclic ligand, dibenzo-36-crown-12. Much smaller molar amounts of either the polymer (substoichiometric) or crown (approximately stoichiometic) are required, in comparison to basic solvent (several-fold excess), in order to induce isomerization in nitromethane as the initial solvent. The possible general utility of the redox isomerization concept in time-resolved intramolecular charge-transfer studies and in optical studies of competitive hole- and electron hole- and electron-transfer pathways is mentioned.

  8. LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Self-sustained exothermic reaction of anti-Stokes gamma transitions in long-lived isomeric nuclei. I

    NASA Astrophysics Data System (ADS)

    Rivlin, Lev A.

    2000-06-01

    The conditions for implementing a self-sustained exothermic nuclear (combustion) reaction in a system comprising long-lived metastable isomers and quasi-equilibrium high-temperature black-body radiation are examined. In this system the radiative decay of the metastable state is a result of an anti-Stokes process bypassing a strongly forbidden isomeric transition. The anti-Stokes transition in the reaction zone is triggered by the corresponding resonance spectral components of the quasi-equilibrium radiation, the temperature of which, sufficient to close the energy reaction cycle, is in its turn maintained by the absorption of hard photons, emitted by nuclei, in the reaction zone.

  9. A search for thermal isomerization of olefins to carbenes: Thermal generations of the silicon-nitrogen double bond

    SciTech Connect

    Zhang, Xianping.

    1990-09-21

    The first part of this thesis will search for the thermal isomerization of olefins to carbenes which is predicted to be a high energy process by calculations and has only been observed in a few strained olefins. The possibility of thermal isomerization of simple olefins to carbenes will be explored. Substitution of a silyl group on the double bond of an olefin allows a potential intermediate which has a {beta}-radical to the silyl group during the cis-trans isomerization. The effects of a trimethylsilyl group on this isomerization are the subject of this study. The second part of this thesis will include the generation and chemistry of intermediates containing a silicon-nitrogen double bond. The isomerization of parent silanimine to the aminosilylene was calculated to be a high energy process. New approaches to the silicon-nitrogen double bond will also be presented. 92 refs., 12 figs., 11 tabs.

  10. Isomerization of the uncomplexed actinidin molecule: kinetic accessibility of additional steps in enzyme catalysis provided by solvent perturbation.

    PubMed Central

    Reid, James D; Hussain, Syeed; Bailey, Tamara S F; Sonkaria, Sanjiv; Sreedharan, Suneal K; Thomas, Emrys W; Resmini, Marina; Brocklehurst, Keith

    2004-01-01

    The effects of increasing the content of the aprotic dipolar organic co-solvent acetonitrile on the observed first-order rate constant (k(obs)) of the pre-steady state acylation phases of the hydrolysis of N-acetyl-Phe-Gly methyl thionester catalysed by the cysteine proteinase variants actinidin and papain in sodium acetate buffer, pH 5.3, were investigated by stopped-flow spectral analysis. With low acetonitrile content, plots of k(obs) against [S]0 for the actinidin reaction are linear with an ordinate intercept of magnitude consistent with a five-step mechanism involving a post-acylation conformational change. Increasing the acetonitrile content results in marked deviations of the plots from linearity with a rate minimum around [S]0=150 microM. The unusual negative dependence of k(obs) on [S]0 in the range 25-150 microM is characteristic of a rate-determining isomerization of the free enzyme before substrate binding, additional to the five-step mechanism. There was no evidence for this phenomenon nor for the post-acylation conformational change in the analogous reaction with papain. For this enzyme, however, acetonitrile acts as an inhibitor with approximately uncompetitive characteristics. Possible mechanistic consequences of the differential solvent-perturbed kinetics are indicated. The free enzyme isomerization of actinidin may provide an explanation for the marked difference in sensitivity between this enzyme and papain of binding site-catalytic site signalling in reactions of substrate-derived 2-pyridyl disulphide reactivity probes. PMID:14640975

  11. Structural Diversity of Cadmium(II) Coordination Polymers Induced by Tuning the Coordination Sites of Isomeric Ligands.

    PubMed

    Liu, Bo; Zhou, Hui-Fang; Hou, Lei; Wang, Jian-Ping; Wang, Yao-Yu; Zhu, Zhonghua

    2016-09-01

    When the coordination sites of ligands were shifted, the solvothermal reactions of four positional isomeric asymmetrical pyridyldicarboxylatic acids with Cd(NO3)2 generated four new coordination polymers, [Cd(L1)(DMF)3]·DMF·H2O (1), [H2N(CH3)2]2[Cd(L2)2]·3DMF·H2O (2), [Cd(L3)(H2O)2] (3), and [Cd(L4)]·1.5DMF (4), where DMF = N,N-dimethylformamide, H2L1 = 2-(3'-carboxylphenyl)isonicotinic acid, H2L2 = 2-(4'-carboxylphenyl)isonicotinic acid, H2L3 = 5-(3'-carboxylphenyl)nicotic acid, and H2L4 = 2-(3'-pyridyl)terephthalic acid. 1 shows a rare 2D fabric structure. 2 discloses a grid-layer structure with heterochiral helical chains and in which three sets of layers stack in different directions, affording an unprecedented 2D + 2D + 2D → 3D polycatenating framework with 3D intersecting porous systems. 3 also displays a 2D layer possessing strong intralayer π···π interactions and interlayer hydrogen bonds. 4 contains a rare Cd2(COO)4 paddle-wheel unit and forms a 3D framework with 1D open channels. The carboxyl and pyridyl groups of the positional isomeric H2L1-H2L4 ligands show distinct bridging fashions, which leads to the production of versatile architectures of 1-4, and their effects on the crystal structures are discussed. 1-4 reveal solid-state photoluminescence stemming from intraligand charge transfer. 2 and 4 show high selectivity for CO2 over CH4 but with different CO2 adsorption enthalpies. Grand canonical Monte Carlo simulations identified the multiple adsorption sites in 2 for CO2. PMID:27513092

  12. Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.

    PubMed Central

    Hodel, A.; Rice, L. M.; Simonson, T.; Fox, R. O.; Brünger, A. T.

    1995-01-01

    Staphylococcal nuclease A exists in two folded forms that differ in the isomerization state of the Lys 116-Pro 117 peptide bond. The dominant form (90% occupancy) adopts a cis peptide bond, which is observed in the crystal structure. NMR studies show that the relatively small difference in free energy between the cis and trans forms (delta Gcis-->trans approximately 1.2 kcal/mol) results from large and nearly compensating differences in enthalpy and entropy (delta Hcis-->trans approximately delta TScis-->trans approximately 10 kcal/mol). There is evidence from X-ray crystal structures that the structural differences between the cis and the trans forms of nuclease are confined to the conformation of residues 112-117, a solvated protein loop. Here, we obtain a thermodynamic and structural description of the conformational equilibrium of this protein loop through an exhaustive conformational search that identified several substates followed by free energy simulations between the substrates. By partitioning the search into conformational substates, we overcame the multiple minima problem in this particular case and obtained precise and reproducible free energy values. The protein and water environment was implicitly modeled by appropriately chosen nonbonded terms between the explicitly treated loop and the rest of the protein. These simulations correctly predicted a small free energy difference between the cis and trans forms composed of larger, compensating differences in enthalpy and entropy. The structural predictions of these simulations were qualitatively consistent with known X-ray structures of nuclease variants and yield a model of the unknown minor trans conformation. PMID:7613463

  13. Linkage Isomerization in Heme–NOx Compounds: Understanding NO, Nitrite, and Hyponitrite Interactions with Iron Porphyrins

    PubMed Central

    Xu, Nan; Yi, Jun

    2011-01-01

    Nitric oxide (NO) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. Much of their physiological relevance stems from their interactions with the iron centers in heme proteins. The chemical reactivities displayed by the heme-NOx species (NOx = NO, nitrite, hyponitrite) are a function of the binding modes of the NOx ligands. Hence, an understanding of the types of binding modes extant in heme-NOx compounds is important if we are to unravel the inherent chemical properties of these NOx metabolites. In this Forum article, the experimentally characterized linkage isomers of heme-NOx models and proteins are presented and reviewed. Nitrosyl linkage isomers of synthetic Fe and Ru porphyrins have been generated by photolysis at low temperatures and characterized by spectroscopy and DFT calculations. Nitrite linkage isomers in synthetic metalloporphyrin derivatives have been generated from photolysis experiments and in low-temperature matrices. In the case of nitrite adducts of heme proteins, both N-binding and O-binding have been determined crystallographically, and the role of the distal Hbonding residue in myoglobin in directing the O-binding mode of nitrite has been explored using mutagenesis. To date, only one synthetic metalloporphyrin complex containing a hyponitrite ligand (displaying an O-binding mode) has been characterized by crystallography. This is contrasted with other hyponitrite binding modes experimentally determined for coordination compounds and computationally for NO reductase enzymes. Although linkage isomerism in heme-NOx derivatives is still in its infancy, opportunities now exist for a detailed exploration of the existence and stabilities of the metastable states in both heme models and heme proteins. PMID:20666385

  14. Linkage isomerization in heme-NOx compounds: understanding NO, nitrite, and hyponitrite interactions with iron porphyrins.

    PubMed

    Xu, Nan; Yi, Jun; Richter-Addo, George B

    2010-07-19

    Nitric oxide (NO) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. Much of their physiological relevance stems from their interactions with the iron centers in heme proteins. The chemical reactivities displayed by the heme-NOx species (NOx = NO, nitrite, hyponitrite) are a function of the binding modes of the NOx ligands. Hence, an understanding of the types of binding modes extant in heme-NOx compounds is important if we are to unravel the inherent chemical properties of these NOx metabolites. In this Forum Article, the experimentally characterized linkage isomers of heme-NOx models and proteins are presented and reviewed. Nitrosyl linkage isomers of synthetic iron and ruthenium porphyrins have been generated by photolysis at low temperatures and characterized by spectroscopy and density functional theory calculations. Nitrite linkage isomers in synthetic metalloporphyrin derivatives have been generated from photolysis experiments and in low-temperature matrices. In the case of nitrite adducts of heme proteins, both N and O binding have been determined crystallographically, and the role of the distal H-bonding residue in myoglobin in directing the O-binding mode of nitrite has been explored using mutagenesis. To date, only one synthetic metalloporphyrin complex containing a hyponitrite ligand (displaying an O-binding mode) has been characterized by crystallography. This is contrasted with other hyponitrite binding modes experimentally determined for coordination compounds and computationally for NO reductase enzymes. Although linkage isomerism in heme-NOx derivatives is still in its infancy, opportunities now exist for a detailed exploration of the existence and stabilities of the metastable states in both heme models and heme proteins. PMID:20666385

  15. How Accurate Are the Minnesota Density Functionals for Noncovalent Interactions, Isomerization Energies, Thermochemistry, and Barrier Heights Involving Molecules Composed of Main-Group Elements?

    PubMed

    Mardirossian, Narbe; Head-Gordon, Martin

    2016-09-13

    The 14 Minnesota density functionals published between the years 2005 and early 2016 are benchmarked on a comprehensive database of 4986 data points (84 data sets) involving molecules composed of main-group elements. The database includes noncovalent interactions, isomerization energies, thermochemistry, and barrier heights, as well as equilibrium bond lengths and equilibrium binding energies of noncovalent dimers. Additionally, the sensitivity of the Minnesota density functionals to the choice of basis set and integration grid is explored for both noncovalent interactions and thermochemistry. Overall, the main strength of the hybrid Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., M06-2X), barrier heights (e.g., M08-HX, M08-SO, MN15), and systems heavily characterized by self-interaction error (e.g., M06-2X, M08-HX, M08-SO, MN15), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-2X is recommended from the 10 hybrid Minnesota functionals). Similarly, the main strength of the local Minnesota density functionals is that the best ones provide very good performance for thermochemistry (e.g., MN15-L), barrier heights (e.g., MN12-L), and systems heavily characterized by self-interaction error (e.g., MN12-L and MN15-L), while the main weakness is that none of them are state-of-the-art for the full spectrum of noncovalent interactions and isomerization energies (although M06-L is clearly the best from the four local Minnesota functionals). As an overall guide, M06-2X and MN15 are perhaps the most broadly useful hybrid Minnesota functionals, while M06-L and MN15-L are perhaps the most broadly useful local Minnesota functionals, although each has different strengths and weaknesses. PMID:27537680

  16. Spectroscopic and structural studies of quinoline derivatives—II. Forrier transform i.r. spectroscopy. 1. Rotational isomerism in 3-ethoxycarbonyl-4(1H)-quinolone and some of its substituted derivatives,

    NASA Astrophysics Data System (ADS)

    Mirek, Julian; Urbanek, Zbigniew H.

    Rotational isomerism associated with internal rotation about the ring carbon(3)-ester carbonyl carbon single bond in a series of 3-ethoxycarbonyl-4(1H)-quinolones have been investigated spectroscopically in the solid state using Fourier transform i.r. and laser Raman spectroscopy. Particular attention is given to the 1700, 1300 and 1100 cm -1 spectral regions related primarily to the vibrations of the CO 2C 2H 5 group. Within these regions rotational isomerism appeared in the compounds examined. The conformational changes are discussed and evidence is reported for occurrence of the unsubstituted compound 1 itself in the solid state at ambient temperature as an equilibrium mixture of both the s-trans ( 1a) and s-cis ( 1b) rotamers (this is in contrast to previous findings), and of its Bz-substituted derivatives.

  17. Asymmetric synthesis of trifluoromethylated amines via catalytic enantioselective isomerization of imines.

    PubMed

    Wu, Yongwei; Deng, Li

    2012-09-01

    A new approach toward the asymmetric synthesis of optically active trifluoromethylated amines was enabled by an unprecedented, highly enantioselective catalytic isomerization of trifluoromethyl imines with a new chiral organic catalyst. Not only aryl but also alkyl trifluoromethylated amines could be obtained in high enantioselectivities. PMID:22906148

  18. Bio-olefins via tandem isomerization-decarboxylation catalysis upon fatty acids

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A facile Ru-catalyzed route to bio-alkenes from alkenoic fatty acids will be discussed. A readily accessible pre-catalyst [Ru(CO)2RCO2]n. apparently functions in a tandem mode by dynamically isomerizing the positions of double bonds in an aliphatic chain and, subsequently, decarboxylating specific i...

  19. Tandem isomerization-decarboxylation for converting alkenoic fatty acids into alkenes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report a facile Ru-catalyzed route to alkenes from alkenoic fatty acids via a readily accessible pre-catalyst [Ru(CO)2RCO2]n. The catalyst apparently functions in a tandem mode by dynamically isomerizing the positions of double bonds in an aliphatic chain and, subsequently, decarboxylating specif...

  20. Xylose isomerization with zeolites in a two-step alcohol-water process.

    PubMed

    Paniagua, Marta; Saravanamurugan, Shunmugavel; Melian-Rodriguez, Mayra; Melero, Juan A; Riisager, Anders

    2015-03-01

    Isomerization of xylose to xylulose was efficiently catalyzed by large-pore zeolites in a two-step methanol-water process that enhanced the product yield significantly. The reaction pathway involves xylose isomerization to xylulose, which, in part, subsequently reacts with methanol to form methyl xyluloside (step 1) followed by hydrolysis after water addition to form additional xylulose (step 2). NMR spectroscopy studies performed with (13) C-labeled xylose confirmed the proposed reaction pathway. The most active catalyst examined was zeolite Y, which proved more active than zeolite beta, ZSM-5, and mordenite. The yield of xylulose obtained over H-USY (Si/Al=6) after 1 h of reaction at 100 °C was 39%. After water hydrolysis in the second reaction step, the yield increased to 47%. Results obtained from pyridine adsorption studies confirm that H-USY (6) is a catalyst that combines Brønsted and Lewis acid sites, and isomerizes xylose in alcohol media to form xylulose at low temperature. The applied zeolites are commercially available; do not contain any auxiliary tetravalent metals, for example, tin, titanium, or zirconium; isomerize xylose efficiently; are easy to regenerate; and are prone to recycling. PMID:25703506

  1. Surprising photochemical and thermal isomerizations of a cyclic 1,2,3-butatriene

    SciTech Connect

    Chen, Yiyuan; Ma, Zhongxin; Ijadi-Maghsoodi, Sina; Barton, T.J.

    1997-12-31

    Photolysis of cyclic 1,2,3-butatriene 1 exclusively affords cyclopropane 2 for which an unprecedented initial isomerization to a methylenecyclopropanylidene is proposed. Thermolysis of 1 produces butadiene 3 in 83% yield. Formation of 3 is an apparent disallowed S, A [2+2] cycloaddition but we will argue that it is actually an allowed [4+2] cycloaddition.

  2. Twice primed: cyclin E is phosphorylated and isomerized before being ubiquitinated.

    PubMed

    Shumway, Stuart D; Xiong, Yue

    2006-07-21

    Targeting proteins for irreversible degradation must be under tight control and is often regulated at the level of substrate-receptor binding. But does a protein really need to be marked twice with two different modifications, first phosphorylation and then isomerization, to bind its receptor, as van Drogen et al. (2006) show for cyclin E? PMID:16857579

  3. The Isomerization of (-)-Menthone to (+)-Isomenthone Catalyzed by an Ion-Exchange Resin

    ERIC Educational Resources Information Center

    Ginzburg, Aurora L.; Baca, Nicholas A.; Hampton, Philip D.

    2014-01-01

    A traditional organic chemistry laboratory experiment involves the acid-catalyzed isomerization of (-)-menthone to (+)-isomenthone. This experiment generates large quantities of organic and aqueous waste, and only allows the final ratio of isomers to be determined. A "green" modification has been developed that replaces the mineral acid…

  4. Fuel properties of heptadecene isomers prepared via tandem isomerization-decarboxylation of oleic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heptadecene isomers were prepared via tandem isomerization-decarboxylation of oleic acid using catalytic triruthenium dodecacarbonyl [Ru3(CO)12]. Chromatographic and spectroscopic characterization of the isolated heptadecene mixture indicated that it consisted of 96% internal trans isomers and 4% ar...

  5. Studies on the simultaneous enzymatic isomerization and yeast fermentation of D-xylose

    SciTech Connect

    Roman de Rodriguez Ganduglia, G.N.

    1983-01-01

    The addition of the enzyme D-xylose isomerase (glucose isomerase) to fermentation medium facilitates the conversion of D-xylose into ethanol by a two step process in which D-xylose is first isomerized to D-xylose, which is in turn converted to ethanol by yeast. Detailed kinetic studies were conducted independently for the isomerization reaction and for the fermentation of D-xylose by the yeast Schizosaccharomyces pombe. The kinetics of the isomerization reaction has been examined using a differential batch reactor at different temperatures and pH value. The kinetics of the utilization of D-xylose by the yeast Schizosaccharomyces pombe has been examined in presence of D-xylose and ethanol under anaerobic batch conditions. The effects of the concentration of each of the two sugars upon the production of ethanol were also examined. A combined model has been formulated that predicts the performance of the batch conversion of D-xylose to ethanol by the simultaneous isomerization/fermentation process. A reasonable agreement was found between experimental data and values calculated from the model.

  6. Isomerization of 4-vinylcyclohexene radical cation. A tandem mass spectrometry study

    SciTech Connect

    Vollmer, D.; Rempel, D.L.; Gross, M. L. ); Williams, F. )

    1995-02-08

    Investigation by matrix-isolation ESR has shown that 4-vinylcyclohexene, 1, surprisingly undergoes isomerization to the bicyclo[3.2.1]oct-2-ene ion, 3. Here we demonstrate the occurrence of this isomerization in the gas phase by use of tandem (MS/MS) sector and Fourier transform (FT) mass spectrometries. The radical cations of 4-vinylcyclohexene (IE = 8.93 eV) or bicyclo[3.2.1]oct-2-ene (approximately 14 kcal/mol more stable than that of 4-vinylcyclohexene) were formed, in separate trials, in a chemical ionization (CI) source by electron ionization (EI). The radical cations were then studied by obtaining their collisionally activated decomposition (CAD) spectra. The CAD spectra are similar, indicating that the isomerization has occurred. Both the sector and the FT mass spectrometer results reflect those obtained in the matrix-isolation ESR investigation. That is isomerizes to 3 at high internal energy, but is stable at low internal energy. Two mechanisms explain this rearrangement. The second mechanism is questionable because the most stable olefin radical cation formed from 5 is that of bicyclo[2.2.2]-2-octene, which gives different ESR and CAD spectra than those of 1 or 3. The CAD spectrum of bicyclo[2.2.2]-2-octene radical cation indicates that the retro-Diels-Alder loss of ethylene is more facile than that from 1 or 3. 18 refs., 3 figs.

  7. A classical trajectory study of the intramolecular dynamics, isomerization, and unimolecular dissociation of HO2

    NASA Astrophysics Data System (ADS)

    Perry, Jamin W.; Dawes, Richard; Wagner, Albert F.; Thompson, Donald L.

    2013-08-01

    The classical dynamics and rates of isomerization and dissociation of HO2 have been studied using two potential energy surfaces (PESs) based on interpolative fittings of ab initio data: An interpolative moving least-squares (IMLS) surface [A. Li, D. Xie, R. Dawes, A. W. Jasper, J. Ma, and H. Guo, J. Chem. Phys. 133, 144306 (2010)] and the cubic-spline-fitted PES reported by Xu, Xie, Zhang, Lin, and Guo (XXZLG) [J. Chem. Phys. 127, 024304 (2007)]. Both PESs are based on similar, though not identical, internally contracted multi-reference configuration interaction with Davidson correction (icMRCI+Q) electronic structure calculations; the IMLS PES includes complete basis set (CBS) extrapolation. The coordinate range of the IMLS PES is limited to non-reactive processes. Surfaces-of-section show similar generally regular phase space structures for the IMLS and XXZLG PESs with increasing energy. The intramolecular vibrational energy redistribution (IVR) at energies above and below the threshold of isomerization is slow, especially for O-O stretch excitations, consistent with the regularity in the surfaces-of-section. The slow IVR rates lead to mode-specific effects that are prominent for isomerization (on both the IMLS and XXZLG) and modest for unimolecular dissociation to H + O2 (accessible only on the XXZLG PES). Even with statistical distributions of initial energy, slow IVR rates result in double exponential decay for isomerization, with the slower rate correlated with slow IVR rates for O-O vibrational excitation. The IVR and isomerization rates computed for the IMLS and XXZLG PESs are quantitatively, but not qualitatively, different from one another with the largest differences ascribed to the ˜2 kcal/mol difference in the isomerization barrier heights. The IMLS and XXZLG results are compared with those obtained using the global, semi-empirical double-many-body expansion DMBE-IV PES [M. R. Pastrana, L. A. M. Quintales, J. Brandão, and A. J. C. Varandas, J. Chem

  8. Ibuprofen Impairs Allosterically Peroxynitrite Isomerization by Ferric Human Serum Heme-Albumin*

    PubMed Central

    Ascenzi, Paolo; di Masi, Alessandra; Coletta, Massimo; Ciaccio, Chiara; Fanali, Gabriella; Nicoletti, Francesco P.; Smulevich, Giulietta; Fasano, Mauro

    2009-01-01

    Human serum albumin (HSA) participates in heme scavenging; in turn, heme endows HSA with myoglobin-like reactivity and spectroscopic properties. Here, the allosteric effect of ibuprofen on peroxynitrite isomerization to NO3− catalyzed by ferric human serum heme-albumin (HSA-heme-Fe(III)) is reported. Data were obtained at 22.0 °C. HSA-heme-Fe(III) catalyzes peroxynitrite isomerization in the absence and presence of CO2; the values of the second order catalytic rate constant (kon) are 4.1 × 105 and 4.5 × 105 m−1 s−1, respectively. Moreover, HSA-heme-Fe(III) prevents peroxynitrite-mediated nitration of free added l-tyrosine. The pH dependence of kon (pKa = 6.9) suggests that peroxynitrous acid reacts preferentially with the heme-Fe(III) atom, in the absence and presence of CO2. The HSA-heme-Fe(III)-catalyzed isomerization of peroxynitrite has been ascribed to the reactive pentacoordinated heme-Fe(III) atom. In the absence and presence of CO2, ibuprofen impairs dose-dependently peroxynitrite isomerization by HSA-heme-Fe(III) and facilitates the nitration of free added l-tyrosine; the value of the dissociation equilibrium constant for ibuprofen binding to HSA-heme-Fe(III) (L) ranges between 7.7 × 10−4 and 9.7 × 10−4 m. Under conditions where [ibuprofen] is ≫L, the kinetics of HSA-heme-Fe(III)-catalyzed isomerization of peroxynitrite is superimposable to that obtained in the absence of HSA-heme-Fe(III) or in the presence of non-catalytic HSA-heme-Fe(III)-cyanide complex and HSA. Ibuprofen binding impairs allosterically peroxynitrite isomerization by HSA-heme-Fe(III), inducing the hexacoordination of the heme-Fe(III) atom. These results represent the first evidence for peroxynitrite isomerization by HSA-heme-Fe(III), highlighting the allosteric modulation of HSA-heme-Fe(III) reactivity by heterotropic interaction(s), and outlining the role of drugs in modulating HSA functions. The present results could be relevant for the drug-dependent protective role

  9. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    NASA Astrophysics Data System (ADS)

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-06-01

    Photodissociation pathways of nitromethane following π → π* electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH3 and NO2 (2B2) is formed by direct dissociation from the S1 state. Important pathways involving S1 and S0 states for production of various dissociation products CH3NO + O (1D), CH3O(X2E) + NO (X2Π), CH2NO + OH, and CH2O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH3NO2, the OH radical roaming in OH dissociation from CH2N(O)(OH), and the NO roaming in NO dissociation from CH3ONO.

  10. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths.

    PubMed

    Isegawa, Miho; Liu, Fengyi; Maeda, Satoshi; Morokuma, Keiji

    2014-06-28

    Photodissociation pathways of nitromethane following π → π(*) electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH3 and NO2 ((2)B2) is formed by direct dissociation from the S1 state. Important pathways involving S1 and S0 states for production of various dissociation products CH3NO + O ((1)D), CH3O(X(2)E) + NO (X(2)Π), CH2NO + OH, and CH2O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH3NO2, the OH radical roaming in OH dissociation from CH2N(O)(OH), and the NO roaming in NO dissociation from CH3ONO. PMID:24985641

  11. Ab initio reaction pathways for photodissociation and isomerization of nitromethane on four singlet potential energy surfaces with three roaming paths

    SciTech Connect

    Isegawa, Miho; Liu, Fengyi; Morokuma, Keiji; Maeda, Satoshi

    2014-06-28

    Photodissociation pathways of nitromethane following π → π{sup *} electronic excitation are reported. The potential energy surfaces for four lowest singlet states are explored, and structures of many intermediates, dissociation limits, transition states, and minimum energy conical intersections were determined using the automated searching algorism called the global reaction route mapping strategy. Geometries are finally optimized at CASSCF(14e,11o) level and energies are computed at CAS(14o,11e)PT2 level. The calculated preferable pathways and important products qualitatively explain experimental observations. The major photodissociation product CH{sub 3} and NO{sub 2} ({sup 2}B{sub 2}) is formed by direct dissociation from the S{sub 1} state. Important pathways involving S{sub 1} and S{sub 0} states for production of various dissociation products CH{sub 3}NO + O ({sup 1}D), CH{sub 3}O(X{sup 2}E) + NO (X{sup 2}Π), CH{sub 2}NO + OH, and CH{sub 2}O + HNO, as well as various isomerization pathways have been identified. Three roaming processes also have been identified: the O atom roaming in O dissociation from CH{sub 3}NO{sub 2}, the OH radical roaming in OH dissociation from CH{sub 2}N(O)(OH), and the NO roaming in NO dissociation from CH{sub 3}ONO.

  12. Photoinduced proton transfer and isomerization in a hydrogen-bonded aromatic azo compound: a CASPT2//CASSCF study.

    PubMed

    Cui, Ganglong; Guan, Pei-Jie; Fang, Wei-Hai

    2014-07-01

    Intramolecularly hydrogen-bonded aromatic azo compound 1-cyclopropyldiazo-2-naphthol (CPDNO) exhibits complicated excited-state behaviors, e.g., wavelength-dependent photoinduced proton transfer and photoproducts. Its photochemistry differs from that of common aromatic azo compounds in which cis-trans photoisomerization is dominant. To rationalize the intriguing photochemistry of CPDNO at the atomic level, we have in this work employed the complete active space self-consistent field (CASSCF) and its second-order perturbation (CASPT2) methods to explore the S0, S1, and S2 potential-energy profiles relevant to enol-keto proton transfer and isomerization reactions. It is found that the proton transfer along the bright diabatic (1)ππ* potential-energy profile is almost barrierless, quickly forming the fluorescent (1)ππ* keto minimum. In this process, the dark (1)nπ* state is populated via a (1)ππ*/(1)nπ* crossing point, but the proton transfer on this dark state is suppressed heavily as a result of a large barrier. In addition, two deactivation paths that decay the S1 enol and keto minima to the S0 state, respectively, were uncovered. For the former, it is exoenergetic and thereby thermodynamically favorable; for the latter, it is a little endothermic (ca. 5 kcal/mol). Both are energetically allowable concerning the available total energy. Finally, on the basis of the present results, the experimentally observed wavelength-dependent photoproducts were explained very well. PMID:24940848

  13. Thrombocytosis in the Setting of Isomerism and a Functionally Univentricular Heart

    PubMed Central

    2015-01-01

    Introduction Bodily isomerism, also known as heterotaxy, is a unique entity in which there is mirror imagery in various organ systems. Those with isomerism will often have congenital malformations of the heart requiring functionally univentricular palliation. Anecdotally, thrombocytosis has been noted with higher frequency in patients with isomerism. This study aimed to determine the prevalence of thrombocytosis at different stages and identify independent predictors of thrombocytosis. Methods We identified patients with isomerism and a functionally univentricular heart who received care at our institution between January 1998 and January 2014. Clinical data regarding these patients was collected via chart review. Platelet counts were collected before initial surgical palliation, the day prior to second surgical palliation, and the day prior to the third surgical palliation. Platelet counts from the first postoperative day following all three surgical palliations was also collected. Mean platelet counts were compared between consecutive stages as well as to the initial platelet count. The frequency of thrombocytosis was also calculated at each point with a binomial logistic regression conducted to determine independent risk factors of thrombocytosis at each time point. Results A total of 57 patients were included in the analysis. The mean platelet count before initial surgical palliation was 349.21 x 109/L and decreased with age. Thrombocytosis was noted in 15.8% prior to initial surgical palliation and 23.6% prior to second surgical palliation. Thrombocytosis was no longer noted after second surgical palliation. No independent risk factors for thrombocytosis were identified. Conclusion Thrombocytosis is not infrequent during the first year of life in those with isomerism. It is important to be vigilant of platelet counts in this population as thrombocytosis may lead to increased thromboembolic events, particularly in the setting of a Blalock-Taussig shunt

  14. Isomeric Selective Studies of the Dominant Addition Channel in OH Initiated Oxidation of Isoprene

    NASA Astrophysics Data System (ADS)

    Ghosh, B.; Bugarin, A.; Connell, B.; North, S. W.

    2009-12-01

    We report the first isomeric selective study of the dominant isomeric pathway in the OH initiated oxidation of isoprene in the presence of O2 and NO using the Laser Photolysis-Laser Induced Fluorescence (LP-LIF) technique. The photolysis of monodeuterated/non deuterated 2-iodo-2-methyl-but-3-en-1-ol results exclusively in the dominant OH-isoprene addition product, providing important insight into the oxidation mechanism. Based on kinetic analysis of OH cycling experiments we have determined the rate constant for O2 addition to the hydroxy alkyl radical to be (1.0±0.5) × 10^(-12) cm^(3) s^(-1) and we find a value of (8.05±2.3) × 10^(-12) cm^(3) s^(-1) for the overall reaction rate constant of the hydroxy peroxy radical with NO. We also report the first clear experimental evidence of the (E-) form of the δ-hydroxyalkoxy channel through isotopic labeling experiments and quantify its branching ratio to be 0.1±0.025. Since it corresponds to missing carbon balance in isoprene oxidation, we have been able to identify some of the missing carbon balance. Since our measured isomeric selective rate constants for the dominant outer channel in OH initiated isoprene chemistry are similar to the overall rate constants derived from non isomeric kinetics, we predict that the remaining outer addition channel will have similar reactivity. We have extended this study to the OH initiated oxidation of 1,3-butadiene. We have obtained isomeric selective rate constants on the dominant channel of the butadiene oxidation chemistry and measured the branching ratio for the δ-hydroxyalkoxy channel. These results on butadiene studies will be discussed.

  15. Bronchial isomerism in a Kabuki syndrome patient with a novel mutation in MLL2 gene

    PubMed Central

    2014-01-01

    Background Kabuki syndrome (KS) is a rare, multiple congenital anomalies/intellectual disability syndrome caused by mutations of MLL2 gene, which codifies for a histone methyltrasferase that regulates the embryogenesis and the tissue development. Left-bronchial isomerism is a rare congenital abnormality that can be defined as the absence of the normal lateralizing features which distinguish right and left-sides in the lungs. To date, this is the first report of left-bronchial isomerism in association with KS. Case presentation A one-month-old Caucasian male patient underwent our attention for microcephaly, dysmorphic features (long palpebral fissures, eyebrows with sparse lateral third, everted lower eyelids, blue sclerae, large dysplastic ears, lower lip pits), persistent fetal fingertip pads, short stature, heart defects (interventricular defect and aortic coarctation), unilateral cryptorchidism, hypotonia and delay in gross motor skills. These features suggested a diagnosis of KS and a molecular analysis confirmed a novel frame-shift mutation in the exon 11 of MLL2 gene. Subsequently, given recurrent respiratory infections with a normal immunological status, he underwent a chest CT scan that showed a left bronchial isomerism. Conclusion We report a patient affected by KS, with a novel MLL2 mutation and an atypical phenotype characterized by left-side bronchial isomerism. Interestingly, genes involved in the heterotaxia/isomerism such as ROCK2 and SHROOM3 are known to interact with MLL2 gene. In order to achieve a correct diagnosis and an appropriate therapy, the presence of pulmonary anatomical variations should be investigated in KS patients with respiratory signs not associated to immunological deficiency. Finally, our findings support the hypothesis that the mutations leading to a complete loss of function of MLL2 gene is often associated with complex visceral malformations. PMID:24472332

  16. Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore: 2. Cis-Trans Isomerization in Water.

    PubMed

    Polyakov, Igor; Epifanovsky, Evgeny; Grigorenko, Bella; Krylov, Anna I; Nemukhin, Alexander

    2009-07-14

    We present quantum chemical calculations of the properties of the anionic form of the green fluorescent protein (GFP) chromophore that can be directly compared to the results of experimental measurements: the cis-trans isomerization energy profile in water. Calculations of the cis-trans chromophore isomerization pathway in the gas phase and in water reveal a problematic behavior of density functional theory and scaled opposite-spin-MP2 due to the multiconfigurational character of the wave function at twisted geometries. The solvent effects treated with the continuum solvation models, as well as with the water cluster model, are found to be important and can reduce the activation energy by more than 10 kcal/mol. Strong solvent effects are explained by the change in charge localization patterns along the isomerization coordinate. At the equilibrium, the negative charge is almost equally delocalized between the phenyl and imidazolin rings due to the interaction of two resonance structures, whereas at the transition state the charge is localized on the imidazolin moiety. Our best estimate of the barrier obtained in cluster calculations employing the effective fragment potential-based quantum mechanics/molecular mechanics method with the complete active space self-consistent field description of the chromophore augmented by perturbation theory correction and the TIP3P water model is 14.8 kcal/mol, which is in excellent agreement with the experimental value of 15.4 kcal/mol. This result helps to resolve previously reported disagreements between experimental measurements and theoretical estimates. PMID:26610015

  17. Nitrosyl isomerism in amorphous Mn(TPP)(NO) solids.

    PubMed

    Kurtikyan, Tigran S; Hayrapetyan, Vardan A; Martirosyan, Garik G; Ghazaryan, Robert K; Iretskii, Alexei V; Zhao, Hailiang; Pierloot, Kristine; Ford, Peter C

    2012-12-25

    Reaction of NO with amorphous Mn(TPP) layers gives two Mn(TPP)(NO) isomers with linear and bent Mn-N-O geometries that reversibly interconvert with changes in temperature. DFT computations predict that the linear complex is the singlet ground state while the bent structure is a triplet state. PMID:23143019

  18. Energetics of the all-trans{yields}13-cis isomerization of the retinal chromophore of bacteriorhodopsin: Electronic structure calculations for a simple model system

    SciTech Connect

    Woywod, Clemens; Vallet, Valerie; Li, Jingrui; Goerling, Andreas

    2008-12-08

    Understanding the molecular mechanism for the photoinduced transmembrane proton pump in the bacteriorhodopsin system is of fundamental importance. This study attempts to investigate the energetics of the initial step of the proton transport cycle, the photoisomerization of the retinal chromophore. The exact reaction pathway and the question of how many excited electronic states are involved in the internal conversion process are still unresolved. The problem is approached by constructing a reaction coordinate suggested by crystallographic studies for a simplified chromophore model system. The CASSCF and CASPT2 electronic structure methods are employed to calculate the energies of the four lowest lying singlet states as a function of the reaction coordinate. The effect of negatively charged protein residues on the reaction is simulated by inclusion of a negative point charge in the model. The results indicate that trans{yields}cis isomerization around the C{sub {beta}} = C{sub {gamma}} bond may be accompanied by twisting around the C{sub {alpha}}-C{sub {beta}} bond in order to drive the proton pump. The presence of a counterion does not seem to reduce the barrier for isomerization or the S{sub 0}-S{sub 1} energy difference but clearly stabilizes the cis--product. At first sight the results appear to support the idea of a participation of no other electronic states beyond S{sub 0} and first singly {pi}{pi}* excited state in the photoreaction. However, the relevance of this prediction is rather limited because of the small size of the model system. Other states of retinal, corresponding in particular to the partly doubly {pi}{pi}* excited S{sub 2} state of the model, are likely to have a vertical excitation energy similar to the first singly {pi}{pi}* excited state or even below.

  19. Fluorine for Hydrogen Exchange in the Hydrofluorobenzene Derivatives C6HxF(6-x), where x = 2, 3, 4 and 5 by Monomeric [1,2,4-(Me3C)3C5H2]2CeH; The Solid State Isomerization of [1,2,4-(Me3C)3C5H2]2Ce(2,3,4,5-C6HF4) to [1,2,4-(Me3C)3C5H2]2Ce(2,3,4,6-C6HF4)

    SciTech Connect

    Andersen, Richard; Werkema, Evan L.; Andersen, Richard A.

    2008-04-21

    The reaction between monomeric bis(1,2,4-tri-t-butylcyclopentadienyl)cerium hydride, Cp'2CeH, and several hydrofluorobenzene derivatives is described. The aryl derivatives that are the primary products, Cp'2Ce(C6H5-xFx) where x = 1,2,3,4, are thermally stable enough to be isolated in only two cases, since all of them decompose at different rates to Cp'2CeF and a fluorobenzyne; the latter is trapped by either solvent when C6D6 is used or by a Cp'H ring when C6D12 is the solvent. The trapped products are identified by GCMS analysis after hydrolysis. The aryl derivatives are generated cleanly by reaction of the metallacycle, Cp'((Me3C)2C5H2C(Me2)CH2)Ce, with a hydrofluorobenzene and the resulting arylcerium products, in each case, are identified by their 1H and 19F NMR spectra at 20oC. The stereochemical principle that evolves from these studies is that the thermodynamic isomer is the one in which the CeC bond is flanked by two ortho-CF bonds. This orientation is suggested to arise from the negative charge that is localized on the ipso-carbon atom due to Co(delta+)-Fo(delta-) polarization. The preferred regioisomer is determined by thermodynamic rather than kinetic effects; this is illustrated by the quantitative, irreversible solid-state conversion at 25oC over two months of Cp'2Ce(2,3,4,5-C6HF4) to Cp'2Ce(2,3,4,6-C6HF4), an isomerization that involves a CeC(ipso) for C(ortho)F site exchange.

  20. Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam

    PubMed Central

    Asciutto, Eliana K.; Madura, Jeffry D.; Pochapsky, Susan Sondej; OuYang, Bo; Pochapsky, Thomas C.

    2009-01-01

    Experimental evidence has been provided for a functionally relevant cis-trans isomerization of the Ile 88-Pro 89 peptide bond in cytochrome P450cam (CYP101). The isomerization is proposed to be a key element of the structural reorganization leading to the catalytically competent form of CYP101 upon binding of the effector protein putidaredoxin (Pdx). A detailed comparison of the results of molecular dynamics simulations on the cis and trans conformations of substrate- and carbonmonoxy-bound ferrous CYP101 with sequence-specific Pdx-induced structural perturbations identified by nuclear magnetic resonance is presented, providing insight into the structural and dynamic consequences of the isomerization. The mechanical coupling between the Pdx binding site on the proximal face of CYP101 and the site of isomerization is described. PMID:19327368

  1. Structural and dynamic implications of an effector-induced backbone amide cis-trans isomerization in cytochrome P450cam.

    PubMed

    Asciutto, Eliana K; Madura, Jeffry D; Pochapsky, Susan Sondej; OuYang, Bo; Pochapsky, Thomas C

    2009-05-15

    Experimental evidence has been provided for a functionally relevant cis-trans isomerization of the Ile88-Pro89 peptide bond in cytochrome P450(cam) (CYP101). The isomerization is proposed to be a key element of the structural reorganization leading to the catalytically competent form of CYP101 upon binding of the effector protein putidaredoxin (Pdx). A detailed comparison of the results of molecular dynamics simulations on the cis and trans conformations of substrate- and carbonmonoxy-bound ferrous CYP101 with sequence-specific Pdx-induced structural perturbations identified by nuclear magnetic resonance is presented, providing insight into the structural and dynamic consequences of the isomerization. The mechanical coupling between the Pdx binding site on the proximal face of CYP101 and the site of isomerization is described. PMID:19327368

  2. Distinguishing PCB Isomeric Congeners with their Gas Chromatographic and Mass Spectrometric Ortho Effect using Comprehensive Gas Chromatography

    EPA Science Inventory

    The 209 polychlorinated biphenyl (PCB) congeners and associated nine isomeric groups (nine groups of PCBs with the same degree of chlorination) have been long recorded as high endocrine disrupting chemicals in the environment. Difficult analytical problems exist, in those frequen...

  3. Identification of the altered pyrrole in the isomeric sulfmyoglobins: hyperfine shift patterns as indicators of ring saturation in ferric chlorins

    SciTech Connect

    Chatfield, M.J.; La Mar, G.N.; Smith, K.M.; Leung, H.K.; Pandey, R.K.

    1988-03-08

    Analysis of the /sup 1/H NMR hyperfine shift patterns of isomeric sulfmyoglobins is carried out in the met-aquo and met-cyano states to determine the site of saturation in each protein. The utility of the patterns for structure elucidation is established by specific deuterium labeling of heme methyls of the terminal base product. On the basis of the know saturation of ring B in this isomer. The methyl resonance of the saturated ring is found to have strongly attenuated contact shift. Thus, the heme methyl contact shift pattern is diagnostic for the saturated pyrrole in the high-spin state. This rationale is then applied to analyze the assigned NMR spectra of the initial and terminal acid sulfmyoglobin products, revealing that the same ring B is saturated in each isomer. In contrast, the heme methyl contact shift pattern in low-spin ferric complexes reveals that the methyls both on the affected pyrrole and on the trans pyrrole are influenced similarly on sulfmyoglobin formation, precluding the use of this methyl shift pattern as a unique indicator of the site of saturation. Identification of exchangeable proximal histidine resonances for met-aquo sulfmyoglobin complexes with shifts similar to that in native myoglobin dictates inconsequential axial alterations in the sulfmyoglobins, while location of downfield meso proton resonances analogous to those of the native protein demonstrates the retention of the coordinate water in the active site of met-sulfmyoglobin.

  4. Stereo and enantioselective separation and identification of synthetic pyrethroids, and photolytical isomerization analysis.

    PubMed

    Li, Z Y; Luo, X N; Li, Q L; Zhang, E Q; Zhao, J H; Zhang, W S

    2015-02-01

    Permethrin, cypermethrin and cyfluthrin are three important pyrethroids with similar structures and contain four, eight and eight stereoisomers, respectively. All the stereoisomers were completely resolved by a combination of achiral and chiral high-performance liquid chromatography with hexane/isopropanol as the mobile phase. The absolute configurations for the stereoisomers were also assigned on the basis of enantioselective resolution of permethrinic acid. For cypermethrin and cyfluthrin, although there is the only difference being one F atom substitution in cyfluthrin, the cis-I diastereomer exhibited a reversal of enantiomer order. Three specific stereoisomers were further isolated to investigate the photolysis and chiral stability of synthetic pyrethroids at the enantiomeric level. The results clearly revealed that significant isomerization occurred along with the photolysis process. The isomerization occurred at chiral 1-C position, 3-C position or both in the cyclopropyl ring, and the chiral 3-C exhibited a higher inversion tendency. PMID:25319199

  5. The isomerization of 1-methylcyclopropene: A multichannel unimolecular reaction induced by overtone excitation

    NASA Astrophysics Data System (ADS)

    Baggott, J. E.; Law, D. W.

    1988-01-01

    The distribution of products resulting from the isomerization of gas phase 1-methylcyclopropene (1) induced by C-H stretch overtone excitation has been studied in a search for mode specific effects. Quantum yields for the disappearance of 1 have been determined as a function of the total pressure of a mixture of 1 and methylenecyclopropane and of the added bath gases SF6 and Ar using a combination of intracavity dye laser photolysis and end product analysis by gas chromatography. These data, together with the ratios of the yields of the major isomerization products, are adequately reproduced by RRKM theory and a weak collisional energy transfer model: no evidence for mode specificity is obtained. The experimental data demonstrate the importance of inefficient collisional energy transfer but allow some conclusions to be drawn concerning the applicability of RRKM theory which are not strongly dependent upon the details of the energy transfer model.

  6. Synthesis of Isomeric Phosphoubiquitin Chains Reveals that Phosphorylation Controls Deubiquitinase Activity and Specificity.

    PubMed

    Huguenin-Dezot, Nicolas; De Cesare, Virginia; Peltier, Julien; Knebel, Axel; Kristaryianto, Yosua Adi; Rogerson, Daniel T; Kulathu, Yogesh; Trost, Matthias; Chin, Jason W

    2016-07-26

    Ubiquitin is post-translationally modified by phosphorylation at several sites, but the consequences of these modifications are largely unknown. Here, we synthesize multi-milligram quantities of ubiquitin phosphorylated at serine 20, serine 57, and serine 65 via genetic code expansion. We use these phosphoubiquitins for the enzymatic assembly of 20 isomeric phosphoubiquitin dimers, with different sites of isopeptide linkage and/or phosphorylation. We discover that phosphorylation of serine 20 on ubiquitin converts UBE3C from a dual-specificity E3 ligase into a ligase that primarily synthesizes K48 chains. We profile the activity of 31 deubiquitinases on the isomeric phosphoubiquitin dimers in 837 reactions, and we discover that phosphorylation at distinct sites in ubiquitin can activate or repress cleavage of a particular linkage by deubiquitinases and that phosphorylation at a single site in ubiquitin can control the specificity of deubiquitinases for distinct ubiquitin linkages. PMID:27425610

  7. Ethanol production from xylose by enzymic isomerization and yeast fermentation. [Schizosaccharomyces pombe

    SciTech Connect

    Chiang, L.C.; Hsiao, H.Y.; Ueng, P.P.; Chen, L.F.; Tsao, G.T.

    1981-01-01

    Repetitive enzymic isomerization of xylose followed by yeast fermentation of xylulose, and simultaneous enzymic isomerization and yeast fermentation, were proven to be methods capable of converting xylose to EtOH. The fermentation product (EtOH, xylitol, or glycerol) has little inhibitory or deactivation effect on the activity of isomerase. In a comparison of the ability of yeasts to ferment xylulose to EtOH, Schizosaccharomyces pombe was found to be superior to industrial bakers' yeast. Under optimal conditions (pH 6, temperature 30 degrees), a final EtOH concentration of 6.3% was obtained from simulated hemicellulose hydrolyzate using a simultaneous fermentation process. The EtOH yield was more than 80% of theoretical.

  8. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

    PubMed

    Pande, Kanupriya; Hutchison, Christopher D M; Groenhof, Gerrit; Aquila, Andy; Robinson, Josef S; Tenboer, Jason; Basu, Shibom; Boutet, Sébastien; DePonte, Daniel P; Liang, Mengning; White, Thomas A; Zatsepin, Nadia A; Yefanov, Oleksandr; Morozov, Dmitry; Oberthuer, Dominik; Gati, Cornelius; Subramanian, Ganesh; James, Daniel; Zhao, Yun; Koralek, Jake; Brayshaw, Jennifer; Kupitz, Christopher; Conrad, Chelsie; Roy-Chowdhury, Shatabdi; Coe, Jesse D; Metz, Markus; Xavier, Paulraj Lourdu; Grant, Thomas D; Koglin, Jason E; Ketawala, Gihan; Fromme, Raimund; Šrajer, Vukica; Henning, Robert; Spence, John C H; Ourmazd, Abbas; Schwander, Peter; Weierstall, Uwe; Frank, Matthias; Fromme, Petra; Barty, Anton; Chapman, Henry N; Moffat, Keith; van Thor, Jasper J; Schmidt, Marius

    2016-05-01

    A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction. PMID:27151871

  9. Isomerization of One Molecule Observed through Tip-Enhanced Raman Spectroscopy.

    PubMed

    Tallarida, Nicholas; Rios, Laura; Apkarian, Vartkess A; Lee, Joonhee

    2015-10-14

    While exploring photoisomerization of azobenzyl thiols (ABT) adsorbed on Au(111), through joint scanning tunneling microscopy (STM) and tip-enhanced Raman scattering (TERS) studies, the reversible photoisomerization of one molecule is captured in TERS trajectories. The unique signature of single molecule isomerization is observed in the form of anticorrelated flip-flops between two distinct spectra with two discrete, on- and off-levels. The apparently heterogeneously photocatalyzed reaction is assigned to cis-trans isomerization of an outlier, which is chemisorbed on the silver tip of the STM. Otherwise, the ensemble of ABT molecules that lie flat on Au(111) remain strongly coupled to the surface, excluding the possibility of photoisomerization or detection through TERS. PMID:26348440

  10. Thermal Z,E-isomerization of imines. IV. Anils of acetone

    SciTech Connect

    Prosyanik, A.V.; Kol'tsov, N.Yu.; Romanchenko, V.A.

    1986-12-20

    It has been established by the correlation between the values of log k/sub 298/ and the sigma constants that the degenerate thermal Z,E-isomerization of anils of acetone takes place according to an inversion mechanism, with the exception of acetone p-dimethylaminophenylimine, which isomerizes predominantly according to a rotation mechanism. The increase in the steric stresses upon the introduction of ortho substituents into the aryl ring of anils of acetone results in significant lowering of the barriers to the inversion of the nitrogen atom. The raising of the barriers to inversion in phenylimines as the electron-acceptor properties of the substituents on the imino carbon atom are enhanced is due to the weakening of the n/sub ..pi../N-..pi../sub Ph/* interaction as a consequence of the increase in the energy gap between the interacting orbitals as a result of the lowering of the energy of the n/sub ..pi../N orbital.

  11. Ru-Catalyzed Isomerization Provides Access to Alternating Copolymers via Ring-Opening Metathesis Polymerization

    PubMed Central

    2016-01-01

    We describe an isomerization–alternating ROMP protocol that gives linear copolymers with rigorous sequence alternation. Bicyclo[4.2.0]oct-7-ene-7-carboxamides of primary amines are isomerized in the presence of (3-BrPyr)2Cl2(H2IMes)Ru=CHPh to the corresponding bicyclo[4.2.0]oct-1(8)-ene-8-carboxamides in which the olefinic bond is tetrasubstituted. The isomerized amides undergo alternating ring-opening metathesis polymerization with cyclohexene to provide soluble and linear copolymers with molecular weights up to ∼130 kDa. This process provides efficient entry to strictly alternating copolymers that can display diverse functional groups. PMID:26243969

  12. Large-amplitude dynamics in vinyl radical: The role of quantum tunneling as an isomerization mechanism

    NASA Astrophysics Data System (ADS)

    Sharma, Amit R.; Bowman, Joel M.; Nesbitt, David J.

    2012-01-01

    We report tunneling splittings associated with the large amplitude 1,2 H-atom migration to the global minima in the vinyl radical. These are obtained using a recent full-dimensional ab initio potential energy surface (PES) [A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman, J. Chem. Phys. 130(17), 174301 (2009)] and independently, directly calculated "reaction paths." The PES is a multidimensional fit to coupled cluster single and double and perturbative treatment of triple excitations coupled-cluster single double triple (CCSD(T)) with the augmented correlation consistent triple zeta basis set (aug-cc-pVTZ). The reaction path potentials are obtained from a series of CCSD(T)/aug-cc-pVnTZ calculations extrapolated to the complete basis set limit. Approximate 1D calculations of the tunneling splitting for these 1,2-H atom migrations are obtained using each of these potentials as well as quite different 1D Hamiltonians. The splittings are calculated over a large energy ranges, with results from the two sets of calculations in excellent agreement. Though negligibly slow (>1 s) for the vibrational ground state, this work predicts tunneling-promoted 1,2 hydride shift dynamics in vinyl to exhibit exponential growth with internal vibrational excitation, specifically achieving rates on the sub-μs time scale at energies above E ≈ 7500 cm-1. Most importantly, these results begin to elucidate the possible role of quantum isomerization through barriers without dissociation, in competition with the more conventional picture of classical roaming permitted over a much narrower window of energies immediately below the bond dissociation limit. Furthermore, when integrated over a Boltzmann distribution of thermal energies, these microcanonical tunneling rates are consistent with sub-μs time scales for 1,2 hydride shift dynamics at T > 1400 K. These results have potential relevance for combustion modeling of low-pressure flames, as well as recent observations

  13. Large-amplitude dynamics in vinyl radical: the role of quantum tunneling as an isomerization mechanism.

    PubMed

    Sharma, Amit R; Bowman, Joel M; Nesbitt, David J

    2012-01-21

    We report tunneling splittings associated with the large amplitude 1,2 H-atom migration to the global minima in the vinyl radical. These are obtained using a recent full-dimensional ab initio potential energy surface (PES) [A. R. Sharma, B. J. Braams, S. Carter, B. C. Shepler, and J. M. Bowman, J. Chem. Phys. 130(17), 174301 (2009)] and independently, directly calculated "reaction paths." The PES is a multidimensional fit to coupled cluster single and double and perturbative treatment of triple excitations coupled-cluster single double triple (CCSD(T)) with the augmented correlation consistent triple zeta basis set (aug-cc-pVTZ). The reaction path potentials are obtained from a series of CCSD(T)/aug-cc-pVnTZ calculations extrapolated to the complete basis set limit. Approximate 1D calculations of the tunneling splitting for these 1,2-H atom migrations are obtained using each of these potentials as well as quite different 1D Hamiltonians. The splittings are calculated over a large energy ranges, with results from the two sets of calculations in excellent agreement. Though negligibly slow (>1 s) for the vibrational ground state, this work predicts tunneling-promoted 1,2 hydride shift dynamics in vinyl to exhibit exponential growth with internal vibrational excitation, specifically achieving rates on the sub-μs time scale at energies above E ≈ 7500 cm(-1). Most importantly, these results begin to elucidate the possible role of quantum isomerization through barriers without dissociation, in competition with the more conventional picture of classical roaming permitted over a much narrower window of energies immediately below the bond dissociation limit. Furthermore, when integrated over a Boltzmann distribution of thermal energies, these microcanonical tunneling rates are consistent with sub-μs time scales for 1,2 hydride shift dynamics at T > 1400 K. These results have potential relevance for combustion modeling of low-pressure flames, as well as recent

  14. Proline Isomerization of the Immune Receptor-Interacting Protein RIN4 by a Cyclophilin Inhibits Effector-Triggered Immunity in Arabidopsis

    PubMed Central

    Li, Meng; Ma, Xiqing; Chiang, Yi-Hsuan; Yadeta, Koste A.; Ding, Pengfei; Dong, Liansai; Zhao, Yan; Li, Xiuming; Yu, Yufei; Zhang, Ling; Shen, Qian-Hua; Xia, Bin; Coaker, Gitta; Liu, Dong; Zhou, Jian-Min

    2016-01-01

    SUMMARY In the absence of pathogen infection, plant effector-triggered immune (ETI) receptors are maintained in a preactivation state by intermolecular interactions with other host proteins. Pathogen effector-induced alterations activate the receptor. In Arabidopsis, the ETI receptor RPM1 is activated via bacterial effector AvrB-induced phosphorylation of the RPM1-interacting protein RIN4 at Threonine 166. We find that RIN4 also interacts with the prolyl-peptidyl isomerase (PPIase) ROC1, which is reduced upon RIN4 Thr166 phosphorylation. ROC1 suppresses RPM1 immunity in a PPIase-dependent manner. Consistent with this, RIN4 Pro149 undergoes cis/trans isomerization in the presence of ROC1. While the RIN4P149V mutation abolishes RPM1 resistance, the deletion of Pro149 leads to RPM1 activation in the absence of RIN4 phosphorylation. These results support a model in which RPM1 directly senses conformational changes in RIN4 surrounding Pro149 that is controlled by ROC1. RIN4 Thr166 phosphorylation indirectly regulates RPM1 resistance by modulating the ROC1-mediated RIN4 isomerization. PMID:25299333

  15. The Isomerization of Δ5-Androstene-3,17-dione by the Human Glutathione Transferase A3-3 Proceeds via a Conjugated Heteroannular Diene Intermediate*

    PubMed Central

    Daka, Jonathan L.; Achilonu, Ikechukwu; Dirr, Heini W.

    2014-01-01

    The seemingly simple proton abstraction reactions underpin many chemical transformations, including isomerization reactions, and are thus of immense biological significance. Despite the energetic cost, enzyme-catalyzed proton abstraction reactions show remarkable rate enhancements. The pathways leading to these accelerated rates are numerous and on occasion partly enigmatic. The isomerization of the steroid Δ5-androstene-3,17-dione by the glutathione transferase A3-3 in mammals was investigated to gain insight into the mechanism. Particular emphasis was placed on the nature of the transition state, the intermediate suspected of aiding this process, and the hydrogen bonds postulated to be the stabilizing forces of these transient species. The UV-visible detection of the intermediate places this species in the catalytic pathway, whereas fluorescence spectroscopy is used to obtain the binding constant of the analog intermediate, equilenin. Solvent isotope exchange reveals that proton abstraction from the substrate to form the intermediate is rate-limiting. Analysis of the data in terms of the Marcus formalism indicates that the human glutathione transferase A3-3 lowers the intrinsic kinetic barrier by 3 kcal/mol. The results lead to the conclusion that this reaction proceeds through an enforced concerted mechanism in which the barrier to product formation is kinetically insignificant. PMID:25248748

  16. Isomeric yield ratios of 87m,gY from different nuclear reactions

    NASA Astrophysics Data System (ADS)

    Naik, H.; Kim, G. N.; Kim, K.; Zaman, M.; Sahid, M.; Yang, S.-C.; Lee, M. W.; Kang, Y. R.; Shin, S. G.; Cho, M.-H.; Goswami, A.; Song, T. Y.

    2014-07-01

    The independent isomeric yield ratios of 87m,gY produced from the 93Nb( γ, α2n) and natZr( γ, p xn) reactions with the end-point bremsstrahlung energy of 45-70 MeV have been determined by an off-line γ-ray spectrometric technique using 100 MeV electron linac at the Pohang accelerator laboratory, Korea. The isomeric yield ratios of 87m,gY were also determined from the natZr(p, αxn) and the 89Y(p,p2n) reactions with E P = 15-45 MeV as well as those from the 89Y( α, α2n) reaction with E α = 32-43 MeV using the MC-50 cyclotron at the Korea Institute of Radiological and Medical Science, Korea. The isomeric yield ratios of 87m,gY from the present work in the 93Nb( γ, α2n), natZr( γ, p xn), natZr(p, αxn), 89Y(p,p2n), and 89Y( α, α2n) reactions were compared with those of the literature data in the 85Rb( α, 2n), the 86,87,88Sr(d, xn), 89Y(n,3n), and the 89Y( γ, 2n) reactions to examine the role of target, projectiles, and ejectiles through compound nucleus excitation energy and input angular momentum. The isomeric yield ratios of 87m,gY in the above eleven reactions were also calculated using the computer code TALYS 1.4 and compared with the experimental data. The different behaviors between photon- and neutron-induced reactions and charged-particle-induced reactions are discussed from the viewpoint of compound and non-compound (pre-equilibrium) process.

  17. An unexpected isomerization of 1,3-benzothiazine and isoquinoline-condensed β-lactams

    NASA Astrophysics Data System (ADS)

    Fodor, Lajos; Csomós, Péter; Fülöp, Ferenc; Csámpai, Antal; Sohár, Pál

    2010-11-01

    A series of novel aryl-substituted β-lactams condensed with 1,3-benzothiazines, isoquinolines or 1,4-benzothiazepine were obtained by means of the Staudinger reaction and isomerized in the presence of sodium methoxide to the thermodynamically more stable form. The structures of the new molecules were determined by NMR spectroscopy. Theoretical calculations corroborate the experimentally observed structure-reactivity relationships.

  18. Isomeric ratio measurements for the radiative neutron capture 176Lu(n,γ) at DANCE

    NASA Astrophysics Data System (ADS)

    Denis-Petit, D.; Roig, O.; Méot, V.; Jandel, M.; Vieira, D. J.; Bond, E. M.; Bredeweg, T. A.; Couture, A. J.; Haight, R. C.; Keksis, A. L.; Rundberg, R. S.; Ullmann, J. L.

    2016-03-01

    The isomeric ratio for the neutron capture reaction 176Lu(n,γ) on the Jπ= 5/2-, 761.7 keV, T1/2=32.8 ns level of 177mLu, has been determined in the neutron energy range 8.5 eV-100 keV for the first time using the DANCE array at the Los Alamos National Laboratory.

  19. Novel domino procedures for the synthesis of chromene derivatives and their isomerization.

    PubMed

    Zonouzi, Afsaneh; Izakian, Zakieh; Ng, Seik Weng

    2016-08-01

    Novel tricyclic keto diesters have been synthesized by a one-pot three-component procedure via DABCO-catalyzed domino Knoevenagel-Michael addition reactions. Also, an efficient four-component reaction for the synthesis of another new group of tricyclic keto diesters has been developed via domino Knoevenagel-intramolecular oxo-Diels-Alder reactions. A selective thermal isomerization of the synthesized chromenes to fumarates is also described. X-ray analyses confirm unambiguously the structures of the products. PMID:27003393

  20. Radio-wave trajectories in a linear layer with isomerous irregularities

    NASA Astrophysics Data System (ADS)

    Golynskii, S. M.; Khlybov, G. N.

    1983-12-01

    A numerical analysis is made of deviations of the most probable trajectory of rays in a linear ionospheric layer with isomerous irregularities from the undisturbed trajectory described by the Snellius law. It is shown that the presence of scattering irregularities in the medium leads to an increase in the length of the radio path and to a change in the inclination angle of the trajectory at the exit from the layer.

  1. Rhodium(II)-Catalyzed Isomerization of Cyclopropenylmethyl Esters into (Acyloxymethylene)cyclopropanes.

    PubMed

    Archambeau, Alexis; Nguyen, Dinh-Vu; Meyer, Christophe; Cossy, Janine

    2016-04-18

    In the presence of a rhodium(II) catalyst, 3,3-disubstituted cyclopropenylmethyl esters that possess an electron-rich or neutral aromatic group undergo isomerization into (acyloxymethylene)cyclopropanes. This transformation, which proceeds with inversion of configuration at the stereogenic center, complements the previously disclosed rearrangement reactions of cyclopropenylmethyl esters. The products arising from this new rhodium-catalyzed rearrangement contain an enol ester group that can be subsequently functionalized to access stereodefined arylcyclopropanes. PMID:26990014

  2. Simulation of chemical isomerization reaction dynamics on a NMR quantum simulator.

    PubMed

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future. PMID:21797586

  3. A classical trajectory study of the dissociation and isomerization of C2H5.

    PubMed

    Wagner, Albert F; Rivera-Rivera, Luis A; Bachellerie, Damien; Perry, Jamin W; Thompson, Donald L

    2013-11-21

    Motivated by photodissociation experiments in which non-RRKM nanosecond lifetimes of the ethyl radical were reported, we have performed a classical trajectory study of the dissociation and isomerization of C2H5 over the energy range 100-150 kcal/mol. We used a customized version of the AIREBO semiempirical potential (Stuart, S. J.; et al. J. Chem. Phys. 2000, 112, 6472-6486) to more accurately describe the gas-phase decomposition of C2H5. This study constitutes one of the first gas-phase applications of this potential form. At each energy, 10,000 trajectories were run and all underwent dissociation in less than 100 ps. The calculated dissociation rate constants are consistent with RRKM models; no evidence was found for nanosecond lifetimes. An analytic kinetics model of isomerization/dissociation competition was developed that incorporated incomplete mode mixing through a postulated divided phase space. The fits of the model to the trajectory data are good and represent the trajectory results in detail through repeated isomerizations at all energies. The model correctly displays single exponential decay at lower energies, but at higher energies, multiexponential decay due to incomplete mode mixing becomes more apparent. At both ends of the energy range, we carried out similar trajectory studies on CD2CH3 to examine isotopic scrambling. The results largely support the assumption that a H or a D atom is equally likely to dissociate from the mixed-isotope methyl end of the molecule. The calculated fraction of products that have the D atom dissociation is ∼20%, twice the experimental value available at one energy within our range. The calculated degree of isotopic scrambling is non-monotonic with respect to energy due to a non-monotonic ratio of the isomerization to dissociation rate constants. PMID:23448205

  4. IR-induced conformational isomerization of a helical peptide in a cold ion trap.

    PubMed

    Seaiby, Caroline; Zabuga, Aleksandra V; Svendsen, Annette; Rizzo, Thomas R

    2016-01-01

    In this work, we use laser-induced population transfer techniques to study the conformational isomerization of a helical peptide, Ac-Phe-(Ala)5-LysH(+), in a cold ion trap. In one scheme, called IR-UV hole-filling spectroscopy, a single conformation is selectively excited with an IR pump laser via a distinct NH stretch vibration. After giving the vibrationally excited ions sufficient time to isomerize and re-cool in the trap, the new conformational redistribution is detected by UV photofragment spectroscopy. While we clearly observe a redistribution of the conformer populations due to isomerization, only those conformations that initially have population participate in this redistribution-we do not form conformers that were not initially present in the trap. In a second scheme, called IR-induced population transfer spectroscopy, we determine the fractional populations of the four stable conformations of Ac-Phe-(Ala)5-LysH(+) by scanning the IR laser while selectively detecting a specific conformation using UV photofragment spectroscopy. PMID:26747803

  5. Human infrared vision is triggered by two-photon chromophore isomerization

    PubMed Central

    Palczewska, Grazyna; Vinberg, Frans; Stremplewski, Patrycjusz; Bircher, Martin P.; Salom, David; Komar, Katarzyna; Zhang, Jianye; Cascella, Michele; Wojtkowski, Maciej; Kefalov, Vladimir J.; Palczewski, Krzysztof

    2014-01-01

    Vision relies on photoactivation of visual pigments in rod and cone photoreceptor cells of the retina. The human eye structure and the absorption spectra of pigments limit our visual perception of light. Our visual perception is most responsive to stimulating light in the 400- to 720-nm (visible) range. First, we demonstrate by psychophysical experiments that humans can perceive infrared laser emission as visible light. Moreover, we show that mammalian photoreceptors can be directly activated by near infrared light with a sensitivity that paradoxically increases at wavelengths above 900 nm, and display quadratic dependence on laser power, indicating a nonlinear optical process. Biochemical experiments with rhodopsin, cone visual pigments, and a chromophore model compound 11-cis-retinyl-propylamine Schiff base demonstrate the direct isomerization of visual chromophore by a two-photon chromophore isomerization. Indeed, quantum mechanics modeling indicates the feasibility of this mechanism. Together, these findings clearly show that human visual perception of near infrared light occurs by two-photon isomerization of visual pigments. PMID:25453064

  6. Minimizing geometric isomerization of α-cypermethrin in the residue analysis.

    PubMed

    Liu, Xueke; Shen, Zhigang; Wang, Peng; Liu, Chang; Yao, Guojun; He, Jiayuan; Liu, Donghui; Zhou, Zhiqiang

    2016-04-01

    Isomerization of chiral pesticides in residue analysis has not drawn much attention which can cause wrong decisions on the enantioselective environmental behavior. A residue analysis method for α-cypermethrin and its three acid metabolites, cis/trans-3-(2,2-dichlorovinyl)-2,2-dimethyl cyclopropanecarboxylic acid (cis/trans-DCVA) and 3-phenoxybenzoic acid (3-PBA), in foods such as chicken, honey, milk and pork has been established, in which the isomerization of α-cypermethrin was minimized. The target compounds were determined by GC-ECD after a derivatization reaction with 1,1,1,3,3,3-hexafluoroisopropanol. The conditions of the method were optimized by Taguchi orthogonal experiment. Under the optimized conditions, good linearity was obtained with correlation coefficients ranging from 0.9964 to 0.9998. The limits of detection were 0.001-0.005 mg kg(-1). The recoveries were 70.9-114.9% with relative standard deviations of 0.6-15%. In addition, ratios of isomerization ranged only from 2.3% to 7.0%. This method was applied in commercial animal food products. PMID:26593561

  7. Reversible photochemical isomerization of N,N'-di(t-butoxycarbonyl)indigos.

    PubMed

    Farka, Dominik; Scharber, Markus; Głowacki, Eric Daniel; Sariciftci, Niyazi Serdar

    2015-04-16

    We report on the photophysics of N,N'-di(t-butoxycarbonyl)indigos (tBOC indigos), finding that reversible photochemical trans-cis and cis-trans isomerization reactions proceed with high quantum yields (0.10-0.46). Absorption of wavelengths in the 500-600 nm region induces trans-cis isomerism, while blue light leads to the reverse cis-trans process. Like their parent indigos, trans-BOC indigos have low fluorescence yields (∼1 × 10(-3)), while the cis isomers have no measurable emission. These compounds are the first examples of photoisomerizable indigoid dyes in which photochemical isomerism effectively outcompetes radiative decay processes. Though indigo dyes typically have poor solubility in organic solvents, tBOC indigos can be dissolved at concentrations up to 8 w% in common organic solvents like acetone. Furthermore, unlike other photoisomerizable indigoids, tBOC indigos are not sensitive to quenching by proton and electron donors. These features, combined with high quantum yields of reversible photoisomerism induced by relatively low-energy photons (∼2 eV), make tBOC indigo derivatives potentially interesting for photochromic applications, such as photomechanically actuated materials. PMID:25811428

  8. Structure-Dependent cis/trans Isomerization of Tetraphenylethene Derivatives: Consequences for Aggregation-Induced Emission.

    PubMed

    Zhang, Chong-Jing; Feng, Guangxue; Xu, Shidang; Zhu, Zhenshu; Lu, Xianmao; Wu, Jien; Liu, Bin

    2016-05-17

    The isomerization and optical properties of the cis and trans isomers of tetraphenylethene (TPE) derivatives with aggregation-induced emission (AIEgens) have been sparsely explored. We have now observed the tautomerization-induced isomerization of a hydroxy-substituted derivative, TPETH-OH, under acidic but not under basic conditions. Replacing the proton of the hydroxy group in TPETH-OH with an alkyl group leads to the formation of TPETH-MAL, for which the pure cis and trans isomers were obtained and characterized by HPLC analysis and NMR spectroscopy. Importantly, cis-TPETH-MAL emits yellow fluorescence in DMSO at -20 °C whereas trans-TPETH-MAL shows red fluorescence under the same conditions. Moreover, the geometry of cis- and trans-TPETH-MAL remains unchanged when they undergo thiol-ene reactions to form cis- and trans-TPETH-cRGD, respectively. Collectively, our findings improve our fundamental understanding of the cis/trans isomerization and photophysical properties of TPE derivatives, which will guide further AIEgen design for various applications. PMID:27071955

  9. Differential mobility spectrometry of isomeric protonated dipeptides: modifier and field effects on ion mobility and stability.

    PubMed

    Blagojevic, Voislav; Chramow, Alexander; Schneider, Bradley B; Covey, Thomas R; Bohme, Diethard K

    2011-05-01

    The ability to resolve isomeric protonated dipeptides was investigated with the new technique of differential ion mobility mass spectrometry that uses "modifier" molecules to enhance differential mobility. Two pairs of protonated peptides [glycine-alanine (GlyAla) and alanine-glycine (AlaGly), glycine-serine (GlySer) and serine-glycine (SerGly)] and eight different modifiers (water, 2-propanol, 1,5-hexadiene, 2-chloropropane, chlorobenzene, dichloromethane, acetonitrile, and cyclohexane) were used in the initial study. Separation of the protonated peptides was found to be dependent on the mass and proton affinity of the modifier and combinations of functionalities present in the modifier and the analyte ion. Six of the eight modifiers (water, 2-propanol, chlorobenzene, cyclohexane, dichloromethane, and acetonitrile) were able to separate the protonated isomeric peptide pairs, and generally, modifiers with electron-rich groups performed the best. In the presence of some modifiers, a reduction of ion current was observed under the highest field conditions (>115 Td). Dopant-catalyzed isomerization, likely by proton-transport catalysis, and field-induced fragmentation may have contributed to these losses. Two high vapor pressure modifiers, 1,5-hexadiene and 2-chloropropane, significantly influenced ion formation leading to the formation of stable cluster populations that could be observed in the mass spectrometer. Although not a major concern, both fragmentation and influence of modifier evaporation warrant further studies in order to fully understand and possibly eliminate them. PMID:21504141

  10. Photochemical chromophore isomerization in histidine kinase rhodopsin HKR1.

    PubMed

    Luck, Meike; Bruun, Sara; Keidel, Anke; Hegemann, Peter; Hildebrandt, Peter

    2015-04-28

    Histidine kinase rhodopsin 1 is a photoreceptor in green algae functioning as a UV-light sensor. It switches between a UV-absorbing state (Rh-UV) and a blue-absorbing state (Rh-Bl) with a protonated retinal Schiff base (RSB) cofactor in a mixture of 13-trans,15-anti and 13-cis,15-syn isomers. The present spectroscopic study now shows that cofactor-protein assembly stabilizes the protonated 13-trans,15-anti RSB isomer. Formation of the active photoswitch requires the photoinduced conversion to Rh-UV. The transitions between the Rh-Bl isomers and the deprotonated 13-cis,15-anti and 13-trans,15-syn isomers of Rh-UV proceed via multiple photoisomerizations of one or simultaneously two double bonds. PMID:25836735

  11. pH control of photoreactivity of Ru(II) pyridyltriazole complexes: Photoinduced linkage isomerism and photoanation

    SciTech Connect

    Wang, R.; Vos, J.G.; Schmehl, R.H.

    1992-03-11

    The photophysical and photochemical behavior of mixed ligand complexes of Ru(II) with 3-(pyridin-2-yl)-1,2,4-triazole (HPTN) have been examined in solutions of varying acidity. Protonation of both the N-2 bound (HPTN-2) and the N-4 bound (HPTN-4) isomers of [(bpy){sub 2}Ru(HPTN)]{sup +} results in a decrease in the luminescence lifetime in solution and an increase in reactivity upon photolysis in CH{sub 2}Cl{sub 2}. The excited state of the deprotonated form of both complexes decays by a single exponential at pHs above 3; the data were fit to a general expression for excited-state decay involving protonation of the excited complex. Results of temperature-dependent luminescence decays suggest the protonated complexes decay via population of a metal-centered excited state, while the deprotonated complexes do not efficiently populate this state at temperatures at or below room temperature. Photolysis of either protonated isomer in CH{sub 2}Cl{sub 2} results in linkage isomerism; equilibrium is established for photolysis at 4:1 [(bpy){sub 2}Ru(HPTN-4)]{sup 2+} to [(bpy){sub 2}Ru(HPTN-2)]{sup 2+}. In the presence of coordinating counterions photoanation occurs to yield the cis-anion complex with loss of pyridyltriazole. The deprotonated form of both isomers is inert to photosubstitution in CH{sub 2}Cl{sub 2} at room temperature. Thus, the substitutional photolability can be controlled by controlling protonation of the ground state of the complex. 41 refs., 9 figs., 3 tabs.

  12. A Crystallographic Study of Bright Far-Red Fluorescent Protein mKate Reveals pH-induced cis-trans Isomerization of the Chromophore

    SciTech Connect

    Pletnev, Sergei; Shcherbo, Dmitry; Chudakov, Dmitry M.; Pletneva, Nadezhda; Merzlyak, Ekaterina M.; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Vladimir

    2008-11-03

    The far-red fluorescent protein mKate {lambda}{sup ex}, 588 nm; {lambda}{sub em}, 635 nm; chromophore-forming triad Met{sup 63}-Tyr{sup 64}-Gly{sup 65}, originating from wild-type red fluorescent progenitor eqFP578 (sea anemone Entacmaea quadricolor), is monomeric and characterized by the pronounced pH dependence of fluorescence, relatively high brightness, and high photostability. The protein has been crystallized at a pH ranging from 2 to 9 in three space groups, and four structures have been determined by x-ray crystallography at the resolution of 1.75--2.6 {angstrom}. The pH-dependent fluorescence of mKate has been shown to be due to reversible cis-trans isomerization of the chromophore phenolic ring. In the non-fluorescent state at pH 2.0, the chromophore of mKate is in the trans-isomeric form. The weakly fluorescent state of the protein at pH 4.2 is characterized by a mixture of trans and cis isomers. The chromophore in a highly fluorescent state at pH 7.0/9.0 adopts the cis form. Three key residues, Ser{sup 143}, Leu{sup 174}, and Arg{sup 197} residing in the vicinity of the chromophore, have been identified as being primarily responsible for the far-red shift in the spectra. A group of residues consisting of Val{sup 93}, Arg{sup 122}, Glu{sup 155}, Arg{sup 157}, Asp{sup 159}, His{sup 169}, Ile{sup 171}, Asn{sup 173}, Val{sup 192}, Tyr{sup 194}, and Val{sup 216}, are most likely responsible for the observed monomeric state of the protein in solution.

  13. Isomerization and fragmentation of acetonitrile upon interaction with N(4S) atoms: the chemistry of nitrogen in dense molecular clouds

    NASA Astrophysics Data System (ADS)

    Mencos, Alejandro; Krim, Lahouari

    2016-08-01

    We experimentally show that the reaction between ground state nitrogen atoms N(4S) and acetonitrile CH3CN can lead to two distinct chemical pathways that are both thermally activated at very low temperatures. First is CH3CN isomerization which produces CH3NC and H2CCNH. Second is CH3CN decomposition which produces HNC and CH3CNH+CN- fragments, with the possible release of H2. Our results reveal that the mobility of N(4S)-atoms is stimulated in the 3-11 K temperature range, and that its subsequent encounter with one acetonitrile molecule is sufficient for the aforementioned reactions to occur without the need for additional energy to be supplied to the CH3CN + N(4S) system. These findings shed more light on the nitrogen chemistry that can possibly take place in dense molecular clouds, which until now was thought to only involve high-energy processes and therefore be unlikely to occur in such cold and dark interstellar regions. The reaction pathways we propose in this study have very important astrochemical implications, as it was shown recently that the atomic nitrogen might be more abundant, in many interstellar icy grain mantles, than previously thought. Also, these reaction pathways can now be considered within dense molecular clouds, and possibly affect the branching ratios for N-bearing molecules computed in astrochemical modelling.

  14. Dynamic Permutational Isomerism in a closo-Cluster.

    PubMed

    Fu, Junhong; Morshedi, Mahbod; Moxey, Graeme J; Barlow, Adam; Cifuentes, Marie P; Humphrey, Mark G

    2016-04-01

    Permutational isomers of trigonal bipyramidal [W2 RhIr2 (CO)9 (η(5) -C5 H5 )2 (η(5) -C5 HMe4 )] result from competitive capping of either a W2 Ir or a WIr2 face of the tetrahedral cluster [W2 Ir2 (CO)10 (η(5) -C5 H5 )2 ] from its reaction with [Rh(CO)2 (η(5) -C5 HMe4 )]. The permutational isomers slowly interconvert in solution by a cluster metal vertex exchange that is proposed to proceed by Rh-Ir and Rh-W bond cleavage and reformation, and via the intermediacy of an edge-bridged tetrahedral transition state. The permutational isomers display differing chemical and physical properties: replacement of CO by PPh3 occurs at one permutational isomer only, while the isomers display distinct optical power limiting behavior. PMID:26868979

  15. Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization

    PubMed Central

    Stensitzki, T.; Yang, Y.; Muders, V.; Schlesinger, R.; Heberle, J.; Heyne, K.

    2016-01-01

    Vibrational dynamics of the retinal all-trans to 13-cis photoisomerization in channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by femtosecond visible pump mid-IR probe spectroscopy. After photoexcitation, the transient infrared absorption of C-C stretching modes was detected. The formation of the 13-cis photoproduct marker band at 1193 cm−1 was observed within the time resolution of 0.3 ps. We estimated the photoisomerization yield to (60 ± 6) %. We found additional time constants of (0.55 ± 0.05) ps and (6 ± 1) ps, assigned to cooling, and cooling processes with a back-reaction pathway. An additional bleaching band demonstrates the ground-state heterogeneity of retinal. PMID:27191011

  16. Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization.

    PubMed

    Stensitzki, T; Yang, Y; Muders, V; Schlesinger, R; Heberle, J; Heyne, K

    2016-07-01

    Vibrational dynamics of the retinal all-trans to 13-cis photoisomerization in channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by femtosecond visible pump mid-IR probe spectroscopy. After photoexcitation, the transient infrared absorption of C-C stretching modes was detected. The formation of the 13-cis photoproduct marker band at 1193 cm(-1) was observed within the time resolution of 0.3 ps. We estimated the photoisomerization yield to (60 ± 6) %. We found additional time constants of (0.55 ± 0.05) ps and (6 ± 1) ps, assigned to cooling, and cooling processes with a back-reaction pathway. An additional bleaching band demonstrates the ground-state heterogeneity of retinal. PMID:27191011

  17. Advances in Tagging Methods for Lifetimes of Isomeric- and Proton-Unbound States

    SciTech Connect

    Cullen, D. M.

    2008-11-11

    This paper summarises the programme of Recoil-isomer tagging that has been performed over the last ten years at the University of Jyvaeskylae, Finland. The nuclei studied lie in the mass 130-140 region of the Segre chart very close to the proton drip line. The evolution of the isomer character is seen to change from K-isomers, at N = 74, to shape-isomers in the gamma soft N = 77 nuclei to seniority-isomers around N = 82. The influence of the proton drip line on the N = 74 isomers and possible critical-point symmetries in the N = 77 nuclei are discussed and the latest results presented. Developments of the isomer-tagging technique, using large beam currents with a dual Multi-Wire Proportional Counter setup, and an Isomer-tagged Differential-Plunger setup are discussed along with a future programme of work at Jyvaeskylae.

  18. Isomerization and dissociation of n-butylbenzene radical cation.

    PubMed

    Halbert, Stéphanie; Bouchoux, Guy

    2012-02-01

    Fragmentation mechanisms of ionized butylbenzene to give m/z 91 and m/z 92 fragment ions have been examined at the G3B3 and G3MP2B3 levels of theory. It is shown that the energetically favored pathways lead to tropylium, Tr(+), and methylene-2,4-cyclohexadiene, MCD(•+), ions. Formation of m/z 91 benzyl ions, Bz(+), by a simple bond fission (SBF) process, needs about 30 kJ/mol more energy than Tr(+). Possible formation of C(7)H(8)(•+) ions of structures different from the retro-ene rearrangement (RER) product, MCD(•+), has been also considered. Comparison with experimental data of this "thermometer" system is done through a kinetic modeling using Rice-Ramsperger-Kassel-Marcus (RRKM) and orbiting transition state (OTS) rate constant calculations on the G3MP2B3 0 K energy surface. The results agree with previous experimental observation if (i) the competitive formation of Tr(+) and Bz(+) is taken into account in the m/z 91 pathway, and (ii) the stepwise character of the RER fragmentation is introduced in the m/z 92 fragmentation route. PMID:22229805

  19. An Optimized Glutamate Receptor Photoswitch with Sensitized Azobenzene Isomerization.

    PubMed

    Gascón-Moya, Marta; Pejoan, Arnau; Izquierdo-Serra, Mercè; Pittolo, Silvia; Cabré, Gisela; Hernando, Jordi; Alibés, Ramon; Gorostiza, Pau; Busqué, Félix

    2015-10-16

    A new azobenzene-based photoswitch, 2, has been designed to enable optical control of ionotropic glutamate receptors in neurons via sensitized two-photon excitation with NIR light. In order to develop an efficient and versatile synthetic route for this molecule, a modular strategy is described which relies on the use of a new linear fully protected glutamate derivative stable in basic media. The resulting compound undergoes one-photon trans-cis photoisomerization via two different mechanisms: direct excitation of its azoaromatic unit and irradiation of the pyrene sensitizer, a well-known two-photon sensitive chromophore. Moreover, 2 presents large thermal stability of its cis isomer, in contrast to other two-photon responsive switches relying on the intrinsic nonlinear optical properties of push-pull substituted azobenzenes. As a result, the molecular system developed herein is a very promising candidate for evoking large photoinduced biological responses during the multiphoton operation of neuronal glutamate receptors with NIR light, which require accumulation of the protein-bound cis state of the switch upon repeated illumination. PMID:26414427

  20. Development of ultrafast photochromic organometallics and photoinduced linkage isomerization of arene chromium carbonyl derivatives.

    PubMed

    To, Tung T; Heilweil, Edwin J; Duke, Charles B; Ruddick, Kristie R; Webster, Charles Edwin; Burkey, Theodore J

    2009-03-26

    We review recent studies of processes relevant to photoinduced linkage isomerization of organometallic systems with the goal of preparing organometallics with an efficient and ultrafast photochromic response. The organometallic system thus corresponds to two linkage isomers with different electronic environments that are responsible for different optical properties. Much of this work has focused on examining processes following irradiation of cyclopentadienyl manganese tricarbonyl derivatives (compounds 3-21) including solvent coordination, thermal relaxation, solvent displacement by tethered functional groups (chelation), dissociation of tethered functional groups, and linkage isomerization. A new platform is investigated for obtaining a photochromic response in new experiments with arene chromium dicarbonyl complexes. A photochromic response is observed for arene chromium dicarbonyl complexes with tethered pyridine and olefin functional groups based on light-driven linkage isomerization on the nanosecond time scale. Irradiation at 532 nm of 23 ([Cr{eta(6)-C(6)H(5)CH(2-Py-kappaN)CH(2)CH=CH(2)}(CO)(2)]) (Py = pyridine) results in the isomerization to 22 ([Cr{eta(6)-C(6)H(5)CH(2-Py)CH(2)-eta(2)-CH=CH(2)}(CO)(2)]), and 355 nm irradiation isomerizes 22 to 23. The ultrafast linkage isomerization has been investigated at room temperature in n-heptane solution on the picosecond to microsecond time scale with UV- or visible-pump and IR-probe transient absorption spectroscopy by comparing the dynamics with model compounds containing only a tethered pyridine. Irradiation of 24 ([Cr{eta(6)-C(6)H(5)(CH(2))(3)(2-Py)}(CO)(3)]) and 25 ([Cr{eta(6)-C(6)H(5)(CH(2))(2)(2-Py)}(CO)(3)]) at 289 nm induces CO loss to immediately yield a Cr-heptane solvent coordinated intermediate of the unsaturated Cr fragment, which then converts to the kappaN(1)-pyridine chelate within 200 and 100 ns, respectively. Irradiation of 26 ([Cr{eta(6)-C(6)H(5)CH(2)(2-Py)}(CO)(3)]) also induces CO loss to

  1. Palladium-Catalyzed Long-Range Deconjugative Isomerization of Highly Substituted α,β-Unsaturated Carbonyl Compounds.

    PubMed

    Lin, Luqing; Romano, Ciro; Mazet, Clément

    2016-08-17

    The long-range deconjugative isomerization of a broad range of α,β-unsaturated amides, esters, and ketones by an in situ generated palladium hydride catalyst is described. This redox-economical process is triggered by a hydrometalation event and is thermodynamically driven by the refunctionalization of a primary or a secondary alcohol into an aldehyde or a ketone. Di-, tri-, and tetrasubstituted carbon-carbon double bonds react with similar efficiency; the system is tolerant toward a variety of functional groups, and olefin migration can be sustained over 30 carbon atoms. The refunctionalized products are usually isolated in good to excellent yield. Mechanistic investigations are in support of a chain-walking process consisting of repeated migratory insertions and β-H eliminations. The bidirectionality of the isomerization reaction was established by isotopic labeling experiments using a substrate with a double bond isolated from both terminal functions. The palladium hydride was also found to be directly involved in the product-forming tautomerization step. The ambiphilic character of the in situ generated [Pd-H] was demonstrated using isomeric trisubstituted α,β-unsaturated esters. Finally, the high levels of enantioselectivity obtained in the isomerization of a small set of α-substituted α,β-unsaturated ketones augur well for the successful development of an enantioselective version of this unconventional isomerization. PMID:27434728

  2. Spatiotemporal manipulation of retinoic acid activity in zebrafish hindbrain development via photo-isomerization.

    PubMed

    Xu, Lijun; Feng, Zhiping; Sinha, Deepak; Ducos, Bertrand; Ebenstein, Yuval; Tadmor, Arbel D; Gauron, Carole; Le Saux, Thomas; Lin, Shuo; Weiss, Shimon; Vriz, Sophie; Jullien, Ludovic; Bensimon, David

    2012-09-01

    All-trans retinoic acid (RA) is a key player in many developmental pathways. Most methods used to study its effects in development involve continuous all-trans RA activation by incubation in a solution of all-trans RA or by implanting all-trans RA-soaked beads at desired locations in the embryo. Here we show that the UV-driven photo-isomerization of 13-cis RA to the trans-isomer (and vice versa) can be used to non-invasively and quantitatively control the concentration of all-trans RA in a developing embryo in time and space. This facilitates the global or local perturbation of developmental pathways with a pulse of all-trans RA of known concentration or its inactivation by UV illumination. In zebrafish embryos in which endogenous synthesis of all-trans RA is impaired, incubation for as little as 5 minutes in 1 nM all-trans RA (a pulse) or 5 nM 13-cis RA followed by 1-minute UV illumination is sufficient to rescue the development of the hindbrain if performed no later than bud stage. However, if subsequent to this all-trans RA pulse the embryo is illuminated (no later than bud stage) for 1 minute with UV light (to isomerize, i.e. deactivate, all-trans RA), the rescue of hindbrain development is impaired. This suggests that all-trans RA is sequestered in embryos that have been transiently exposed to it. Using 13-cis RA isomerization with UV light, we further show that local illumination at bud stage of the head region (but not the tail) is sufficient to rescue hindbrain formation in embryos whose all-trans RA synthetic pathway has been impaired. PMID:22874920

  3. Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity*

    PubMed Central

    Golczak, Marcin; Kiser, Philip D.; Lodowski, David T.; Maeda, Akiko; Palczewski, Krzysztof

    2010-01-01

    Regeneration of visual chromophore in the vertebrate visual cycle involves the retinal pigment epithelium-specific protein RPE65, the key enzyme catalyzing the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol. Although RPE65 has no predicted membrane spanning domains, this protein predominantly associates with microsomal fractions isolated from bovine retinal pigment epithelium (RPE). We have re-examined the nature of RPE65 interactions with native microsomal membranes by using extraction and phase separation experiments. We observe that hydrophobic interactions are the dominant forces that promote RPE65 association with these membranes. These results are consistent with the crystallographic model of RPE65, which features a large lipophilic surface that surrounds the entrance to the catalytic site of this enzyme and likely interacts with the hydrophobic core of the endoplasmic reticulum membrane. Moreover, we report a critical role for phospholipid membranes in preserving the retinoid isomerization activity and physical properties of RPE65. Isomerase activity measured in bovine RPE was highly sensitive to phospholipase A2 treatment, but the observed decline in 11-cis-retinol production did not directly reflect inhibition by products of lipid hydrolysis. Instead, a direct correlation between the kinetics of phospholipid hydrolysis and retinoid isomerization suggests that the lipid membrane structure is critical for RPE65 enzymatic activity. We also provide evidence that RPE65 operates in a multiprotein complex with retinol dehydrogenase 5 and retinal G protein-coupled receptor in RPE microsomes. Modifications in the phospholipid environment affecting interactions with these protein components may be responsible for the alterations in retinoid metabolism observed in phospholipid-depleted RPE microsomes. Thus, our results indicate that the enzymatic activity of native RPE65 strongly depends on its membrane binding and phospholipid

  4. Racemized and Isomerized Proteins in Aging Rat Teeth and Eye Lens.

    PubMed

    Warmack, Rebeccah A; Mansilla, Eduardo; Goya, Rodolfo G; Clarke, Steven G

    2016-08-01

    The quantification of aspartic acid racemization in the proteins of nonmetabolically active tissues can be used as a measure of chronological aging in humans and other long-lived organisms. However, very few studies have been conducted in shorter-lived animals such as rodents, which are increasingly used as genetic and metabolic models of aging. An initial study had reported significant changes in the ratio of d- to l-aspartate in rat molars with age. Using a sensitive HPLC method for the determination of d- and l-aspartate from protein hydrolysates, we found no accumulation of d-aspartate in the molars of 17 rats that ranged in age from 2 to 44 months, and the amount of d-aspartate per molar did not correspond with molar eruption date as had been previously reported. However, developing an alternate approach, we found significant accumulation of isomerized aspartyl residues in eye lens proteins that are also formed by spontaneous degradation processes. In this study, we used the human protein l-isoaspartate/d-aspartate O-methyltransferase (PCMT1) as an analytical reagent in a sensitive and convenient procedure that could be used to rapidly examine multiple samples simultaneously. We found levels of isomerized aspartyl residues to be about 35 times higher in the lens extracts of 18-month-old rats versus 2-month-old rats, suggesting that isomerization may be an effective marker for biological aging in this range of ages. Importantly, we found that the accumulation appeared to plateau in rats of 18 months and older, indicating that potentially novel mechanisms for removing altered proteins may develop with age. PMID:26650547

  5. Minute Time Scale Prolyl Isomerization Governs Antibody Recognition of an Intrinsically Disordered Immunodominant Epitope*

    PubMed Central

    Fassolari, Marisol; Chemes, Lucia B.; Gallo, Mariana; Smal, Clara; Sánchez, Ignacio E.; de Prat-Gay, Gonzalo

    2013-01-01

    Conformational rearrangements in antibody·antigen recognition are essential events where kinetic discrimination of isomers expands the universe of combinations. We investigated the interaction mechanism of a monoclonal antibody, M1, raised against E7 from human papillomavirus, a prototypic viral oncoprotein and a model intrinsically disordered protein. The mapped 12-amino acid immunodominant epitope lies within a “hinge” region between the N-terminal intrinsically disordered and the C-terminal globular domains. Kinetic experiments show that despite being within an intrinsically disordered region, the hinge E7 epitope has at least two populations separated by a high energy barrier. Nuclear magnetic resonance traced the origin of this barrier to a very slow (t½ ∼4 min) trans-cis prolyl isomerization event involving changes in secondary structure. The less populated (10%) cis isomer is the binding-competent species, thus requiring the 90% of molecules in the trans configuration to isomerize before binding. The association rate for the cis isomer approaches 6 × 107 m−1 s−1, a ceiling for antigen-antibody interactions. Mutagenesis experiments showed that Pro-41 in E7Ep was required for both binding and isomerization. After a slow postbinding unimolecular rearrangement, a consolidated complex with KD = 1.2 × 10−7 m is reached. Our results suggest that presentation of this viral epitope by the antigen-presenting cells would have to be “locked” in the cis conformation, in opposition to the most populated trans isomer, in order to select the specific antibody clone that goes through affinity and kinetic maturation. PMID:23504368

  6. Isomerization and dissociation in competition: The two-component dissociation rates of methyl propionate ions

    SciTech Connect

    Mazyar, O.A.; Baer, T.

    1999-03-04

    Threshold photoelectron-photoion coincidence (TPEPICO) spectroscopy has been used to investigate the unimolecular chemistry of gas-phase methyl propionate ions. This ion undergoes isomerization to a lower energy enol structure, CH{sub 3}CHC(OH)OCH{sub 3}{sup {sm_bullet}+}, via two different pathways involving two distonic isomers, {sup {sm_bullet}}CH{sub 2}CH{sub 2}C{sup +}(OH)OCH{sub 3} and CH{sub 3}CH{sub 2}C{sup +}(OH)OCH{sub 2}{sup {sm_bullet}}. This isomerization reaction is in competition with the direct CH{sub 3}O{sup {sm_bullet}} loss reaction, which leads to two-component dissociation rates of the methyl propionate ions. Detailed modeling of this complex reaction permitted the extraction of the dissociative photoionization threshold for methyl propionate, which at 0 K is 10.83 {+-} 0.01 eV, as well as the isomerization barrier between the distonic CH{sub 3}CH{sub 2}C{sup +}(OH)OCH{sub 2}{sup {sm_bullet}} and enol CH{sub 3}CHC(OH)OCH{sub 3}{sup {sm_bullet}+} ions of 8.5 kcal/mol (relative to the methyl propionate ion). By combining this with the 0 K heats of formation of methyl propionate and the methoxy radical, the authors derive a 0 K heat of formation of the product propanoyl ion of 147 kcal/mol. Also measured was the adiabatic ionization energy of methyl propionate, 10.03 {+-} 0.05 eV.

  7. Thermodynamic driving forces for PAH isomerization and growth during thermal treatment of polluted soils.

    PubMed

    Pope, C J; Peters, W A; Howard, J B

    2000-12-01

    For a limiting case of thermodynamic equilibrium, the importance of two classes of thermal chemical reactions that modify the structure and bioactivity of polycyclic aromatic hydrocarbons (PAH) was assessed computationally. These reactions are molecular weight (MW) growth by acetylene addition, and intramolecular rearrangement (isomerization). Temperatures (300-1100 degrees C), and the chemical environment (C(2)H(2)/H(2) molar ratios) were selected for relevancy to thermal treatment of PAH-contaminated soils under oxygen-free conditions. Molecular mechanics methods [MM3(92)] were used to compute thermochemical properties for calculation of equilibrium constants, i.e., heats of formation, standard entropies, and heat capacities for 30 PAH with empirical formulae C(14)H(10), C(16)H(10), C(18)H(10), C(18)H(12), C(20)H(10), and C(20)H(12). Included were 11 PAH containing only six-membered rings and 19 PAH containing both five- and six-membered rings. For each of these PAH the calculations predict that with increasing temperature, isomerization increases the "complexity" of the PAH mixture, i.e., the relative abundance of each PAH isomer in the mixture other than the most stable isomer, increases. Isomerization also partially transforms non-mutagens to mutagens, e.g., pyrene and benzo[e]pyrene to fluoranthene and benzo[a]pyrene, respectively, and partially converts cyclopenta[c, d]pyrene (CPEP) and chrysene, both human cell mutagens, to one and three additional human cell mutagens, respectively. Acetylene addition transforms the non-mutagens phenanthrene and pyrene to the mutagens triphenylene and CPEP, respectively. Some of the predicted PAH have been observed elsewhere among the products of aromatics pyrolysis. This study elucidates PAH reactivity for comparison with measurements, and identifies PAH reactions to be monitored and avoided in soil thermal decontamination and other waste remediation processes. PMID:11040395

  8. Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

    SciTech Connect

    Golczak, Marcin; Kiser, Philip D.; Lodowski, David T.; Maeda, Akiko; Palczewski, Krzysztof

    2010-04-05

    Regeneration of visual chromophore in the vertebrate visual cycle involves the retinal pigment epithelium-specific protein RPE65, the key enzyme catalyzing the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol. Although RPE65 has no predicted membrane spanning domains, this protein predominantly associates with microsomal fractions isolated from bovine retinal pigment epithelium (RPE). We have re-examined the nature of RPE65 interactions with native microsomal membranes by using extraction and phase separation experiments. We observe that hydrophobic interactions are the dominant forces that promote RPE65 association with these membranes. These results are consistent with the crystallographic model of RPE65, which features a large lipophilic surface that surrounds the entrance to the catalytic site of this enzyme and likely interacts with the hydrophobic core of the endoplasmic reticulum membrane. Moreover, we report a critical role for phospholipid membranes in preserving the retinoid isomerization activity and physical properties of RPE65. Isomerase activity measured in bovine RPE was highly sensitive to phospholipase A{sup 2} treatment, but the observed decline in 11-cis-retinol production did not directly reflect inhibition by products of lipid hydrolysis. Instead, a direct correlation between the kinetics of phospholipid hydrolysis and retinoid isomerization suggests that the lipid membrane structure is critical for RPE65 enzymatic activity. We also provide evidence that RPE65 operates in a multiprotein complex with retinol dehydrogenase 5 and retinal G protein-coupled receptor in RPE microsomes. Modifications in the phospholipid environment affecting interactions with these protein components may be responsible for the alterations in retinoid metabolism observed in phospholipid-depleted RPE microsomes. Thus, our results indicate that the enzymatic activity of native RPE65 strongly depends on its membrane binding and

  9. Spectroscopic identification of isomeric jet-cooled benzyl-type radicals formed from 3-fluoro-o-xylene by corona discharge

    NASA Astrophysics Data System (ADS)

    Yoon, Young Wook; Chae, Sang Youl; Lee, Sang Kuk

    2013-10-01

    By means of a pinhole-type glass nozzle designed for supersonic jet expansion along with corona discharge, vibronically excited but jet-cooled isomeric benzyl-type radicals were generated from the precursor 3-fluoro-o-xylene. The visible vibronic emission spectrum was recorded from the discharge system with a long-path monochromator. From an analysis of the spectrum observed, we identified the formation of two isomers, 2-methyl-3-fluorobenzyl and 2-methyl-6-fluorobenzyl radicals in the corona discharge of precursor, and determined for the first time the electronic energy in the D1 → D0 transition and vibrational mode frequencies in the D0 state for both isomers.

  10. Establishing the Two-Photon Linkage Isomerization Mechanism in the Nitrosyl Complex trans-[RuCl(NO)(py)4](2+) by DFT and TDDFT.

    PubMed

    Sanz García, Juan; Alary, Fabienne; Boggio-Pasqua, Martial; Dixon, Isabelle M; Malfant, Isabelle; Heully, Jean-Louis

    2015-09-01

    The density functional theory calculations presented in this work allow the first rationalization of the full linkage photoisomerization mechanism of trans-[RuCl(NO)(py)4](2+), in both the forward and reverse directions. These mechanisms are consistent with the experimental data establishing that blue-light irradiation triggers the forward process, while red or IR photons trigger the reverse process. Characterization of the singlet and lowest triplet potential energy surfaces shows that, despite the unfavorable thermodynamic character of the forward process, the topologies of the surfaces and particularly some crucial surface crossings enable the isomerization. In the forward Ru-NO → Ru-ON direction, a sequential two-photon absorption mechanism is unraveled that involves a sideways-bonded metastable state. In contrast, in the reverse reaction, two mechanisms are proposed involving either one or two photons. PMID:26274397

  11. Isomeric differentiation of polycyclic aromatic hydrocarbons using silver nitrate reactive desorption electrospray ionization mass spectrometry

    PubMed Central

    Eftekhari, Mohammad; Ismail, Ali I.; Zare, Richard N.

    2014-01-01

    RATIONALE Polycyclic aromatic hydrocarbons (PAHs) are nonpolar and difficult to detect by desorption electrospray ionization. We present a new detection method based on cationization with silver ions, which has the added advantage of being able to differentiate PAHs with the same mass but different structure. METHODS 9,10-Diphenylanthracene and triptycene, in addition to four different groups of PAH isomers: (1) anthracene and phenanthrene, (2) pyrene and fluoranthene, (3) benz[a]anthracene, benz[b]anthracene (tetracene), and chrysene (4) benzo[a]pyrene and benzo[k]fluoranthene, were deposited on a paper surface and bombarded with methanol droplets containing silver nitrate. The resulting microdroplets entered a quadruple mass spectrometer for mass analysis. RESULTS The mass spectrum shows [PAH]+, [Ag + OH + PAH]+, and [Ag(PAH)n]+ n (n = 1, 2) (and [PAH + O2]+ in the case of benz[b]anthracene) ions. PAHs having a bay structure, such as phenanthrene, showed a different tendency to interact with silver ions from those PAHs having a linear arrangement of the fused benzene rings, such as anthracene. The ratios of the [PAH]+ peak intensity to that of [Ag–PAH]+, [Ag + OH + PAH]+, [Ag(PAH)2]+, and [PAH + O2]+ were used to differentiate the PAH isomers sharing the same molecular formula with different structures. For isomeric mixtures the [PAH]+ to [Ag + OH + PAH]+ ratio was found to be the most useful parameter. The uncertainty in the mole fraction of an isomeric mixture was ±0.09, 0.13, ±0.25, and ±0.1 for phenanthrene-anthracene, fl benz[a] anthracene-chrysene, and benzo[a]pyrene-benzo[k]fluoranthene, respectively. CONCLUSIONS A simple method has been developed for the detection of PAHs in desorption electrospray ionization mass spectrometry based on Ag(I) cationization. The method showed a capability to differentiate PAHs isomers (having the same molecular mass) in isomeric mixture with an uncertainty in the mole fraction of about 0.1. At high inlet temperature

  12. Xylose Isomerization to Xylulose and Its Dehydration to Furfural in Aqueous Media

    SciTech Connect

    Choudhary, Vinit; Pinar, Ana B; Sandler, Stanley I; Vlachos, Dion G.; Lobo, Raul F

    2011-12-02

    A nonenzymatic route for xylose isomerization in an aqueous medium using zeolite Sn-beta as a catalyst is demonstrated. Xylulose and lyxose are the primary and secondary products. The maximum yield to xylulose is 27%, with an 11% yield to lyxose at ~60% xylose conversion at 100 °C. When the Sn-beta zeolite is combined with a Brønsted acid catalyst, furfural forms in a single pot from xylose in an aqueous medium at much lower temperatures than typically employed for this reaction.

  13. Energy density analysis (EDA) of cis, trans-enol isomerization in malonaldehyde, tropolone and 9-hydroxyphenalenone

    NASA Astrophysics Data System (ADS)

    Nakai, Hiromi; Sodeyama, Keitaro

    2002-10-01

    We have recently proposed an energy density analysis (EDA) that partitions the total energy of a molecular system into atomic energy densities. In this study, the EDA is applied to cis, trans-enol isomerization reactions of malonaldehyde, tropolone and 9-hydroxyphenalenone. Energy density changes in the reactions are shown to be closely related to the formation and breaking of the chemical bonds. By analyzing the energy density changes, we can find the reason why the hydrogen atom moves through the out-of-plane pathway instead of the in-plane pathway.

  14. Photo- and thermochromic spirans. XVII. Tautomerism and photoinduced isomerizations of aldonitrone vinylogs

    SciTech Connect

    Metelitsa, A.V.; Lyashik, O.T.; Volbushko, N.V.; Andreeva, I.M.; Knyazhanskii, M.I.; Medyantseva, E.A.; Minkin, V.I.

    1986-12-10

    Nitrones of o-hydroxycinnamaldehyde and its benzoannelated derivatives were prepared. A benzoid-quinoid tautomeric equilibrium was observed for 3-(1-hydroxy-4-methyl-2-naphthyl)propenal and 3-(1-hydroxy-4-naphthyl)-propenal nitrones in a polar solvent. On irradiation of o-cetyl derivatives (77-293/sup 0/K), oxaziranes are formed and reversible cis-trans-isomerization reactions with respect to the CH=CH bond are recorded. In the case of hydroxynitrones, the phototransformations are due to a proton transfer from the hydroxylic group to the nitrogen oxide group, followed by cyclization, leading to isomers with a cyclic 2H-chromene structure.

  15. Modeling of xylose fermentation to ethanol by sequential isomerization and fermentation. [Schizosaccharomyces pombe

    SciTech Connect

    Kabel, J.J.; Robinson, C.W.; Moo-Young, M.

    1983-01-01

    Economic utilization of the hemicellulose fraction of lignocellulosics is required to enable the commercial exploitation of ethanol-from-lignocellulosics processes. By isomerizing xylose, the major hemicellulose sugar, to xylulose this substrate becomes fermentable by many yeasts. It is thought that conversion of xylose to ethanol is optimal in a packed-bed reactor system employing both immobilized glucose isomerase and immobilized Schizosaccharomyces pombe. Plug-flow models are employed in a preliminary discrimination between possible reactor schemes. A combined enzyme-yeast bed reactor is shown to be the most technically feasible and least costly alternative. 36 references, 8 figures, 5 tables.

  16. Quantum control of isomerization by robust navigation in the energy spectrum

    SciTech Connect

    Murgida, G. E.; Arranz, F. J.; Borondo, F.

    2015-12-07

    In this paper, we present a detailed study on the application of the quantum control technique of navigation in the energy spectrum to chemical isomerization processes, namely, CN–Li⇆ Li–CN. This technique is based on the controlled time variation of a Hamiltonian parameter, an external uniform electric field in our case. The main result of our work establishes that the navigation involved in the method is robust, in the sense that quite sizable deviations from a pre-established control parameter time profile can be introduced and still get good final results. This is specially relevant thinking of a experimental implementation of the method.

  17. Single bubble sonochemistry: decomposition of alkyl bromide and the isomerization reaction of maleic acid.

    PubMed

    Troia, A; Ripa, D Madonna; Spagnolo, R; Maurino, V

    2006-07-01

    Single bubble cavitation offers an unique opportunity to evaluate the effect of bubble activity in promoting chemical reactions. In this paper we study the isomerization reaction of maleic acid into fumaric acid using an aqueous solution of maleic acid saturated with CH2Br2. The Br* radicals are generated at the bubble surface and a whitish thread forms. For comparison, the same reaction was conducted in a sonochemical bath. A possible scheme of the reactions activated at bubble surface after the decomposition of organic brominated substances is proposed. PMID:16168698

  18. Dielectric characteristic of photoinduced isomerization in azo-dye doped polymeric matrices

    SciTech Connect

    Luo Duanbin; Deng Li

    2006-05-01

    The dielectric permittivities and losses of poly(methyl methacrylate) doped with different concentrations of azo dye are investigated under the irradiation of 532 nm light for the first time. The dielectric permittivities increase with the concentration of chromophores increasing, and the dielectric relaxation is mainly influenced by the doped azo-dye chromophores. Given the dye concentration, the dielectric permittivities depend on the pump power of 532 nm light. With the increase of pumping light power, the low frequency dielectric losses increase while the high frequency dielectric losses decrease. The results are explained based on the photoinduced isomerization of chromophores and the interaction between the chromophores and polymer matrices.

  19. RhNGF slow unfolding is not due to proline isomerization: possibility of a cystine knot loop-threading mechanism.

    PubMed Central

    De Young, L. R.; Burton, L. E.; Liu, J.; Powell, M. F.; Schmelzer, C. H.; Skelton, N. J.

    1996-01-01

    The unfolding of recombinant human beta-NGF (NGF) in guanidine hydrochloride (GdnHCl) was found to be time dependent with the denaturation midpoint moving to lower GdnHCl concentration over time. Dissociation and extensive unfolding of the NGF dimer occurred rapidly in 5 M GdnHCl, but further unfolding of the molecule occurred over many days at 25 degrees C. Fluorescence spectroscopy, size-exclusion and reversed-phase HPLC, ultra-centrifugation, and proton NMR spectroscopy were used to ascertain that the slow unfolding step was between two denatured monomeric states of NGF (M1 and M2). Proton NMR showed the monomer formed at early times in GdnHCl (M1) had little beta-sheet structure, but retained residual structure in the tryptophan indole and high-field methyl regions of the spectrum. This residual structure was lost after prolonged incubation in GdnHCl giving a more fully unfolded monomer, M2. From kinetic unfolding experiments in 5 M GdnHCl it was determined that the conversion of M1 to M2 had an activation energy of 26.5 kcal/mol, a half-life of 23 h at 25 degrees C, and the rate of formation of M2 was dependent on the GdnHCl concentration between 5 and 7.1 M GdnHCl. These properties of the slow unfolding step are inconsistent with a proline isomerization mechanism. The rate of formation of the slow folding monomer M2 increases with truncation of five and nine amino acids from the NGF N-terminus. A model for the slow unfolding reaction is proposed where the N-terminus threads through the cystine knot to form M2, a loop-threading reaction, increasing the conformational freedom of the denatured state. PMID:8844846

  20. Effects of Infrared Laser Radiation on the In Vitro Isomerization of All-Trans Retinal to 11-Cis Retinal

    PubMed Central

    Liegner, J.; Taboada, J.; Tsin, A. T. C.

    2015-01-01

    The in vitro effect of infrared laser light on the isomerization of all-trans retinal dissolved in an ether/hexane and also an ethanol solvent was studied. Pulsed laser energy at 1064 nm was used to drive the molecular reconfiguration of all-trans retinal to 11-cis retinal. High pressure liquid chromatography (HPLC) was used to quantify the conversion. Overall isomerization was minimal (0.2 percent to 1.0 percent), yet, a significant difference in isomerization due to pulsed infrared laser energy over non-modulated monochromatic laser light was detected (up to 168 percent difference). Potentially, pulsed laser radiation tuned to the ethylenic stretch frequency of the C11=C12 bond of retinal may induce rotational changes to the chromophore. PMID:26321787

  1. Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

    PubMed Central

    Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

    2014-01-01

    Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

  2. Coulomb excitation of a {sup 242}Am isomeric target : E2, E3 strengths, rotational alignment, and collective enhancement.

    SciTech Connect

    Hayes, A. B.; Cline, D.; Moody, K. J.; Ragnarsson, I.; Wu, C. Y.; Becker, J. A.; Carpenter, M. P.; Carroll, J. J.; Gohlke, D.; Greene, J. P.; Hecht, A. A.; Janssens, R. V. F.; Karamian, S. A.; Lauritsen, T.; Lister, C. J.; Macri, R. A.; Propri, R.; Seweryniak, D.; Wang, X.; Wheeler, R.; Zhu, S.

    2010-10-29

    A 98% pure {sup 242m}Am (K=5{sup -}, t{sub 1/2} = 141 years) isomeric target was Coulomb excited with a 170.5-MeV {sup 40}Ar beam. The selectivity of Coulomb excitation, coupled with the sensitivity of Gammasphere plus CHICO, was sufficient to identify 46 new states up to spin 18 {h_bar} in at least four rotational bands; 11 of these new states lie in the isomer band, 13 in a previously unknown yrast K{sup {pi}} = 6{sup -} rotational band, and 13 in a band tentatively identified as the predicted yrast K{sup {pi}} = 5{sup +} band. The rotational bands based on the K{sup {pi}} = 5{sup -} isomer and the 6{sup -} bandhead were populated by Coulomb excitation with unexpectedly equal cross sections. The {gamma}-ray yields are reproduced by Coulomb excitation calculations using a two-particle plus rotor model (PRM), implying nearly complete {Delta}K = 1 mixing of the two almost-degenerate rotational bands, but recovering the Alaga rule for the unperturbed states. The degeneracy of the 5{sup -} and 6{sup -} bands allows for precise determination of the mixing interaction strength V, which approaches the strong-mixing limit; this agrees with the 50% attenuation of the Coriolis matrix element assumed in the model calculations. The fractional admixture of the I{sub K}{sup {pi}} = 6{sub 6{sup -}} state in the nominal 6{sub 5{sup -}} isomer band state is measured within the PRM as 45.6{sub -1.1}{sup +0.3}%. The E2 and M1 strengths coupling the 5{sup -} and 6{sup -} bands are enhanced significantly by the mixing, while E1 and E2 couplings to other low-K bands are not measurably enhanced. The yields of the 5{sup +} band are reproduced by an E3 strength of {approx}15 W.u., competitive with the interband E2 strength. Alignments of the identified two-particle Nilsson states in {sup 242}Am are compared with the single-particle alignments in {sup 241}Am.

  3. Ion Mobility Separation of Isomeric Carbohydrate Precursor Ions and Acquisition of their Independent Tandem Mass Spectra

    PubMed Central

    Zhu, Maolei; Bendiak, Brad; Clowers, Brian; Hill, Herbert H.

    2010-01-01

    The rapid separation of isomeric precursor ions of oligosaccharides prior to their analysis by MSn was demonstrated using an ambient pressure ion mobility spectrometer (IMS) interfaced with a quadrupole ion trap. Separations were not limited to specific types of isomers; representative isomers differing solely in the stereochemistry of sugars, in their anomeric configurations, and in their overall branching patterns and linkage positions could be resolved in the millisecond time frame. Physical separation of precursor ions permitted independent mass spectra of individual oligosaccharide isomers to be acquired to at least MS3, the number of stages of dissociation limited only practically by the abundance of specific product ions. IMS-MSn analysis was particularly valuable in the evaluation of isomeric oligosaccharides that yielded identical sets of product ions in MS/MS experiments, revealing pairs of isomers that would otherwise not be known to be present in a mixture if evaluated solely by MS dissociation methods alone. A practical example of IMS-MSn analysis of a set of isomers included within a single HPLC fraction of oligosaccharides released from bovine submaxillary mucin is described. PMID:19562326

  4. Isomerization and decomposition reactions in the pyrolysis of branched hydrocarbons: 4-methyl-1-pentyl radical.

    PubMed

    McGivern, W Sean; Awan, Iftikhar A; Tsang, Wing; Manion, Jeffrey A

    2008-07-31

    The kinetics of the decomposition of 4-methyl-1-pentyl radicals have been studied from 927-1068 K at pressures of 1.78-2.44 bar using a single pulse shock tube with product analysis. The reactant radicals were formed from the thermal C-I bond fission of 1-iodo-4-methylpentane, and a radical inhibitor was used to prevent interference from bimolecular reactions. 4-Methyl-1-pentyl radicals undergo competing decomposition and isomerization reactions via beta-bond scission and 1, x-hydrogen migrations (x = 4, 5), respectively, to form short-chain radicals and alkenes. Major alkene products, in decreasing order of concentration, were propene, ethene, isobutene, and 1-pentene. The observed products are used to validate a RRKM/master equation (ME) chemical kinetics model of the pyrolysis. The presence of the branched methyl moiety has a significant impact on the observed reaction rates relative to analogous reaction rates in straight-chain radical systems. Systems that result in the formation of substituted radical or alkene products are found to be faster than reactions that form primary radical and alkene species. Pressure-dependent reaction rate constants from the RRKM/ME analysis are provided for all four H-transfer isomers at 500-1900 K and 0.1-1000 bar pressure for all of the decomposition and isomerization reactions in this system. PMID:18613654

  5. Silver complexation and tandem mass spectrometry for differentiation of isomeric flavonoid diglycosides.

    PubMed

    Zhang, Junmei; Brodbelt, Jennifer S

    2005-03-15

    For detection and differentiation of isomeric flavonoids, electrospray ionization mass spectrometry is used to generate silver complexes of the type (Ag + flavonoid)+. Collisionally activated dissociation (CAD) of the resulting 1:1 silver/flavonoid complexes allows isomer differentiation of flavonoids. Eighteen flavonoid diglycosides constituting seven isomeric series are distinguishable from each other based on the CAD patterns of their silver complexes. Characteristic dissociation pathways allow identification of the site of glycosylation, the type of disaccharide (rutinose versus neohesperidose), and the type of aglycon (flavonol versus flavone versus flavanone). This silver complexation method is more universal than previous metal complexation methods, as intense silver complexes are observed even for flavonoids that lack the typical metal chelation sites. To demonstrate the feasibility of using silver complexation and tandem mass spectrometry to characterize flavonoids in complex mixtures, flavonoids extracted from grapefruit juice are separated by high-performance liquid chromatography and analyzed via a postcolumn complexation ESI-MS/MS strategy. Diagnostic fragmentation pathways of the silver complexes of the individual eluting flavonoids allow successful identification of the six flavonoids in the extract. PMID:15762583

  6. Roaming-mediated ultrafast isomerization of geminal tri-bromides in the gas and liquid phases

    NASA Astrophysics Data System (ADS)

    Mereshchenko, Andrey S.; Butaeva, Evgeniia V.; Borin, Veniamin A.; Eyzips, Anna; Tarnovsky, Alexander N.

    2015-07-01

    ‘Roaming’ is a new and unusual class of reaction mechanism that has recently been discovered in unimolecular dissociation reactions of isolated molecules in the gas phase. It is characterized by frustrated bond cleavage, after which the two incipient fragments ‘roam’ on a flat region of the potential energy surface before reacting with one another. Here, we provide evidence that supports roaming in the liquid phase. We are now able to explain previous solution-phase experiments by comparing them with new ultrafast transient absorption data showing the photoisomerization of gas-phase CHBr3. We see that, upon S0-S1 excitation, gas-phase CHBr3 isomerizes within 100 fs into the BrHCBr-Br species, which is identical to what has been observed in solution. Similar sub-100 fs isomerization is now also observed for BBr3 and PBr3 in solution upon S1 excitation. Quantum chemical simulations of XBr3 (X = B, P or CH) suggest that photochemical reactivity in all three cases studied is governed by S1/S0 conical intersections and can best be described as occurring through roaming-mediated pathways.

  7. Roaming-mediated ultrafast isomerization of geminal tri-bromides in the gas and liquid phases.

    PubMed

    Mereshchenko, Andrey S; Butaeva, Evgeniia V; Borin, Veniamin A; Eyzips, Anna; Tarnovsky, Alexander N

    2015-07-01

    'Roaming' is a new and unusual class of reaction mechanism that has recently been discovered in unimolecular dissociation reactions of isolated molecules in the gas phase. It is characterized by frustrated bond cleavage, after which the two incipient fragments 'roam' on a flat region of the potential energy surface before reacting with one another. Here, we provide evidence that supports roaming in the liquid phase. We are now able to explain previous solution-phase experiments by comparing them with new ultrafast transient absorption data showing the photoisomerization of gas-phase CHBr3. We see that, upon S0-S1 excitation, gas-phase CHBr3 isomerizes within 100 fs into the BrHCBr-Br species, which is identical to what has been observed in solution. Similar sub-100 fs isomerization is now also observed for BBr3 and PBr3 in solution upon S1 excitation. Quantum chemical simulations of XBr3 (X = B, P or CH) suggest that photochemical reactivity in all three cases studied is governed by S1/S0 conical intersections and can best be described as occurring through roaming-mediated pathways. PMID:26100804

  8. Fast Photochromism Involving Thermally-Activated Valence Isomerization of Phenoxyl-Imidazolyl Radical Complex Derivatives.

    PubMed

    Kobayashi, Yoichi; Shima, Kentaro; Mutoh, Katsuya; Abe, Jiro

    2016-08-18

    Open-shell biradicals have received considerable attention in material science because of their high two-photon absorption cross sections and broad and high absorptive features over the visible region. However, the instability of the biradical caused by the open-shell nature was one of the drawbacks; therefore, novel radical compounds which can suppress unwanted reactions by tuning the open-shell features are desired to expand the versatility of the radical compounds. Here, we report a novel radical-dissociation-type photochromic compound whose photochromic reaction involves a valence isomerization from the open-shell biradical to closed-shell quinoidal forms by using a phenoxyl-imidazolyl radical complex framework. The valence isomerization from the biradical to quinoid forms effectively tunes the open-shell feature in time and drastically changes the spectral features, which were revealed by time-resolved Fourier transform infrared spectroscopy. This novel fast photochromic property not only is important for fundamental spin chemistry but also expands the versatility of the radical compounds for novel advanced photofunctional materials. PMID:27454008

  9. Kinetics of the geometric isomerization of cyclohexene in a stochastic bath

    NASA Astrophysics Data System (ADS)

    Depaepe, J. M.; Ryckaert, J. P.; Bellemans, A.

    Rare-events molecular dynamics techniques are used to study the interconversion between the two half-chair isomers of cyclohexene (C6H10), in a solvent modelled through a stochastic bath, in order to investigate dynamic solvent effects on the isomerization rate. Adopting the torsional angle around the C-C sigma bond opposite to the double bond as the reaction coordinate, we calculate the equilibrium distribution of this coordinate (using umbrella sampling), and estimate the isomerization rate, including the transmission coefficient κ. The paper also contains methodological developments. A variant of Andersen's stochastic collision method (canonical ensemble sampling) is developed for molecules with constraints: by resampling Cartesian velocities of a localized subgroup of atoms of the molecule and leaving all other atomic velocity components unchanged, one mimics the collision of a virtual gas molecule with a subpart of the molecule of interest. To evaluate the transmission coefficient κ, the initial conditions for trajectories 'crossing the top' are automatically generated during the run, using a biased potential to obtain the probability of being at the saddle point.

  10. Isomeric signatures in the fragmentation of pyridazine and pyrimidine induced by fast ion impact

    SciTech Connect

    Wolff, Wania Luna, Hugo; Montenegro, Eduardo C.

    2015-07-28

    We present fast proton impact induced fragmentations of pyrimidine and pyridazine as an experimental resource to investigate isomeric signatures. Major isomeric imprints are identified for few fragment ions and differences of more than an order of magnitude for the cross sections of fragments of the same mass were measured. The observation of the molecular structure of these isomers gives no apparent indication for the reasons for such substantial differences. It is verified that the simple displacement of the position of one nitrogen atom strongly inhibits or favors the production of some ionic fragment species. The dependency of the fragmentation cross sections on the proton impact energy, investigated by means of time of flight mass spectroscopy and of a model calculation based in first order perturbation theory, allows us to disentangle the complex collision dynamics of the ionic fragments. The proton-induced fragmentation discriminates rather directly the association between a molecular orbital ionization and the fragment-ions creation and abundance, as well as how the redistribution of the energy imparted to the molecules takes place, triggering not only single but also double vacancy and leads to specific fragmentation pathways.

  11. Isomerization of n-butene to isobutene by ferrierite and modified ferrierite catalysts

    SciTech Connect

    Pellet, R.J.; Casey, D.G.; Huang, H.M.

    1995-12-01

    n-Butene was isomerized to isobutene over fresh and used ferrierite catalysts. Activity and selectivity for skeletal isomerization and biproduct formation were measured and changes following extended use were related to changes in ferrierite`s aluminum distribution. MAS-NMR of the deactivated catalyst showed a decrease in zeolitic, tetrahedral aluminum and an increase in octahedral aluminum. In order to understand changes occurring following extended use, ferrierite powders were modified by steam and by steam plus acid-wash treatments. A steamed-acid-washed ferrierite catalyst also exhibited reduced initial n-butene conversion but high isobutene selectivity throughout the run. Biproduct formation was greatly reduced. Characterization indicated that acid-wash treatment after steaming had no effect on framework aluminum but partially reduced the amount of nonframework aluminum. Steamed-acid-washed ferrierite was much less sensitive to subsequent hydrothermal treatments than was the starting ferrierite. The study suggests a catalytic role for nonframework alumina, generated upon extended use of unmodified ferrierite and present in steamed ferrierite. Catalytically active, nonframework sites contribute to the production of non-C{sub 4} products and reduced isobutene selectivity. Steamed-acid-washed ferrierite with the active nonframe-work phase removed exhibits excellent isobutene selectivity and catalytic stability. 29 refs., 11 figs., 4 tabs.

  12. Sulfated nanozirconia: an investigation on acid-base properties and n-butane isomerization activity.

    PubMed

    Mishra, H K; Dalai, A K; Das, D D; Parida, K M; Pradhan, N C

    2004-04-15

    Hydrated zirconia was synthesized by an organo-inorganic route employing surfactant and was sulfated using aqueous ammonium persulfate, followed by drying at 110 degrees C. The sample thus obtained was calcined at 600 degrees C to obtain sulfated zirconia and was characterized by several physicochemical methods. Crystallite sizes of sulfated zirconia were calculated from X-ray line broadening using the Debye-Scherer equation and were found to be in the range of 25 nm. When pretreated in air, the catalyst was found to exhibit butane isomerization activity at a temperature as low as 35 degrees C under atmospheric pressure. It showed conversion as high as 37% at 100 degrees C under normal pressure when pretreated in air, whereas nitrogen-pretreated catalyst showed zero activity under similar conditions. NH(3) and CO(2) temperature-programmed desorption studies on air- and helium-pretreated samples indicated that the catalyst surface changes appreciably during air pretreatment. Results on butane isomerization in conjunction with TPD studies suggest that zirconium-oxy sites play an important role in butane activation during the reaction. PMID:15028501

  13. Suffrutines A and B: a pair of Z/E isomeric indolizidine alkaloids from the roots of Flueggea suffruticosa.

    PubMed

    Wu, Zhen-Long; Zhao, Bing-Xin; Huang, Xiao-Jun; Tang, Gen-Yun; Shi, Lei; Jiang, Ren-Wang; Liu, Xin; Wang, Ying; Ye, Wen-Cai

    2014-06-01

    Suffrutines A (1) and B (2), a pair of novel photochemical Z/E isomeric indolizidine alkaloids, with a unique and highly conjugated C20 skeleton, were isolated from the roots of Flueggea suffruticosa. The structures were elucidated by extensive analysis of NMR spectra and single-crystal X-ray diffraction. The light-induced isomerization and hypothetical biogenetic pathway to 1 and 2, as well as their activity for regulating the morphology of Neuro-2a cells are also discussed. PMID:24729281

  14. MNDO barrier heights for catalyzed bicycle-pedal, hula-twist, and ordinary cis-trans isomerizations of protonated retinal Schiff base

    SciTech Connect

    Seltzer, S.

    1987-03-18

    Energy barriers to dark cis-trans isomerization in a protonated retinal Schiff base model in the presence and absence of electrostatic and nucleophilic catalysts have been calculated by the MNDO method. Three general processes - ordinary double bond isomerization, concerted isomerization about two double bonds by bicycle-pedal motion, and one-step double bond and adjacent single bond isomerization by hula-twist motion - are considered. Point negative charges or negatively charged nucleophiles near the protonated nitrogen substantially increase the barrier to cis-trans isomerization over what they would be in the absence of these agents. Negative charge or a nucleophile near C13 lowers the barrier to bicycle-pedal isomerization. Dark isomerization by a hula-twist motion required greater energy and is not substantially aided by the placement of a negative charge or nucleophile near any of the skeletal atoms in the isomerizing system. The importance of this to the mechanism of dark-light adaptation of bacteriorhodopsin is discussed.

  15. Computational Studies Of Chemical Reactions: The Hnc-Hcn And Ch[subscript3]Nc-Ch[subscript3]Cn Isomerizations

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2006-01-01

    The application of computational methods to the isomerization of hydrogen isocyanide to hydrogen cyanide, HNC-HCN is described. The logical extension to the exercise is presented to the isomerization of the methyl-substituted compounds, methylisocyanide and methylcyanide, Ch[subscript 3]NC-CH[subscript3]CN.

  16. Folding of barstar C40A/C82A/P27A and catalysis of the peptidyl-prolyl cis/trans isomerization by human cytosolic cyclophilin (Cyp18).

    PubMed Central

    Golbik, R.; Fischer, G.; Fersht, A. R.

    1999-01-01

    Refolding of b*C40A/C82A/P27A is comprised of several kinetically detectable folding phases. The slowest phase in refolding originates from trans-->cis isomerization of the Tyr47-Pro48 peptide bond being in cis conformation in the native state. This refolding phase can be accelerated by the peptidyl-prolyl cis/trans isomerase human cytosolic cyclophilin (Cyp18) with a kcat/K(M) of 254,000 M(-1) s(-1). The fast refolding phase is not influenced by the enzyme. PMID:10422840

  17. A fluorescent sensor for Zn(2+) and NO2(-) based on the rational control of C[double bond, length as m-dash]N isomerization.

    PubMed

    Liu, Zheng; Peng, Cuina; Wang, Ying; Pei, Meishan; Zhang, Guangyou

    2016-05-01

    A new strategy for the ultrasensitive sensing of cations and anions based on the control of C[double bond, length as m-dash]N isomerization has been developed. Imine-derived ligand is non-fluorescent due to the C[double bond, length as m-dash]N isomerization process, whereas its ternary complex with ZnCl2 is moderately fluorescent because of the partial inhibition of C[double bond, length as m-dash]N isomerization. Such a ternary complex can give a remarkable fluorescence increase when it interacts with nitrite because of the much more efficient suppression of C[double bond, length as m-dash]N isomerization. This modulation process of C[double bond, length as m-dash]N isomerization can thus be used for the highly selective detection of Zn(2+) and NO2(-) in an aqueous solution. PMID:27075971

  18. Isomeric [RuCl2(dmso)2(indazole)2] complexes: ruthenium(II)-mediated coupling reaction of acetonitrile with 1H-indazole.

    PubMed

    Reisner, Erwin; Arion, Vladimir B; Rufińska, Anna; Chiorescu, Ion; Schmid, Wolfgang F; Keppler, Bernhard K

    2005-07-21

    Reaction of the antitumor complex trans-[Ru(III)Cl4(Hind)2]- (Hind = indazole) with an excess of dimethyl sulfoxide (dmso) in acetone afforded the complex trans,trans,trans-[Ru(II)Cl2(dmso)2(Hind)2] (1). Two other isomeric compounds trans,cis,cis-[Ru(II)Cl2(dmso)2(Hind)2] (2) and cis,cis,cis-[Ru(II)Cl2(dmso)2(Hind)2] (3) have been obtained on refluxing cis-[Ru(II)Cl(2)(dmso)(4)] with 2 equiv. of indazole in ethanol and methanol, respectively. Isomers 1 and 2 react with acetonitrile yielding the complexes trans-[Ru(II)Cl2(dmso)(Hind){HN=C(Me)ind}].CH3CN (4.CH3CN) and trans,cis-[Ru(II)Cl2(dmso)2{HN=C(Me)ind}].H2O (5.H2O), respectively, containing a cyclic amidine ligand resulting from insertion of the acetonitrile C triple bond N group in the N1-H bond of the N2-coordinated indazole ligand in the nomenclature used for 1H-indazole. These are the first examples of the metal-assisted iminoacylation of indazole. The products isolated have been characterized by elemental analysis, IR spectroscopy, UV-vis spectroscopy, electrospray mass-spectrometry, thermogravimetry, differential scanning calorimetry, 1H NMR spectroscopy, and solid-state 13C CP MAS NMR spectroscopy. The isomeric structures of 1-3 and the presence of a chelating amidine ligand in 4 and 5 have been confirmed by X-ray crystallography. The electrochemical behavior of 1-5 and the formation of 5 have been studied by cyclic voltammetry. PMID:15995743

  19. Management and outcome of infants and children with right atrial isomerism.

    PubMed Central

    Sadiq, M.; Stümper, O.; De Giovanni, J. V.; Wright, J. G.; Sethia, B.; Brawn, W. J.; Silove, E. D.

    1996-01-01

    OBJECTIVES: To assess the current results and outcome of surgery in infants and children with right atrial isomerism and complex congenital heart disease. SETTING: Tertiary referral centre. METHODS: 20 consecutive children with right atrial isomerism and complex congenital heart disease underwent surgery over a 6 year period between August 1987 and July 1993. The results and outcome were analysed according to age, presentation, and surgical procedures. RESULTS: Patients were divided into two groups depending on age at presentation and initial surgery: group A comprised 11 patients who required surgical intervention in the first month of life (mean age 5 days); and group B comprised nine patients who required initial surgical intervention after the first month of life (mean age 6.8 months). Seven (64%) of the 11 patients in group A had obstructed pulmonary venous drainage and ten (91%) had pulmonary atresia. There were seven early deaths (64%), including the five patients who required systemic to pulmonary artery shunt and simultaneous repair of obstructed pulmonary veins. The long-term survival rate in this group was 18% (two of 11). Pulmonary venous obstruction was present in two (22%) of the nine patients in group B and four (44%) had pulmonary atresia. There were no early deaths. One patient died after a second palliative procedure. There was one late sudden death. Four patients had a Fontan operation with no deaths. Two of the remaining three patients meet the Fontan criteria. The long-term survival rate in this group was 78% (seven of nine). CONCLUSIONS: Surgical management of patients with right atrial isomerism who have complex congenital heart disease carries a high mortality and remains palliative. The overall survival rate was 45% (nine of 20); 18% in patients requiring surgery in the first month of life (group A) and 78% in patients requiring surgery after the first month of life (group B) (P < 0.001). Of the total of 20 patients, nine were potential

  20. Nitrite-Reductase and Peroxynitrite Isomerization Activities of Methanosarcina acetivorans Protoglobin

    PubMed Central

    Ascenzi, Paolo; Leboffe, Loris; Pesce, Alessandra; Ciaccio, Chiara; Sbardella, Diego; Bolognesi, Martino; Coletta, Massimo

    2014-01-01

    Within the globin superfamily, protoglobins (Pgb) belong phylogenetically to the same cluster of two-domain globin-coupled sensors and single-domain sensor globins. Multiple functional roles have been postulated for Methanosarcina acetivorans Pgb (Ma-Pgb), since the detoxification of reactive nitrogen and oxygen species might co-exist with enzymatic activity(ies) to facilitate the conversion of CO to methane. Here, the nitrite-reductase and peroxynitrite isomerization activities of the CysE20Ser mutant of Ma-Pgb (Ma-Pgb*) are reported and analyzed in parallel with those of related heme-proteins. Kinetics of nitrite-reductase activity of ferrous Ma-Pgb* (Ma-Pgb*-Fe(II)) is biphasic and values of the second-order rate constant for the reduction of NO2– to NO and the concomitant formation of nitrosylated Ma-Pgb*-Fe(II) (Ma-Pgb*-Fe(II)-NO) are kapp1 = 9.6±0.2 M–1 s–1 and kapp2 = 1.2±0.1 M–1 s–1 (at pH 7.4 and 20°C). The kapp1 and kapp2 values increase by about one order of magnitude for each pH unit decrease, between pH 8.3 and 6.2, indicating that the reaction requires one proton. On the other hand, kinetics of peroxynitrite isomerization catalyzed by ferric Ma-Pgb* (Ma-Pgb*-Fe(III)) is monophasic and values of the second order rate constant for peroxynitrite isomerization by Ma-Pgb*-Fe(III) and of the first order rate constant for the spontaneous conversion of peroxynitrite to nitrate are happ = 3.8×104 M–1 s–1 and h0 = 2.8×10–1 s–1 (at pH 7.4 and 20°C). The pH-dependence of hon and h0 values reflects the acid-base equilibrium of peroxynitrite (pKa = 6.7 and 6.9, respectively; at 20°C), indicating that HOONO is the species that reacts preferentially with the heme-Fe(III) atom. These results highlight the potential role of Pgbs in the biosynthesis and scavenging of reactive nitrogen and oxygen species. PMID:24827820

  1. Acid-catalyzed isomerization of rhenium alkyne complexes to rhenium allene complexes via 1-metallacyclopropene intermediates

    SciTech Connect

    Casey, C.P.; Brady, J.T.

    1998-10-12

    The alkyne complexes C{sub 5}Me{sub 5}(CO){sub 2}Re({eta}{sup 2}-MeC{triple_bond}CMe) (1) and C{sub 5}H{sub 5}(CO){sub 2}Re({eta}{sup 2}-MeC{triple_bond}CMe) (6) underwent acid-catalyzed isomerization by way of 1-metallacyclopropene intermediates to form the allene complexes C{sub 5}Me{sub 5}(CO){sub 2}Re({eta}{sup 2}-2,3-MeHC{double_bond}C{double_bond}CH{sub 2}) (5) and C{sub 5}H{sub 5}(CO){sub 2}Re({eta}{sup 2}-2,3-MeHC{double_bond}C{double_bond}CH{sub 2}) (7). Stoichiometric reaction of 1 with CF{sub 3}CO{sub 2}H initially produced the kinetic addition product C{sub 5}Me{sub 5}(CO){sub 2}Re[{eta}{sup 2}-(Z)-MeHC{double_bond}CMeO{sub 2}CCF{sub 3}] (8-Z), which slowly isomerized to the thermodynamically more stable E isomer 8-E. The reaction of 6 with CF{sub 3}CO{sub 2}H at {minus}73 C produced only C{sub 5}H{sub 5}(CO){sub 2}Re[{eta}{sup 2}-(E)-MeHC{double_bond}CMeO{sub 2}CCF{sub 3}] (9-E), which isomerized at -60 C to a 80:20 equilibrium mixture of 9-E and 9-Z. Treatment of 9-E and 9-Z with base led to formation of allene complex 7. The rate of this elimination was independent of base concentration. Labeling studies showed that the 1-metallacyclopropene intermediate C{sub 5}H{sub 5}(CO){sub 2}({eta}{sup 2}-CMeCHMe){sup +}CF{sub 3}CO{sub 2}{sup {minus}} (12-CF{sub 3}CO{sub 2}) undergoes a number of important reactions which include, in order of decreasing relative rates: (1) addition of trifluoroacetate to give enol trifluoroacetate complexes, (2) deprotonation to give complexed allenes, (3) degenerate 1,2-hydride migrations, (4) hydride migrations to give {eta}{sup 3}-allyl complexes, and (5) deprotonation to give complexed alkynes.

  2. Mechanism of D-fructose isomerization by Arthrobacter D-xylose isomerase.

    PubMed Central

    Rangarajan, M; Hartley, B S

    1992-01-01

    The mechanism of D-fructose isomerization by Arthrobacter D-xylose isomerase suggested from X-ray-crystallographic studies was tested by detailed kinetic analysis of the enzyme with various metal ions at different pH values and temperatures. At D-fructose concentrations used in commercial processes Mg2+ is the best activator with an apparent dissociation constant of 63 microM; Co2+ and Mn2+ bind more strongly (apparent Kd 20 microM and 10 microM respectively) but give less activity (45% and 8% respectively). Ca2+ is a strict competitive inhibitor versus Mg2+ (Ki 3 microM) or Co2+ (Ki 105 microM). The kinetics show a compulsory order of binding; Co2+ binds first to Site 2 and then to Site 1; then D-fructose binds at Site 1. At normal concentrations Mg2+ binds at Site 1, then D-fructose and then Mg2+ at Site 2. At very high Mg2+ concentrations (greater than 10 mM) the order is Mg2+ at Site 1, Mg2+ at Site 2, then D-fructose. The turnover rate (kcat.) is controlled by ionization of a residue with apparent pKa at 30 degrees C of 6.0 +/- 0.07 (Mg2+) or 5.3 +/- 0.08 (Co2+) and delta H = 23.5 kJ/mol. This appears to be His-219, which is co-ordinated to M[2]; protonation destroys isomerization by displacing M[2]; Co2+ binds more strongly at Site 2 than Mg2+, so competes more strongly against H+. The inhibition constant (Ki) for the two competitive inhibitors 5-thio-alpha-D-glucopyranose and D-sorbitol is invariant with pH, but Km(app.) in the Mg[1]-enzyme is controlled by ionization of a group with pKa 6.8 +/- 0.07 and delta H = 27 kJ/mol, which appears to be His-53. This shows that Km(app.) is a complex constant that includes the rate of the ring-opening step catalysed by His-53, which explains the pH-dependence. In the Mg[1]Mg[2]-enzyme or Co[1]Co[2]-enzyme, the pKa is lower (6.2 +/- 0.1 or 5.6 +/- 0.08) because of the extra adjacent cation. Hence the results fit the previously proposed pathway, but show that the mechanisms differ for Mg2+ and Co2+ and that the rate

  3. Environmental factors affecting the low temperature isomerization of homohopanes in acidic peat deposits, central China

    NASA Astrophysics Data System (ADS)

    Huang, Xianyu; Meyers, Philip A.; Xue, Jiantao; Gong, Linfeng; Wang, Xinxin; Xie, Shucheng

    2015-04-01

    Progressively more evidence reveals the abundant occurrence of the C31 homohopane with a 17α, 21β-configuration (C31 αβ) in immature peats. This compound is commonly considered to be an indicator of thermal maturity in petroleum source rocks, but in peats it has also been interpreted to reflect the oxidation and subsequent decarboxylation reactions of bacteriohopanepolyols with microbially mediated epimerization at C-17 that is catalyzed by the acidic peat conditions. To learn more about the environmental factors that affect the low-temperature isomerization of homohopanes, we investigated the distribution patterns of homohopanes in a well-studied peat core from the Dajiuhu peatland, central China, together with data from modern surface peat samples from Dajiuhu and three other locations. From comparison with paleotemperature and paleohydrologic records in the peat core, we hypothesize that the ratio of C31 αβ hopane relative to the ββ isomer (C31 αβ/ββ) is mainly influenced on a centennial to millennial timescale by ambient temperature with a secondary effect from redox conditions that are defined by peatland water levels. The surface peat samples revealed that relatively high C31 αβ/ββ values occurred under pH < 6. These results suggest that pH is indeed an important factor in the low-temperature isomerization of C31 homohopanes, although the magnitude of the pH effect may be less than those of ambient temperature and redox conditions. In both surface peat and peat horizons from the Dajiuhu peatland, the amount of the C31 αβ compound with R configuration relative to that with S configuration (C31 R/S) varied closely with C31 αβ/ββ, suggesting that the epimerization at both C-17 and C-22 may happen synchronously and at similar rates. This study reveals that the isomerization of homohopanes has the potential to reflect paleoenvironmental changes in acidic peat deposits. In addition, acidic peat samples investigated in this and previous studies

  4. Flavylium based dual photochromism: addressing cis-trans isomerization and ring opening-closure by different light inputs.

    PubMed

    Gago, Sandra; Basílio, Nuno; Moro, Artur J; Pina, Fernando

    2015-04-30

    The multistate system of 4',7-dihydroxy-3-methoxyflavylium is constituted by a multiequilibrium involving trans-chalcone, cis-chalcone, hemiketal, flavylium cation and quinoidal base. This system possesses two independently addressable inter-connected photochromic systems based on the cis-trans isomerization and ring opening-closure of the hemiketal. PMID:25820365

  5. Enantioselective Nickel-Catalyzed anti-Carbometallative Cyclizations of Alkynyl Electrophiles Enabled by Reversible Alkenylnickel E/Z Isomerization.

    PubMed

    Clarke, Christopher; Incerti-Pradillos, Celia A; Lam, Hon Wai

    2016-07-01

    Nickel-catalyzed additions of arylboronic acids to alkynes, followed by enantioselective cyclizations of the alkenylnickel species onto tethered ketones or enones, are reported. These reactions are reliant upon the formal anti-carbonickelation of the alkyne, which is postulated to occur by the reversible E/Z isomerization of an alkenylnickel species. PMID:27333360

  6. Tandem semi-hydrogenation/isomerization of propargyl alcohols to saturated carbonyl analogues by dodecanethiolate-capped palladium nanoparticle catalysts†

    PubMed Central

    Gavia, Diego J.; Koeppen, Jordan; Sadeghmoghaddam, Elham; Shon, Young-Seok

    2016-01-01

    The efficient one-pot conversion of propargyl alcohols to their saturated carbonyl analogues is carried out for the first time using metal nanoparticle catalysts, dodecanethiolate-capped Pd nanoparticles. Kinetic studies reveal that the reaction progresses through a semi-hydrogenation intermediate (allyl alcohols) followed by isomerization to carbonyls.

  7. Tandem isomerization-decarboxylation of unsaturated fatty acids to olefins via ruthenium metal-as-ligand catalysts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new facile Ru-catalyzed route to bio-olefins3 from unsaturated fatty acids via readily accessible metal-as-ligand type catalyst precursors, [Ru(CO)2RCO2]n and Ru3(CO)12, will be described. The catalyst apparently functions in a tandem mode by dynamically isomerizing the positions of double bonds i...

  8. Mechanistic interpretation of selective catalytic hydrogenation and isomerization of alkenes and dienes by ligand deactivated Pd nanoparticles

    NASA Astrophysics Data System (ADS)

    Zhu, Jie S.; Shon, Young-Seok

    2015-10-01

    Unsupported thiolate-capped palladium nanoparticle catalysts are found to be highly substrate-selective for alkene hydrogenation and isomerization. Steric and poisoning effects from thiolate ligands on the nanoparticle surface control reactivity and selectivity by influencing alkene adsorption and directing either di-σ or mono-σ bond formation. The presence of overlapping p orbitals and α protons in alkenes greatly influences the catalytic properties of deactivated palladium nanoparticles leading to easily predictable hydrogenation or isomerization products.Unsupported thiolate-capped palladium nanoparticle catalysts are found to be highly substrate-selective for alkene hydrogenation and isomerization. Steric and poisoning effects from thiolate ligands on the nanoparticle surface control reactivity and selectivity by influencing alkene adsorption and directing either di-σ or mono-σ bond formation. The presence of overlapping p orbitals and α protons in alkenes greatly influences the catalytic properties of deactivated palladium nanoparticles leading to easily predictable hydrogenation or isomerization products. Electronic supplementary information (ESI) available: Supplementary figures, methods, materials, and characterization data. See DOI: 10.1039/c5nr05090a

  9. Enantioselective Nickel-Catalyzed anti-Carbometallative Cyclizations of Alkynyl Electrophiles Enabled by Reversible Alkenylnickel E/Z Isomerization

    PubMed Central

    2016-01-01

    Nickel-catalyzed additions of arylboronic acids to alkynes, followed by enantioselective cyclizations of the alkenylnickel species onto tethered ketones or enones, are reported. These reactions are reliant upon the formal anti-carbonickelation of the alkyne, which is postulated to occur by the reversible E/Z isomerization of an alkenylnickel species. PMID:27333360

  10. Synthesis and polymerization of renewable 1,3-cyclohexadiene using metathesis, isomerization, and cascade reactions with late-metal catalysts.

    PubMed

    Mathers, Robert T; Shreve, Michael J; Meyler, Etan; Damodaran, Krishnan; Iwig, David F; Kelley, Diana J

    2011-09-01

    Synthesis and subsequent polymerization of renewable 1,3-cyclohexadiene (1,3-CHD) from plant oils is reported via metathesis and isomerization reactions. The metathesis reaction required no plant oil purification, minimal catalyst loading, no organic solvents, and simple product recovery by distillation. After treating soybean oil with a ruthenium metathesis catalyst, the resulting 1,4-cyclohexadiene (1,4-CHD) was isomerized with RuHCl(CO)(PPh3)3. The isomerization reaction was conducted for 1 h in neat 1,4-CHD with [1,4-CHD]/[RuHCl(CO)(PPh3)3] ratios as high as 5000. The isomerization and subsequent polymerization of the renewable 1,3-CHD was examined as a two-step sequence and as a one-step cascade reaction. The polymerization was catalyzed with nickel(II)acetylacetonate/methaluminoxane in neat monomer, hydrogenated d-limonene, and toluene. The resulting polymers were characterized by FTIR, DSC, and TGA. PMID:21648003

  11. A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction.

    PubMed

    Gao, Li; Tu, Yaoquan; Wegman, Pia; Wingren, Sten; Eriksson, Leif A

    2011-09-26

    We provide a detailed description of the cis-trans isomerization of 4-hydroxytamoxifen/endoxifen catalyzed by several isoforms from the cytochrome P450 (CYP) superfamily, including CYP1B1, CYP2B6, and CYP2C19. We show that the reactions mainly involve redox processes catalyzed by CYP. DFT calculation results strongly suggest that the isomerization occurs via a cationic intermediate. The cationic cis-isomer is more than 3 kcal/mol more stable than the trans form, resulting in an easier conversion from trans-to-cis than cis-to-trans. The cis-trans isomerization is a rarely reported CYP reaction and is ascribed to the lack of a second abstractable proton on the ethenyl group of the triarylvinyl class of substrates. The cationic intermediates thus formed instead of the stable dehydrogenation products allow for isomerization to occur. As a comparison, the reactions for the tamoxifen derivatives are compared to those of other substrates, 4-hydroxyacetanilide and raloxifene, for which the stable dehydrogenation products are formed. PMID:21870861

  12. Tandem Copper-Catalyzed Propargylation/Alkyne Azacyclization/Isomerization Reaction under Microwave Irradiation: Synthesis of Fully Substituted Pyrroles.

    PubMed

    Zhang, Xiao-Yan; Yang, Zhi-Wei; Chen, Zhongzhu; Wang, Jun; Yang, Dong-Lin; Shen, Ze; Hu, Li-Li; Xie, Jian-Wu; Zhang, Jin; Cui, Hai-Lei

    2016-03-01

    A copper-catalyzed and microwave-assisted synthesis of fully substituted pyrroles has been developed. A series of pentasubstituted pyrroles, especially α-arylpyrroles, could be obtained in moderate to good yields (up to 93%) through a tandem propargylation/alkyne azacyclization/isomerization sequence from readily available β-enamino compounds and propargyl acetates. PMID:26872395

  13. Identification of novel isomeric pectic oligosaccharides using hydrophilic interaction chromatography coupled to traveling-wave ion mobility mass spectrometry.

    PubMed

    Leijdekkers, Antonius G M; Huang, Jie-Hong; Bakx, Edwin J; Gruppen, Harry; Schols, Henk A

    2015-03-01

    Separation and characterization of complex mixtures of pectic oligosaccharides still remains challenging and often requires the use of multiple analytical techniques, especially when isomeric structures are present. In this work, it is demonstrated that the coupling of hydrophilic interaction chromatography (HILIC) to traveling-wave ion mobility mass spectrometry (TWIMMS) enabled the simultaneous separation and characterization of complex mixtures of various isomeric pectic oligosaccharides. Labeling of oligosaccharides with 3-aminoquinoline (3-AQ) improved MS-ionization efficiency of the oligosaccharides and reduced the complexity of the product ion mass spectra, without losing resolution of the HILIC separation. In addition, labeling enabled quantification of oligosaccharides on molar basis using in-line fluorescence detection. Isomeric structures were distinguished using TWIMMS. The 3-AQ-HILIC-TWIMMS method was used to characterize a series of isomeric sugar beet rhamnogalacturonan I derived oligosaccharides carrying a glucuronic acid substituent. Thereby, some novel structural features were identified for the first time: glucuronic acid was attached to O-3 or to O-2 of galacturonic acid residues and a single galacturonic acid residue within an oligomer could contain both an acetyl group and a glucuronic acid substituent. PMID:25647688

  14. Induction of E/Z isomerization in a pendant metal-bound azobenzene: a synthetic, spectroscopic and theoretical study.

    PubMed

    Hasheminasab, A; Wang, L; Dawadi, M B; Bass, J; Herrick, R S; Rack, J J; Ziegler, C J

    2015-09-21

    Re(CO)3 conjugates 1 and 2 that incorporate azobenzenes can be readily generated via one-pot reactions using Schiff base reaction forming conditions. Excitation of the MLCT bands in 1 and 2 results in isomerization of the azobenzene moiety, and this process has been investigated via time-resolved photophysics and TDDFT calculations. PMID:26252161

  15. Investigation of glassy state molecular motions in thermoset polymers

    NASA Astrophysics Data System (ADS)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  16. Mechanism Elucidation of the cis–trans Isomerization of an Azole Ruthenium–Nitrosyl Complex and Its Osmium Counterpart

    PubMed Central

    2013-01-01

    Synthesis and X-ray diffraction structures of cis and trans isomers of ruthenium and osmium metal complexes of general formulas (nBu4N)[cis-MCl4(NO)(Hind)], where M = Ru (1) and Os (3), and (nBu4N)[trans-MCl4(NO)(Hind)], where M = Ru (2) and Os (4) and Hind = 1H-indazole are reported. Interconversion between cis and trans isomers at high temperatures (80–130 °C) has been observed and studied by NMR spectroscopy. Kinetic data indicate that isomerizations correspond to reversible first order reactions. The rates of isomerization reactions even at 110 °C are very low with rate constants of 10–5 s–1 and 10–6 s–1 for ruthenium and osmium complexes, respectively, and the estimated rate constants of isomerization at room temperature are of ca. 10–10 s–1. The activation parameters, which have been obtained from fitting the reaction rates at different temperatures to the Eyring equation for ruthenium [ΔHcis-trans‡= 122.8 ± 1.3; ΔHtrans-cis‡= 138.8 ± 1.0 kJ/mol; ΔScis-trans‡= −18.7 ± 3.6; ΔStrans-cis‡= 31.8 ± 2.7 J/(mol·K)] and osmium [ΔHcis-trans‡= 200.7 ± 0.7; ΔHtrans-cis‡= 168.2 ± 0.6 kJ/mol; ΔScis-trans‡= 142.7 ± 8.9; ΔStrans-cis‡= 85.9 ± 3.9 J/(mol·K)] reflect the inertness of these systems. The entropy of activation for the osmium complexes is highly positive and suggests the dissociative mechanism of isomerization. In the case of ruthenium, the activation entropy for the cis to trans isomerization is negative [−18.6 J/(mol·K)], while being positive [31.0 J/(mol·K)] for the trans to cis conversion. The thermodynamic parameters for cis to trans isomerization of [RuCl4(NO)(Hind)]−, viz. ΔH° = 13.5 ± 1.5 kJ/mol and ΔS° = −5.2 ± 3.4 J/(mol·K) indicate the low difference between the energies of cis and trans isomers. The theoretical calculation has been carried out on isomerization of ruthenium complexes with DFT methods. The dissociative, associative, and intramolecular twist isomerization mechanisms have

  17. Mechanism elucidation of the cis-trans isomerization of an azole ruthenium-nitrosyl complex and its osmium counterpart.

    PubMed

    Gavriluta, Anatolie; Büchel, Gabriel E; Freitag, Leon; Novitchi, Ghenadie; Tommasino, Jean Bernard; Jeanneau, Erwann; Kuhn, Paul-Steffen; González, Leticia; Arion, Vladimir B; Luneau, Dominique

    2013-06-01

    Synthesis and X-ray diffraction structures of cis and trans isomers of ruthenium and osmium metal complexes of general formulas (nBu4N)[cis-MCl4(NO)(Hind)], where M = Ru (1) and Os (3), and (nBu4N)[trans-MCl4(NO)(Hind)], where M = Ru (2) and Os (4) and Hind = 1H-indazole are reported. Interconversion between cis and trans isomers at high temperatures (80-130 °C) has been observed and studied by NMR spectroscopy. Kinetic data indicate that isomerizations correspond to reversible first order reactions. The rates of isomerization reactions even at 110 °C are very low with rate constants of 10(-5) s(-1) and 10(-6) s(-1) for ruthenium and osmium complexes, respectively, and the estimated rate constants of isomerization at room temperature are of ca. 10(-10) s(-1). The activation parameters, which have been obtained from fitting the reaction rates at different temperatures to the Eyring equation for ruthenium [ΔH(cis-trans)‡ = 122.8 ± 1.3; ΔH(trans-cis)‡ = 138.8 ± 1.0 kJ/mol; ΔS(cis-trans)‡ = -18.7 ± 3.6; ΔS(trans-cis)‡ = 31.8 ± 2.7 J/(mol·K)] and osmium [ΔH(cis-trans)‡ = 200.7 ± 0.7; ΔH(trans-cis)‡ = 168.2 ± 0.6 kJ/mol; ΔS(cis-trans)‡ = 142.7 ± 8.9; ΔS(trans-cis)‡ = 85.9 ± 3.9 J/(mol·K)] reflect the inertness of these systems. The entropy of activation for the osmium complexes is highly positive and suggests the dissociative mechanism of isomerization. In the case of ruthenium, the activation entropy for the cis to trans isomerization is negative [-18.6 J/(mol·K)], while being positive [31.0 J/(mol·K)] for the trans to cis conversion. The thermodynamic parameters for cis to trans isomerization of [RuCl4(NO)(Hind)]-, viz. ΔH° = 13.5 ± 1.5 kJ/mol and ΔS° = -5.2 ± 3.4 J/(mol·K) indicate the low difference between the energies of cis and trans isomers. The theoretical calculation has been carried out on isomerization of ruthenium complexes with DFT methods. The dissociative, associative, and intramolecular twist isomerization

  18. Holographic recording materials development. [development of cis-trans isomerization for holographic memory

    NASA Technical Reports Server (NTRS)

    1974-01-01

    Developments in the area of organic cis-trans isomerization systems for holographic memory applications are reported. The chemical research effort consisted of photochemical studies leading to the selection of a stilbene derivative and a polymer matrix system which have greatly improved refractive index differences between the cis and trans isomers as well as demonstrated efficiency of the photoisomerization process. In work on lithium niobate effects of sample stoichiometry and of read and write beam polarizations on recording efficiency were investigated. LiNbO3 was used for a study of angular sensitivity and of capability for simultaneous recording of extended objects without interference. The current status of LiNbO3 as a holographic recording material is summarized.

  19. Structural Isomerization of the Gas Phase 2-NORBORNYL Cation Revealed with Infrared Spectroscopy and Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Mauney, Daniel; Mosley, Jonathan; Duncan, Michael A.

    2014-06-01

    The non-classical structure of the 2-norborny cation (C_7H11+) which was at the center of "the most heated chemical controversy of our time" has been observed in the condensed phase and recently using X-ray crystallography. However, no gas phase vibrational spectrum has been collected. The C_7H11+ cation is produced via H_3+ protonation of norbornene by pulsed discharge in a supersonic expansion of H_2/Ar. Ions are mass-selected and probed using infrared photodissociation spectroscopy. Due to high exothermicity, protonation via H_3+ leads to a structural isomerization to the global minimum structure 1,3-dimethylcyclopentenyl (DMCP+). Experiments are currently being conducted to find softer protonation techniques that could lead to the authentic 2-norbornyl cation. Schleyer,P.v.R. et. al.; Stable Carbocation Chemistry, John Wiley & Sons,Inc.; New York, 1997, Chapter 2

  20. Calcineurin Undergoes a Conformational Switch Evoked via Peptidyl-Prolyl Isomerization

    PubMed Central

    Guasch, Alicia; Aranguren-Ibáñez, Álvaro; Pérez-Luque, Rosa; Aparicio, David; Martínez-Høyer, Sergio; Mulero, M. Carmen; Serrano-Candelas, Eva

    2015-01-01

    A limited repertoire of PPP family of serine/threonine phosphatases with a highly conserved catalytic domain acts on thousands of protein targets to orchestrate myriad central biological roles. A major structural reorganization of human calcineurin, a ubiquitous Ser/Thr PPP regulated by calcium and calmodulin and targeted by immunosuppressant drugs cyclosporin A and FK506, is unveiled here. The new conformation involves trans- to cis- isomerization of proline in the SAPNY sequence, highly conserved across PPPs, and remodels the main regulatory site where NFATc transcription factors bind. Transitions between cis- and trans- conformations may involve peptidyl prolyl isomerases such as cyclophilin A and FKBP12, which are known to physically interact with and modulate calcineurin even in the absence of immunosuppressant drugs. Alternative conformations in PPPs provide a new perspective on interactions with substrates and other protein partners and may foster development of more specific inhibitors as drug candidates. PMID:26248042

  1. Molecular recognition of isomeric protonated amino acid esters monitored by ESI-mass spectrometry.

    PubMed

    Liesenfeld, Andrea; Lützen, Arne

    2014-01-01

    Two new 9,9'-spirobifluorene-derived crown ethers were prepared and used to recognise constitutionally isomeric amino acid derivatives. The performance of the receptors was evaluated by ESI-mass spectrometry using the isomer labelled guest method (ILGM). This method revealed the preferred binding of L-norleucine and L-leucine compared to L-isoleucine for both receptors. Furthermore, non-covalent isotope effects demonstrate the relevance of dispersive interactions for the overall binding event. These effects also provide hints for the relative spatial orientation of the guest molecules within the host-guest complex, and thereby prove the importance of the spirobifluorene moiety for the observed binding of the protonated amino acid esters. PMID:24778737

  2. Mechanistic Study on Oxorhenium-Catalyzed Deoxydehydration and Allylic Alcohol Isomerization.

    PubMed

    Wu, Di; Zhang, Yugen; Su, Haibin

    2016-05-20

    The reaction mechanism of 1,2×n-deoxydehydration (DODH; n=1, 2, 3 …) reactions with 1-butanol as a reductant in the presence of methyltrioxorhenium(VII) catalyst has been investigated by DFT. The reduced rhenium compound, methyloxodihydroxyrhenium(V), serves as the catalytically relevant species in both allylic alcohol isomerization and subsequent DODH processes. Compared with three-step pathway A, involving [1,3]-transposition of allylic alcohols, direct two-step pathway B is an alternative option with lower activation barriers. The rate-limiting step of the DODH reaction is the first hydrogen transfer in methyltrioxorhenium(VII) reduction. Moreover, the increase in the distance between two hydroxyl groups in direct 1,2×n-DODH reactions for C4 and C6 diols results in a higher barrier height. PMID:26991093

  3. Differentiation of Isomeric Ginsenosides by Using Electron-Induced Dissociation Mass Spectrometry.

    PubMed

    Wong, Y-L Elaine; Chen, Xiangfeng; Li, Wan; Wang, Ze; Hung, Y-L Winnie; Wu, Ri; Chan, T-W Dominic

    2016-06-01

    Current phytochemical research on ginsengs focuses on the structural characterization and isomer differentiation of ginsenosides. In this Letter, electron-induced dissociation (EID) was initially investigated by analyzing isomeric ginsenosides. EID provided more structural information on their differentiation than collision-induced dissociation (CID) did. Glycosyl group migration previously observed in the CID of oligosaccharide ions could also be found in the EID of protonated Rg1. This rearrangement reaction would show substantial ambiguities in differentiating Rg1 from Rf. Although other charge carriers could alleviate this problem, the use of EID in dissociating deprotonated ginsenoside ions was superior to other techniques in terms of eliminating glycosyl group migration and generating diagnostic fragment ions for the differentiation of structural isomers. This study demonstrates a potential method to analyze natural products and thus help discover and evaluate novel compounds. PMID:27181402

  4. Catalytic glucose isomerization by porous coordination polymers with open metal sites.

    PubMed

    Akiyama, George; Matsuda, Ryotaro; Sato, Hiroshi; Kitagawa, Susumu

    2014-10-01

    Highly efficient catalytic isomerization reactions from glucose to fructose in aqueous media using porous coordination polymers (PCPs) or metal-organic frameworks (MOFs) is reported for the first time. The catalytic activity of PCPs functionalized with -NH2, -(CH3)2, -NO2, and -SO3H groups on the pore surface is systematically tested. The catalytic activity can be tuned by the acidity of open metal sites (OMSs) by modifying the organic linkers with the functional groups. As a result, it is demonstrated that MIL-101 functionalized with -SO3H not only shows high conversion of glucose but also selectively produces fructose. Further, catalytic one-pot conversion of amylose to fructose is achieved, thanks to the high stability of the framework in an acidic solution. These results show that MOF/PCP compounds having OMSs are promising materials for various useful heterogeneous catalytic reactions, in particular in the biomass field. PMID:25080129

  5. IODINE MONOCHLORIDE FACILITATED DEGLYCOSYLATION, ANOMERIZATION, AND ISOMERIZATION OF 3-SUBSTITUTED THYMIDINE ANALOGUES

    PubMed Central

    Khalil, Ahmed; Ishita, Keisuke; Ali, Tehane; Tiwari, Rohit; Riachy, Ramy; Toppino, Antonio; Hasabelnaby, Sherifa; Sayfullin, Naum; Oliver, Allen G.; Gallucci, Judith; Huang, Zhenguo; Tjarks, Werner

    2014-01-01

    The reaction of thymidine, 3-mono-, and 3,3′,5′-trialkylsubstitued thymidine analogues with iodine monochloride (ICl) was investigated. Treatment with ICl resulted in rapid deglycosylation, anomerization, and isomerization of thymidine and 3-substituted thymidine analogues under various reaction conditions leading to the formation of the nucleobases as the major products accompanied by minor formation of α-furanosidic-, α-pyranosidic- and β-pyranosidic nucleosides. On the other hand, 3,3′,5′-trisubstitued thymidine analogues were only deglycosylated and anomerized. These results are similar to those observed for the acidic hydrolysis of the glycoside bond in nucleosides, but were presumably caused by the Lewis acid character of an iodine electrophile. PMID:25372994

  6. Isomeric differentiation of chloroanilines by gas chromatography-mass spectrometry in combination with tosylation.

    PubMed

    Wang, Shanshan; Zhu, Guohua; Chen, Mengmeng; Liu, Jinsong; Jiang, Kezhi

    2016-01-01

    p-Chloroaniline is one of the banned aromatic amines in azo dyes, but it is very difficult to distinguish it from its isomers due to their identical retention time in chromatography and similar mass spectra. In this work, derivatization of the isomeric chloroanilines was carried out to yield the corresponding N-tosyl chloroanilines, which were completely separated by gas chromatography and also possessed clearly different electron ionization mass spectra. Thus, the three isomers could be differentiated and determined at the same time. Density functional theory calculation results indicated that the effect of the substituent pattern in electron ionization mass spectrometry is mainly due to the difference in the stability of the product ion (P2) at m/z 126, originating from the loss of tosyl radical from the precursor ion. PMID:27553734

  7. Coherent chemistry with THz pulses: Ultrafast field-driven isomerization of LiNC

    NASA Astrophysics Data System (ADS)

    Pellouchoud, L. A.; Reed, E. J.

    2015-05-01

    The ability to coherently rearrange structures at the atomic scale is among the grand challenges of physical science. Some of the primary obstacles are nonadiabatic increases in energy, such as intramolecular vibrational relaxation (IVR) and electronic excitations. Motivated by recent advances in strong terahertz (THz) pulse generation, we investigate the potential of THz to circumvent these obstacles. Employing TDDFT-Ehrenfest simulations, we discover that strong THz pulses can drive isomerization of the LiNC molecule over barriers greater than 0.2 eV with very low ionization rates and, in the best case, less than 3 meV of residual excess energy. This work points to new possibilities in predictively manipulating chemical bonds in molecules and materials.

  8. Antifungal activity and isomerization of octadecyl p-coumarates from Ipomoea carnea subsp. fistulosa.

    PubMed

    Nidiry, Eugene Sebastian J; Ganeshan, Girija; Lokesha, Ankanahalli N

    2011-12-01

    Bioassay monitored HPLC assisted isolation and purification of the chief antifungal fraction of the leaves of Ipomoea carnea subsp. fistulosa (Convulvulaceae) were achieved using Colletotrichum gloeosporioides and Cladosporium cucumerinum as test organisms. The activity of the purified fraction was further confirmed by the dose dependent inhibition of the spore germination of Alternaria alternata and A. porri. The active fraction was identified as a mixture of (E)-octadecyl p-coumarate and (Z)-octadecyl p-coumarate. The two isomers were detected on an HPLC column with substantially different retention times, but once eluted from the column, one form was partly converted to the other in daylight. Conclusive evidence for the structures and their isomerization were obtained from the HPLC behavior, IR, UV, HRESIMS, CIMS and and NMR spectral data. Important 1H NMR and 13C NMR signals could be separately assigned for the isomers using 2D NMR techniques. PMID:22312731

  9. Two new isomerous fluorescent chemosensors for Al3+ based on photoinduced electron transfer

    NASA Astrophysics Data System (ADS)

    Jiang, Xiu-Juan; Tang, Hao; Li, Xiao-Yuan; Zang, Shuang-Quan; Hou, Hong-Wei; Mak, Thomas C. W.

    2013-11-01

    Two new isomerous PET fluorescent chemosensors (L and L‧) for Al3+ have been designed, synthesized and characterized. The two chemosensors exhibited fluorescence enhancement upon binding Al3+ in CH3CN by PET inhibition processes from both the sulfur and the nitrogen donors to anthracene. The job's plot, Benesi-Hildebrand plot and 1H NMR titration experiments indicate that both chemosensors form a 1:1 complex with Al3+. The binding constants were calculated to be (1.432 ± 0.186) × 105 and (1.427 ± 0.970) × 105, respectively. Furthermore, the lowest detection limit for Al3+ in CH3CN was determined to be 4.8 × 10-7 M and 2.2 × 10-7 M, respectively.

  10. The diene isomerization energies dataset: A difficult test for double-hybrid density functionals?

    NASA Astrophysics Data System (ADS)

    Wykes, M.; Pérez-Jiménez, A. J.; Adamo, C.; Sancho-García, J. C.

    2015-06-01

    We have systematically analyzed the performance of some representative double-hybrid density functionals (including PBE0-DH, PBE-QIDH, PBE0-2, XYG3, XYGJ-OS, and xDH-PBE0) for a recently introduced database of diene isomerization energies. Double-hybrid models outperform their corresponding hybrid forms (for example, PBE0-DH, PBE0-2, and PBE-QIDH are more accurate than PBE0) and the XYG3, XYGJ-OS, and xDH-PBE0 functionals perform excellently, providing root mean square deviation values within "calibration accuracy." XYGJ-OS and xDH-PBE0 also rival the best performing post-Hartree-Fock methods at a substantially lower cost.

  11. Single-Molecule Observation of a Mechanically Activated Cis-to-Trans Cyclopropane Isomerization.

    PubMed

    Wang, Junpeng; Kouznetsova, Tatiana B; Craig, Stephen L

    2016-08-24

    The mechanochemical activation of cis-gem-difluorocyclopropane (cis-gDFC) mechanophore in toluene was characterized with single-molecule force spectroscopy. Unlike previously reported behavior in methyl benzoate (MB), two transitions are observed in the force vs extension curves of cis-gDFC polymers in toluene. The first transition occurs at the same force of ∼1300 pN observed previously in MB, but a second transition is observed at forces of ∼1800 pN that reveal the partial formation of the trans-gDFC isomer. The behavior is attributed to competing reactions of the cis-gDFC at the 1300 pN plateau: addition of oxygen to a ring-opened diradicaloid intermediate, and isomerization of cis-gDFC to its trans isomer. PMID:27500711

  12. Screening method for stimulants in urine by UHPLC-MS/MS: identification of isomeric compounds.

    PubMed

    Monfort, Núria; Martínez, Laura; Bergés, Rosa; Segura, Jordi; Ventura, Rosa

    2015-09-01

    A fast screening method for the detection of more than 60 stimulants in urine was developed. The method consisted of a dilution of the urine (1:5 v/v) and analysis by ultra high performance liquid chromatography coupled to tandem mass spectrometry, using a C18 column (1.7 µm particle size), a mobile phase containing deionized water and acetonitrile with formic acid, and gradient elution. The chromatographic run time was 5 min. The detection was performed in positive mode electrospray ionization, monitoring one or two specific ion transitions for each analyte. Appropriate repeatability was obtained, with relative standard deviation (RSD) values below 25% for most of the analytes. Regarding intermediate precision, estimated during routine work, higher RSDs were obtained, probably due to between-day differences in the status of the mass spectrometer and in the chromatographic system. Matrix effect ranged from 60 to 255% with RSD lower than 35% for the majority of compounds. Despite the matrix effect observed, the signal/noise ratio of the analytes spiked at 50 ng/mL was greater than three in all tested samples, allowing a correct detection of all substances at the minimum required performance levels required by the World Anti-Doping Agency and demonstrating the suitability of the method. The method was tested in administration study samples and satisfactorily in operation for more than one year with routine doping samples. The presence of isomeric stimulants with closely similar chromatographic and/or mass spectrometric properties did not allow the unequivocal identification of these compounds after the first analysis. Different possibilities for separation and identification of isomeric compounds are presented. PMID:25728759

  13. Investigation of bone disease using isomerized and racemized fragments of type I collagen.

    PubMed

    Cloos, P A C; Fledelius, C; Christgau, S; Christiansen, C; Engsig, M; Delmas, P; Body, J-J; Garnero, P

    2003-01-01

    In the collagen type I C-telopeptide an aspartyl-glycine site within the sequence AHDGGR is susceptible to molecular rearrangement. In newly synthesized collagen this site is in the native form, denoted alpha L. During aging a spontaneous reaction occurs resulting in three age-modified forms: an isomerized form (beta L) a racemized form (alpha D), and an isomerized/racemized form (beta D). In this study, we measured the urinary excretion of the four forms of C-telopeptides (CTX) in healthy adults and in patients with bone diseases. Levels of all CTX forms were higher in healthy postmenopausal women (P<0.001) compared with premenopausal controls. Levels decreased within 3 days of bisphosphonate treatment indicating that all CTX forms reflect bone resorption. In hyperthyroidism, characterized by a generalized increased bone turnover, native (alpha L) and age-modified (beta L, alpha D and beta D) forms increased to a similar extent compared to controls, resulting in normal ratios between the alpha L and age-modified forms of CTX. Conversely, in Paget's disease and prostate cancer-induced bone metastases, conditions characterized by focal increased bone turnover, alpha L CTX levels were more elevated than those of age-related CTX forms, resulting in increased ratios between native and age-modified CTX. For example, the ratio alpha L/alpha D was increased 7-fold in Paget's disease (P<0.001) and 2-fold in prostate cancer-induced bone metastases (P<0.002). In conclusion, the study suggests that in conditions with a localized alteration in bone turnover the ratio between alpha L CTX and the age-modified forms is significantly elevated. This may provide a new diagnostic and monitoring tool for diseases such as metastatic bone cancer and Paget's disease. PMID:12384813

  14. Spectroscopic Investigation on the Primary Photoreaction of Bathy Phytochrome Agp2-Pr of Agrobacterium fabrum: Isomerization in a pH-dependent H-bond Network.

    PubMed

    Singer, Patrick; Wörner, Sybille; Lamparter, Tilman; Diller, Rolf

    2016-05-01

    Bathy phytochrome Agp2 from Agrobacterium fabrum exhibits an unusually low pKa =7.6 in the Pr state in contrast to a pKa >11 in the Pfr state, indicating a pH-dependent charge distribution and H-bond network in the Pr chromophore binding pocket around neutral pH. Here, we report on ultrafast UV/Vis absorption spectroscopy of the primary Pr photoisomerization of Agp2 at pH 6 and pH 9 and upon H2 O/D2 O buffer exchange. The triexponential Pr kinetics slows down at increased pH and pronounced pH-dependent kinetic isotope effects are observed. The results on the Pr photoreaction suggest: 1) component-wise hindered dynamics on the chromophore excited-state potential energy surface at high pH and 2) proton translocation processes either via single-proton transfer or via significant reorganization of H-bond networks. Both effects reflect the interplay between the pH-dependent charge distribution in the Pr chromophore binding pocket on the one hand and chromophore excitation and its Z→E isomerization on the other hand. PMID:27075723

  15. Vibrational memory in quantum localized states

    NASA Astrophysics Data System (ADS)

    Ajili, Y.; Trabelsi, T.; Denis-Alpizar, O.; Stoecklin, T.; Császár, A. G.; Mogren Al-Mogren, M.; Francisco, J. S.; Hochlaf, M.

    2016-05-01

    The rovibrational eigenenergy set of molecular systems is a key feature needed to understand and model elementary chemical reactions. A unique class of molecular systems, represented by an 4A'' excited electronic state of the [H,S ,N ] - system comprising several distinct dipole-bound isomers, is found to contain both bent and linear minima separated by relatively small barriers. Full-dimensional nuclear-motion computations performed in Jacobi coordinates using three-dimensional potential energy surfaces describing the stable isomers and the related transition states yield rovibrational eigenstates located both below and above the barriers. The rovibrational wave functions are well localized, regardless of whether the state's energy is below or above the barriers. We also show that the states preserve the memory of the isomeric forms they "originate from," which is signature of a strong vibrational memory effect above isomerization barriers.

  16. Ag(I)-catalyzed tandem [6+3] annulation/isomerization of isocyanoacetates with fulvenes: an expedient approach to synthesize fused dihydropyridines.

    PubMed

    He, Zhao-Lin; Wang, Chun-Jiang

    2015-01-11

    An unprecedented Ag(i)-catalyzed tandem [6+3] cycloaddition/isomerization of isocyanoacetates with fulvenes has been developed, affording the fused dihydropyridine derivatives in good yields with exclusive regioselectivities. PMID:25412446

  17. Theoretical study of 1,2-hydride shift associated with the isomerization of glyceraldehyde to dihydroxy acetone by Lewis acid active site models.

    PubMed

    Assary, Rajeev S; Curtiss, Larry A

    2011-08-11

    The isomerization of glyceraldehyde to dihydroxy acetone catalyzed by the active site of Sn-beta zeolite is investigated using the B3LYP density functional and MP2 levels of theory. Structural studies were aimed to understanding the binding modes of glyceraldehyde with the active site, and the detailed free energy landscape was computed for the isomerization process. The rate-limiting step for the isomerization is the 1,2-hydride shift, which is enhanced by the active participation of the hydroxyl group in the hydrolyzed Sn-beta active site analogues to the one seen in the xylose isomerase. On the basis of the assessment of the activation barriers for isomerization by the Sn, Zr, Ti, and Si zeolite models, the activity of the catalysts are in the order of Sn > Zr > Ti > Si in aqueous dielectric media. PMID:21707087

  18. Theoretical study of 1,2-hydride shift associated with the isomerization of glyceraldehyde to dihydroxy acetone by Lewis acid active site models.

    SciTech Connect

    Assary, R. S.; Curtiss, L. A.

    2011-08-01

    The isomerization of glyceraldehyde to dihydroxy acetone catalyzed by the active site of Sn-beta zeolite is investigated using the B3LYP density functional and MP2 levels of theory. Structural studies were aimed to understanding the binding modes of glyceraldehyde with the active site, and the detailed free energy landscape was computed for the isomerization process. The rate-limiting step for the isomerization is the 1,2-hydride shift, which is enhanced by the active participation of the hydroxyl group in the hydrolyzed Sn-beta active site analogues to the one seen in the xylose isomerase. On the basis of the assessment of the activation barriers for isomerization by the Sn, Zr, Ti, and Si zeolite models, the activity of the catalysts are in the order of Sn > Zr > Ti > Si in aqueous dielectric media.

  19. Theoretical Study of 1,2-Hydride Shift Associated with the Isomerization of Glyceraldehyde to Dihydroxy Acetone by Lewis Acid Active Site Models

    SciTech Connect

    Assary, Rajeev S.; Curtiss, Larry A.

    2011-08-11

    The isomerization of glyceraldehyde to dihydroxy acetone catalyzed by the active site of Sn-beta zeolite is investigated using the B3LYP density functional and MP2 levels of theory. Structural studies were aimed to understanding the binding modes of glyceraldehyde with the active site, and the detailed free energy landscape was computed for the isomerization process. The rate-limiting step for the isomerization is the 1,2-hydride shift, which is enhanced by the active participation of the hydroxyl group in the hydrolyzed Sn-beta active site analogues to the one seen in the xylose isomerase. On the basis of the assessment of the activation barriers for isomerization by the Sn, Zr, Ti, and Si zeolite models, the activity of the catalysts are in the order of Sn > Zr > Ti > Si in aqueous dielectric media.

  20. Crystallographic study of red fluorescent protein eqFP578 and its far-red variant Katushka reveals opposite pH-induced isomerization of chromophore

    SciTech Connect

    Pletneva, Nadya V.; Pletnev, Vladimir Z.; Shemiakina, Irina I.; Chudakov, Dmitriy M.; Artemyev, Igor; Wlodawer, Alexander; Dauter, Zbigniew; Pletnev, Sergei

    2012-08-10

    The wild type red fluorescent protein eqFP578 (from sea anemone Entacmaea quadricolor, {lambda}{sub ex} = 552 nm, {lambda}{sub em} = 578 nm) and its bright far-red fluorescent variant Katushka ({lambda}{sub ex} = 588 nm, {lambda}{sub em} = 635 nm) are characterized by the pronounced pH dependence of their fluorescence. The crystal structures of eqFP578f (eqFP578 with two point mutations improving the protein folding) and Katushka have been determined at the resolution ranging from 1.15 to 1.85 {angstrom} at two pH values, corresponding to low and high level of fluorescence. The observed extinguishing of fluorescence upon reducing pH in eqFP578f and Katushka has been shown to be accompanied by the opposite trans-cis and cis-trans chromophore isomerization, respectively. Asn143, Ser158, His197 and Ser143, Leu174, and Arg197 have been shown to stabilize the respective trans and cis fluorescent states of the chromophores in eqFP578f and Katushka at higher pH. The cis state has been suggested as being primarily responsible for the observed far-red shift of the emission maximum of Katushka relative to that of eqFP578f.

  1. Accurate prediction of diradical chemistry from a single-reference density-matrix method: Model application to the bicyclobutane to gauche-1,3-butadiene isomerization

    SciTech Connect

    Bertels, Luke W.; Mazziotti, David A.

    2014-07-28

    Multireference correlation in diradical molecules can be captured by a single-reference 2-electron reduced-density-matrix (2-RDM) calculation with only single and double excitations in the 2-RDM parametrization. The 2-RDM parametrization is determined by N-representability conditions that are non-perturbative in their treatment of the electron correlation. Conventional single-reference wave function methods cannot describe the entanglement within diradical molecules without employing triple- and potentially even higher-order excitations of the mean-field determinant. In the isomerization of bicyclobutane to gauche-1,3-butadiene the parametric 2-RDM (p2-RDM) method predicts that the diradical disrotatory transition state is 58.9 kcal/mol above bicyclobutane. This barrier is in agreement with previous multireference calculations as well as recent Monte Carlo and higher-order coupled cluster calculations. The p2-RDM method predicts the Nth natural-orbital occupation number of the transition state to be 0.635, revealing its diradical character. The optimized geometry from the p2-RDM method differs in important details from the complete-active-space self-consistent-field geometry used in many previous studies including the Monte Carlo calculation.

  2. An isomerization-induced cage-breaking process in a molecular glass former below T{sub g}

    SciTech Connect

    Teboul, V.; Saiddine, M.; Accary, J.-B.; Nunzi, J.-M.

    2011-03-21

    A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials.

  3. Synthesis of 1,3-Dienes via a Sequential Suzuki-Miyaura Coupling/Palladium-Mediated Allene Isomerization Sequence.

    PubMed

    Al-Jawaheri, Yassir; Kimber, Marc C

    2016-07-15

    We report a facile method for the synthesis of 1,3-dienes by a sequential process consisting of a palladium-catalyzed, base-free, Suzuki-Miyaura coupling/isomerization sequence. This sequence couples boronic acids with propargyl alcohols, generating the requisite allene in situ, followed by conversion of the unactivated allene to its 1,3-diene via a hydro-palladation/dehydro-palladation process. This process is general for a range of boronic acids, including boronic acids with electron-donating and -withdrawing groups, as well as heteroarylboronic acids. Key to this process is the boric acid byproduct of the base-free Suzuki-Miyauru coupling, which generates the required palladium-hydrido complex [H-Pd(II)-OB(OH)2] required for the isomerization. PMID:27355240

  4. Mesoporous Aluminosilicate Catalysts for the Selective Isomerization of n-Hexane: The Roles of Surface Acidity and Platinum Metal.

    PubMed

    Musselwhite, Nathan; Na, Kyungsu; Sabyrov, Kairat; Alayoglu, Selim; Somorjai, Gabor A

    2015-08-19

    Several types of mesoporous aluminosilicates were synthesized and evaluated in the catalytic isomerization of n-hexane, both with and without Pt nanoparticles loaded into the mesopores. The materials investigated included mesoporous MFI and BEA type zeolites, MCF-17 mesoporous silica, and an aluminum modified MCF-17. The acidity of the materials was investigated through pyridine adsorption and Fourier Transform-Infrared Spectroscopy (FT-IR). It was found that the strong Brönsted acid sites in the micropores of the zeolite catalysts facilitated the cracking of hexane. However, the medium strength acid sites on the Al modified MCF-17 mesoporous silica greatly enhanced the isomerization reaction. Through the loading of different amounts of Pt into the mesopores of the Al modified MCF-17, the relationship between the metal nanoparticles and acidic sites on the support was revealed. PMID:26168190

  5. Results of a Direct Search Using Synchrotron Radiation for the Low-Energy (229)Th Nuclear Isomeric Transition.

    PubMed

    Jeet, Justin; Schneider, Christian; Sullivan, Scott T; Rellergert, Wade G; Mirzadeh, Saed; Cassanho, A; Jenssen, H P; Tkalya, Eugene V; Hudson, Eric R

    2015-06-26

    We report the results of a direct search for the (229)Th (I(π)=3/2(+)←5/2(+)) nuclear isomeric transition, performed by exposing (229)Th-doped LiSrAlF(6) crystals to tunable vacuum-ultraviolet synchrotron radiation and observing any resulting fluorescence. We also use existing nuclear physics data to establish a range of possible transition strengths for the isomeric transition. We find no evidence for the thorium nuclear transition between 7.3 eV and 8.8 eV with transition lifetime (1-2) s≲τ≲(2000-5600)  s. This measurement excludes roughly half of the favored transition search area and can be used to direct future searches. PMID:26197124

  6. Thermodynamic characteristics of the adsorption of isomeric molecules of fluoroadamantanes on the surface of the basal face of graphite

    NASA Astrophysics Data System (ADS)

    Yashkin, S. N.; Svetlov, D. A.; Klimochkin, Yu. N.

    2011-10-01

    The thermodynamic characteristics of adsorption (TCA) for isomeric molecules of mono-, di-, tri-, and tetrafluoroadamantanes were determined for the first time experimentally and by molecular statistics on the surface of graphitized thermal black (GTB). The parameters of atom-atom potential function of pair intermolecular interaction (φ( r)) for F atoms included in fluoroadamantanes with C atoms on the basal face of graphite were calculated for the first time within an atom-atom approximation of the semi-empirical molecular statistical theory of adsorption. The adsorption non-equivalence of F atoms in various positions of an adamantane framework, a consequence of the mutual effect of atoms in a framework molecule, was determined. On the basis of the definite TCA values, the conclusion was drawn as to the possibility of isolation of isomeric fluoroadamantanes under the conditions of gas-adsorption chromatography on GTB.

  7. Effects of normal and reverse micellar environment on the spectral properties, isomerization and aggregation of a hydrophilic cyanine dye

    NASA Astrophysics Data System (ADS)

    Tatikolov, Alexander S.; Costa, Sílvia M. B.

    2001-10-01

    The spectral properties, cis→ trans isomerization and aggregation of the anionic hydrophilic cyanine 1, were studied in isooctane/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/water, cyclohexane-hexanol/Triton X-100/water reverse micelles and in aqueous solutions in the presence of surfactants. The incorporation of 1 into micelles leads to dimer→monomer decomposition and cis→ trans isomerization. In AOT reverse micelles with w0⩾5 ( w0=[H 2O]/[AOT]) 1 forms J aggregates at concentrations much lower than one dye molecule per one micelle; at w0=50 the most probable aggregation number is 3. Premicellar J aggregates of 1 are observed with both cationic and anionic surfactants, but not with Triton X-100.

  8. Acidic and basic properties of zeolite-containing cracking catalyst in the process of butene-1 isomerization

    NASA Astrophysics Data System (ADS)

    Mursalova, L. A.; Guseinova, E. A.; Adzhamov, K. Yu.

    2016-08-01

    The process of butene-1 isomerization in the presence of two groups of samples of zeolite-containing catalyst (ZCC) that earlier participated in the traditional and oxidative catalytic cracking of vacuum gasoil is investigated. It is established that the nature of the reaction mixture and conditions of the cracking process are key factors in forming the acidic and basic properties of the catalyst. It is shown that the highest activity in the butene-1 isomerization into cis-/ trans-butene-2 is demonstrated by ZCC samples that participated in the oxidative catalytic cracking (oxycracking). It is suggested that the enhanced catalytic activity of this group of ZCC samples was related to the availability of acid-base centers in the form of radical-like oxygen along with protic- and aprotic-type acidic centers in the structure of the oxidative compaction products.

  9. Cat's claw oxindole alkaloid isomerization induced by cell incubation and cytotoxic activity against T24 and RT4 human bladder cancer cell lines.

    PubMed

    Kaiser, Samuel; Dietrich, Fabrícia; de Resende, Pedro Ernesto; Verza, Simone Gasparin; Moraes, Renata Cougo; Morrone, Fernanda Bueno; Batastini, Ana Maria Oliveira; Ortega, George González

    2013-10-01

    The antitumor activity of Uncaria tomentosa, a native vine from the Amazonian rainforest, has been ascribed to pentacyclic oxindole alkaloids occurring in its bark. Former studies have shown that this activity, as well as its intensity, depends on whether cat's claw alkaloids occur as original compounds or isomerized derivatives. This work addresses this aspect, using T24 and RT4 human bladder cancer cell lines for that purpose. Bark samples were extracted by dynamic maceration, prepurified with cross-linked polyvinylpyrrolidone and properly fractioned by an ion exchange process to obtain an oxindole alkaloid purified fraction. Alkaloid isomerization was induced by heating it under reflux at 85 °C. Samples collected after 5, 15, and 45 min of heating were analyzed by HPLC-PDA, freeze-dried at once, and separately assayed using the non-isomerized purified fraction for comparison purposes. The latter showed significant and dose-dependent cytotoxic activity against both T24 and RT4 cancer cell lines (IC50: 164.13 and 137.23 µg/mL, respectively). However, results for both cell lines were equivalent to those observed for isomerized samples (p > 0.05). The alkaloid isomerization induced by the incubation conditions (buffered medium pH 7.4 and temperature 37 °C) helps to explain the similar results obtained from non-isomerized and isomerized samples. Mitraphylline, speciophylline, uncarine F, and, to a lesser degree, pteropodine were more susceptible to isomerization under the incubation conditions. Thus, the alkaloid profile of all fractions and their cytotoxic activities against T24 and RT4 human bladder cancer cell lines are determined to a large extent by the incubation conditions. PMID:23975868

  10. Thermal cis-trans isomerization of cis,cis-3,7-decadiene - A model for cis-1,4-polybutadiene

    NASA Technical Reports Server (NTRS)

    Golub, M. A.; Lee, W. M.

    1983-01-01

    The thermal cis-trans isomerization of cis,cis-3,7-decadiene (DD), a model compound for cis-PBD, is reported. It is demonstrated that the rather low E for the polyalkenamer isomerizations compared with that for the 2-olefins is not an artifact of the solid polymer structures, but rather is characteristic of both small and large molecules possessing pairs of nonconjugated vinylene double bonds in a suitable arrangement.

  11. Chalcogenation of the 1,4-C2P4 ring: oxidation, isomerization, insertion, and ring contraction.

    PubMed

    Elder, Philip J W; Chivers, Tristram

    2013-07-01

    The reaction of H2C(PCl2)2 with 4 equiv of (t)BuMgCl in tetrahydrofuran (THF) produces 1,4-(CH2)2(P(t)Bu)4, 1, in about 65% yield. This six-membered ring reacts directly with elemental sulfur or selenium in toluene at low temperatures to give the mono- and dichalcogenides 1,4-(CH2)2(P(t)BuE)(P(t)Bu)3 (E = S, 2a, E = Se, 2b) and 1,4-(CH2)2-2,5-(P(t)BuE)2(P(t)Bu)2 (E = S, 3a, E = Se, 3b). X-ray structural determinations showed that 3a and 3b are isostructural in the solid state; the six-membered C2P4 ring exhibits a twist-boat geometry with chalcogen substituents in syn positions in each case. Density functional theory (DFT) calculations for the three possible isomers of disubstitution were performed to elucidate the factors that favor the 2,5-isomer. Thermal isomerism was observed in solutions of 3b or 3a in toluene at 60 and 95 °C, respectively, to give the corresponding 2,6-isomers. With an excess of chalcogen in toluene at reflux, the four-membered rings (H2C)(P(t)BuE)2E (E = S, 4a, E = Se, 4b) were obtained and identified by multinuclear NMR spectroscopy and single crystal X-ray crystallography, which showed the (t)Bu groups in a trans orientation with respect to the CP2E ring. With a large excess of chalcogen, the five-membered rings (H2C)(P(t)BuE)2E2 (E = S, 5a, E = Se, 5b) were also observed; the X-ray structure of 5b revealed a half-envelope conformation for the CP2Se2 ring. The direct reaction of 4a with sulfur in boiling toluene does not produce 5a, whereas 5b is formed slowly and in low yields from 4b and selenium under similar conditions. On the basis of DFT calculations of the relative energies of likely intermediates, chalcogen insertion into the P-P bonds of 3a and 3b to give eight-membered C2P4E2 rings, followed by monomerization, is proposed as a feasible pathway for the formation of the four-membered CP2E heterocycles 4a and 4b. PMID:23786389

  12. Biosynthesis of monoterpenes: Stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to camphane and isocamphane monoterpenes

    SciTech Connect

    Croteau, R.; Gershenzon, J.; Wheeler, C.J.; Satterwhite, D.M. )

    1990-03-01

    The conversion of geranyl pyrophosphate to (+)-bornyl pyrophosphate and (+)-camphene is considered to proceed by the initial isomerization of the substrate to (-)-(3R)-linalyl pyrophosphate and the subsequent cyclization of this bound intermediate. In the case of (-)-bornyl pyrophosphate and (-)-camphene, isomerization of the substrate to the (+)-(3S)-linalyl intermediate precedes cyclization. The geranyl and linalyl precursors were shown to be mutually competitive substrates (inhibitors) of the relevant cyclization enzymes isolated from Salvia officinalis (sage) and Tanacetum vulgare (tansy) by the mixed substrate analysis method, demonstrating that isomerization and cyclization take place at the same active site. Incubation of partially purified enzyme preparations with (3R)-(1Z-3H)linalyl pyrophosphate plus (1-14C)geranyl pyrophosphate gave rise to double-labeled (+)-bornyl pyrophosphate and (+)-camphene, whereas incubation of enzyme preparations catalyzing the antipodal cyclizations with (3S)-(1Z-3H)-linalyl pyrophosphate plus (1-14C)geranyl pyrophosphate yielded double-labeled (-)-bornyl pyrophosphate and (-)-camphene. Each product was then transformed to the corresponding (+)- or (-)-camphor without change in the 3H:14C isotope ratio, and the location of the tritium label was deduced in each case by stereoselective, base-catalyzed exchange of the exo-alpha-hydrogen of the derived ketone. The finding that the 1Z-3H of the linalyl precursor was positioned at the endo-alpha-hydrogen of the corresponding camphor in all cases, coupled to the previously demonstrated retention of configuration at C1 of the geranyl substrate in these transformations, confirmed the syn-isomerization of geranyl pyrophosphate to linalyl pyrophosphate and the cyclization of the latter via the anti,endo- conformer.

  13. Synthesis of isomeric, oxathiolone fused chalcones, and comparison of their activity toward various microorganisms and human cancer cells line.

    PubMed

    Konieczny, Marek Tadeusz; Konieczny, Wojciech; Sabisz, Michał; Skladanowski, Andrzej; Wakieć, Roland; Augustynowicz-Kopeć, Ewa; Zwolska, Zofia

    2007-05-01

    Isomeric oxathiolone fused chalcones were prepared by condensation of appropriate acetylbenzo[1,3]oxathiol-2-ones with benzaldehydes under acidic conditions. The synthesized compounds were screened for cytotoxic activity using HeLa cells, as well as for antibacterial activity against Micrococcus luteus, Staphylococcus aureus, Salmonella typhimurium, Escherichia coli, Proteus vulgaris, antifungal activity against Candida albicans, and tuberculostatic activity against Mycobacterium tuberculosis H(37)Rv and Mycobacterium kansasii strains. PMID:17473478

  14. Olefin Isomerization Regiochemistries during Tandem Action of BacA and BacB on Prephenate in Bacilysin Biosynthesis†

    PubMed Central

    Parker, Jared B.; Walsh, Christopher T.

    2012-01-01

    BacA and BacB, the first two enzymes of the bacilysin pathway, convert prephenate to an exocylic regioisomer of dihydrohydroxyphenylpyruvate (ex-H2HPP) on the way to the epoxycyclohexanone warhead in the dipeptide antibiotic, bacilysin. BacA decarboxylates prephenate without aromatization, converting the 1,4-diene in prephenate to the endocyclic 1,3 diene in Δ4Δ8-dihydrohydroxyphenylpyruvate (en-H2HPP). BacB then performs an allylic isomerization to bring the diene into conjugation with the 2-ketone in the product Δ3Δ5-dihydrohydroxyphenylpyruvate (ex-H2HPP). To prove that BacA acts regiospecifically on one of the two prochiral olefins in prephenate, we generated 1,5,8-[13C]-chorismate from bacterial fermentation of 5-[13C]-glucose and in turn produced 2,4,6-[13C]-prephenate via chorismate mutase. Tandem action of BacA and BacB gave 2,4,8-[13C]-7R-ex-H2HPP, showing that BacA isomerizes only the pro-R double bond in prephenate. Nonenzymatic isomerization of the BacA product into conjugation gives only the Δ3 E-geometric isomer of Δ3Δ5-ex-H2HPP. On the other hand, acceleration of the allylic isomerization by BacB gives a mixture of the E- and Z-geometric isomers of the 7R-product, indicating some rerouting of the flux, likely through dienolate geometric isomers. PMID:22483065

  15. Mechanism of hydrogenolysis and isomerization of oxacycloalkanes on metals. IV. Mechanism of transformation of oxiranes on Cu catalyst

    SciTech Connect

    Notheisz, F.; Molnar, A.; Zsigmond, A.G.; Bartok, M.

    1986-03-01

    The mechanism of isomerization of methyloxirane to propanal and acetone was studied on a Cu catalyst. During the transformation, the deoxidation reaction causes the oxidation of the catalyst surface, and Lewis acid site-basic site pairs are produced. Propanal is formed predominantly on these centers. The rate of formation of such active centers, and hence that of propanal, is maximum on the partially oxidized surface. Acetone is formed on the reduced metal surface. Both reactions may be regarded as hydroisomerization.

  16. Sensitized Two-NIR-Photon Z→E Isomerization of a Visible-Light-Addressable Bistable Azobenzene Derivative.

    PubMed

    Moreno, Javier; Gerecke, Mario; Grubert, Lutz; Kovalenko, Sergey A; Hecht, Stefan

    2016-01-22

    Two-NIR-photon-triggered Z→E isomerization of an azobenzene was accomplished by covalently linking a two-photon-harvesting triarylamine antenna to a thermally stable ortho-fluorinated azobenzene derivative. The obtained photoswitch is fully addressable with visible and NIR light by using one-photon and two-photon excitation, respectively, with the latter offering enhanced penetration depth and improved spatial resolution. PMID:26679769

  17. Emerging Disinfection Byproducts, Halobenzoquinones: Effects of Isomeric Structure and Halogen Substitution on Cytotoxicity, Formation of Reactive Oxygen Species, and Genotoxicity.

    PubMed

    Li, Jinhua; Moe, Birget; Vemula, Sai; Wang, Wei; Li, Xing-Fang

    2016-07-01

    Halobenzoquinones (HBQs) are a structurally diverse class of water disinfection byproducts. Here, we report a systematic study on the effects of isomeric structure and the type and number of halogen substitutions of HBQs on their cytotoxicity, formation of reactive oxygen species (ROS), and genotoxicity. Dynamic responses and IC50 histograms were obtained using real-time cell analysis, clearly ranking the cytotoxicity of the HBQs in Chinese hamster ovary (CHO-K1) cells. Strong isomeric structure effects were shown with 2,5-HBQ isomers inducing greater cytotoxicity than their corresponding 2,6-HBQ isomers (P < 0.05). HBQ-halogen substitution groups also influence cytotoxicity, as cytotoxicity increases across the dihalogenated HBQs: iodo- > bromo- > chloro-HBQs (P < 0.05). Determination of HBQ-induced ROS further supports isomeric structure and halogen substitution effects. HBQ-induced genotoxicity was shown as increased levels of 8-hydroxy-2'-deoxyguanosine and p53 protein. Pearson correlation analysis of the HBQ toxicity measurements with their physicochemical parameters demonstrates that dipole moment and the lowest unoccupied molecular orbital energy are two major structural influences on toxicity (r = -0.721 or -0.766, P < 0.05). Dipole moment also correlates with isomer toxicity. This study suggests that formation and occurrence of highly toxic iodo-HBQs and 2,5-HBQs warrant further investigation to fully assess the impact of HBQs in drinking water. PMID:26812484

  18. 25-Hydroxyvitamin D isomerizes to pre-25-hydroxyvitamin D in solution: considerations for calibration in clinical measurements.

    PubMed

    Bedner, Mary; Lippa, Katrice A

    2015-10-01

    Reference standards for the vitamin D metabolites 25-hydroxyvitamin D3, 25-hydroxyvitamin D2, and 3-epi-25-hydroxyvitamin D3 were evaluated using liquid chromatography (LC) with ultraviolet (UV) absorbance and mass spectrometric (MS) detection to assess purity. The chromatograms for solutions of all three 25(OH)D compounds, obtained using a pentafluorophenyl (PFP) stationary phase, revealed peaks that increased in area over time and had MS spectra that were nearly identical to the parent compound, indicating isomers had formed in solution that were unrelated to the reference standard purity. However, when the purity evaluations were completed with a cyanopropyl stationary phase, the isomeric products coeluted with the parent compounds and were not observable. The rates of formation of the isomeric products were found to increase when heated and were confirmed to be pre-25-hydroxyvitamin D compounds using spectral information from both MS detection and nuclear magnetic resonance (NMR) spectroscopy. The rates of conversion of 25(OH)D3 to pre-25(OH)D3 was studied in solutions of ethanol and bovine serum albumin (BSA) in phosphate-buffered saline (PBS). The solutions prepared with BSA/PBS were found to form twice as much pre-25(OH)D3 as the solutions in ethanol. The isomerization of 25(OH)D in solution has implications for calibration of 25(OH)D in clinical measurements, which are discussed. PMID:26359234

  19. Nutritional value and safety of methionine derivatives, isomeric dipeptides and hydroxy analogs in mice.

    PubMed

    Friedman, M; Gumbmann, M R

    1988-03-01

    Weight gains in mice fed amino acid diets containing methionine and 16 methionine derivatives and analogs were compared at graded dietary concentrations. Linear response was closely approximated for concentrations below those yielding maximum growth. Derivatization of L-methionine generally lowered potency, calculated as the ratio of the slopes of the two dose-response curves. However, the three isomeric dipeptides L-L-, L-D- and D-L-methionylmethionine, N-acetyl- and N-formyl-L-methionine, L-methionine sulfoxide and D-methionine were well utilized. The double derivative N-acetyl-L-methionine sulfoxide reduced potency below 60%. D-Methionine sulfoxide, N-acetyl-D-methionine and D-methionyl-D-methionine had potencies between 4 and 40%. The calcium salts of L- and D-alpha-hydroxy analogs of methionine had potencies of 55.4 and 85.7%, respectively. Several of the analogs were less growth-inhibiting or toxic at high concentrations in the diet than was L-methionine. These results imply that some methionine dipeptides or analogs may be better candidates for fortifying foods than L-methionine. Possible biochemical pathways for the utilization of methionine derivatives and analogs are also described. PMID:3351635

  20. LC-MS n Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

    NASA Astrophysics Data System (ADS)

    Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

    2011-09-01

    Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MS n . The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MS n fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MS n experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MS n methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications.

  1. Chemical and enzymatic reductive activation of acylfulvene to isomeric cytotoxic reactive intermediates

    PubMed Central

    Pietsch, Kathryn E.; Neels, James F.; Yu, Xiang; Gong, Jiachang; Sturla, Shana J.

    2011-01-01

    Acylfulvenes, a class of semisynthetic analogues of the sesquiterpene natural product illudin S, are cytotoxic towards cancer cells. The minor structural changes between illudin S and AFs translate to an improved therapeutic window in preclinical cell-based assays and xenograft models. AFs are, therefore, unique tools for addressing the chemical and biochemical basis of cytotoxic selectivity. AFs elicit cytotoxic responses by alkylation of biological targets, including DNA. While AFs are capable of direct alkylation, cytosolic reductive bioactivation to an electrophilic intermediate is correlated with enhanced cytotoxicity. Data obtained in this study illustrates chemical aspects of the process of AF activation. By tracking reaction mechanisms with stable isotope-labeled reagents, enzymatic versus chemical activation pathways for AF were compared for reactions involving the NADPH-dependent enzyme prostaglandin reductase 1 (PTGR1) or sodium borohydride, respectively. These two processes resulted in isomeric products that appear to give rise to similar patterns of DNA modification. The chemically activated isomer has been newly isolated and chemically characterized in this study, including an assessment of its relative stereochemistry, and stability at varying pH and under bioassay conditions. In mammalian cancer cells, this chemically activated analog was shown to not rely on further cellular activation to significantly enhance cytotoxic potency, in contrast to the requirements of AF. On the basis of this study, we anticipate that the chemically activated form of AF will serve as a useful chemical probe for evaluating biomolecular interactions independent of enzyme-mediated activation. PMID:21939268

  2. Investigating the position isomerism effect of dihydroxybenzoic acid compounds by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Yong; Hao, Guohui; Zhao, Rongjiao; Hong, Zhi

    2012-03-01

    Far-infrared vibrational absorption of a series of dihydroxybenzoic acid (DHBA) compounds with different substituted hydroxy group at different positions have been investigated using terahertz time-domain spectroscopy (THz-TDS) at room temperature. The experimental results show large difference among absorption spectra of different DHBA (2,3-DHBA, 2,4-DHBA, 2,5-DHBA, 2,6-DHBA) compounds in 0.2 ~ 2.0 THz region, which probably originated from the difference of intra-molecular and inter-molecular hydrogen bonds due to the presence of two hydroxyl group in different positions with respect to the carboxylic group in different DHBAs. All the experimental DHBAs vibrational modes showed distinct fingerprint absorption in THz region and theorectical calculation based on density functional theory (DFT) was carried out to assist the analysis and assignment of the vibrational modes. The results indicate that THz-TDS technology can not only give a new experimental method to identify and characterize the position isomerism effect of hydroxyl group between such different kinds of DHBAs from molecule-level, but also provide a useful suggestion for further assessing the possible relationships between the DHBAs vibrational properties and the effects of the substituted hydroxy group position to better know their biochemical activities in food, pharmaceutical and cosmetic fields.

  3. Investigating the position isomerism effect of dihydroxybenzoic acid compounds by terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Du, Yong; Hao, Guohui; Zhao, Rongjiao; Hong, Zhi

    2011-11-01

    Far-infrared vibrational absorption of a series of dihydroxybenzoic acid (DHBA) compounds with different substituted hydroxy group at different positions have been investigated using terahertz time-domain spectroscopy (THz-TDS) at room temperature. The experimental results show large difference among absorption spectra of different DHBA (2,3-DHBA, 2,4-DHBA, 2,5-DHBA, 2,6-DHBA) compounds in 0.2 ~ 2.0 THz region, which probably originated from the difference of intra-molecular and inter-molecular hydrogen bonds due to the presence of two hydroxyl group in different positions with respect to the carboxylic group in different DHBAs. All the experimental DHBAs vibrational modes showed distinct fingerprint absorption in THz region and theorectical calculation based on density functional theory (DFT) was carried out to assist the analysis and assignment of the vibrational modes. The results indicate that THz-TDS technology can not only give a new experimental method to identify and characterize the position isomerism effect of hydroxyl group between such different kinds of DHBAs from molecule-level, but also provide a useful suggestion for further assessing the possible relationships between the DHBAs vibrational properties and the effects of the substituted hydroxy group position to better know their biochemical activities in food, pharmaceutical and cosmetic fields.

  4. Monomer exchange kinetics, radial diffusion, and hydrocarbon chain isomerization of sodium dodecylsulfate micelles in water.

    PubMed

    Polacek, R; Kaatze, U

    2007-02-22

    Molecular relaxation properties of sodium dodecylsulfate in aqueous solutions with surfactant concentrations between 0.009 and 0.4 mol/L have been studied using broadband ultrasonic spectrometry in the frequency range 0.1-2000 MHz. Ultrasonic excess attenuation characteristics were found that could be well represented by a sum of three relaxation terms, each one characterized by a discrete relaxation time. The low-frequency term with concentration-dependent relaxation time, tau1, between 0.06 and 3.5 micros is discussed in terms of the surfactant monomer exchange. The noticeable effect from the incomplete dissociation of the surfactant counter ions and the variation of the monomer concentration following thereby is discussed. The second relaxation term (0.9 isomerizations of the hydrocarbon chains in the micellar cores, largely resembling those of liquid alkanes. PMID:17261063

  5. n-Hexane hydro-isomerization over promoted Pd/HZSM-5 catalysts

    NASA Astrophysics Data System (ADS)

    Thoa Dao, Thi Kim; Loc Luu, Cam

    2015-09-01

    A series of Pd/HZSM-5 catalysts modified by various metallic species, including Co, Ni, Fe, Re, and Cu, was prepared by sequential impregnation. Contents of Pd and second metals in modified catalysts were 0.8 and 1.0 wt%, respectively. Physico-chemical characteristics of catalysts were investigated by nitrogen physi-sorption (BET), x-ray diffraction (XRD), transmission electron microscopy (TEM), ammonia temperature programmed desorption (NH3-TPD), temperature programmed reduction (TPR) and hydrogen pulse chemisorption (HPC). Coke formation was studied by the method of thermogravimetric analysis (TGA). The activities of catalysts in n-hexane isomerization were studied in a micro-flow reactor under atmospheric pressure at 250 °C, and molar ratio of H2: n-hexane of 5.92. It was found that Co, Ni, Fe, and Re additives exhibited geometric and electronic effects toward Pd/HZSM-5 catalyst, leading to an enhancement of its activity and stability. On the contrary, Cu additive caused Pd/HZSM-5 to become poorer in activity and stability.

  6. Light olefin production, skeletal olefin isomerization and etherification for oxygenated fuel production

    SciTech Connect

    Gaffney, A.M.

    1994-12-31

    ARCO`s newly developed SUPERFLEX{sup SM} process offers opportunities to product high yields of light olefins, from a variety of readily available refinery and petrochemical feedstocks. The process is unique in that it employs a catalytic reactor system which is lower in capital and operating costs than conventional steam cracking reactors. The SUPERFLEX process is also more selective for production of propylene and butylenes (including isobutylene) than conventional steam cracking operations. The C{sub 4} product stream from the SUPERFLEX process contains about 20 to 30 percent isobutylene. The SUPERFLEX C{sub 4} product is, therefore, an excellent feedstock for producing MTBE via reaction of the contained isobutylene with methanol. After MTBE production, the isobutylene depleted C{sub 4} stream may be recycled to the SUPERFLEX process to produce additional isobutylene and propylene. This paper will focus on the chemistry and mechanism of catalytic cracking and skeletal olefin isomerization. In addition, there will be some discussion on catalyst activation, life and characterization.

  7. Sugar Profile, Mineral Content, and Rheological and Thermal Properties of an Isomerized Sweet Potato Starch Syrup

    PubMed Central

    Dominque, Brunson; Gichuhi, Peter N.; Rangari, Vijay; Bovell-Benjamin, Adelia C.

    2013-01-01

    Currently, corn is used to produce more than 85% of the world's high fructose syrup (HFS). There is a search for alternative HFS substrates because of increased food demand and shrinking economies, especially in the developing world. The sweet potato is a feasible, alternative raw material. This study isomerized a high glucose sweet potato starch syrup (SPSS) and determined its sugar profile, mineral content, and rheological and thermal properties. Rheological and thermal properties were measured using a rheometer and DSC, respectively. Sweet potato starch was hydrolyzed to syrup with a mean fructose content of 7.6 ± 0.4%. The SPSS had significantly higher (P < 0.05) mineral content when compared to commercial ginger and pancake syrups. During 70 days of storage, the SPSS acted as a non-Newtonian, shear-thinning liquid in which the viscosity decreased as shear stress increased. Water loss temperature of the SPSS continually decreased during storage, while pancake and ginger syrups' peak water loss temperature decreased initially and then increased. Further and more detailed studies should be designed to further enhance the fructose content of the syrup and observe its stability beyond 70 days. The SPSS has the potential to be used in human food systems in space and on Earth. PMID:26904593

  8. A rapid ambient ionization-mass spectrometry approach to monitoring the relative abundance of isomeric glycerophospholipids.

    PubMed

    Kozlowski, Rachel L; Mitchell, Todd W; Blanksby, Stephen J

    2015-01-01

    Glycerophospholipids with two, non-equivalent fatty acyl chains can adopt one of two isomeric forms depending on the relative position of substitutions on the glycerol backbone. These so-called sn-positional isomers can have distinct biophysical and biochemical behaviors making it desirable to uniquely assign their regiochemistries. Unambiguous assignment of such similar molecular structures in complex biological extracts is a significant challenge to current analytical technologies. We have recently reported a novel mass spectrometric method that combines collision- and ozone-induced dissociation in series (CID/OzID) to yield product ions characteristic of acyl chain substitution patterns in glycerophospholipids. Here phosphatidylcholines are examined using the CID/OzID protocol combined with desorption electrospray ionization (DESI) to facilitate the rapid exploration of sample arrays comprised of a wide variety of synthetic and biological sources. Comparison of the spectra acquired from different extracts reveals that the sn-positional isomers PC 16:0/18:1 and PC 18:1/16:0 (where the 18:1 chain is present at the sn-2 and sn-1 position of the glycerol backbone, respectively) are most often found together in lipids of either natural or synthetic origin. Moreover, the proportions of the two isomers vary significantly between extracts from different organisms or even between adjacent tissues from the same organism. PMID:25880027

  9. Association of chlorophyll with amides on plasticized polyethylene particles. II. The isomeric N-(pyridyl)myristamides

    SciTech Connect

    Kusumoto, Y.; Seely, G.R.; Senthilathipan, V.

    1982-01-01

    When chlorophyll, together with certain other amphiphilic substances, is adsorbed to particles of polyethylene plasticized by incorporation of tetradecane, it is maintained in monomeric or oligomeric forms with characteristic absorption and fluorescence spectra. The present work describes the properties of chlorophyll a on such particles in the presence of the three isomeric N-(pyridyl)myristamides, and of the similarly shaped but not basic compound myristanilide, in an effort to ascertain the structural factors governing associations of these species. Absorption and fluorescence spectra at room temperature are resolved into minimal sets of Gaussian components, and relations between the component sets are proposed. The positions of the component bands and their relative abundance are characteristic of the amide used. The 3- and 4-pyridyl isomers bind more strongly to chlorophyll, probably by ligation of the pyridine nitrogen to Mg of the pigment. The 2-pyridyl isomer and myristanilide bind more weakly, probably through the amide carbonyl group. The association of chlorophyll into species with characteristic absorption and fluorescence bands is promoted more strongly by the 3- and 4-isomers than by the 2-isomer and myristanilide, and probably involves hydrogen bonding to chlorophyll carbonyl groups. A possible manner of association of chlorophyll in the presence of N,N-dimethylmyristamide is also presented. By way of comparison, chlorophyll adsorbed with dodecylpyridinium bromide, which lacks a nucleophilic function, is mainly in the microcrystalline hydrate form absorbing near 740 nm.

  10. Structure of the room-temperature ionic liquid 1-hexyl-3-methylimidazolium hydrogen sulfate: conformational isomerism.

    PubMed

    Kiefer, Johannes; Pye, Cory C

    2010-06-24

    The acidic room-temperature ionic liquid 1-hexyl-3-methylimidazolium hydrogen sulfate has recently been identified to have beneficial properties for practical applications in catalysis and electrochemistry. In the present work, the conformational isomerism of this ionic liquid is studied by means of density functional theory calculations and experiments in terms of infrared absorption and Raman scattering spectroscopy. For the hydrogen sulfate anion, the trans conformer is found to be the favored isomer in the ionic liquid. For the 1-hexyl-3-methylimidazolium cation, three different low-energy conformations were obtained, differing only in the orientation of the hexyl chain. The comparison of vibrational frequencies with IR and Raman data showed good agreement for all three conformations, indicating their presence in the ionic liquid. Beyond revealing the conformational information, the experimental spectra indicate strong interionic interactions. Vibrations of sulfuric acid could be observed, indicating possible proton transfer from the cation to the anion. This is further supported by the appearance of modes around 2000 cm(-1) in the IR spectrum, which could tentatively be assigned to C2-H stretching vibrations red-shifted as a result of strong interionic hydrogen bonds as a prerequisite of proton transfer. PMID:20509684

  11. Statistical thermodynamics of the isomerization reaction between n-heptane and isoheptane.

    PubMed

    Yu, Tao; Zheng, Jingjing; Truhlar, Donald G

    2012-01-14

    We have employed electronic structure calculations and the recently proposed multi-structural (MS) anharmonicity method to calculate partition functions and thermodynamic quantities, in particular entropy and heat capacity, for n-heptane and isoheptane. We included all structures, of which there are 59 for n-heptane and 37 for isoheptane, and we carried out the calculations both in the local harmonic approximation and by including torsional (T) anharmonicity. In addition, ΔS°, ΔH, and ΔG° for the isomerization reaction between these two species were also calculated. It is found that all calculated thermodynamic quantities based on the MS-T approximation in the temperature range from 298 K to 1500 K agree well with experimental data from the American Petroleum Institute (API) tables or Thermodynamics Research Center (TRC) data series and with values obtained from Benson's empirical parameters fit to experiment. This demonstrates not only the high accuracy of the electronic structure calculations but also that the MS-T method can be used to include both multiple-structure anharmonicity and torsional anharmonicity in the calculation of thermodynamic properties for complex molecules that contain many torsions. It also gives us confidence that we can apply the MS-T statistical thermodynamic method to obtain thermodynamic properties (i) over a broader temperature range than that for which data are available in the API tables, TRC data series, or from empirical estimation and (ii) to the many molecules for which experimental data are not available at any temperature. PMID:22119933

  12. Pharmacokinetics and tissue distribution of two novel isomerism anticancer platinum compounds.

    PubMed

    He, Donglin; Yin, Shuhui; Han, Fuguo; Zhu, Jingjie; Shi, Yun; Tong, Zhiyuan; Liu, Qingfei

    2016-11-01

    LLC-0601(S,S) and LLC-0601(R,R) are two novel synthesized isomerism platinum compounds both with encouraging anticancer activity. However, the previous study showed that toxicity of LLC-0601(R,R) was much higher than that of LLC-0601(S,S) with higher body weight loss and mortality rate of tested rats. This paper is focused on the comparison of the two compounds with their pharmacokinetic (PK) profiles in rats and tissue distribution in mice after intravenous administration. The atomic absorption spectrometry (AAS) method was successfully developed and applied for the determination of platinum in plasma and tissues. The results showed that main PK parameters such as half-life, AUC and MRT of the two compounds had no significant difference after intravenous administration to rats (p  > 0.05). The tissue distribution after intravenous administration to mice showed that the concentration of LLC-0601(R,R) in heart at 0.083 h was higher than that of LLC-0601(S,S) (p  < 0.05) and it was the same case for AUC5min-4 h (p  < 0.05). Different distribution of the two compounds in heart was possibly the main reason of different toxicity and more in-depth research on the metabolites and other mechanism are needed to investigate the toxicity. PMID:27042965

  13. A rapid ambient ionization-mass spectrometry approach to monitoring the relative abundance of isomeric glycerophospholipids

    NASA Astrophysics Data System (ADS)

    Kozlowski, Rachel L.; Mitchell, Todd W.; Blanksby, Stephen J.

    2015-04-01

    Glycerophospholipids with two, non-equivalent fatty acyl chains can adopt one of two isomeric forms depending on the relative position of substitutions on the glycerol backbone. These so-called sn-positional isomers can have distinct biophysical and biochemical behaviors making it desirable to uniquely assign their regiochemistries. Unambiguous assignment of such similar molecular structures in complex biological extracts is a significant challenge to current analytical technologies. We have recently reported a novel mass spectrometric method that combines collision- and ozone-induced dissociation in series (CID/OzID) to yield product ions characteristic of acyl chain substitution patterns in glycerophospholipids. Here phosphatidylcholines are examined using the CID/OzID protocol combined with desorption electrospray ionization (DESI) to facilitate the rapid exploration of sample arrays comprised of a wide variety of synthetic and biological sources. Comparison of the spectra acquired from different extracts reveals that the sn-positional isomers PC 16:0/18:1 and PC 18:1/16:0 (where the 18:1 chain is present at the sn-2 and sn-1 position of the glycerol backbone, respectively) are most often found together in lipids of either natural or synthetic origin. Moreover, the proportions of the two isomers vary significantly between extracts from different organisms or even between adjacent tissues from the same organism.

  14. Hemin-functionalized reduced graphene oxide nanosheets reveal peroxynitrite reduction and isomerization activity.

    PubMed

    Vernekar, Amit A; Mugesh, Govindasamy

    2012-11-19

    Facile and efficient reduction of graphene oxide (GO) and novel applications of the reduced graphene oxide (RGO) based materials are of current interest. Herein, we report a novel and facile method for the reduction of GO by using a biocompatible reducing agent dithiothreitol (DTT). Stabilization of DTT by the formation of a six-membered ring with internal disulfide linkage upon oxidation is responsible for the reduction of GO. The reduced graphene oxide is characterized by several spectroscopic and microscopic techniques. Dispersion of RGO in DMF remained stable for several weeks suggesting that the RGO obtained by DTT-mediated reduction is hydrophobic in nature. This method can be considered for large scale production of good quality RGO. Treatment of RGO with hemin afforded a functional hemin-reduced graphene oxide (H-RGO) hybrid material that exhibited remarkable protective effects against the potentially harmful peroxynitrite (PN). A detailed inhibition study on PN-mediated oxidation and nitration reactions indicate that the interaction between hemin and RGO results in a synergistic effect, which leads to an efficient reduction of PN to nitrate. The RGO also catalyzes the isomerization of PN to nitrate as the RGO layers facilitate the rapid recombination of (·)NO(2) with Fe(IV)=O species. In the presence of reducing agents such as ascorbic acid, the Fe(IV)=O species can be reduced to Fe(III), thus helping to maintain the PN reductase cycle. PMID:23042238

  15. Comparisons of Caenorhabditis Fucosyltransferase Mutants Reveal a Multiplicity of Isomeric N-Glycan Structures

    PubMed Central

    2015-01-01

    Recent studies have shown a remarkable degree of plasticity in the N-glycome of the model nematode Caenorhabditis elegans; ablation of glycosylation-relevant genes can result in radically altered N-glycan profiles despite only minor biological phenotypic effects. Up to four fucose residues and five different linkages of fucose are known on the N-glycans of C. elegans. Due to the complexity in the wild type, we established three mutant strains defective in two core fucosyltransferases each (fut-1;fut-6, fut-1;fut-8, and fut-6;fut-8). Enzymatically released N-glycans were subject to HPLC and MALDI-TOF MS/MS, in combination with various treatments, to verify structural details. The N-glycome of the fut-1;fut-6 mutant was the most complex of the three double-mutant strains due to the extension of the core α1,6-fucose as well as the presence of fucose on the bisecting galactose. In contrast, maximally two fucoses were found on N-glycans of the fut-1;fut-8 and fut-6;fut-8 strains. The different locations and capping of fucose meant that up to 13 isomeric structures, many highly galactosylated, were determined for some single masses. These data not only show the high variability of the N-glycomic capacity of a “simple” nematode but also exemplify the need for multiple approaches to reveal individual glycan structures within complex invertebrate glycomes. PMID:26538210

  16. Synthesis of azo-conjugated metalladithiolenes and their photo- and proton-responsive isomerization reactions.

    PubMed

    Nihei, Masayuki; Kurihara, Masato; Mizutani, Jun; Nishihara, Hiroshi

    2003-03-12

    A versatile synthetic method of azo-conjugated metalladithiolenes was developed, and new complexes with various central metals and substituent groups were synthesized. Molecular structures of the azo-conjugated metalladithiolenes of Ni(II), Pd(II), and Pt(II) with diphenylphosphinoethane as a co-ligand were determined by X-ray crystallography. While the energy of the reversible trans-to-cis photoisomerization is considerably lower than that of azobenzene, the thermal stability of the cis form is much higher than that of the organic azobenzene derivatives showing similar low-energy trans-to-cis photoisomerization. A novel proton response of the azo group occurs, and the combination of photoisomerization and protonation leads to a novel proton-catalyzed cis-to-trans isomerization, the rate of which correlates with the redox potential of the metalladithiolene moiety. The study including other azo-conjugated metalladithiolenes has indicated that the protonation is a common feature for the azo-conjugated metalladithiolenes, but trans-to-cis photoisomerization is strongly dependent on the electronic structure of the trans form or a steric effect in the cis form. PMID:12617664

  17. Strong-field isomerization dynamics of fast beams of hydrocarbon ions

    NASA Astrophysics Data System (ADS)

    Jochim, Bethany; Rajput, Jyoti; Berry, Ben; Severt, T.; Zohrabi, M.; Feizollah, Peyman; Carnes, K. D.; Esry, B. D.; Ben-Itzhak, I.

    2016-05-01

    Bond rearrangement and fragmentation of hydrocarbons in intense laser fields has been a topic of considerable interest in the strong-field community in recent years. We study the interactions of keV hydrocarbon ion beams with ultrafast, intense laser pulses, employing coincidence 3D momentum imaging to elucidate the fragmentation dynamics and identify laser parameters that might be used for controlling outcomes such as the branching ratios. We focus on dissociation to ensure that isomerization occurs on the particular electronic channels of the molecular ion investigated. In C2 H2+, for example, we measure the intensity-dependent branching ratios of the acetylene (CH++CH) and vinylidene (e . g . , C++ CH2) channels. The relative fragmentation rates between the acetylene and vinylidene channels change by a factor of ~ 2 over the range of experimental intensities (1013- 1015 W/ cm2). Other hydrocarbons of interest include not only cations but also anions, such as C2 H 2 -. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. Department of Energy. BJ was also supported in part by DOE-SCGF (DE-AC05-06OR23100).

  18. Understanding M-ligand bonding and mer-/fac-isomerism in tris(8-hydroxyquinolinate) metallic complexes.

    PubMed

    Lima, Carlos F R A C; Taveira, Ricardo J S; Costa, José C S; Fernandes, Ana M; Melo, André; Silva, Artur M S; Santos, Luís M N B F

    2016-06-28

    Tris(8-hydroxyquinolinate) metallic complexes, Mq3, are one of the most important classes of organic semiconductor materials. Herein, the nature of the chemical bond in Mq3 complexes and its implications on their molecular properties were investigated by a combined experimental and computational approach. Various Mq3 complexes, resulting from the alteration of the metal and substitution of the 8-hydroxyquinoline ligand in different positions, were prepared. The mer-/fac-isomerism in Mq3 was explored by FTIR and NMR spectroscopy, evidencing that, irrespective of the substituent, mer- and fac-are the most stable molecular configurations of Al(iii) and In(iii) complexes, respectively. The relative M-ligand bond dissociation energies were evaluated experimentally by electrospray ionization tandem mass spectrometry (ESI-MS-MS), showing a non-monotonous variation along the group (Al > In > Ga). The results reveal a strong covalent character in M-ligand bonding, which allows for through-ligand electron delocalization, and explain the preferred molecular structures of Mq3 complexes as resulting from the interplay between bonding and steric factors. The mer-isomer reduces intraligand repulsions, being preferred for smaller metals, while the fac-isomer is favoured for larger metals where stronger covalent M-ligand bonds can be formed due to more extensive through-ligand conjugation mediated by metal "d" orbitals. PMID:27273193

  19. Structure refinement and photocatalytic properties of porous POMCPs by selecting the isomerous PYTTZ.

    PubMed

    Li, Liang; Sun, Jing-Wen; Sha, Jing-Quan; Li, Guang-Ming; Yan, Peng-Fei; Wang, Cheng; Yu, Lian

    2015-01-28

    Two polyoxometalate-based coordination polymers (POMCPs) constructed form Keggin POMs and Ag(+) with pyttz were synthesized: [Ag4(H2pyttz-I)(H2pyttz-II)(Hpyttz-II)][HSiW12O40]·4H2O (1) and [Ag4(H2pyttz-II)(Hpyttz-II)2][H2SiW12O40]·3H2O (2) (H2pyttz-I = 3-(pyrid-2-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl; H2pyttz-II = 3-(pyrid-4-yl)-5-(1H-1,2,4-triazol-3-yl)-1,2,4-triazolyl). Both compounds have similar building units, similar stick-like units and similar 1D inorganic chains, but finally form the different motifs of tunnels (tunnel A in 1 and tunnel A&B in 2). By careful inspection of the structures of 1 and 2, it is believed that the isomerous pyttz molecules can precisely refine the structure of porous POMCPs without changing the underlying framework, which favors the study of the structure-activity relationship of POMCPs. Furthermore, the results of the photocatalytic activities show that compound 2 exhibits higher photocatalytic activity than that of compound 1, which is consistent with their structural characterization. PMID:25492257

  20. Simulated (n,f) cross section of isomeric 235m-U

    SciTech Connect

    Becker, J; Britt, H; Younes, W

    2003-12-18

    The neutron-induced fission cross section on the {sup 235}U, T{sub 1/2} {approx} 26 min isomer has been deduced for incident neutron energies in the range E{sub n}=0.1-2.5 MeV, using the surrogate-reaction technique. In this technique, {sup 236}U fission probabilities measured in the {sup 234}U(t, pf) reaction have been converted into {sup 235}U(n,f) and {sup 235m}U(n,f) cross sections, using reaction theory to compensate for the differences in angular-momentum and parity distributions in the fissioning systems, transferred by the (t,p) and neutron-induced reactions. Based on the comparison between the {sup 235}U(n,f) cross section extracted in this work and independent experimental data, the deduced {sup 235m}U(n,f) cross section is believed to be reliable to 20% below E{sub n} {approx} 0.5 MeV and 10% at higher energies. The surrogate-reaction technique, its validation in the case of the {sup 235}U(n,f) cross section, and the deduced {sup 235m}U(n,f) cross section are discussed. Validation of this method allows (n,f) cross sections for many short-lived nuclei, as well as isomeric nuclei, to be extracted from measured fission probabilities.

  1. Sugar Profile, Mineral Content, and Rheological and Thermal Properties of an Isomerized Sweet Potato Starch Syrup.

    PubMed

    Dominque, Brunson; Gichuhi, Peter N; Rangari, Vijay; Bovell-Benjamin, Adelia C

    2013-01-01

    Currently, corn is used to produce more than 85% of the world's high fructose syrup (HFS). There is a search for alternative HFS substrates because of increased food demand and shrinking economies, especially in the developing world. The sweet potato is a feasible, alternative raw material. This study isomerized a high glucose sweet potato starch syrup (SPSS) and determined its sugar profile, mineral content, and rheological and thermal properties. Rheological and thermal properties were measured using a rheometer and DSC, respectively. Sweet potato starch was hydrolyzed to syrup with a mean fructose content of 7.6 ± 0.4%. The SPSS had significantly higher (P < 0.05) mineral content when compared to commercial ginger and pancake syrups. During 70 days of storage, the SPSS acted as a non-Newtonian, shear-thinning liquid in which the viscosity decreased as shear stress increased. Water loss temperature of the SPSS continually decreased during storage, while pancake and ginger syrups' peak water loss temperature decreased initially and then increased. Further and more detailed studies should be designed to further enhance the fructose content of the syrup and observe its stability beyond 70 days. The SPSS has the potential to be used in human food systems in space and on Earth. PMID:26904593

  2. DETECTION OF TWO ISOMERIC BINDING CONFIGURATIONS IN A PROTEIN-APTAMER COMPLEX WITH A BIOLOGICAL NANOPORE

    PubMed Central

    Van Meervelt, Veerle; Soskine, Misha; Maglia, Giovanni

    2015-01-01

    Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we have shown that folded proteins can be internalised inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalisation of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement, and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores might provide a new approach to probe conformational heterogeneity in protein:DNA interactions. PMID:25493908

  3. Detection of two isomeric binding configurations in a protein-aptamer complex with a biological nanopore.

    PubMed

    Van Meervelt, Veerle; Soskine, Misha; Maglia, Giovanni

    2014-12-23

    Protein-DNA interactions play critical roles in biological systems, and they often involve complex mechanisms and dynamics that are not easily measured by ensemble experiments. Recently, we showed that folded proteins can be internalized inside ClyA nanopores and studied by ionic current recordings at the single-molecule level. Here, we use ClyA nanopores to sample the interaction between the G-quadruplex fold of the thrombin binding aptamer (TBA) and human thrombin (HT). Surprisingly, the internalization of the HT:TBA complex inside the nanopore induced two types of current blockades with distinguished residual current and lifetime. Using single nucleobase substitutions to TBA we showed that these two types of blockades originate from TBA binding to thrombin with two isomeric orientations. Voltage dependencies and the use of ClyA nanopores with two different diameters allowed assessing the effect of the applied potential and confinement and revealed that the two binding configurations of TBA to HT display different lifetimes. These results show that the ClyA nanopores can be used to probe conformational heterogeneity in protein:DNA interactions. PMID:25493908

  4. Benzimidazole-Branched Isomeric Dyes: Effect of Molecular Constitution on Photophysical, Electrochemical, and Photovoltaic Properties.

    PubMed

    Bodedla, Govardhana Babu; Justin Thomas, K R; Fan, Miao-Syuan; Ho, Kuo-Chuan

    2016-01-15

    Three benzimidazole-based isomeric organic dyes possessing two triphenylamine donors and a cyanoacrylic acid acceptor are prepared by stoichiometrically controlled Stille or Suzuki-Miyaura coupling reaction which predominantly occurs on the N-butyl side of benzimidazole due to electronic preferences. Combined with the steric effect of the N-butyl substituent, placement of the acceptor segment at various nuclear positions of benzimidazole such as C2, C4, and C7 led to remarkable variations in intramolecular charge transfer absorption, electron injection efficiency, and charge recombination kinetics. The substitution of acceptor on the C4 led to red-shifted absorption, while that on C7 retarded the charge transfer due to twisting in the structure caused by the butyl group. Because of the cross-conjugation nature and poor electronic interaction between the donor and acceptor, the dye containing triphenylamine units on C4 and C7 and the acceptor unit on C2 showed the low oxidation potential. Thus, this dye possesses favorable HOMO and LUMO energy levels to render efficient sensitizing action in solar cells. Consequently, it results in high power conversion efficiency (5.01%) in the series with high photocurrent density and open circuit voltage. The high photocurrent generation by this dye is reasoned to it exceptional charge collection efficiency as determined from the electron impedance spectroscopy. PMID:26679036

  5. Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues.

    PubMed

    Batoon, Patrick; Ren, Jianhua

    2016-08-18

    Conformational effects on the proton affinity of oligopeptides have been studied using six alanine (A)-based acetylated dipeptides containing a basic probe that is placed closest to either the C- or the N-terminus. The basic probe includes Lysine (Lys) and two nonproteinogenic Lys-homologues, ornithine (Orn) and 2,3-diaminopropionic acid (Dap). The proton affinities of the peptides have been determined using the extended Cooks kinetic method in a triple quadrupole mass spectrometer. Computational studies have been carried out to search for the lowest energy conformers and to calculate theoretical proton affinities as well as various molecular properties using the density functional theory. The dipeptides containing a C-terminal probe, ALys, AOrn, and ADap, were determined to have a higher proton affinity by 1-4 kcal/mol than the corresponding dipeptides containing an N-terminal probe, LysA, OrnA, and DapA. For either the C-probe peptides or the N-probe peptides, the proton affinity reduces systematically as the side-chain of the probe residue is shortened. The difference in the proton affinities between isomeric peptides is largely associated with the variation of the conformations. The peptides with higher values of the proton affinity adopt a relatively compact conformation such that the protonated peptides can be stabilized through more efficient internal solvation. PMID:27459294

  6. Measurement of flux-weighted average cross sections for 197Au(γ, xn) reactions and isomeric yield ratios of 196m,gAu with bremsstrahlung

    NASA Astrophysics Data System (ADS)

    Naik, Haladhara; Kim, Guinyun; Kim, Kwangsoo; Zaman, Muhammad; Goswami, Ashok; Lee, Man Woo; Yang, Sung-Chul; Lee, Young-Ouk; Shin, Sung-Gyun; Cho, Moo-Hyun

    2016-04-01

    Photo-neutron cross sections of 197Au were experimentally determined for the bremsstrahlung end-point energies of 50, 60, and 70 MeV, by utilizing activation and off-line γ-ray spectrometric technique, using the 100 MeV electron linac at the Pohang Accelerator Laboratory (PAL), Pohang, Korea. The 197Au(γ, xn; x = 1- 6) reaction cross sections were calculated as a function of the bombarding photon energy by using the TALYS 1.6 computer code with default parameters. The flux-weighted average cross sections were obtained from the literature data and the theoretical values of TALYS 1.6 and TENDL-2014, for mono-energetic photons, and are found to be in good agreement with the present data. Isomeric yield ratios of 196m2,gAu from the 197Au(γ, n) reaction were also determined for the bremsstrahlung end-point energies of 50, 60, and 70 MeV, from the reaction cross sections of m2- and g-states, based on the present experimental data, and are found to be in good agreement with the theoretical values based on TALYS 1.6 and TENDL-2014.

  7. Part A. Neutron activation analysis of selenium and vanadium in biological matrices. Part B. Isomeric transition activation in aqueous solutions of alkyl bromides

    SciTech Connect

    Ebrahim, A.

    1988-01-01

    Several procedures were evaluated for determination of selenium in biological fluids and vanadium in biological tissues by neutron activation analysis (NAA) employing {sup 77m}Se and {sup 52}V isotopes, respectively. Procedures for determination of total selenium, trimethylselenonium (TMSe) ion and selenite (SeO{sub 3}{sup 2{minus}}) ion in urine and serum and for total selenoamino acids in urine were developed by utilizing anion exchange chromatography and molecular NAA. A pre-column derivatization of selenoamino acids with o-phthalaldehyde was necessary for their determination. Also an analytical approach was developed for determination of trace vanadium in liver samples from normal and diabetic rats as well as human and cow. Reactions of bromine-80 activated by radiative neutron capture and bromine-82 activated by isomeric transition were investigated in aqueous solutions of bromomethane and 1-bromobutane. Bromine-80 organic yields decreased with decreasing solute concentrations. The tendency for aggregation of the solute molecules diminished as the solute concentration approached zero where the probable state of the solute approached a monomolecular dispersion. Unlike reactions of {sup 80}Br born by {sup 79}Br(n,{gamma}){sup 80}Br reaction, the total organic product yields resulting from the {sup 82m}Br(I.T.){sup 82}Br process showed no solute concentration dependence.

  8. {gamma}-vibrational states in superheavy nuclei

    SciTech Connect

    Sun Yang; Long Guilu; Al-Khudair, Falih; Sheikh, Javid A.

    2008-04-15

    Recent experimental advances have made it possible to study excited structure in superheavy nuclei. The observed states have often been interpreted as quasiparticle excitations. We show that in superheavy nuclei collective vibrations systematically appear as low-energy excitation modes. By using the microscopic Triaxial Projected Shell Model, we make a detailed prediction on {gamma}-vibrational states and their E2 transition probabilities to the ground state band in fermium and nobelium isotopes where active structure research is going on, and in {sup 270}Ds, the heaviest isotope where decay data have been obtained for the ground-state and for an isomeric state.

  9. Isomerization and Fragmentation of Cyclohexanone in a Heated Micro-Reactor.

    PubMed

    Porterfield, Jessica P; Nguyen, Thanh Lam; Baraban, Joshua H; Buckingham, Grant T; Troy, Tyler P; Kostko, Oleg; Ahmed, Musahid; Stanton, John F; Daily, John W; Ellison, G Barney

    2015-12-24

    The thermal decomposition of cyclohexanone (C6H10═O) has been studied in a set of flash-pyrolysis microreactors. Decomposition of the ketone was observed when dilute samples of C6H10═O were heated to 1200 K in a continuous flow microreactor. Pyrolysis products were detected and identified by tunable VUV photoionization mass spectroscopy and by photoionization appearance thresholds. Complementary product identification was provided by matrix infrared absorption spectroscopy. Pyrolysis pressures were roughly 100 Torr, and contact times with the microreactors were roughly 100 μs. Thermal cracking of cyclohexanone appeared to result from a variety of competing pathways, all of which open roughly simultaneously. Isomerization of cyclohexanone to the enol, cyclohexen-1-ol (C6H9OH), is followed by retro-Diels-Alder cleavage to CH2═CH2 and CH2═C(OH)-CH═CH2. Further isomerization of CH2═C(OH)-CH═CH2 to methyl vinyl ketone (CH3CO-CH═CH2, MVK) was also observed. Photoionization spectra identified both enols, C6H9OH and CH2═C(OH)-CH═CH2, and the ionization threshold of C6H9OH was measured to be 8.2 ± 0.1 eV. Coupled cluster electronic structure calculations were used to establish the energetics of MVK. The heats of formation of MVK and its enol were calculated to be ΔfH298(cis-CH3CO-CH═CH2) = -26.1 ± 0.5 kcal mol(-1) and ΔfH298(s-cis-1-CH2═C(OH)-CH═CH2) = -13.7 ± 0.5 kcal mol(-1). The reaction enthalpy ΔrxnH298(C6H10═O → CH2═CH2 + s-cis-1-CH2═C(OH)-CH═CH2) is 53 ± 1 kcal mol(-1) and ΔrxnH298(C6H10═O → CH2═CH2 + cis-CH3CO-CH═CH2) is 41 ± 1 kcal mol(-1). At 1200 K, the products of cyclohexanone pyrolysis were found to be C6H9OH, CH2═C(OH)-CH═CH2, MVK, CH2CHCH2, CO, CH2═C═O, CH3, CH2═C═CH2, CH2═CH-CH═CH2, CH2═CHCH2CH3, CH2═CH2, and HC≡CH. PMID:26617252

  10. Experimental and Computational Studies of the Isomerization Reactions of Bidentate Phosphine Ligands in Triosmium Clusters

    SciTech Connect

    Xue, Zhang; Kandala, Srikanth; Yang, Li; Watson, William H.; Wang, Xiaoping; Hrovat, David A.

    2011-01-01

    The diphosphine ligand 1,2-bis(diphenylphosphino)benzene (dppbz) reacts with the activated cluster 1,2-Os{sub 3}(CO){sub 10}(MeCN){sub 2} (1) at room temperature to furnish a mixture of the triosmium clusters 1,2-Os{sub 3}(CO){sub 10}(dppbz) (2) and 1,1-Os{sub 3}(CO){sub 10}(dppbz) (3), along with a trace amount of the hydride cluster HOs{sub 3}(CO){sub 9}[{mu}-1,2-PhP(C{sub 6}H{sub 4}-{eta}{sup 1})C{sub 6}H{sub 4}PPh{sub 2}] (4). The dppbz-bridged cluster 2 forms as the kinetically controlled product and irreversibly transforms to the corresponding chelated isomer 3 at ambient temperature. The disposition of the dppbz ligand in 2 and 3 has been established by X-ray crystallography and {sup 31}P NMR spectroscopy, and the kinetics for the conversion 2 {yields} 3 have been followed by UV-vis spectroscopy in toluene over the temperature range 318-343 K. The calculated activation parameters ({Delta}H{sub {+-}} = 21.6(3) kcal/mol; {Delta}S{sub {+-}} = -11(1) eu) and lack of CO inhibition support an intramolecular isomerization mechanism that involves the simultaneous migration of phosphine and CO groups about the cluster polyhedron. The reaction between 1 and the fluorinated diphosphine ligand 1,2-bis(diphenylphosphino)tetrafluorobenzene (dppbzF{sub 4}) was examined under similar reaction conditions and was found to afford the chelated cluster 1,1-Os{sub 3}(CO){sub 10}(dppbzF{sub 4}) (6) as the sole observable product. The absence of the expected bridged isomer 1,2-Os{sub 3}(CO){sub 10}(dppbzF{sub 4}) (5) suggests that the dppbzF{sub 4} ligand destabilizes 5, thus accounting for the rapid isomerization of 5 to 6. Near-UV irradiation of clusters 3 and 6 leads to CO loss and ortho metalation of an ancillary aryl group. The resulting hydride clusters 4 and HOs{sub 3}(CO){sub 9}[{mu}-1,2-PhP(C{sub 6}H{sub 4}-{eta}{sup 1})C{sub 6}F{sub 4}PPh{sub 2}] (7) have been isolated and fully characterized by spectroscopic and X-ray diffraction analyses. Both 4 and 7 react with added

  11. Cis→Trans Isomerization of Pro(7) in Oxytocin Regulates Zn(2+) Binding.

    PubMed

    Fuller, Daniel R; Glover, Matthew S; Pierson, Nicholas A; Kim, DoYong; Russell, David H; Clemmer, David E

    2016-08-01

    Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn(2+) to the nine-residue peptide hormone oxytocin (OT, Cys(1)-Tyr(2)-Ile(3)-Gln(4)-Asn(5)-Cys(6)-Pro(7)-Leu(8)-Gly(9)-NH2, having a disulfide bond between Cys(1) and Cys(6) residues). Zn(2+) binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899-3906 (1979)]. In the absence of Zn(2+), we find evidence for two primary OT conformations, which arise because the Cys(6)-Pro(7) peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn(2+), we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM(-1), for the trans- and cis-configured populations, respectively. The Zn(2+) bound form of OT, having a cross section of Ω = 235 Å(2), has Pro(7) in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993-6000 (2008)], in which it was proposed that Zn(2+) binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro(7)-Leu(8)-Gly(9)-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn(2+). In this way, the proline residue regulates Zn(2+) binding to OT and, hence, is important in receptor binding. Graphical Abstract ᅟ. PMID:27154022

  12. Theoretical investigation on the vibrational and electronic spectra of three isomeric forms of dicobalt octacarbonyl

    NASA Astrophysics Data System (ADS)

    Karakaş, Duran; Kariper, Sultan Erkan

    2014-03-01

    Three isomeric forms of dicobalt octacarbonyl, [Co2(CO)8], with C2v, D3d and D2d point group were optimized by using density functional theory (DFT/B3LYP) method with LANL2DZ basis set for the cobalt atoms and 6-31G(d) basis set for the other atoms in the gas phase. Electronic structures, carbonyl stretching frequencies and Mulliken population analysis were determined from the optimized structures. Electronic structures indicate that each of the dicobalt octacarbonyl isomers have been constituted from two trigonal bipyramidal geometry. While the isomer C2v has two bridged carbonyl groups, in the isomers D3d and D2d all carbonyl groups are coordinating as terminal. The calculated C-O stretching frequencies are in a good agreement with experimental frequencies. Experimental C-O stretching frequencies were assigned to isomers according to the calculated frequencies. Mulliken population analysis show that free carbonyl ligands transfer their electron to the cobalt atoms during formation of the complexes. The electronic spectra of isomers were obtained by using time dependent density functional theory (TD-DFT/B3LYP) method with LANL2DZ basis set for the cobalt atoms and 6-31G(d) basis set for the other atoms in the gas phase. The theoretical electronic spectra of isomers are in a good agreement with experimental spectra. The calculated bands at 277.9, 278.1 and 284.1 nm for isomers C2v, D2d and D3d were assigned to metal-ligand charge transfer transitions and the shoulder at 344.6 nm was assigned to pure metal center transitions for isomer D3d.

  13. Notable differences between oxidized diruthenium complexes bridged by four isomeric diethynyl benzodithiophene ligands.

    PubMed

    Ou, Ya-Ping; Zhang, Jing; Zhang, Fuxing; Kuang, Daizhi; Hartl, František; Rao, Li; Liu, Sheng Hua

    2016-04-12

    Four new diruthenium complexes [{(η(5)-C5Me5)Ru(dppe)}2(μ-C[triple bond, length as m-dash]C-L-C[triple bond, length as m-dash]C)] featuring different bridging isomeric diethynyl benzodithiophenes viz. L = benzo[1,2-b;4,5-b']dithiophene (complex ), benzo[2,1-b;4,5-b']dithiophene (complex ), benzo[1,2-b;3,4-b']dithiophene (complex ) and benzo[1,2-b;4,3-b']dithiophene (complex ), were synthesized and characterized by molecular spectroscopic and crystallographic methods. The subtle changes in the molecular structure introduced by the diethynyl benzodithiophene isomers have a notable impact on the stability of the oxidized complexes and their absorption characteristics in the visible-NIR and IR spectral domains. Electronic properties of stable oxidized complexes [](n+) and [](n+) (n = 1, 2) were investigated by cyclic voltammetry, UV-vis-NIR and IR spectroelectrochemistry as well as DFT and TDDFT calculations. The results document the largely bridge-localized character of the oxidation of parents and . Cations [](+) and [](+) are too unstable at ambient temperature to afford their unambiguous characterization. UV-vis-NIR absorption spectral data combined with TDDFT calculations (BLYP35) reveal that the broad electronic absorption of [](+) and [](+) in the NIR region has a mixed intraligand π-π* and MLCT character, with similar contribution from their spin-delocalized trans and cis conformers. A spin-localized (mixed-valence) rotamer was only observed for [](+) at ambient temperature as a minor component on the time scale of IR spectroscopy. PMID:26953807

  14. Cis→Trans Isomerization of Pro7 in Oxytocin Regulates Zn2+ Binding

    NASA Astrophysics Data System (ADS)

    Fuller, Daniel R.; Glover, Matthew S.; Pierson, Nicholas A.; Kim, DoYong; Russell, David H.; Clemmer, David E.

    2016-05-01

    Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn2+ to the nine-residue peptide hormone oxytocin (OT, Cys1-Tyr2-Ile3-Gln4-Asn5-Cys6-Pro7-Leu8-Gly9-NH2, having a disulfide bond between Cys1 and Cys6 residues). Zn2+ binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899-3906 (1979)]. In the absence of Zn2+, we find evidence for two primary OT conformations, which arise because the Cys6-Pro7 peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn2+, we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM-1, for the trans- and cis-configured populations, respectively. The Zn2+ bound form of OT, having a cross section of Ω = 235 Å2, has Pro7 in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993-6000 (2008)], in which it was proposed that Zn2+ binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro7-Leu8-Gly9-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn2+. In this way, the proline residue regulates Zn2+ binding to OT and, hence, is important in receptor binding.

  15. Cis→Trans Isomerization of Pro7 in Oxytocin Regulates Zn2+ Binding

    NASA Astrophysics Data System (ADS)

    Fuller, Daniel R.; Glover, Matthew S.; Pierson, Nicholas A.; Kim, DoYong; Russell, David H.; Clemmer, David E.

    2016-08-01

    Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn2+ to the nine-residue peptide hormone oxytocin (OT, Cys1-Tyr2-Ile3-Gln4-Asn5-Cys6-Pro7-Leu8-Gly9-NH2, having a disulfide bond between Cys1 and Cys6 residues). Zn2+ binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899-3906 (1979)]. In the absence of Zn2+, we find evidence for two primary OT conformations, which arise because the Cys6-Pro7 peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn2+, we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM-1, for the trans- and cis-configured populations, respectively. The Zn2+ bound form of OT, having a cross section of Ω = 235 Å2, has Pro7 in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993-6000 (2008)], in which it was proposed that Zn2+ binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro7-Leu8-Gly9-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn2+. In this way, the proline residue regulates Zn2+ binding to OT and, hence, is important in receptor binding.

  16. Isomeric Distinction of Small Oligosaccharides: A Bottom-Up Approach Using the Kinetic Method

    NASA Astrophysics Data System (ADS)

    Major, Mohamed; Fouquet, Thierry; Charles, Laurence

    2011-07-01

    Isomeric distinction of di- and tri-saccharides could be efficiently achieved by using data previously obtained while performing experiments aimed at discriminating monosaccharides using trimeric ion dissociation with data analysis by the kinetic method. This study shows that effects observed for lower homologues when one of the partners is changed in the metal/reference system (typically a transition metal divalent cation associated to amino acids) can be extrapolated to upper homologues, at least for the tested analyte series. Systems allowing galactose, glucose, and fructose distinction were used as starting conditions to resolve cellobiose, lactose, maltose, and saccharose disaccharides. When a unique dissociation reaction was observed from the trimeric clusters, a new reference was selected based on its propensity to favor the analyte or the reference release, as revealed from monosaccharide experiments, depending on the desired effect. The same approach could be implemented from data obtained for disaccharides to select efficient metal/reference systems to distinguish cellotriose, isomaltotriose, maltotriose, and panose trisaccharides. As a result, method optimization is greatly improved due to an enhanced rationalization of the search for discriminant systems. While 40 systems had to be tested for monosaccharides, by screening five transition metals and eight amino acids, the proposed approach allowed efficient metal/reference systems to be found for disaccharides after testing 18 combinations; then, only four systems had to be scrutinized to achieve trisaccharide distinction. Accurate quantitative analyses could be performed in binary mixtures using three-point calibration curves to correct for competition effects between analytes for the formation of the trimeric clusters.

  17. Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds

    PubMed Central

    Kim, Judy E.; McCamant, David W.; Zhu, Leyun; Mathies, Richard A.

    2005-01-01

    Picosecond time-resolved resonance Raman spectroscopy is used to probe the structural changes of rhodopsin's retinal chromophore as the cis-to-trans isomerization reaction occurs that initiates vision. Room-temperature resonance Raman spectra of rhodopsin's photoproduct with time delays from −0.7 to 20.8 ps are measured using 2.2 ps, 480 nm pump and 1.5 ps, 600 nm probe pulses. Hydrogen-out-of-plane (HOOP) modes at 852, 871, and 919 cm−1, fingerprint peaks at 1272, 1236, 1211, and 1166 cm−1, and a broad red-shifted ethylenic band at 1530 cm−1 are present at the earliest positive pump−probe time delay of 0.8 ps, indicating that the chromophore is already in a strained, all-trans configuration. Kinetic analyses of both the HOOP and ethylenic regions of the photoproduct spectra reveal that these features grow in with fast (∼ 200 fs) and slow (∼ 2–3 ps) components. These data provide the first structural evidence that photorhodopsin has a thermally unrelaxed, torsionally strained all-trans chromophore within ∼1 ps, and possibly within 200 fs, of photon absorption. Following this ultrafast product formation, the all-trans chromophore cools and conformationally relaxes within a few picoseconds to form bathorhodopsin. This cooling process is revealed as an ethylenic frequency blue-shift of 6 cm−1 (τ ∼ 3.5 ps) as well as an ethylenic width narrowing (τ ∼ 2 ps). The ultrafast production of photorhodopsin is likely accompanied by an impulsively driven, localized protein response. More delocalized protein modes are unable to relax on this ultrafast time scale enabling the chromophore-protein complex to store the large amounts of photon energy (30–35 kcal/mol) that are subsequently used to drive activating protein conformational changes. PMID:16755302

  18. Anomalous magnetic hyperfine structure of the 229Th ground-state doublet in muonic atoms

    NASA Astrophysics Data System (ADS)

    Tkalya, E. V.

    2016-07-01

    The magnetic hyperfine (MHF) splitting of the ground and low-energy 3 /2+(7.8 ±0.5 eV) levels in the 229Th nucleus in the muonic atom (μ1S1 /2 -229Th) * is calculated considering the distribution of the nuclear magnetization in the framework of the collective nuclear model with wave functions of the Nilsson model for the unpaired neutron. It is shown that (a) deviation of the MHF structure of the isomeric state exceeds 100% from its value for a pointlike nuclear magnetic dipole (the order of sublevels is reversed); (b) partial inversion of levels of the 229Th ground-state doublet and spontaneous decay of the ground state to the isomeric state occur; (c) the E 0 transition, which is sensitive to differences in the mean-square charge radii of the doublet states, is possible between mixed sublevels with F =2 ; and (d) MHF splitting of the 3 /2+ isomeric state may be in the optical range for certain values of the intrinsic gK factor and a reduced probability of a nuclear transition between the isomeric and the ground states.

  19. 1H NMR, electronic-absorption and resonance-Raman spectra of isomeric okenone as compared with those of isomeric β-carotene, canthaxanthin, β-apo-8'-carotenal and spheroidene

    NASA Astrophysics Data System (ADS)

    Fujii, Ritsuko; Chen, Chun-Hai; Mizoguchi, Tadashi; Koyama, Yasushi

    1998-05-01

    Eleven cis- trans isomers of okenone were isolated by means of HPLC using a silica-gel column from an isomeric mixture which was obtained by iodine-sensitized photo-isomerization of the all- trans isomer. The configurations of eight isomers among them were determined by NMR spectroscopy using the isomerization shifts of the olefinic 1Hs and the 1H- 1H NOE correlations to be all- trans, 7- cis, 7- cis,8-s- cis, 9- cis, 9'- cis, 13- cis, 13'- cis and 9,9'-di- cis, and their electronic-absorption and resonance-Raman spectra were recorded. Based on the results: (1) the chemical shifts of the olefinic 1Hs in NMR; (2) the wavelength of the A g-→B u+ transition; and (3) the relative intensity of the A g-→A g+ versus the A g-→B u+ transition in electronic absorption; (4) the CC stretching frequency; and (5) the relative intensity of the C10-C11 (C10'-C11') versus the C14-C15 (C14'-C15') stretching vibration in resonance Raman were compared among the all- trans, 7- cis, 9- cis (9'- cis) and 13- cis (13'- cis) isomers of β-carotene, canthaxanthin, β-apo-8'-carotenal, neurosporene, spheroidene and okenone. Relevance of the systematic changes in the above five different parameters originally found in β-carotene was examined in the rest of the carotenoids, and the effects of the peripheral groups on them were explained in terms of the length and asymmetry of the conjugated system consisting of the CC and CO bonds.

  20. Non-adiabatic dynamics investigation of the radiationless decay mechanism of trans-urocanic acid in the S2 state.

    PubMed

    Zhao, Li; Zhou, Pan-Wang; Zhao, Guang-Jiu

    2016-07-28

    The trans-urocanic acid, a UV chromophore in the epidermis of human skin, was found to exhibit a wavelength dependent isomerization property. The isomerization quantum yield to cis-urocanic is greatest when being excited to the S1 state, whereas exciting the molecule to the S2 state causes almost no isomerization. The comparative photochemical behavior of the trans-urocanic on the S1 and S2 states continues to be the subject of intense research effort. This study is concerned with the unique photo-behavior of this interesting molecule on the S2 state. Combining the on-the-fly surface hopping dynamics simulations and static electronic structure calculations, three decay channels were observed following excitation to the S2 state. An overwhelming majority of the molecules decay to the S1 state through a planar or pucker characterized minimum energy conical intersection (MECI), and then decay to the ground state along a relaxation coordinate driven by a pucker deformation of the ring. A very small fraction of molecules decay to the S1 state by a MECI characterized by a twisting motion around the CC double bond, which continues to drive the molecule to deactivate to the ground state. The latter channel is related with the photoisomerization process, whereas the former one will only generate the original trans-form products. The present work provides a novel S2 state decay mechanism of this molecule, which offers useful information to explain the wavelength dependent isomerization behavior. PMID:27475370

  1. Non-adiabatic dynamics investigation of the radiationless decay mechanism of trans-urocanic acid in the S2 state

    NASA Astrophysics Data System (ADS)

    Zhao, Li; Zhou, Pan-Wang; Zhao, Guang-Jiu

    2016-07-01

    The trans-urocanic acid, a UV chromophore in the epidermis of human skin, was found to exhibit a wavelength dependent isomerization property. The isomerization quantum yield to cis-urocanic is greatest when being excited to the S1 state, whereas exciting the molecule to the S2 state causes almost no isomerization. The comparative photochemical behavior of the trans-urocanic on the S1 and S2 states continues to be the subject of intense research effort. This study is concerned with the unique photo-behavior of this interesting molecule on the S2 state. Combining the on-the-fly surface hopping dynamics simulations and static electronic structure calculations, three decay channels were observed following excitation to the S2 state. An overwhelming majority of the molecules decay to the S1 state through a planar or pucker characterized minimum energy conical intersection (MECI), and then decay to the ground state along a relaxation coordinate driven by a pucker deformation of the ring. A very small fraction of molecules decay to the S1 state by a MECI characterized by a twisting motion around the CC double bond, which continues to drive the molecule to deactivate to the ground state. The latter channel is related with the photoisomerization process, whereas the former one will only generate the original trans-form products. The present work provides a novel S2 state decay mechanism of this molecule, which offers useful information to explain the wavelength dependent isomerization behavior.

  2. Excited-state properties and physiological functions of biological polyenes: the triplet-excited region of retinoids and carotenoids

    NASA Astrophysics Data System (ADS)

    Koyama, Y.; Mukai, Yumiko; Kuki, Michitaka

    1993-06-01

    Both experimental and theoretical results which indicate the presence of the triplet-excited region in retinoids and carotenoids are reviewed. The triplet- excited region is defined as a region where changes in the bond order take place, upon triplet excitation, toward its inversion, i.e., a double bond becomes more signal bond-like and a single bond becomes more double bond-like. (1) It has a span of approximately six conjugated double bonds, (2) it is localized in the central part of a conjugated chain, and (3) it triggers `cis' to `trans' isomerization in the T1 state. The experimental and theoretical results include: (1) the T1 Raman spectra of all-trans-retinal and its homologues; (2) the T1-state isomerization of isomeric retinal; (3) the T1-state isomerization of isomeric (beta) -carotene; (4) the PPP-SD-CI calculations of the bond orders of the carbon-carbon bonds in a set of model polyenes; and (5) the normal-coordinate analysis of the T1 Raman lines of undeuterated and deuterated all-trans-retinal. Finally, (6) the biological implication of 'the triplet-excited region' is discussed in relation to the photo-protective function of a 15-cis carotenoid bound to the bacterial photoreaction center.

  3. Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a d-isomerized serine residue.

    PubMed

    Alsanousi, Nesreen; Sugiki, Toshihiko; Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi; Kojima, Chojiro

    2016-09-01

    Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from l to d form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin d-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin d-Ser14 by nuclear magnetic resonance (NMR) and showed that d-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin d-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure-function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by d-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. PMID:27349871

  4. Isomerization of delta-9-THC to delta-8-THC when tested as trifluoroacetyl-, pentafluoropropionyl-, or heptafluorobutyryl- derivatives.

    PubMed

    Holler, Justin M; Smith, Michael L; Paul, Shom N; Past, Marilyn R; Paul, Buddha D

    2008-05-01

    For GC-MS analysis of delta-9-tetrahydrocannabinol (delta-9-THC), perfluoroacid anhydrides in combination with perfluoroalcohols are commonly used for derivatization. This reagent mixture is preferred because it allows simultaneous derivatization of delta-9-THC and its acid metabolite, 11-nor-delta-9-THC-9-carboxylic acid present in biological samples. When delta-9-THC was derivatized by trifluoroacetic anhydride/hexafluoroisopropanol (TFAA/HFIPOH) and analyzed by GC-MS using full scan mode (50-550 amu), two peaks (P1 and P2) with an identical molecular mass of 410 amu were observed. On the basis of the total ion chromatogram (TIC), P1 with a shorter retention time (RT) was the major peak (TIC 84%). To identify the peaks, delta-8-THC was also tested under the same conditions. The RT and spectra of the major peak (TIC 95%) were identical with that of P1 for delta-9-THC. A minor peak (5%) present also correlated well with the latter peak (P2) for the delta-9-THC derivative. The fragmentation pathway of P1 was primarily demethylation followed by retro Diels-Alder fragmentation (M - 15-68, base peak 100%) indicating P1 as a delta-8-THC-trifluoroacetyl compound. This indicated that delta-9-THC isomerized to delta-8-THC during derivatization with TFAA/HFIPOH. Similar results were also observed when delta-9-THC was derivatized with pentafluoropropionic anhydride/pentafluoropropanol or heptafluorobutyric anhydride/heptafluorobutanol. No isomerization was observed when chloroform was used in derivatization with TFAA. In this reaction, the peaks of delta-8-THC-TFA and delta-9-THC-TFA had retention times and mass spectra matching with P1 and P2, respectively. Because of isomerization, perfluoroacid anhydrides/perfluoroalcohols are not suitable derivatizing agents for analysis of delta-9-THC; whereas the TFAA in chloroform is suitable for the analysis. PMID:18205240

  5. Isolation and identification of 2,4,6-trihydroxyphenanthrene as a byproduct of trans-resveratrol photochemical isomerization and electrocyclization.

    PubMed

    Francioso, Antonio; Boffi, Alberto; Villani, Claudio; Manzi, Lucio; D'Erme, Maria; Macone, Alberto; Mosca, Luciana

    2014-10-01

    UV irradiation of trans-resveratrol leads to its photochemical isomerization and electrocyclization, giving rise to different byproducts. Preliminary attempts to purify and characterize these products were in the majority of cases unsuccessful. In the present work, the resveratrol photoreaction products were analyzed by HPLC, and one of these compounds, 2,4,6-trihydroxyphenanthrene (THP), was purified and unambiguously identified. The structure of THP was unequivocally characterized for the first time by combined GC-MS, ESI-MS/MS, NMR, and FT-IR analyses. PMID:25198795

  6. A Novel Chromone Schiff-Base Fluorescent Chemosensor for Cd(II) Based on C=N Isomerization.

    PubMed

    Yan, Jun; Fan, Long; Qin, Jing-Can; Li, Chao-Rui; Yang, Zheng-Yin

    2016-05-01

    A new chromone Schiff-base fluorescent probe 7'-methoxychromone-3'-methylidene-1,2,4-triazole-3-imine (L) was designed and synthesized for selective recognition Cd(2+). With the fluorescence titration and the ESI-MS data, we reach the conclusion that the binding mode of the ligand-metal (L-Cd (2+) ) complex is 1:1. The sensor showed a strong fluorescence enhancement in ethanol system of Cd(2+) (excitation 409 nm and emission 462 nm) and the sensing mechanism based on the fact that C=N isomerization can be used to explain this phenomenon. PMID:27048223

  7. Soft Propargylic Deprotonation: Designed Ligand Enables Au-Catalyzed Isomerization of Alkynes to 1,3-Dienes

    PubMed Central

    2015-01-01

    By functionalizing the privileged biphenyl-2-ylphosphine with a basic amino group at the rarely explored 3′ position, the derived gold(I) complex possesses orthogonally positioned “push” and “pull” forces, which enable for the first time soft propargylic deprotonation and permit the bridging of a difference of >26 pKa units (in DMSO) between a propargylic hydrogen and a protonated tertiary aniline. The application of this design led to efficient isomerization of alkynes into versatile 1,3-dienes with synthetically useful scope under mild reaction conditions. PMID:24911158

  8. From a Sequential to a Concurrent Reaction in Aqueous Medium: Ruthenium-Catalyzed Allylic Alcohol Isomerization and Asymmetric Bioreduction.

    PubMed

    Ríos-Lombardía, Nicolás; Vidal, Cristian; Liardo, Elisa; Morís, Francisco; García-Álvarez, Joaquín; González-Sabín, Javier

    2016-07-18

    The ruthenium-catalyzed redox isomerization of allylic alcohols was successfully coupled with the enantioselective enzymatic ketone reduction (mediated by KREDs) in a concurrent process in aqueous medium. The overall transformation, formally the asymmetric reduction of allylic alcohols, took place with excellent conversions and enantioselectivities, under mild reaction conditions, employing commercially and readily available catalytic systems, and without external coenzymes or cofactors. Optimization resulted in a multistep approach and a genuine cascade reaction where the metal catalyst and biocatalyst coexist from the beginning. PMID:27258838

  9. The oxidation of n-butane and n-heptane in a CFR engine; Isomerization reactions and delay of autoignition

    SciTech Connect

    Sahetchian, K.A.; Blin, N.; Rigny, R.; Seydi, A. ); Murat, M. )

    1990-03-01

    During the oxidation of {ital n}-butane in a flow system and also in a motored CFR engine (600 rpm) hydrogen peroxide, primary and secondary butylhydroperoxides, and peracetic acid are formed. In the CFR engine these peroxides appear only when the compression ratio is larger than 10:1 ({ital T}{sub max} = 650 K). No autoignition has been observed. A comparison of {ital n}-butane and {ital n}-heptane oxidation is presented. Isomerization reactions,which are correlated with the alkane structure and the octane number, account for the differences in the experimental results.

  10. A Photoresponsive Surface Covalent Organic Framework: Surface-Confined Synthesis, Isomerization, and Controlled Guest Capture and Release.

    PubMed

    Liu, Chunhua; Zhang, Wei; Zeng, Qingdao; Lei, Shengbin

    2016-05-10

    By introducing an azobenzene group to the backbone of diboronic acid, we have obtained a surface-confined, photoresponsive single-layer covalent organic framework with long-range order and almost entire surface coverage. Scanning tunneling microscopic characterization indicates that though the covalent linkage provides a significant locking effect, isomerization can still happen under UV irradiation, which causes destruction of the surface COF. Furthermore, the decomposed surface COF can recover upon annealing. This photoinduced decomposition provides a facile approach for the controlled capture and release of targeted objects using these nanoporous surface COFs as a host, which has been demonstrated in this work using copper phthalocyanine as a model guest. PMID:26990558

  11. Regioselective Isomerization of 2,3-Disubstituted Epoxides to Ketones: An Alternative to the Wacker Oxidation of Internal Alkenes.

    PubMed

    Lamb, Jessica R; Mulzer, Michael; LaPointe, Anne M; Coates, Geoffrey W

    2015-12-01

    We report an alternative pathway to the Wacker oxidation of internal olefins involving epoxidation of trans-alkenes followed by a mild and highly regioselective isomerization to give the major ketone isomers in 66-98% yield. Preliminary kinetics and isotope labeling studies suggest epoxide ring opening as the turnover limiting step in our proposed mechanism. A similar catalytic system was applied to the kinetic resolution of select trans-epoxides to give synthetically useful selectivity factors of 17-23 for benzyl-substituted substrates. PMID:26522052

  12. Five chiral Cd(II) complexes with dual chiral components: Effect of positional isomerism, luminescence and SHG response

    NASA Astrophysics Data System (ADS)

    Cheng, Lin; Wang, Jun; Yu, Hai-Yan; Zhang, Xiu-Ying; Gou, Shao-Hua; Fang, Lei

    2015-01-01

    Five chiral Cd(II) complexes with dual chiral components have been synthesized by using a series of (1R,2R)-N1,N2-bis(pyridinylmethyl)cyclohexane-1,2-diamine ligands with different N-positions of pyridyl rings and Cd(NO3)2. The circular dichroism (CD) spectra and second-harmonic generation (SHG) efficiency measurements confirmed that they are of structural chirality in the bulk samples. The luminescent properties indicated that they may have potential applications as optical materials. The formation of discrete mononuclear and binuclear complexes, and one-dimensional chains may be attributed to positional isomerism of the ligands.

  13. ‘Horror vacui’ or topological in-out isomerism in perhydrogenated fullerenes: C60H60 and monoalkylated perhydrogenated fullerenes

    NASA Astrophysics Data System (ADS)

    Dodziuk, Helena; Nowinski, Krzysztof

    1996-02-01

    In endohedral chemistry, one of the exciting prospects offered by the cage-like structure of fullerenes, several aspects of the calculations on in-out isomerism of perhydrogenated fullerene and their consequences went unnoticed, e.g. the topological character of the isomerism, the instability of C 60F 60, which was thought to revolutionize industry as an ideal lubricant, as well as the possibility of in-out isomerism in alkylated fulleranes. Molecular mechanics calculations indicate that for smaller alkyl groups the 'in' isomer is significantly more stable extending the possibility of endohedral fullerene chemistry. C 60H 60 and its derivatives can be considered as examples of a manifestation of the ancient 'horror vacui' concept.

  14. Linkage Isomerism in Silver Acylpyrazolonato Complexes and Correlation with Their Antibacterial Activity.

    PubMed

    Marchetti, Fabio; Palmucci, Jessica; Pettinari, Claudio; Pettinari, Riccardo; Scuri, Stefania; Grappasonni, Iolanda; Cocchioni, Mario; Amati, Mario; Lelj, Francesco; Crispini, Alessandra

    2016-06-01

    Novel silver(I) acylpyrazolonato coordination polymers of formula [Ag(Q(R))]n (1-3) have been synthesized by interaction of silver nitrate with HQ(R) in methanol in the presence of an equivalent quantity of KOH (in general HQ(R) = 1-phenyl-3-methyl-4-RC(═O)-5-pyrazolone, in detail HQ(fb), R = -CF2CF2CF3; HQ(cy), R = -cyclo-C6H11; HQ(be), R = -C(H)═C(CH3)2). [Ag(Q(R))]n react with 2-ethylimidazole (2EtimH), 1-methylimidazole (Meim), and triphenylphosphine (PPh3), affording the mononuclear Ag(Q(fb))(EtimH) (4), Ag(Q(cy))(Meim)2 (5), Ag(Q(be))(Meim) (6), and Ag(Q(R))(PPh3)2 (7-9). All complexes have been analytically and spectroscopically characterized, and for some of them the X-ray crystal structure has been resolved. In particular, the single crystal molecular structure determination of Ag(Q(fb))(EtimH) and Ag(Q(be))(PPh3)2 has confirmed the different coordination modes of the HQ(fb) and HQ(be) acylpyrazolone ligands, the former being bound to the silver(I) ion in a monodentate fashion while the latter in the O2-chelating mode. Density functional theory computations suggest new insights about metal-ligand interactions and the observed linkage isomerism. While phosphine-containing complexes Ag(Q(R))(PPh3)2 (7-9) seem not to be able to efficiently inhibit the growth of Escherichia coli and Staphylococcus aureus, the polynuclear complexes [Ag(Q(R))]n (1-3) and the mononuclear Ag(Q(fb))(EtimH) (4), Ag(Q(cy))(Meim)2 (5), and Ag(Q(be))(Meim) (6) show a high and almost steady in time antibacterial activity, comparable to that of AgNO3. This activity is likely related to the degree of saturation of the silver center and to the presence of different ancillary ligands in the diverse typologies of complexes. PMID:27177324

  15. Spectroscopic separation of (13) C NMR spectra of complex isomeric mixtures by the CSSF-TOCSY-INEPT experiment.

    PubMed

    Yang, Lu; Moreno, Aitor; Fieber, Wolfgang; Brauchli, Robert; Sommer, Horst

    2015-04-01

    Isomeric mixtures from synthetic or natural origins can pose fundamental challenges for their chromatographic separation and spectroscopic identification. A novel 1D selective NMR experiment, chemical shift selective filter (CSSF)-TOCSY-INEPT, is presented that allows the extraction of (13) C NMR subspectra of discrete isomers in complex mixtures without physical separation. This is achieved via CSS excitation of proton signals in the (1) H NMR mixture spectrum, propagation of the selectivity by polarization transfer within coupled (1) H spins, and subsequent relaying of the magnetization from (1) H to (13) C by direct INEPT transfer to generate (13) C NMR subspectra. Simple consolidation of the subspectra yields (13) C NMR spectra for individual isomers. Alternatively, CSSF-INEPT with heteronuclear long-range transfer can correlate the isolated networks of coupled spins and therefore facilitate the reconstruction of the (13) C NMR spectra for isomers containing multiple spin systems. A proof-of-principle validation of the CSSF-TOCSY-INEPT experiment is demonstrated on three mixtures with different spectral and structural complexities. The results show that CSSF-TOCSY-INEPT is a versatile, powerful tool for deconvoluting isomeric mixtures within the NMR tube with unprecedented resolution and offers unique, unambiguous spectral information for structure elucidation. PMID:25616134

  16. Influence of ligand and environment substitution on photo-triggered linkage isomerization of photochromic ruthenium sulfoxide complexes

    NASA Astrophysics Data System (ADS)

    Springfeld, Kristin; Dieckmann, Volker; Eicke, Sebastian; Imlau, Mirco

    2012-02-01

    The group of ruthenium polypyridine sulfoxides features a pronounced photochromism in the UV/VIS spectral range based on an ultrafast photo-triggered linkage isomerization located at the SO-ligand. This isomerization exhibits a tremendous photosensitivity and a high thermal stability of the two metastable structural isomers. Here, we discuss the characteristic photochromic properties of the compounds in the frame of ligand substitution and the replacement of the dielectric environment. The complex [Ru(bpy)2(ROSO)].PF6 [1] (with OSO: 2-methylsulfinylbenzoate) has been modified with the groups R = H, Bn, BnCl and BnMe [2] and studied in different solvents as well as in polydimethylsiloxane. The analysis is performed by cw-pump-probe technique as a function of temperature and exposure. Our results reveal a selective adjustability of the thermal stability in the compounds, while the photosensitivity and the characteristic absorption spectra remain unchanged. We discuss the impact of sulfoxide compounds with the desired features in view of application in molecular photonic devices.[4pt] [1] V. Dieckmann et al., Opt. Express 17, 15052 (2009)[2] V. Dieckmann et al., Opt. Express 18, 23495 (2010)

  17. A sugar isomerization reaction established on various (βα)₈-barrel scaffolds is based on substrate-assisted catalysis.

    PubMed

    Reisinger, Bernd; Bocola, Marco; List, Felix; Claren, Jörg; Rajendran, Chitra; Sterner, Reinhard

    2012-11-01

    In the course of tryptophan biosynthesis, the isomerization of phosphoribosylanthranilate (PRA) is catalyzed by the (βα)₈-barrel enzyme TrpF. The reaction occurs via a general acid-base mechanism with an aspartate and a cysteine residue acting as acid and base, respectively. PRA isomerase activity could be established on two (βα)₈-barrel enzymes involved in histidine biosynthesis, namely HisA and HisF, and on a HisAF chimera, by introducing two aspartate-to-valine substitutions. We have analyzed the reaction mechanism underlying this engineered activity by measuring its pH dependence, solving the crystal structure of a HisF variant with bound product analogue, and applying molecular dynamics simulations and mixed quantum and molecular mechanics calculations. The results suggest that PRA is anchored by the C-terminal phosphate-binding sites of HisA, HisF and HisAF. As a consequence, a conserved aspartate residue, which is equivalent to Cys7 from TrpF, is properly positioned to act as catalytic base. However, no obvious catalytic acid corresponding to Asp126 from TrpF could be identified in the three proteins. Instead, this role appears to be carried out by the carboxylate group of the anthranilate moiety of PRA. Thus, the engineered PRA isomerization activity is based on a reaction mechanism including substrate-assisted catalysis and thus differs substantially from the naturally evolved reaction mechanism used by TrpF. PMID:23109729

  18. Playing with isomerism and N substitution in pentalenedione derivatives for organic electrode batteries: how high are the stakes?

    PubMed

    Tomerini, Daniele; Gatti, Carlo; Frayret, Christine

    2016-01-28

    New concepts to design innovating and top-performing redox-active organic molecules based electrodes should push forward and promote an eco-friendly alternative to classical Li-ion batteries. In this promising research area, density functional theory calculations lend support to experiments through the prediction of redox voltage and give promise to rationalize the trends, thus providing a general approach for engineering advanced materials. In this study in which we analysed spin density/net atomic charges distribution along with global energy decomposition thanks to Bader's partitioning of the molecular space, a vision for designing pentalenedione derivatives by fine tuning of the redox potential properties is presented. The concept relies on combined effects of isomerism and N single/double substitution for CH on the parent backbone. Such dual nature modification is able to provide a series of compounds within the range of 2.2-3.6 V vs. Li(+)/Li (against a more restricted range of 2.2-2.8 V vs. Li(+)/Li for the sole effect of isomerism on the unsubstituted parent compounds). The incidence of double N substitution alone generally follows an almost additive rule based on the combined actions of the composing single N substitutions. Few exceptions to the rule were, however, also observed and rationalized. Beyond learning gained for this peculiar family, these results may have exciting implications for future design strategies. PMID:26701642

  19. Using Variable Ionization Energy Time-of-Flight Mass Spectrometry with Comprehensive GC×GC To Identify Isomeric Species.

    PubMed

    Alam, Mohammed S; Stark, Christopher; Harrison, Roy M

    2016-04-19

    Although GC×GC-ToF-MS allows the separation of thousands of peaks, many of these peaks are not positively identified owing to the lack of mass spectral library data and/or standard materials, leading to a substantial amount of information being inaccessible. The fragmentation patterns of molecules in mass spectrometers using electron impact ionization at 70 eV can be useful for molecule identification, provided a match is available in a published EI MS library, but are indistinguishable for many isomeric organic compounds (for example, linear and branched alkanes). Lower ionization energies have been exploited leading to organic compounds being ionized with lower excess internal energy and less fragmentation, retaining the molecular ion and maximizing its relative signal. This has enabled the identification of a large number of isomeric organic compounds, both aliphatic and aromatic, between C12-C36, in the previously unresolved complex mixture (UCM) of two motor oil samples. This technique also demonstrates problems associated with separation of coeluting isomers, particularly for the n-alkanes, which are routinely measured by 1D GC/MS and may be overestimated, due to coelution. As a consequence retention times in 2 dimensions and mass spectra at variable ionization energies are shown to give unparalleled power to identify specific isomers. PMID:26981641

  20. Direct measurement of the energy thresholds to conformational isomerization. II. 3-indole-propionic acid and its water-containing complex.

    PubMed

    Clarkson, Jasper R; Baquero, Esteban; Zwier, Timothy S

    2005-06-01

    The methods of stimulated emission pumping-hole-filling spectroscopy (SEP-HFS) and population transfer spectroscopy (SEP-PTS) were used to place direct experimental bounds on the energetic barriers to conformational isomerization in 3-indole-propionic acid (IPA) and its water-containing complex. By contrast with tryptamine (Paper I), IPA has only two conformations with significant population in them. The structures of the two conformers are known from previous work [P. M. Felker, J. Phys. Chem. 96, 7844 (1992)]. The energy thresholds for A-->B and B-->A isomerizations are placed at 854 and 754 cm(-1), respectively. Lower bounds on the isomerization barrier in the two directions are determined from the last transition not observed in the SEP-PT spectra. These are placed at 800 and 644 cm(-1) for A-->B and B-->A, respectively. The combined results place bounds on the relative energies of the A and B minima, with E(B)-E(A)=46-210 cm(-1). Like the IPA monomer, the IPA-H2O complex forms two conformational isomers. Both these isomers incorporate the water molecule as a bridge between the carbonyl and OH groups of the carboxylic acid. Previous rotational coherence measurements (L. L. Connell, Ph.D. thesis, UCLA, 1991) have determined that these complexes retain the same IPA conformational structure as the monomers. SEP-PTS and SEP-HFS were carried out on the IPA-H2O complexes. It was demonstrated that it is possible to use SEP to drive conformational isomerization between the two conformational isomers of IPA-H2O. Bounds on the energy barriers to conformational isomerization are not effected greatly by the presence of the water molecule, with Ebarrier(A-->B)=771-830 cm(-1) and Ebarrier(B-->A)=583-750 cm(-1). This is a simple consequence of the fact that the barrier is an intramolecular barrier, and the water molecule is held fixed in the COOH pocket, where it interacts with the ring only peripherally during the isomerization process. Finally, changes in the SEP