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Sample records for 94ag isomeric states

  1. 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.

  2. 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.

  3. New isomeric state in {sup 116}Ag

    SciTech Connect

    Batchelder, J.C.; Carter, H.K.; Spejewski, E.H.; Bingham, C.R.; Fong, D.; Hamilton, J.H.; Hwang, J.K.; Ramayya, A.V.; Garrett, P.E.; Hartley, D.J.; Krolas, W.; Kulp, W.D.; Wood, J.L.; Larochelle, Y.; Tantawy, M.N.; Piechaczek, A.

    2005-10-01

    A new isomer in {sup 116}Ag with a half-life of 20(1) s has been discovered through the use of conversion electron, {beta}, and {gamma} spectroscopy of on-line mass-separated radioactivities at the Holifield Radioactive Ion Beam Facility at ORNL. The observed electron peaks at 22.5, 44.42, and 47.33 keV were interpreted as the K,L, and M conversion electron lines resulting from a 47.9-keV E3 transition associated with the decay of a second isomeric level in {sup 116}Ag. A new level structure of {sup 116}Ag is proposed, with the levels identified as the 0{sup -} ground-state and isomers at 47.9 and 128.8 keV having spin/parities of 3{sup +} and 6{sup -} respectively.

  4. 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)

  5. 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

  6. 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.

  7. Proton-proton correlations observed in two-proton radioactivity of 94Ag.

    PubMed

    Mukha, Ivan; Roeckl, Ernst; Batist, Leonid; Blazhev, Andrey; Döring, Joachim; Grawe, Hubert; Grigorenko, Leonid; Huyse, Mark; Janas, Zenon; Kirchner, Reinhard; La Commara, Marco; Mazzocchi, Chiara; Tabor, Sam L; Van Duppen, Piet

    2006-01-19

    The stability and spontaneous decay of naturally occurring atomic nuclei have been much studied ever since Becquerel discovered natural radioactivity in 1896. In 1960, proton-rich nuclei with an odd or an even atomic number Z were predicted to decay through one- and two-proton radioactivity, respectively. The experimental observation of one-proton radioactivity was first reported in 1982, and two-proton radioactivity has now also been detected by experimentally studying the decay properties of 45Fe (refs 3, 4) and 54Zn (ref. 5). Here we report proton-proton correlations observed during the radioactive decay of a spinning long-lived state of the lightest known isotope of silver, 94Ag, which is known to undergo one-proton decay. We infer from these correlations that the long-lived state must also decay through simultaneous two-proton emission, making 94Ag the first nucleus to exhibit one- as well as two-proton radioactivity. We attribute the two-proton emission behaviour and the unexpectedly large probability for this decay mechanism to a very large deformation of the parent nucleus into a prolate (cigar-like) shape, which facilitates emission of protons either from the same or from opposite ends of the 'cigar'.

  8. 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.

  9. Half-life measurements of isomeric states populated in projectile fragmentation

    SciTech Connect

    Bowry, M.; Podolay, Zs.

    2012-10-20

    The half-lives of excited isomeric states observed in {sup 195}Au, {sup 201}Tl and {sup 215}Rn are reported for the first time. Delayed {gamma}-rays were correlated with nuclei produced in the projectile fragmentation of relativistic {sup 238}U ions, unambiguously identified in terms of their atomic number (Z) and mass-to-charge ratio (A/Q) after traversing an in-flight separator. The observation of a long-lived isomeric state in {sup 195}Au with t{sub 1/2} = 16{sub -4}{sup +8}{mu}s is presented. Two shorter-lived isomeric states were detected in {sup 201}Tl and {sup 215}Rn with t{sub 1/2} = 95{sub -21}{sup +39} and 57{sub -12}{sup +21} ns respectively. In total 24 isomeric states were identified in different nuclei from Pt to Rn (A {approx} 200) during the current study, the majority of which were previously reported. The wealth of spectroscopic data provides the opportunity to determine the isomeric ratios over a wide range of Z, A and angular momentum (I h) of the reaction products. In particular, high-spin states with I Greater-Than-Or-Equivalent-To 18 h provide a robust test of theoretical models of fragmentation.

  10. 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.

  11. 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.

  12. 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.

  13. Calculation of the production cross sections of high-spin isomeric states in hafnium

    SciTech Connect

    Chadwick, M.B.; Young, P.G. . Nuclear Physics Lab.; Los Alamos National Lab., NM )

    1989-01-01

    The J{sup {pi}} = 16{sup +} isomeric state in {sup 178}Hf(E{sub x} = 2.447 MeV), which has a halflife of 31 years, poses a threat for serious radioactive activation problems in some fusion reactor designs if its production in 14-MeV neutron reactions is significant. The relatively high excitation energy (2.447 MeV) of this state results in it lying in the continuum region, so it is necessary in a calculation to reconstruct the salient nuclear structure around the state, particularly rotational band levels that might be populated and would feed into it. Using preequilibrium and Hauser-Feshbach statistical theories, the cross sections for this and other hafnium isomeric states are calculated and compared with experimental measurements, where available. 13 refs., 6 figs., 3 tabs.

  14. {alpha} decay of nuclei in the range 67{<=}Z{<=}91 from the ground state and isomeric state

    SciTech Connect

    Santhosh, K. P.; Joseph, Jayesh George; Sahadevan, Sabina

    2010-12-15

    The Coulomb and proximity potential model for deformed nuclei (CPPMDN) is used to study the favored and unfavored {alpha} decay of nuclei in the range 67{<=}Z{<=}91 from both the ground state (g.s.) and isomeric state (i.s.). The computed half-lives are in good agreement with experimental data. The standard deviation of half-life is found to be 0.44. Geiger-Nuttall (GN) plots for various parent isotopes are studied. It is found that all four types of transitions (g.s.{yields}g.s., g.s.{yields}i.s., i.s.{yields}g.s., i.s.{yields}i.s.) lie on a straight line. The isomeric state {alpha} decay shows a behavior similar to that of the ground state and the nuclear structure of the isomeric states imitates that of the ground states. Some predictions are done for {alpha} transition from both ground and isomeric states, which will be useful for future experiments.

  15. 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.

  16. Multi-quasiparticle high-K isomeric states in deformed nuclei

    NASA Astrophysics Data System (ADS)

    Xu, F. R.; Shi, Y.; Liu, H. L.; Liang, W. Y.; Walker, P. M.; Dracoulis, G. D.

    2016-09-01

    In the past years, we have made many theoretical investigations on multi-quasiparticle high-K isomeric states. A deformation-pairing-configuration self-consistent calculation has been developed by calculating a configuration-constrained multi-quasiparticle potential energy surface (PES). The specific single-particle orbits that define the high-K configuration are identified and tracked (adiabatically blocked) by calculating the average Nilsson numbers. The deformed Woods-Saxon potential was taken to give single-particle orbits. The configuration-constrained PES takes into account the shape polarization effect. Such calculations give good results on excitation energies, deformations and other structure information about multi-quasiparticle high-K isomeric states. Many different mass regions have been investigated.

  17. 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.

  18. 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.

  19. 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.

  20. Study of Shape Isomeric States in Fission Fragments

    NASA Astrophysics Data System (ADS)

    Pyatkov, Yu. V.; Kamanin, D. V.; Alexandrov, A. A.; Alexandrova, I. A.; Kondtatyev, N. A.; Kuznetsova, , E. A.; Strekalovsky, A. O.; Strekalovsky, O. V.; Zhuchko, V. E.; Mkaza, N.

    2015-06-01

    For the first time the brake-up of the fission fragments crossing metal foil was observed. The effect takes place predominantly in front impacts. To treat the data we suppose the bulk of the fragments from the conventional binary fission to be borne in shape-isomer states which look like di-nuclear systems with magic cores.

  1. 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.

  2. Subpicosecond Excited-State Proton Transfer Preceding Isomerization During the Photorecovery of Photoactive Yellow Protein

    PubMed Central

    Carroll, Elizabeth C.; Song, Sang-Hun; Kumauchi, Masato; van Stokkum, Ivo H. M.; Jailaubekov, Askat; Hoff, Wouter D.; Larsen, Delmar S.

    2010-01-01

    The ultrafast excited-state dynamics underlying the receptor state photorecovery is resolved in the M100A mutant of the photoactive yellow protein (PYP) from Halorhodospira halophila. The M100A PYP mutant, with its distinctly slower photocycle than wt PYP, allows isolation of the pB signaling state for study of the photodynamics of the protonated chromophore cis-p-coumaric acid. Transient absorption signals indicate a subpicosecond excited-state proton-transfer reaction in the pB state that results in chromophore deprotonation prior to the cis–trans isomerization required in the photorecovery dynamics of the pG state. Two terminal photoproducts are observed, a blue-absorbing species presumed to be deprotonated trans-p-coumaric acid and an ultraviolet-absorbing protonated photoproduct. These two photoproducts are hypothesized to originate from an equilibrium of open and closed folded forms of the signaling state, I2 and I2’. PMID:20953237

  3. Remeasurement of the Lifetime of the Isomeric 9/2+ State in 155Dy

    NASA Astrophysics Data System (ADS)

    Katajanheimo, R.; Siivola, A.; Liukkonen, E.; Hammarén, E.

    1982-12-01

    The isomeric 9/2+ state at 132.2 keV in the nucleus 155Dy has been populated through 3He bombardment (E = 27 MeV) of a 155Gd target. The half-life of the the 9/2+ level has been determined as 51 ± 3 ns. The decay modes of the 11/2-, 234.2 keV level have been confirmed. For both levels the hindrance factors calculated with the particle-rotor model have been compared with other predictions available.

  4. 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 )% .

  5. 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.

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Gao, Fei; Weiland, Lisa Mauck; Kitchin, John

    2008-03-01

    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 CO II 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.

  9. 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)

  10. A dipole band above the Iπ= 31/2- isomeric state in 189Pb

    NASA Astrophysics Data System (ADS)

    Cullen, D. M.

    2016-09-01

    This contribution focuses on the new observation of a dipole band built upon an Iπ=31/2- isomeric state in 189Pb, identified using recoil-isomer tagging at the University of Jyväskylä, Finland. This is the lightest odd-mass Pb isotope in which a dipole band is known. By comparison with the heavier-mass dipole bands, the dipole band in 189Pb was deduced to be based upon a π {≤ft( {s1/2 - 2{h9/2}{i13/2}} right){{11^ - }}} otimes v{≤ft( {i13/2 - 1} right)13/{2^ + }} configuration. However, in the 189Pb dipole band, the initial aligned angular momentum was larger than that exhibited by the dipole bands in the heavier-mass isotopes. This may be evidence for a reduced repulsive proton/neutron-hole interaction in 189Pb.

  11. Isomeric and ground state energy level measurements of natural tellurium isotopes via (γ,n) reaction

    NASA Astrophysics Data System (ADS)

    Tamkas, M.; Akcali, O.; Durusoy, A.

    2015-04-01

    We have planned to measure isomeric and ground state energy levels in 120Te(γ,n)119m,gTe, 122Te(γ,n)121m,gTe, 128Te(γ,n)127m,gTe, 130Te(γ,n)129m,gTe photonuclear reactions of natural tellurium induced by bremsstrahlung photons with end-point energy at 18 MeV. The sample was irradiated in the clinical linear electron accelerator (Philips SLi-25) at Akdeniz University Hospital. The gamma spectrum of the tellurium sample was measured using HP(Ge) semiconductor detector (ORTEC) and multi channel analyzer. We used both MAESTRO (ORTEC) and home made root based gui program (Theia) for data analyzing. The obtained experimental data values are compared with NUDAT energy values.

  12. 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.

  13. 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

  14. 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.

  15. Effect of nuclear-reaction mechanisms on the population of excited nuclear states and isomeric ratios

    NASA Astrophysics Data System (ADS)

    Skobelev, N. K.

    2016-07-01

    Experimental data on the cross sections for channels of fusion and transfer reactions induced by beams of radioactive halo nuclei and clustered and stable loosely bound nuclei were analyzed, and the results of this analysis were summarized. The interplay of the excitation of single-particle states in reaction-product nuclei and direct reaction channels was established for transfer reactions. Respective experiments were performed in stable (6Li) and radioactive (6He) beams of the DRIBs accelerator complex at the Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, and in deuteron and 3He beams of the U-120M cyclotron at the Nuclear Physics Institute, Academy Sciences of Czech Republic (Řež and Prague, Czech Republic). Data on subbarrier and near-barrier fusion reactions involving clustered and loosely bound light nuclei (6Li and 3He) can be described quite reliably within simple evaporation models with allowance for different reaction Q-values and couple channels. In reactions involving halo nuclei, their structure manifests itself most strongly in the region of energies below the Coulomb barrier. Neutron transfer occurs with a high probability in the interactions of all loosely bound nuclei with light and heavy stable nuclei at positive Q-values. The cross sections for such reactions and the respective isomeric ratios differ drastically for nucleon stripping and nucleon pickup mechanisms. This is due to the difference in the population probabilities for excited single-particle states.

  16. 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.

  17. Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide.

    PubMed

    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. PMID:19694484

  18. 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.

  19. Thorium silicate compound as a solid-state target for production of isomeric thorium-229 nuclei by electron beam irradiation

    NASA Astrophysics Data System (ADS)

    Borisyuk, P. V.; Vasilyev, O. S.; Lebedinskii, Y. Y.; Krasavin, A. V.; Tkalya, E. V.; Troyan, V. I.; Habibulina, R. F.; Chubunova, E. V.; Yakovlev, V. P.

    2016-09-01

    In this paper, we discuss an idea of the experiment for excitation of the isomeric transition in thorium-229 nuclei by irradiating with electron beam targets with necessary physical characteristics. The chemical composition and bandgap of ThSi10O22 were determined by X-ray photoelectron spectroscopy and reflection electron energy loss spectroscopy. It was found that the energy gap is equal to 7.7 eV and does not change when the target is exposed to a medium energy electron beam for a long time. This indicates that the compound possesses high electron-beam resistance. A quantitative estimation of the output function of isomeric thorium-229 nuclei generated by interaction of nuclei with the secondary electron flow formed by irradiating the solid-state ThSi10O22-based target is given. The estimation shows that ThSi10O22 is a promising thorium-containing target for investigating excitation of the nuclear low-lying isomeric transition in the thorium-229 isotope using medium-energy electrons.

  20. 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.

  1. 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.

  2. 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.

  3. Excitation of 11/2- isomeric state in 137Ce in (γ,n) reaction within 10-22MeV energy range

    NASA Astrophysics Data System (ADS)

    Mazur, V. M.; Bigan, Z. M.; Derechkey, P. S.; Symochko, D. M.

    2016-09-01

    Isomeric yields ratios and energy differential cross-section of metastable state excitation in the 138Ce(γ,n)137m,gCe reaction has been studied in the 10-22MeV end-point energy range of bremsstrahlung beams. Experimental data are compared with Hauser-Feshbach calculations performed with TALYS-1.6 statistical model code.

  4. Multipath variational transition state theory: rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical.

    PubMed

    Yu, Tao; Zheng, Jingjing; Truhlar, Donald G

    2012-01-12

    We propose a new formulation of variational transition state theory called multipath variational transition state theory (MP-VTST). We employ this new formulation to calculate the forward and reverse thermal rate constant of the 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical in the gas phase. First, we find and optimize all the local-minimum-energy structures of the reaction, product, and transition state. Then, for the lowest-energy transition state structures, we calculate the reaction path by using multiconfiguration Shepard interpolation (MSCI) method to represent the potential energy surface, and, from this representation, we also calculate the ground-state vibrationally adiabatic potential energy curve, the reaction-path curvature vector, and the generalized free energy of activation profile. With this information, the path-averaged generalized transmission coefficients <γ> are evaluated. Then, thermal rate constant containing the multiple-structure anharmonicity and torsional anharmonicity effects is calculated using multistructural transition state theory (MS-TST). The final MP-VTST thermal rate constant is obtained by multiplying k(MS-T)(MS-TST) by <γ>. In these calculations, the M06 density functional is utilized to compute the energy, gradient, and Hessian at the Shepard points, and the M06-2X density functional is used to obtain the structures (conformers) of the reactant, product, and the saddle point for computing the multistructural anharmonicity factors.

  5. 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

  6. 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.

  7. Proposed experimental method to determine alpha sensitivity of splitting between ground and 7.6 eV isomeric states in 229Th.

    PubMed

    Berengut, J C; Dzuba, V A; Flambaum, V V; Porsev, S G

    2009-05-29

    The 7.6 eV electromagnetic transition between the nearly degenerate ground state and first excited state in the 229Th nucleus may be very sensitive to potential changes in the fine-structure constant, alpha=e2/variant Planck's over 2pic. However, the sensitivity is not known, and nuclear calculations are currently unable to determine it. We propose measurements of the differences of atomic transition frequencies between thorium atoms (or ions) with the nucleus in the ground state and in the first excited (isomeric) state. This will enable extraction of the change in nuclear charge radius and electric-quadrupole moment between the isomers, and hence the alpha dependence of the isomeric transition frequency with reasonable accuracy.

  8. 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.

  9. Photophysics of the Red Chromophore of HcRed: Evidence for Cis-Trans Isomerization and Protonation-State Changes

    SciTech Connect

    Cotlet, M.; Mudalige, K.; Habuchi, S.; Goodwin, P.M.; Pai, R.K.; De Schryver, F.

    2010-03-15

    HcRed is a dimeric intrinsically fluorescent protein with origins in the sea anemone Heteractis crispa. This protein exhibits deep red absorption and emission properties. Using a combination of ensemble and single molecule methods and by varying environmental parameters such as temperature and pH, we found spectroscopic evidence for the presence of two ground state conformers, trans and cis chromophores that are in thermal equilibrium and that follow different excited-state pathways upon exposure to light. The photocycle of HcRed appears to be a combination of both kindling proteins and bright emitting GFP/GFP-like proteins: the trans chromophore undergoes light driven isomerization followed by radiative relaxation with a fluorescence lifetime of 0.5 ns. The cis chromophore exhibits a photocycle similar to bright GFPs and GFP-like proteins such as enhanced GFP, enhanced YFP or DsRed, with radiative relaxation with a fluorescence lifetime of 1.5 ns, singlet-triplet deactivation on a microsecond time scale and solvent controlled protonation/deprotonation in tens of microseconds. Using single molecule spectroscopy, we identify trans and cis conformers at the level of individual moieties and show that it is possible that the two conformers can coexist in a single protein due to the dimeric nature of HcRed.

  10. Experiments with neutron-rich isomeric beams

    SciTech Connect

    Rykaczewski, K. |; Grzywacz, R. |; Lewitowicz, M.; Pfuetzner, M.; Grawe, H.

    1998-01-01

    A review of experimental results obtained on microsecond-isomeric states in neutron-rich nuclei produced in fragmentation reactions and studied with SISSI-Alpha-LISE3 spectrometer system at GANIL Caen is given. The perspectives of experiments based on secondary reactions with isomeric beams are presented.

  11. A theoretical study of the solid-state thermal isomerization reaction of methyl 4-(dimethylamino)benzenesulfonate in the energetic aspect

    NASA Astrophysics Data System (ADS)

    Oda, Masao; Sato, Naoki

    1997-08-01

    The thermal isomerization reaction from methyl 4-(dimethylamino)benzenesulfonate (MDBS) to N,N,N-trimethylbenzenaminium-4-sulfonate (TBS) in the crystalline state has been studied to understand the origin of its exothermic nature. Ab initio MO calculations of these molecules with their molecular geometries realized in crystals and recalculations of coulombic contributions to the lattice energies based on those results show that the heat exhausted by the solid-state reaction of interest can be elucidated by the lattice energy of TBS, which is much higher than that of MDBS, although the energetic stability of a TBS zwitterion is lower than that of MDBS.

  12. 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.

  13. 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.

  14. 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…

  15. 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

  16. Isomeric states observed in heavy neutron-rich nuclei populated in the fragmentation of a 208Pb beam

    NASA Astrophysics Data System (ADS)

    Steer, S. J.; Podolyák, Zs.; Pietri, S.; Górska, M.; Grawe, H.; Maier, K. H.; Regan, P. H.; Rudolph, D.; Garnsworthy, A. B.; Hoischen, R.; Gerl, J.; Wollersheim, H. J.; Becker, F.; Bednarczyk, P.; Cáceres, L.; Doornenbal, P.; Geissel, H.; Grębosz, J.; Kelic, A.; Kojouharov, I.; Kurz, N.; Montes, F.; Prokopwicz, W.; Saito, T.; Schaffner, H.; Tashenov, S.; Heinz, A.; Pfützner, M.; Kurtukian-Nieto, T.; Benzoni, G.; Jungclaus, A.; Balabanski, D. L.; Bowry, M.; Brandau, C.; Brown, A.; Bruce, A. M.; Catford, W. N.; Cullen, I. J.; Dombrádi, Zs.; Estevez, M. E.; Gelletly, W.; Ilie, G.; Jolie, J.; Jones, G. A.; Kmiecik, M.; Kondev, F. G.; Krücken, R.; Lalkovski, S.; Liu, Z.; Maj, A.; Myalski, S.; Schwertel, S.; Shizuma, T.; Walker, P. M.; Werner-Malento, E.; Wieland, O.

    2011-10-01

    Heavy neutron-rich nuclei were populated via the fragmentation of a E/A=1 GeV 20882Pb beam. Secondary fragments were separated and identified and subsequently implanted in a passive stopper. By the detection of delayed γ rays, isomeric decays associated with these nuclei have been identified. A total of 49 isomers were detected, with the majority of them observed for the first time. The newly discovered isomers are in 204,20580Hg, 201,202,204,20579Au, 197,203,20478Pt, 195,199-20377Ir, 193,197-19976Os, 19675Re, 190,19174W, and 18973Ta. Possible level schemes are constructed and the structure of the nuclei discussed. To aid the interpretation, shell-model as well as BCS calculations were performed.

  17. 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.

  18. 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.

  19. 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.

  20. The importance of being isomeric.

    PubMed

    Anderson, Robert H; Brown, Nigel A; Meno, Chikara; Spicer, Diane E

    2015-05-01

    In the normal individual, the parietal components of the body are mirror-imaged and appropriately described as isomeric. The thoraco-abdominal organs, in contrast, are lateralized. However, in "visceral heterotaxy," the thoraco-abdominal organs also show some degree of isomerism, best seen in the arrangement of the bronchial tree. Whether isomerism can be found within the heart remains controversial. One of two recent publications in this journal emphasized the crucial features of bronchial isomerism; the other, in contrast, confused the situation of isomerism within the heart. In this review, we show how the topic of cardiac isomerism is clarified by concentrating on the anatomical features of the cardiac components and determining how best they can be described. Appropriate manipulation of developing mice produces unequivocal evidence of isomerism of the atrial appendages, but with no evidence of ventricular isomerism. In hearts from patients with so-called "heterotaxy," only the atrial appendages, distinguished on the basis of the pectinate muscles lining their walls, are uniformly isomeric, permitting the syndrome to be differentiated into the subsets of left as opposed to right atrial appendage isomerism. Thus, controversies are defused by simply describing the isomerism of the atrial appendages rather than "atrial isomerism," recognizing the frequency of abnormal venoatrial connections in these settings. Any suggestion of ambiguity is removed by the equally simple expedient of describing all the variable cardiac features, describing the arrangements of the thoracic and abdominal organs separately should there be discordances. PMID:25782978

  1. Low-lying isomeric state in {sup 80}Ga from the {beta}{sup -} decay of {sup 80}Zn

    SciTech Connect

    LicA, R.; Marginean, N.; Ghita, D.G.; and others

    2012-10-20

    A new level scheme was constructed for {sup 80}Ga which is significantly different from the one previously reported. The excitation energy of a new low-lying state recently reported in [2] was identified at 22.4 keV. Properties of the level scheme suggest that the ground state has spin J = 6 and the first excited state has spin J = 3. The spin assignments are in agreement with laser spectroscopy values previously measured. Our work provides the first evidence for the J = 6 being the ground state.

  2. Systematic study of favored α -decay half-lives of closed shell odd-A and doubly-odd nuclei related to ground and isomeric states

    NASA Astrophysics Data System (ADS)

    Sun, Xiao-Dong; Guo, Ping; Li, Xiao-Hua

    2016-08-01

    In this work, we systematically investigate the favored α -decay half-lives and α preformation probabilities of both odd-A and doubly-odd nuclei related to ground and isomeric states around the doubly magic cores at Z =82 , N =82 and at Z =82 , N =126 , respectively, within a two-potential approach from the view of the valence nucleon (or hole). The results show that the α preformation probability is linearly related to NpNn or NpNnI , where Np, Nn, and I are the number of valence protons (or holes), the number of valence neutrons (or holes), and the isospin of the parent nucleus, respectively. Fitting the α preformation probabilities data extracted from the differences between experimental data and calculated half-lives without a shell correction, we give two analytic formulas of the α preformation probabilities and the values of corresponding parameters. Using those formulas and the parameters, we calculate the α -decay half-lives for those nuclei. The calculated results can well reproduce the experimental data.

  3. Multi-Structural Variational Transition State Theory. Kinetics of the 1,4-Hydrogen Shift Isomerization of the Pentyl Radical with Torsional Anharmonicity

    SciTech Connect

    Yu, T.; Zheng, J.; Truhlar, D. G.

    2011-01-01

    We present a new formulation of variational transition state theory (VTST) called multi-structural VTST (MS-VTST) and the use of this to calculate the rate constant for the 1,4-hydrogen shift isomerization reaction of 1-pentyl radical and that for the reverse reaction. MS-VTST uses a multi-faceted dividing surface and provides a convenient way to include the contributions of many structures (typically conformers) of the reactant and the transition state in rate constant calculations. In this particular application, we also account for the torsional anharmonicity. We used the multi-configuration Shepard interpolation method to efficiently generate a semi-global portion of the potential energy surface from a small number of high-level electronic structure calculations using the M06 density functional in order to compute the energies and Hessians of Shepard points along a reaction path. The M06-2X density functional was used to calculate the multi-structural anharmonicity effect, including all of the structures of the reactant, product and transition state. To predict the thermal rate constant, VTST calculations were performed to obtain the canonical variational rate constant over the temperature range 200–2000 K. A transmission coefficient is calculated by the multidimensional small-curvature tunneling (SCT) approximation. The final MS-CVT/SCT thermal rate constant was determined by combining a reaction rate calculation in the single-structural harmonic oscillator approximation (including tunneling) with the multi-structural anharmonicity torsional factor. The calculated forward rate constant agrees very well with experimentally-based evaluations of the high-pressure limit for the temperature range 300–1300 K, although it is a factor of 2.5–3.0 lower than the single-structural harmonic oscillator approximation over this temperature range. We anticipate that MS-VTST will be generally useful for calculating the reaction rates of complex molecules with multiple

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Theoretical and Experimental Evidence of Hydrogen Migration rather than Isomerization in the Acetylene Dication

    NASA Astrophysics Data System (ADS)

    Liekhus-Schmaltz, Chelsea; Li, Zheng; Petrovic, Vladimir; Martinez, Todd; Bucksbaum, Phil; AMO75113 Collaboration

    2016-05-01

    Theoretical calculations and experimental results in the acetylene dication have long agreed that isomerization after x-ray excitation occurs in the first singlet state, where the carbon-carbon bond lives long enough for isomerization to complete. These same calculations predict that a large barrier to isomerization exists that would cause isomerization to occur in about a picosecond, while there is some evidence for ultrafast isomerization in under 100 fs. However, new ab initio calculations of the acetylene dication reveal that ultrafast isomerization after x-ray excitation is unlikely. In this talk, we present evidence that signatures of hydrogen migration observed in recent time resolved LCLS data are mostly due to hydrogen migration in an excited state which dissociates too quickly for isomerization to complete. This material is based upon work supported by the National Science Foundation under Grant No. PHY-0649578.

  9. 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.

  10. 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.

  11. 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.

  12. Exercises in anatomy: cardiac isomerism.

    PubMed

    Anderson, Robert H; Sarwark, Anne E; Spicer, Diane E; Backer, Carl L

    2014-01-01

    It is well recognized that the patients with the most complex cardiac malformations are those with so-called visceral heterotaxy. At present, it remains a fact that most investigators segregate these patients on the basis of their splenic anatomy, describing syndromes of so-called asplenia and polysplenia. It has also been known for quite some time, nonetheless, that the morphology of the tracheobronchial tree is usually isomeric in the setting of heterotaxy. And it has been shown that the isomerism found in terms of bronchial arrangement correlates in a better fashion with the cardiac anatomy than does the presence of multiple spleens, or the absence of any splenic tissue. In this exercise in anatomy, we use hearts from the Idriss archive of Lurie Children's Hospital in Chicago to demonstrate the isomeric features found in the hearts obtained from patients known to have had heterotaxy. We first demonstrate the normal arrangements, showing how it is the extent of the pectinate muscles in the atrial appendages relative to the atrioventricular junctions that distinguishes between morphologically right and left atrial chambers. We also show the asymmetry of the normal bronchial tree, and the relationships of the first bronchial branches to the pulmonary arteries supplying the lower lobes of the lungs. We then demonstrate that diagnosis of multiple spleens requires the finding of splenic tissue on either side of the dorsal mesogastrium. Turning to hearts obtained from patients with heterotaxy, we illustrate isomeric right and left atrial appendages. We emphasize that it is only the appendages that are universally isomeric, but point out that other features support the notion of cardiac isomerism. We then show that description also requires a full account of veno-atrial connections, since these can seemingly be mirror-imaged when the arrangement within the heart is one of isomerism of the atrial appendages. We show how failure to recognize the presence of such isomeric

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. Mechanistic imperatives for aldose-ketose isomerization in water: specific, general base- and metal ion-catalyzed isomerization of glyceraldehyde with proton and hydride transfer.

    PubMed

    Nagorski, R W; Richard, J P

    2001-02-01

    The deuterium enrichment of dihydroxyacetone obtained from the aldose-ketose isomerization of D,L-glyceraldehyde in D(2)O at 25 degrees C was determined by (1)H NMR spectroscopy from the integrated areas of the signals for the alpha-CH(2) and alpha-CHD groups of the product. One mole equivalent of deuterium is incorporated into the product when the isomerization is carried out in 150 mM pyrophosphate buffer at pD 8.4, but only 0.6 mol equiv of deuterium is incorporated into the product of isomerization in the presence of 0.01 M deuterioxide ion, so that 40% of the latter isomerization reaction proceeds by the intramolecular transfer of hydride ion. Several pathways were identified for catalysis of the isomerization of glyceraldehyde to give dihydroxyacetone. The isomerization with hydride transfer is strongly catalyzed by added Zn(2+). Deprotonation of glyceraldehyde is rate-determining for isomerization with proton transfer, and this proton-transfer reaction is catalyzed by Brønsted bases. Proton transfer also occurs by a termolecular pathway with catalysis by the combined action of Brønsted bases and Zn(2+). These results show that there is no large advantage to the spontaneous isomerization of glyceraldehyde in alkaline solution with either proton or hydride transfer, and that effective catalytic pathways exist to stabilize the transition states for both of these reactions in water. The existence of separate enzymes that catalyze the isomerization of sugars with hydride transfer and the isomerization of sugar phosphates with proton transfer is proposed to be a consequence of the lack of any large advantage to reaction by either of these pathways for the corresponding nonenzymatic isomerization in water.

  18. 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.

  19. 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.

  20. Simple, chemoselective, catalytic olefin isomerization.

    PubMed

    Crossley, Steven W M; Barabé, Francis; Shenvi, Ryan A

    2014-12-01

    Catalytic amounts of Co(Sal(tBu,tBu))Cl and organosilane irreversibly isomerize terminal alkenes by one position. The same catalysts effect cycloisomerization of dienes and retrocycloisomerization of strained rings. Strong Lewis bases like amines and imidazoles, and labile functionalities like epoxides, are tolerated.

  1. Theoretical aspects of cephalosporin isomerism

    SciTech Connect

    Pop, E.; Brewster, M.E.; Bodor, N. Univ. of Florida, Gainesville ); Kaminski, J.J. )

    1989-01-01

    The {triangle}{sup 3} double bond of cephalosporins isomerizes to the {triangle}{sup 2} position, resulting in biological inactivation of these antibiotics. This phenomenon occurs slowly in the case of cephalosporanic acids, but is rapid when the 4-carboxylate moiety is esterified or otherwise derivatized, leading to an equilibrium between the {triangle}{sup 2} and {triangle}{sup 3} forms. A theoretical study of this isomerization is described in the framework of two semiempirical all-valence electron molecular orbital (MO) approximations, namely MNDO and AMI. Specifically, the methyl ester and free carboxylate derivatives of both the {triangle}{sup 3} and {triangle}{sup 2} isomers of 7-phenylacetamidocephalosporin were studied. The results obtained indicated that the {triangle}{sup 3} derivatives were thermodynamically more stable than were the {triangle}{sup 2} isomers both in the case of the free acids and methyl esters. These data are consistent with experimental findings and suggest that the more rapid isomerization demonstrated in the case of the esters is due primarily to kinetic rather than to thermodynamic factors. Examination of the calculated molecular structures lend support to various theories that correlate the inactivity of the {triangle}{sup 2} isomers with spatial considerations and the degree of {beta}-lactam amide resonance.

  2. Trans-cis isomerization of lipophilic dyes probing membrane microviscosity in biological membranes and in live cells.

    PubMed

    Chmyrov, Volodymyr; Spielmann, Thiemo; Hevekerl, Heike; Widengren, Jerker

    2015-06-01

    Membrane environment and fluidity can modulate the dynamics and interactions of membrane proteins and can thereby strongly influence the function of cells and organisms in general. In this work, we demonstrate that trans-cis isomerization of lipophilic dyes is a useful parameter to monitor packaging and fluidity of biomembranes. Fluorescence fluctuations, generated by trans-cis isomerization of the thiocarbocyanine dye Merocyanine 540 (MC540), were first analyzed by fluorescence correlation spectroscopy (FCS) in different alcohol solutions. Similar isomerization kinetics of MC540 in lipid vesicles could then also be monitored, and the influence of lipid polarity, membrane curvature, and cholesterol content was investigated. While no influence of membrane curvature and lipid polarity could be observed, a clear decrease in the isomerization rates could be observed with increasing cholesterol contents in the vesicle membranes. Finally, procedures to spatially map photoinduced and thermal isomerization rates on live cells by transient state (TRAST) imaging were established. On the basis of these procedures, MC540 isomerization was studied on live MCF7 cells, and TRAST images of the cells at different temperatures were found to reliably detect differences in the isomerization parameters. Our studies indicate that trans-cis isomerization is a useful parameter for probing membrane dynamics and that the TRAST imaging technique can provide spatial maps of photoinduced isomerization as well as both photoinduced and thermal back-isomerization, resolving differences in local membrane microviscosity in live cells.

  3. Catalysis of protein disulfide bond isomerization in a homogeneous substrate.

    PubMed

    Kersteen, Elizabeth A; Barrows, Seth R; Raines, Ronald T

    2005-09-13

    Protein disulfide isomerase (PDI) catalyzes the rearrangement of nonnative disulfide bonds in the endoplasmic reticulum of eukaryotic cells, a process that often limits the rate at which polypeptide chains fold into a native protein conformation. The mechanism of the reaction catalyzed by PDI is unclear. In assays involving protein substrates, the reaction appears to involve the complete reduction of some or all of its nonnative disulfide bonds followed by oxidation of the resulting dithiols. The substrates in these assays are, however, heterogeneous, which complicates mechanistic analyses. Here, we report the first analysis of disulfide bond isomerization in a homogeneous substrate. Our substrate is based on tachyplesin I, a 17-mer peptide that folds into a beta hairpin stabilized by two disulfide bonds. We describe the chemical synthesis of a variant of tachyplesin I in which its two disulfide bonds are in a nonnative state and side chains near its N and C terminus contain a fluorescence donor (tryptophan) and acceptor (N(epsilon)-dansyllysine). Fluorescence resonance energy transfer from 280 to 465 nm increases by 28-fold upon isomerization of the disulfide bonds into their native state (which has a lower E(o') = -0.313 V than does PDI). We use this continuous assay to analyze catalysis by wild-type human PDI and a variant in which the C-terminal cysteine residue within each Cys-Gly-His-Cys active site is replaced with alanine. We find that wild-type PDI catalyzes the isomerization of the substrate with kcat/K(M) = 1.7 x 10(5) M(-1) s(-1), which is the largest value yet reported for catalysis of disulfide bond isomerization. The variant, which is a poor catalyst of disulfide bond reduction and dithiol oxidation, retains virtually all of the activity of wild-type PDI in catalysis of disulfide bond isomerization. Thus, the C-terminal cysteine residues play an insignificant role in the isomerization of the disulfide bonds in nonnative tachyplesin I. We conclude

  4. Femtosecond Isomerization Dynamics in the Ethylene Molecule

    NASA Astrophysics Data System (ADS)

    Belkacem, Ali

    2009-05-01

    The ethylene molecule plays a fundamental and prototypical role for the understanding of photo-isomerizaton processes and particularly for ultrafast energy conversion through nonadiabatic transitions and state crossing via conical intersections. We have developed a high power femtosecond laser based pump-probe system to study femtosecond isomerization dynamics in various model molecules. By focusing 25-mJ laser pulses into a 5-cm-long xenon-filled gas cell, we can deliver about 10^9 photons per harmonic per pulse onto a target gas, with the photons ranging in energy from 8 to 40 eV. In this talk I will present the results of our studies of the dynamics in the excited ethylene cation (C2H4^+) using a high intensity high harmonic source. The dynamics in the excited ethylene cation leads, among other channels, to isomerization to the ethyledene configuration (CH3CH^+), which is predicted to be a transient configuration for electronic relaxation. With an intense femtosecond EUV pulse as pump, and a NIR (near infra-red) pulse as probe, we measure a time scale of 45±10 fs for formation of the transient ethylidene configuration (lifetime of 60±15 fs ) through detection of the NIR-induced fragmentation to CH3^+ and CH^+. Also, a H2-stretch transient configuration (believed to succeed ethylidene), yielding H2^+, is found to be populated after 100±10 fs. These studies were also extended to excited state dynamics in the neutral ethylene using a recently developed split mirror technique enabling XUV pump - XUV probe capability. In order to achieve this we optimized our high harmonic system for high power in order to produce a very intense source of high harmonics that allows multiphoton (XUV) absorption by a single molecule. In particular, we were able to measure two-photon double-ionization of Ethelyne and argon and three-photon double ionization of neon.

  5. Intersystem Crossing Pathway in Quinoline-Pyrazole Isomerism: A Time-Dependent Density Functional Theory Study on Excited-State Intramolecular Proton Transfer.

    PubMed

    Liu, Yu-Hui; Lan, Sheng-Cheng; Zhu, Chaoyuan; Lin, Sheng-Hsien

    2015-06-18

    The dynamics of the excited-state intramolecular proton-transfer (ESIPT) reaction of quinoline-pyrazole (QP) isomers, designated as QP-I and QP-II, has been investigated by means of time-dependent density functional theory (TDDFT). A lower barrier has been found in the potential energy curve for the lowest singlet excited state (S1) along the proton-transfer coordinate of QP-II compared with that of QP-I; however, this is at variance with a recent experimental report [J. Phys. Chem. A 2010, 114, 7886-7891], in which the authors proposed that the ESIPT reaction would only proceed in QP-I due to the absence of a PT emission for QP-II. Therefore, several deactivating pathways have been investigated to determine whether fluorescence quenching occurs in the PT form of QP-II (PT-II). The S1 state of PT-II has nπ* character, which is a well-known dark state. Moreover, the energy gap between the S1 and T2 states is only 0.29 eV, implying that an intersystem crossing (ISC) process would occur rapidly following the ESIPT reaction. Therefore, it is demonstrated that the ESIPT could successfully proceed in QP-II and that the PT emission would be quenched by the ISC process.

  6. 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.

  7. 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

  8. 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.

  9. Isomerization reactions on single adsorbed molecules.

    PubMed

    Morgenstern, Karina

    2009-02-17

    Molecular switches occur throughout nature. In one prominent example, light induces the isomerization of retinal from the compact 11-cis form to the elongated all-trans form, a conversion that triggers the transformation of light into a neural impulse in the eye. Applying these natural principles to synthetic systems offers a promising way to construct smaller and faster nanoelectronic devices. In such systems, electronic switches are essential components for storage and logical operations. The development of molecular switches on the single-molecule level would represent a major step toward incorporating molecules as building units into nanoelectronic circuits. Molecular switches must be both reversible and bistable. To meet these requirements, a molecule must have at least two different thermally stable forms and a way to repeatedly interconvert between those forms based on changes in light, heat, pressure, magnetic or electric fields, pH, mechanical forces, or electric currents. The conversion should be connected to a measurable change in electronic, optical, magnetic, or mechanical properties. Because isomers can differ significantly in physical and chemical properties, isomerization could serve as a molecular switching mechanism. Integration of molecular switches into larger circuits will probably require arranging them on surfaces, which will require a better understanding of isomerization reactions in these environments. In this Account, we describe our scanning tunneling microscopy studies of the isomerization of individual molecules adsorbed on metal surfaces. Investigating chlorobenzene and azobenzene derivatives on the fcc(111) faces of Ag, Cu, and Au, we explored the influence of substituents and the substrate on the excitation mechanism of the isomerization reaction induced by inelastically tunneling electrons. We achieved an irreversible configurational (cis-trans) isomerization of individual 4-dimethyl-amino-azobenzene-4-sulfonic acid molecules on Au

  10. 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.

  11. 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

  12. 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

  13. Ultrafast structural dynamics and isomerization in Rydberg-exited Quadricyclane

    SciTech Connect

    Rudakov, Fedor M

    2012-01-01

    The quadricyclane - norbornadiene system is an important model for the isomerization dynamics between highly strained molecules. In a breakthrough observation for a polyatomic molecular system of that complexity, we follow the photoionization from Rydberg states in the time-domain to derive a measure for the time-dependent structural dynamics and the time-evolving structural dispersion even while the molecule is crossing electronic surfaces. The photoexcitation to the 3s and 3p Rydberg states deposits significant amounts of energy into vibrational motions. We observe the formation and evolution of the vibrational wavepacket on the Rydberg surface and the internal conversion from the 3p Rydberg states to the 3s state. In that state, quadricyclane isomerizes to norbornadiene with a time constant of {tau}{sub 2} = 136(45) fs. The lifetime of the 3p Rydberg state in quadricyclane is {tau}{sub 1} = 320(31) and the lifetime of the 3s Rydberg state in norbornadiene is {tau}{sub 3} = 394(32).

  14. Isomerization mechanism in hydrazone-based rotary switches: lateral shift, rotation, or tautomerization?

    PubMed

    Landge, Shainaz M; Tkatchouk, Ekatarina; Benítez, Diego; Lanfranchi, Don Antoine; Elhabiri, Mourad; Goddard, William A; Aprahamian, Ivan

    2011-06-29

    Two intramolecularly hydrogen-bonded arylhydrazone (aryl = phenyl or naphthyl) molecular switches have been synthesized, and their full and reversible switching between the E and Z configurations have been demonstrated. These chemically controlled configurational rotary switches exist primarily as the E isomer at equilibrium and can be switched to the protonated Z configuration (Z-H(+)) by the addition of trifluoroacetic acid. The protonation of the pyridine moiety in the switch induces a rotation around the hydrazone C=N double bond, leading to isomerization. Treating Z-H(+) with base (K(2)CO(3)) yields a mixture of E and "metastable" Z isomers. The latter thermally equilibrates to reinstate the initial isomer ratio. The rate of the Z → E isomerization process showed small changes as a function of solvent polarity, indicating that the isomerization might be going through the inversion mechanism (nonpolar transition state). However, the plot of the logarithm of the rate constant k vs the Dimroth parameter (E(T)) gave a linear fit, demonstrating the involvement of a polar transition state (rotation mechanism). These two seemingly contradicting kinetic data were not enough to determine whether the isomerization mechanism goes through the rotation or inversion pathways. The highly negative entropy values obtained for both the forward (E → Z-H(+)) and backward (Z → E) processes strongly suggest that the isomerization involves a polarized transition state that is highly organized (possibly involving a high degree of solvent organization), and hence it proceeds via a rotation mechanism as opposed to inversion. Computations of the Z ↔ E isomerization using density functional theory (DFT) at the M06/cc-pVTZ level and natural bond orbital (NBO) wave function analyses have shown that the favorable isomerization mechanism in these hydrogen-bonded systems is hydrazone-azo tautomerization followed by rotation around a C-N single bond, as opposed to the more common

  15. Nuclear moments of μ-second isomeric fragments at BigRIPS

    NASA Astrophysics Data System (ADS)

    Chevrier, R.; Daugas, J. M.; Gaudefroy, L.; Hass, M.; Haas, H.; Ueno, H.; Aoi, N.; Fukuda, N.; Ichikawa, Y.; Inabe, N.; Ishihara, M.; Kameda, D.; Kubo, T.; Ohnishi, T.; Takeda, H.; Watanabe, H.; Yoshimi, A.; Asahi, K.; Furukawa, T.; Hayashi, H.; Iijima, H.; Inoue, T.; Ishii, Y.; Nanao, T.; Suzuki, K.; Tsuchiya, M.; Balabanski, D. L.; Georgiev, G.; Cootenier, S.; Neyens, G.; Rajabali, M.

    2013-09-01

    The measurement of nuclear moments of a μ-second isomeric state have been successfully performed using the RIKEN Radioactive Ion Beam Facility. The Time Dependent Perturbed Angular Distribution technique was applied on the 43S isomeric state produced by the fragmentation of a 48Ca beam and selected with the BigRIPS spectrometer. Following the measurement of the known g-factor of the isomer the quadrupole moment of this state was measured. Its spectroscopic quadrupole moment |QS| = 23(3) efm2 agreed with both shell model and beyond mean field calculations.

  16. Direct Dynamics Study of Hydrogen-Transfer Isomerization of 1-Pentyl and 1-Hexyl Radicals

    NASA Astrophysics Data System (ADS)

    Zheng, Jingjing; Truhlar, Donald G.

    2009-07-01

    The rate constants of three intramolecular hydrogen-transfer isomerization reactions, namely, 1-4 isomerization of the 1-pentyl radical and 1-4 and 1-5 isomerizations of the 1-hexyl radical, are calculated using variational transition state theory with multidimensional tunneling, in particular by using canonical variational theory (CVT, which is the version of variational transition state theory in which the transition state dividing surface is optimized for a canonical ensemble) with small-curvature tunneling (SCT) for the transmission coefficient. The required potential energy surfaces were obtained implicitly by direct dynamics employing interpolated variational transition state theory with mapping (IVTST-M) and variational transition state theory with interpolated single-point energies (VTST-ISPE). Single-level direct dynamics calculations were performed for all of the reactions by IVTST-M using M06-2X/MG3S or M08-HX/cc-pVTZ+ potential energy surfaces or both. The stationary points of 1-4 isomerization of 1-pentyl and the stationary points for the forward reactions of 1-4 and 1-5 isomerizations of 1-hexyl were also optimized by BMC-CCSD, and for all three reactions we also performed dual-level direct dynamics calculations using VTST-ISPE in which MCG3-MPW single-point energies served as the higher level. The calculated MCG3-MPW//M06-2X/MG3S rate constants agree well with experimental values for 1-4 isomerization of the 1-pentyl radical at high temperature, and this validates the accuracy of this theoretical method for 1-4 isomerization. The MCG3-MPW//M06-2X/MG3S method was therefore used to make a reliable prediction for the rata constants of 1-4 isomerization of the 1-hexyl radical for which a direct experimental measurement is not available. The calculated CVT/SCT/M08-HX/cc-pVTZ+ rate constants agree well with experimental values for 1-5 isomerization of the 1-hexyl radical, and they show that the tunneling effect for these reactions was underestimated in

  17. 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.

  18. Isomerization of Asp residues plays an important role in αA-crystallin dissociation.

    PubMed

    Takata, Takumi; Fujii, Noriko

    2016-03-01

    Aged cataract formation is caused by the accumulative precipitation of lens proteins incorporating diverse post-translational modifications. α-Crystallin, a major structural and functional lens protein, consists of a large polymeric structure that is dissociated and insolubilized with accumulative post-translational modifications. One such modification, isomerization of Asp, was recently identified in αB-crystallin monomers derived from aged lens. However, the distributions of Asp isomers in each lens fraction remain unknown. Here, α-crystallin fractions from aged lens were separated into heteropolymeric and monomeric forms to determine the Asp isomerization ratios in each fraction. Lens of four different ages were homogenized and centrifuged, and the soluble fraction was applied to size-exclusion chromatography. The heteropolymeric α-crystallin and monomeric crystallin fractions were obtained and concentrated. After trypsin digestion, each fraction was independently applied to liquid chromatography equipped with mass spectrometry to extract α-crystallin-derived peptides containing Asp isomers. The results showed that Asp58, Asp84 and Asp151 of αA-crystallin were highly isomerized in the monomeric fraction, but not isomerized to the same level in the heteropolymeric fraction. Each type of Asp isomerization increased in an age-dependent manner, was site-specific and was similar to previous results from lens water-insoluble fractions. These results imply that isomerization of Asp residues leads to dissociation of αA-crystallin from the heteropolymeric state and induces insolubilization in aged lens. Taken together, our findings suggest that isomerization of Asp might disrupt the higher order polymeric state of α-crystallin, resulting in decreased solubility and function, ultimately contributing to lens protein impairment and cataract formation with aging. PMID:26700637

  19. Isomerization of Asp residues plays an important role in αA-crystallin dissociation.

    PubMed

    Takata, Takumi; Fujii, Noriko

    2016-03-01

    Aged cataract formation is caused by the accumulative precipitation of lens proteins incorporating diverse post-translational modifications. α-Crystallin, a major structural and functional lens protein, consists of a large polymeric structure that is dissociated and insolubilized with accumulative post-translational modifications. One such modification, isomerization of Asp, was recently identified in αB-crystallin monomers derived from aged lens. However, the distributions of Asp isomers in each lens fraction remain unknown. Here, α-crystallin fractions from aged lens were separated into heteropolymeric and monomeric forms to determine the Asp isomerization ratios in each fraction. Lens of four different ages were homogenized and centrifuged, and the soluble fraction was applied to size-exclusion chromatography. The heteropolymeric α-crystallin and monomeric crystallin fractions were obtained and concentrated. After trypsin digestion, each fraction was independently applied to liquid chromatography equipped with mass spectrometry to extract α-crystallin-derived peptides containing Asp isomers. The results showed that Asp58, Asp84 and Asp151 of αA-crystallin were highly isomerized in the monomeric fraction, but not isomerized to the same level in the heteropolymeric fraction. Each type of Asp isomerization increased in an age-dependent manner, was site-specific and was similar to previous results from lens water-insoluble fractions. These results imply that isomerization of Asp residues leads to dissociation of αA-crystallin from the heteropolymeric state and induces insolubilization in aged lens. Taken together, our findings suggest that isomerization of Asp might disrupt the higher order polymeric state of α-crystallin, resulting in decreased solubility and function, ultimately contributing to lens protein impairment and cataract formation with aging.

  20. 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.

  1. 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.

  2. Consequences of acid strength for isomerization and elimination catalysis on solid acids.

    PubMed

    Macht, Josef; Carr, Robert T; Iglesia, Enrique

    2009-05-13

    We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal-acid mixtures designed to maintain alkane-alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activation barriers increased with increasing DPE, as also shown for alkanol dehydration reactions. These trends are consistent with thermochemical analyses of the transition states involved in isomerization and elimination steps. For all reactions, barriers increased by less than the concomitant increase in DPE upon changes in composition, because electrostatic stabilization of ion-pairs at the relevant transition states becomes more effective for weaker acids, as a result of their higher charge density at the anionic conjugate base. Alkoxide isomerization barriers were more sensitive to DPE than for elimination from H-bonded alkanols, the step that limits 2-butanol and 1-butanol dehydration rates; the latter two reactions showed similar DPE sensitivities, despite significant differences in their rates and activation barriers, indicating that slower reactions are not necessarily more sensitive to acid strength, but instead reflect the involvement of more unstable organic

  3. 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.

  4. Arrhythmias in Adult Congenital Patients With Bodily Isomerism.

    PubMed

    Loomba, Rohit S; Aggarwal, Saurabh; Gupta, Navdeep; Buelow, Matthew; Alla, Venkata; Arora, Rohit R; Anderson, Robert H

    2016-02-01

    There are an increasing number of adults with congenital heart disease, some of whom have bodily isomerism. Bodily isomerism or heterotaxy is a unique clinical entity associated with congenital malformations of the heart which further increases the risk for future cardiovascular complications. We aimed to investigate the frequency of arrhythmias in adults with bodily isomerism. We utilized the 2012 iteration of the Nationwide Inpatient Sample to identify adult inpatient admissions associated with arrhythmias in patients with isomerism. Data regarding demographics, comorbidities, and various procedures were collected and compared between those with and without isomerism. A total of 6,907,109 admissions were analyzed with a total of 861 being associated isomerism. The frequency of arrhythmias was greater in those with isomerism (20.8 vs. 15.4 %). Those with isomerism were also more five times more likely to undergo invasive electrophysiology studies. Length and cost of hospitalization for patients with arrhythmias also tended to be greater in those with isomerism. Mortality did not differ between the two groups. Arrhythmias are more prevalent in those with isomerism, with a majority of arrhythmias in isomerism being atrial. Those with isomerism and arrhythmias also tended to have greater length and cost of hospitalization.

  5. IR laser manipulation of cis{r_reversible}trans isomerization of 2-naphthol and its hydrogen-bonded clusters

    SciTech Connect

    Kouyama, Kyouko; Miyazaki, Mitsuhiko; Mikami, Naohiko; Ebata, Takayuki

    2006-02-07

    The cis{r_reversible}trans isomerization reaction has been carried out for 2-naphthol and its hydrogen (H) bonded clusters by infrared (IR) laser in the electronic excited state (S{sub 1}) in supersonic jets. A specific isomer in the jet was pumped to the X-H stretching vibration in the S{sub 1} state, where X refers to C, O, or N atom, by using a stepwise UV-IR excitation, and the dispersed emission spectra of the excited species or generated fragments were observed. It was found that the isomerization occurs only in the H-bonded clusters but a bare molecule does not exhibit the isomerization in the examined energy region of E{sub v}{<=}3610 cm{sup -1}, indicating a reduction of the isomerization barrier height upon the H bonding. The relative yield of the isomerization was observed as a function of internal energy. The isomerization yield was found to be very high at the low IR frequency excitation, and was rapidly reduced with the IR frequency due to the competition of the dissociation of the H bond within the isomer. Density-functional theory (DFT) and time-dependent DFT calculations were performed for estimating the barrier height of the isomerization for bare 2-naphthol and its cluster for electronic ground and excited states. The calculation showed that the isomerization barrier height is highly dependent on the electronic states. However, the reduction of the height upon the hydrogen bonding was not suggested at the level of our calculation.

  6. Cryo-EM Structure of Isomeric Molluscan Hemocyanin Triggered by Viral Infection

    PubMed Central

    Feng, Hongli; Liang, Rongfeng; Wang, Jiangyong; Xie, Lianhui; Zhu, Ping

    2014-01-01

    Hemocyanins (Hcs) of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs). In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8 Å cryo-electron microscopy (cryo-EM) structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV) infected abalone (Halitotis diversicolor), and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1). Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs) present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens. PMID:24887432

  7. 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.

  8. Cryo-EM structure of isomeric molluscan hemocyanin triggered by viral infection.

    PubMed

    Zhu, Hongtao; Zhuang, Jun; Feng, Hongli; Liang, Rongfeng; Wang, Jiangyong; Xie, Lianhui; Zhu, Ping

    2014-01-01

    Hemocyanins (Hcs) of arthropods and mollusks function not only as oxygen transporters, but also as phenoloxidases (POs). In invertebrates, PO is an important component in the innate immune cascade, where it functions as the initiator of melanin synthesis, a pigment involved in encapsulating and killing of pathogenic microbes. Although structures of Hc from several species of invertebrates have been reported, the structural basis for how PO activity is triggered by structural changes of Hc in vivo remains poorly understood. Here, we report a 6.8 Å cryo-electron microscopy (cryo-EM) structure of the isomeric form of hemocyanin, which was isolated from Abalone Shriveling syndrome-associated Virus (AbSV) infected abalone (Halitotis diversicolor), and build a pseudoatomic model of isomeric H. diversicolor hemocyanin 1 (HdH1). Our results show that, compared with native form of HdH1, the architecture of isomeric HdH1 turns into a more relaxed form. The interactions between certain functional units (FUs) present in the native form of Hc either decreased or were totally abolished in the isomeric form of Hc. As a result of that, native state Hc switches to its isomeric form, enabling it to play its role in innate immune responses against invading pathogens.

  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. 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.

  11. Characterizing gamma fields using isomeric activation ratios

    NASA Astrophysics Data System (ADS)

    Venkataraman, Ramkumar; Fleming, Ronald F.

    1994-12-01

    Isomeric activities were induced in indium by gamma irradiation in three different gamma fields, through the reactions 115In(γ, γ') 115mIn and 113In(γ, γ') 113mIn. The irradiation fields were (i) the 15 kCi 60Co source available in the University, (ii) the spent fuel gamma irradiator in the pool of the University's Ford Nuclear Reactor (FNR) and (iii) south face of the core of the FNR during routine shut downs. Isomeric activation ratios can serve to characterize gamma fields, provided the response functions of the two (γ, γ') reactions sample different energy regimes of the gamma spectrum present in the irradiation fields. The response of an isomeric activation detector, in turn, depends on the number of activation energy levels of the nuclide and the probabilities with which the activation levels de-populate to the isomeric level. The reaction rate ratio RIn115m/ RIn113m was measured in the three gamma fields. The measured ratios were (i) 1.210 ± 0.011 in the 60Co source, (ii) 1.314 ± 0.060 in the spent fuel gamma irradiator and (iii) 1.298 ± 0.039 in a location alongside the FNR core during routine shut downs. The measured reaction rate ratios are not only close to each other, but close to unity as well. This indicates that the excitation functions for the reactions 115In(γ, γ') 115mIn and 113In(γ, γ') 113mIn have similar shapes and that for the nuclides 115In and 113In, the number of activation energy levels and the probabilities with which they populate the isomeric levels are very similar to each other. Thus, the ratio RIn115m/ RIn113m will not yield any information regarding the shape of gamma spectrum in the field of measurement. However by choosing (γ, γ') reactions with different shapes for the excitation functions one can measure a set of isomeric activation ratios that characterize a given gamma field.

  12. Aryl isomerization during aliphatic CH bond activation

    SciTech Connect

    Chamberlain, L.R.; Rothwell, I.P.

    1983-03-23

    The transition-metal-stablized benzyne or o-phenylene (n/sup 2/-C/sub 6/H/sub 4/) ligand has been shown to be both an interesting and reactive group. The ligand is normally generated in mononuclear systems by ..beta..- (ortho-) hydrogen abstraction from an aryl group, and this synthetic approach has allowed a stable example to be isolated and structurally characterized. Here the conclusive identification of a benzyne intermediate during the isomerization of a tantalum-aryl compound is reported. The reaction is interesting in that the ortho hydrogen is transferred to the carbon atom of a cyclometalated chelate, the reverse (isomerization) step thus involving the activation of an aliphatic CH bond by the intermediate benzyne.

  13. Direct measurement of the energy thresholds to conformational isomerization in tryptamine: experiment and theory.

    PubMed

    Clarkson, Jasper R; Dian, Brian C; Moriggi, Loïck; DeFusco, Albert; McCarthy, Valerie; Jordan, Kenneth D; Zwier, Timothy S

    2005-06-01

    The methods of stimulated emission pumping-hole filling spectroscopy (SEP-HFS) and stimulated emission pumping population transfer spectroscopy (SEP-PTS) were applied to the conformation-specific study of conformational isomerization in tryptamine [TRA, 3-(2-aminoethyl)indole]. These experimental methods employ stimulated emission pumping to selectively excite a fraction of the population of a single conformation of TRA to well-defined ground-state vibrational levels. This produces single conformations with well-defined internal energy, tunable over a range of energies from near the zero-point level to well above the lowest barriers to conformational isomerization. When the SEP step overcomes a barrier to isomerization, a fraction of the excited population isomerizes to form that product. By carrying out SEP excitation early in a supersonic expansion, these product molecules are subsequently cooled to their zero-point vibrational levels, where they can be detected downstream with a third tunable laser that probes the ground-state population of a particular product conformer via a unique ultraviolet transition using laser-induced fluorescence. The population transfer spectra (recorded by tuning the SEP dump laser while holding the pump and probe lasers fixed) exhibit sharp onsets that directly determine the energy thresholds for conformational isomerization in a given reactant-product conformer pair. In the absence of tunneling effects, the first observed transition in a given X-Y PTS constitutes an upper bound to the energy barrier to conformational isomerization, while the last transition not observed constitutes a lower bound. The bounds for isomerizing conformer A of tryptamine to B(688-748 cm(-1)), C(1)(860-1000 cm(-1)), C(2)(1219-1316 cm(-1)), D(1219-1282 cm(-1)), E(1219-1316 cm(-1)), and F(688-748 cm(-1)) are determined. In addition, thresholds for isomerizing from B to A(<1562 cm(-1)), B to F(562-688 cm(-1)), and out of C(2) to B(<747 cm(-1)) are also

  14. Direct measurement of the energy thresholds to conformational isomerization in Tryptamine: Experiment and theory

    NASA Astrophysics Data System (ADS)

    Clarkson, Jasper R.; Dian, Brian C.; Moriggi, Loïck; DeFusco, Albert; McCarthy, Valerie; Jordan, Kenneth D.; Zwier, Timothy S.

    2005-06-01

    The methods of stimulated emission pumping-hole filling spectroscopy (SEP-HFS) and stimulated emission pumping population transfer spectroscopy (SEP-PTS) were applied to the conformation-specific study of conformational isomerization in tryptamine [TRA, 3-(2-aminoethyl)indole]. These experimental methods employ stimulated emission pumping to selectively excite a fraction of the population of a single conformation of TRA to well-defined ground-state vibrational levels. This produces single conformations with well-defined internal energy, tunable over a range of energies from near the zero-point level to well above the lowest barriers to conformational isomerization. When the SEP step overcomes a barrier to isomerization, a fraction of the excited population isomerizes to form that product. By carrying out SEP excitation early in a supersonic expansion, these product molecules are subsequently cooled to their zero-point vibrational levels, where they can be detected downstream with a third tunable laser that probes the ground-state population of a particular product conformer via a unique ultraviolet transition using laser-induced fluorescence. The population transfer spectra (recorded by tuning the SEP dump laser while holding the pump and probe lasers fixed) exhibit sharp onsets that directly determine the energy thresholds for conformational isomerization in a given reactant-product conformer pair. In the absence of tunneling effects, the first observed transition in a given X -Y PTS constitutes an upper bound to the energy barrier to conformational isomerization, while the last transition not observed constitutes a lower bound. The bounds for isomerizing conformer A of tryptamine to B(688-748cm-1), C(1)(860-1000cm-1), C(2)(1219-1316cm-1), D(1219-1282cm-1), E(1219-1316cm-1), and F(688-748cm-1) are determined. In addition, thresholds for isomerizing from B to A(<1562cm-1), B to F(562-688cm-1), and out of C(2) to B(<747cm-1) are also determined. The A →B and B

  15. 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.

  16. JYFLTRAP: Mass Spectrometry and Isomerically Clean Beams

    NASA Astrophysics Data System (ADS)

    Eronen, T.; Elomaa, V.-V.; Hager, U.; Hakala, J.; Jokinen, A.; Kankainen, A.; Rahaman, S.; Rissanen, J.; Weber, C.; Aeystoe, J.

    2008-02-01

    A radiofrequency quadrupole (RFQ) cooler and buncher and two Penning traps form the JYFLTRAP setup, which is located at the Department of Physics, University of JyvxE4skylxE4, Finland. It is used as a high-resolution mass filter for decay-spectroscopy experiments as well as for high-precision mass measurements. Recent developments have enabled JYFLTRAP to prepare isomerically clean beams with a mass resolving power R = { M over Delta M} geq 106.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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)

  2. Kinetics of Hydrogen-Transfer Isomerizations of Butoxyl Radicals

    SciTech Connect

    Zheng, J.; Truhlar, D. G.

    2010-01-01

    Five isomerization reactions involving intramolecular hydrogen-transfer in butoxyl radicals have been studied using variational transition state theory with small curvature tunneling. A set of best estimates of barrier heights and reaction energies for these five reactions was obtained by using coupled cluster theory including single and double excitations with a quasiperturbative treatment of connected triple excitations and a basis set extrapolated to the complete basis set limit plus core–valence correlation contributions and scalar relativistic corrections. This work predicts high-pressure limiting rate constants of these five reactions over the temperature range 200–2500 K and clarifies the available experimental data from indirect measurements. This study shows the importance of performing rate calculations with proper accounting for tunneling and torsional anharmonicity. We also proposed two new models for use in fitting rate constants over wide ranges of temperature.

  3. Lycopene degradation and isomerization kinetics during thermal processing of an olive oil/tomato emulsion.

    PubMed

    Colle, Ines J P; Lemmens, Lien; Tolesa, Getachew N; Van Buggenhout, Sandy; De Vleeschouwer, Kristel; Van Loey, Ann M; Hendrickx, Marc E

    2010-12-22

    The stability of lycopene in an olive oil/tomato emulsion during thermal processing (80-140 °C) was studied. Initially, the degradation of total lycopene (all-E plus Z-forms) occurred quickly at temperatures above 100 °C. However, a nonzero plateau value, depending on the processing temperature, was attained after longer treatment times. Besides degradation, the isomerization of total-Z-lycopene as well as the individual isomerization of all-E-, 5-Z-, 9-Z-, and 13-Z-lycopene was studied in detail. After prolonged heating, the isomer conversion reached a temperature-dependent equilibrium state. The degradation of total lycopene and the isomerization could be described by a fractional conversion model. The temperature dependency of the corresponding reaction rate constants was quantified by the Arrhenius equation. The activation energy of degradation was estimated to be 28 kJ/mol, and the activation energy of overall (all-E and total-Z) isomerization was estimated to be 52 kJ/mol.

  4. 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.

  5. 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.

  6. Isomerizing olefin metathesis as a strategy to access defined distributions of unsaturated compounds from fatty acids.

    PubMed

    Ohlmann, Dominik M; Tschauder, Nicole; Stockis, Jean-Pierre; Goossen, Käthe; Dierker, Markus; Goossen, Lukas J

    2012-08-22

    The dimeric palladium(I) complex [Pd(μ-Br)(t)Bu(3)P](2) was found to possess unique activity for the catalytic double-bond migration within unsaturated compounds. This isomerization catalyst is fully compatible with state-of-the-art olefin metathesis catalysts. In the presence of bifunctional catalyst systems consisting of [Pd(μ-Br)(t)Bu(3)P](2) and NHC-indylidene ruthenium complexes, unsaturated compounds are continuously converted into equilibrium mixtures of double-bond isomers, which concurrently undergo catalytic olefin metathesis. Using such highly active catalyst systems, the isomerizing olefin metathesis becomes an efficient way to access defined distributions of unsaturated compounds from olefinic substrates. Computational models were designed to predict the outcome of such reactions. The synthetic utility of isomerizing metatheses is demonstrated by various new applications. Thus, the isomerizing self-metathesis of oleic and other fatty acids and esters provides olefins along with unsaturated mono- and dicarboxylates in distributions with adjustable widths. The cross-metathesis of two olefins with different chain lengths leads to regular distributions with a mean chain length that depends on the chain length of both starting materials and their ratio. The cross-metathesis of oleic acid with ethylene serves to access olefin blends with mean chain lengths below 18 carbons, while its analogous reaction with hex-3-enedioic acid gives unsaturated dicarboxylic acids with adjustable mean chain lengths as major products. Overall, the concept of isomerizing metatheses promises to open up new synthetic opportunities for the incorporation of oleochemicals as renewable feedstocks into the chemical value chain.

  7. 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.

  8. 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.

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

    PubMed

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

    2016-03-14

    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

  10. 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.

  11. 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.

  12. 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.

  13. The photoinduced E → Z isomerization of bisazobenzenes: a surface hopping molecular dynamics study.

    PubMed

    Floss, Gereon; Saalfrank, Peter

    2015-05-21

    The photoinduced E → Z isomerization of azobenzene is a prototypical example of molecular switching. On the way toward rigid molecular rods such as those for opto-mechanical applications, multiazobenzene structures have been suggested in which several switching units are linked together within the same molecule (Bléger et al., J. Phys. Chem. B 2011, 115, 9930-9940). Large differences in the switching efficiency of multiazobenzenes have been observed, depending on whether the switching units are electronically decoupled or not. In this paper we study, on a time-resolved molecular level, the E→ Z isomerization of the simplest multiazobenzene, bisazobenzene (BAB). Two isomers (ortho- and para-BAB), differing only in the connectivity of two azo groups on a shared phenyl ring will be considered.To do so, nonadiabatic semiclassical dynamics after photoexcitation of the isomers are studied by employing an "on-the-fly", fewest switches surface hopping approach. States and couplings are calculated by Configuration Interaction (CI) based on a semiempirical (AM1) Hamiltonian (Persico and co-workers, Chem. Eur. J. 2004, 10, 2327-2341). In the case of para-BAB, computed quantum yields for photoswitching are drastically reduced compared to pristine azobenzene, due to electronic coupling of both switching units. A reason for this (apart from altered absorption spectra and reduced photochromicity) is the drastically reduced lifetimes of electronically excited states which are transiently populated. In contrast for meta-connected species, electronic subsystems are largely decoupled, and computed quantum yields are slightly higher than that for pristine azobenzene because of new isomerization channels. In this case we can also distinguish between single- and double-switch events and we find a cooperative effect: The isomerization of a single azo group is facilitated if the other azo group is already in the Z-configuration.

  14. New butane isomerization unit is unvieled by Andrews Petroleum

    SciTech Connect

    McWilliams, H.

    1990-06-01

    This article discusses the development of a butane isomerization unit which will help reduce butane surplus by fractionating it into other LPG products. Other features of this California project increase on-site storage.

  15. Photoinduced trans-to-cis isomerization of cyclocurcumin.

    PubMed

    Adhikary, Ramkrishna; Barnes, Charles A; Trampel, Rachel L; Wallace, Samuel J; Kee, Tak W; Petrich, Jacob W

    2011-09-15

    The photophysical properties of cyclocurcumin in various solvents are studied for the first time to shed light on the nonradiative processes of the parent compound, curcumin, which has a range of medicinal properties. Steady-state fluorescence and fluorescence-excitation spectra of cyclocurcumin in polar aprotic solvents are strongly dependent on excitation (λ(ex)) and emission (λ(em)) wavelength, respectively. The fluorescence quantum yield also depends on λ(ex) and increases with the viscosity of the medium. Time-resolved studies show nonexponential fluorescence decay in all solvents studied. The two fluorescence decay components of cyclocurcumin in alcohols exhibit a strong dependence on viscosity and temperature. NMR spectroscopy indicates that cyclocurcumin is entirely in the trans form with respect to the C6-C7 double bond in methanol, chloroform, and acetone. It is suggested that at least two conformational isomers about another single bond (C5-C6 or C7-C1″ or both) and that trans-to-cis isomerization about the C6-C7 double bond of these isomers provide the most likely means of rationalizing the steady-state spectra and the nonradiative decay mechanisms in both protic and aprotic polar solvents.

  16. Isomerization dynamics and thermodynamics of ionic argon clusters

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Gadéa, F. X.; Lombardi, A.; Aquilanti, V.

    2006-09-01

    The dynamics and thermodynamics of small Arn+ clusters, n =3, 6, and 9, are investigated using molecular dynamics (MD) and exchange Monte Carlo (MC) simulations. A diatomic-in-molecule Hamiltonian provides an accurate model for the electronic ground state potential energy surface. The microcanonical caloric curves calculated from MD and MC methods are shown to agree with each other, provided that the rigorous conservation of angular momentum is accounted for in the phase space density of the MC simulations. The previously proposed projective partition of the kinetic energy is used to assist MD simulations in interpreting the cluster dynamics in terms of inertial, internal, and external modes. The thermal behavior is correlated with the nature of the charged core in the cluster by computing a dedicated charge localization order parameter. We also perform systematic quenches to establish a connection with the various isomers. We find that the Ar3+ cluster is very stable in its linear ground state geometry up to about 300K, and then isomerizes to a T-shaped isomer in which a quasineutral atom lies around a charged dimer. In Ar6+ and Ar9+, the covalent trimer core is solvated by neutral atoms, and the weakly bound solvent shell melts at much lower energies, occasionally leading to a tetramer or pentamer core with weakly charged extremities. At high energies the core itself becomes metastable and the cluster transforms into Ar2+ solvated by a fluid of neutral argon atoms.

  17. Theoretical study of isomerization and decomposition of propenal

    SciTech Connect

    Chin, Chih-Hao; Lee, Shih-Huang

    2011-01-28

    We investigated the dynamics of isomerization and multi-channel dissociation of propenal (CH{sub 2}CHCHO), methyl ketene (CH{sub 3}CHCO), hydroxyl propadiene (CH{sub 2}CH{sub 2}CHOH), and hydroxyl cyclopropene (cyclic-C{sub 3}H{sub 3}-OH) in the ground potential-energy surface using quantum-chemical calculations. Optimized structures and vibrational frequencies of molecular species were computed with method B3LYP/6-311G(d,p). Total energies of molecules at optimized structures were computed at the CCSD(T)/6-311+G(3df,2p) level of theory. We established the potential-energy surface for decomposition to CH{sub 2}CHCO + H, CH{sub 2}CH + HCO, CH{sub 2}CH{sub 2}/CH{sub 3}CH + CO, CHCH/CH{sub 2}C + H{sub 2}CO, CHCCHO/CH{sub 2}CCO + H{sub 2}, CHCH + CO + H{sub 2}, CH{sub 3}+ HCCO, CH{sub 2}CCH + OH, and CH{sub 2}CC/cyclic-C{sub 3}H{sub 2}+ H{sub 2}O. Microcanonical rate coefficients of various reactions of trans-propenal with internal energies 148 and 182 kcal mol{sup -1} were calculated using Rice-Ramsperger-Kassel-Marcus and Variational transition state theories. Product branching ratios were derivable using numerical integration of kinetic master equations and the steady-state approximation. The concerted three-body dissociation of trans-propenal to fragments C{sub 2}H{sub 2}+ CO + H{sub 2} is the prevailing channel in present calculations. In contrast, C{sub 3}H{sub 3}O + H, C{sub 2}H{sub 3}+ HCO and C{sub 2}H{sub 4}+ CO were identified as major channels in the photolysis of trans-propenal. The discrepancy between calculations and experiments in product branching ratios indicates that the three major photodissociation channels occur mainly on an excited potential-energy surface whereas the other channels occur mainly on the ground potential-energy surface. This work provides profound insight in the mechanisms of isomerization and multichannel dissociation of the system C{sub 3}H{sub 4}O.

  18. 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.

  19. Lewis acid catalysis of photochemical reactions. 4. Selective isomerization of cinnamic esters

    SciTech Connect

    Lewis, F.D.; Oxman, J.D.; Gibson, L.L.; Hampsch, H.L.; Quillen, S.L.

    1986-05-28

    The spectroscopic properties and photoisomerization reactions of several (E)- and (Z)-cinnamic esters, bis cinnamic esters, and model esters and lactones in the presence and absence of Lewis acids have been investigated. The use of Lewis acids such as BF/sub 3/ or EtAlCl/sub 2/ results in enhanced photoisomerization efficiency and a shift in the photoequilibrium toward the thermodynamically less stable Z isomer. Enhanced E ..-->.. Z photoisomerization results from selective excitation of ground-state ester-Lewis acid complexes. These complexes have been characterized by /sup 1/H NMR, ultraviolet, and fluorescence spectroscopies. The equilibrium constants for complexation are dependent upon both the electron donor strength of the ester and its conformational mobility. These factors also determine the magnitude of the red shifts in the electronic absorption spectra observed upon complexation. Enhanced E ..-->.. Z photoisomerization upon complex formation is a consequence of selective excitation of the E vs. Z complex, more efficient isomerization of the excited E vs. Z complex, and larger equilibrium constants for complexation of E vs. Z esters. The photoequilibria obtained for bis cinnamic esters are highly enriched in the Z,Z and Z,E isomers in accord with independent isomerization of the two cinnamate groups; however, in the case of 1,3-trimethylenebis(cinnamate), two-bond isomerization of the E,E to Z,Z isomer is observed at low conversions.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Solution and solid-state study of the structure of azo-coupling products from isomeric enaminones possessing tert-butyl group: An unprecedented observation of pure hydrazo form in azo coupled N-alkyl β-enaminones

    NASA Astrophysics Data System (ADS)

    Šimůnek, Petr; Padělková, Zdeňka; Macháček, Vladimír

    2014-10-01

    The structure of the azo-coupling products from enaminones derived from 4,4-dimethyl-1-phenylpentane-1,3-dione has been studied by means of solution-state 1H, 13C and 15N NMR spectroscopy and X-ray diffractometry. The presence of bulky tert-butyl group hinders or even prevents from the formation of planar conjugated heterodiene system Hsbnd Nsbnd Cdbnd Csbnd Ndbnd N with an intramolecular hydrogen bond Nsbnd H⋯Ndbnd which is the prerequisite for fast tautomeric exchange imino-hydrazo - enamino-azo. The minor amount of azo compounds is formed by a proton exchange through a hydrogen bond Nsbnd H⋯N, which is either intramolecular (in solution) or intermolecular (solid state). The intermolecular exchange proceeds via the dimers of the azo coupling products. This is unprecedented result among the similar molecules hitherto studied.

  6. Isomerism or heterotaxy: which term leads to better understanding?

    PubMed

    Loomba, Rohit S; Hlavacek, Anthony M; Spicer, Diane E; Anderson, Robert H

    2015-08-01

    Use of correct nomenclature is important in all aspects of medicine. Many of the controversies that have bedeviled paediatric cardiology have devolved from the inappropriate use of words to describe the lesions to be found when the heart is congenitally abnormal. A continuing area of disagreement is the situation currently described by many as representing "heterotaxy". When used literally, this word means any departure from the normal. Thus, all congenitally malformed hearts represent examples of heterotaxy. By convention, nonetheless, the term is used to describe the arrangement in which the bodily organs, including parts of the heart, are not in their usual or in their mirror-imaged patterns. The arrangements, therefore, represent the presence of the organs on the right and left sides of the body being mirror imaged, in other words isomeric; however, not all the organs are uniformly isomeric. In this review, we show that, when assessed on the basis of the morphology of the atrial appendages, specifically the extent of the pectinate muscles relative to the atrioventricular junctions, isomerism is an unequivocal finding within the heart. Only the atrial appendages, however, are truly isomeric. The potential problem of disharmony between the various systems of organs is resolved simply by accounting specifically for each of the systems. On these bases, we suggest that the isomeric arrangements can now readily be diagnosed in the clinical setting, and differentiated into their right and left isomeric variants. We propose that such distinctions will provide the key for establishing the genetic cues responsible for the formation of the isomeric as opposed to the lateralised arrangements. PMID:26088959

  7. Isomeric Island in the Vicinity of 66Fe

    SciTech Connect

    Daugas, J. M.; Sawicka, M.; Pfutzner, M.; Matea, I.; Grawe, H.; Grzywacz, Robert Kazimierz; Bingham, Carrol R; Grzywacz-Jones, K. L.; Rykaczewski, Krzysztof Piotr

    2006-01-01

    An island of isomers have recently been observed on both sides of the N=40 shell below the Ni isotopes. Isomeric states in the 65Fe and 67Fe allow the knowledge of the single particle structure around the g9/2 shell. Moreover, the excitation energy of the first 2+ and 4+ states in the 68Fe have been established by − correlation. The evolution of the structure of the Fe isotopes going far away from the valley of stability is, for the first time, given for N>40.

  8. 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

  9. 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.

  10. Phototriggered sulfoxide isomerization in [Ru(pic)2(dmso)2].

    PubMed

    Rachford, Aaron A; Petersen, Jeffrey L; Rack, Jeffrey J

    2007-08-14

    We report the characterization and photochemistry of a simple ruthenium coordination complex containing only picolinate (pic) and dmso, which exhibits a large isomerization quantum yield (Phi(SS-->OO) = 0.50) in various solvents. The picolinate ligands of [Ru(pic)(2)(dmso)(2)] are in a cis arrangement so that the carboxylate oxygen of one pic ligand (O1) is trans to the pyridine of the second picolinate (N2). One dmso ligand (S1) is trans to a pyridine nitrogen (N1), while the second dmso (S2) is trans to a carboxylate oxygen (O3). The cyclic voltammetry, (1)H NMR, IR, and UV-vis spectroscopy data suggest that while both dmso ligands isomerize photochemically, only one dmso ligand isomerizes electrochemically. Isomerization quantum yields for each dmso ligand differ by an order of magnitude (Phi(SS-->SO) = 0.46 and Phi(SO-->OO) = 0.036). In agreement with previous results, the isomerization quantum yield for each dmso is dependent on the ligand that is trans to the dmso.

  11. 100 fs photo-isomerization with vibrational coherences but low quantum yield in Anabaena Sensory Rhodopsin.

    PubMed

    Cheminal, Alexandre; Léonard, Jérémie; Kim, So-Young; Jung, Kwang-Hwan; Kandori, Hideki; Haacke, Stefan

    2015-10-14

    Anabaena Sensory Rhodopsin (ASR) stands out among the microbial retinal proteins in that, under light-adaptation (LA) conditions, it binds both the 13-cis isomer and the all-trans isomer of the protonated Schiff base of retinal (PSBR). In the dark-adapted (DA) state, more than 95% of the proteins bear all-trans PSBR, and the protein environment adopts a different equilibrium state. We report the excited state and photo-isomerization kinetics of ASR under different LA conditions. The full data set allows confirming that the photoisomerization of the 13C isomer occurs within 100 fs and indications of an excited and ground state wavepacket launched by the ultrafast non-adiabatic reaction are reported. Even though this recalls the record isomerization time and the coherent reaction scenario of 11-cis PSBR in rhodopsin, the photoisomerization quantum yield (QY) is much lower, actually the lowest value ever reported for retinal proteins (<15%). Noticeably, in ASR the excited state lifetime (ESL) is at least five times larger and the QY is more than twice as large for AT PSBR as compared to 13C PSBR. We argue that ESL and QY cannot be expected to be correlated at all, but that the latter is decided on, as often anticipated, by the wavepacket pathways leading to the conical intersection seam.

  12. 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

  13. 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.

  14. Catalytic Isomerization of Biomass‐Derived Aldoses: A Review

    PubMed Central

    Delidovich, Irina

    2016-01-01

    Abstract 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

  15. 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.

  16. 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.

  17. Heart Transplantation in a Patient with Left Isomerism

    PubMed Central

    Bang, Ji Hyun; Oh, You Na; Yoo, Jae Suk; Kim, Jae-Joong; Park, Chun Soo; Park, Jeong-Jun

    2015-01-01

    We report the case of a 37-year-old man who suffered from biventricular failure due to left isomerism, inferior vena cava interruption with azygos vein continuation, bilateral superior vena cava, double outlet of right ventricle, complete atrioventricular septal defect, pulmonary stenosis, and isolated dextrocardia. Heart transplantation in patients with systemic venous anomalies often requires the correction and reconstruction of the upper & lower venous drainage. We present a case of heart transplantation in a patient with left isomerism, highlighting technical modifications to the procedure, including the unifocalization of the caval veins and reconstruction with patch augmentation. PMID:26290840

  18. 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.

  19. Ultrafast studies of solvent effects in the isomerization of cis-stilbene

    SciTech Connect

    Rice, J.K.; Baronavski, A.P.

    1992-04-16

    Using a femtosecond pump-probe laser system, the excited-state lifetimes of cis-stilbene in n-hexane, tetradecane, methanol, 1,4-dioxane, and cyclohexane are measured and correlated with solvent bulk viscosity. The measured lifetimes in n-hexane and tetradecane correlate well to solvent bulk viscosity, but methanol, 1,4-dioxane, and cyclohexane do not. Polarity-influenced solvent-solute interactions occur in methanol and 1,4-dioxane and a slow isomerization rate in cyclohexane occurs with cis-stilbene. 39 refs., 7 figs., 2 tabs.

  20. 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.

  1. 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)

  2. 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.

  3. Fast (E)-(Z) Isomerization Mechanisms of Substituted Allyloxy Radicals in Isoprene Oxidation.

    PubMed

    Nguyen, Vinh Son; Peeters, Jozef

    2015-07-16

    Unusually rapid (E) ⇌ (Z) isomerization mechanisms are proposed and theoretically quantified for substituted allyloxy radicals, R'RC═CH-CH2O(•), with R and R' alkyl or oxygenated substituents, termed below β,γ-enoxy radicals. These conversions are shown to occur by a sequence of (i) ring closure to nearly isoergic oxiranyl-C(•)RR' radicals, (ii) internal rotation of the oxiranyl-moiety over 180°, and (iii) oxiranyl-ring reopening to yield the (E) ⇌ (Z)-isomerized oxy radicals. The barriers for all three steps were computed at the CCSD(T)/aug-cc-pVTZ//QCISD/6-311(d,p) level of theory to be only ≈5 ± 2 kcal mol(-1), and the rate constants at 298 K for the overall reactions were evaluated using transition-state theory to be in the range of 10(8)-10(9) s(-1). Specifically, and of relevance to the isoprene oxidation mechanism, it is predicted that the (E)-δ-hydroxy-isoprenyloxy radicals resulting from isoprene oxidation at high NO levels should isomerize to their (Z)-analogues at a rate of about 1.5 × 10(9) s(-1), much faster than the competing 1,5-H shift that was proposed earlier as the major fate of these (E)-oxy radicals ( Dibble, T. S. J. Phys. Chem. A 2002, 106, 6643-6650 ). It is concluded that under high-NO conditions the (E)- and (Z)-δ-hydroxy-isoprenylperoxy precursors should yield identical and therefore indistinguishable C5-hydroxycarbonyls as main products.

  4. Coherent control of the isomerization of retinal in bacteriorhodopsin in the high intensity regime

    SciTech Connect

    Prokhorenko, Valentyn I.; Halpin, Alexei; Johnson, Philip J. M.; Miller, R. J. Dwayne; Brown, Leonid S.

    2011-02-28

    Coherent control protocols provide a direct experimental determination of the relative importance of quantum interference or phase relationships of coupled states along a selected pathway. These effects are most readily observed in the high intensity regime where the field amplitude is sufficient to overcome decoherence effects. The coherent response of retinal photoisomerization in bacteriorhodopsin to the phase of the photoexcitation pulses was examined at fluences of 10{sup 15}- 2.5 x 10{sup 16} photons per square centimeter, comparable to or higher than the saturation excitation level of the S{sub 0}-S{sub 1} retinal electronic transition. At moderate excitation levels of {approx}6 x 10{sup 15} photons/cm{sup 2} (<100 GW/cm{sup 2}), chirping the excitation pulses increases the all-trans to 13-cis isomerization yield by up to 16% relative to transform limited pulses. The reported results extend previous weak-field studies [Prokhorenko et al., Science 313, 1257 (2006)] and further illustrate that quantum coherence effects persist along the reaction coordinate in strong fields even for systems as complex as biological molecules. However, for higher excitation levels of {approx}200 GW/cm{sup 2}, there is a dramatic change in photophysics that leads to multiphoton generated photoproducts unrelated to the target isomerization reaction channel and drastically changes the observed isomerization kinetics that appears, in particular, as a red shift of the transient spectra. These results explain the apparent contradictions of the work by Florean et al.[Proc. Natl. Acad. Sci. U.S.A. 106, 10896 (2009)] in the high intensity regime. We are able to show that the difference in observations and interpretation is due to artifacts associated with additional multiphoton-induced photoproducts. At the proper monitoring wavelengths, coherent control in the high intensity regime is clearly observable. The present work highlights the importance of conducting coherent control

  5. 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.

  6. Initiation of Phage Infection by Partial Unfolding and Prolyl Isomerization*♦

    PubMed Central

    Hoffmann-Thoms, Stephanie; Weininger, Ulrich; Eckert, Barbara; Jakob, Roman P.; Koch, Johanna R.; Balbach, Jochen; Schmid, Franz X.

    2013-01-01

    Infection of Escherichia coli by the filamentous phage fd starts with the binding of the N2 domain of the phage gene-3-protein to an F pilus. This interaction triggers partial unfolding of the gene-3-protein, cis → trans isomerization at Pro-213, and domain disassembly, thereby exposing its binding site for the ultimate receptor TolA. The trans-proline sets a molecular timer to maintain the binding-active state long enough for the phage to interact with TolA. We elucidated the changes in structure and local stability that lead to partial unfolding and thus to the activation of the gene-3-protein for phage infection. Protein folding and TolA binding experiments were combined with real-time NMR spectroscopy, amide hydrogen exchange measurements, and phage infectivity assays. In combination, the results provide a molecular picture of how a local unfolding reaction couples with prolyl isomerization not only to generate the activated state of a protein but also to maintain it for an extended time. PMID:23486474

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Complementing ultrafast shape recognition with an optical isomerism descriptor.

    PubMed

    Zhou, Ting; Lafleur, Karine; Caflisch, Amedeo

    2010-11-01

    We introduce the mixed product of three vectors spanning four molecular locations as a descriptor of optical isomerism. This descriptor is very efficient as it does not require molecular superposition, and is very robust in discriminating between a given isomer and its mirror image. In particular, conformational isomers that are mirror images of each other, as well as optical isomers have opposite sign of the descriptor value. For efficient database searches, the optical isomerism descriptor can be used to complement an available ultrafast shape recognition (USR) method based solely on distances, which is not able to distinguish enantiomers. By an extensive comparison of the USR-based similarity score with an approach based on Gaussian molecular volume overlap, the accuracy and completeness of the former are discussed.

  16. Fragrance material review on isotridecan-1-ol (isomeric mixture).

    PubMed

    McGinty, D; Bhatia, S P; Scognamiglio, J; Letizia, C S; Api, A M

    2010-07-01

    A toxicologic and dermatologic review of isotridecan-1-ol (isomeric mixture) when used as a fragrance ingredient is presented. Isotridecan-1-ol (isomeric mixture) is a member of the fragrance structural group branched chain saturated alcohols. The common characteristic structural elements of the alcohols with saturated branched chain are one hydroxyl group per molecule, and a C(4)-C(12) carbon chain with one or several methyl side chains. This review contains a detailed summary of all available toxicology and dermatology papers that are related to this individual fragrance ingredient and is not intended as a stand-alone document. A safety assessment of the entire branched chain saturated alcohol group will be published simultaneously with this document; please refer to Belsito et al. (2010) for an overall assessment of the safe use of this material and all other branched chain saturated alcohols in fragrances.

  17. 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.

  18. The isomerization barrier in cyanocyclobutadienes: an ab initio multireference average quadratic coupled cluster study.

    PubMed

    Eckert-Maksić, Mirjana; Lischka, Hans; Maksić, Zvonimir B; Vazdar, Mario

    2009-07-23

    The energy profiles of the isomerization of mono, di-, and tetracyano-substituted cyclobutadienes (CBDs) are computed at the multireference average quadratic coupled cluster/complete active space self-consistent field level of theory. It was found that the energy barrier heights for the automerization reaction are 2.6 (tetracyano-CBD), 5.1 (1,3-dicyano-CBD), and 6.4 (cyano-CBD) kcal mol(-1), implying that they are lowered relative to that in the parent CBD (6.4 kcal mol(-1)), the monosubstituted derivative being an exception. Since the free CBD shuttles between two equivalent structures even at low temperature of 10 K, it follows that bond-stretch isomerism does not take place in cyanocyclobutadienes. Instead, these compounds exhibit rapid fluxional interconversion at room temperature between two bond-stretch isomers by the double bond flipping mechanism. The reason behind the decrease in the barrier heights is identified as a slightly enhanced resonance effect at the saddle points separating two (equivalent) bond-stretch isomers, compared to that in the equilibrium structures, predominantly due to the diradical character of the former. It is also shown that the energy gap between the singlet ground state saddle point structure and the first triplet equilibrium geometry decreases upon multiple substitution by the cyano groups. The splitting of the S and T energy is small being within the range of 6.5-8.2 kcal mol(-1).

  19. 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

  20. 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

  1. 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.

  2. Photoinduced isomerization of lycopene and application to tomato cultivation.

    PubMed

    Heymann, Thomas; Raeke, Julia; Glomb, Marcus A

    2013-11-20

    The present study aimed to investigate if growth conditions have an impact on the isomeric composition of lycopene in tomatoes. First a model system for photoinduced isomerization was established. Tomato extracts were irradiated with a halogen lamp, whose wavelength spectrum is close to the spectrum of daylight and thus mimics field-grown cultivation. Different optical filters were interposed between lamp and samples to simulate greenhouse conditions. 5-cis-Lycopene was formed preferentially while the concentration of 7-cis-lycopene decreased in field-grown model systems. The change of isomerization in greenhouse model systems led to a significantly different ratio. Consequently 5-cis- and 7-cis-lycopene were identified as potent markers for the differentiation of various lighting conditions during cultivation. This result was verified in biological samples. Authentic field-grown tomatoes (var. Lycopersicon esculentum Mill. var. commune L. H. Bailey "Harzfeuer") showed a significantly higher content of 5-cis-lycopene 5.90 ± 0.45% compared to tomatoes of the same variety grown under electric lighting 4.11 ± 0.10%. Additionally, the ratio of 7-cis-lycopene was significantly lower under field-grown conditions. PMID:24191648

  3. [Ion mobility spectrometry for the isomeric volatile organic compounds].

    PubMed

    Han, Hai-yan; Jia, Xian-de; Huang, Guo-dong; Wang, Hong-mei; Li, Jian-quan; Jin, Shun-ping; Jiang, Hai-he; Chu, Yan-nan; Zhou, Shi-kang

    2007-10-01

    Ion mobility spectrometry (IMS) is based on determining the drift velocities, which the ionized sample molecules attain in the weak electric field of a drift tube at atmospheric pressure. The drift behavior can be affected by structural differences of the analytes, so that ion mobility spectrometry has the ability to separated isomeric compounds. In the present article, an introduction to IMS is given, followed by a description of the instrument used for the experiments to differentiate isomeric compounds. Positive ion mobility spectras of three kinds of isomeric volatile organic compounds were studied in a homemade high-resolution IMS apparatus with a discharge ionization source. The study includes the differences in the structure of carbon chain, the style of function group, and the position of function group. The reduced mobility values were determined, which are in very good agreement with the previously reported theoretical values using neural network theory. The influence of the structural features of the substances and including the size and shape of the molecule has been investigated. The reduced mobility values increases in the order: alcohols < acetones < aromas, linears < branches < cycles, and para- < meta- < ortho-. The deviating ion mobility spectra of the constitutional isomers studied reflect the influence of structural features. In order to calibrate or determine the detection limits and the sensitivity of the ion mobility spectrometry, the exponential dilution flask (EDF) was used. Using this method, the detection limit of the analytes can reach the order of magnitude of ng x L(-1).

  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. 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.

  6. 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.

  7. Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

    SciTech Connect

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

    2009-07-28

    Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open{yields}cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O{sub 2}+O asymptote on the O{sub 3} ground-state {sup 1}A{sup '} potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O{sub 2}+O dissociation channel lie at {approx}0.05, {approx}0.086, and {approx}0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O{sub 2}+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

  8. Polarity controlled reaction path and kinetics of thermal cis-to-trans isomerization of 4-aminoazobenzene.

    PubMed

    Joshi, Neeraj Kumar; Fuyuki, Masanori; Wada, Akihide

    2014-02-20

    Spectral and kinetic behavior of thermal cis-to-trans isomerization of 4-aminoazobenzene (AAB) is examined in various solvents of different polarities. In contrast to azobenzene (AB), it is found the rate of thermal isomerization of AAB is highly dependent on solvent polarity. Accelerated rates are observed in polar solvents as compared to nonpolar solvents. Moreover, a decrease in the barrier height with an increase in medium polarity is observed. Our observations suggest that inversion is the preferred pathway in cis-to-trans thermal isomerization in a nonpolar medium; however, in a polar medium, the isomerization path deviates from the inversion route and rotational behavior is incorporated. Differences in the kinetics and in mechanisms of isomerization in different media are rationalized in terms of modulation in barrier height by polarity of the medium and solute-solvent interaction. It is found that kinetics as well as the mechanism of thermal isomerization in AAB is controlled by the polarity of the medium.

  9. Observation of M3 isomeric transition from 156mPm through the βdecay of 156Nd

    NASA Astrophysics Data System (ADS)

    Shibata, M.; Suematsu, O.; Kojima, Y.; Kawade, K.; Taniguchi, A.; Kawase, Y.

    2007-02-01

    An M3 transition in a doubly odd nucleus of 156Pm was identified by internal conversion electron measurement through the β-decay of 156Nd which was separated from the fission products of 235U using the on-line mass separator KUR-ISOL. The isomeric state at 150.3keV de-excites to the ground state with the M3 transition, and the spin-parity is considered to be 1-. Nilsson configurations are also discussed on the basis of the systematics.

  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. beta decay and isomeric properties of neutron-rich Ca and Sc isotopes

    SciTech Connect

    Crawford, H. L.; Mantica, P. F.; Berryman, J. S.; Stoker, J. B.; Janssens, R. V. F.; Carpenter, M. P.; Kay, B. P.; Lauritsen, T.; Zhu, S.; Broda, R.; Cieplicka, N.; Fornal, B.; Grinyer, G. F.; Minamisono, K.; Hoteling, N.; Stefanescu, I.; Walters, W. B.

    2010-07-15

    The isomeric and beta-decay properties of neutron-rich {sup 53-57}Sc and {sup 53,54}Ca nuclei near neutron number N=32 are reported, and the low-energy level schemes of {sup 53,54,56}Sc and {sup 53-57}Ti are presented. The low-energy level structures of the {sub 21}Sc isotopes are discussed in terms of the coupling of the valence 1f{sub 7/2} proton to states in the corresponding {sub 20}Ca cores. Implications with respect to the robustness of the N=32 subshell closure are discussed, as well as the repercussions for a possible N=34 subshell closure.

  13. First-principles investigation of isomerization by proton transfer in β-fumaric acid crystal

    NASA Astrophysics Data System (ADS)

    Dopieralski, P.; Panek, J.; Latajka, Z.

    2009-04-01

    Crystal structure of fumaric acid was investigated by Car-Parrinello molecular dynamics and Path Integral molecular dynamics. We propose a mechanism of isomerization by proton transfer in the solid state. It is shown that the three conformers of fumaric acid observed in cryogenic Ar matrix are also present in the solid. Standard ab initio Car-Parrinello dynamics of the studied solid at 100 K indicates that barrier height for proton transfer is too high to enable thermal jump over the barrier. Path Integral method in this particular case significantly changes proton behavior in the hydrogen bridge, and the proton tunneling process is observed. Vibrational spectra of investigated system HOOC-CH=CH-COOH and its deuterated analog DOOC-CH=CH-COOD were calculated and compared with experimental data.

  14. First-principles investigation of isomerization by proton transfer in beta-fumaric acid crystal.

    PubMed

    Dopieralski, P; Panek, J; Latajka, Z

    2009-04-28

    Crystal structure of fumaric acid was investigated by Car-Parrinello molecular dynamics and Path Integral molecular dynamics. We propose a mechanism of isomerization by proton transfer in the solid state. It is shown that the three conformers of fumaric acid observed in cryogenic Ar matrix are also present in the solid. Standard ab initio Car-Parrinello dynamics of the studied solid at 100 K indicates that barrier height for proton transfer is too high to enable thermal jump over the barrier. Path Integral method in this particular case significantly changes proton behavior in the hydrogen bridge, and the proton tunneling process is observed. Vibrational spectra of investigated system HOOC-CH=CH-COOH and its deuterated analog DOOC-CH=CH-COOD were calculated and compared with experimental data. PMID:19405604

  15. 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

  16. 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.

  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 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.

  19. Photochromic isomerization of spirobenzopyran in nanoholes of anodic alumina

    SciTech Connect

    Saito, Mitsunori; Tsubokura, Yasuhiro

    2006-11-01

    A notable change in the photochromic characteristics was observed when the benzene solution of spirobenzopyran was put in nanoholes of anodic alumina. The absorption peak that appeared in the ultraviolet irradiation process shifted to a shorter wavelength, and the decay time of the decoloration process became?200 times longer than that of the original solution. After a preservation period of several days, however, both the absorption wavelength and the decay time recovered to those of the original solution. These experimental results suggest that the photochromic isomerization in the alumina nanoholes is affected by the large surface area of the matrix rather than the limited free volume.

  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.

  1. 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.

  2. 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

  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. Tandem ring-closing metathesis/isomerization reactions for the total synthesis of violacein.

    PubMed

    Petersen, Mette T; Nielsen, Thomas E

    2013-04-19

    A series of 5-substituted 2-pyrrolidinones was synthesized through a one-pot ruthenium alkylidene-catalyzed tandem RCM/isomerization/nucleophilic addition sequence. The intermediates resulting from RCM/isomerization showed reactivity toward electrophiles in aldol condensation reactions which provided a new entry for the total synthesis of the antileukemic natural product violacein.

  6. 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.

  7. Iridium-Catalyzed Dynamic Kinetic Isomerization: Expedient Synthesis of Carbohydrates from Achmatowicz Rearrangement Products.

    PubMed

    Wang, Hao-Yuan; Yang, Ka; Bennett, Scott R; Guo, Sheng-rong; Tang, Weiping

    2015-07-20

    A highly stereoselective dynamic kinetic isomerization of Achmatowicz rearrangement products was discovered. This new internal redox isomerization provided ready access to key intermediates for the enantio- and diastereoselective synthesis of a series of naturally occurring sugars. The nature of the de novo synthesis also enables the preparation of both enantiomers.

  8. Effects of alkali or acid treatment on the isomerization of amino acids.

    PubMed

    Ohmori, Taketo; Mutaguchi, Yuta; Doi, Katsumi; Ohshima, Toshihisa

    2012-10-01

    The effect of alkali treatment on the isomerization of amino acids was investigated. The 100×D/(D+L) values of amino acids from peptide increased with increase in the number of constituent amino acid residues. Furthermore, the N-terminal amino acid of a dipeptide was isomerized to a greater extent than the C-terminal residue.

  9. Identification of Asp isomerization in proteins by ¹⁸O labeling and tandem mass spectrometry.

    PubMed

    Zhang, Jennifer; Katta, Viswanatham

    2012-01-01

    Isomerization of aspartic acid (Asp) to isoaspartic acid (isoAsp) via succinimide intermediate is a common route of degradation for proteins that can affect their structural integrity. As Asp/isoAsp is isobaric in mass, it is difficult to identify the site of modification by LC-MS/MS peptide mapping. Here, we describe an approach to label the Asp residue involved in isomerization at the protein level by hydrolyzing the succinimide intermediate in H₂¹⁸O. Tryptic digestion of this labeled protein will result in peptides containing the site of isomerization being 2 Da heavier than the ¹⁶O-containing counterparts, due to ¹⁸O incorporation during the hydrolysis process. Comparison of tandem mass spectra of isomerized peptides with and without ¹⁸O incorporation allows easy identification of the Asp residue involved. This method proved to be especially useful in identifying the sites when isomerization occurs in Asp-Asp motifs.

  10. 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.

  11. Effect of protonation on the isomerization properties of n-butylamine Schiff base of isomeric retinal as revealed by direct HPLC analyses: selection of isomerization pathways by retinal proteins.

    PubMed

    Koyama, Y; Kubo, K; Komori, M; Yasuda, H; Mukai, Y

    1991-09-01

    Alumina adsorption chromatography and ion-pair reversed-phase chromatography were developed to analyze the isomers of unprotonated and protonated n-butylamine Schiff base of retinal (RSB and PRSB), respectively. Photoisomerization starting from the all-trans, 11-cis and 13-cis isomers was traced for RSB in n-hexane, acetonitrile, methanol and 1-butanol, and for PRSB in methanol, acetonitrile and 1-butanol. The quantum yields of photoisomerization for the all-trans, 9-cis, 11-cis and 13-cis isomers were determined for RSB and PRSB in the above solvents except 1-butanol. On the other hand, photoisomerization of isomeric retinal bound (through Schiff base linkage) to bovine serum albumin (RBSA) in aqueous solution (pH 3, 7 and 12) as well as thermal isomerization of RSB (in n-hexane), PRSB (in methanol) and RBSA (in aqueous solution, pH 7) were traced starting from the all-trans, 11-cis, and 13-cis isomers. Protonation of RSB drastically changes the pathway of photoisomerization and increases the quantum yields of isomeric RSB. The solvent polarity increases the quantum yields of RSB differently depending on the configuration. Protonation enhances thermal isomerization also. The results of the above model systems are compared with those of retinal proteins to rationalize their selection of the particular isomerization pathways.

  12. Optical Pumping and Laser Induced Nuclear Orientation of a Microsecond Isomeric Level in BARIUM-134

    NASA Astrophysics Data System (ADS)

    Bell, Curtis John

    Using optical pumping techniques, on and off-line experiments were performed on a microsecond nuclear isomer (('134m)Ba 10('+) ). Shifts in atomic resonances detected by changes in the angular distribution of characteristic nuclear radiations (expressed as changes in shape and size) yield information on changes in nuclear structure. The 10('+) isomeric state was produced using a 49 MeV pulsed beam of ('13)C on an isotopically enriched ('124)Sn target. The reaction products recoil out of the target and are slowed to thermal velocities in 10 torr of xenon in a region illuminated with circularly polarized light (553.5 nm) from a Coherent 699-21 dye laser. Nuclear parameters measured were the lifetime (3.8(2)(mu)s) and g-factor (g = -.20(1)) of the 10('+) state. Atomic parameters measured for barium were the depolarization cross sections of the ('1)P(,1) atomic level (6.0(6) nm('2)) in xenon, the quenching cross section for hydrogen (0.042(4) nm('2)), and the branching ratio of the metastable (('1,3)D(,1,2,3)) atomic states (0.011(1)). A possible anisotropy signal and the cumulative results (no measurable anisotropy) are presented. Difficulties encountered were insufficient neutralization, and unexpectedly large spatial distribution, and 'trapping' in metastable atomic states.

  13. Measuring picosecond isomerization kinetics via broadband microwave spectroscopy.

    PubMed

    Dian, Brian C; Brown, Gordon G; Douglass, Kevin O; Pate, Brooks H

    2008-05-16

    The rotational spectrum of a highly excited molecule is qualitatively different from its pure rotational spectrum and contains information about the intramolecular dynamics. We have developed a broadband Fourier transform microwave spectrometer that uses chirped-pulse excitation to measure a rotational spectrum in the 7.5- to 18.5-gigahertz range in a single shot and thereby reduces acquisition time sufficiently to couple molecular rotational spectroscopy with tunable laser excitation. After vibrationally exciting a single molecular conformation of cyclopropane carboxaldehyde above the barrier to C-C single-bond isomerization, we applied line-shape analysis of the dynamic rotational spectrum to reveal a product yield and picosecond reaction rate that were significantly different from statistical predictions. The technique should be widely applicable to dynamical studies of radical intermediates, molecular complexes, and conformationally flexible molecules with biological interest.

  14. 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.

  15. Mass spectrometric profiling of flavonoid glycoconjugates possessing isomeric aglycones.

    PubMed

    Abrankó, László; Szilvássy, Blanka

    2015-01-01

    In fields such as food and nutrition science or plant physiology, interest in untargeted profiling of flavonoids continues to expand. The group of flavonoids encompasses several thousands of chemically distinguishable compounds, among which are a number of isobaric compounds with the same elemental composition. Thus, the mass spectrometric identification of these compounds is challenging, especially when reference standards are not available to support their identification. Many different types of isomers of flavonoid glycoconjugates are known, i.e. compounds that differ in their glycosylation position, glycan sequence or type of interglycosidic linkage. This work focuses on the mass spectrometric identification of flavonoid glycoconjugate isomers possessing the same glycan mass and differing only in their aglycone core. A non-targeted HPLC-ESI-MS/MS profiling method using a triple quadrupole MS is presented herein, which utilizes in-source fragmentation and a pseudo-MS(3) approach for the selective analysis of flavonoid glycoconjugates with isomeric/isobaric aglycones. A selective MRM-based identification of the in-source formed isobaric aglycone fragments was established. Additionally, utilizing the precursor scanning capability of the employed triple quadrupole instrument, the developed method enabled the determination of the molecular weight of the studied intact flavonoid glycoconjugate. The versatility of the method was proven with various types of flavonoid aglycones, i.e. anthocyanins, flavonols, flavones, flavanones and isoflavones, along with their representative glycoconjugates. The developed method was also successfully applied to a commercially available sour cherry sample, in which 16 different glycoconjugates of pelargonidin, genistein, cyanidin, kaempferol and quercetin could be tentatively identified, including a number of compounds containing isomeric/isobaric aglycones. PMID:25601677

  16. 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

  17. Morphological considerations pertaining to recognition of atrial isomerism. Consequences for sequential chamber localisation.

    PubMed Central

    Macartney, F J; Zuberbuhler, J R; Anderson, R H

    1980-01-01

    The atrial morphology and venous connections were assessed "blind" in 51 necropsy specimens from patients with visceral heterotaxy. This was compared with bronchial morphology as established by dissection. Six specimens were found to have both atria and bronchi in situs solitus or inversus, and were rejected. In the remainder, atrial isomerism was diagnosed, though this required minor revision of the atrial assessment in two patients. Thirty-four patients had isomeric right atria and bronchi, while 11 had isomeric left atria and bronchi. In seven cases, splenic status was unknown, but in seven of the remaining 38 (18.4%) atrial isomerism was not associated with either asplenia or polysplenia. Nevertheless, right isomerism was strongly associated with total anomalous pulmonary venous drainage (as is asplenia) and left isomerism was likewise associated with interruption of the inferior vena cava (as is polysplenia). Bilateral superior venae cavae and hepatic veins, and absence of the coronary sinus, were frequent in both forms of isomerism (as they are in asplenia and polysplenia). These findings suggest that atrial situs can be defined as solitus inversus, right isomerism, and left isomerism. This determination of atrial situs is quite independent of any other abnormalities of visceral situs. The high incidence of anomalies of both venous return and common atrium resulted in presumed complete mixing of blood at atrial level in all but one patient (97.8%), making the haemodynamic connection between atria and ventricles almost always ambiguous. To describe this anatomical connection as ambiguous when there are two ventricles present is therefore no more than recognition of anatomical and haemodynamic reality. Images PMID:7459148

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    To study the steric effect of the flexible dicarboxylate ligands on the resultant formations of coordination polymers (CPs), four new PbII CPs [Pb(1,2-pda)(H2O)]n (1), [Pb(1,3-pda)]n·nH2O (2), [Pb2(1,4-pda)2(H2O)]n·2nH2O (3a and 3b) have been produced by the isomeric phenylenediacetic acids (H2pda). The X-ray crystallography study reveals that CP 1 is a two-dimensional (2D) 4-connected sql (44.62) network via the weak Pb···O interactions built on 1D chain-like structure. CP 2 crystallizes in orthorhombic system with chiral space group P212121, showing a 4-connected sra (42.63.8) framework where a left-handed helical motif is formed by PbII 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 66 motif, while that of 3b is a (4,6)-connected fsh (43.63)2(46.66.83) 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 H2pda tectons has a positive role in directing the final products of PbII CPs. Also, the fluorescent properties of the CPs were studied in the solid state at room temperature.

  19. Reorientation of Isomeric Butanols: The Multiple Effects of Steric Bulk Arrangement on Hydrogen-Bond Dynamics.

    PubMed

    Mesele, Oluwaseun O; Vartia, Anthony A; Laage, Damien; Thompson, Ward H

    2016-03-01

    Molecular dynamics simulations are used to investigate OH reorientation in the four isomeric butanols in their bulk liquid state to examine the influence of the arrangement of the steric bulk on the alcohol reorientational and hydrogen-bond (H-bond) dynamics. The results are interpreted within the extended jump model in which the OH reorientation is decomposed into contributions due to "jumps" between H-bond partners and "frame" reorientation of the intact H-bonded pair. Reorientation is fastest in iso-butanol and slowest in tert-butanol, while sec- and n-butanol have similar reorientation times. This latter result is a fortuitous cancellation between the jump and frame reorientation in the two alcohols. The extended jump model is shown to provide a quantitative description of the OH reorientation times. A detailed analysis of the jump times shows that a combination of entropic, enthalpic, and dynamical factors, including transition state recrossing effects, all play a role. A simple model based on the liquid structure is proposed to estimate the energetic and entropic contributions to the jump time. This represents the groundwork for a predictive model of OH reorientation in alcohols, but additional studies are required to better understand the frame reorientation and transition state recrossing effects.

  20. 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.

  1. cis-trans-Isomerization of unsaturated fatty acids during /γ-irradiation of barley grains

    NASA Astrophysics Data System (ADS)

    Geißler, Christian; Brede, Ortwin; Reinhardt, Jürgen

    2003-06-01

    Gamma-irradiating barley grains with doses of 10-100 kGy, a dose dependent isomerization of the naturally occurring cis-unsaturated fatty acids such as oleic, cis-vaccenic, linoleic and also of linolenic acid was found. Whereas the effect was negligible up to 10 kGy, at 50 kGy the trans-fatty acid level became comparable to that of other natural products like butter fat which means that there is no essential nutrition danger. The cis-trans-isomerization found in barley grains is explained mainly by a thiyl radical driven process rather than direct isomerization.

  2. 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...

  3. Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining.

    PubMed

    Wedler, Henry B; Pemberton, Ryan P; Lounnas, Valère; Vriend, Gert; Tantillo, Dean J; Wang, Selina C

    2015-05-01

    Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined.

  4. Communication: Effective spectroscopic Hamiltonian for multiple minima with above barrier motion: Isomerization in HO2

    NASA Astrophysics Data System (ADS)

    Barnes, George L.; Kellman, Michael E.

    2010-09-01

    We present a two-dimensional potential surface for the isomerization in the hydroperoxyl radical HO2 and calculate the vibrational spectrum. We then show that a simple effective spectroscopic fitting Hamiltonian is capable of reproducing large scale vibrational spectral structure above the isomerization barrier. Polyad breaking with multiple resonances is necessary to adequately describe the spectral features of the system. Insight into the dynamical nature of isomerization related to the effective Hamiltonian is gained through classical trajectories on the model potential. Contrary to physical intuition, the bend mode is not a "reaction mode," but rather isomerization requires excitation in both stretch and bend. The dynamics reveals a Farey tree formed from the 2:1 and 3:1 resonances, corresponding to the resonance coupling terms in the effective Hamiltonian, with the prominent 5:2 (2:1+3:1) feature dividing the tree into parts that we call the 3:1 and 2:1 portions.

  5. Communication: Effective spectroscopic Hamiltonian for multiple minima with above barrier motion: Isomerization in HO(2).

    PubMed

    Barnes, George L; Kellman, Michael E

    2010-09-14

    We present a two-dimensional potential surface for the isomerization in the hydroperoxyl radical HO(2) and calculate the vibrational spectrum. We then show that a simple effective spectroscopic fitting Hamiltonian is capable of reproducing large scale vibrational spectral structure above the isomerization barrier. Polyad breaking with multiple resonances is necessary to adequately describe the spectral features of the system. Insight into the dynamical nature of isomerization related to the effective Hamiltonian is gained through classical trajectories on the model potential. Contrary to physical intuition, the bend mode is not a "reaction mode," but rather isomerization requires excitation in both stretch and bend. The dynamics reveals a Farey tree formed from the 2:1 and 3:1 resonances, corresponding to the resonance coupling terms in the effective Hamiltonian, with the prominent 5:2 (2:1+3:1) feature dividing the tree into parts that we call the 3:1 and 2:1 portions. PMID:20849156

  6. 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.

  7. 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.

  8. "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.

  9. Spectrophotometric studies on alkaline isomerization of spinach ferredoxin.

    PubMed

    Hasumi, H; Nagata, E; Nakamura, S

    1985-10-01

    The gross protein structure, the microenvironment of the iron-sulfur cluster, and the effect of neutral salts on the molecular structure of spinach ferredoxin were studied by CD and absorption spectroscopy in the alkaline pH range. In the pH range of 7-11, the existence of reversible isomerization which consisted of at least two proton dissociation processes was indicated by the statical CD and absorption spectra. The CD changes in the visible and far-UV regions were dramatic upon elevation of the pH from neutral to alkaline, indicating a significant alteration of the microenvironment of the cluster and a decrease in the ordered secondary structures. The absorption change in the visible region due to pH elevation was small but clearly observed with a high signal-to-noise ratio. The numbers of protons involved in the respective processes and the apparent pK values obtained from the pH-dependence of the CD changes were in good agreement with those obtained from the pH-dependence of the absorption changes in the visible region. In addition, the rate constants obtained from the time courses of the CD and absorption changes agreed with one another. By the addition of 1 M NaCl, the CD and absorption spectra at alkaline pH were reversed almost to those at neutral pH without significant pH change. On the other hand, above pH 11, ferredoxin was found to be irreversibly denatured. Based on analyses of the statical CD and absorption spectra and of the time courses of the CD changes, the probable mechanism of the isomerization was considered to be as follows: (Formula: see text) where H stands for a proton, N-form for native ferredoxin at neutral pH, N*-form for alkaline ferredoxin below pH 11 which still has the iron-sulfur cluster but with disordered secondary structures of the polypeptide chain, and D-form for completely denatured ferredoxin above pH 11. These results lead to the conclusions that (1) the interaction between the protein moiety and the iron-sulfur cluster is

  10. 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

  11. Light-induced isomerization of the LHCII-bound xanthophyll neoxanthin: possible implications for photoprotection in plants.

    PubMed

    Zubik, Monika; Luchowski, Rafał; Grudzinski, Wojciech; Gospodarek, Małgorzata; Gryczynski, Ignacy; Gryczynski, Zygmunt; Dobrucki, Jerzy W; Gruszecki, Wiesław I

    2011-09-01

    Light-harvesting pigment-protein complex of Photosystem II (LHCII) is the largest photosynthetic antenna complex of plants and the most abundant membrane protein in the biosphere. Plant fitness and productivity depend directly on a balance between excitations in the photosynthetic apparatus, generated by captured light quanta, and the rate of photochemical processes. Excess excitation energy leads to oxidative damage of the photosynthetic apparatus and entire organism and therefore the balance between the excitation density and photosynthesis requires precise and efficient regulation, operating also at the level of antenna complexes. We show that illumination of the isolated LHCII leads to isomerization of the protein-bound neoxanthin from conformation 9'-cis to 9',13- and 9',13'-dicis forms. At the same time light-driven excitation quenching is observed, manifested by a decrease in chlorophyll a fluorescence intensity and shortened fluorescence lifetimes. Both processes, the neoxanthin isomerization and the chlorophyll excitation quenching, are reversible in dim light. The results of the 77K florescence measurements of LHCII show that illumination is associated with appearance of the low-energy states, which can serve as energy traps in the pigment-protein complex subjected to excess excitation. Possible sequence of the molecular events is proposed, leading to a protective excess excitation energy quenching: neoxanthin photo-isomerization→formation of LHCII supramolecular structures which potentiate creation of energy traps→excitation quenching.

  12. 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

  13. Bistable molecular switches based on linkage isomerization in ruthenium polypyridyl complexes with a ligand-bound ambidentate motif.

    PubMed

    Johansson, Olof; Johannissen, Linus O; Lomoth, Reiner

    2009-01-01

    Electron-transfer-induced linkage isomerization was investigated in a series of bis-tridentate Ru polypyridyl complexes [Ru(L-X-OH)(Y-tpy)](2+) with ambidentate ligand L-X-OH=bpy-C(R)(OH)-py (bpy=2,2'-bipyridine; py=pyridine; R=H, Me, Ph, or tBu) and spectator ligand Y-tpy (tpy=2,2':6',2''-terpyridine; Y=p-tolyl, p-PhCO(2)Me, Cl, OEt, N-pyrrolidine). The ligand-bound ambidentate motif switches reversibly between N and O coordination in the Ru(II) and Ru(III) state, respectively. The potentials of the Ru(III/II) couple differ by about 0.5 V between the isomers, and this results in a bistable electrochemical response of the molecular switches. The effects of structural modifications in form of substituents on the linking carbon atom of the ambidentate ligand and on the central pyridine moiety of the spectator ligand were investigated by electrochemical and computational methods. Differences in isomerization behavior span six orders of magnitude in rate constants and two orders of magnitude in equilibrium constants. The results can be interpreted in terms of steric and electronic substituent effects and their influence on rotational barriers, ligation geometry, and electron deficiency of the metal center. PMID:19072945

  14. 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

  15. Kinetic analysis for the isomerization of glucose, fructose, and mannose in subcritical aqueous ethanol.

    PubMed

    Gao, Da-Ming; Kobayashi, Takashi; Adachi, Shuji

    2015-01-01

    Fructose, glucose, and mannose were treated with subcritical aqueous ethanol for ethanol concentrations ranging from 0 to 80% (v/v) at 180-200 °C. The aldose-ketose isomerization was more favorable than ketose-aldose isomerization and glucose-mannose epimerization. The isomerization of the monosaccharides was promoted by the addition of ethanol. In particular, mannose was isomerized most easily to fructose in subcritical aqueous ethanol. The apparent equilibrium constants for the isomerizations of mannose to fructose, Keq,M→F, and glucose to fructose, Keq,G→F, were independent of ethanol concentration and increased with increasing temperature. Moreover, the Keq,M→F value was much larger than the Keq,G→F value. The enthalpies for the isomerization of mannose to fructose, ΔHM→F, and glucose to fructose, ΔHG→F, were estimated to be 18 and 24 kJ/mol, respectively, according to van't Hoff equation. Subcritical aqueous ethanol can be used to produce fructose from glucose and mannose efficiently.

  16. Carrot β-carotene degradation and isomerization kinetics during thermal processing in the presence of oil.

    PubMed

    Knockaert, Griet; Pulissery, Sudheer K; Lemmens, Lien; Van Buggenhout, Sandy; Hendrickx, Marc; Van Loey, Ann

    2012-10-17

    The effect of thermal processing (85-130 °C) on the stability and isomerization of β-carotene in both an olive oil/carrot emulsion and an olive oil phase enriched with carrot β-carotene was studied. During processing, degradation of total β-carotene took place. Initially, total β-carotene concentration decreased quickly, after which a plateau value was reached, which was dependent on the applied temperature. In the oil/carrot emulsion, the total β-carotene concentration could be modeled by a fractional conversion model. The temperature dependence of the degradation rate constants was described by the activation energy and was estimated to be 45.0 kJ/mol. In the enriched oil phase, less degradation took place and the results could not be modeled. Besides degradation, β-carotene isomerization was studied. In both matrices, a fractional conversion model could be used to model total isomerization and formation of 13-Z- and 15-Z-β-carotene. β-Carotene isomerization was similar in both the oil/carrot emulsion and enriched oil phase as the simultaneously estimated kinetic parameters (isomerization reaction rate constant and activation energy) of both matrices did not differ significantly. The activation energies of isomerization were estimated to be 70.5 and 75.0 kJ/mol in the oil/carrot emulsion and enriched oil phase, respectively.

  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. RNA-guided isomerization of uridine to pseudouridine—pseudouridylation

    PubMed Central

    Yu, Yi-Tao; Meier, U Thomas

    2014-01-01

    Box H/ACA ribonucleoproteins (RNPs), each consisting of one unique guide RNA and 4 common core proteins, constitute a family of complex enzymes that catalyze, in an RNA-guided manner, the isomerization of uridines to pseudouridines (Ψs) in RNAs, a reaction known as pseudouridylation. Over the years, box H/ACA RNPs have been extensively studied revealing many important aspects of these RNA modifying machines. In this review, we focus on the composition, structure, and biogenesis of H/ACA RNPs. We explain the mechanism of how this enzyme family recognizes and specifies its target uridine in a substrate RNA. We discuss the substrates of box H/ACA RNPs, focusing on rRNA (rRNA) and spliceosomal small nuclear RNA (snRNA). We describe the modification product Ψ and its contribution to RNA function. Finally, we consider possible mechanisms of the bone marrow failure syndrome dyskeratosis congenita and of prostate and other cancers linked to mutations in H/ACA RNPs. PMID:25590339

  19. 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.

  20. 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.

  1. Assembly of a Tyr122 Hydrophobic Cluster in Sarcoplasmic Reticulum Ca2+-ATPase Synchronizes Ca2+ Affinity Reduction and Release with Phosphoenzyme Isomerization.

    PubMed

    Yamasaki, Kazuo; Daiho, Takashi; Danko, Stefania; Suzuki, Hiroshi

    2015-11-13

    The mechanism whereby events in and around the catalytic site/head of Ca(2+)-ATPase effect Ca(2+) release to the lumen from the transmembrane helices remains elusive. We developed a method to determine deoccluded bound Ca(2+) by taking advantage of its rapid occlusion upon formation of E1PCa2 and of stabilization afforded by a high concentration of Ca(2+). The assay is applicable to minute amounts of Ca(2+)-ATPase expressed in COS-1 cells. It was validated by measuring the Ca(2+) binding properties of unphosphorylated Ca(2+)-ATPase. The method was then applied to the isomerization of the phosphorylated intermediate associated with the Ca(2+) release process E1PCa2 → E2PCa2 → E2P + 2Ca(2+). In the wild type, Ca(2+) release occurs concomitantly with EP isomerization fitting with rate-limiting isomerization (E1PCa2 → E2PCa2) followed by very rapid Ca(2+) release. In contrast, with alanine mutants of Leu(119) and Tyr(122) on the cytoplasmic part of the second transmembrane helix (M2) and Ile(179) on the A domain, Ca(2+) release in 10 μm Ca(2+) lags EP isomerization, indicating the presence of a transient E2P state with bound Ca(2+). The results suggest that these residues function in Ca(2+) affinity reduction in E2P, likely via a structural rearrangement at the cytoplasmic part of M2 and a resulting association with the A and P domains, therefore leading to Ca(2+) release.

  2. Tuning structural topologies of three photoluminescent metal-organic frameworks via isomeric biphenyldicarboxylates.

    PubMed

    Guo, Feng; Wang, Fei; Yang, Hui; Zhang, Xiuling; Zhang, Jian

    2012-09-17

    Three new cadmium compounds, [Cd(2,4'-bpdc)(bib)(0.5)] (1; 2,4'-bpdc = biphenyl-2,4'-dicarboxylate and bib = 1,4-bis(2-methyl-imidazol-1-yl)butane), {[Cd(2)(3,4'-bpdc)(2)(bib)(1.5)(H(2)O)](n)·H(2)O}(n) (2; 3,4'-bpdc = biphenyl-3,4'-dicarboxylate), and [Cd (4,4'-bpdc)(bib)] (3; 4,4'-bpdc = biphenyl-4,4'-dicarboxylate), have been successfully synthesized by the assembly of Cd(2+) ions, bib ligands, and isomeric bpdc ligands, respectively. This paper presents a comparative study on the tuning of structural topologies using three isomers of biphenyldicarboxylates as bridging ligands. Compound 1 based on 2,4'-bpdc features a three-dimensional (3D) framework with 6-connected mab topology. Compound 2 based on 3,4'-bpdc is another 3D framework, but it possesses a rare 3-fold interpenetrating 4,6-connected fsh net, while compound 3 based on linear 4,4'-bpdc shows unusual 2D → 3D parallel polycatenation of (4,4) layers. Furthermore, the luminescent properties of three compounds are investigated in the solid state.

  3. 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.

  4. 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

  5. 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.

  6. Modeling trans-cis chromophore isomerization for the asFP595 kindling protein

    NASA Astrophysics Data System (ADS)

    Grigorenko, Bella L.; Nemukhin, Alexander V.

    2007-02-01

    We present the results of modeling properties of the chromophore, 2-acetyl-4-(p-hydroxybenzylidene)-1-methyl-5- imidazolone (AHBMI), from the newly discovered fluorescent protein asFP595 inside the protein environment by using the combined quantum mechanical - molecular mechanical (QM/MM) method. In this approach, the chromophore unit and the side chains of the nearest amino acid residues are assigned to the quantum subsystem. The starting coordinates of heavy atoms were taken from the relevant crystal structures of the protein. Hydrogen atoms were added manually, and the structure of the model protein system was optimized by using QM/MM energy minimization for the trans-form of the chromophore. The Hartree-Fock/6-31G quantum chemical approximation and the AMBER force field parameters were employed in geometry optimization. The points on potential energy surfaces of the ground and first and second excited electronic states were computed with the complete active space self-consistent field approximation in the quantum subsystem under different choices of the QM/MM partitioning. Possible pathways for the trans-cis photo isomerization presumably responsible for the kindling properties of asFP595 as well as other mechanisms of photo excitation are discussed.

  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. 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].

  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. Analysis of atrioventricular junction, ventricular mass, and ventriculoarterial junction in 43 specimens with atrial isomerism.

    PubMed

    De Tommasi, S; Daliento, L; Ho, S Y; Macartney, F J; Anderson, R H

    1981-03-01

    We have analysed the atrioventricular junction, ventricular mass, and ventriculoarterial junction in 43 hearts with isomeric atrial chambers. Of the hearts, 32 had atrial chambers of bilateral right morphology while 11 had atrial chambers with bilateral left atrial characteristics. Among the hearts with right atrial isomerism, there were 13 biventricular hearts, all with ambiguous atrioventricular connection. Eight had a common valve and five had two atrioventricular valves. In the other 19 hearts, the atrial chambers were connected to only one ventricular chamber, 18 having double inlet ventricle through a common valve and the other having absence of the left atrioventricular connection. In these univentricular hearts, all possible types of ventricular morphology were found. The ventriculoarterial junction among these hearts with right isomerism showed great variation. In the hearts with left atrial isomerism, nine hearts had two ventricles and two were univentricular. The biventricular hearts all had ambiguous atrioventricular connection, six via a common valve and three via two valves. The two univentricular hearts both had double inlet via a common valve, one to a chamber of right ventricular type and the other to a chamber of left ventricular type. Both had rudimentary chambers of complementary pattern. The ventriculoarterial junction again showed much variation. Statistical analysis showed that pulmonary obstruction and a univentricular heart were both significantly more frequent in association with right compared with left isomerism. Significant differences were also noted in the two groups in terms of ventriculoarterial connections and infundibular morphology.

  11. A Bio-Inspired, Catalytic E → Z Isomerization of Activated Olefins.

    PubMed

    Metternich, Jan B; Gilmour, Ryan

    2015-09-01

    Herein, Nature's flavin-mediated activation of complex (poly)enes has been translated to a small molecule paradigm culminating in a highly (Z)-selective, catalytic isomerization of activated olefins using (-)-riboflavin (up to 99:1 Z/E). In contrast to the prominent Z → E isomerization of the natural system, it was possible to invert the directionality of the isomerization (E → Z) by simultaneously truncating the retinal scaffold, and introducing a third olefin substituent to augment A1,3-strain upon isomerization. Consequently, conjugation is reduced in the product chromophore leading to a substrate/product combination with discrete photophysical signatures. The operationally simple isomerization protocol has been applied to a variety of enone-derived substrates and showcased in the preparation of the medically relevant 4-substituted coumarin scaffold. A correlation of sensitizer triplet energy (ET) and reaction efficiency, together with the study of additive effects and mechanistic probes, is consistent with a triplet energy transfer mechanism.

  12. Kinetics of the thermal decomposition and isomerization of pyrazine (1,4 diazine)

    SciTech Connect

    Doughty, A.; Mackie, J.C.; Palmer, J.M.

    1994-12-31

    The isomerization and decomposition of pyrazine have been studied over the temperature range 1,200--1,480 K. The major products of decomposition were found to be acetylene and HCN, with cyanoacetylene and acrylonitrile also being significant products, although lower yields of these products were observed. The decomposition has been successfully modeled using a free radical mechanisms, with the major chain carriers being CN radicals and H atoms. The initiation reaction was found to be C{single_bond}H bond fission, to yield H atoms and pyrazyl radicals. Kinetic modeling allowed the rate of initiation to be determined, yielding a first-order rate constant given by the expression k = 10{sup 15.7} exp({minus}96.5 kcal/mol/RT) s{sup {minus}1}. The importance of CN radicals as chain carriers appears to be a significant difference in the decomposition of the dizziness compared with pyridine or 2-picoline. Accompanying the decomposition of pyrazine was the isomerization of pyrazine to pyrimidine. By kinetic modeling, the isomerization of pyrazine to pyrimidine was found to occur via a fulvenelike intermediate. The rate and mechanism of the isomerization are analogous to the isomerization of fulvene to benzene described by Melius and Miller. The thermal reactions of these species are being studied because of their relevance to the mechanism of formation of NO{sub x} through the oxidation of fuel-bound nitrogen (FBN) in coal during the combustion of coal and heavy fuels.

  13. 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

  14. Kinetics of trans-cis isomerization in azobenzene dimers at an air-water interface

    SciTech Connect

    Kumar, Bharat; Suresh, K. A.

    2009-08-15

    We have studied the kinetics of trans to cis isomerization under the illumination of ultraviolet light, in the Langmuir monolayer of mesogenic azobenzene dimer, bis-[5-(4{sup '}-n-dodecyloxy benzoyloxy)-2-(4{sup ''}-methylphenylazo)phenyl] adipate, at an air-water interface. We find that the trans to cis isomerization reaction of the molecules in the monolayer shows deviation from the first-order kinetics unlike those reported on Langmuir monolayers of azobenzene molecules. We attribute the deviation from first-order kinetics to the simultaneous photoisomerization of trans isomers to form cis isomers and the reverse thermal isomerization of cis isomers to form trans isomers. Our analysis of the rate of change of mole fraction of trans isomers to form cis isomers indicates a first-order kinetics for trans to cis photoisomerization reaction and a second-order kinetics for cis to trans thermal isomerization reaction. This second-order kinetics mechanism is similar to the Lindemann-Hinshelwood mechanism for the unimolecular reactions at low concentration of reactants. The formation of the activated cis isomer by collisions is a slow process as compared to the decay of the activated cis isomer to trans isomer in the liquid expanded phase. This results in the second-order kinetics for the thermal isomerization of cis isomers.

  15. Formation, isomerization, and dissociation of alpha-carbon-centered and pi-centered glycylglycyltryptophan radical cations

    SciTech Connect

    Ng, Dominic C.; Song, Tao; Siu, Shiu On; Siu, Chi-Kit; Laskin, Julia; Chu, Ivan K.

    2010-02-11

    Gas phase fragmentations of two isomeric radical cationic tripeptides of glycylglycyltryptophan-G•GW+ and [GGW]•+—with well-defined initial radical sites at the α-carbon atom and the 3-methylindole ring, respectively, have been studied using collision-induced dissociation (CID), density functional theory (DFT), and Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Substantially different low-energy CID spectra were obtained for these two isomeric GGW structures, suggesting that they did not interconvert on the time scale of these experiments. DFT and RRKM calculations were used to investigate the influence of the kinetics, stabilities, and locations of the radicals on the competition between the isomerization and dissociation channels. The calculated isomerization barrier between the GGW radical cations (>35.4 kcal/mol) was slightly higher than the barrier for competitive dissociation of these species (<30.5 kcal/mol); the corresponding microcanonical rate constants for isomerization obtained from RRKM calculations were all considerably lower than the dissociation rates at all internal energies. Thus, interconversion between the GGW isomers examined in this study cannot compete with their fragmentations.

  16. 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.

  17. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO ↔ HOCN Isomerization.

    PubMed

    Lattanzi, Valerio; Thorwirth, Sven; Gottlieb, Carl A; McCarthy, Michael C

    2012-12-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH(+) have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO(+) with C2v symmetry and a low-lying bent chain HNCOH(+), guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH(+) is found to be more abundant than H2NCO(+), even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH(+) serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH(+) may play an analogous role in the conversion of HNCO to HOCN.

  18. Experimental apparatus at KUR-ISOL to identify isomeric transitions from fission products, and decay spectroscopy of 151Ce

    NASA Astrophysics Data System (ADS)

    Kojima, Y.; Shibata, M.; Taniguchi, A.; Kawase, Y.; Doi, R.; Nagao, A.; Shizuma, K.

    2006-08-01

    Decay studies on 151Ce have been performed using the on-line isotope separator connected to the Kyoto University Reactor. In addition to conventional γ and conversion electron spectroscopy, β-gated measurements were carried out on mass-separated 151Ce to identify an isomeric transition. From the analysis of the obtained data, the half-life of the isotope was ascertained to be 1.76(6) s and a decay scheme containing six excited levels was constructed for the first time. The excited level at 35.1 keV in 151Pr was found to be a long-lived state (a half-life of approximately 10 μs or longer).

  19. 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

  20. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO-HOCN Isomerization

    NASA Astrophysics Data System (ADS)

    Lattanzi, V.; Thorwirth, S.; Gottlieb, C. A.; McCarthy, M. C.

    2012-11-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH+ have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO+ with C2v symmetry and a low-lying bent chain HNCOH+, guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH+ is found to be more abundant than H2NCO+, even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH+ serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH+ may play an analogous role in the conversion of HNCO to HOCN.

  1. Two Isomers of Protonated Isocyanic Acid: Evidence for an Ion-Molecule Pathway for HNCO ↔ HOCN Isomerization.

    PubMed

    Lattanzi, Valerio; Thorwirth, Sven; Gottlieb, Carl A; McCarthy, Michael C

    2012-12-01

    Ion-molecule reactions are thought to play a crucial role in the formation of metastable isomers, but relatively few protonated intermediates beyond HNCH(+) have been characterized at high spectral resolution. We present here laboratory measurements of the rotational spectra of protonated isocyanic acid in two isomeric forms, the ground state H2NCO(+) with C2v symmetry and a low-lying bent chain HNCOH(+), guided by coupled cluster calculations of their molecular structure. Somewhat surprisingly, HNCOH(+) is found to be more abundant than H2NCO(+), even though this metastable isomer is calculated to lie approximately 15-20 kcal/mol higher in energy. In the same way that HCNH(+) serves as a key intermediate in ion-molecule reactions that form HNC via dissociative electron recombination in cold dense interstellar molecular clouds, HNCOH(+) may play an analogous role in the conversion of HNCO to HOCN. PMID:26290966

  2. Formation and decay of fluorobenzene radical anions affected by their isomeric structures and the number of fluorine atoms.

    PubMed

    Higashino, Saki; Saeki, Akinori; Okamoto, Kazumasa; Tagawa, Seiichi; Kozawa, Takahiro

    2010-08-12

    Aryl fluoride has attracted much attention as a resist component for extreme ultraviolet (EUV) lithography, because of the high absorption cross section of fluorine for EUV photons; however, less is known about electron attachment to fluorobenzene (FBz) and the stability of the reduced state. Picosecond and nanosecond pulse radiolysis of tetrahydrofuran solutions of FBz from mono-, di-, tri-, tetra-, penta-, and hexafluorobenzene was performed, and the effects of isomeric structure and number of fluorine atoms were examined. Scavenging of solvated electrons was found to correlate with the electron affinity obtained by density functional theory in the gas phase, whereas the decay of FBz radical anions was dominated by the activation energy of fluorine anion dissociation calculated using a polarized continuum model (PCM). A sharp contrast in the lifetimes of ortho-, meta-, and para-position difluorobenzene was observed, which could provide information on the molecular design of functional materials.

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Mechanism of isomerization of 11-cis-retinal in lipid dispersions by aromatic amines

    SciTech Connect

    Fulton, B.S.; Rando, R.R.

    1987-01-13

    It has previously been shown that retinotoxic, primary aromatic amines catalyze the isomerization of 11-cis-retinal to its all-trans congener after Schiff base formation. This process led to the short-circuiting of the visual cycle and the observed retinotoxicity when it occurred in vivo. The catalysis was also observed to occur in vitro in phosphatidylcholine-based vesicles but not in hydrocarbon solutions. The rate of isomerization of an aromatic amine Schiff base of 11-cis-retinal in the phospholipid vesicles was typically 10/sup 3/-fold more rapid than in hydrocarbon solutions. In this article, the mechanistic basis of this apparently membrane-specific catalysis is described. It was found that the rate enhancement effect observed was independent of the lipid used. Moreover, a bilayer structure was not important because rate enhancements were also observed in micelles. The rapid isomerization rates observed in lipid dispersions appear not be free radical initiated because free radical quenching agents, such as ..cap alpha..-tocopherol and BETA-carotene, had little effect on the isomerization rates. It was further found that aliphatic amines, such as n-dodecylamine, could be substituted for the aromatic amines in phospholipid. Finally, and most importantly, it was found that the isomerization of the aromatic amine retinal Schiff bases in phospholipid vesicles was acid-catalyzed. It is concluded that the rate enhancements observed for the isomerization of 11-cis-retinal aromatic amine Schiff bases in lipid dispersions over that in hydrocarbon solvents are due to the occurrence of acid-base catalysis in the former.

  11. Lycopene inhibits the isomerization of β-carotene during quenching of singlet oxygen and free radicals.

    PubMed

    Heymann, Thomas; Heinz, Philipp; Glomb, Marcus A

    2015-04-01

    The present study aimed to investigate the influence of singlet oxygen and radical species on the isomerization of carotenoids. On the one hand, lycopene and β-carotene standards were incubated with 1,4-dimethylnaphthalene-1,4-endoperoxide that produced singlet oxygen in situ. (13Z)- and (15Z)-β-carotene were preferentially generated at low concentrations of singlet oxygen, while high concentrations resulted in formation of (9Z)-β-carotene. The addition of different concentrations of lycopene led to the same isomerization progress of β-carotene, but resulted in a decreased formation of (9Z)-β-carotene and retarded degradation of (all-E)-β-carotene. On the other hand, isomerization of β-carotene and lycopene was induced by ABTS-radicals, too. As expected from the literature, chemical quenching was observed especially for lycopene, while physical quenching was preferred for β-carotene. Mixtures of β-carotene and lycopene resulted in a different isomerization progress compared to the separate β-carotene model. As long as lycopene was present, almost no isomerization of β-carotene was triggered; after that, strong formation of (13Z)-, (9Z)-, and (15Z)-β-carotene was initiated. In summary, lycopene protected β-carotene against isomerization during reactions with singlet oxygen and radicals. These findings can explain the pattern of carotenoid isomers analyzed in fruits and vegetables, where lycopene containing samples showed higher (all-E)/(9Z)-β-carotene ratios, and also in in vivo samples such as human blood plasma.

  12. cis-trans isomerization of carbon double bonds in monounsaturated triacylglycerols via generation of free radicals.

    PubMed

    Tsuzuki, Wakako

    2010-09-01

    We investigated the heat-induced cis/trans isomerization of double bonds in monounsaturated lipids. When triolein (9-cis, 18:1) was heated around 180 degrees C, small amounts of isomerization products were obtained depending on the heating period. The heat-induced isomerization of triolein was considerably suppressed by the addition of different antioxidants or under nitrogen stream, and these additives simultaneously inhibited the thermal oxidation of double bonds in triolein. Therefore, an intermediate of the thermal oxidation reaction might be responsible for the heat-induced isomerization of the double bonds in triolein. The thermodynamics of the heat-induced isomerization of triolein (9-cis, 18:1) and trielaidin (9-trans, 18:1) were investigated using Arrhenius plot. The Arrhenius activation energies of cis double bonds in triolein and trans double bonds in trielaidin were 106 kJ/mol and 137 kJ/mol, respectively. The calculated internal rotational barrier heights of these double bonds were similar to those of the double bond of 2-butene radical and significantly lower than those of non-radicalized double bonds in 2-butene. These results suggest that heat-induced cis/trans isomerization of triolein and trielaidin occurs mainly through the formation of radical species, which are the intermediates produced during thermal oxidation. The activation energy difference between the two forms suggests that trans trielaidin radicals are more stable than cis triolein radicals. The high thermodynamic stability of the trans double bonds in lipid radicals would influence the population of cis and trans isomers in edible oils and contribute to slight accumulation of trans-18:1 isomers during heating or industrial processing.

  13. Lycopene inhibits the isomerization of β-carotene during quenching of singlet oxygen and free radicals.

    PubMed

    Heymann, Thomas; Heinz, Philipp; Glomb, Marcus A

    2015-04-01

    The present study aimed to investigate the influence of singlet oxygen and radical species on the isomerization of carotenoids. On the one hand, lycopene and β-carotene standards were incubated with 1,4-dimethylnaphthalene-1,4-endoperoxide that produced singlet oxygen in situ. (13Z)- and (15Z)-β-carotene were preferentially generated at low concentrations of singlet oxygen, while high concentrations resulted in formation of (9Z)-β-carotene. The addition of different concentrations of lycopene led to the same isomerization progress of β-carotene, but resulted in a decreased formation of (9Z)-β-carotene and retarded degradation of (all-E)-β-carotene. On the other hand, isomerization of β-carotene and lycopene was induced by ABTS-radicals, too. As expected from the literature, chemical quenching was observed especially for lycopene, while physical quenching was preferred for β-carotene. Mixtures of β-carotene and lycopene resulted in a different isomerization progress compared to the separate β-carotene model. As long as lycopene was present, almost no isomerization of β-carotene was triggered; after that, strong formation of (13Z)-, (9Z)-, and (15Z)-β-carotene was initiated. In summary, lycopene protected β-carotene against isomerization during reactions with singlet oxygen and radicals. These findings can explain the pattern of carotenoid isomers analyzed in fruits and vegetables, where lycopene containing samples showed higher (all-E)/(9Z)-β-carotene ratios, and also in in vivo samples such as human blood plasma. PMID:25803572

  14. Metamorphic protein IscU changes conformation by cis-trans isomerizations of two peptidyl-prolyl peptide bonds.

    PubMed

    Dai, Ziqi; Tonelli, Marco; Markley, John L

    2012-12-01

    IscU from Escherichia coli, the scaffold protein for iron-sulfur cluster biosynthesis and transfer, populates two conformational states with similar free energies and with lifetimes on the order of 1 s that interconvert in an apparent two-state reaction. One state (S) is structured, and the other (D) is largely disordered; however, both play essential functional roles. We report here nuclear magnetic resonance studies demonstrating that all four prolyl residues of apo-IscU (P14, P35, P100, and P101) are trans in the S state but that two absolutely conserved residues (P14 and P101) become cis in the D state. The peptidyl-prolyl peptide bond configurations were determined by analyzing assigned chemical shifts and were confirmed by measurements of nuclear Overhauser effects. We conclude that the S ⇄ D interconversion involves concerted trans-cis isomerization of the N13-P14 and P100-P101 peptide bonds. Although the D state is largely disordered, we show that it contains an ordered domain that accounts for the stabilization of two high-energy cis peptide bonds. Thus, IscU may be classified as a metamorphic protein.

  15. Identification of a new isomer from a reversible isomerization of ceftriaxone in aqueous solution.

    PubMed

    Tian, Ye; Lu, Li; Chang, Yan; Zhang, Dou-sheng; Li, Jin; Feng, Yan-Chun; Hu, Chang-Qin

    2015-01-01

    A reversible isomerization of ceftriaxone in aqueous solution was observed, and the structure of the isomer was determined by mass spectrometry and various 1D and 2D NMR techniques. The mechanism of isomerization was also discussed. Finally, molecular docking simulations were performed and the antimicrobial activities of the isomers were measured. This showed that the biological activity of ceftriaxone was stronger than that of its isomer. The results reported in this article may be important to quality control requirements and to the stability of ceftriaxone products.

  16. Preparing isomerically pure beams of short-lived nuclei at JYFLTRAP

    NASA Astrophysics Data System (ADS)

    Eronen, T.; Elomaa, V.-V.; Hager, U.; Hakala, J.; Jokinen, A.; Kankainen, A.; Rahaman, S.; Rissanen, J.; Weber, C.; Äystö, J.

    2008-10-01

    A new procedure to prepare isomerically clean samples of short-lived ions with a mass resolving power of more than 1 × 105 has been developed at the JYFLTRAP tandem Penning trap system. The method utilises a dipolar rf-excitation of the ion motion with separated oscillatory fields in the precision trap. During a subsequent retransfer to the purification trap, the contaminants are rejected and as a consequence, the remaining bunch is isomerically cleaned. This newly-developed method is suitable for very high-resolution cleaning and is at least a factor of five faster than the methods used so far in Penning trap mass spectrometry.

  17. Ruthenium hydride-promoted dienyl isomerization: access to highly substituted 1,3-dienes.

    PubMed

    Clark, Joseph R; Griffiths, Justin R; Diver, Steven T

    2013-03-01

    Ruthenium hydrides were found to promote the positional isomerization of 1,3-dienes into more highly substituted 1,3-dienes in a stereoconvergent manner. The reaction can be conducted in one pot starting with terminal alkynes and alkenes by triggering decomposition of the Grubbs catalyst into a ruthenium hydride, which promotes the dienyl isomerization. The presence of an alcohol additive plays a helpful role in the reaction, significantly increasing the chemical yields. Mechanistic studies are consistent with hydrometalation of the geminally substituted alkene of the 1,3-diene and transit of the ruthenium atom across the diene framework via a π-allylruthenium intermediate. PMID:23427813

  18. Unprecedented cobalt-catalyzed isomerization reactions to single skipped 2,4,7-trienes applied in the synthesis of urushiol.

    PubMed

    Schmidt, Anastasia; Hilt, Gerhard

    2014-09-01

    The cobalt-catalyzed isomerization of 1,3-dienes to 2Z,4E-dienes was realized for the very challenging substrates with an additional double bond in the side chain. An isomerization to the conjugated 3,5,7-triene derivative was not observed, which is in stark contrast to observations with many other isomerization catalysts. Accordingly, the synthesis of the natural product urushiol, which has a sensitive 2Z,4E,7Z-triene subunit in the side chain, was investigated. The O-protected urushiol derivative was generated selectively without isomerization to the conjugated 3,5,7-triene or Z/E-isomerization of the double bond at position 7.

  19. 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.

  20. 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

  1. 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

  2. Experimental and density functional theoretical investigations of linkage isomerism in six-coordinate FeNO(6) iron porphyrins with axial nitrosyl and nitro ligands.

    PubMed

    Novozhilova, Irina V; Coppens, Philip; Lee, Jonghyuk; Richter-Addo, George B; Bagley, Kimberly A

    2006-02-15

    A critical component of the biological activity of NO and nitrite involves their coordination to the iron center in heme proteins. Irradiation (330 < lambda < 500 nm) of the nitrosyl-nitro compound (TPP)Fe(NO)(NO(2)) (TPP = tetraphenylporphyrinato dianion) at 11 K results in changes in the IR spectrum associated with both nitro-to-nitrito and nitrosyl-to-isonitrosyl linkage isomerism. Only the nitro-to-nitrito linkage isomer is obtained at 200 K, indicating that the isonitrosyl linkage isomer is less stable than the nitrito linkage isomer. DFT calculations reveal two ground-state conformations of (porphine)Fe(NO)(NO(2)) that differ in the relative axial ligand orientations (i.e., GS parallel and GS perpendicular). In both conformations, the FeNO group is bent (156.4 degrees for GS parallel, 159.8 degrees for GS perpendicular) for this formally {FeNO}(6) compound. Three conformations of the nitrosyl-nitrito isomer (porphine)Fe(NO)(ONO) (MSa parallel, MSa perpendicular, and MSa(L)) and two conformations of the isonitrosyl-nitro isomer (porphine)Fe(ON)(NO(2)) (MSb parallel and MSb perpendicular) are identified, as are three conformations of the double-linkage isomer (porphine)Fe(ON)(ONO) (MSc parallel, MSc perpendicular, MSc(L)). Only 2 of the 10 optimized geometries contain near-linear FeNO (MSa(L)) and FeON (MSc(L)) bonds. The energies of the ground-state and isomeric structures increase in the order GS < MSa < MSb < MSc. Vibrational frequencies for all of the linkage isomers have been calculated, and the theoretical gas-phase absorption spectrum of (porphine)Fe(NO)(NO(2)) has been analyzed to obtain information on the electronic transitions responsible for the linkage isomerization. Comparison of the experimental and theoretical IR spectra does not provide evidence for the existence of a double linkage isomer of (TPP)Fe(NO)(NO(2)).

  3. 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.

  4. 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

  5. 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...

  6. 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.

  7. A novel base-induced isomerization gives access to unprecedented (E)-exo-glycals.

    PubMed

    Eppe, Guillaume; Dumitrescu, Lidia; Pierrot, Olivier; Li, Tianlei; Pan, Weidong; Vincent, Stéphane P

    2013-08-26

    Bump the base: This study reports the discovery of the base-induced Z-to-E isomerization of exo-glycals bearing an electron-withdrawing group (EWG). The scope of this novel transformation regarding the carbohydrate unit is also discussed. After elucidating the mechanism, preparation of novel (E)-exo- glycals was performed (TBS = tert-butyldimethylsilyl).

  8. 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…

  9. 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.

  10. 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

  11. 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

  12. Asymmetric Synthesis of Trifluoromethylated Amines via Catalytic Enantioselective Isomerization of Imines

    PubMed Central

    Wu, Yongwei

    2012-01-01

    A new approach toward the asymmetric synthesis of optically active trifluromethylated 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 enantioselecitivities. PMID:22906148

  13. Relation of the acidity of amorphous aluminosilicates with their activity and selectivity in isomerization of xylenes

    SciTech Connect

    Zadymov, V.V.; Lupina, M.I.; Kaliko, M.A.

    1981-01-01

    Conversion of m-xylene on amorphous aluminosilicates is determined by overall surface acidity. The formation of acid centres with pK a greater than or equal toapprox. =-10 as a result of heat-steam treatment of aluminosilicates and a reduction in the number of strong centres increases selectivity in isomerization of m-xylene.

  14. Water-assisted isomerization of the [H, C, N, O] system.

    PubMed

    Cao, Jia; Wang, Zhi Xiang; Gao, Lou Jun; Fu, Feng

    2015-03-01

    Ten minima of [H, C, N, O] isomers were investigated in gas phase and water solution using the polarizable continuum model at the CCSD(T)//M06-2X/6-311 + G(3df,2p) level of theory. The results show that the stability order of all isomers in water solution is HNCO > HOCN > HCNO > HONC > Y-OC(H)N > cycl-OCN(H)-a ≈ cycl-OCN(H)-b > cycl-NCO(H) > HNOC > HCON, i.e., the same as that in the gas phase. Potential energy surfaces of [H, C, N, O] system isomerization were constructed in gas phase and in water solution, showing that the isomerization of [H, C, N, O] isomers in gas phase is unfavorable because of the high barrier height. Interestingly, although the water solvent has a little impact on the isomeric mechanism, water molecules (H2O)n(n = 1-3) acting as catalyst dramatically lower the barrier height in the hydrogen transfer processes (HCNO → HONC, HNCO → HOCN, and HCON → HNOC). Water is the most abundant compound in the interstellar area. These results give new insight into the mechanism of [H, C, N, O] system isomerization in interstellar gas. Enthalpies of formation of the isomers were predicted at the CBS-QB3, G4MP2 and W1U levels. PMID:25739567

  15. 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...

  16. Isomerization of cis-1,2-dimethylcyclohexane in single-pulse shock tube experiments.

    PubMed

    Rosado-Reyes, Claudette M; Tsang, Wing

    2014-09-11

    Cyclic hydrocarbons are major constituents of jet fuels and reference compounds in jet fuel surrogates. The kinetic and thermal stability and reaction mechanisms of fuel molecules are essential input parameters in the models and simulations used in the design of novel fuels, renewable energy technologies, and devices. A detailed study and analysis of the pyrolytic chemistry of cis-1,2-dimethylcyclohexane has been performed in single-pulse shock tube experiments. The investigations are carried out over the temperature range of 1100 to 1200 K at about 2.5 atm pressure. The isomeric products are trans-1,2-dimethylcyclohexane, 1-octene, and (cis + trans)-2-octene. The three octene isomers can be attributed to internal disproportionation processes. Assuming a diradical mechanism and that cis-1,2-dimethylcyclohexane is formed in equal amount with respect to its trans isomer, the total rate expression for isomerization is kC-C = 10(15.5±0.8) exp(-38,644 ± 2061 K/T) s(-1). The rate constants are over an order of magnitude smaller than the equivalent noncyclic hydrocarbon system. The presence of the isomeric octenes suggests that internal disproportionation is an important component of the isomerization process. PMID:25083602

  17. 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...

  18. 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

  19. 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

  20. 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.

  1. 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

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

    PubMed

    Loomba, Rohit

    2015-11-19

    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 10(9)/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

  3. 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

  4. A coupled cluster study of the structures, spectroscopic properties, and isomerization path of NCS - and CNS -

    NASA Astrophysics Data System (ADS)

    Pak, Youngshang; Woods, R. Claude; Peterson, Kirk A.

    1995-12-01

    Three-dimensional near-equilibrium potential energy surfaces and dipole moment functions have been calculated for the X 1Σ+ ground states of NCS- and CNS-, using the coupled cluster method with single and double substitutions augmented by a perturbative estimate of triple excitations [CCSD(T)] with a set of 154 contracted Gaussian-type orbitals. The corresponding equilibrium bond lengths at their linear geometries are re(NC)=1.1788 Å and re(CS)=1.6737 Å for NCS-, and re(CN)=1.1805 Å and re(NS)=1.6874 Å for CNS-. The predicted equilibrium rotational constants Be of NCS- and CNS- are 5918.2 and 6282.7 MHz, respectively. The former agrees very well with the known experimental value (5919.0 MHz). Full three-dimensional variational calculations have also been carried out using the CCSD(T) potential energy and dipole moment functions to determine the rovibrational energy levels and dipole moment matrix elements for both NCS- and CNS-. The corresponding fundamental band origins (cm-1) ν1, ν2, and ν3 and their absolute intensities (km/mol) at the CCSD(T) level are 2060.9/306.1, 451.5/2.2, and 707.5/12.8, respectively, for NCS- and 2011.4/6.6, 343.7/2.3, and 624.9/0.2 for CNS-. The calculated ν1 (CN stretching) value for NCS- is in very good agreement with the experimental result, 2065.9 cm-1. The calculated dipole moments of NCS- and CNS- in their ground vibrational states are 1.427 and 1.347 D, respectively. The transition state geometry (saddle point) for the isomerization of NCS-→CNS- is predicted at the CCSD(T) level to be r(NC)=1.2044 Å, R(CS)=1.9411 Å and θ(∠NCS)=86.8°. Its calculated energy is 62.6 and 26.5 kcal/mol above the minima of NCS- and CNS-, respectively, including zero-point energy corrections. The structure of the NCS radical was also optimized at the same level of theory, yielding ion to neutral bond length shifts in excellent agreement with those derived from recent photoelectron spectroscopy experiments.

  5. Identification of isomerization and racemization of aspartate in the Asp-Asp motifs of a therapeutic protein.

    PubMed

    Zhang, Jennifer; Yip, Holly; Katta, Viswanatham

    2011-03-15

    A thermally stressed Fab molecule showed a significant increase of basic variants in imaged capillary isoelectric focusing (iCIEF) analysis. Mass analyses of the reduced protein found an increase in -18Da species from both light chain and heavy chain. A tryptic peptide map identified two isoAsp-containing peptides, both containing Asp-Asp motifs and located in complementarity-determining regions (CDRs) of light chains and heavy chains, respectively. The approaches of hydrolyzing succinimide in H(2)(18)O followed by tryptic digestion were used to label and identify the sites of isomerization. This method enabled identification of the isomerization site by comparing the MS/MS spectra of isomerized peptides with and without (18)O incorporation. The light chain peptide L2 VTITCITSTDID(12)DDMNWYQQKPGK underwent simultaneous isomerization and recemization at residue Asp-12 after thermal stress as evidenced by the coinjection of synthetic peptide L2 with l-Asp-12, l-isoAsp-12, d-Asp-12, and d-isoAsp-12, respectively. A thermal stress study of the synthetic peptide (l-)L2 showed that the isomerization and racemization did not occur, indicating that the Asp degradation in this Asp-Asp motif is more related to the protein conformation than the primary sequence. Another isomerization site was identified as Asp-24 in the heavy chain peptide H5 QAPGQGLEWMGWINTYTGETTYAD(24)DFK. No other isomerizations were detected in CDR peptides containing either Asp-Ser or Asp-Thr motifs.

  6. 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.

  7. 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.

  8. Core-coupled states and split proton-neutron quasiparticle multiplets in 122-126Ag

    NASA Astrophysics Data System (ADS)

    Lalkovski, S.; Bruce, A. M.; Jungclaus, A.; Górska, M.; Pfützner, M.; Cáceres, L.; Naqvi, F.; Pietri, S.; Podolyák, Zs.; Simpson, G. S.; Andgren, K.; Bednarczyk, P.; Beck, T.; Benlliure, J.; Benzoni, G.; Casarejos, E.; Cederwall, B.; Crespi, F. C. L.; Cuenca-García, J. J.; Cullen, I. J.; Denis Bacelar, A. M.; Detistov, P.; Doornenbal, P.; Farrelly, G. F.; Garnsworthy, A. B.; Geissel, H.; Gelletly, W.; Gerl, J.; Grebosz, J.; Hadinia, B.; Hellström, M.; Hinke, C.; Hoischen, R.; Ilie, G.; Jaworski, G.; Jolie, J.; Khaplanov, A.; Kisyov, S.; Kmiecik, M.; Kojouharov, I.; Kumar, R.; Kurz, N.; Maj, A.; Mandal, S.; Modamio, V.; Montes, F.; Myalski, S.; Palacz, M.; Prokopowicz, W.; Reiter, P.; Regan, P. H.; Rudolph, D.; Schaffner, H.; Sohler, D.; Steer, S. J.; Tashenov, S.; Walker, J.; Walker, P. M.; Weick, H.; Werner-Malento, E.; Wieland, O.; Wollersheim, H. J.; Zhekova, M.

    2013-03-01

    Neutron-rich silver isotopes were populated in the fragmentation of a 136Xe beam and the relativistic fission of 238U. The fragments were mass analyzed with the GSI Fragment Separator and subsequently implanted into a passive stopper. Isomeric transitions were detected by 105 high-purity germanium detectors. Eight isomeric states were observed in 122-126Ag nuclei. The level schemes of 122,123,125Ag were revised and extended with isomeric transitions being observed for the first time. The excited states in the odd-mass silver isotopes are interpreted as core-coupled states. The isomeric states in the even-mass silver isotopes are discussed in the framework of the proton-neutron split multiplets. The results of shell-model calculations, performed for the most neutron-rich silver nuclei are compared to the experimental data.

  9. Fetal Heterotaxy with Tricuspid Atresia, Pulmonary Atresia, and Isomerism of the Right Atrial Appendages at 22 Weeks

    PubMed Central

    Solomon, Julia E.; Stock, John H.; Richardson, Randy R.; Silverman, Norman H.

    2013-01-01

    We report the accurate prenatal diagnosis at 22 weeks gestation of right atrial isomerism in association with tricuspid atresia. Several distinctive sonographic features of isomerism of the right atrial appendages were present in this fetus: complex cardiac abnormality, ventriculoarterial discordance, juxtaposition of the aorta and the inferior vena cava to the right side, pulmonary atresia, and anomalous pulmonary venous return to the morphological right atrium. Tricuspid atresia, which is an extremely rare lesion within heterotaxy spectrum disorders, was present. Postnatal investigations confirmed all prenatally diagnosed abnormalities, with additional findings of pulmonary atresia with discontinuous pulmonary arteries and bilateral arterial ducts, asplenia, and bilateral eparterial bronchi. To our knowledge, tricuspid atresia in the setting of isomerism of the right atrial appendages has not previously been diagnosed or reported prenatally. Because of the complexity of cardiac lesions that may be present in cases of atrial isomerism, these disorders should be considered even if sonographic findings are uncommon or atypical. PMID:24147244

  10. 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...

  11. 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

  12. Green-lighting green fluorescent protein: Faster and more efficient folding by eliminating a cis–trans peptide isomerization event

    PubMed Central

    Rosenman, David J; Huang, Yao-ming; Xia, Ke; Fraser, Keith; Jones, Victoria E; Lamberson, Colleen M; Van Roey, Patrick; Colón, Wilfredo; Bystroff, Christopher

    2014-01-01

    Wild-type green fluorescent protein (GFP) folds on a time scale of minutes. The slow step in folding is a cis–trans peptide bond isomerization. The only conserved cis-peptide bond in the native GFP structure, at P89, was remodeled by the insertion of two residues, followed by iterative energy minimization and side chain design. The engineered GFP was synthesized and found to fold faster and more efficiently than its template protein, recovering 50% more of its fluorescence upon refolding. The slow phase of folding is faster and smaller in amplitude, and hysteresis in refolding has been eliminated. The elimination of a previously reported kinetically trapped state in refolding suggests that X-P89 is trans in the trapped state. A 2.55 Å resolution crystal structure revealed that the new variant contains only trans-peptide bonds, as designed. This is the first instance of a computationally remodeled fluorescent protein that folds faster and more efficiently than wild type. PMID:24408076

  13. 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

  14. Reversible Z-E isomerism and pharmaceutical implications for SU5416.

    PubMed

    Sistla, Anand; Shenoy, Narmada

    2005-12-01

    SU5416 (Z-isomer), the first in its class of angiogenesis inhibitors, in solution converts to the E-isomer following light exposure and reverts to the Z-isomer in the dark. Kinetics of this Z-E isomerism in pharmaceutical media is reported. Analytical solutions need light protection at 5 degrees C to maintain integrity. While E-isomer in light-exposed product increased to 0.9% in 24 hours, light-protected product showed no change (25 degrees C, 18 months). Infusate studies indicated that < 1.9% E-isomer will be dosed to patients and would likely convert to the Z-isomer, following administration. This report implies Z-E isomerism in SU5416 is controllable with no limitations towards ensuring pharmaceutical product quality.

  15. The a sequence is dispensable for isomerization of the herpes simplex virus type 1 genome.

    PubMed

    Martin, D W; Weber, P C

    1996-12-01

    The herpes simplex virus type 1 (HSV-1) genome consists of two components, L (long) and S (short), that invert relative to each other during productive infection to generate four equimolar isomeric forms of viral DNA. Recent studies have indicated that this genome isomerization is the result of DNA replication-mediated homologous recombination between the large inverted repeat sequences that exist in the genome, rather than site-specific recombination through the terminal repeat a sequences present at the L-S junctions. However, there has never been an unequivocal demonstration of the dispensability of the latter element for this process using a recombinant virus whose genome lacks a sequences at its L-S junctions. This is because the genetic manipulations required to generate such a viral mutant are not possible using simple marker transfer, since the cleavage and encapsidation signals of the a sequence represent essential cis-acting elements which cannot be deleted outright from the viral DNA. To circumvent this problem, a simple two-step strategy was devised by which essential cis-acting sites like the a sequence can be readily deleted from their natural loci in large viral DNA genomes. This method involved initial duplication of the element at a neutral site in the viral DNA and subsequent deletion of the element from its native site. By using this approach, the a sequence at the L-S junction was rendered dispensable for virus replication through the insertion of a second copy into the thymidine kinase (TK) gene of the viral DNA; the original copies at the L-S junctions were then successfully deleted from this virus by conventional marker transfer. The final recombinant virus, HSV-1::L-S(delta)a, was found to be capable of undergoing normal levels of genome isomerization on the basis of the presence of equimolar concentrations of restriction fragments unique to each of the four isomeric forms of the viral DNA. Interestingly, only two of these genomic isomers

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. Experimental study of water-ice catalyzed thermal isomerization of cyanamide into carbodiimide: implication for prebiotic chemistry.

    PubMed

    Duvernay, Fabrice; Chiavassa, Thierry; Borget, Fabien; Aycard, Jean-Pierre

    2004-06-30

    Cyanamide (NH2CN) is a molecule of interstellar interest which can be implied in prebiotic chemistry. We showed, by FTIR spectroscopy, that cyanamide can be isomerized in carbodiimide (HNCNH), another interstellar relevant molecule, by a reaction involving the amorphous water-ice surface as catalyst. This isomerization occurs at low temperature (T < 100 K) which agrees quite well with that expected in the interstellar clouds composed of dust grains in which water is the most predominant constituent.

  1. Synthesis of Z-alkenes from Rh(I)-catalyzed olefin isomerization of β,γ-unsaturated ketones.

    PubMed

    Zhuo, Lian-Gang; Yao, Zhong-Ke; Yu, Zhi-Xiang

    2013-09-20

    Developing olefin isomerization reactions to reach kinetically controlled Z-alkenes is challenging because formation of trans-alkenes is thermodynamically favored under the traditional catalytic conditions using acids, bases, or transition metals as the catalysts. A new synthesis of Z-alkenes from Rh(I)-catalyzed olefin isomerization of β,γ-unsaturated ketones to α,β-unsaturated ketones was developed, providing an easy and efficient way to access various Z-enones.

  2. 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

  3. 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.

  4. Simulation of Chemical Isomerization Reaction Dynamics on a NMR Quantum Simulator

    NASA Astrophysics Data System (ADS)

    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.

  5. Preparation of aliphatic ketones through a ruthenium-catalyzed tandem cross-metathesis/allylic alcohol isomerization.

    PubMed

    Finnegan, David; Seigal, Benjamin A; Snapper, Marc L

    2006-06-01

    Grubbs' 2nd generation and Hoveyda-Grubbs' ruthenium alkylidenes are shown to be effective catalysts for cross-metatheses of allylic alcohols with cyclic and acyclic olefins, as well as isomerization of the resulting allylic alcohols to alkyl ketones. The net result of this new tandem methodology is a single-flask process that provides highly functionalized, ketone-containing products from simple allylic alcohol precursors. [reaction: see text

  6. Mechanism of Glucose Isomerization Using a Solid Lewis Acid Catalyst in Water

    SciTech Connect

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

    2010-10-20

    1H and 13C NMR spectroscopy on isotopically labeled glucose reveals that in the presence of tin-containing zeolite Sn-Beta, the isomerization reaction of glucose in water proceeds by way of an intramolecular hydride shift rather than proton transfer. This is the first mechanistic demonstration of Sn-Beta acting as a Lewis acid in a purely aqueous environment.

  7. Effect of fluorine groups and different terminal chains on the electro-isomerization of azobenzene liquid crystals

    NASA Astrophysics Data System (ADS)

    Xiong, Jing-Jing; Shen, Dong; Zheng, Zhi-Gang; Wang, Xiao-Qian

    2016-09-01

    A series of azobenzene liquid crystals with one or two terminal acrylate groups were synthesized and their polymers were fabricated. The azobenzene liquid crystals and their polymers achieved the photoisomerization from the liquid crystalline trans-isomer to the isotropic cis-isomer with UV irradiation. Then, the cis to trans isomerization induced by an electric field was studied, the time required for electro-isomerization was measured, the texture change and absorption variation from cis to trans form induced by the electric field were observed clearly, and the time required for electro-isomerization was much shorter than that for thermal relaxation. The influence of the polar group (fluorine), terminal acrylate group, and flexible alkyl chain on the time of electro-isomerization was studied. The results show that the compounds with polar fluorine group require shorter time for electro-isomerization and the polymerization of terminal acrylate group delays the electro-isomerization. Project supported by the National Natural Science Foundation of China (Grant Nos. 61435008 and 61575063).

  8. 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

  9. Characteristic structural features of indolicidin: effects of the cis-trans isomerism on its conformation.

    PubMed

    Leitgeb, Balázs

    2014-01-01

    Indolicidin is an antimicrobial peptide showing a broad spectrum of antibacterial and antifungal activities, and according to the cis-trans isomerism of three Xaa-Pro peptide bonds, eight different stereoisomers could be distinguished for this peptide. As the cis-trans isomerism about the Xaa-Pro peptide bonds was not considered in previous studies, the structural features of distinct stereoisomeric forms were not characterized in detail, so far. In this theoretical study, the influences of cis-trans isomerism on the conformation of indolicidin were investigated, as well as the typical structural properties of each stereoisomer were determined, focusing on the secondary structures and intramolecular interactions. Based on the results derived from the molecular dynamics simulations, it could be concluded that the eight different stereoisomeric forms of indolicidin adopted characteristic conformational features. Nevertheless, the appearance of various turn structures and intramolecular interactions proved to be dependent on the cis or trans nature of Xaa-Pro peptide bonds, indicating the relevant role of Pro amino acids in determining the three-dimensional structure of this peptide.

  10. 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

  11. Human infrared vision is triggered by two-photon chromophore isomerization.

    PubMed

    Palczewska, Grazyna; Vinberg, Frans; Stremplewski, Patrycjusz; Bircher, Martin P; Salom, David; Komar, Katarzyna; Zhang, Jianye; Cascella, Michele; Wojtkowski, Maciej; Kefalov, Vladimir J; Palczewski, Krzysztof

    2014-12-16

    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.

  12. Spectroscopic and Theoretical Identification of Two Thermal Isomerization Pathways for Bistable Chiral Overcrowded Alkenes.

    PubMed

    Kistemaker, Jos C M; Pizzolato, Stefano F; van Leeuwen, Thomas; Pijper, Thomas C; Feringa, Ben L

    2016-09-12

    Chiroptical molecular switches play an important role in responsive materials and dynamic molecular systems. Here we present the synthesis of four chiral overcrowded alkenes and the experimental and computational study of their photochemical and thermal behavior. By irradiation with UV light, metastable diastereoisomers with opposite helicity were generated through high yielding E-Z isomerizations. Kinetic studies on metastable 1-4 using CD spectroscopy and HPLC analysis revealed two pathways at higher temperatures for the thermal isomerization, namely a thermal E-Z isomerization (TEZI) and a thermal helix inversion (THI). These processes were also studied computationally whereby a new strategy was developed for calculating the TEZI barrier for second-generation overcrowded alkenes. To demonstrate that these overcrowded alkenes can be employed as bistable switches, photochromic cycling was performed, which showed that the alkenes display good selectivity and fatigue resistance over multiple irradiation cycles. In particular, switch 3 displayed the best performance in forward and backward photoswitching, while 1 excelled in thermal stability of the photogenerated metastable form. Overall, the alkenes studied showed a remarkable and unprecedented combination of switching properties including dynamic helicity, reversibility, selectivity, fatigue resistance, and thermal stability. PMID:27471009

  13. Photo-isomerization and oxidation of bilirubin in mammals is dependent on albumin binding.

    PubMed

    Goncharova, Iryna; Jašprová, Jana; Vítek, Libor; Urbanová, Marie

    2015-12-01

    The bilirubin (BR) photo-conversion in the human body is a protein-dependent process; an effective photo-isomerization of the potentially neurotoxic Z,Z-BR as well as its oxidation to biliverdin in the antioxidant redox cycle is possible only when BR is bound on serum albumin. We present a novel analytical concept in the study of linear tetrapyrroles metabolic processes based on an in-depth mapping of binding sites in the structure of human serum albumin (HSA). A combination of fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling methods was used for recognition of the binding site for BR, its derivatives (mesobilirubin and bilirubin ditaurate), and the products of the photo-isomerization and oxidation (lumirubin, biliverdin, and xanthobilirubic acid) on HSA. The CD spectra and fluorescent quenching of the Trp-HSA were used to calculate the binding constants. The results of the CD displacement experiments performed with hemin were interpreted together with the findings of molecular docking performed on the pigment-HSA complexes. We estimated that Z,Z-BR and its metabolic products bind on two independent binding sites. Our findings support the existence of a reversible antioxidant redox cycle for BR and explain an additional pathway of the photo-isomerization process (increase of HSA binding capacity; the excess free [unbound] BR can be converted and also bound to HSA).

  14. Comparison of homogeneous and heterogeneous catalysts for glucose-to-fructose isomerization in aqueous media.

    PubMed

    Choudhary, Vinit; Pinar, Ana B; Lobo, Raul F; Vlachos, Dionisios G; Sandler, Stanley I

    2013-12-01

    Herein, the first comparison of the mechanisms of glucose-to-fructose isomerization in aqueous media enabled by homogeneous (CrCl3 and AlCl3 ) and heterogeneous catalysts (Sn-beta) by using isotopic-labeling studies is reported. A pronounced kinetic isotope effect (KIE) was observed if the deuterium label was at the C2 position, thus suggesting that a hydrogen shift from the C2 to C1 positions was the rate-limiting step with the three catalysts. (13) C and (1) H NMR spectroscopic investigations confirmed that an intra-hydride-transfer reaction pathway was the predominant reaction channel for all three catalysts in aqueous media. Furthermore, the deuterium atom in the labeled glucose could be mapped onto hydroxymethylfurfural and formic acid through reactions that followed the isomerization step in the presence of Brønsted acids. In all three catalysts, the active site appeared to be a bifunctional Lewis-acidic/Brønsted-basic site, based on a speciation model and first-principles calculations. For the first time, a mechanistic similarities between the homogeneous and heterogeneous catalysis of aldose-to-ketose isomerization is established and it is suggested that learning from homogeneous catalysis could assist in the development of improved heterogeneous catalysts.

  15. 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.

  16. Spectroscopic and Theoretical Identification of Two Thermal Isomerization Pathways for Bistable Chiral Overcrowded Alkenes.

    PubMed

    Kistemaker, Jos C M; Pizzolato, Stefano F; van Leeuwen, Thomas; Pijper, Thomas C; Feringa, Ben L

    2016-09-12

    Chiroptical molecular switches play an important role in responsive materials and dynamic molecular systems. Here we present the synthesis of four chiral overcrowded alkenes and the experimental and computational study of their photochemical and thermal behavior. By irradiation with UV light, metastable diastereoisomers with opposite helicity were generated through high yielding E-Z isomerizations. Kinetic studies on metastable 1-4 using CD spectroscopy and HPLC analysis revealed two pathways at higher temperatures for the thermal isomerization, namely a thermal E-Z isomerization (TEZI) and a thermal helix inversion (THI). These processes were also studied computationally whereby a new strategy was developed for calculating the TEZI barrier for second-generation overcrowded alkenes. To demonstrate that these overcrowded alkenes can be employed as bistable switches, photochromic cycling was performed, which showed that the alkenes display good selectivity and fatigue resistance over multiple irradiation cycles. In particular, switch 3 displayed the best performance in forward and backward photoswitching, while 1 excelled in thermal stability of the photogenerated metastable form. Overall, the alkenes studied showed a remarkable and unprecedented combination of switching properties including dynamic helicity, reversibility, selectivity, fatigue resistance, and thermal stability.

  17. Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of dihydroxyacetone phosphate in D2O.

    PubMed

    O'Donoghue, Annmarie C; Amyes, Tina L; Richard, John P

    2005-02-22

    The product distributions for the reactions of dihydroxyacetone phosphate (DHAP) in D(2)O at pD 7.9 catalyzed by triosephosphate isomerase (TIM) from chicken and rabbit muscle were determined by (1)H NMR spectroscopy using glyceraldehyde 3-phosphate dehydrogenase to trap the first-formed products of the thermodynamically unfavorable isomerization reaction, (R)-glyceraldehyde 3-phosphate (GAP) and [2(R)-(2)H]-GAP (d-GAP). Three products were observed from the reactions catalyzed by TIM: GAP from isomerization with intramolecular transfer of hydrogen (18% of the enzymatic products), d-GAP from isomerization with incorporation of deuterium from D(2)O into C-2 of GAP (43% of the enzymatic products), and [1(R)-(2)H]-DHAP (d-DHAP) from incorporation of deuterium from D(2)O into C-1 of DHAP (40% of the enzymatic products). The ratios of the yields of the deuterium-labeled products d-DHAP and d-GAP from partitioning of the intermediate of the TIM-catalyzed reactions of GAP and DHAP in D(2)O are 1.48 and 0.93, respectively. This provides evidence that the reaction of these two substrates does not proceed through a single, common, reaction intermediate but, rather, through distinct intermediates that differ in the bonding and arrangement of catalytic residues at the enediolate O-1 and O-2 oxyanions formed on deprotonation of GAP and DHAP, respectively.

  18. Kinetic analysis for the isomerization of cellobiose to cellobiulose in subcritical aqueous ethanol.

    PubMed

    Soisangwan, Nontanut; Gao, Da-Ming; Kobayashi, Takashi; Khuwijitjaru, Pramote; Adachi, Shuji

    2016-10-01

    The isomerization of cellobiose to cellobiulose, and other degradation reactions of cellobiose were investigated in subcritical aqueous ethanol with concentrations of ethanol ranging from 0 to 60% (w/w) and at temperatures ranging from 170 to 200 °C. The maximum yield of cellobiulose (ca. 40%) was obtained from the treatment of cellobiose in 60% (w/w) aqueous ethanol at 190 °C. Glucose and fructose were also detected as byproducts. The concentration-time integral method was employed to analyze the rate constants for the isomerization and degradation processes. The rate constant of cellobiose isomerization to cellobiulose was greater than those of the degradation reactions under all experimental conditions, and it increased significantly with treatment temperature and ethanol concentration. However, the use of higher temperatures and ethanol concentrations was restricted due to decomposition of the saccharides and the low solubility of cellobiose, respectively. The effect of initial feed concentration (0.5-5.5% w/w) was also studied. The maximum productivity of cellobiulose, 54.1 kg/(h m(3)-reactor), was accomplished at a feed concentration of 5.5% (w/w) in 20% (w/w) subcritical aqueous ethanol. PMID:27454654

  19. Differences in sequence selectivity of DNA alkylation by isomeric intercalating aniline mustards.

    PubMed

    Prakash, A S; Denny, W A; Wakelin, L P

    1990-01-01

    Two DNA-targeted mustard derivatives, N,N-bis(2-chloroethyl)-4-(5-[9-acridinylamino]-pentamido)aniline and 4-(9-[acridinylamino]butyl 4-(N,N-bis[2-chloroethyl]-aminobenzamide, which are isomeric compounds where the mustard is linked to the DNA-binding 9-aminoacridine moiety by either a -CONH- or a -NHCO- group, show significant differences in the sequence selectivity of their alkylation of DNA. The CONH isomer is a more efficient alxylating agent than the NHCO compound by an order of magnitude, consistent with the larger electron release of the CONH group to the aniline ring. However, the pattern of alkylation by the two compounds is also very different, with the CONH isomer preferring alkylation of guanines adjacent to 3'- or 5'-adenines and cytosines (for example those in sequences 5'-CGC, 5'-AGC, 5'-CGG and 5'-AGA) while the isomeric NHCO compound shows preference for guanines in runs of Gs. In addition, both isomers alkylate 3'-adenines in runs of adenines. Both compounds also show completely different patterns of alkylation to their untargeted mustard counterparts, since 4-MeCONH-aniline mustard alkylates all guanines and adenines in runs of adenines, while 4-Me2NCO-aniline mustard fails to alkylate DNA at all. These differences in alkylation patterns between the CONH- and its isomeric NHCO- compounds and their relationships between the alkylation patterns of the isomers and their biological activities are discussed.

  20. HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358

    PubMed Central

    2013-01-01

    Background Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown. Results Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positioned to allow single-bond resonance stabilisation of exposed capsid residue P90. NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid. In contrast, the distantly related feline lentivirus FIV can bind NUP358 but is neither isomerized by it nor requires it for infection. Conclusion Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating. PMID:23902822

  1. 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.

  2. 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

  3. 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

  4. Role of Solvent and Effect of Substituent on Azobenzene Isomerization by Using Room-Temperature Ionic Liquids as Reaction Media.

    PubMed

    Angelini, Guido; Canilho, Nadia; Emo, Mélanie; Kingsley, Molly; Gasbarri, Carla

    2015-08-01

    The effects of a para substituent, as the electron-donating -OCH3 and -OtBu groups and the electron-withdrawing -Br and -F atoms, on azobenzene isomerization have been investigated in a series of imidazolium ionic liquids (BMIM PF6, BMIM BF4, BMIM Tf2N, EMIM Tf2N, BM2IM Tf2N, and HMIM Tf2N). The thermal cis-trans conversion tends to be improved in the presence of the substituent, as pointed out by the first-order rate constants measured at 25 °C. Both the rotation and the inversion mechanisms occur in BMIM Tf2N, EMIM Tf2N, and HMIM Tf2N, as highlighted by typical V-shape Hammett plots, but only rotation takes place in BMIM PF6, BMIM BF4, and BM2IM Tf2N. The possible interactions between the cation and the anion of the solvent and both the isomers of the azobenzene derivatives have been studied by small-wide-angle X-ray scattering (SWAXS). The calculated cis population in the photostationary state and the hardness parameter η of the trans isomer show that azobenzene and F-azobenzene are the less reactive molecules for the trans-cis conversion in all the investigated ionic liquids.

  5. 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.

  6. 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.

  7. 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.

  8. Parallel channels and rate-limiting steps in complex protein folding reactions: prolyl isomerization and the alpha subunit of Trp synthase, a TIM barrel protein.

    PubMed

    Wu, Ying; Matthews, C Robert

    2002-10-18

    A kinetic folding mechanism for the alpha subunit of tryptophan synthase (alphaTS) from Escherichia coli, involving four parallel channels with multiple native, intermediate and unfolded forms, has recently been proposed. The hypothesis that cis/trans isomerization of several Xaa-Pro peptide bonds is the source of the multiple folding channels was tested by measuring the sensitivity of the three rate-limiting phases (tau(1), tau(2), tau(3)) to catalysis by cyclophilin, a peptidyl-prolyl isomerase. Although the absence of catalysis for the tau(1) (fast) phase leaves its assignment ambiguous, our previous mutational analysis demonstrated its connection to the unique cis peptide bond preceding proline 28. The acceleration of the tau(2) (medium) and tau(3) (slow) refolding phases by cyclophilin demonstrated that cis/trans prolyl isomerization is also the source of these phases. A collection of proline mutants, which covered all of the remaining 18 trans proline residues of alphaTS, was constructed to obtain specific assignments for these phases. Almost all of the mutant proteins retained the complex equilibrium and kinetic folding properties of wild-type alphaTS; only the P217A, P217G and P261A mutations caused significant changes in the equilibrium free energy surface. Both the P78A and P96A mutations selectively eliminated the tau(1) folding phase, while the P217M and P261A mutations eliminated the tau(2) and tau(3) folding phases, respectively. The redundant assignment of the tau(1) phase to Pro28, Pro78 and Pro96 may reflect their mutual interactions in non-random structure in the unfolded state. The non-native cis isomers for Pro217 and Pro261 may destabilize an autonomous C-terminal folding unit, thereby giving rise to kinetically distinct unfolded forms. The nature of the preceding amino acid, the solvent exposure, or the participation in specific elements of secondary structure in the native state, in general, are not determinative of the proline residues whose

  9. Thermal Degradation and Isomerization of β-Carotene in Oil-in-Water Nanoemulsions Supplemented with Natural Antioxidants.

    PubMed

    Yi, Jiang; Fan, Yuting; Yokoyama, Wallace; Zhang, Yuzhu; Zhao, Liqing

    2016-03-01

    The goal of this study was to see the impact on the retention and isomerization of encapsulated β-carotene (BC) in nanoemulsions fortified with natural antioxidants (α-tocopherol (AT) and l-ascorbic acid (AA)). The physical stability of nanoemulsion, oxidative stability, and isomerization of all-trans-β-carotene (BC) in oil-in-water (O/W) nanoemulsions were determined in the presence or absence of natural antioxidants at 25 and 50 °C at certain intervals of time by high-performance liquid chromatography (HPLC). Sodium caseinate was used as the emulsifier, and corn oil (CO) was more protective than medium-chain triglycerides (MCT) and used for isomerization studies. Mean diameters of control (without antioxidants) and AA- and AT-fortified particles were similar. Mean particle diameter of nanoemulsions increased from 10 to 25 nm at 25 °C and from 40 to 50 nm at 50 °C during 30 days of storage. The isomerization from all-trans-BC to cis-BC isomers was inhibited by antioxidants. The isomerization rates were in the following order: 13-cis-BC > 15-cis-BC > 9-cis-BC. AT had better antioxidant activities than AA in inhibiting BC degradation in O/W nanoemulsions. The results indicated that BC encapsulated in nanoemulsions supplemented with antioxidants could significantly improve BC's chemical stability.

  10. Thermal Degradation and Isomerization of β-Carotene in Oil-in-Water Nanoemulsions Supplemented with Natural Antioxidants.

    PubMed

    Yi, Jiang; Fan, Yuting; Yokoyama, Wallace; Zhang, Yuzhu; Zhao, Liqing

    2016-03-01

    The goal of this study was to see the impact on the retention and isomerization of encapsulated β-carotene (BC) in nanoemulsions fortified with natural antioxidants (α-tocopherol (AT) and l-ascorbic acid (AA)). The physical stability of nanoemulsion, oxidative stability, and isomerization of all-trans-β-carotene (BC) in oil-in-water (O/W) nanoemulsions were determined in the presence or absence of natural antioxidants at 25 and 50 °C at certain intervals of time by high-performance liquid chromatography (HPLC). Sodium caseinate was used as the emulsifier, and corn oil (CO) was more protective than medium-chain triglycerides (MCT) and used for isomerization studies. Mean diameters of control (without antioxidants) and AA- and AT-fortified particles were similar. Mean particle diameter of nanoemulsions increased from 10 to 25 nm at 25 °C and from 40 to 50 nm at 50 °C during 30 days of storage. The isomerization from all-trans-BC to cis-BC isomers was inhibited by antioxidants. The isomerization rates were in the following order: 13-cis-BC > 15-cis-BC > 9-cis-BC. AT had better antioxidant activities than AA in inhibiting BC degradation in O/W nanoemulsions. The results indicated that BC encapsulated in nanoemulsions supplemented with antioxidants could significantly improve BC's chemical stability. PMID:26881704

  11. Detailed analysis of polyad-breaking spectroscopic Hamiltonians for multiple minima with above barrier motion: Isomerization in HO2

    NASA Astrophysics Data System (ADS)

    Barnes, George L.; Kellman, Michael E.

    2011-02-01

    We present a two-dimensional model for isomerization in the hydroperoxyl radical (HO2). We then show that spectroscopic fitting Hamiltonians are capable of reproducing large scale vibrational structure above isomerization barriers. Two resonances, the 2:1 and 3:1, are necessary to describe the pertinent physical features of the system and, hence, a polyad-breaking Hamiltonian is required. We further illustrate, through the use of approximate wave functions, that inclusion of additional coupling terms yields physically unrealistic results despite an improved agreement with the exact energy levels. Instead, the use of a single diagonal term, rather than "extra" couplings, yields good fits with realistic results. Insight into the dynamical nature of isomerization is also gained through classical trajectories. Contrary to physical intuition the bend mode is not the initial "reaction mode," but rather isomerization requires excitation in both the stretch and bend modes. The dynamics reveals a Farey tree formed between the 2:1 and 3:1 resonances with the prominent 5:2 (2:1 + 3:1) feature effectively dividing the tree into portions. The 3:1 portion is associated with isomerization, while the 2:1 portion leads to "localization" and perhaps dissociation at higher energies than those considered in this work. Simple single resonance models analyzed on polyad phase spheres are able to account in a qualitative way for the spectral, periodic orbit, and wave function patterns that we observe.

  12. Detailed analysis of polyad-breaking spectroscopic Hamiltonians for multiple minima with above barrier motion: isomerization in HO2.

    PubMed

    Barnes, George L; Kellman, Michael E

    2011-02-21

    We present a two-dimensional model for isomerization in the hydroperoxyl radical (HO(2)). We then show that spectroscopic fitting Hamiltonians are capable of reproducing large scale vibrational structure above isomerization barriers. Two resonances, the 2:1 and 3:1, are necessary to describe the pertinent physical features of the system and, hence, a polyad-breaking Hamiltonian is required. We further illustrate, through the use of approximate wave functions, that inclusion of additional coupling terms yields physically unrealistic results despite an improved agreement with the exact energy levels. Instead, the use of a single diagonal term, rather than "extra" couplings, yields good fits with realistic results. Insight into the dynamical nature of isomerization is also gained through classical trajectories. Contrary to physical intuition the bend mode is not the initial "reaction mode," but rather isomerization requires excitation in both the stretch and bend modes. The dynamics reveals a Farey tree formed between the 2:1 and 3:1 resonances with the prominent 5:2 (2:1 + 3:1) feature effectively dividing the tree into portions. The 3:1 portion is associated with isomerization, while the 2:1 portion leads to "localization" and perhaps dissociation at higher energies than those considered in this work. Simple single resonance models analyzed on polyad phase spheres are able to account in a qualitative way for the spectral, periodic orbit, and wave function patterns that we observe. PMID:21341829

  13. 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

  14. 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

  15. Photochemistry of visual pigments: an interpretation of spectral changes in terms of molecular associations and isomerization.

    PubMed

    Hárosi, F I; Favrot, J; Leclercq, J M; Vocelle, D; Sándorfy, C

    1978-12-01

    A unified view of the photochemical part of the visual process is presented. It is proposed that both conformational changes and changes in intermolecular interactions in the sequence that leads from rhodopsin through batho-lumi- and meta-I to meta-II- rhodopsin have to be considered in order to elucidate the mechanism of the visual process. The main intermolocular associations are assumed to be the hydrogen bond involving the nitrogen atom of the Schiff base and the interaction between a negative group and the beta-ionone ring. The two together can be used to explain the absorption wavelength of rhodopsin without actual protonation. The main line of thought is as follows: when light is absorbed the basicity of the Schiff base increases significantly. This triggers proton transfer in the H-bond. At the same time cis-trans isomerization begins but it only reaches the coplanar all-trans stage at metarhodopsin-II. Lumi-, meta-I and meta-II are way stations in the stepwise isomerization whereby the energy of the photon is used together with thermal energy. Batho- is probably still close to 11-cis which then becomes successively strained 13-cis and 15-cis. In vertebrate rhodopsins at the meta-II stage both the H-bond and the beta-ionone interaction are severed and meta-II becomes exposed to attack by water molecules. The importance of syn-anti isomerization on the C=N bond is emphasized. The irreversibility necessary for the production of a signal requires that the proton does not return to its original donor. The possible identity of the donor is discussed: it might be an amino acid or the polar part of a lipid. Relevant observations made on bacteriorhodopsin, squid rhodopsin and chicken iodopsin are discussed.

  16. 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

  17. Probing Photochemically and Thermally Induced Isomerization Reactions in α-Pyrone.

    PubMed

    Murdock, Daniel; Clark, Ian P; Ashfold, Michael N R

    2016-09-22

    The isomerization dynamics of α-pyrone dissolved in CH3CN have been probed by femtosecond 267 nm pump/broadband infrared (IR) probe spectroscopy. A novel experimental setup allowed the populations of the parent molecule and ring-opened photoproducts to be monitored over pump/probe time delays ranging between 2 ps and 100 μs within a single experiment, and at 5 different temperatures between 0 and 40 °C. The photochemically prepared α-pyrone(S1) molecules decay rapidly (<10 ps) through internal conversion to the S0 potential energy surface, with an initial quantum yield for parent molecule re-formation of ∼60%. Probing the antisymmetric ketene stretch region (2100-2150 cm(-1)) confirms the presence of at least two ring-opened photoproducts, which are assumed to have an E-configuration with respect to the central C═C double bond. These ketenes are observed to undergo two distinct, thermally driven, isomerization processes which occur on the nanosecond and microsecond time scales, respectively. The former reaction is ascribed to thermalization of the initially prepared E-isomer populations, while the slower (microsecond) process involves rotation around the central C═C double bond leading to formation of Z-isomers. Subsequent rapid Z → Z isomerizations (occurring on a nanosecond time scale) result in ring-closure and a second, longer time recovery of parent molecule population. By determining rates as a function of the sample temperature, barrier heights of 0.23(3) eV and 0.43(2) eV are obtained for the E → E and E → Z transformations, respectively. PMID:27584030

  18. Molecular Structures of Isomeric Ortho, Meta, and Para Bromo-Substituted α-Methylsulfonyl-α-diethoxyphosphoryl Acetophenones by X-ray and DFT Molecular Orbital Calculations.

    PubMed

    Rodrigues, Alessandro; Olivato, Paulo R; Zukerman-Schpector, Julio; Maganhi, Stella H; Reis, Adriana K C A; Tiekink, Edward R T

    2015-08-13

    The X-ray single crystal analysis of isomeric ortho, meta, and para bromo-substituted α-methylsulfonyl-α-diethoxyphosphoryl acetophenones showed that this class of compound adopts synclinal (gauche) conformations for both [-P(O)(OEt)2] and [-S(O)2Me] groups, with respect to the carbonyl functional group. The phosphonate, sulfonyl, and carbonyl functional groups are joined through an intramolecular network of attractive interactions, as detected by molecular orbital calculations at the M06-2X/6-31G(d,p) level. These interactions are responsible for the more stable conformations in the gas phase, which also persist in the solid-state structures. The main structural distinction in the title compounds relates to the torsion angle of the aryl group (with respect to the carbonyl group), which gives rise to different interactions in the crystal packing, due to the different positions of the Br atom.

  19. Adsorption of surfactants on mineral oxide surfaces from aqueous solutions. Part 1. Isomerically pure anionic surfactants

    SciTech Connect

    Scamehorn, J.F.; Schechter, R.S.; Wade, W.H.

    1982-02-01

    The adsorption of surfactants on minerals is detrimental to surfactant-enhanced oil recovery. To minimize adsorption, the forces tending to cause it must be understood. This requires the study of relatively simple, well-defined systems. The majority of surfactant adsorption studies on mineral oxides has been made with surfactant mixtures and not with monoisomerically pure species. Some of the observed results may be due to complex surfactant intercomponent interactions. In this study, the adsorption of 3 isomerically pure alkylbenzene sulfonates was measured on alumina and kaolinite from very low concentrations to well above the critical micelle concentration and a thermodynamic model was developed, which describes the observed isotherms. 59 references.

  20. 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

  1. A theoretical study of the carbocation formation energy involved in the isomerization of α-pinene

    NASA Astrophysics Data System (ADS)

    Flores-Holguín, Norma; Aguilar-Elguézabal, Alfredo; Rodríguez-Valdez, Luz-María; Glossman-Mitnik, Daniel

    2012-09-01

    α-Pinene isomerization starts with the formation of the pinanyl carbocation, which then undergoes rearrangement into two different isomers. One isomer yields monocyclic rings as final products, such as limonene, α-terpinene, and terpinolene while the other isomer yields bicyclic compounds, including camphene. In this Letter, a computational study is carried out in order to find the optimal temperature and solvent for the promotion of the second path considering that the bicyclical compounds are of greater economical interest. The energies of formation of the carbocations at different temperatures were calculated in vacuum and in solvents using the PBEPBE/6-31+G(d,p) model chemistry.

  2. 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.

  3. Fluorescence excitation spectrum and solvent-assisted conformational isomerization (SACI) of jet-cooled acetaminophen

    NASA Astrophysics Data System (ADS)

    Sohn, Woon Yong; Kang, Jeong Seok; Lee, So Young; Kang, Hyuk

    2013-08-01

    Fluorescence excitation spectrum of jet-cooled acetaminophen was obtained. When AAP was expanded with a buffer gas containing 0.3-1.1% of water, absorption peaks of the less stable trans conformer was significantly reduced by solvent-assisted conformational isomerization (SACI), which is confirmed by a separately measured UV-UV hole burning spectroscopy. It is also confirmed by quantum mechanical calculation and RRKM calculation that it is energetically and kinetically possible to induce SACI in AAP with water. The SACI mechanism suggests a possible pathway that acetaminophen can adopt an active conformation in vivo, which is need for molecular recognition and drug activity.

  4. 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.

  5. 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.

  6. 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

  7. Unimolecular reactions in the CF3CH2Cl ↔ CF2ClCH2F system: isomerization by interchange of Cl and F atoms.

    PubMed

    Enstice, Erin C; Duncan, Juliana R; Setser, D W; Holmes, Bert E

    2011-02-17

    The recombination of CF(2)Cl and CH(2)F radicals was used to prepare CF(2)ClCH(2)F* molecules with 93 ± 2 kcal mol(-1) of vibrational energy in a room temperature bath gas. The observed unimolecular reactions in order of relative importance were: (1) 1,2-ClH elimination to give CF(2)═CHF, (2) isomerization to CF(3)CH(2)Cl by the interchange of F and Cl atoms and (3) 1,2-FH elimination to give E- and Z-CFCl═CHF. Since the isomerization reaction is 12 kcal mol(-1) exothermic, the CF(3)CH(2)Cl* molecules have 105 kcal mol(-1) of internal energy and they can eliminate HF to give CF(2)═CHCl, decompose by rupture of the C-Cl bond, or isomerize back to CF(2)ClCH(2)F. These data, which provide experimental rate constants, are combined with previously published results for chemically activated CF(3)CH(2)Cl* formed by the recombination of CF(3) and CH(2)Cl radicals to provide a comprehensive view of the CF(3)CH(2)Cl* ↔ CF(2)ClCH(2)F* unimolecular reaction system. The experimental rate constants are matched to calculated statistical rate constants to assign threshold energies for the observed reactions. The models for the molecules and transition states needed for the rate constant calculations were obtained from electronic structures calculated from density functional theory. The previously proposed explanation for the formation of CF(2)═CHF in thermal and infrared multiphoton excitation studies of CF(3)CH(2)Cl, which was 2,2-HCl elimination from CF(3)CH(2)Cl followed by migration of the F atom in CF(3)CH, should be replaced by the Cl/F interchange reaction followed by a conventional 1,2-ClH elimination from CF(2)ClCH(2)F. The unimolecular reactions are augmented by free-radical chemistry initiated by reactions of Cl and F atoms in the thermal decomposition of CF(3)CH(2)Cl and CF(2)ClCH(2)F. PMID:21244059

  8. 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.

  9. Isomeric signatures in the fragmentation of pyridazine and pyrimidine induced by fast ion impact

    NASA Astrophysics Data System (ADS)

    Wolff, Wania; Luna, Hugo; Montenegro, Eduardo C.

    2015-07-01

    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.

  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. Light-induced oxidation and isomerization of all-trans-β-cryptoxanthin in a model system.

    PubMed

    Li, Dajing; Xiao, Yadong; Zhang, Zhongyuan; Liu, Chunquan

    2015-01-01

    The oxidation and isomerization of all-trans-β-cryptoxanthin as affected by iodine-catalysed illumination and non-iodine-catalysed illumination were studied. Seven cis-isomers and two oxidation products were separated by HPLC method using a C30 column. The identification and structural elucidation of the compounds were determined by HPLC-DAD-APCI-MS. Five compounds were identified in details for the first time, namely, β-β-carotene-3-one, 5,6-epoxy-β-β-carotene-3-one, 13,15-di-cis-, 9,13-di-cis- and 9,9'-di-cis-β-cryptoxanthin. Sum of 13- and 13'-cis-β-cryptoxanthin was the major cis-isomer of β-cryptoxanthin formed, accounting for 59.0% and 30.6%, respectively. The formation of di-cis isomers may prefer in the present of iodine. 13,15-di-cis-β-cryptoxanthin was the major di-cis-isomer of the iodine-catalysed photo-isomerization.

  12. Separation and identification of isomeric glycopeptides by high field asymmetric waveform ion mobility spectrometry.

    PubMed

    Creese, Andrew J; Cooper, Helen J

    2012-03-01

    The analysis of intact glycopeptides by mass spectrometry is challenging due to the numerous possibilities for isomerization, both within the attached glycan and the location of the modification on the peptide backbone. Here, we demonstrate that high field asymmetric wave ion mobility spectrometry (FAIMS), also known as differential ion mobility, is able to separate isomeric O-linked glycopeptides that have identical sequences but differing sites of glycosylation. Two glycopeptides from the glycoprotein mucin 5AC, GT(GalNAc)TPSPVPTTSTTSAP and GTTPSPVPTTST(GalNAc)TSAP (where GalNAc is O-linked N-acetylgalactosamine), were shown to coelute following reversed-phase liquid chromatography. However, FAIMS analysis of the glycopeptides revealed that the compensation voltage ranges in which the peptides were transmitted differed. Thus, it is possible at certain compensation voltages to completely separate the glycopeptides. Separation of the glycopeptides was confirmed by unique reporter ions produced by supplemental activation electron transfer dissociation mass spectrometry. These fragments also enable localization of the site of glycosylation. The results suggest that glycan position plays a key role in determining gas-phase glycopeptide structure and have implications for the application of FAIMS in glycoproteomics.

  13. 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.

  14. 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.

  15. Highly efficient redox isomerization of allylic alcohols at ambient temperature catalyzed by novel ruthenium-cyclopentadienyl complexes--new insight into the mechanism.

    PubMed

    Martín-Matute, Belén; Bogár, Krisztián; Edin, Michaela; Kaynak, F Betül; Bäckvall, Jan-E

    2005-10-01

    A range of ruthenium cyclopentadienyl (Cp) complexes have been prepared and used for isomerization of allylic alcohols to the corresponding saturated carbonyl compounds. Complexes bearing CO ligands show higher activity than those with PPh3 ligands. The isomerization rate is highly affected by the substituents on the Cp ring. Tetra(phenyl)methyl-substituted catalysts rapidly isomerize allylic alcohols under very mild reaction conditions (ambient temperature) with short reaction times. Substituted allylic alcohols have been isomerized by employing Ru-Cp complexes. A study of the isomerization catalyzed by [Ru(Ph5Cp)(CO)2H] (14) indicates that the isomerization catalyzed by ruthenium hydrides partly follows a different mechanism than that of ruthenium halides activated by KOtBu. Furthermore, the lack of ketone exchange when the isomerization was performed in the presence of an unsaturated ketone (1 equiv), different from that obtained by dehydrogenation of the starting allylic alcohol, supports a mechanism in which the isomerization takes place within the coordination sphere of the ruthenium catalyst. PMID:16028298

  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. 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

  18. 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

  19. Structural characterization of the HIV-1 Vpr N terminus: evidence of cis/trans-proline isomerism.

    PubMed

    Bruns, Karsten; Fossen, Torgils; Wray, Victor; Henklein, Peter; Tessmer, Uwe; Schubert, Ulrich

    2003-10-31

    The 96-residue human immunodeficiency virus (HIV) accessory protein Vpr serves manifold functions in the retroviral life cycle including augmentation of viral replication in non-dividing host cells, induction of G2 cell cycle arrest, and modulation of HIV-induced apoptosis. Using a combination of dynamic light scattering, circular dichroism, and NMR spectroscopy the N terminus of Vpr is shown to be a unique domain of the molecule that behaves differently from the C-terminal domain in terms of self-association and secondary structure folding. Interestingly, the four highly conserved proline residues in the N terminus are predicted to have a high propensity for cis/trans isomerism. Thus the high resolution structure and folding of a synthetic N-terminal peptide (Vpr1-40) and smaller fragments thereof have been investigated. 1H NMR data indicate Vpr1-40 possesses helical structure between residues 17-32, and for the first time, this helix, which is bound by proline residues, was observed even in aqueous solution devoid of any detergent supplements. In addition, NMR data revealed that all of the proline residues undergo a cis/ trans isomerism to such an extent that approximately 40% of all Vpr molecules possess at least one proline in a cis conformation. This phenomenon of cis/trans isomerism, which is unprecedented for HIV-1 Vpr, not only provides an explanation for the molecular heterogeneity observed in the full-length molecule but also indicates that in vivo the folding and function of Vpr should depend on a cis/trans-proline isomerase activity, particularly as two of the proline residues in positions 14 and 35 show considerable amounts of cis isomers. This prediction correlates well with our recent observation (Zander, K., Sherman, M. P., Tessmer, U., Bruns, K., Wray, V., Prechtel, A. T., Schubert, E., Henklein, P., Luban, J., Neidleman, J., Greene, W. C., and Schubert, U. (2003) J. Biol. Chem. 278, 43170-43181) of a functional interaction between the major

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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...

  6. Absence of isomerization of retinyl palmitate, retinol, and retinal in chlorinated and nonchlorinated solvents under gold light

    SciTech Connect

    Landers, G.M.; Olson, J.A.

    1986-01-01

    Purified solutions of all-trans retinyl palmitate, retinol, and retinaldehyde in chloroform, methylene chloride, or hexane were exposed to white light or gold fluorescent light or were kept in the dark, and the resulting isomer distributions were determined by LC (liquid chromatography). No significant isomerization of any of the retinoids occurred either in the dark or on exposure to gold light in any of the solvents tested. However, a large amount of the 9-cis isomer and only much smaller amounts of other cis isomers were produced when retinol or retinyl palmitate in chloroform or methylene chloride solution was exposed to white light. The isomerization pattern of retinyl palmitate in chloroform was not altered by the addition of free-radical scavengers, addition of an organic base, or substitution of deuterochloroform for chloroform as solvent. Use of other polar solvents such as tetrahydrofuran, acetone, or methanol produced isomer distributions similar to those obtained in chloroform solution. Retinol and retinyl palmitate in hexane solution, on exposure to white light, were isomerized much less extensively than in chloroform or methylene chloride and produced a significant amount of the 13-cis, as well as the 9-cis, isomer. Isomerization of retinaldehyde in chloroform or in methylene chloride solution under white light yielded 13-cis, 11-cis, 9-cis, and 7-cis isomers, in order of decreasing amount, whereas in hexane solution, only the 13-cis and 9-cis isomers were produced in significant quantity.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Relaxation dynamics and structural isomerism in Nb10 and Nb10+

    NASA Astrophysics Data System (ADS)

    Walsh, T. R.

    2006-05-01

    The structure, energetics, and interconversion of isomers of Nb10 and Nb10+ are studied using density functional theory with Gaussian basis sets, using guess structures derived from basin-hopping simulations with the Finnis-Sinclair [Philos. Mag. A 50, 45 (1984)] potential. These results are used as input to a master equation approach to model the relaxation of these clusters. Ionization potentials are calculated for all relevant minima, as are the infrared spectra. On the basis of these data, and known experimental results, plausible explanations are given for the biexponential reaction kinetics observed for Nb10 and Nb10+ with respect to small molecule adsorbates. In principle, this approach could be extended to investigate any midsized transition metal cluster that exhibits structural isomerism.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. Linkage Isomerism in Transition-Metal Complexes of Mixed (Arylcarboxamido)(arylimino)pyridine Ligands

    PubMed Central

    2015-01-01

    The synthesis of a series of asymmetric mixed 2,6-disubstituted (arylcarboxamido)(arylimino)pyridine ligands and their coordination chemistry toward a series of divalent first-row transition metals (Cu, Co, and Zn) have been explored. Complexes featuring both anionic N,N′,N″-carboxamido and neutral O,N,N′-carboxamide coordination have been prepared and characterized by X-ray crystallography, cyclic voltammetry, and UV–visible and EPR spectroscopy. Specifically, RLM(X) (M = Cu; X = Cl–, OAc–) and RL(H)MX2 (M = Cu, Co, Zn; X = Cl–, SbF6–) complexes that feature N,N′,N″- or O,N,N′-coordination are presented. Base-induced linkage isomerization from O,N,N′-carboxamide to N,N′,N″-carboxamido coordination is also confirmed by multiple forms of spectroscopy. PMID:24819403

  1. 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

  2. Isomerization and Fragmentation of Cyclohexanone in a Heated Micro-Reactor

    NASA Astrophysics Data System (ADS)

    Porterfield, Jessica P.; Nguyen, Thanh Lam; Baraban, Joshua H.; Buckingham, Grant; Troy, Tyler; Kostko, Oleg; Ahmed, Musahid; Stanton, John F.; Daily, John W.; Ellison, Barney

    2016-06-01

    he thermal decomposition of cyclohexanone (C_6H10=O) has been studied in a set of flash-pyrolysis micro-reactors. Samples of C_6H10=O were first observed to decompose at 1200 K. Short residence times of 100 μsec and dilution of samples (<0.1%) isolate unimolecular decomposition. Products were identified by tunable VUV photoionization mass spectroscopy, photoionization appearance thresholds, and complementary matrix infrared absorption spectroscopy. Thermal cracking of cyclohexanone appeared to result from a variety of competing pathways pictured to the right. Isomerization of cyclohexanone to the enol, cyclohexen-1-ol (C_6H_9OH), is followed by retro-Diels-Alder cleavage to CH_2=CH_2 and CH_2=C(OH)-CH=CH_2. Further isomerization of CH_2=C(OH)CH=CH_2 to methyl vinyl ketone (CH_3COCH=CH_2, MVK) was also observed. Photoionization spectra identified both enols, C_6H_9OH and CH=C(OH)CH=CH_2, and the ionization threshold of C_6H_9OH was measured to be 8.2 ± 0.1 eV. At 1200 K, the products of cyclohexanone pyrolysis were found to be: C_6H_9OH, CH_2=C(OH)CH=CH_2, MVK, CH_2CHCH_2, CO, CH_2=C=O, CH_3, CH_2=C=CH_2, CH_2=CH-CH=CH_2, CH_2=CHCH_2CH_3, CH_2=CH_2, and HCCH.

  3. Evaluation of ion mobility-mass spectrometry for determining the isomeric heterogeneity of oligosaccharide-alditols derived from bovine submaxillary mucin.

    PubMed

    Li, Hongli; Bendiak, Brad; Kaplan, Kimberly; Davis, Eric; Siems, William F; Hill, Herbert H

    2013-10-15

    Rapid separation and independent analysis of isomeric species are needed for the structural characterization of carbohydrates in glycomics research. Ion mobility-mass spectrometry techniques were used to examine a series of isomeric neutral oligosaccharide-alditols derived from bovine submaxillary mucin. Several analytical techniques were employed: (1) off line separation of the oligosaccharide-alditol mixture by HPLC; (2) direct and rapid evaluation of isomeric heterogeneity of oligosaccharides by electrospray ionization-ion mobility-time of flight mass spectrometry; and (3) mobility-selected MS(2) and MS(3) to evaluate isomeric mobility peaks by dual gate ion mobility-tandem mass spectrometry. Multiple isomeric ion mobility peaks were observed for the majority of oligosaccharide-alditols, which was achieved on the millisecond time scale after LC separation. Fragmentation spectra obtained from the collision-induced dissociation of isomeric precursor ions could be essentially identical, or dramatically different for a given precursor m/z using the dual-gate ion mobility quadrupole ion trap mass spectrometer. This further confirmed the need for rapid physical resolution of isomeric precursor species prior to their tandem mass spectral analysis.

  4. 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

  5. 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.

  6. Is the 7/21- Isomer State of S43 Spherical?

    NASA Astrophysics Data System (ADS)

    Chevrier, R.; Daugas, J. M.; Gaudefroy, L.; Ichikawa, Y.; Ueno, H.; Hass, M.; Haas, H.; Cottenier, S.; Aoi, N.; Asahi, K.; Balabanski, D. L.; Fukuda, N.; Furukawa, T.; Georgiev, G.; Hayashi, H.; Iijima, H.; Inabe, N.; Inoue, T.; Ishihara, M.; Ishii, Y.; Kameda, D.; Kubo, T.; Nanao, T.; Neyens, G.; Ohnishi, T.; Rajabali, M. M.; Suzuki, K.; Takeda, H.; Tsuchiya, M.; Vermeulen, N.; Watanabe, H.; Yoshimi, A.

    2012-04-01

    We report on the spectroscopic quadrupole moment measurement of the 7/21- isomeric state in S271643 [E*=320.5(5)keV, T1/2=415(3)ns], using the time dependent perturbed angular distribution technique at the RIKEN RIBF facility. Our value, ∣Qs∣=23(3)efm2, is larger than that expected for a single-particle state. Shell model calculations using the modern SDPF-U interaction for this mass region reproduce remarkably well the measured ∣Qs∣, and show that non-negligible correlations drive the isomeric state away from a purely spherical shape.

  7. 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.

  8. 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.

  9. Discrimination of Isomeric Carbohydrates as the Electron Transfer Products of Group II Cation Adducts by Ion Mobility Spectrometry and Tandem Mass Spectrometry.

    PubMed

    Huang, Yuting; Dodds, Eric D

    2015-06-01

    The rapid and unambiguous distinction of isomeric carbohydrate structures persists as a tremendous analytical challenge. This paper reports the first exploitation of carbohydrate/metal ion interactions in concert with gas-phase ion chemistry to improve discrimination of oligosaccharide isomers by both ion mobility spectrometry and tandem mass spectrometry. This is demonstrated for two isomeric pentasaccharides and two isomeric hexasaccharides, each studied in an underivatized form as their calcium ion adducts, barium ion adducts, and gas-phase electron transfer products thereof. With appropriate selection of the charge carrier, transfer of a single electron to the carbohydrate metal ion adducts resulted in isomer-distinguishing shifts in their ion/neutral collision cross sections and the appearance of unique features in their vibrational activation/dissociation spectra. These findings suggest novel and elegant gas-phase strategies for rapid differentiation of isomeric oligosaccharides.

  10. 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.

  11. 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.

  12. Chain branching and termination in the low-temperature combustion of n-alkanes: 2-pentyl radical + O2, isomerization and association of the second O2.

    PubMed

    Asatryan, Rubik; Bozzelli, Joseph W

    2010-07-29

    Association of alkyl radicals with ground-state oxygen (3)Sigma(g)(+)(O(2)) generates chemically activated peroxy intermediates, which can isomerize or further react to form new products before collisional stabilization. The lowest-energy reaction (approximately 19 kcal mol(-1)) for alkylperoxy derivatives of C(3) and larger n-hydrocarbons is an isomerization (intramolecular H-atom transfer) that forms a hydroperoxide alkyl radical, and there is a approximately 30 kcal mol(-1) barrier path to olefin plus HO(2), which is a termination step at lower temperatures. The low-energy-barrier product, hydroperoxide alkyl radical intermediate, can experience additional chemical activation via association with a second oxygen molecule, where there are three important paths that result in chain branching. The competition between this HO(2) + olefin termination step of the first O(2) association and the chain branching processes from the second chemical activation step plays a dominant role at temperatures below 1000 K. Secondary n-pentyl radicals are used in this study as surrogates to analyze the thermochemistry and detailed kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination. As these radicals provide six- member ring transition states for H-atom transfer between secondary carbons, they represent the detailed kinetics of larger alkane radicals, such as the common fuel components n-heptane and n-decane. Comprehensive potential energy diagrams developed from multilevel CBS-QB3, G3MP2, and CBS-APNO and single-level ab initio and density functional theory methods are used to analyze secondary 2-pentyl (n-pentan-2-yl) and interrelated 2-hydroperoxide-pentan-4-yl radical interactions with O(2). The thermochemistry and kinetics of the chemical activation and stabilized adduct reactions important to chain branching and termination are reported and discussed. Results show that the chain branching reactions have faster

  13. 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.

  14. 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

  15. Two water-bridged cobalt(II) chains with isomeric naphthoate spacers: from metamagnetic to single-chain magnetic behaviour.

    PubMed

    Liu, Zhong-Yi; Xia, Yan-Fei; Jiao, Jiao; Yang, En-Cui; Zhao, Xiao-Jun

    2015-12-14

    The crystal structures and magnetic behaviours of two water-bridged one-dimensional (1D) cobalt(II) chains with different isomeric naphthoate (na(-)) terminals, [Co(H2O)3(2-na)2]n (1) and {[Co(H2O)3(1-na)2]·2H2O}n (2), were reported to investigate the effect of interchain distance on their magnetic properties. Complex 1 with trans-2-na(-) blocks and dense interchain separation exhibits a metamagnetic transition from antiferromagnetic ordering to a saturated paramagnetic phase. By contrast, complex 2 possessing cis-arranged 1-na(-) spacers and good interchain isolation shows unusual single-chain magnetic behavior under a zero dc field. Thus, completely different interchain packing by isomeric naphthoate ligands governs the ratio of intra- to inter-chain magnetic interactions and further results in different magnetic phenomena, which provide significant magnetostructural information on 1D magnetic systems. PMID:26514974

  16. Infrared-induced rotational isomerization of 1,2-ethanediamine in argon matrices and conformational analysis by DFT calculation

    NASA Astrophysics Data System (ADS)

    Kudoh, Satoshi; Takayanagi, Masao; Nakata, Munetaka; Ishibashi, Takaaki; Tasumi, Mitsuo

    1999-04-01

    Infrared spectra of 1,2-ethanediamine and its two deuterated species, ND 2CH 2CH 2ND 2 and NH 2CD 2CD 2NH 2, were measured by matrix-isolation FTIR spectroscopy. Isomerization around the central C-C axis from two gauche conformers to one trans conformer was found to occur upon infrared irradiation. With an aid of density functional theory, DFT, calculations, where the 6-31++G** basis set was used to optimize geometrical structures, the gauche conformers were assigned to G +G +G - and TG +G -, and the trans conformer to TTT. Wavelength dependence of the isomerization rates was examined using a tunable narrow band pass filter. It was found that relative quantum yields depend on excitation energy but not on the type of vibrational modes which absorb infrared rays.

  17. Complementary in situ reactivity of isomeric dipyridylamide precursors and its effect on dimensionality of cadmium 5-nitroisophthalate coordination polymers

    NASA Astrophysics Data System (ADS)

    O'Donovan, Megan E.; LaDuca, Robert L.

    2014-07-01

    Hydrothermal treatment of cadmium nitrate, 5-nitroisophthalic acid (H2nip) and one of two isomeric dipyridylamides resulted in coordination polymer crystalline solids that manifested different in situ reactivity and dimensionality, as ascertained by single crystal X-ray diffraction. Hydrolysis of 3-pyridylisonicotinamide (3-pina) afforded the 3-aminopyridine (3-ampyr) ligands observed in the 1-D ladder polymer {[Cd(nip)(3-ampyr)(H2O)]ṡ2H2O}n (1). Conversely, hydrolysis of the isomeric precursor 3-pyridylnicotinamide (3-pna) generated the monoanionic nicotinate ligands in the 2-D coordination polymer [Cd2(nip)(nic)2(H2O)2]n (2). Compound 2 displays {Cd2(OCO)2} eight-membered ring dimeric units linked into (6,3) graphite-type slab motifs. Luminescent properties of these two new materials are also presented.

  18. Results of a Direct Search Using Synchrotron Radiation for the Low-Energy Th229 Nuclear Isomeric Transition

    DOE PAGES

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

    2015-06-23

    We report the results of a direct search for the 229Tn (Iπ = 3/2+ ← 5/2+) nuclear isomeric transition, performed by exposing 229Tn-doped LiSrAlF6 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. Lastly, this measurement excludes roughly half of the favored transition search area and can be used to direct future searches.

  19. 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.

  20. 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.

  1. 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

  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. 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.

  4. Intramolecular C-H bond activation and redox isomerization across two-electron mixed valence diiridium cores.

    SciTech Connect

    Esswein, A. J.; Veige, A. S.; Piccoli, P. M. B.; Schultz, A. J.; Nocera, D. G.; MIT

    2008-03-24

    Metal-metal cooperativity enables the reaction of carbon-based substrates at diiridium two-electron mixed valence centers. Arylation of Ir{sub 2}{sup 0,II}(tfepma){sub 3}Cl{sub 2} (1) (tfepma = bis[(bistrifluoroethoxy)phosphino]methylamine) with RMgBr (R = C{sub 6}H{sub 5} and C{sub 6}D{sub 5}) is followed by C-H bond activation to furnish the bridging benzyne complex Ir{sub 2}II,II(tfepma){sub 3}({mu}-C{sub 6}H4)(C{sub 6}H{sub 5})H (2), as the kinetic product. At ambient temperature, 2 isomerizes to Ir{sub 2}{sup I,III}(tfepma){sub 3}({mu}-C{sub 6}H4)(C{sub 6}H{sub 5})H (3) (k{sub obs} = 9.57 {+-} 0.10 x 10{sup -5} s{sup -1} at 31.8 C, {Delta}H{sup {+-}} = 21.7 {+-} 0.3 kcal/mol, {Delta}S{sup {+-}} = -7.4 {+-} 0.9 eu), in which the benzyne moiety is conserved and the Ir{sup III} center is ligated by terminal hydride and phenyl groups. The same reaction course is observed for arylation of 1 with C{sub 6}D{sub 5}MgBr to produce 2-d{sub 10} and 3-d{sub 10} accompanied by an inverse isotope effect, k{sub h}/k{sub d} = 0.44 (k{sub obs} = 2.17 {+-} 0.10 x 10{sup -4} s{sup -1} in C{sub 6}D{sub 6} solution at 31.8 C, {Delta}H{sup {+-}} = 24.9 {+-} 0.7 kcal/mol, {Delta}S{sup {+-}} = -6.4 {+-} 2.4 eu). 2 reacts swiftly with hydrogen to provide Ir{sub 2}{sup II,II}(tfepma){sub 3}H{sub 4} as both the syn and anti isomers (4-syn and 4-anti, respectively). The hydrides of 4-syn were directly located by neutron diffraction analysis. X-ray crystallographic examination of 2, 2-d{sub 10}, 3, and 4-syn indicates that cooperative reactivity at the bimetallic diiridium core is facilitated by the ability of the two-electron mixed valence framework to accommodate the oxidation state changes and ligand rearrangements attendant to the reaction of the substrate.

  5. 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.

  6. Effect of Asp 96 isomerization on the properties of a lens αB-crystallin-derived short peptide.

    PubMed

    Takata, Takumi; Fujii, Noriko

    2015-12-10

    One of the major reasons for age-related cataract formation is an accumulation of insoluble lens proteins. In particular, higher-order α-crystallin aggregates, comprising αA and αB subunits, are insolubilized by the build up of various post-translational modifications over time. Although we previously found an exceptional amount of Asp96 isomerization in αB-crystallin from aged human lens, the biological effect remains unknown. To approximate the effect of Asp 96 isomerization in αB-crystallin, here residues 93-103 of αB-crystallin were chemically synthesized as peptides in which l-α-Asp was replaced with l-β-Asp, D-α-Asp, or D-β-Asp. The resulting peptides were then compared in a biological assay. The results showed that isomerization of Asp 96 altered both the local structure of peptide and its stability against enzymatic digestion. In addition, the synthesized peptides decreased the insoluble fraction of heated α-crystallin. The D-β-Asp-containing peptide further decreased heat-induced precipitation of α-crystallin, and a chaperone assay based on heated alcohol dehydrogenase implied differential interaction of the peptides with substrate depending on the Asp isomer present in each. Our results suggest that the formation of Asp isomers is likely to affect the higher-order oligomer structure of α-crystallin and thereby its chaperone functions in aged lens.

  7. 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

  8. Effect of Pt and H{sub 2} on n-butane isomerization over Fe and Mn promoted sulfated zirconia

    SciTech Connect

    Song, Xuemin; Reddy, K.R.; Sayari, A.

    1996-06-01

    The activity of a 0.4 wt% Pt-containing Fe and Mn promoted sulfated zirconia (PtSFMZ) catalyst in n-butane isomerization at 35{degrees}C was compared to that of a Pt-free catalyst (SFMZ). The maximum rate of n-butane conversion observed in helium over PtSFMZ was found to be 2.5 times higher than that over the SFMZ catalyst under the same conditions. It is believed that n-butane isomerization proceeds via a bimolecular mechanism in which the formation of hydrogen-deficient intermediates (carbenium ions and butenes), is necessary and the presence of transition metals such as Pt, Fe, and Mn on sulfated zirconia facilitates the formation/accumulation of these intermediates and increases their stability on the catalyst surface. The presence of H{sub 2} had a strong negative effect on n-butane conversion over PtSFMZ, but had no effect over SFMZ. The negative effect of H{sub 2} on PtSFMZ catalyst in n-butane isomerization reaction was attributed to the decreased concentration of butenes in the presence of hydrogen atoms which are formed by the dissociation of H{sub 2} on Pt. The ability of calcined Pt-containing catalysts to activate hydrogen at 35{degrees}C was demonstrated. Reduced SFMZ with or without Pt was not active at 35{degrees}C regardless of the nature of the carrier gas. 42 refs., 5 figs.

  9. Analysis of isomeric polycyclic aromatic hydrocarbons by charge-exchange chemical ionization mass spectrometry

    SciTech Connect

    Simonsick, W.J. Jr.; Hites, R.A.

    1984-12-01

    Charge-exchange chemical ionization mass spectrometry (using a 15% mixture of methane in argon) yields abundant M/sup +/, M + H/sup +/, M + C/sub 2/H/sub 5//sup +/ ions of polycyclic aromatic hydrocarbons (PAH). On the basis of the relative intensities of the M + H/sup +/ ion to the M/sup +/ ion, this technique can differentiate, in a predictable manner, isomeric structures of PAH. The operating conditions were evaluated and optimized; the most significant contributions to the variations in the (M + H)/sup +//M/sup +/ ratios are the temperature, pressure, and condition of the ion source. The optimum ion source temperature (250/sup 0/C) and pressure (0.8 torr) are easily controlled and regulated. The variable contamination of the ion source is compensated by an internal standard 1,2,3,5-tetrafluorobenzene. The analyses of Standard Reference Materials 1648 and 1649 (air particulate samples) and a carbon black extract are reported. Triphenylene and chrysene, although not chromatographically resolved, can be quantitated by using this technique. The identification of acephenanthrylene based on the measurement of ratios and calculated ionization potentials is also presented.

  10. Electron Anisotropy as a Signature of Mode Specific Isomerization in Vinylidene

    NASA Astrophysics Data System (ADS)

    Gibson, Stephen T.; Laws, Benjamin A.; Mabbs, Richard; Neumark, Daniel; Lineberger, Carl; Field, Robert W.

    2016-06-01

    he nature of the isomerization process that turns vinylidene into acetylene has been awaiting advances in experimental methods, to better define fractionation widths beyond those available in the seminal 1989 photoelectron spectrum measurement. This has proven a challenge. The technique of velocity-map imaging (VMI) is one avenue of approach. Images of electrons photodetached from vinylidene negative-ions, at various wavelengths, 1064 nm shown, provide more detail, including unassigned structure, but only an incremental improvement in the instrument line width. Intriguingly, the VMIs demonstrate a mode dependent variation in the electron anisotropy. Most notable in the figure, the inner-ring transition clusters are discontinuously, more isotropic. Electron anisotropy may provide an alternative key to examine the character of vinylidene transitions, mediating the necessity for an extreme resolution measurement. Vibrational dependent anisotropy has previously been observed in diatomic photoelectron spectra, associated with the coupling of electronic and nuclear motions. Research supported by the Australian Research Council Discovery Project Grant DP160102585. K. M. Ervin, J. Ho, and W. C. Lineberger, J. Chem. Phys. 91, 5974 (1989). doi:10.1063/1.457415 M. van Duzor et al. J. Chem. Phys. 133, 174311 (2010). doi:10.1063/1.3493349

  11. Isomerization and Oligomerization of Truncated and Mutated Tau Forms by FKBP52 are Independent Processes.

    PubMed

    Kamah, A; Cantrelle, F X; Huvent, I; Giustiniani, J; Guillemeau, K; Byrne, C; Jacquot, Y; Landrieu, I; Baulieu, E E; Smet, C; Chambraud, B; Lippens, G

    2016-03-27

    The aggregation of the neuronal Tau protein is one molecular hallmark of Alzheimer's disease and other related tauopathies, but the precise molecular mechanisms of the aggregation process remain unclear. The FK506 binding protein FKBP52 is able to induce oligomers in the pathogenic Tau P301L mutant and in a truncated form of the wild-type human Tau protein. Here, we investigate whether FKBP52's capacity to induce Tau oligomers depends on its prolyl cis/trans isomerase activity. We find that FKBP52 indeed can isomerize selected prolyl bonds in the different Tau proteins, and that this activity is carried solely by its first FK506 binding domain. Its capacity to oligomerize Tau is, however, not linked to this peptidyl-prolyl isomerase activity. In addition, we identified a novel molecular interaction implying the PHF6 peptide of Tau and the FK1/FK2 domains of FKBP52 independent of FK506 binding; these data point toward a non-catalytic molecular interaction that might govern the effect of FKBP52 on Tau.

  12. Cyanides and isocyanides of first-row transition metals: molecular structure, bonding, and isomerization barriers.

    PubMed

    Rayón, Víctor M; Redondo, Pilar; Valdés, Haydee; Barrientos, Carmen; Largo, Antonio

    2007-07-19

    Cyanides and isocyanides of first-row transition metal M(CN) (M=Sc-Zn) are investigated with quantum chemistry techniques, providing predictions for their molecular properties. A careful analysis of the competition between cyanide and isocyanide isomers along the transition series has been carried out. In agreement with the experimental observations, late transition metals (Co-Zn) clearly prefer a cyanide arrangement. On the other hand, early transition metals (Sc-Fe), with the only exception of the Cr(CN) system, favor the isocyanide isomer. The theoretical calculations predict the following unknown isocyanides, ScNC(3Delta), TiNC(4Phi), VNC(5Delta), and MnNC(7Sigma+), and agree with the experimental observation of FeNC(6Delta) and the CrCN(6Sigma+) cyanide. First-row transition metal cyanides and isocyanides are predicted to have relatively large dissociation energies with values within the range 80-101 kcal mol(-1), except Zn(CN), which has a dissociation energy around 50-55 kcal mol(-1), and low isomerization barriers. A detailed analysis of the bonding has been carried out employing the topological analysis of the charge density and an energy decomposition analysis. The role of the covalent and electrostatic contributions to the metal-ligand bonding, as well as the importance of pi bonding, are discussed. PMID:17580838

  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. 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.

  15. KSHV Reactivation and Novel Implications of Protein Isomerization on Lytic Switch Control

    PubMed Central

    Guito, Jonathan; Lukac, David M.

    2015-01-01

    In Kaposi’s sarcoma-associated herpesvirus (KSHV) oncogenesis, both latency and reactivation are hypothesized to potentiate tumor growth. The KSHV Rta protein is the lytic switch for reactivation. Rta transactivates essential genes via interactions with cofactors such as the cellular RBP-Jk and Oct-1 proteins, and the viral Mta protein. Given that robust viral reactivation would facilitate antiviral responses and culminate in host cell lysis, regulation of Rta’s expression and function is a major determinant of the latent-lytic balance and the fate of infected cells. Our lab recently showed that Rta transactivation requires the cellular peptidyl-prolyl cis/trans isomerase Pin1. Our data suggest that proline‑directed phosphorylation regulates Rta by licensing binding to Pin1. Despite Pin1’s ability to stimulate Rta transactivation, unchecked Pin1 activity inhibited virus production. Dysregulation of Pin1 is implicated in human cancers, and KSHV is the latest virus known to co-opt Pin1 function. We propose that Pin1 is a molecular timer that can regulate the balance between viral lytic gene expression and host cell lysis. Intriguing scenarios for Pin1’s underlying activities, and the potential broader significance for isomerization of Rta and reactivation, are highlighted. PMID:25588053

  16. Isomerization and Oligomerization of Truncated and Mutated Tau Forms by FKBP52 are Independent Processes.

    PubMed

    Kamah, A; Cantrelle, F X; Huvent, I; Giustiniani, J; Guillemeau, K; Byrne, C; Jacquot, Y; Landrieu, I; Baulieu, E E; Smet, C; Chambraud, B; Lippens, G

    2016-03-27

    The aggregation of the neuronal Tau protein is one molecular hallmark of Alzheimer's disease and other related tauopathies, but the precise molecular mechanisms of the aggregation process remain unclear. The FK506 binding protein FKBP52 is able to induce oligomers in the pathogenic Tau P301L mutant and in a truncated form of the wild-type human Tau protein. Here, we investigate whether FKBP52's capacity to induce Tau oligomers depends on its prolyl cis/trans isomerase activity. We find that FKBP52 indeed can isomerize selected prolyl bonds in the different Tau proteins, and that this activity is carried solely by its first FK506 binding domain. Its capacity to oligomerize Tau is, however, not linked to this peptidyl-prolyl isomerase activity. In addition, we identified a novel molecular interaction implying the PHF6 peptide of Tau and the FK1/FK2 domains of FKBP52 independent of FK506 binding; these data point toward a non-catalytic molecular interaction that might govern the effect of FKBP52 on Tau. PMID:26903089

  17. Cationic Methylene-Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies.

    PubMed

    Rapacioli, Mathias; Simon, Aude; Marshall, Charlotte C M; Cuny, Jérôme; Kokkin, Damian; Spiegelman, Fernand; Joblin, Christine

    2015-12-24

    This paper provides spectral characterizations of the two isomers of the 1-methylenepyrene cation, namely, the 1-pyrenemethylium and a pyrene-like isomer owing a tropylium cycle. Both are possible photodissociation products of the 1-methylpyrene cation and were proposed as potential contributors to the diffuse interstellar bands. In that respect, vibrational and electronic spectra are computed for the optimized structures at the density functional theory (DFT) and time-dependent (TD-)DFT levels. Finite temperature effects on these spectra are estimated from molecular dynamics simulations within the density functional-based tight-binding (DFTB) and TD-DFTB frameworks, these methods being first benchmarked against DFT and TD-DFT calculations. The computed spectra allow discrimination of the two isomers. When the temperature increases, bands are observed to redshift and merge. The isomerization mechanism is investigated with the metadynamics technique, a biased dynamics scheme allowing to probe reaction mechanisms with high energy barriers by investigating the free energy surface at various temperatures. Four pathways with similar barrier heights (3.5-4 eV) are found, showing that the interconversion process would only occur in interstellar clouds under photoactivation. The present study opens the way to simulations on larger methyl- and methylenePAHs of astrophysical interest and their experimental investigation.

  18. 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.

  19. Chemical protection of pheromones containing an internal conjugated diene system from isomerization and oxidation.

    PubMed

    Ideses, R; Shani, A

    1988-08-01

    Conjugated diene systems are common in natural products, including pheromones. The systems are sensitive to heat, light, and oxygen, among other things. They can be protected by antioxidants and UV absorbers, which slow downcis-trans isomerization and oxidation. Three sex pheromones (one as an analog) containingZ,E, E,Z, andE,E units were studied: (Z,E)-9,11-C14OAc, (E,Z)-7,9-C12OAc, and (E,E)-10,12-C16OAc. The UV absorber 2-hydroxy-4-methoxybenzophenone and the antioxidants BHT and BHA were found to be effective in solution. The protective effect of the UV absorber against photoisomerization on paper carriers was not as good as that in solution. Preliminary studies on the utilization of formulations containing these compounds and (Z,E)-9,11-C14OAc in the mass trapping of Egyptian cotton leafworm male in cotton fields showed the new combinations to be as good as a previously used formulation with UOP 688, a compound which is unpleasant to handle.

  20. Failure in closure of the anterior neural tube causes left isomerization of the zebrafish epithalamus.

    PubMed

    Lu, Po-Nien; Lund, Caroline; Khuansuwan, Sataree; Schumann, Adelle; Harney-Tolo, Marijah; Gamse, Joshua T; Liang, Jennifer O

    2013-02-15

    Differences between the left and right sides of the brain are present in many animal species. For instance, in humans the left cerebral hemisphere is largely responsible for language and tool use and the right for processing spatial information. Zebrafish have prominent left-right asymmetries in their epithalamus that have been associated with differential left and right eye use and navigational behavior. In wild-type (WT) zebrafish embryos, Nodal pathway genes are expressed in the left side of the pineal anlage. Shortly thereafter, a parapineal organ forms to the left of the pineal. The parapineal organ causes differences in gene expression, neuropil density, and connectivity of the left and right habenula nuclei. In embryos that have an open neural tube, such as embryos that are deficient in Nodal signaling or the cell adhesion protein N-cadherin, the left and right sides of the developing epithalamus remain separated from one another. We find that the brains of these embryos often become left isomerized: both sides of the brain develop morphology and gene expression patterns that are characteristic of the left side. However, other aspects of epithalamic development, such as differentiation of specific neuronal cell types, are intact. We propose that there is a mechanism in embryos with closed neural tubes that prevents both sides from developing like the left side. This mechanism fails when the two sides of the epithalamus are widely separated from one another, suggesting that it is dependent upon a signaling protein with limited range.

  1. 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.

  2. A comparative cytotoxicity study of isomeric alkylphthalates to metabolically variant bacteria.

    PubMed

    Sandy, Edward H; Yao, Jun; Zheng, Shixue; Gogra, Alhaji B; Chen, Huilun; Zheng, Hui; Yormah, Thomas B R; Zhang, Xin; Zaray, Gyula; Ceccanti, Brunello; Choi, Martin M F

    2010-10-15

    This work investigated the toxicity of two isomeric alkylphthalates, i.e., di-n-octyl phthalate (DOP) and di-2-ethylhexyl phthalate (DEHP) to two model bacteria, Escherichia coli (E. coli) and Bacillus subtilis (B. subtilis), which have been previously used to study the toxicity of environmental pollutants. Microcalorimetry was used as the key analytical tool alongside scanning electron microscopy (SEM) and traditional microbiology techniques. The thermokinetic parameters from microcalorimetry showed that the phthalates had a biphasic effect on the metabolic activities of the bacteria; serving as energy sources for the bacteria thereby stimulating their growth at low dosages (< or = 150 microg/mL), but displaying inhibitory effects at higher dosages (> or = 300 microg/mL), indicated by a sharp decrease in growth rate constants at 450 microg/mL. The SEM revealed that the bacterial cells were morphological deformed, with shrunk cells and elongated strands at 600 microg/mL of both phthalates. The elongated strands inferred that the phthalates inhibited the reproductive processes of the bacteria by possibly impeding some stages of cell division. The half inhibitory concentrations of the phthalates showed that DEHP was more toxic than DOP. Additionally, E. coli, a facultative anaerobe, was more susceptible to the toxic effects of phthalates than B. subtilis, an obligate aerobe capable of forming endospores crucial for tolerating extreme environmental conditions.

  3. Isomerization of all-trans-retinoids to 11-cis-retinoids in vitro

    SciTech Connect

    Bernstein, P.S.; Law, W.C.; Rando, R.R.

    1987-04-01

    The key biochemical process of the vertebrate visual cycle required for rhodopsin regeneration, 11-cis-retinoid production from all-trans-retinoids, is shown to occur in vitro. A 600 X g supernatant from a frog retina/pigment epithelium homogenate transforms added all-trans-(/sup 3/H)retinol, in a time-dependent fashion, to a mixture of 11-cis-retinol, 11-cis-retinal, and 11-cis-retinyl palmitate. 13-cis-Retinoids are formed in only minor amounts by nonspecific processes. Studies using washed particulate fractions of the 600 X g supernatant indicate that all-trans-(/sup 3/H)retinol is isomerized to 11-cis-retinoids much more effectively than is all-trans-(/sup 3/H)retinal or all-trans-(/sup 3/H)retinyl palmitate. The 11-cis-retinoid biosynthetic activity is heat-labile, sedimentable by high-speed centrifugation, and largely found in the pigment epithelium rather than in the neural retina.

  4. Cationic Methylene-Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies.

    PubMed

    Rapacioli, Mathias; Simon, Aude; Marshall, Charlotte C M; Cuny, Jérôme; Kokkin, Damian; Spiegelman, Fernand; Joblin, Christine

    2015-12-24

    This paper provides spectral characterizations of the two isomers of the 1-methylenepyrene cation, namely, the 1-pyrenemethylium and a pyrene-like isomer owing a tropylium cycle. Both are possible photodissociation products of the 1-methylpyrene cation and were proposed as potential contributors to the diffuse interstellar bands. In that respect, vibrational and electronic spectra are computed for the optimized structures at the density functional theory (DFT) and time-dependent (TD-)DFT levels. Finite temperature effects on these spectra are estimated from molecular dynamics simulations within the density functional-based tight-binding (DFTB) and TD-DFTB frameworks, these methods being first benchmarked against DFT and TD-DFT calculations. The computed spectra allow discrimination of the two isomers. When the temperature increases, bands are observed to redshift and merge. The isomerization mechanism is investigated with the metadynamics technique, a biased dynamics scheme allowing to probe reaction mechanisms with high energy barriers by investigating the free energy surface at various temperatures. Four pathways with similar barrier heights (3.5-4 eV) are found, showing that the interconversion process would only occur in interstellar clouds under photoactivation. The present study opens the way to simulations on larger methyl- and methylenePAHs of astrophysical interest and their experimental investigation. PMID:26600076

  5. 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

  6. 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.

  7. Secondary deuterium kinetic isotope effects on the isomerization of the trimethylene diradical to cyclopropane

    SciTech Connect

    Baldwin, J.E.; Freedman, T.B.; Yamaguchi, Yukio; Schaefer, H.F. III

    1996-11-06

    The trimethylene diradical (1-d{sub 0}) has long been considered a possible or even a likely short-lived reactive intermediate. The precise character of the trimethylene intermediate is of course not revealed unambiguously through the agreement between calculated relative lifetimes and measured lifetimes shown here. The local energetic minimum in the many-dimensional potential energy surface for the trimethylene intermediate is quite shallow, and the diradical may exist in a variety of conformational forms characterized by different C-C-C bond angles and H-C-C-H dihedral angles without any substantial variations in energy. For such a molecular entity, nearly a `twixtyl`, `a molecule or a range of molecular conformations` having no minimum on a potential energy surface but `which operationally behaves as a true intermediate`, isomerization rates and lifetimes may be dictated more by the requirement that various vibrational modes must attain appropriate phase relationships with one another rather than by any all-important activation energy criterion. 26 refs., 3 tabs.

  8. 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

  9. 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).

  10. 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

  11. Stereochemical aspects of the metabolism of the isomeric methylcyclohexanols and methylcyclohexanones

    PubMed Central

    Elliott, T. H.; Tao, Rosaline C. C.; Williams, R. T.

    1965-01-01

    1. The seven isomeric optically inactive forms of methylcyclohexanol (i.e. 1-, and cis- and trans-2-, -3- and -4-) are excreted by rabbits mainly as glucuronides of the thermodynamically more stable forms of the alcohols. The eighth isomer, cyclohexylmethanol, however, undergoes aromatization in vivo, giving rise to benzoic acid and hippuric acid. The (±)-2-, (±-3- and 4-methylcyclohexanones are reduced in the rabbit and excreted mainly as the glucuronides of the thermodynamically more stable forms of the corresponding methylcyclohexanols. 2. Racemic cis- and trans-2-methylcyclohexanol and 2-methylcyclohexanone are all excreted as conjugated trans-2-methylcyclohexanol. However, when the (±)-cis-alcohol or the (±)-ketone is fed, (+)-trans-2-methylcyclohexanol is excreted, whereas when the (±)-trans-alcohol is fed it is excreted as the (±)-trans-alcohol. 3. Racemic cis- and trans-3-methylcyclohexanol and 3-methylcyclohexanone are all excreted as conjugated racemic cis-3-methylcyclohexanol. cis- and trans-4-Methylcyclohexanol and 4-methylcyclohexanone are all excreted as conjugated trans-4-methylcyclohexanol. 4. The metabolic differences between the various methylcyclohexanols are explicable in terms of their conformations and of Vennesland's (1958) hypothesis of the role of NADH in dehydrogenation reactions. PMID:14333568

  12. STEREOCHEMICAL ASPECTS OF THE METABOLISM OF THE ISOMERIC METHYLCYCLOHEXANOLS AND METHYLCYCLOHEXANONES.

    PubMed

    ELLIOTT, T H; TAO, R C; WILLIAMS, R T

    1965-04-01

    1. The seven isomeric optically inactive forms of methylcyclohexanol (i.e. 1-, and cis- and trans-2-, -3- and -4-) are excreted by rabbits mainly as glucuronides of the thermodynamically more stable forms of the alcohols. The eighth isomer, cyclohexylmethanol, however, undergoes aromatization in vivo, giving rise to benzoic acid and hippuric acid. The (+/-)-2-, (+/--3- and 4-methylcyclohexanones are reduced in the rabbit and excreted mainly as the glucuronides of the thermodynamically more stable forms of the corresponding methylcyclohexanols. 2. Racemic cis- and trans-2-methylcyclohexanol and 2-methylcyclohexanone are all excreted as conjugated trans-2-methylcyclohexanol. However, when the (+/-)-cis-alcohol or the (+/-)-ketone is fed, (+)-trans-2-methylcyclohexanol is excreted, whereas when the (+/-)-trans-alcohol is fed it is excreted as the (+/-)-trans-alcohol. 3. Racemic cis- and trans-3-methylcyclohexanol and 3-methylcyclohexanone are all excreted as conjugated racemic cis-3-methylcyclohexanol. cis- and trans-4-Methylcyclohexanol and 4-methylcyclohexanone are all excreted as conjugated trans-4-methylcyclohexanol. 4. The metabolic differences between the various methylcyclohexanols are explicable in terms of their conformations and of Vennesland's (1958) hypothesis of the role of NADH in dehydrogenation reactions.

  13. 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.

  14. Comparisons of Caenorhabditis Fucosyltransferase Mutants Reveal a Multiplicity of Isomeric N-Glycan Structures.

    PubMed

    Yan, Shi; Jin, Chunsheng; Wilson, Iain B H; Paschinger, Katharina

    2015-12-01

    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.

  15. 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

  16. 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

  17. The intrinsic energy of the gating isomerization of a neuromuscular acetylcholine receptor channel.

    PubMed

    Nayak, Tapan K; Purohit, Prasad G; Auerbach, Anthony

    2012-05-01

    Nicotinic acetylcholine receptor (AChR) channels at neuromuscular synapses rarely open in the absence of agonists, but many different mutations increase the unliganded gating equilibrium constant (E0) to generate AChRs that are active constitutively. We measured E0 for two different sets of mutant combinations and by extrapolation estimated E0 for wild-type AChRs. The estimates were 7.6 and 7.8×10(-7) in adult-type mouse AChRs (-100 mV at 23°C). The values are in excellent agreement with one obtained previously by using a completely different method (6.5×10(-7), from monoliganded gating). E0 decreases with depolarization to the same extent as does the diliganded gating equilibrium constant, e-fold with ∼60 mV. We estimate that at -100 mV the intrinsic energy of the unliganded gating isomerization is +8.4 kcal/mol (35 kJ/mol), and that in the absence of a membrane potential, the intrinsic chemical energy of this global conformational change is +9.4 kcal/mol (39 kJ/mol). Na+ and K+ in the extracellular solution have no measureable effect on E0, which suggests that unliganded gating occurs with only water occupying the transmitter binding sites. The results are discussed with regard to the energy changes in receptor activation and the competitive antagonism of ions in agonist binding.

  18. Cyanides and isocyanides of first-row transition metals: molecular structure, bonding, and isomerization barriers.

    PubMed

    Rayón, Víctor M; Redondo, Pilar; Valdés, Haydee; Barrientos, Carmen; Largo, Antonio

    2007-07-19

    Cyanides and isocyanides of first-row transition metal M(CN) (M=Sc-Zn) are investigated with quantum chemistry techniques, providing predictions for their molecular properties. A careful analysis of the competition between cyanide and isocyanide isomers along the transition series has been carried out. In agreement with the experimental observations, late transition metals (Co-Zn) clearly prefer a cyanide arrangement. On the other hand, early transition metals (Sc-Fe), with the only exception of the Cr(CN) system, favor the isocyanide isomer. The theoretical calculations predict the following unknown isocyanides, ScNC(3Delta), TiNC(4Phi), VNC(5Delta), and MnNC(7Sigma+), and agree with the experimental observation of FeNC(6Delta) and the CrCN(6Sigma+) cyanide. First-row transition metal cyanides and isocyanides are predicted to have relatively large dissociation energies with values within the range 80-101 kcal mol(-1), except Zn(CN), which has a dissociation energy around 50-55 kcal mol(-1), and low isomerization barriers. A detailed analysis of the bonding has been carried out employing the topological analysis of the charge density and an energy decomposition analysis. The role of the covalent and electrostatic contributions to the metal-ligand bonding, as well as the importance of pi bonding, are discussed.

  19. 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

  20. 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.

  1. Rargb regulates organ laterality in a zebrafish model of right atrial isomerism

    PubMed Central

    Garnaas, Maija K.; Cutting, Claire C.; Meyers, Alison; Kelsey, Peter B.; Harris, James M.; North, Trista E.; Goessling, Wolfram

    2013-01-01

    Developmental signals determine organ morphology and position during embryogenesis. To discover novel modifiers of liver development, we performed a chemical genetic screen in zebrafish and identified retinoic acid as a positive regulator of hepatogenesis. Knockdown of the four RA receptors revealed that all receptors affect liver formation, however specific receptors exert differential effects. Rargb knockdown results in bilateral livers but does not impact organ size, revealing a unique role for Rargb in conferring left–right positional information. Bilateral populations of hepatoblasts are detectable in rargb morphants, indicating Rargb acts during hepatic specification to position the liver, and primitive endoderm is competent to form liver on both sides. Hearts remain at the midline and gut looping is perturbed in rargb morphants, suggesting Rargb affects lateral plate mesoderm migration. Overexpression of Bmp during somitogenesis similarly results in bilateral livers and midline hearts, and inhibition of Bmp signaling rescues the rargb morphant phenotype, indicating Rargb functions upstream of Bmp to regulate organ sidedness. Loss of rargb causes biliary and organ laterality defects as well as asplenia, paralleling symptoms of the human condition right atrial isomerism. Our findings uncover a novel role for RA in regulating organ laterality and provide an animal model of one form of human heterotaxia. PMID:22982668

  2. Lysergamides of isomeric 2,4-dimethylazetidines map the binding orientation of the diethylamide moiety in the potent hallucinogenic agent N,N-diethyllysergamide (LSD).

    PubMed

    Nichols, David E; Frescas, Stewart; Marona-Lewicka, Danuta; Kurrasch-Orbaugh, Deborah M

    2002-09-12

    Lysergic acid amides were prepared from (R,R)-(-)-, (S,S)-(+)-, and cis-2,4-dimethyl azetidine. The dimethylazetidine moiety is considered here to be a rigid analogue of diethylamine, and thus, the target compounds are all conformationally constrained analogues of the potent hallucinogenic agent, N,N-diethyllysergamide, LSD-25. Pharmacological evaluation showed that (S,S)-(+)-2,4-dimethylazetidine gave a lysergamide with the highest LSD-like behavioral activity in the rat two lever drug discrimination model that was slightly more potent than LSD itself. This same diastereomer also had the highest affinity and functional potency at the rat serotonin 5-HT(2A) receptor, the presumed target for hallucinogenic agents, and a receptor affinity profile in a panel of screens that was most similar to that of LSD itself. Both cis- and the (R,R)-trans-dimethylazetidines gave lysergamides that were less potent in all relevant assays. The finding that the S,S-dimethylazetidine gave a lysergamide with pharmacology most similar to LSD indicates that the N,N-diethyl groups of LSD optimally bind when they are oriented in a conformation distinct from that observed in the solid state by X-ray crystallography. The incorporation of isomeric dialkylazetidines into other biologically active molecules may be a useful strategy to model the active conformations of dialkylamines and dialkylamides.

  3. Shape isomers as candidates for the gamma ray laser storage state

    SciTech Connect

    Weiss, M.S.

    1987-12-01

    Three Dimension Nuclear Hartree-Fock calculations have been performed for isotopes of Osmium, Mercury, and Tungsten. Many of the calculated potential energy surfaces show a second minimum at large prolate deformation indicating the possibility of shape isomeric states. Several are at sufficiently low energy to be possible candidates as storage states for the gamma ray laser. 9 refs., 4 figs., 1 tab.

  4. {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.

  5. Isomerization of all-trans-Retinol to cis-Retinols in Bovine Retinal Pigment Epithelial Cells: Dependence on the Specificity of Retinoid-Binding Proteins†

    PubMed Central

    McBee, Joshua K.; Kuksa, Vladimir; Alvarez, Rosana; de Lera, Angel R.; Prezhdo, Oleg; Haeseleer, Françoise; Sokal, Izabela; Palczewski, Krzysztof

    2006-01-01

    In the retinal rod and cone photoreceptors, light photoactivates rhodopsin or cone visual pigments by converting 11-cis-retinal to all-trans-retinal, the process that ultimately results in phototransduction and visual sensation. The production of 11-cis-retinal in adjacent retinal pigment epithelial (RPE) cells is a fundamental process that allows regeneration of the vertebrate visual system. Here, we present evidence that all-trans-retinol is unstable in the presence of H+ and rearranges to anhydroretinol through a carbocation intermediate, which can be trapped by alcohols to form retro-retinyl ethers. This ability of all-trans-retinol to form a carbocation could be relevant for isomerization. The calculated activation energy of isomerization of all-trans-retinyl carbocation to the 11-cis-isomer was only ~18 kcal/mol, as compared to ~36 kcal/mol for all-trans-retinol. This activation energy is similar to ~17 kcal/mol obtained experimentally for the isomerization reaction in RPE microsomes. Mass spectrometric (MS) analysis of isotopically labeled retinoids showed that isomerization proceeds via alkyl cleavage mechanism, but the product of isomerization depended on the specificity of the retinoid-binding protein(s) as evidenced by the production of 13-cis-retinol in the presence of cellular retinoid-binding protein (CRBP). To test the influence of an electron-withdrawing group on the polyene chain, which would inhibit carbocation formation, 11-fluoro-all-trans-retinol was used in the isomerization assay and was shown to be inactive. Together, these results strengthen the idea that the isomerization reaction is driven by mass action and may occur via carbocation intermediate. PMID:10985782

  6. 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.

  7. o-Benzyne fragmentation and isomerization pathways: a CASPT2 study.

    PubMed

    Ghigo, Giovanni; Maranzana, Andrea; Tonachini, Glauco

    2014-11-21

    The mechanisms of the fragmentation and isomerization pathways of o-benzyne were studied at the multi-configurational second-order perturbative level [CAS(12,12)-PT2]. The direct fragmentation of o-benzyne to C2H2 + C4H2 follows two mechanisms: a concerted mechanism and a stepwise mechanism. Although the concerted mechanism is characterized by a single closed-shell transition structure, the stepwise pathway is more complex and structures with a strong diradical character are seen. A third diradicaloid fragmentation pathway of o-benzyne yields C6H2 as the final product. As an alternative to fragmentation, o-benzyne can also undergo rearrangement to its meta and para isomers and to the open chain cis and trans isomers of hexa-3-en-1,6-diyne (HED). These easily fragment to C2H2 + C4H2 or C6H2. Kinetic modelling at several different temperatures between 800 and 3000 K predicted that the thermal decomposition of o-benzyne should yield C2H2, C4H2 and C6H2 as the main products. Small amounts of the HED isomers accumulated at temperatures <1200 K, but they rapidly decompose at higher temperatures. Between 1000 and 1400 K, C2H2 + C4H2 are formed exclusively from the decomposition of trans-HED. At temperatures >1400 K, C2H2 + C4H2 also form from the direct fragmentation of o-benzyne. The formation of C2H2 + C4H2 prevails up to 1600 K but above this temperature the formation of C6H2 prevails. At temperatures >2400 K, the direct fragmentation of o-benzyne again leads to the formation of C2H2 + C4H2. The formation of hydrogen atoms is also explained by our proposed mechanisms. PMID:25283147

  8. o-Benzyne fragmentation and isomerization pathways: a CASPT2 study.

    PubMed

    Ghigo, Giovanni; Maranzana, Andrea; Tonachini, Glauco

    2014-11-21

    The mechanisms of the fragmentation and isomerization pathways of o-benzyne were studied at the multi-configurational second-order perturbative level [CAS(12,12)-PT2]. The direct fragmentation of o-benzyne to C2H2 + C4H2 follows two mechanisms: a concerted mechanism and a stepwise mechanism. Although the concerted mechanism is characterized by a single closed-shell transition structure, the stepwise pathway is more complex and structures with a strong diradical character are seen. A third diradicaloid fragmentation pathway of o-benzyne yields C6H2 as the final product. As an alternative to fragmentation, o-benzyne can also undergo rearrangement to its meta and para isomers and to the open chain cis and trans isomers of hexa-3-en-1,6-diyne (HED). These easily fragment to C2H2 + C4H2 or C6H2. Kinetic modelling at several different temperatures between 800 and 3000 K predicted that the thermal decomposition of o-benzyne should yield C2H2, C4H2 and C6H2 as the main products. Small amounts of the HED isomers accumulated at temperatures <1200 K, but they rapidly decompose at higher temperatures. Between 1000 and 1400 K, C2H2 + C4H2 are formed exclusively from the decomposition of trans-HED. At temperatures >1400 K, C2H2 + C4H2 also form from the direct fragmentation of o-benzyne. The formation of C2H2 + C4H2 prevails up to 1600 K but above this temperature the formation of C6H2 prevails. At temperatures >2400 K, the direct fragmentation of o-benzyne again leads to the formation of C2H2 + C4H2. The formation of hydrogen atoms is also explained by our proposed mechanisms.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Investigation of isomeric flavanol structures in black tea thearubigins using ultraperformance liquid chromatography coupled to hybrid quadrupole/ion mobility/time of flight mass spectrometry.

    PubMed

    Yassin, Ghada H; Grun, Christian; Koek, Jean H; Assaf, Khaleel I; Kuhnert, Nikolai

    2014-11-01

    Ultra performance liquid chromatography (UPLC) when coupled to ion mobility (IMS)/orthogonal acceleration time of flight mass spectrometry is a suitable technique for analyzing complex mixtures such as the black tea thearubigins. With the aid of this advanced instrumental analysis, we were able to separate and identify different isomeric components in the complex mixture which could previously not be differentiated by a conventional high performance liquid chromatography/tandem mass spectrometry. In this study, the difference between isomeric structures theasinensins, proanthocyanidins B-type and rutin (quercetin-3O-rutinoside) were studied, and these are present abundantly in many botanical sources. The differentiation between these structures was accomplished according to their acquired mobility drift times differing from the traditional investigations in mass spectrometry, where calculation of theoretical collisional cross sections allowed assignment of the individual isomeric structures. The present work demonstrates UPLC-IMS-MS as an efficient technology for isolating and separating isobaric and isomeric structures existing in complex mixtures discriminating between them according to their characteristic fragment ions and mobility drift times. Therefore, a rational assignment of isomeric structures in many phenolic secondary metabolites based on the ion mobility data might be useful in mass spectrometry-based structure analysis in the future.

  15. High-voltage electric-field-induced growth of aligned ``cow-nipple-like'' submicro-nano carbon isomeric structure via chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Liao, Chengwei; Zhang, Yupeng; Pan, Chunxu

    2012-12-01

    In this study, a novel vertically aligned carbon material, named "cow-nipple-like" submicro-nano carbon isomeric structure, was synthesized by the thermal decomposition of C2H2 in a chemical-vapor deposition system with a high-voltage external electric field. The microstructures were characterized by using scanning electron microscopy, high-resolution transmission electron microscopy, and Raman spectroscopy, respectively. The results revealed that (1) the total height of the carbon isomeric structure was in a rang of 90-250 nm; (2) the carbon isomeric structure consisted of a submicro- or nano-sized hemisphere carbon ball with 30-120 nm in diameter at the bottom and a vertically grown carbon nanotube with 10-40 nm in diameter upon the carbon ball; (3) there was a sudden change in diameter at the junction of the carbon ball and carbon nanotube. In addition, the carbon isomeric structure showed an excellent controllability, that is, the density, height, and diameter could be controlled effectively by adjusting the precursor ferrocene concentration in the catalytic solution and C2H2 ventilation time. A possible growth model was proposed to describe the formation mechanism, and a theoretic calculation was carried out to discuss the effect of high-voltage electric field upon the growth of the carbon isomeric structure.

  16. Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of (R)-glyceraldehyde 3-phosphate in D2O.

    PubMed

    O'Donoghue, Annmarie C; Amyes, Tina L; Richard, John P

    2005-02-22

    The product distributions for the reactions of (R)-glyceraldehyde 3-phosphate (GAP) in D(2)O at pD 7.5-7.9 catalyzed by triosephosphate isomerase (TIM) from chicken and rabbit muscle were determined by (1)H NMR spectroscopy. Three products were observed from the reactions catalyzed by TIM: dihydroxyacetone phosphate (DHAP) from isomerization with intramolecular transfer of hydrogen (49% of the enzymatic products), [1(R)-(2)H]-DHAP from isomerization with incorporation of deuterium from D(2)O into C-1 of DHAP (31% of the enzymatic products), and [2(R)-(2)H]-GAP from incorporation of deuterium from D(2)O into C-2 of GAP (21% of the enzymatic products). The similar yields of [1(R)-(2)H]-DHAP and [2(R)-(2)H]-GAP from partitioning of the enzyme-bound enediol(ate) intermediate between hydron transfer to C-1 and C-2 is consistent with earlier results, which showed that there are similar barriers for conversion of this intermediate to the alpha-hydroxy ketone and aldehyde products (Knowles, J. R., and Albery, W. J. (1977) Acc. Chem. Res. 10, 105-111). However, the observation that the TIM-catalyzed isomerization of GAP in D(2)O proceeds with 49% intramolecular transfer of the (1)H label from substrate to product DHAP stands in sharp contrast with the

  17. 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

  18. A rare association of major aorto-pulmonary collaterals with right isomerism and totally anomalous pulmonary venous drainage.

    PubMed

    Kumar, Sanjay; Ansari, Junaid; Weerasena, Nihal

    2005-12-01

    A female neonate, born at term, presented with complex cardiac anatomy dominated by right isomerism and infra-diaphragmatic totally anomalous pulmonary venous connection. Surgical repair was performed using circulatory arrest under deep hypothermia. In the postoperative period, the patient could not be weaned off mechanical ventilation, and underwent cardiac catheterization. This revealed major aortopulmonary collateral arteries, which were occluded with coils. We review the literature with specific focus on the occurrence of this unusual combination and its implication in the management during the postoperative period.

  19. 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

  20. 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

  1. 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.

  2. Journey through the potential energy surfaces for the isomerization and decomposition reactions of the telluroformaldehyde analogues: H2A═Te and HFA═Te (A = C, Si, and Ge).

    PubMed

    Jaufeerally, Naziah B; Abdallah, Hassan H; Ramasami, Ponnadurai; Schaefer, Henry F

    2013-07-11

    The unavailability of monomeric heavy ketone analogues has been ascribed to the evanescence of the very reactive A═E double bond (A and E are the heavier group 14 and group 16 elements, respectively). Can the isolation of any of the monomeric telluro-ketones be assisted by an energetic favorability on its potential energy surface (PES)? In this light, the reaction pathways for the isomerization and decomposition reactions of H2A═Te and HFA═Te (A = C, Si, and Ge) molecules on their singlet state PES have been studied using second-order Møller-Plesset perturbation theory (MP2). The barrier heights reported suggest that telluroformaldehyde, silanetellone, and germatellone are kinetically more resistant to unimolecular reactions than the corresponding lighter chalcogen analogues. However, upon replacing a hydrogen atom by fluorine, the barrier heights of most of the isomerization and decomposition reactions are lowered. Among the unimolecular reactions studied for the H2A═Te and HFA═Te (A = C, Si, and Ge) molecules, the decomposition of cis-FGeTeH into HF and GeTe is found to be the most facile reaction, with a barrier height of only 4.6 kcal/mol. We also predict the ground state telluro-ketones to be viable molecules, as they have no imaginary vibrational frequencies and their lowest vibrational frequencies are always >100 cm(-1). In view of the scarcity of information on the chemistry of the mentioned telluro-ketones, the molecular parameters of various isomers and decomposition products have been reported, and should be useful for future experimental investigations.

  3. Structural isomerization of synephrine influences its uptake and ensuing glutathione depletion in rat-isolated cardiomyocytes.

    PubMed

    Rossato, Luciana Grazziotin; Costa, Vera Marisa; de Pinho, Paula Guedes; Carvalho, Félix; de Lourdes Bastos, Maria; Remião, Fernando

    2011-08-01

    depletion showing that this effect is independent of α(1)-adrenoceptor stimulation. In conclusion, both positional isomers require OCT3 and OCT1-mediated transport to enter into the cardiomyocytes; however, the hydroxyl group in the p-position favours the OCT-mediated transport into cardiomyocytes. Furthermore, the structural isomerization of synephrine influences its toxicological profile since only m-synephrine caused GSH depletion.

  4. ‘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.

  5. High performance liquid chromatographic separation and pH-dependent electrochemical properties of pyrroloquinoline quinone and three closely related isomeric analogues.

    PubMed

    Zhang, Z; Tillekeratne, L M; Kirchhoff, J R; Hudson, R A

    1995-07-01

    Pyrroloquinoline quinone 1 (PQQ, methoxatin, 4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid) is a novel coenzyme. Closely related isomeric analogues of PQQ may be formed in nature and may possess PQQ-like functions. Here, the electrochemical pH-dependent properties and the high performance liquid chromatographic (HPLC) separation protocols are reported for three major isomeric PQQ analogues likely to be formed in nature. The electrochemical data (cyclic voltammetry) provided the pKas of the five ionizable groups in each isomeric PQQ. The HPLC protocols provide the means of investigating the formation of PQQ and the PQQ isomers reported here during the normal turnover of eukaryotic amine oxidases containing integral topaquinone residues, as well as from direct enzyme-mediated reactions which remain to be characterized.

  6. 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)

  7. Detailed study of the direct numerical observation of the Kramers turnover in the LiNC⇌LiCN isomerization rate

    NASA Astrophysics Data System (ADS)

    Müller, P. L. García; Hernandez, Rigoberto; Benito, R. M.; Borondo, F.

    2012-11-01

    According to Kramers, rates of molecular process are expected to follow a rise and fall from low friction (at little to no interaction with the environment) to high friction (at typical liquid densities and above). This so-called Kramers turnover was recently observed and delineated in the case of the LiNC⇌LiCN isomerization reaction in the presence of an argon bath [P. García-Müller, R. Hernandez, R. M. Benito, and F. Borondo, Phys. Rev. Lett. 101, 178302 (2008)], 10.1103/PhysRevLett.101.178302. The rates were obtained using direct molecular dynamics of an all-atom representation and the Langevin dynamics of a projected representation. We now provide further evidence that the forward and backward rates are indeed exhibiting the turnover. The rates are also seen to agree remarkably well with the Pollak-Grabert-Hänggi rate formulas in regimes satisfying the theory underlying assumptions. At higher temperatures, when the theory is expected to fail, the solvated LiCN isomerization continues to exhibit activated dynamics following the turnover.

  8. Mechanism responsible for D-transposition of the great arteries: Is this part of the spectrum of right isomerism?

    PubMed

    Nakajima, Yuji

    2016-09-01

    D-transposition of the great arteries (TGA) is one of the most common conotruncal heart defects at birth and is characterized by a discordant ventriculoarterial connection with a concordant atrioventricular connection. The morphological etiology of TGA is an inverted or arrested rotation of the heart outflow tract (OFT, conotruncus), by which the aorta is transposed in the right ventral direction to the pulmonary trunk. The rotational defect of the OFT is thought to be attributed to hypoplasia of the subpulmonic conus, which originates from the left anterior heart field (AHF) residing in the mesodermal core of the first and second pharyngeal arches. AHF, especially on the left, at the early looped heart stage (corresponding to Carnegie stage 10-11 in the human embryo) is one of the regions responsible for the impediment that causes TGA morphology. In human or experimentally produced right isomerism, malposition of the great arteries including D-TGA is frequently associated. Mutations in genes involving left-right (L-R) asymmetry, such as NODAL, ACTRIIB and downstream target FOXH1, have been found in patients with right isomerism as well as in isolated TGA. The downstream pathways of Nodal-Foxh1 play a critical role not only in L-R determination in the lateral plate mesoderm but also in myocardial specification and differentiation in the AHF, suggesting that TGA is a phenotype in heterotaxia as well as the primary developmental defect of the AHF.

  9. Kinetics of glucose isomerization to fructose by immobilized glucose isomerase: anomeric reactivity of D-glucose in kinetic model.

    PubMed

    Lee, H S; Hong, J

    2001-11-30

    The substrate specificity of immobilized D-glucose isomerase (EC 5.3. 1.5) is investigated with an immobilized enzyme-packed reactor. A series of isomerization experiments with alpha-, beta-, and equilibrated D-glucose solutions indicates that beta anomer as well as alpha anomer is a substrate of the glucose isomerase at pH 7.5 and 60 degrees C. For substrate concentration of 0.028 mol l(-1) (1% w/v), the initial conversion rate of alpha-D-glucose was 43% higher than that with equilibrated glucose at the same concentration and 113% higher than beta-D-glucose conversion rate. This anomeric reactivity of glucose isomerase is mathematically described with a set of kinetic equations based on the reaction steps complying with Briggs-Haldane mechanism and the experimentally determined kinetic constants. The proposed reaction mechanism includes the mutarotation and the isomerization reactions of alpha- and beta-D-glucose with different rate constants.

  10. cis/trans isomerization of unsaturated fatty acids as possible control mechanism of membrane fluidity in Pseudomonas putida P8.

    PubMed

    Loffeld, B; Keweloh, H

    1996-08-01

    Exponentially growing cells of Pseudomonas putida had an increased ratio of saturated to unsaturated fatty acids in response to increased growth temperatures. Resting cells in which fatty acid biosynthesis was stopped reacted to a thermal increase by converting cis-monounsaturated fatty acids to trans isomers. cis/trans Isomerization of up to 60% of the unsaturated fatty acids was also activated by alcohols of different chain length. Their effective concentrations apparently depended on the lipophilic character of the alcohols. Also, a salt shock caused by the addition of NaCl resulted in the production of trans fatty acids. However, cells that were adapted to growth media of high osmolarity synthesized cyclopropane fatty acids instead of trans fatty acids. Activity of cis/trans-isomerase was dependent on the growth phase and was significantly higher during logarithmic growth than during the stationary phase. The results of this study agree with the hypothesis that the isomerization of cis into trans unsaturated fatty acids is an emergency action of cells of P. putida to adapt membrane fluidity to drastic changes of environmental conditions.

  11. The Acid Catalyzed Dehydration of an Isomeric 2-Methylcyclohexanol Mixture: A Kinetic and Regiochemical Study of the Evelyn Effect

    NASA Astrophysics Data System (ADS)

    Cawley, John J.; Linder, Patrick E.

    1997-01-01

    This paper details an experiment which serves as an introduction to organic laboratory research. The reaction is the dehydration of a cis, trans mixture of 2-methylcyclohexanols. At intervals of times the reactant mixture is sampled for the cis and trans reactants. At those same intervals of times the receiver flasks of product cyclohexanes being collected are changed, such that sequential fractions of material are obtained. The reactant aliquots are quantitatively assayed by proton NMR, measuring each hydroxyl proton of the isomeric alcohols against the hydroxyl proton of an internal standard amount of cyclohexanol. The product fractions are analyzed for the relative amounts of the three cyclohexene isomers formed, again by proton NMR, this time measuring the vinyl hydrogens of one isomer against another. The resultant data are then analyzed, such that kisomeric cyclohexene, for example 1-methylcyclohexene.

  12. Mechanism responsible for D-transposition of the great arteries: Is this part of the spectrum of right isomerism?

    PubMed

    Nakajima, Yuji

    2016-09-01

    D-transposition of the great arteries (TGA) is one of the most common conotruncal heart defects at birth and is characterized by a discordant ventriculoarterial connection with a concordant atrioventricular connection. The morphological etiology of TGA is an inverted or arrested rotation of the heart outflow tract (OFT, conotruncus), by which the aorta is transposed in the right ventral direction to the pulmonary trunk. The rotational defect of the OFT is thought to be attributed to hypoplasia of the subpulmonic conus, which originates from the left anterior heart field (AHF) residing in the mesodermal core of the first and second pharyngeal arches. AHF, especially on the left, at the early looped heart stage (corresponding to Carnegie stage 10-11 in the human embryo) is one of the regions responsible for the impediment that causes TGA morphology. In human or experimentally produced right isomerism, malposition of the great arteries including D-TGA is frequently associated. Mutations in genes involving left-right (L-R) asymmetry, such as NODAL, ACTRIIB and downstream target FOXH1, have been found in patients with right isomerism as well as in isolated TGA. The downstream pathways of Nodal-Foxh1 play a critical role not only in L-R determination in the lateral plate mesoderm but also in myocardial specification and differentiation in the AHF, suggesting that TGA is a phenotype in heterotaxia as well as the primary developmental defect of the AHF. PMID:27329052

  13. Capillary electrophoresis analysis of hydrolysis, isomerization and enantiomerization of aspartyl model tripeptides in acidic and alkaline solution.

    PubMed

    De Boni, Silvia; Scriba, Gerhard K E

    2007-01-01

    In order to investigate the degradation of two aspartyl tripeptides, Gly-Asp-PheNH2 and Phe-Asp-GlyNH2 in solution capillary, electrophoresis methods were developed and validated. Separation of most degradation products including those arising from isomerization and enantiomerization of the Asp residues was achieved in a 50 mM sodium phosphate buffer, pH 3.0. Resolution of comigrating compounds could be achieved by addition of cyclodextrins to the background electrolyte. For tripeptide derivatives the assays were linear in the range of 0.015-3.0 mmol/l. Some dipeptides and amino acids exhibited a narrower linear range due to low UV absorbance. The limits of detection were in the range of 0.005-0.1 mmol/l. Incubation of the model peptides was carried out at pH 2 and 10. At pH 2, degradation of the peptides proceeded via C-terminal deamidation and peptide backbone hydrolysis. In contrast, isomerization and enantiomerization were observed in combination with deamidation at pH 10. Generally, degradation of Phe-Asp-GlyNH2 proceeded faster compared to Gly-Asp-PheNH2 due to steric hindrance by the phenyl side chain.

  14. 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

  15. Alpha-hydroxyalkyl heterocycles via chiral allylic boronates: Pd-catalyzed borylation leading to a formal enantioselective isomerization of allylic ether and amine.

    PubMed

    Lessard, Stéphanie; Peng, Feng; Hall, Dennis G

    2009-07-22

    An efficient catalytic enantioselective preparation of synthetically useful pyranyl and piperidinyl allylic boronates was achieved via a palladium-catalyzed borylation/isomerization reaction on the corresponding alkenyl triflates. The influence of the base and solvent was found to be crucial on the regio- and enantioselectivity of this reaction. The overall borylation process constitutes a successful example of formal asymmetric isomerization of allylic ether/amine. The resulting allylic boronate reagents add to various aldehydes in a one-pot process to give synthetically useful alpha-hydroxyalkyl derivatives in high stereoselectivity. PMID:19552416

  16. N-Heterocyclic Carbenes as Promotors for the Rearrangement of Phosphaketenes to Phosphaheteroallenes: A Case Study for OCP to OPC Constitutional Isomerism.

    PubMed

    Li, Zhongshu; Chen, Xiaodan; Benkő, Zoltán; Liu, Liu; Ruiz, David A; Peltier, Jesse L; Bertrand, Guy; Su, Chen-Yong; Grützmacher, Hansjörg

    2016-05-10

    The concept of isomerism is essential to chemistry and allows defining molecules with an identical composition but different connectivity (bonds) between their atoms (constitutional isomers) and/or a different arrangement in space (stereoisomers). The reaction of phosphanyl ketenes, (NHP)-P=C=O (NHP=N-heterocyclic phosphenium) with N-heterocyclic carbenes (NHCs) leads to phosphaheteroallenes (NHP)-O-P=C=NHC in which the PCO unit has been isomerized to OPC. Based on the isolation of several intermediates and DFT calculations, a mechanism for this fundamental isomerisation process is proposed. PMID:27060924

  17. Application of Orbitrap-mass spectrometry to differentiate isomeric sildenafil- and thiosildenafil-like analogues used for the adulteration of dietary supplements.

    PubMed

    Kee, Chee-Leong; Ge, Xiaowei; Low, Min-Yong

    2015-01-01

    Two groups of isomeric phosphodiestrase-type 5 inhibitors (PDE-5), consisting of four sildenafil- and three thiosildenafil-like analogues, have been successfully differentiated using high-resolution MS/MS. The optimised MS/MS data obtained from each compound were used to build a database with the aid of mass processing software. Isomeric compounds with very close chromatographic separation like dimethylsildenafil and homosildenafil could be distinguished by their unique fingerprint fragment ions in the MS/MS database. All fragment ions were within the mass tolerance of 5 ppm. One case study using an adulterated dietary supplement is included to provide more insights into this application. PMID:26179419

  18. Titanium-Beta Zeolites Catalyze the Stereospecific Isomerization of D-Glucose to L-Sorbose via Intramolecular C5-C1 Hydride Shift

    SciTech Connect

    Gounder, Rajamani; Davis, Mark E.

    2013-06-03

    Pure-silica zeolite beta containing Lewis acidic framework Ti4+ centers (Ti-Beta) is shown to catalyze the isomerization of D-glucose to L-sorbose via an intramolecular C5–C1 hydride shift. Glucose–sorbose isomerization occurs in parallel to glucose–fructose isomerization on Ti-Beta in both water and methanol solvents, with fructose formed as the predominant product in water and sorbose as the predominant product in methanol (at 373 K) at initial times and over the course of >10 turnovers. Isotopic tracer studies demonstrate that 13C and D labels placed respectively at the C1 and C2 positions of glucose are retained respectively at the C6 and C5 positions of sorbose, consistent with its formation via an intramolecular C5–C1 hydride shift isomerization mechanism. This direct Lewis acid-mediated pathway for glucose–sorbose isomerization appears to be unprecedented among heterogeneous or biological catalysts and sharply contrasts indirect base-mediated glucose–sorbose isomerization via 3,4-enediol intermediates or via retro-aldol fragmentation and recombination of sugar fragments. Measured first-order glucose–sorbose isomerization rate constants (per total Ti; 373 K) for Ti-Beta in methanol are similar for glucose and glucose deuterated at the C2 position (within a factor of ~1.1), but are a factor of ~2.3 lower for glucose deuterated at each carbon position, leading to H/D kinetic isotope effects expected for kinetically relevant intramolecular C5–C1 hydride shift steps. Optical rotation measurements show that isomerization of D-(+)-glucose (92% enantiomeric purity) with Ti-Beta in water (373 K) led to the formation of L-(-)-sorbose (73% enantiomeric purity) and D-(-)-fructose (87% enantiomeric purity) as the predominant stereoisomers, indicating that stereochemistry is preserved at carbon centers not directly involved in intramolecular C5–C1 or C2–C1 hydride shift steps, respectively. This new Lewis acid

  19. New Cluster States in {sup 12}Be

    SciTech Connect

    Dufour, M.; Nowacki, F.

    2009-08-26

    This work is devoted to new investigations of the {sup 12}Be spectrum with No-core Shell Model (NCSM) calculations and with the Generator Coordinate Method (GCM). The NCSM calculations do not reproduce the breaking of the N 8 shell closure. The NCSM and the GCM calculations do not support the existence of a band based on the ground state. The GCM calculations lead to a good description of the molecular band of Freer et al. and Saito et al.. The 0{sub 2}{sup +} isomeric state and the 2{sub 2}{sup +} state are also well described by the GCM. New bands of positive and negative parities are proposed.

  20. Unimolecular isomerization of CH2FCD2Cl via the interchange of Cl and F atoms: assignment of the threshold energy to the 1,2-dyotropic rearrangement.

    PubMed

    Tucker, Mary K; Rossabi, Samuel M; McClintock, Corey E; Heard, George L; Setser, D W; Holmes, Bert E

    2013-08-01

    The room-temperature gas-phase recombination of CH2F and CD2Cl radicals was used to prepare CH2FCD2Cl molecules with 91 kcal mol(-1) of vibrational energy. Three unimolecular processes are in competition with collisional deactivation of CH2FCD2Cl; HCl and DF elimination to give CHF═CD2 and CH2═CDCl plus isomerization to give CH2ClCD2F by the interchange of F and Cl atoms. The Cl/F interchange reaction was observed, and the rate constant was assigned from measurement of CHCl═CD2 as a product, which is formed by HF elimination from CH2ClCD2F. These experiments plus previously published results from chemically activated CH2ClCH2F and electronic structure and RRKM calculations for the kinetic-isotope effects permit assignment of the three rate constants for CH2FCD2Cl (and for CH2ClCD2F). The product branching ratio for the interchange reaction versus elimination is 0.24 ± 0.04. Comparison of the experimental rate constant with the RRKM calculated rate constant permitted the assignment of a threshold energy of 62 ± 3 kcal mol(-1) for this type-1 dyotropic rearrangement. On the basis of electronic structure calculations, the nature of the transition state for the rearrangement reaction is discussed. The radical recombination reactions in the chemical system also generate vibrationally excited CD2ClCD2Cl and CH2FCH2F molecules, and the rate constants for DCl and HF elimination were measured in order to confirm that the photolysis of CD2ClI and (CH2F)2CO mixtures was giving reliable data for CH2FCD2Cl. PMID:23837645