Photoinduced Trans-to-cis Phase Transition of Polycrystalline Azobenzene at Low Irradiance Occurs in the Solid State

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

Bhattacharjee, Ujjal; Freppon, Daniel; Men, Long

2017-07-09

The ability to produce large-scale, reversible structural changes in a variety of materials by photoexcitation of a wide variety of azobenzene derivatives has been recognized for almost two decades. Because photoexcitation of trans-azobenzene produces the cis-isomer in solution, it has generally been inferred that the macroscopic structural changes occurring in materials are also initiated by a similar large-amplitude trans-to-cis isomerization. This paper provides the first demonstration that a trans-to-cis photoisomerization occurs in polycrystalline azobenzene, and is consistent with the previously hypothesized nature of the trigger in the photoactuated mechanisms of the materials in question. It is also demonstrated that undermore » low irradiance, trans-to-cis isomerization occurs in the solid (not via a pre-melted phase); and the presence of the cis-isomer thus lowers the melting point of the sample, providing a liquid phase. A variety of experimental techniques were employed, including X-ray diffraction measurements of polycrystalline azobenzene during exposure to laser irradiation and fluorescence measurements of the solid sample. Finally, a practical consequence of this work is that it establishes trans-azobenzene as an easily obtainable and well-defined control for monitoring photoinduced structural changes in X-ray diffraction experiments, using easily accessible laser wavelengths.« less

Half-life measurements of isomeric states populated in projectile fragmentation

NASA Astrophysics Data System (ADS)

Bowry, M.; Podolyák, Zs.; Kurcewicz, J.; Pietri, S.; Bunce, M.; Regan, P. H.; Farinon, F.; Geissel, H.; Nociforo, C.; Prochazka, A.; Weick, H.; Allegro, P.; Benlliure, J.; Benzoni, G.; Boutachkov, P.; Gerl, J.; Gorska, M.; Gottardo, A.; Gregor, N.; Janik, R.; Knöbel, R.; Kojouharov, I.; Kubo, T.; Litvinov, Y. A.; Merchan, E.; Mukha, I.; Naqvi, F.; Pfeiffer, B.; Pfützner, M.; Plaß, W.; Pomorski, M.; Riese, B.; Ricciardi, M. V.; Schmidt, K.-H.; Schaffner, H.; Kurz, N.; Denis Bacelar, A. M.; Bruce, A. M.; Farrelly, G. F.; Alkhomashi, N.; Al-Dahan, N.; Scheidenberger, C.; Sitar, B.; Spiller, P.; Stadlmann, J.; Strmen, P.; Sun, B.; Takeda, H.; Tanihata, I.; Terashima, S.; Valiente Dobon, J. J.; Winfield, J. S.; Wollersheim, H.-J.; Woods, P. J.

2012-10-01

The half-lives of excited isomeric states observed in 195Au, 201Tl and 215Rn are reported for the first time. Delayed γ-rays were correlated with nuclei produced in the projectile fragmentation of relativistic 238U 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 195Au with t1/2 = 16-4+8 μs is presented. Two shorter-lived isomeric states were detected in 201Tl and 215Rn with t1/2 = 95-21+39 and 57-12+21 ns respectively. In total 24 isomeric states were identified in different nuclei from Pt to Rn (A ˜ 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 ħ) of the reaction products. In particular, high-spin states with I ≳ 18 ħ provide a robust test of theoretical models of fragmentation.

Formation of an Isomeric State of Zn$sup 67$ by Bombardment with Slow Neutrons; FORMACION DE UN ESTADO ISOMERO DEL ZN$sup 67$$sub 30$ MEDIANTE BOMBARDEO CON NEUTRONES LENTOS

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

Montes Ponce De Leon, J.; Sanchez Del Rio, C.

1956-01-01

In this paper the identification of the isomeric state of Zn/sup 67/ by a new method is described. The isotopes Zn/sup 68/ and Zn/sup 67/ being both stable, the capture of slow neutrons by Zn/sup 68/ leads sometimes to the formation of the isomeric state of Zn/sup 67/; the state is identified by its half life, measured by delayed coincidences between the capture and the isomeric gamma rays. (auth)

Nanoporous frameworks exhibiting multiple stimuli responsiveness

NASA Astrophysics Data System (ADS)

Kundu, Pintu K.; Olsen, Gregory L.; Kiss, Vladimir; Klajn, Rafal

2014-04-01

Nanoporous frameworks are polymeric materials built from rigid molecules, which give rise to their nanoporous structures with applications in gas sorption and storage, catalysis and others. Conceptually new applications could emerge, should these beneficial properties be manipulated by external stimuli in a reversible manner. One approach to render nanoporous frameworks responsive to external signals would be to immobilize molecular switches within their nanopores. Although the majority of molecular switches require conformational freedom to isomerize, and switching in the solid state is prohibited, the nanopores may provide enough room for the switches to efficiently isomerize. Here we describe two families of nanoporous materials incorporating the spiropyran molecular switch. These materials exhibit a variety of interesting properties, including reversible photochromism and acidochromism under solvent-free conditions, light-controlled capture and release of metal ions, as well reversible chromism induced by solvation/desolvation.

Preformation probability inside α emitters around the shell closures Z = 50 and N = 82

NASA Astrophysics Data System (ADS)

Seif, W. M.; Ismail, M.; Zeini, E. T.

2017-05-01

The preformation of an α-particle as a distinct entity inside the α-emitter is the first move towards α-decay. We investigate the α-particle preformation probability (S α ) in ordinary and exotic α-decays. We consider favored and unfavored decays at which the α-emitters and the produced daughter nuclides are in their ground or isomeric states. The study of 244 α-decay modes with 52≤slant Z≤slant 81 and 53≤slant N≤slant 112 is accomplished using the preformed cluster model. The preformation probabilities were estimated from the experimental half-lives and the computed decay widths based on the Wentzel-Kramers-Brillouin tunneling penetrability and knocking frequency, and the Skyrme-SLy4 interaction potential. We found that the favored α-decay mode from a ground state to an isomeric state shows larger α-preformation probability than the favored and unfavored decays of the same isotope but from isomeric to ground states. The favored decay mode from isomeric- to ground-state exhibits rather less S α relative to the other decay modes from the same nuclide. The favored decay modes between two isomeric states tend to yield larger S α and less partial half-life compared with the favored and unfavored decays from the same nuclides but between two ground states. For the decays involving two ground states, the preformation probability is larger for the favored decay modes than for the unfavored ones. The unfavored α-decay modes from ground- to isomeric-states are rare. The unfavored decay modes from isomeric- to ground-states show less S α than that for the favored decays from the ground states of the same emitters. The unfavored α-decay modes between two isomeric states exhibit larger S α than the other α-decay modes from the same isomers.

Second-Chance Forward Isomerization Dynamics of the Red/Green Cyanobacteriochrome NpR6012g4 from Nostoc punctiforme

PubMed Central

Kim, Peter W.; Freer, Lucy H.; Rockwell, Nathan C.; Martin, Shelley S.; Lagarias, J. Clark; Larsen, Delmar S.

2011-01-01

The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome (CBCR) NpR6012g4 from N. punctiforme were studied by transient absorption pump-dump-probe spectroscopy. A 2-ps dump pulse resonant with the stimulated emission band depleted 21 % of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11 %. We observe a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to fully isomerize. Multi-component global analysis implicates the generation of additional Lumi-R from GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy of excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40 % for the primary isomerization step in the forward reaction of NpR6012g4. PMID:22107125

Second-chance forward isomerization dynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme.

PubMed

Kim, Peter W; Freer, Lucy H; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark; Larsen, Delmar S

2012-01-11

The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump-dump-probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the forward reaction of NpR6012g4. © 2011 American Chemical Society

Regioselective Copper-Catalyzed Amination of Chlorobenzoic Acids: Synthesis and Solid-State Structures of N-Aryl Anthranilic Acid Derivatives

PubMed Central

Mei, Xuefeng; August, Adam T.; Wolf, Christian

2008-01-01

A chemo- and regioselective copper-catalyzed cross-coupling reaction for effective amination of 2-chlorobenzoic acids with aniline derivatives has been developed. The method eliminates the need for acid protection and produces a wide range of N-aryl anthranilic acid derivatives in up to 99%. The amination was found to proceed with both electron-rich and electron-deficient aryl chlorides and anilines and also utilizes sterically hindered anilines such as 2,6-dimethylaniline and 2-tert-butylaniline. The conformational isomerism of appropriately substituted N-aryl anthranilic acids has been investigated in the solid state. Crystallographic analysis of seven anthranilic acid derivatives showed formation of two distinct supramolecular architectures exhibiting trans-anti- and unprecedented trans-syn-dimeric structures. PMID:16388629

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations

PubMed Central

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, PK

2009-01-01

Background Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. Results We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (α-phase) and the facial (δ-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the α-phase and the δ-phase, although the fluorescence emission shows no substantial difference between the α-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the α-phase. Conclusion The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the α-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation. PMID:19900275

Characterisation of different polymorphs of tris(8-hydroxyquinolinato)aluminium(III) using solid-state NMR and DFT calculations.

PubMed

Goswami, Mithun; Nayak, Pabitra K; Periasamy, N; Madhu, P K

2009-11-09

Organic light emitting devices (OLED) are becoming important and characterisation of them, in terms of structure, charge distribution, and intermolecular interactions, is important. Tris(8-hydroxyquinolinato)-aluminium(III), known as Alq3, an organomettalic complex has become a reference material of great importance in OLED. It is important to elucidate the structural details of Alq3 in its various isomeric and solvated forms. Solid-state nuclear magnetic resonance (NMR) is a useful tool for this which can also complement the information obtained with X-ray diffraction studies. We report here 27Al one-dimensional (1D) and two-dimensional (2D) multiple-quantum magic-angle spinning (MQMAS) NMR studies of the meridional (alpha-phase) and the facial (delta-phase) isomeric forms of Alq3. Quadrupolar parameters are estimated from the 1D spectra under MAS and anisotropic slices of the 2D spectra and also calculated using DFT (density functional theory) quantum-chemical calculations. We have also studied solvated phase of Alq3 containing ethanol in its lattice. We show that both the XRD patterns and the quadrupolar parameters of the solvated phase are different from both the alpha-phase and the delta-phase, although the fluorescence emission shows no substantial difference between the alpha-phase and the solvated phase. Moreover, we have shown that after the removal of ethanol from the matrix the solvated Alq3 has similar XRD patterns and quadrupolar parameters to that of the alpha-phase. The 2D MQMAS experiments have shown that all the different modifications of Alq3 have 27Al in single unique crystallographic site. The quadrupolar parameters predicted using the DFT calculation under the isodensity polarisable continuum model resemble closely the experimentally obtained values. The solvated phase of Alq3 containing ethanol has structural difference from the alpha-phase of Alq3 (containing meridional isomer) from the solid-state NMR studies. Solid-state NMR can hence be used as an effective complementary tool to XRD for characterisation and structural elucidation.

Study of isomeric states in 198,200,202,206Pb and 206Hg populated in fragmentation reactions

NASA Astrophysics Data System (ADS)

Lalović, N.; Rudolph, D.; Podolyák, Zs; Sarmiento, L. G.; Simpson, E. C.; Alexander, T.; Cortés, M. L.; Gerl, J.; Golubev, P.; Ameil, F.; Arici, T.; Bauer, Ch; Bazzacco, D.; Bentley, M. A.; Boutachkov, P.; Bowry, M.; Fahlander, C.; Gadea, A.; Gellanki, J.; Givechev, A.; Goel, N.; Górska, M.; Gottardo, A.; Gregor, E.; Guastalla, G.; Habermann, T.; Hackstein, M.; Jungclaus, A.; Kojouharov, I.; Kumar, R.; Kurz, N.; Lettmann, M.; Lizarazo, C.; Louchart, C.; Merchán, E.; Michelagnoli, C.; Moeller, Th; Moschner, K.; Patel, Z.; Pietralla, N.; Pietri, S.; Ralet, D.; Reese, M.; Regan, P. H.; Reiter, P.; Schaffner, H.; Singh, P.; Stahl, C.; Stegmann, R.; Stezowski, O.; Taprogge, J.; Thöle, P.; Wendt, A.; Wieland, O.; Wilson, E.; Wood, R.; Wollersheim, H.-J.; Birkenbach, B.; Bruyneel, B.; Burrows, I.; Clément, E.; Désesquelles, P.; Domingo-Pardo, C.; Eberth, J.; González, V.; Hess, H.; Jolie, J.; Judson, D. S.; Menegazzo, R.; Mengoni, D.; Napoli, D. R.; Pullia, A.; Quintana, B.; Rainovski, G.; Salsac, M. D.; Sanchis, E.; Simpson, J.; Valiente Dóbon, J. J.; AGATA Collaboration

2018-03-01

Isomeric states in isotopes in the vicinity of doubly-magic 208Pb were populated following reactions of a relativistic 208Pb primary beam impinging on a 9Be fragmentation target. Secondary beams of 198,200,202,206Pb and 206Hg were isotopically separated and implanted in a passive stopper positioned in the focal plane of the GSI Fragment Separator. Delayed γ rays were detected with the Advanced Gamma Tracking Array (AGATA). Decay schemes were re-evaluated and interpreted with shell-model calculations. The momentum-dependent population of isomeric states in the two-nucleon hole nuclei 206Pb/206Hg was found to differ from the population of multi neutron-hole isomeric states in 198,200,202Pb.

Solid-state molecular organometallic chemistry. Single-crystal to single-crystal reactivity and catalysis with light hydrocarbon substrates† †Electronic supplementary information (ESI) available: Full details of experimental details, spectroscopic and other analytical data, X-ray crystallography, catalytic conditions, and computational studies. CCDC 1539832–1539836. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01491k

PubMed Central

Chadwick, F. Mark; McKay, Alasdair I.; Martinez-Martinez, Antonio J.; Rees, Nicholas H.; Krämer, Tobias

2017-01-01

Single-crystal to single-crystal solid/gas reactivity and catalysis starting from the precursor sigma-alkane complex [Rh(Cy2PCH2CH2PCy2)(η2η2-NBA)][BArF4] (NBA = norbornane; ArF = 3,5-(CF3)2C6H3) is reported. By adding ethene, propene and 1-butene to this precursor in solid/gas reactions the resulting alkene complexes [Rh(Cy2PCH2CH2PCy2)(alkene)x][BArF4] are formed. The ethene (x = 2) complex, [Rh(Cy2PCH2CH2PCy2)(ethene)2][BArF4]-Oct, has been characterized in the solid-state (single-crystal X-ray diffraction) and by solution and solid-state NMR spectroscopy. Rapid, low temperature recrystallization using solution methods results in a different crystalline modification, [Rh(Cy2PCH2CH2PCy2)(ethene)2][BArF4]-Hex, that has a hexagonal microporous structure (P6322). The propene complex (x = 1) [Rh(Cy2PCH2CH2PCy2)(propene)][BArF4] is characterized as having a π-bound alkene with a supporting γ-agostic Rh···H3C interaction at low temperature by single-crystal X-ray diffraction, variable temperature solution and solid-state NMR spectroscopy, as well as periodic density functional theory (DFT) calculations. A fluxional process occurs in both the solid-state and solution that is proposed to proceed via a tautomeric allyl-hydride. Gas/solid catalytic isomerization of d3-propene, H2C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 CHCD3, using [Rh(Cy2PCH2CH2PCy2)(η2η2-NBA)][BArF4] scrambles the D-label into all possible positions of the propene, as shown by isotopic perturbation of equilibrium measurements for the agostic interaction. Periodic DFT calculations show a low barrier to H/D exchange (10.9 kcal mol–1, PBE-D3 level), and GIPAW chemical shift calculations guide the assignment of the experimental data. When synthesized using solution routes a bis-propene complex, [Rh(Cy2PCH2CH2PCy2)(propene)2][BArF4], is formed. [Rh(Cy2PCH2CH2PCy2)(butene)][BArF4] (x = 1) is characterized as having 2-butene bound as the cis-isomer and a single Rh···H3C agostic interaction. In the solid-state two low-energy fluxional processes are proposed. The first is a simple libration of the 2-butene that exchanges the agostic interaction, and the second is a butene isomerization process that proceeds via an allyl-hydride intermediate with a low computed barrier of 14.5 kcal mol–1. [Rh(Cy2PCH2CH2PCy2)(η2η2-NBA)][BArF4] and the polymorphs of [Rh(Cy2PCH2CH2PCy2)(ethene)2][BArF4] are shown to be effective in solid-state molecular organometallic catalysis (SMOM-Cat) for the isomerization of 1-butene to a mixture of cis- and trans-2-butene at 298 K and 1 atm, and studies suggest that catalysis is likely dominated by surface-active species. [Rh(Cy2PCH2CH2PCy2)(η2η2-NBA)][BArF4] is also shown to catalyze the transfer dehydrogenation of butane to 2-butene at 298 K using ethene as the sacrificial acceptor. PMID:28989631

Coulomb excitation of the K π= 8⁻ isomeric band in 178Hf

DOE PAGES

Napiorkovsk, P. J.; Srebrny, J.; Czosnyka, T.; ...

2001-12-01

The Coulomb excitation experiment on the 178Hf was performed using 650 MeV beam of 136Xe. The first observation of discrete transitions in the K π = 8 - isomeric band. Coulomb excited from K π = 0+ ground state, is reported. The possible mechanisms of El coupling of the ground state band and the isomeric band is discussed.

Operando Solid-State NMR Observation of Solvent-Mediated Adsorption-Reaction of Carbohydrates in Zeolites

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

Qi, Long; Alamillo, Ricardo; Elliott, William A.

Liquid-phase processing of molecules using heterogeneous catalysts – an important strategy for obtaining renewable chemicals sustainably from biomass – involves reactions that occur at solid-liquid interfaces. In glucose isomerization catalyzed by basic faujasite zeolites, the catalytic activity depends strongly on the solvent composition: initially, it declines precipitously when water is mixed with a small amount of the organic co-solvent γ-valerolactone (GVL), then recovers as the GVL content increases. Using solid-state 13C NMR spectroscopy, we observed glucose isomers located inside the zeolite pores directly, and followed their transformations into fructose and mannose in real time. At low GVL concentrations, glucose ismore » depleted in the zeolite pores relative to the liquid phase, while higher GVL concentrations in solution drive glucose inside the pores, resulting in up to a 32 enhancement in the local glucose concentration. Although their populations exchange rapidly, molecules present at the reactive interface experience a significantly different environment from the bulk solution.« less

Benzil-tethered precipitons for controlling solubility: a round-trip energy-transfer mechanism in the isomerization of extended stilbene analogues.

PubMed

Ams, Mark R; Wilcox, Craig S

2007-04-04

We are investigating photoresponsive molecules called "precipitons" that undergo a solubility change co-incident with isomerization. Isomerization can be induced by light or by catalytic reagents. Previous work demonstrated that covalent attachment of a metal complex, Ru(II)(bpy)3, greatly accelerates photoisomerization and influences the photostationary state. In this paper, we describe precipitons (1,2-biphenylethenes; analogous to stilbenes) that are activated by a covalently attached organic sensitizer (benzil). We find that isomerization of these stilbene analogues is little effected by the presence of benzil in solution but that the intramolecular benzil effect is to increase the rate of isomerization and to significantly change the photostationary state. What is most interesting about these observations is that the precipiton is the primary chromophore in this bichromophoric system (precipiton absorbance is many times greater than benzil absorbance in the 300-400 nm range), yet the neighboring benzil has a significant effect on the rate and the photostationary state. The effect of unattached benzil on the rate was small, about a 24% increase in rate as compared with 4-6-fold changes for an attached benzil. We speculate that the isomerization process occurs by a "round-trip" energy-transfer mechanism. Initial excitation of the precipiton chromophore initiates a sequence that includes (1) formation of the precipiton singlet state, (2) singlet excitation transfer from the precipiton unit to the benzil, (3) benzil-centered intersystem crossing to the localized benzil triplet state, (4) triplet energy transfer from the benzil moiety back to the precipiton, and (5) isomerization.

n-hydrocarbons conversions over metal-modified solid acid catalysts

NASA Astrophysics Data System (ADS)

Zarubica, A.; Ranđelović, M.; Momčilović, M.; Radulović, N.; Putanov, P.

2013-12-01

The quality of a straight-run fuel oil can be improved if saturated n-hydrocarbons of low octane number are converted to their branched counterparts. Poor reactivity of traditional catalysts in isomerization reactions imposed the need for the development of new catalysts among which noble metal promoted acid catalysts, liquid and/or solid acid catalysts take a prominent place. Sulfated zirconia and metal promoted sulfated zirconia exhibit high activity for the isomerization of light alkanes at low temperatures. The present paper highlights the original results which indicate that the modification of sulfated zirconia by incorporation of metals (platinum and rhenium) significantly affects catalytic performances in n-hydrocarbon conversion reactions. Favourable activity/selectivity of the promoted sulfated zirconia depends on the crystal phase composition, critical crystallites sizes, platinum dispersion, total acidity and type of acidity. Attention is also paid to the recently developed solid acid catalysts used in other conversion reactions of hydrocarbons.

Reaction pathways of photoexcited retinal in proteorhodopsin studied by pump-dump-probe spectroscopy.

PubMed

Rupenyan, Alisa; van Stokkum, Ivo H M; Arents, Jos C; van Grondelle, Rienk; Hellingwerf, Klaas J; Groot, Marie Louise

2009-12-17

Proteorhodopsin (pR) is a membrane-embedded proton pump from the microbial rhodopsin family. Light absorption by its retinal chromophore initiates a photocycle, driven by trans/cis isomerization on the femtosecond to picosecond time scales. Here, we report a study on the photoisomerization dynamics of the retinal chromophore of pR, using dispersed ultrafast pump-dump-probe spectroscopy. The application of a pump pulse initiates the photocycle, and with an appropriately tuned dump pulse applied at a time delay after the dump, the molecules in the initial stages of the photochemical process can be de-excited and driven back to the ground state. In this way, we were able to resolve an intermediate on the electronic ground state that represents chromophores that are unsuccessful in isomerization. In particular, the fractions of molecules that undergo slow isomerization (20 ps) have a high probability to enter this state rather than the isomerized K-state. On the ground state reaction surface, return to the stable ground state conformation via a structural or vibrational relaxation occurs in 2-3 ps. Inclusion of this intermediate in the kinetic scheme led to more consistent spectra of the retinal-excited state, and to a more accurate estimation of the quantum yield of isomerization (Phi = 0.4 at pH 6).

Experiments with neutron-rich isomeric beams

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

Rykaczewski, K.; Grzywacz, R.; Lewitowicz, M.

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.

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.

Systematic study of α preformation probability of nuclear isomeric and ground states

NASA Astrophysics Data System (ADS)

Sun, Xiao-Dong; Wu, Xi-Jun; Zheng, Bo; Xiang, Dong; Guo, Ping; Li, Xiao-Hua

2017-01-01

In this paper, based on the two-potential approach combining with the isospin dependent nuclear potential, we systematically compare the α preformation probabilities of odd-A nuclei between nuclear isomeric states and ground states. The results indicate that during the process of α particle preforming, the low lying nuclear isomeric states are similar to ground states. Meanwhile, in the framework of single nucleon energy level structure, we find that for nuclei with nucleon number below the magic numbers, the α preformation probabilities of high-spin states seem to be larger than low ones. For nuclei with nucleon number above the magic numbers, the α preformation probabilities of isomeric states are larger than those of ground states. Supported by National Natural Science Foundation of China (11205083), Construct Program of Key Discipline in Hunan Province, Research Foundation of Education Bureau of Hunan Province, China (15A159), Natural Science Foundation of Hunan Province, China (2015JJ3103, 2015JJ2123), Innovation Group of Nuclear and Particle Physics in USC, Hunan Provincial Innovation Foundation for Postgraduate (CX2015B398)

One-way Z→E isomerization around the double bond of N-methoxy- 1- (2-anthryl) ethanimine in the excited triplet state. Direct observation of one-way isomerization from Z triplet to E triplet of the C dbnd N bond

NASA Astrophysics Data System (ADS)

Arai, Tatsuo; Furuya, Yasunori; Furuuchi, Hideo; Tokumaru, Katsumi

1993-09-01

On direct as well as benzil-sensitized irradiation in degassed benzene N-methoxy-1-(2-anthryl) ethanimine ( I), ArC (CH 3) dbnd N sbnd OCH 3 (Ar: 2-anthryl), underwent one-way Z→E isomerization through a quantum chain process. The barrier to Z→E isomerization of I in the excited triplet state was determined by directly observing the change of T—T absorption spectra from the Z triplet to the E triplet. Based on these results the potential energy surface of photoisomerization of I is discussed.

Centrohexaindane: six benzene rings mutually fixed in three dimensions - solid-state structure and six-fold nitration.

PubMed

Kuck, Dietmar; Linke, Jens; Teichmann, Lisa Christin; Barth, Dieter; Tellenbröker, Jörg; Gestmann, Detlef; Neumann, Beate; Stammler, Hans-Georg; Bögge, Hartmut

2016-04-28

The solid-state molecular structure of centrohexaindane (), a unique hydrocarbon comprising six benzene rings clamped to each other in three dimensions around a neopentane core, and the molecular packing in crystals of ·CHCl3 are reported. The molecular Td-symmetry and the Cartesian orientation of the six indane wings of in the solid state have been confirmed. The course and limitation of electrophilic aromatic substitution of are demonstrated for the case of nitration. Based on nitration experiments of a lower congener of , tribenzotriquinacene , the six-fold nitrofunctionalisation of has been achieved in excellent yield, giving four constitutional isomers, two nonsymmetrical ( and ) and two C3-symmetrical ones ( and ), all of which contain one single nitro group in each of the six benzene rings. The relative yields of the four isomers (∼3 : 1 : 1 : 3) point to a random electrophilic attack of the electrophiles at the twelve formally equivalent outer positions of the aromatic periphery of , suggesting electronic independence of its six aromatic π-electron systems. In turn, the pronounced conformational rigidity of the centrohexacyclic framework of enables the unequivocal structural identification of the isomeric hexanitrocentrohexaindanes by (1)H NMR spectroscopy.

A green emissive amorphous fac-Alq3 solid generated by grinding crystalline blue fac-Alq3 powder.

PubMed

Bi, Hai; Chen, Dong; Li, Di; Yuan, Yang; Xia, Dandan; Zhang, Zuolun; Zhang, Hongyu; Wang, Yue

2011-04-14

A novel green emissive Alq(3) solid with a facial isomeric form has been obtained by grinding the typical blue luminescent fac-Alq(3) crystalline powder. This is the first report, to the best of our knowledge, that a fac-Alq(3) isomer emits green light.

Syn/anti isomerization of 2,4-dinitrophenylhydrazones in the determination of airborne unsymmetrical aldehydes and ketones using 2,4-dinitrophenylhydrazine derivation.

PubMed

Binding, N; Müller, W; Witting, U

1996-10-01

Aldehydes and ketones readily react with 2,4-dinitrophenylhydrazine (2,4-DNPH) to form the corresponding hydrazones. This reaction has been frequently used for the quantification of airborne carbonyl compounds. Since unsymmetrical aldehydes and ketones are known to form isomeric 2,4-dinitrophenylhydrazones (syn/ anti-isomers), the influence of isomerization on the practicability and accuracy of the 2,4-DNPH-method using 2,4-dinitrophenylhydrazine-coated solid sorbent samplers has been studied with three ketones (methyl ethyl ketone (MEK), methyl isopropyl ketone (MIPK), and methyl isobutyl ketone (MIBK)). With all three ketones the reaction with 2,4-DNPH resulted in mixtures of the isomeric hydrazones which were separated by HPLC and GC and identified by mass spectroscopy and (1)H nuclear magnetic resonance spectroscopy. The isomers show similar chromatographic behaviour in HPLC as well as in GC, thus leading to problems in quantification and interpretation of chromatographic results.

Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon.

PubMed

Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei

2016-07-11

A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

Moliner, Manuel; Román-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 (150 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].

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

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

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

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) mannosemore » 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].« less

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

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

Miernik, K., E-mail: kmiernik@fuw.edu.pl; Gross, C.J.; Grzywacz, R.

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.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides.

PubMed

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-01-13

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

NASA Astrophysics Data System (ADS)

Engin, Ozge; Sayar, Mehmet; Erman, Burak

2009-03-01

Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

Alkene Isomerization Using a Solid Acid as Activator and Support for a Homogeneous Catalyst

ERIC Educational Resources Information Center

Seen, Andrew J.

2004-01-01

An upper-level undergraduate experiment that, in addition to introducing students to catalysis using an air sensitive transition-metal complex, introduces the use of a solid acid as an activator and support for the catalyst is developed. The increased stability acquired in the course of the process affords the opportunity to characterize the…

Searching for high-K isomers in the proton-rich A ˜ 80 mass region

NASA Astrophysics Data System (ADS)

Bai, Zhi-Jun; Jiao, Chang-Feng; Gao, Yuan; Xu, Fu-Rong

2016-09-01

Configuration-constrained potential-energy-surface calculations have been performed to investigate the K isomerism in the proton-rich A ˜ 80 mass region. An abundance of high-K states are predicted. These high-K states arise from two and four-quasi-particle excitations, with Kπ = 8+ and Kπ = 16+, respectively. Their excitation energies are comparatively low, making them good candidates for long-lived isomers. Since most nuclei under study are prolate spheroids in their ground states, the oblate shapes of the predicted high-K states may indicate a combination of K isomerism and shape isomerism. Supported by National Key Basic Research Program of China (2013CB834402) and National Natural Science Foundation of China (11235001, 11320101004 and 11575007)

Mechanistic insights into Pin1 peptidyl-prolyl cis-trans isomerization from umbrella sampling simulations.

PubMed

Di Martino, Giovanni Paolo; Masetti, Matteo; Cavalli, Andrea; Recanatini, Maurizio

2014-11-01

The peptidyl-proyl isomerase Pin1 plays a key role in the regulation of phospho(p)-Ser/Thr-Pro proteins, acting as a molecular timer of the cell cycle. After recognition of these motifs, Pin1 catalyzes the rapid cis-trans isomerization of proline amide bonds of substrates, contributing to maintain the equilibrium between the two conformations. Although a great interest has arisen on this enzyme, its catalytic mechanism has long been debated. Here, the cis-trans isomerization of a model peptide system was investigated by means of umbrella sampling simulations in the Pin1-bound and unbound states. We obtained free energy barriers consistent with experimental data, and identified several enzymatic features directly linked to the acceleration of the prolyl bond isomerization. In particular, an enhanced autocatalysis, the stabilization of perturbed ground state conformations, and the substrate binding in a procatalytic conformation were found as main contributions to explain the lowering of the isomerization free energy barrier. © 2014 Wiley Periodicals, Inc.

Prompt and delayed spectroscopy of At 203 : Observation of a shears band and a 29 / 2 + isomeric state

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

Auranen, K.; Uusitalo, J.; Juutinen, S.

Using fusion-evaporation reactions, a gas-filled recoil separator, recoil-gating technique and recoil-isomer decay tagging technique we have extended the level scheme of At-203 (N = 118) significantly. We have observed an isomeric [tau = 14.1(3) mu s] state with a spin and parity of 29/2(+). The isomeric state is suggested to originate from the pi(h(9/2)) circle times |Po-202; 11(-)> coupling, and it is depopulated through 286 keV E2 and 366 keV E3 transitions. In addition, we have observed a cascade of magnetic-dipole transitions which is suggested to be generated by the shears mechanism.

Matrix isolation infrared spectra, assignment and DFT investigation on reactions of iron and manganese monoxides with CH3Cl.

PubMed

Zhao, Yanying; Fan, Kexue; Huang, Yongfei; Zheng, Xuming

2013-12-01

The reactions of iron and manganese monoxide molecules (FeO, and MnO) with monochloromethane in solid argon have been studied by matrix isolation infrared spectroscopy and quantum chemistry calculations. When annealing, the reactions of FeO and MnO with CH3Cl first form the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes, which can isomerize to CH3MOCl (MMn, Fe) upon 300<λ<580 nm irradiation. The products were characterized by isotopic IR studies with CD3Cl and (13)CH3Cl and density functional calculations. Based on theoretical calculations, the OFe-(η(Cl)-CH3Cl) and OMn-(η(Cl)-CH3Cl) complexes have (5)A' and (6)A' ground state with Cs symmetry, respectively. The accurate CCSD(T) single point calculations illustrate the CH3MOCl isomerism are 13.8 and 3.1 kcal/mol lower in energy than the OM-(η(Cl)-CH3Cl) (MMn, Fe) complexes. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Concurrent Mass Measurement and Laser Spectroscopy for Unambiguous Isomeric State Assignment

NASA Astrophysics Data System (ADS)

Lascar, Daniel; Babcock, Carla; Henderson, Jack; Pearson, Matt

2017-09-01

Recent work by the TITAN group at TRIUMF on isomeric state mass measurements of odd-A, neutron-rich cadmium nuclei has shown a disconnect between experiment and theory in 127 g , mCd. The spin and parity assignments of the ground and isomeric states are assigned as 3/2+ and 11/2-, respectively, primarily via systematic arguments. Conversely, state of the art shell model and ab initio calculations show a reversal of the states, predicting a ground state of 11/2- and a 3/2+ isomer. Penning Trap Mass Spectrometry (PTMS) can measure the energy separation between the ground state and the isomer without ambiguity but cannot, on its own, comment on the spin and parity. Collinear Laser Spectroscopy (CLS) experiments have been performed on 127Cd and have elegantly demonstrated the existence of both 3/2+ and 11/2- states. What CLS cannot do, on its own, is assign an ordering to those states. If, however, a PTMS and CLS experiment could be performed concurrently using identical beams from the same facility then there exists sufficient information shared between both experiments that a definitive assignment can be made. We present a concept for a new slate of measurements using existing experimental facilities simultaneously, with shared resources, to definitively assign spin and parity for ground and isomeric states in short-lived nuclei.

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

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

Danagulyan, A. S.; Hovhannisyan, G. H., E-mail: hov-gohar@ysu.am; Bakhshiyan, T. M.

2016-05-15

Calculations for (p, n) and (α, p3n) reactions were performed with the aid of the TALYS-1.4 code. Reactions in which the mass numbers of target and product nuclei were identical were examined in the range of A = 44–124. Excitation functions were obtained for product nuclei in ground and isomeric states, and isomeric ratios were calculated. The calculated data reflect well the dependence of the isomeric ratios on the projectile type. A comparison of the calculated and experimental data reveals, that, for some nuclei in a high-spin state, the calculated data fall greatly short of their experimental counterparts. These discrepanciesmore » may be due to the presence of high-spin yrast states and rotational bands in these nuclei. Calculations involving various level-density models included in the TALYS-1.4 code with allowance for the enhancement of collective effects do not remove the discrepancies in the majority of cases.« less

Octupole deformations in high-K isomeric states of heavy and superheavy nuclei

NASA Astrophysics Data System (ADS)

Minkov, N.; Walker, P. M.

2016-01-01

We study the effects of quadrupole-octupole deformations on the energy and magnetic properties of high-K isomeric states in even-even heavy and superheavy nuclei. The neutron two-quasiparticle (2qp) isomeric energies and magnetic dipole moments are calculated within a deformed shell model with the Bardeen-Cooper- Schrieffer (BCS) pairing interaction over a wide range of quadrupole and octupole deformations. We found that in most cases the magnetic moments exhibit a pronounced sensitivity to the octupole deformation, while the 2qp energies indicate regions of nuclei in which the presence of high-K isomeric states may be associated with the presence of octupole softness or even with octupole deformation. In the present work we also examine the influence of the BCS pairing strength on the energy of the blocked isomer configuration. We show that the formation of 2qp energy minima in the space of quadrupole-octupole and eventually higher multipolarity deformations is a subtle effect depending on nuclear pairing correlations.

Model studies on the photosensitized isomerization of bixin.

PubMed

Montenegro, Mariana A; Rios, Alessandro de O; Mercadante, Adriana Z; Nazareno, Mónica A; Borsarelli, Claudio D

2004-01-28

The photosensitized isomerization reaction of the natural cis carotenoid bixin (methyl hydrogen 9'-cis-6, 6'-diapocarotene-6, 6'-dioate) with rose bengal or methylene blue as the sensitizer in acetonitrile/methanol (1:1) solution was studied using UV-vis spectroscopy, high-performance liquid chromatography (HPLC), and time-resolved spectroscopic techniques, such as laser-flash photolysis and singlet oxygen phosphorescence detection. In both N(2)- and air-saturated solutions, the main product formed was all-trans-bixin. The observed isomerization rate constants, k(obs), decreased in the presence of air or with increase in the bixin concentration, suggesting the participation of the excited triplet state of bixin, (3)Bix, as precursor of the cis--> trans process. On the other hand, bixin solutions in the absence of sensitizer and/or light did not degrade, indicating that the ground state of bixin is stable to thermal isomerization at room temperature. Time-resolved spectroscopic experiments confirmed the formation of the excited triplet state of bixin and its deactivation by ground state bixin and molecular oxygen quenching processes. The primary isomerization products only degraded in the presence of air and under prolonged illumination conditions, probably due to the formation of oxidation products by reaction with singlet molecular oxygen. An energy-transfer mechanism was used to explain the observed results for the bixin transformations, and the consequences for food color are discussed.

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water.

PubMed

Yonezawa, Yasushige; Nakata, Kazuto; Sakakura, Kota; Takada, Toshikazu; Nakamura, Haruki

2009-04-01

The cis-trans isomerization of the peptide bond preceding a proline plays important roles in protein folding and biological function. Although many experimental and theoretical studies have been done, the mechanism has not yet been clearly elucidated. We studied the cis-trans isomerization of the proline dipeptide (Ace-Pro-NMe) in explicit water by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. We obtained the free energy landscape during the isomerization by using the umbrella sampling method. The free energy landscape is in good accordance with previous experimental and theoretical values. We observed that in the middle of the isomerization, the prolyl nitrogen transiently takes pyramidal conformations in two polarized directions and that, simultaneously, the prolyl C-N bond extends. We show that these geometrical changes cooperatively transform the prolyl nitrogen from a sp(2)-hybridized electronic state into a sp(3)-hybridized one, and thus realize a transition state that reduces the rotational barriers separating the cis- and trans-states. We also found that the hydration of the prolyl nitrogen stabilizes the negative pyramidal conformation, while an intramolecular interaction mainly stabilizes the positive one. Fluctuations in the polarity and magnitude of the pyramidal conformation during the isomerization are interpreted as a competition between the hydrogen-bonding partners for the prolyl nitrogen between different sides of the pyrrolidine ring.

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

2015-06-02

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.

Deconstructing field-induced ketene isomerization through Lagrangian descriptors.

PubMed

Craven, Galen T; Hernandez, Rigoberto

2016-02-07

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

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

PubMed

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

2009-09-07

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

Solvent- and DNA-Controlled Phototriggered Linkage Isomerization in a Ruthenium Sulfoxide Complex Incorporating Dipyrido[3,2-a:2',3'-c]phenazine (dppz).

PubMed

Phapale, Daulat; Ghosh, Rajib; Das, Dipanwita

2017-06-05

A new tris-heteroleptic complex [Ru(bpy)(dppz)(OSO)](ClO 4 ), [1](ClO 4 ) (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine and OSO = 2-methylsulfinylbenzoate), was synthesized and characterized to control the photochromic Ru-S → Ru-O linkage isomerization. Details isomerization kinetics studied by UV-visible absorption spectroscopy and cyclic voltammetry revealed that efficient photochromic S → O isomerization and thermal O → S reversal take place in solvents like propylene carbonate (PC), methanol, and dichloromethane. Strikingly, photoisomerization of [1](ClO 4 ) is arrested in water although is active in the analogous compound [Ru(bpy) 2 (OSO)](ClO 4 ). Effective excited state deactivation through dark 3 MLCT state involving dppz ligand of [1](ClO 4 ) switches off photochromism in aqueous medium. Interestingly, the photochromism is activated in aqueous solution in the presence of DNA which shields the dppz localized dark state through intercalation. Ultrafast transient absorption spectroscopic measurement sheds light on the differential behavior of photochromism in aqueous and nonaqueous solvents.

Sunlight-switchable light shutter fabricated using liquid crystals doped with push-pull azobenzene.

PubMed

Oh, Seung-Won; Baek, Jong-Min; Yoon, Tae-Hoon

2016-11-14

We propose a sunlight-switchable light shutter using liquid crystal/polymer composite doped with push-pull azobenzene. The proposed light shutter is switchable between the translucent and transparent states by application of an electric field or by UV irradiation. Switching by UV irradiation is based on the change of the liquid crystal (LC) clearing point by the photo-isomerization effect of push-pull azobenzene. Under sunlight, the light shutter can be switched from the translucent to the transparent state by the nematic-isotropic phase transition of the LC domains triggered by trans-cis photo-isomerization of the push-pull azobenzene molecules. When the amount of sunlight is low because of cloud cover or when there is no sunlight at sunset, the light shutter rapidly relaxes from its transparent state back to its initial translucent state by the isotropic-nematic phase transition induced by cis-trans back-isomerization of the push-pull azobenzene molecules.

Protein side chain rotational isomerization: A minimum perturbation mapping study

NASA Astrophysics Data System (ADS)

Haydock, Christopher

1993-05-01

A theory of the rotational isomerization of the indole side chain of tryptophan-47 of variant-3 scorpion neurotoxin is presented. The isomerization potential energy, entropic part of the isomerization free energy, isomer probabilities, transition state theory reaction rates, and indole order parameters are calculated from a minimum perturbation mapping over tryptophan-47 χ1×χ2 torsion space. A new method for calculating the fluorescence anisotropy from molecular dynamics simulations is proposed. The method is based on an expansion that separates transition dipole orientation from chromophore dynamics. The minimum perturbation potential energy map is inverted and applied as a bias potential for a 100 ns umbrella sampling simulation. The entropic part of the isomerization free energy as calculated by minimum perturbation mapping and umbrella sampling are in fairly close agreement. Throughout, the approximation is made that two glutamine and three tyrosine side chains neighboring tryptophan-47 are truncated at the Cβ atom. Comparison with the previous combination thermodynamic perturbation and umbrella sampling study suggests that this truncated neighbor side chain approximation leads to at least a qualitatively correct theory of tryptophan-47 rotational isomerization in the wild type variant-3 scorpion neurotoxin. Analysis of van der Waals interactions in a transition state region indicates that for the simulation of barrier crossing trajectories a linear combination of three specially defined dihedral angles will be superior to a simple side chain dihedral reaction coordinate.

Non-adiabatic dynamics investigation of the radiationless decay mechanism of trans-urocanic acid in the S{sub 2} state

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

Zhao, Li; University of the Chinese Academy of Sciences, Beijing 100049; Zhou, Pan-Wang, E-mail: pwzhou@dicp.ac.cn, E-mail: gjzhao@dicp.ac.cn

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 S{sub 1} state, whereas exciting the molecule to the S{sub 2} state causes almost no isomerization. The comparative photochemical behavior of the trans-urocanic on the S{sub 1} and S{sub 2} 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 S{sub 2} state. Combining the on-the-fly surface hopping dynamics simulations and staticmore » electronic structure calculations, three decay channels were observed following excitation to the S{sub 2} state. An overwhelming majority of the molecules decay to the S{sub 1} 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 S{sub 1} 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 S{sub 2} state decay mechanism of this molecule, which offers useful information to explain the wavelength dependent isomerization behavior.« less

Ultrafast kinetics of linkage isomerism in Na2[Fe(CN)5NO] aqueous solution revealed by time-resolved photoelectron spectroscopy

PubMed Central

Raheem, Azhr A.; Wilke, Martin; Borgwardt, Mario; Engel, Nicholas; Bokarev, Sergey I.; Grell, Gilbert; Aziz, Saadullah G.; Kühn, Oliver; Kiyan, Igor Yu.; Merschjann, Christoph; Aziz, Emad F.

2017-01-01

The kinetics of ultrafast photoinduced structural changes in linkage isomers is investigated using Na2[Fe(CN)5NO] as a model complex. The buildup of the metastable side-on configuration of the NO ligand, as well as the electronic energy levels of ground, excited, and metastable states, has been revealed by means of time-resolved extreme UV (XUV) photoelectron spectroscopy in aqueous solution, aided by theoretical calculations. Evidence of a short-lived intermediate state in the isomerization process and its nature are discussed, finding that the complete isomerization process occurs in less than 240 fs after photoexcitation. PMID:28713840

Communication: An accurate calculation of the S{sub 1} C{sub 2}H{sub 2} cis-trans isomerization barrier height

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

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

2016-03-21

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

Communication: An accurate calculation of the S 1 C 2H 2 cis-trans isomerization barrier height

DOE PAGES

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

2016-03-16

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

Asp 58 modulates lens αA-crystallin oligomer formation and chaperone function.

PubMed

Takata, Takumi; Nakamura-Hirota, Tooru; Inoue, Rintaro; Morishima, Ken; Sato, Nobuhiro; Sugiyama, Masaaki; Fujii, Noriko

2018-06-01

Senile cataract onset is caused by insolubilization of lens proteins. The lens crystallin protein family correctly orders the formation of homo- or hetero-oligomers in lens fiber cells. Because lens fiber cells do not divide, covalent post-translational modifications, such as isomerization of aspartate residues, accumulate with aging. Although many isomerization sites of αA-crystallin have been reported, their structural and functional contributions have never been identified. In this study, αA-crystallin was extracted from aged human lens and separated into each oligomeric state by size exclusion chromatography and electrophoresis. The novel combination methodology of in-solution/gel tryptic digestion with liquid chromatography equipped with mass spectrometry (LC-MS/MS) was used to evaluate the isomerization of Asp 58. The contributions of isomerization to assembly, solubility, and chaperone functions of αA-crystallin were estimated using a series of mutations of Asp 58 in αA-crystallin. The results indicated that the isomerization of Asp 58 depended on the oligomer size and age of the lens. The substitution of Asp 58 for hydrophobic residues increased αA-crystallin oligomer size and decreased solubility. All substitutions decreased the chaperone function of αA-crystallin for aggregates of bovine βL-crystallin and alcohol dehydrogenase. The data indicated that Asp 58 in αA-crystallin was critical for intermolecular interactions in the lens. Our results also suggested that LC-MS/MS-based isomerization analyses of in-gel-digested products could be useful for investigating the isomerization of Asp residues in oligomeric states. This method could also be used to analyze d/l ratios of amino acid residues in soluble protein aggregates. © 2018 Federation of European Biochemical Societies.

High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.

PubMed

Jeong, Seung Pyo; Renna, Lawrence A; Boyle, Connor J; Kwak, Hyunwook S; Harder, Edward; Damm, Wolfgang; Venkataraman, Dhandapani

2017-12-19

Energy densities of ~510 J/g (max: 698 J/g) have been achieved in azobenzene-based syndiotactic-rich poly(methacrylate) polymers. The processing solvent and polymer-solvent interactions are important to achieve morphologically optimal structures for high-energy density materials. This work shows that morphological changes of solid-state syndiotactic polymers, driven by different solvent processings play an important role in controlling the activation energy of Z-E isomerization as well as the shape of the DSC exotherm. Thus, this study shows the crucial role of processing solvents and thin film structure in achieving higher energy densities.

Proline isomerization in the C-terminal region of HSP27.

PubMed

Alderson, T Reid; Benesch, Justin L P; Baldwin, Andrew J

2017-07-01

In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond. The cis-P194 state is populated to near 15% at physiological temperatures, and, although both cis- and trans-P194 forms of the CTR are flexible and dynamic, both states show a residual but differing tendency to adopt β-strand conformations. In NMR spectra of an isolated CTR peptide, we observed similar evidence for isomerization involving proline 182, found within the IPI/V motif. Collectively, these data indicate a potential role for cis-trans proline isomerization in regulating the oligomerization of sHSPs.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

Investigating the large deformation of the 5 /2+ isomeric state in 73Zn: An indicator for triaxiality

NASA Astrophysics Data System (ADS)

Yang, X. F.; Tsunoda, Y.; Babcock, C.; Billowes, J.; Bissell, M. L.; Blaum, K.; Cheal, B.; Flanagan, K. T.; Garcia Ruiz, R. F.; Gins, W.; Gorges, C.; Grob, L. K.; Heylen, H.; Kaufmann, S.; Kowalska, M.; Krämer, J.; Malbrunot-Ettenauer, S.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Otsuka, T.; Papuga, J.; Sánchez, R.; Wraith, C.; Xie, L.; Yordanov, D. T.

2018-04-01

Recently reported nuclear spins and moments of neutron-rich Zn isotopes measured at ISOLDE-CERN [C. Wraith et al., Phys. Lett. B 771, 385 (2017), 10.1016/j.physletb.2017.05.085] show an uncommon behavior of the isomeric state in 73Zn. Additional details relating to the measurement and analysis of the Znm73 hyperfine structure are addressed here to further support its spin-parity assignment 5 /2+ and to estimate its half-life. A systematic investigation of this 5 /2+ isomer indicates that significant collectivity appears due to proton/neutron E 2 excitations across the proton Z = 28 and neutron N = 50 shell gaps. This is confirmed by the good agreement of the observed quadrupole moments with large scale Monte Carlo shell model calculations. In addition, potential energy surface calculations in combination with T plots reveal a triaxial shape for this isomeric state.

Iodine-Catalyzed Isomerization of Dimethyl Muconate

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

Settle, Amy E.; Berstis, Laura; Zhang, Shuting

cis,cis-Muconic acid is a platform biobased chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate ( ccDMM) to the trans,trans-form ( ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Densitymore » functional theory calculations identified unique regiochemical considerations due to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely due to solvent complexation with iodine. Under select conditions, ttDMM yields of 95% were achieved in <1 h with methanol, followed by high purity recovery (>98%) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Altogether, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for biobased chemicals.« less

Iodine-Catalyzed Isomerization of Dimethyl Muconate

DOE PAGES

Settle, Amy E.; Berstis, Laura; Zhang, Shuting; ...

2018-04-16

cis,cis-Muconic acid is a platform biobased chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate ( ccDMM) to the trans,trans-form ( ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Densitymore » functional theory calculations identified unique regiochemical considerations due to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely due to solvent complexation with iodine. Under select conditions, ttDMM yields of 95% were achieved in <1 h with methanol, followed by high purity recovery (>98%) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Altogether, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for biobased chemicals.« less

Excited state free energy calculations of Cy3 in different environments

NASA Astrophysics Data System (ADS)

Sawangsang, Pilailuk; Buranachai, Chittanon; Punwong, Chutintorn

2015-05-01

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Characterization of the X~ 2A1, A~ 2B1, and X~ 2Π electronic states of the Ga2H molecule and the X~ 2A' and A~ 2A'' isomerization transition states connecting the three minima

NASA Astrophysics Data System (ADS)

Wang, Hongyan; Wang, Suyun; Yan, Ge; Yamaguchi, Yukio; Schaefer, Henry F.

2006-01-01

A wide range of highly correlated ab initio methods has been used to predict the geometrical parameters of the linear (X˜Π2) and H-bridged (X˜A12 and ÃB12) Ga2H isomers and two isomerization transition states (X˜A'2 and ÃA″2) connecting the three minima. Dipole moments and vibrational frequencies are also obtained. The global minimum X˜A12 ground state of the H-bridged GaHGa isomer is predicted to lie only 1.6 [1.9 with the zero-point vibrational energy (ZPVE) corrections] kcalmol-1 below the ÃB12 state. The X˜A12 state lies 5.4kcalmol-1 below the X˜Π2 ground state of the linear GaGaH isomer at the coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] level of theory with the augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set. The full triples coupled-cluster method is found to alter these CCSD(T) predictions by as much as 0.3kcalmol-1. The forward isomerization barriers from the linear ground state to the X˜A'2 and ÃA″2 transition states are determined to be 3.3 and 5.3kcalmol-1, respectively. The reverse isomerization barrier between the X˜A12 GaHGa structure and the X˜Π2 GaGaH structure is predicted to be 8.6 (8.2 with the ZPVE corrections) kcalmol-1 at the aug-cc-pVQZ CCSD(T) level of theory.

Improved zeolite regeneration processes for preparing saturated branched-chain fatty acids

USDA-ARS?s Scientific Manuscript database

Ferrierite zeolite solid is an excellent catalyst for the skeletal isomerization of unsaturated linear-chain fatty acids (i.e., oleic acid) to unsaturated branched-chain fatty acids (i.e., iso-oleic acid) follow by hydrogenation to give saturated branched-chain fatty acids (i.e., isostearic acid). ...

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.

K selection in the decay of the (ν 5/2 [532 ] ⊗3/2 [411 ] ) 4- isomeric state in 102Zr

NASA Astrophysics Data System (ADS)

Browne, F.; Bruce, A. M.; Sumikama, T.; Nishizuka, I.; Nishimura, S.; Doornenbal, P.; Lorusso, G.; Söderström, P.-A.; Watanabe, H.; Daido, R.; Patel, Z.; Rice, S.; Sinclair, L.; Wu, J.; Xu, Z. Y.; Yagi, A.; Baba, H.; Chiga, N.; Carroll, R.; Didierjean, F.; Fang, Y.; Fukuda, N.; Gey, G.; Ideguchi, E.; Inabe, N.; Isobe, T.; Kameda, D.; Kojouharov, I.; Kurz, N.; Kubo, T.; Lalkovski, S.; Li, Z.; Lozeva, R.; Nishibata, N.; Odahara, A.; Podolyák, Zs.; Regan, P. H.; Roberts, O. J.; Sakurai, H.; Schaffner, H.; Simpson, G. S.; Suzuki, H.; Takeda, H.; Tanaka, M.; Taprogge, J.; Werner, V.; Wieland, O.

2017-08-01

The (ν 5/2 [532 ] ⊗3/2 [411 ] ) 4- state in 102Zr, populated in the β decay of 102Y, has been measured to be isomeric with a mean lifetime of 9.5(7) ns. It decays via four transitions, two of which are Δ K =2 (to the 3+ and 4+ members of the 2γ+ band) and one is Δ K =4 (to the 4+ member of the ground state 0+ band). The fourth (low-energy) transition is inferred to decay to an as-yet unassigned state. Hindrances of 106 were derived for the Δ K =2 transitions compared to Weisskopf estimates and the Δ K =4 transition hindered by a factor of 109. These values are consistent with the decay pattern of the analogous isomeric state in the neighboring N =62 nucleus 100Sr and with the broader systematics of such transitions. A comparison of the hindrances for the Δ K =4 transitions suggests that 102Zr is hardened against the γ degree of freedom compared to 100Sr.

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.

Intramolecular charge transfer and trans-cis isomerization of the DCM styrene dye in polar solvents. A CS INDO MRCI study

NASA Astrophysics Data System (ADS)

Marguet, S.; Mialocq, J. C.; Millie, P.; Berthier, G.; Momicchioli, F.

1992-03-01

The solvent-induced changes of trans-cis isomerization efficiency and electronic structure of the excited state of the DCM dye have been considered by means of CS INDO MRCI calculations. The potential energy curves, dipole moments and atomic charge densities as a function of two internal coordinates, namely the rotation angle about the central "double" bond and the twisting of the dimethylamino group, have been obtained for the ground state and the lowest excited states. The structural requirements for the existence of ICT (intramolecular charge transfer) excited states have been investigated by considering internal rotations about three single bonds. The reliability of the potential surfaces and of the solvation models has been discussed with reference to test-calculations on the DMABN molecule. In the first excited singlet state of DCM, the low-energy barrier for the trans-cis isomerization has been found unaffected by the solvent polarity. The only singlet excited state presenting a large ICT character has been found to be the S 2 state for a perpendicularly twisted conformation of the dimethylamino group (TICT state). The assumption of a deactivation of the trans-isomer in the locally excited state through the TICT funnel has been largely discussed with reference to the simplifications of the present theoretical approach.

Iodine-Catalyzed Isomerization of Dimethyl Muconate.

PubMed

Settle, Amy E; Berstis, Laura; Zhang, Shuting; Rorrer, Nicholas A; Hu, Haiming; Richards, Ryan M; Beckham, Gregg T; Crowley, Michael F; Vardon, Derek R

2018-06-11

cis,cis-Muconic acid is a platform bio-based chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate (ccDMM) to the trans,trans-form (ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Density functional theory calculations identified unique regiochemical considerations owing to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely because of solvent complexation with iodine. Under select conditions, ttDMM yields of 95 % were achieved in <1 h with methanol, followed by high purity recovery (>98 %) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Overall, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for bio-based chemicals. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing the Single-Particle Character of Rotational States in F 19 Using a Short-Lived Isomeric Beam

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

Santiago-Gonzalez, D.; Auranen, K.; Avila, M. L.

2018-03-01

A beam containing a substantial component of both the J(pi) = 5(+), T-1/2 = 162 ns isomeric state of F-18 and its 1(+), 109.77-min ground state is utilized to study members of the ground-state rotational band in F-19 through the neutron transfer reaction (d,p) in inverse kinematics. The resulting spectroscopic strengths confirm the single-particle nature of the 13/2(+) band-terminating state. The agreement between shell-model calculations using an interaction constructed within the sd shell, and our experimental results reinforces the idea of a single-particle-collective duality in the descriptions of the structure of atomic nuclei.

Flipping the Switch: Fast Photoisomerization in a Confined Environment.

PubMed

Williams, Derek E; Martin, Corey R; Dolgopolova, Ekaterina A; Swifton, Anton; Godfrey, Danielle C; Ejegbavwo, Otega A; Pellechia, Perry J; Smith, Mark D; Shustova, Natalia B

2018-05-28

Stimuli-responsive materials are vital for addressing emerging demands in the advanced technology sector as well as current industrial challenges. Here, we report for the first time that coordinative integration of photoresponsive building blocks possessing photochromic spiropyran and diarylethene moieties within a rigid scaffold of metal-organic frameworks (MOFs) could control photophysics; in particular, cycloreversion kinetics with the level of control, which is not accessible in the solid state or solution. On the series of photoactive materials, we demonstrated for the first time that photoisomerization rates of photochromic compounds could be tuned within almost two orders of magnitude. Moreover, cycloreversion rates of photoresponsive derivatives could be modulated as a function of the framework structure. Furthermore, through MOF engineering we were able to achieve complete isomerization for coordinatively immobilized spiropyran derivatives, typically exhibiting limited photoswitching behavior in the solid state. For instance, spectroscopic analysis revealed that the novel monosubstituted spiropyran derivative grafted to the backbone of the MOF pillar exhibits a remarkable photoisomerization rate of 0.16 s-1, typical for cycloreversion in solution. We also applied the acquired fundamental principles towards mapping of changes in material properties, which could provide a pathway for monitoring material aging or structural deterioration.

A Novel simultaneous-Saccharification-Fermentation Strategy for Efficient Co-fermentation of C5 and C6 Sugars Using Native, Non-GMO Yeasts

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

Varanasi, Sasidhar; Relue, Patricia

Economic bioethanol production is critically dependent upon the ability to convert both the hexose (C6) and pentose (C5) sugars resulting from cellulose and hemicellulose. C5 sugars are not readily fermentable by native Saccharomyces cerevisiae. Genetically Modified Organisms (GMOs) are designed to ferment xylose, but their stability, ethanol yield, environmental impact, and survival under conditions of industrial fermentation are unproven. In this project, we developed a novel approach for efficient fermentation of both C5 and C6 sugars using native S. Cerevisiae by exploiting its ability to produce ethanol from xylulose - the keto-isomer of xylose. While the isomerization of xylose tomore » xylulose can be accomplished via commercially (and cheaply) available Xylose Isomerase (XI) (Sweetzyme™), this conversion has an extremely unfavorable equilibrium (xylose:xylose is about 5:1). To address this, we developed two alternate strategies. In the first, the two enzymes XI and urease are coimmobilized on solid support particles to enable complete isomerization of xylose to xylulose under pH conditions suitable for fermentation, in a simultaneous-isomerization-fermentation (SIF) mode. The ability of our technology to conduct isomerization of xylose under pH conditions suitable for both saccharification and fermentation opens the possibility of SSF with native yeasts for the first time. Herein, we performed specific research tasks for implementation of our technology in several modes of operation, including simultaneous-isomerization-and-fermentation (SIF), simultaneous-saccharification-and-isomerization (SSI) followed by fermentation, and SSF mode with the biomass feedstock poplar. The projected economics of our process are very favorable in comparison to the costs associated with engineering, licensing and propagating GMOs. This novel fermentation technology is readily accessible to rural farming economies for implementation in cellulosic ethanol production facilities.« less

Identification of Excited States in the N=Z Nucleus 82Nb

NASA Astrophysics Data System (ADS)

Caceres, L. S.; Gorska, M.; Jungclaus, A.; Regan, P. H.; Garnsworthy, A. B.; Pietri, S.; Podolyak, Zs.; Rudolph, D.; Steer, S. J.; Grawe, H.; Balabanski, D. L.; Becker, F.; Bednarczyk, P.; Benzoni, G.; Blank, B.; Brandau, C.; Bruce, A. M.; Camera, F.; Catford, W. N.; Cullen, I. J.; Dombradi, Zs.; Doornenbal, P.; Estevez, E.; Geissel, H.; Gelletly, W.; Gerl, J.; Grebosz, J.; Heinz, A.; Hoischen, R.; Ilie, G.; Jolie, J.; Jones, G. A.; Kmiecik, M.; Kojouharov, I.; Kondev, F. G.; Kurtukian-Nieto, T.; Kurz, N.; Lalkowski, S.; Liu, L.; Maj, A.; Myalski, S.; Montes, F.; Pfuetzner, M.; Prokopowicz, W.; Saito, T.; Schaffner, H.; Schwertel, S.; Shizuma, T.; Simons, A. J.; Tashenov, S.; Walker, P. M.; Werner-Malento, E.; Wieland, O.; Wollersheim, H. J.

2007-04-01

Information on the first excited states in the N=Z=41 nucleus 82Nb sheds light on the competition of isospin T=0 and T=1 states in the A sim 80 region. The measurement was performed at the GSI laboratory using fragmentation of a 107Ag primary beam at 750 MeV/u on a 4 g/cm2 9Be target. The fragments were separated and identified unambiguously in the FRagment Separator. Three excited states were observed and the half-life estimate for the isomeric state was extracted. A tentative spin assignment based on the isobaric analogue states systematics in the Tz=1 nucleus 82Zr, and transition probabilities indicate T=1 character of the first two excited states, and T=0 for the isomeric state.

Isomer-delayed gamma-ray spectroscopy of neutron-rich 166Tb

DOE PAGES

Gurgi, L. A.; Regan, P. H.; Söderström, P. -A.; ...

2017-09-13

Here, this short paper presents the identification of a metastable, isomeric-state decay in the neutron-rich odd-odd, prolate-deformed nucleus 166Tb. The nucleus of interest was formed using the in-flight fission of a 345 MeV per nucleon 238U primary beam at the RIBF facility, RIKEN, Japan. Gamma-ray transitions decaying from the observed isomeric states in 166Tb were identified using the EURICA gamma-ray spectrometer, positioned at the final focus of the BigRIPS fragments separator. The current work identifies a single discrete gamma-ray transition of energy 119 keV which de-excites an isomeric state in 166Tb with a measured half-life of 3.5(4) μs. The multipolaritymore » assignment for this transition is an electric dipole and is made on the basis internal conversion and decay lifetime arguments. Possible two quasi-particle Nilsson configurations for the initial and final states which are linked by this transition in 166Tb are made on the basis of comparison with Blocked BCS Nilsson calculations, with the predicted ground state configuration for this nucleus arising from the coupling of the v(1-/2)[521] and π(3+/2) Nilsson orbitals.« less

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

Gurgi, L. A.; Regan, P. H.; Söderström, P. -A.

Here, this short paper presents the identification of a metastable, isomeric-state decay in the neutron-rich odd-odd, prolate-deformed nucleus 166Tb. The nucleus of interest was formed using the in-flight fission of a 345 MeV per nucleon 238U primary beam at the RIBF facility, RIKEN, Japan. Gamma-ray transitions decaying from the observed isomeric states in 166Tb were identified using the EURICA gamma-ray spectrometer, positioned at the final focus of the BigRIPS fragments separator. The current work identifies a single discrete gamma-ray transition of energy 119 keV which de-excites an isomeric state in 166Tb with a measured half-life of 3.5(4) μs. The multipolaritymore » assignment for this transition is an electric dipole and is made on the basis internal conversion and decay lifetime arguments. Possible two quasi-particle Nilsson configurations for the initial and final states which are linked by this transition in 166Tb are made on the basis of comparison with Blocked BCS Nilsson calculations, with the predicted ground state configuration for this nucleus arising from the coupling of the v(1-/2)[521] and π(3+/2) Nilsson orbitals.« less

Isomer-delayed gamma-ray spectroscopy of neutron-rich 166Tb

NASA Astrophysics Data System (ADS)

Gurgi, L. A.; Regan, P. H.; Söderström, P.-A.; Watanabe, H.; Walker, P. M.; Podolyák, Zs.; Nishimura, S.; Berry, T. A.; Doornenbal, P.; Lorusso, G.; Isobe, T.; Baba, H.; Xu, Z. Y.; Sakurai, H.; Sumikama, T.; Catford, W. N.; Bruce, A. M.; Browne, F.; Lane, G. J.; Kondev, F. G.; Odahara, A.; Wu, J.; Liu, H. L.; Xu, F. R.; Korkulu, Z.; Lee, P.; Liu, J. J.; Phong, V. H.; Yagi, A.; Zhang, G. X.; Alharbi, T.; Carroll, R. J.; Chae, K. Y.; Dombradi, Zs.; Estrade, A.; Fukuda, N.; Griffin, C.; Ideguchi, E.; Inabe, N.; Kanaoka, H.; Kojouharov, I.; Kubo, T.; Kubono, S.; Kurz, N.; Kuti, I.; Lalkovski, S.; Lee, E. J.; Lee, C. S.; Lotay, G.; Moon, C. B.; Nishizuka, I.; Nita, C. R.; Patel, Z.; Roberts, O. J.; Schaffner, H.; Shand, C. M.; Suzuki, H.; Takeda, H.; Terashima, S.; Vajta, Zs.; Kanaya, S.; Valiente-Dobòn, J. J.

2017-09-01

This short paper presents the identification of a metastable, isomeric-state decay in the neutron-rich odd-odd, prolate-deformed nucleus 166Tb. The nucleus of interest was formed using the in-flight fission of a 345 MeV per nucleon 238U primary beam at the RIBF facility, RIKEN, Japan. Gamma-ray transitions decaying from the observed isomeric states in 166Tb were identified using the EURICA gamma-ray spectrometer, positioned at the final focus of the BigRIPS fragments separator. The current work identifies a single discrete gamma-ray transition of energy 119 keV which de-excites an isomeric state in 166Tb with a measured half-life of 3.5(4) μs. The multipolarity assignment for this transition is an electric dipole and is made on the basis internal conversion and decay lifetime arguments. Possible two quasi-particle Nilsson configurations for the initial and final states which are linked by this transition in 166Tb are made on the basis of comparison with Blocked BCS Nilsson calculations, with the predicted ground state configuration for this nucleus arising from the coupling of the v(1-/2)?[521] and ? π(3+/2) Nilsson orbitals.

Conformational Fluctuations in G-Protein-Coupled Receptors

NASA Astrophysics Data System (ADS)

Brown, Michael F.

2014-03-01

G-protein-coupled receptors (GPCRs) comprise almost 50% of pharmaceutical drug targets, where rhodopsin is an important prototype and occurs naturally in a lipid membrane. Rhodopsin photoactivation entails 11-cis to all-trans isomerization of the retinal cofactor, yielding an equilibrium between inactive Meta-I and active Meta-II states. Two important questions are: (1) Is rhodopsin is a simple two-state switch? Or (2) does isomerization of retinal unlock an activated conformational ensemble? For an ensemble-based activation mechanism (EAM) a role for conformational fluctuations is clearly indicated. Solid-state NMR data together with theoretical molecular dynamics (MD) simulations detect increased local mobility of retinal after light activation. Resultant changes in local dynamics of the cofactor initiate large-scale fluctuations of transmembrane helices that expose recognition sites for the signal-transducing G-protein. Time-resolved FTIR studies and electronic spectroscopy further show the conformational ensemble is strongly biased by the membrane lipid composition, as well as pH and osmotic pressure. A new flexible surface model (FSM) describes how the curvature stress field of the membrane governs the energetics of active rhodopsin, due to the spontaneous monolayer curvature of the lipids. Furthermore, influences of osmotic pressure dictate that a large number of bulk water molecules are implicated in rhodopsin activation. Around 60 bulk water molecules activate rhodopsin, which is much larger than the number of structural waters seen in X-ray crystallography, or inferred from studies of bulk hydrostatic pressure. Conformational selection and promoting vibrational motions of rhodopsin lead to activation of the G-protein (transducin). Our biophysical data give a paradigm shift in understanding GPCR activation. The new view is: dynamics and conformational fluctuations involve an ensemble of substates that activate the cognate G-protein in the amplified visual response.

The thermal Z-isomerization-induced change in solubility and physical properties of (all-E)-lycopene.

PubMed

Murakami, Kazuya; Honda, Masaki; Takemura, Ryota; Fukaya, Tetsuya; Kubota, Mitsuhiro; Wahyudiono; Kanda, Hideki; Goto, Motonobu

2017-09-16

The effect of Z-isomerization of (all-E)-lycopene on its solubility in organic solvents and physical properties was investigated. Lycopene samples containing different Z-isomer contents (23.8%, 46.9%, and 75.6% of total lycopene) were prepared from high-purity (all-E)-lycopene by thermal Z-isomerization in dichloromethane (CH 2 Cl 2 ). As the Z-isomer content increased, the relative solubility of lycopene significantly improved. Although (all-E)-lycopene barely dissolved in ethanol (0.6 mg/L), the solubilities of lycopene containing 23.8%, 46.9%, and 75.6% Z-isomers were 484.5, 914.7, and 2401.7 mg/L, respectively. Furthermore, differential scanning calorimetry (DSC), powder X-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses clearly indicated that (all-E)-lycopene was present in the crystal state, while Z-isomers of lycopene were present in amorphous states. A number of studies have suggested that Z-isomers of lycopene are better absorbed in the human body than the all-E-isomer. This may be due to the change in solubility and physical properties of lycopene by the Z-isomerization. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental study of isomeric intruder 1 2 + states in At 197 , 203

DOE PAGES

Auranen, K.; Uusitalo, J.; Juutinen, S.; ...

2017-04-10

A newly observed isomeric intruder ½ + state [T ½=3.5(6)ms] is identified in 203At using a gas-filled recoil separator and fusion-evaporation reactions. The isomer is depopulated through a cascade of E3 and mixed M1/E2 transitions to the 9/2 – ground state, and it is suggested to originate from the π(s ½) –1 configuration. In addition, the structures above the ½ + state in 203At and 197At are studied using in-beam γ-ray spectroscopy, recoil-decay tagging, and recoil-isomer decay tagging methods. As a result, the ½ + state is fed from 3/2 + and 5/2 + states, and the origin of thesemore » states are discussed.« less

High-K Isomers in Light Superheavy Nuclei by PNC-CSM method

NASA Astrophysics Data System (ADS)

He, Xiao-Tao

2018-05-01

The high-K isomeric states in light superheavy nuclei around A = 250 mass region are investigated by the Cranked Shell Model (CSM) with pairing treated by a Particle-Number Conserving (PNC) method. With including the higher-order deformation ɛ6, both of the high-K multi-particle state energies and the rotational bands in 254No and N = 150 isotone are reproduced well. The isomeric state energies and the microscopic mechanism of kinematic moment of inertia variations versus rotational frequency are discussed. The irregularity of the two-neutron Kπ = 8- state band at ħω ≈ 0:17 in 252No is caused by the configuration mixing with the two-proton Kπ = 8- band. .

Activation cross section and isomeric cross section ratios for the (n ,2 n ) reaction on 153Eu

NASA Astrophysics Data System (ADS)

Luo, Junhua; Jiang, Li; Li, Suyuan

2017-10-01

The 153Eu(n ,2 n ) m1,m2,g152Eu cross section was measured by means of the activation technique at three neutron energies in the range 13-15 MeV. The quasimonoenergetic neutron beam was formed via the 3H(d ,n ) 4He reaction, in the Pd-300 Neutron Generator at the Chinese Academy of Engineering Physics (CAEP). The activities induced in the reaction products were measured using high-resolution γ-ray spectroscopy. The cross section of the population of the second high-spin (8-) isomeric state was measured along with the reaction cross section populating both the ground (3-) and the first isomeric state (0-). Cross sections were also evaluated theoretically using the numerical code TALYS-1.8, with different level density options at neutron energies varying from the reaction threshold to 20 MeV. Results are discussed and compared with the corresponding literature.

Engineering the vibrational coherence of vision into a synthetic molecular device.

PubMed

Gueye, Moussa; Manathunga, Madushanka; Agathangelou, Damianos; Orozco, Yoelvis; Paolino, Marco; Fusi, Stefania; Haacke, Stefan; Olivucci, Massimo; Léonard, Jérémie

2018-01-22

The light-induced double-bond isomerization of the visual pigment rhodopsin operates a molecular-level optomechanical energy transduction, which triggers a crucial protein structure change. In fact, rhodopsin isomerization occurs according to a unique, ultrafast mechanism that preserves mode-specific vibrational coherence all the way from the reactant excited state to the primary photoproduct ground state. The engineering of such an energy-funnelling function in synthetic compounds would pave the way towards biomimetic molecular machines capable of achieving optimum light-to-mechanical energy conversion. Here we use resonance and off-resonance vibrational coherence spectroscopy to demonstrate that a rhodopsin-like isomerization operates in a biomimetic molecular switch in solution. Furthermore, by using quantum chemical simulations, we show why the observed coherent nuclear motion critically depends on minor chemical modifications capable to induce specific geometric and electronic effects. This finding provides a strategy for engineering vibrationally coherent motions in other synthetic systems.

Geometrical Optimization Approach to Isomerization: Models and Limitations.

PubMed

Chang, Bo Y; Shin, Seokmin; Engel, Volker; Sola, Ignacio R

2017-11-02

We study laser-driven isomerization reactions through an excited electronic state using the recently developed Geometrical Optimization procedure. Our goal is to analyze whether an initial wave packet in the ground state, with optimized amplitudes and phases, can be used to enhance the yield of the reaction at faster rates, driven by a single picosecond pulse or a pair of femtosecond pulses resonant with the electronic transition. We show that the symmetry of the system imposes limitations in the optimization procedure, such that the method rediscovers the pump-dump mechanism.

Gaseous 83mKr generator for KATRIN

NASA Astrophysics Data System (ADS)

Sentkerestiová, J.; Dragoun, O.; Lebeda, O.; Ryšavý, M.; Sturm, M.; Vénos, D.

2018-04-01

Monoenergetic conversion electrons from the 83mKrKr isomeric state have been proven to be useful in the calibration of several tritium neutrino mass and dark matter experiments. In this paper the design and characteristics of the gaseous 83mKrKr generator, including the 83Rb/83mKrKr source behavior in tritium, for the KATRIN experiment are presented. Using Si(Li) and silicon drift detectors (SDD) detectors, the half-life of the 83mKrKr isomeric state was measured to be 1.8620 ± 0.0019 h.

g factors of coexisting isomeric states in {sup 188}Pb

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

Ionescu-Bujor, M.; Iordachescu, A.; Marginean, N.

2010-02-15

The g factors of the 12{sup +}, 11{sup -}, and 8{sup -} isomeric states in {sup 188}Pb were measured using the time-differential perturbed angular distribution method as g(12{sup +})=-0.179(6), g(11{sup -})=+1.03(3), and g(8{sup -})=-0.037(7). The g factor of the 12{sup +} state follows the observed slight down-sloping evolution of the g factors of the i{sub 13/2}{sup 2} neutron spherical states with decreasing N. The g factors of the 11{sup -} and 8{sup -} isomers proposed as oblate and prolate deformed states, respectively, were interpreted within the rotational model, using calculated and empirical g factor values for the involved single-particle orbitals.

Probing the Single-Particle Character of Rotational States in F 19 Using a Short-Lived Isomeric Beam

NASA Astrophysics Data System (ADS)

Santiago-Gonzalez, D.; Auranen, K.; Avila, M. L.; Ayangeakaa, A. D.; Back, B. B.; Bottoni, S.; Carpenter, M. P.; Chen, J.; Deibel, C. M.; Hood, A. A.; Hoffman, C. R.; Janssens, R. V. F.; Jiang, C. L.; Kay, B. P.; Kuvin, S. A.; Lauer, A.; Schiffer, J. P.; Sethi, J.; Talwar, R.; Wiedenhöver, I.; Winkelbauer, J.; Zhu, S.

2018-03-01

A beam containing a substantial component of both the Jπ=5+ , T1 /2=162 ns isomeric state of F 18 and its 1+, 109.77-min ground state is utilized to study members of the ground-state rotational band in F 19 through the neutron transfer reaction (d ,p ) in inverse kinematics. The resulting spectroscopic strengths confirm the single-particle nature of the 13 /2+ band-terminating state. The agreement between shell-model calculations using an interaction constructed within the s d shell, and our experimental results reinforces the idea of a single-particle-collective duality in the descriptions of the structure of atomic nuclei.

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

NASA Astrophysics Data System (ADS)

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

2009-07-01

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→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 O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜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 O2+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.

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 determined. The A-->B and B-->A transitions are used to place bounds on the relative energies of minima B relative to A, with B lying at least 126 cm(-1) above A. The corresponding barriers have been computed using both density functional and second-order many-body perturbation theory methods in order to establish the level of theory needed to reproduce experimental results. While most of the computed barriers match experiment well, the barriers for the A-F and B-F transitions are too high by almost a factor of 2. Possible reasons for this discrepancy are discussed.

Dipole-resonance assisted isomerization in the electronic ground state using few-cycle infrared pulses.

PubMed

Skocek, Oliver; Uiberacker, Christoph; Jakubetz, Werner

2011-06-30

A computational investigation of HCN → HNC isomerization in the electronic ground state by one- and few-cycle infrared pulses is presented. Starting from a vibrationally pre-excited reagent state, isomerization yields of more than 50% are obtained using single one- to five-cycle pulses. The principal mechanism includes two steps of population transfer by dipole-resonance (DR), and hence, the success of the method is closely linked to the polarity of the system and, in particular, the stepwise change of the dipole moment from reactant to transition state and on to products. The yield drops massively if the diagonal dipole matrix elements are artificially set to zero. In detail, the mechanism includes DR-induced preparation of a delocalized vibrational wavepacket, which traverses the barrier region and is finally trapped in the product well by DR-dominated de-excitation. The excitation and de-excitation steps are triggered by pulse lobes of opposite field direction. As the number of optical cycles is increased, the leading field lobes prepare a vibrational superposition state by off-resonant ladder climbing, which is then subjected to the three steps of the principal isomerization mechanism. DR excitation is more efficient from a preformed vibrational wavepacket than from a molecular eigenstate. The entire process can be loosely described as Tannor-Kosloff-Rice type transfer mechanism on a single potential surface effected by a single pulse, individual field lobes assuming the roles of pump- and dump-pulses. Pre-excitation to a transient wavepacket can be enhanced by applying a separate, comparatively weak few-cycle prepulse, in which the prepulse prepares a vibrational wavepacket. The two-pulse setup corresponds to a double Tannor-Kosloff-Rice control scheme on a single potential surface.

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

NASA Astrophysics Data System (ADS)

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-01

A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) 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-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-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.

Short-lived isomers in 192Po and 194Po

NASA Astrophysics Data System (ADS)

Andel, B.; Andreyev, A. N.; Antalic, S.; Heßberger, F. P.; Ackermann, D.; Hofmann, S.; Huyse, M.; Kalaninová, Z.; Kindler, B.; Kojouharov, I.; Kuusiniemi, P.; Lommel, B.; Nishio, K.; Page, R. D.; Sulignano, B.; Van Duppen, P.

2016-06-01

Isomeric states in 194Po and 192Po were studied at the velocity filter SHIP. The isotopes were produced in the fusion-evaporation reactions 141Pr(56Fe, p 2 n )194Po and 144Sm(51V, p 2 n )192Po . Several new γ -ray transitions were attributed to the isomers and γ -γ coincidences for both isomers were studied for the first time. The 459-keV transition earlier, tentatively proposed as de-exciting the isomeric level in 194Po, was replaced by a new 248-keV transition, and the spin of this isomer was reassigned from (11-) to (10-). The de-excitation of the (11-) isomeric level in 192Po by the 154-keV transition was confirmed and a parallel de-excitation by a 733-keV (E 3 ) transition to (8+) level of the ground-state band was suggested. Moreover, side feeding to the (4+) level of the ground-state band was proposed. The paper also discusses strengths of transitions de-exciting 11- isomers in neighboring Po and Pb isotopes.

Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory.

PubMed

Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

2017-08-09

The thermal [Formula: see text] (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G * including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model-[Formula: see text] isomerization in azobenzene-a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the [Formula: see text] (back-)isomerization of azobenzenes under solvent-free conditions.

Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory

NASA Astrophysics Data System (ADS)

Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

2017-08-01

The thermal Z\\to E (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G* including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model—Z\\to E isomerization in azobenzene—a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the Z\\to E (back-)isomerization of azobenzenes under solvent-free conditions.

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.

Penning trap mass measurement of 72Br

NASA Astrophysics Data System (ADS)

Valverde, A. A.; Bollen, G.; Cooper, K.; Eibach, M.; Gulyuz, K.; Izzo, C.; Morrissey, D. J.; Ringle, R.; Sandler, R.; Schwarz, S.; Sumithrarachchi, C. S.; Villari, A. C. C.

2015-03-01

The Low Energy Beam and Ion Trap (LEBIT) Penning trap mass spectrometer was used to perform an improved-precision mass measurement of 72Br and the low-lying isomeric state, Brm72, giving mass excesses of -59 062.2 (1.0 )keV and -58 960.9 (1.2 )keV , respectively. These values are consistent with the values from the 2012 atomic mass evaluation [Chin. Phys. C 36, 1603 (2012), 10.1088/1674-1137/36/12/003] and the Nubase2012 evaluation of nuclear properties [Chin. Phys. C 36, 1157 (2012), 10.1088/1674-1137/36/12/001]. The uncertainties on the mass of the ground state and isomeric state have been reduced by a factor of seven.

Molecular isomerization induced by ultrashort infrared pulses. II. Pump-dump isomerization using pairs of time-delayed half-cycle pulses.

PubMed

Uiberacker, Christoph; Jakubetz, Werner

2004-06-22

We investigate population transfer across the barrier in a double-well potential, induced by a pair of time-delayed single-lobe half-cycle pulses. We apply this setup both to a one-dimensional (1D) quartic model potential and to a three-dimensional potential representing HCN-->HNC isomerization. Overall the results for the two systems are similar, although in the 3D system some additional features appear not seen in the 1D case. The generic mechanism of population transfer is the preparation by the pump pulse of a wave packet involving delocalized states above the barrier, followed by the essentially 1D motion of the delocalized part of wave packet across the barrier, and the eventual de-excitation by the dump pulse to localized states in the other well. The correct timing is given by the well-to-well passage time of the wave packet and its recurrence properties, and by the signs of the field lobes which determine the direction and acceleration or deceleration of the wave packet motion. In the 3D system an additional pump-pump-dump mechanism linked to wave packet motion in the reagent well can mediate isomerization. Since the transfer time and the pulse durations are of the same order of magnitude, there is also a marked dependence of the dynamics and the transfer yield on the pulse duration. Our analysis also sheds light on the pronounced carrier envelope phase dependence previously observed for isomerization and molecular dissociation with one-cycle and sub-one-cycle pulses. (c) 2004 American Institute of Physics.

Nonradiative decay dynamics of methyl-4-hydroxycinnamate and its hydrated complex revealed by picosecond pump-probe spectroscopy.

PubMed

Shimada, Daiki; Kusaka, Ryoji; Inokuchi, Yoshiya; Ehara, Masahiro; Ebata, Takayuki

2012-07-07

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H(2)O) in the S(1) state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S(1)-S(0) origin is 8-9 ps. On the other hand, the lifetime of the OMpCA-H(2)O complex at the origin is 930 ps, which is ∼100 times longer than that of OMpCA. Furthermore, in the complex the S(1) lifetime shows rapid decrease at an energy of ∼200 cm(-1) above the origin and finally becomes as short as 9 ps at ∼500 cm(-1). Theoretical calculations with a symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that the observed lifetime behavior of the two species is described by nonradiative decay dynamics involving trans → cis isomerization. That is both OMpCA and OMpCA-H(2)O in the S(1) state decay due to the trans → cis isomerization, and the large difference of the lifetimes between them is due to the difference of the isomerization potential energy curve. In OMpCA, the trans → cis isomerization occurs smoothly without a barrier on the S(1) surface, while in the OMpCA-H(2)O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H(2)O is in good agreement with that observed experimentally.

Nature of isomerism of solid isothiourea salts, inhibitors of nitric oxide synthases, as studied by 1H-14N nuclear quadrupole double resonance, X-ray, and density functional theory/quantum theory of atoms in molecules.

PubMed

Latosińska, J N; Latosińska, M; Seliger, J; Žagar, V; Maurin, J K; Kazimierczuk, Z

2012-02-09

Isothioureas, inhibitors of nitric oxide synthases, have been studied experimentally in solid state by nuclear quadrupole double resonance (NQDR) and X-ray methods and theoretically by the quantum theory of atoms in molecules/density functional theory. Resonance frequencies on (14)N have been detected and assigned to particular nitrogen sites in each molecule. The crystal packings of (S)-3,4-dichlorobenzyl-N-methylisothiouronium chloride with the disordered chlorine positions in benzene ring and (S)-butyloisothiouronium bromide have been resolved in X-ray diffraction studies. (14)N NQDR spectra have been found good indicators of isomer type and strength of intra- or intermolecular N-H···X (X = Cl, Br) interactions. From among all salts studied, only for (S)-2,3,4,5,6-pentabromobenzylisothiouronium chloride are both nitrogen sites equivalent, which has been explained by the slow exchange. This unique structural feature can be a key factor in the high biological activity of (S)-2,3,4,5,6-pentabromobenzylisothiouronium salts.

An isomer-specific study of solid nitromethane decomposition pathways - Detection of aci-nitromethane (H2CNO(OH)) and nitrosomethanol (HOCH2NO) intermediates

NASA Astrophysics Data System (ADS)

Maksyutenko, Pavlo; Förstel, Marko; Crandall, Parker; Sun, Bing-Jian; Wu, Mei-Hung; Chang, Agnes H. H.; Kaiser, Ralf I.

2016-08-01

An isomer specific study of energetic electron exposed nitromethane ices was performed via photoionization - reflectron time of flight mass spectrometry (PI-ReTOF-MS) of the subliming products employing tunable vacuum ultraviolet light for ionization. Supported by electronic structure calculations, nitromethane (CH3NO2) was found to isomerize to methyl nitrite (CH3ONO) and also via hydrogen migration to the hitherto elusive aci-nitromethane isomer (H2CNO(OH)). The latter isomerizes to nitrosomethanol (HOCH2NO) through hydroxyl group (OH) migration, and, probably, ring closure to the cyclic 2-hydroxy-oxaziridine isomer (c-H2CON(OH)) as well. The importance of hydrogen migrations was also verified via the nitrosomethane (CH3NO) - formaldehyde oxime isomer (CH2NOH) pair.

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

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

PubMed

Lai, Cheng-Tsung; Li, Huei-Jiun; Yu, Weixuan; Shah, Sonam; Bommineni, Gopal R; Perrone, Victoria; Garcia-Diaz, Miguel; Tonge, Peter J; Simmerling, Carlos

2015-08-04

Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.

A study of Pd/SO4/ZrO2/Al2O3 catalysts in n-hexane isomerization

NASA Astrophysics Data System (ADS)

Dzhikiya, O. V.; Smolikov, M. D.; Kazantsev, K. V.; Yablokova, S. S.; Kireeva, T. V.; Paukshtis, E. A.; Gulyaeva, T. I.; Belyi, A. S.

2017-08-01

The effect of palladium concentration in a range from 0.02 to 1.6 wt.% on characteristics of n-hexane isomerization was studied. The (O2-Hchem) titration and O2 chemisorption study revealed that palladium in Pd/SO4/ZrO2/Al2O3 systems adsorbs hydrogen in a ratio H/Pds = 1.13-1.65 at./at. Investigation of the charge state of the metal by IR spectroscopy of adsorbed CO showed the presence of both the metallic (Pd0) and charged palladium species. Pd/SO4/ZrO2/Al2O3 catalysts with charged palladium atoms exhibit high activity and selectivity in n-hexane isomerization.

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.

Infrared-induced conformational isomerization and vibrational relaxation dynamics in melatonin and 5-methoxy-N-acetyl tryptophan methyl amide

NASA Astrophysics Data System (ADS)

Dian, Brian C.; Florio, Gina M.; Clarkson, Jasper R.; Longarte, Asier; Zwier, Timothy S.

2004-05-01

The conformational isomerization dynamics of melatonin and 5-methoxy N-acetyltryptophan methyl amide (5-methoxy NATMA) have been studied using the methods of IR-UV hole-filling spectroscopy and IR-induced population transfer spectroscopy. Using these techniques, single conformers of melatonin were excited via a well-defined NH stretch fundamental with an IR pump laser. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were re-cooled into their zero-point levels, partially re-filling the hole created in the ground state population of the excited conformer, and creating gains in population of the other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion via an UV probe laser. The isomerization quantum yields for melatonin show some conformation specificity but no hint of vibrational mode specificity. In 5-methoxy NATMA, no isomerization was observed out of the single conformational well populated in the expansion in the absence of the infrared excitation. In order to study the dependence of the isomerization on the cooling rate, the experimental arrangement was modified so that faster cooling conditions could be studied. In this arrangement, the pump and probe lasers were overlapped in space in the high density region of the expansion, and the time dependence of the zero-point level populations of the conformers was probed following selective excitation of a single conformation. The analysis needed to extract isomerization quantum yields from the timing scans was developed and applied to the melatonin timing scans. Comparison between the frequency and time domain isomerization quantum yields under identical experimental conditions produced similar results. Under fast cooling conditions, the product quantum yields were shifted from their values under standard conditions. The results for melatonin are compared with those for N-acetyl tryptophan methyl amide.

Raman studies on molecular and ionic forms in solid layers of nitrogen dioxide - Temperature and light induced effects

NASA Astrophysics Data System (ADS)

Givan, A.; Loewenschuss, A.

1990-12-01

Raman spectra of zero-pressure-formed N2O4 solid layers are reported. Sample composition is extremely dependent upon deposition conditions. For ordered and pure solid N2O4(D2h), produced by slow NO2 deposition, temperature cycling over the range in which the solid is stable shows no significant spectral changes and does not result in autoionization, as argued in a previous Raman study. Fast and low temperature deposited layers are amorphous and multicomponent, showing bands of disordered and isomeric molecular N2O4 and of ionic NO + NO3, nitrosonium nitrate. For nitrosonium nitrate, three solid modifications can be characterized spectroscopically. In the amorphous phase, a light induced, temperature dependent, reversible transition between molecular and ionic nitrogen tetroxide is observed below 150 K. The paths leading to nitrosonium nitrate formation are examined.

A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin.

PubMed

Borin, Veniamin A; Wiebeler, Christian; Schapiro, Igor

2018-04-17

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

The detection of conformational disorder by thermal analysis

NASA Astrophysics Data System (ADS)

Wunderlich, B.

Conformational disorder in crystals is found in many molecules that possess a plurality of conformational isomers. Typical examples are linear macromolecules such as polyethylene, polytetrafluoroethylene and trans-1,4-polybutadiene; and small molecules such as paraffins, cycloparaffins, soaps, lipids and many liquid-crystal forming molecules. Conformational motion is often coupled with the cooperative creation of disorder. In this case a heat and entropy of transition is observed by thermal analysis. Levels of transition entropies can be estimated, assuming most of the disorder can be traced to conformational isomerism. In case there is conformational disorder frozen-in at low temperature, thermal analysis can be used to find the glass transition of a condis crystal. An Advanced Thermal Analysis System has been developed, and will be described that permits a detailed interpretation of the thermal analysis traces. It rests with the establishment of high quality heat capacity for the rigid solid state (vibration only) and the mobile liquid state (vibrations and large amplitude cooperative motion).

The detection of conformational disorder by thermal analysis

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

Wunderlich, B.

1988-01-01

Conformational disorder in crystals is found in many molecules that possess a plurality of conformational isomers. Typical examples are linear macromolecules such as polyethylene, polytetrafluoroethylene and trans-1,4-polybutadiene; and small molecules such as paraffins, cycloparaffins, soaps, lipids and many liquid-crystal forming molecules. Conformational motion is often coupled with the cooperative creation of disorder. In this case a heat and entropy of transition is observed by thermal analysis. Levels of transition entropies can be estimated, assuming most of the disorder can be traced to conformational isomerism. In case there is conformational disorder frozen-in at low temperature, thermal analysis can be used tomore » find the glass transition of a condis crystal. An Advanced Thermal Analysis System has been developed, and will be described that permits a detailed interpretation of the thermal analysis traces. It rests with the establishment of high quality heat capacity for the rigid solid state (vibration only) and the mobile liquid state (vibrations and large amplitude cooperative motion). 36 refs., 3 figs.« less

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

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

Han, Huixian; School of Physics, Northwest University, Xi’an, Shaanxi 710069; Li, Anyang

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 upmore » 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.« less

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy.

PubMed

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P; Nguyen, Huong T H; Dang, Andy; Tureček, František

2018-01-16

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z 4 + H] +● fragment ion-radicals of the R-C ● H-CONH- type, initially formed by N-C α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [ ● DAAR + H] + isomers and used to assign structures to the action spectra. The potential energy surface of [ ● DAAR + H] + isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [ ● XAAR + H] + ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H] ● -ETD fragments containing Asp, Asn, Glu, and Gln residues. Graphical Abstract ᅟ.

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

NASA Astrophysics Data System (ADS)

Imaoka, Naruaki; Houferak, Camille; Murphy, Megan P.; Nguyen, Huong T. H.; Dang, Andy; Tureček, František

2018-01-01

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z4 + H]+● fragment ion-radicals of the R-C●H-CONH- type, initially formed by N-Cα bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [●DAAR + H]+ isomers and used to assign structures to the action spectra. The potential energy surface of [●DAAR + H]+ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [●XAAR + H]+ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone Cα positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]●-ETD fragments containing Asp, Asn, Glu, and Gln residues. [Figure not available: see fulltext.

Communication: Electronic flux induced by crossing the transition state

NASA Astrophysics Data System (ADS)

Jia, Dongming; Manz, Jörn; Yang, Yonggang

2018-01-01

We present a new effect of chemical reactions, e.g., isomerizations, that occurs when the reactants pass along the transition state, on the way to products. It is based on the well-known fact that at the transition state, the electronic structure of one isomer changes to the other. We discover that this switch of electronic structure causes a strong electronic flux that is well distinguishable from the usual flux of electrons that travel with the nuclei. As a simple but clear example, the effect is demonstrated here for bond length isomerization of Na2 (21Σu+), with adiabatic crossing the barrier between the inner and outer wells of the double minimum potential that support different "Rydberg" and "ionic" type electronic structures, respectively.

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

Sun, Jiangman; Dong, Xiao; Wang, Yajie

Geometric isomerism in polyacetylene is a basic concept in chemistry textbooks. Polymerization to cis-isomer is kinetically preferred at low temperature, not only in the classic catalytic reaction in solution but also, unexpectedly, in the crystalline phase when it is driven by external pressure without a catalyst. Until now, no perfect reaction route has been proposed for this pressure-induced polymerization. Using in situ neutron diffraction and meta-dynamic simulation, we discovered that under high pressure, acetylene molecules react along a specific crystallographic direction that is perpendicular to those previously proposed. Moreover, following this route produces a pure cis-isomer and more surprisingly, predictsmore » that graphane is the final product. Experimentally, polycyclic polymers with a layered structure were identified in the recovered product by solid-state nuclear magnetic resonance and neutron pair distribution functions, which indicates the possibility of synthesizing graphane under high pressure.« less

Evolution of nuclear structure in neutron-rich odd-Zn isotopes and isomers

NASA Astrophysics Data System (ADS)

Wraith, C.; Yang, X. F.; Xie, L.; Babcock, C.; Bieroń, J.; Billowes, J.; Bissell, M. L.; Blaum, K.; Cheal, B.; Filippin, L.; Garcia Ruiz, R. F.; Gins, W.; Grob, L. K.; Gaigalas, G.; Godefroid, M.; Gorges, C.; Heylen, H.; Honma, M.; Jönsson, P.; Kaufmann, S.; Kowalska, M.; Krämer, J.; Malbrunot-Ettenauer, S.; Neugart, R.; Neyens, G.; Nörtershäuser, W.; Nowacki, F.; Otsuka, T.; Papuga, J.; Sánchez, R.; Tsunoda, Y.; Yordanov, D. T.

2017-08-01

Collinear laser spectroscopy was performed on Zn (Z = 30) isotopes at ISOLDE, CERN. The study of hyperfine spectra of nuclei across the Zn isotopic chain, N = 33- 49, allowed the measurement of nuclear spins for the ground and isomeric states in odd-A neutron-rich nuclei up to N = 50. Exactly one long-lived (>10 ms) isomeric state has been established in each 69-79Zn isotope. The nuclear magnetic dipole moments and spectroscopic quadrupole moments are well reproduced by large-scale shell-model calculations in the f5pg9 and fpg9d5 model spaces, thus establishing the dominant term in their wave function. The magnetic moment of the intruder Iπ = 1 /2+ isomer in 79Zn is reproduced only if the νs1/2 orbital is added to the valence space, as realized in the recently developed PFSDG-U interaction. The spin and moments of the low-lying isomeric state in 73Zn suggest a strong onset of deformation at N = 43, while the progression towards 79Zn points to the stability of the Z = 28 and N = 50 shell gaps, supporting the magicity of 78Ni.

Improved measurement of the half-life of the J π = 8 - nuclear isomer 152m2 Eu

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

Humby, Peter; Simon, Anna; Beausang, C. W.

2015-02-23

The standard γ-ray energy calibration source 152Eu is well known based on the 13.5 y decay of its ground state. Nevertheless, in addition to this decay 152Eu also has two relatively long-lived isomeric states: a 9 h J π=0 - state at E *=46 keV and a 96 min J π=8 - state at E *=148 keV. Here we report a new measurement of the half-lives of both of these isomeric states. Excited states in 152Eu were populated following the 154Sm (p,3n) reaction using a 25 MeV proton beam from the K-150 cyclotron at the Cyclotron Institute of Texas A&Mmore » University. Post irradiation, γ rays from the de-excitation of the long lived isomeric states were measured using the six BGO shielded high-purity germanium (HPGe) clover detectors that are part of the STARLiTeR array. The half-life of the J π=8 - isomer 152m2Eu was obtained by measuring the decrease in intensity of the 90 keV γ ray from the cascade to the ground state. The half-life of this state was measured to be 95.8(4) min which is in agreement with and significantly more precise than the previously measured value of 96(1) min. In a manner similar to the ground state the second long-lived isomer 151m1Eu, the J π=0 - state at 46 keV, β decays to excited states in 152Gd and 152Sm. Also, the half-life of this state was measured to be 9.39(7) h using five γ-ray transitions.« less

Molecular isomerization induced by ultrashort infrared pulses. I. Few-cycle to sub-one-cycle Gaussian pulses and the role of the carrier-envelope phase.

PubMed

Uiberacker, Christoph; Jakubetz, Werner

2004-06-22

Using 550 previously calculated vibrational energy levels and dipole moments we performed simulations of the HCN-->HNC isomerization dynamics induced by sub-one-cycle and few-cycle IR pulses, which we represent as Gaussian pulses with 0.25-2 optical cycles in the pulse width. Starting from vibrationally pre-excited states, isomerization probabilities of up to 50% are obtained for optimized pulses. With decreasing number of optical cycles a strong dependence on the carrier-envelope phase (CEP) emerges. Although the optimized pulse parameters change significantly with the number of optical cycles, the distortion by the Gaussian envelope produces nearly equal fields, with a positive lobe followed by a negative one. The positions and areas of the lobes are also almost unchanged, irrespective of the number of cycles in the half-width. Isomerization proceeds via a pump-dumplike mechanism induced by the sequential lobes. The first lobe prepares a wave packet incorporating many delocalized states above the barrier. It is the motion of this wave packet across the barrier, which determines the timing of the pump and dump lobes. The role of the pulse parameters, and in particular of the CEP, is to produce the correct lobe sequence, size and timing within a continuous pulse. (c) 2004 American Institute of Physics.

Cyclohexane isomerization. Unimolecular dynamics of the twist-boat intermediate.

PubMed

Kakhiani, Khatuna; Lourderaj, Upakarasamy; Hu, Wenfang; Birney, David; Hase, William L

2009-04-23

Direct dynamics simulations were performed at the HF/6-31G level of theory to investigate the intramolecular and unimolecuar dynamics of the twist-boat (TB) intermediate on the cyclohexane potential energy surface (PES). Additional calculations were performed at the MP2/aug-cc-pVDZ level of theory to further characterize the PES's stationary points. The trajectories were initiated at the C(1) and C(2) half-chair transition states (TSs) connecting a chair conformer with a TB intermediate, via an intrinsic reaction coordinate (IRC). Energy was added in accord with a microcanonical ensemble at the average energy for experiments at 263 K. Important nontransition state theory (TST), non-IRC, and non-RRKM dynamics were observed in the simulations. Trajectories initially directed toward the chair conformer had a high probability of recrossing the TS, with approximately 30% forming a TB intermediate instead of accessing the potential energy well for the conformer. The TB intermediate initially formed was not necessarily the one connected to the TS via the IRC. Of the trajectories initiated at the C(2) half-chair TS and initially directed toward the chair conformer, 35% formed a TB intermediate instead of the chair conformer. Also, of the trajectories forming a TB intermediate, only 16% formed the TB intermediate connected with the C(2) TS via the IRC. Up to eight consecutive TB --> TB isomerizations were followed, and non-RRKM behavior was observed in their dynamics. A TB can isomerize to two different TBs, one by a clockwise rotation of C-C-C-C dihedral angles and the other by a counterclockwise rotation. In contrast to RRKM theory, which predicts equivalent probabilities for these rotations, the trajectory dynamics show they are not equivalent and depend on whether the C(1) or C(2) half-chair TS is initially excited. Non-RRKM dynamics is also observed in the isomerization of the TB intermediates to the chair conformers. RRKM theory assumes equivalent probabilities for isomerizing to the two chair conformers. In contrast, for the first and following TB intermediate formed, there is a preference to isomerize to the chair conformer connected to the TS at which the trajectories were initiated. For the first TB intermediate formed, approximately 30% of the isomerization is to a chair conformer, but this fraction decreases for the later formed TB intermediates and becomes approximately 10% for the eighth consecutive TB intermediate formed.

Configurations and decay hindrances of high- K states in Hf 180

DOE PAGES

Tandel, S. K.; Chowdhury, P.; Kondev, F. G.; ...

2016-12-02

Multi-quasiparticle high-K states, several of which are isomeric, were observed in Hf-180 with the Gammasphere array. We determined the lifetimes in the ns-μs range using centroid-shift and decay measurements within a mu s coincidence time window. The configurations of high-K states involve two and four quasiparticles, with states up to K π = (18 -) established. High-K excitations are found to be progressively more favored with increasing excitation energy. The K quantum number is quite robust up to the highest spins observed, as evidenced by the large values of the reduced hindrance for isomeric decays. Furthermore, rotational bands built onmore » three high-K states are identified, and the measured branching ratios in these sequences enable the assignment of underlying configurations. Multi-quasiparticle calculations using the Lipkin-Nogami approach for pairing, with blocking included, reproduce the observed high-K energies quite well.« less

Configurations and decay hindrances of high-K states in 180Hf

NASA Astrophysics Data System (ADS)

Tandel, S. K.; Chowdhury, P.; Kondev, F. G.; Janssens, R. V. F.; Khoo, T. L.; Carpenter, M. P.; Lauritsen, T.; Lister, C. J.; Seweryniak, D.; Zhu, S.; Deacon, A.; Freeman, S. J.; Hammond, N. J.; Jones, G. D.; Moore, E. F.; Smith, J. F.

2016-12-01

Multi-quasiparticle high-K states, several of which are isomeric, were observed in 180Hf with the Gammasphere array. Lifetimes in the ns-μ s range were determined using centroid-shift and decay measurements within a μ s coincidence time window. The configurations of high-K states involve two and four quasiparticles, with states up to Kπ=(18-) established. High-K excitations are found to be progressively more favored with increasing excitation energy. The K quantum number is quite robust up to the highest spins observed, as evidenced by the large values of the reduced hindrance for isomeric decays. Rotational bands built on three high-K states are identified, and the measured branching ratios in these sequences enable the assignment of underlying configurations. Multi-quasiparticle calculations using the Lipkin-Nogami approach for pairing, with blocking included, reproduce the observed high-K energies quite well.

Configurations and decay hindrances of high- K states in Hf 180

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

Tandel, S. K.; Chowdhury, P.; Kondev, F. G.

Multi-quasiparticle high-K states, several of which are isomeric, were observed in Hf-180 with the Gammasphere array. We determined the lifetimes in the ns-μs range using centroid-shift and decay measurements within a mu s coincidence time window. The configurations of high-K states involve two and four quasiparticles, with states up to K π = (18 -) established. High-K excitations are found to be progressively more favored with increasing excitation energy. The K quantum number is quite robust up to the highest spins observed, as evidenced by the large values of the reduced hindrance for isomeric decays. Furthermore, rotational bands built onmore » three high-K states are identified, and the measured branching ratios in these sequences enable the assignment of underlying configurations. Multi-quasiparticle calculations using the Lipkin-Nogami approach for pairing, with blocking included, reproduce the observed high-K energies quite well.« less

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.

Photodissociation dynamics of nitromethane and methyl nitrite by infrared multiphoton dissociation imaging with quasiclassical trajectory calculations: signatures of the roaming pathway.

PubMed

Dey, Arghya; Fernando, Ravin; Abeysekera, Chamara; Homayoon, Zahra; Bowman, Joel M; Suits, Arthur G

2014-02-07

We combine the techniques of infrared multiphoton dissociation (IRMPD) with state selective ion imaging to probe roaming dynamics in the unimolecular dissociation of nitromethane and methyl nitrite. Recent theoretical calculations suggest a "roaming-mediated isomerization" pathway of nitromethane to methyl nitrite prior to decomposition. State-resolved imaging of the NO product coupled with infrared multiphoton dissociation was carried out to examine this unimolecular decomposition near threshold. The IRMPD images for the NO product from nitromethane are consistent with the earlier IRMPD studies that first suggested the importance of an isomerization pathway. A significant Λ-doublet propensity is seen in nitromethane IRMPD but not methyl nitrite. The experimental observations are augmented by quasiclassical trajectory calculations for nitromethane and methyl nitrite near threshold for each dissociation pathway. The observation of distinct methoxy vibrational excitation for trajectories from nitromethane and methyl nitrite dissociation at the same total energy show that the nitromethane dissociation bears a nonstatistical signature of the roaming isomerization pathway, and this is possibly responsible for the nitromethane Λ-doublet propensity as well.

Role of the Δ Resonance in the Population of a Four-Nucleon State in the 56Fe → 54Fe Reaction at Relativistic Energies

NASA Astrophysics Data System (ADS)

Podolyák, Zs.; Shand, C. M.; Lalović, N.; Gerl, J.; Rudolph, D.; Alexander, T.; Boutachkov, P.; Cortés, M. L.; Górska, M.; Kojouharov, I.; Kurz, N.; Louchart, C.; Merchán, E.; Michelagnoli, C.; Pérez-Vidal, R. M.; Pietri, S.; Ralet, D.; Reese, M.; Schaffner, H.; Stahl, Ch.; Weick, H.; Ameil, F.; de Angelis, G.; Arici, T.; Carroll, R.; Dombrádi, Zs.; Gadea, A.; Golubev, P.; Lettmann, M.; Lizarazo, C.; Mahboub, D.; Pai, H.; Patel, Z.; Pietralla, N.; Regan, P. H.; Sarmiento, L. G.; Wieland, O.; Wilson, E.; Birkenbach, B.; Bruyneel, B.; Burrows, I.; Charles, L.; Clément, E.; Crespi, F. C. L.; Cullen, D. M.; Désesquelles, P.; Eberth, J.; González, V.; Habermann, T.; Harkness-Brennan, L.; Hess, H.; Judson, D. S.; Jungclaus, A.; Korten, W.; Labiche, M.; Maj, A.; Mengoni, D.; Napoli, D. R.; Pullia, A.; Quintana, B.; Rainovski, G.; Reiter, P.; Salsac, M. D.; Sanchis, E.; Valiente Dóbon, J. J.

2016-11-01

The 54Fe nucleus was populated from a 56Fe beam impinging on a Be target with an energy of E /A =500 MeV . The internal decay via γ -ray emission of the 10+ metastable state was observed. As the structure of this isomeric state has to involve at least four unpaired nucleons, it cannot be populated in a simple two-neutron removal reaction from the 56Fe ground state. The isomeric state was produced in the low-momentum (-energy) tail of the parallel momentum (energy) distribution of 54Fe, suggesting that it was populated via the decay of the Δ0 resonance into a proton. This process allows the population of four-nucleon states, such as the observed isomer. Therefore, it is concluded that the observation of this 10+ metastable state in 54Fe is a consequence of the quark structure of the nucleons.

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.

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

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

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

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 excitedmore » 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.« less

Photoisomers of Azobenzene Star with a Flat Core: Theoretical Insights into Multiple States from DFT and MD Perspective.

PubMed

Koch, Markus; Saphiannikova, Marina; Santer, Svetlana; Guskova, Olga

2017-09-21

This study focuses on comparing physical properties of photoisomers of an azobenzene star with benzene-1,3,5-tricarboxamide core. Three azobenzene arms of the molecule undergo a reversible trans-cis isomerization upon UV-vis light illumination giving rise to multiple states from the planar all-trans one, via two mixed states to the kinked all-cis isomer. Employing density functional theory, we characterize the structural and photophysical properties of each state indicating a role the planar core plays in the coupling between azobenzene chromophores. To characterize the light-triggered switching of solvophilicity/solvophobicity of the star, the difference in solvation free energy is calculated for the transfer of an azobenzene star from its gas phase to implicit or explicit solvents. For the latter case, classical all-atom molecular dynamics simulations of aqueous solutions of azobenzene star are performed employing the polymer consistent force field to shed light on the thermodynamics of explicit hydration as a function of the isomerization state and on the structuring of water around the star. From the analysis of two contributions to the free energy of hydration, the nonpolar van der Waals and the electrostatic terms, it is concluded that isomerization specificity largely determines the polarity of the molecule and the solute-solvent electrostatic interactions. This convertible hydrophilicity/hydrophobicity together with readjustable occupied volume and the surface area accessible to water, affects the self-assembly/disassembly of the azobenzene star with a flat core triggered by light.

Manifestation of the structure of heavy nuclei in their alpha decays

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

Adamian, G. G., E-mail: adamian@theor.jinr.ru; Antonenko, N. V.; Bezbakh, A. N.

2016-11-15

Low-lying one- and two-quasiparticle states of heavy nuclei are predicted. Alpha-decay chains, including those that proceed through isomeric states, are examined on the basis of the predicted properties of superheavy nuclei.

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.

PubMed

Nogly, Przemyslaw; Weinert, Tobias; James, Daniel; Carbajo, Sergio; Ozerov, Dmitry; Furrer, Antonia; Gashi, Dardan; Borin, Veniamin; Skopintsev, Petr; Jaeger, Kathrin; Nass, Karol; Båth, Petra; Bosman, Robert; Koglin, Jason; Seaberg, Matthew; Lane, Thomas; Kekilli, Demet; Brünle, Steffen; Tanaka, Tomoyuki; Wu, Wenting; Milne, Christopher; White, Thomas; Barty, Anton; Weierstall, Uwe; Panneels, Valerie; Nango, Eriko; Iwata, So; Hunter, Mark; Schapiro, Igor; Schertler, Gebhard; Neutze, Richard; Standfuss, Jörg

2018-06-14

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion-transport across bacterial membranes. We studied the sub-picosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin using an x-ray laser. A series of structural snapshots with near-atomic spatial and temporal resolution in the femtosecond regime show how the excited all- trans retinal samples conformational states within the protein binding pocket prior to passing through a twisted geometry and emerging in the 13 -cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key ingredient for this stereo-selective and efficient photochemical reaction. Copyright © 2018, American Association for the Advancement of Science.

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.

Molecular dynamics simulations of cis-trans isomerization for a proline-containing tripeptide in solution

NASA Astrophysics Data System (ADS)

Wan, Shun Zhou; Wang, Cun Xin; Xu, Ying Wu; Shi, Yun Yu

1996-11-01

The cis-trans isomerization of X-Pro (X is Pro or any other residue) often plays a rate-limiting role in protein folding. In order to study the dynamic properties of X-Pro in water, we have analyzed the trajectory data obtained from constrained molecular dynamics (MD) simulations of a tripeptide Phe-Pro-Ala in solution. Via calculation of autocorrelation functions and their corresponding spectral densities, we have found that the structural fluctuations of the solute are affected by the motions of various degrees of freedom, and the solvent dynamic behavior is bimodal rather than exponential or Gaussian. In addition, according to the energy and torque analysis, we suggest that both the anti/endo and the syn/endo could be the possible transition state for the cis-trans isomerization of the tripeptide.

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.

Inter-Fullerene Electronic Coupling Controls the Efficiency of Photoinduced Charge Generation in Organic Bulk Heterojunctions

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

Larson, Bryon W.; Reid, Obadiah G.; Coffey, David C.

2016-09-26

Photoinduced charge generation (PCG) dynamics are notoriously difficult to correlate with specific molecular properties in device relevant polymer:fullerene organic photovoltaic blend films due to the highly complex nature of the solid state blend morphology. Here, this study uses six judiciously selected trifluoromethylfullerenes blended with the prototypical polymer poly(3-hexylthiophene) and measure the PCG dynamics in 50 fs-500 ns time scales with time-resolved microwave conductivity and femtosecond transient absorption spectroscopy. The isomeric purity and thorough chemical characterization of the fullerenes used in this study allow for a detailed correlation between molecular properties, driving force, local intermolecular electronic coupling and, ultimately, the efficiencymore » of PCG yield. The findings show that the molecular design of the fullerene not only determines inter-fullerene electronic coupling, but also influences the decay dynamics of free holes in the donor phase even when the polymer microstructure remains unchanged.« less

Pressure-induced polymerization of acetylene: Structure-directed stereoselectivity and a possible route to graphane

DOE PAGES

Sun, Jiangman; Dong, Xiao; Wang, Yajie; ...

2017-05-02

Geometric isomerism in polyacetylene is a basic concept in chemistry textbooks. Polymerization to cis-isomer is kinetically preferred at low temperature, not only in the classic catalytic reaction in solution but also, unexpectedly, in the crystalline phase when it is driven by external pressure without a catalyst. Until now, no perfect reaction route has been proposed for this pressure-induced polymerization. Using in situ neutron diffraction and meta-dynamic simulation, we discovered that under high pressure, acetylene molecules react along a specific crystallographic direction that is perpendicular to those previously proposed. Moreover, following this route produces a pure cis-isomer and more surprisingly, predictsmore » that graphane is the final product. Experimentally, polycyclic polymers with a layered structure were identified in the recovered product by solid-state nuclear magnetic resonance and neutron pair distribution functions, which indicates the possibility of synthesizing graphane under high pressure.« less

Dehydrogenation of n-Alkanes by Solid-Phase Molecular Pincer-Iridium Catalysts. High Yields of α-Olefin Product.

PubMed

Kumar, Akshai; Zhou, Tian; Emge, Thomas J; Mironov, Oleg; Saxton, Robert J; Krogh-Jespersen, Karsten; Goldman, Alan S

2015-08-12

We report the transfer-dehydrogenation of gas-phase alkanes catalyzed by solid-phase, molecular, pincer-ligated iridium catalysts, using ethylene or propene as hydrogen acceptor. Iridium complexes of sterically unhindered pincer ligands such as (iPr4)PCP, in the solid phase, are found to give extremely high rates and turnover numbers for n-alkane dehydrogenation, and yields of terminal dehydrogenation product (α-olefin) that are much higher than those previously reported for solution-phase experiments. These results are explained by mechanistic studies and DFT calculations which jointly lead to the conclusion that olefin isomerization, which limits yields of α-olefin from pincer-Ir catalyzed alkane dehydrogenation, proceeds via two mechanistically distinct pathways in the case of ((iPr4)PCP)Ir. The more conventional pathway involves 2,1-insertion of the α-olefin into an Ir-H bond of ((iPr4)PCP)IrH2, followed by 3,2-β-H elimination. The use of ethylene as hydrogen acceptor, or high pressures of propene, precludes this pathway by rapid hydrogenation of these small olefins by the dihydride. The second isomerization pathway proceeds via α-olefin C-H addition to (pincer)Ir to give an allyl intermediate as was previously reported for ((tBu4)PCP)Ir. The improved understanding of the factors controlling rates and selectivity has led to solution-phase systems that afford improved yields of α-olefin, and provides a framework required for the future development of more active and selective catalytic systems.

Photoinduced electron-transfer in perylenediimide triphenylamine-based dendrimers: single photon timing and femtosecond transient absorption spectroscopy.

PubMed

Fron, Eduard; Pilot, Roberto; Schweitzer, Gerd; Qu, Jianqiang; Herrmann, Andreas; Müllen, Klaus; Hofkens, Johan; Van der Auweraer, Mark; De Schryver, Frans C

2008-05-01

The excited state dynamics of two generations perylenediimide chromophores substituted in the bay area with dendritic branches bearing triphenylamine units as well as those of the respective reference compounds are investigated. Using single photon timing and multi-pulse femtosecond transient absorption experiments a direct proof of a reversible charge transfer occurring from the peripheral triphenylamine to the electron acceptor perylenediimide core is revealed. Femtosecond pump-dump-probe experiments provide evidence for the ground state dynamics by populating excited vibronic levels. It is found by the means of both techniques that the rotational isomerization of the dendritic branches occurs on a time scale that ranges up to 1 ns. This time scale of the isomerization depends on the size of the dendritic arms and is similar both in the ground and excited state.

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

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

Schrauben, Joel N.; Akdag, Akin; Wen, Jin

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.

An automated exploration of the isomerization and dissociation pathways of (E)-1,2-dichloroethene cations and anions

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Nishi, Yuito

2017-04-01

Isomerization and dissociation pathways after the photoionization or electron attachment of (E)-1,2-dichloroethene were calculated with an automated exploration method utilizing a scaled hypersphere search of the anharmonic downward distortion following algorithm at the UB3LYP/6-311G(2d,d,p) level of theory. The potential energies of transition states and dissociation channels were calculated by a composite method ((RO)CBS-QB3) and compared with the breakdown diagrams and electron attachment spectra observed in previous spectroscopic studies. The results of single point calculations with several DFT and post-SCF methods are compared using the root mean square deviations from the (RO)CBS-QB3 energies for six states of anionic dichloroethene.

β-γ and isomeric decay spectroscopy of 168Dy

NASA Astrophysics Data System (ADS)

Zhang, G. X.; Watanabe, H.; Kondev, F. G.; Lane, G. J.; Regan, P. H.; Söderström, P.-A.; Walker, P. M.; Kanaoka, H.; Korkulu, Z.; Lee, P. S.; Liu, J. J.; Nishimura, S.; Wu, J.; Yagi, A.; Ahn, D. S.; Alharbi, T.; Baba, H.; Browne, F.; Bruce, A. M.; Carroll, R. J.; Chae, K. Y.; Dombradi, Zs.; Doornenbal, P.; Estrade, A.; Fukuda, N.; Griffin, C.; Ideguchi, E.; Inabe, N.; Isobe, T.; Kanaya, S.; Kojouharov, I.; Kubo, T.; Kubono, S.; Kurz, N.; Kuti, I.; Lalkovski, S.; Lee, C. S.; Lee, E. J.; Lorusso, G.; Lotay, G.; Moon, C.-B.; Nishizuka, I.; Nita, C. R.; Odahara, A.; Patel, Z.; Phong, V. H.; Podolyák, Zs.; Roberts, O. J.; Sakurai, H.; Schaffner, H.; Shand, C. M.; Shimizu, Y.; Sumikama, T.; Suzuki, H.; Takeda, H.; Terashima, S.; Vajta, Zs.; Valiente-Dóbon, J. J.; Xu, Z. Y.

2018-05-01

This contribution will report on the experimental work on the level structure of 168Dy. The experimental data have been taken as part of the EURICA decay spectroscopy campaign at RIBF, RIKEN in November 2014. In the experiment, a 238U primary beam is accelerated up to 345 MeV/u with an average intensity of 12 pnA. The nuclei of interest are produced by in-flight fission of 238U impinging on Be target with a thickness of 5 mm. The excited states of 168Dy have been populated through the decay from a newly identified isomeric state and via the β decay from 168Tb. In this contribution, scientific motivations, experimental procedure and some preliminary results for this study are presented.

Saddle point localization of molecular wavefunctions.

PubMed

Mellau, Georg Ch; Kyuberis, Alexandra A; Polyansky, Oleg L; Zobov, Nikolai; Field, Robert W

2016-09-15

The quantum mechanical description of isomerization is based on bound eigenstates of the molecular potential energy surface. For the near-minimum regions there is a textbook-based relationship between the potential and eigenenergies. Here we show how the saddle point region that connects the two minima is encoded in the eigenstates of the model quartic potential and in the energy levels of the [H, C, N] potential energy surface. We model the spacing of the eigenenergies with the energy dependent classical oscillation frequency decreasing to zero at the saddle point. The eigenstates with the smallest spacing are localized at the saddle point. The analysis of the HCN ↔ HNC isomerization states shows that the eigenstates with small energy spacing relative to the effective (v1, v3, ℓ) bending potentials are highly localized in the bending coordinate at the transition state. These spectroscopically detectable states represent a chemical marker of the transition state in the eigenenergy spectrum. The method developed here provides a basis for modeling characteristic patterns in the eigenenergy spectrum of bound states.

The origin of absorptive features in the two-dimensional electronic spectra of rhodopsin.

PubMed

Farag, Marwa H; Jansen, Thomas L C; Knoester, Jasper

2018-05-09

In rhodopsin, the absorption of a photon causes the isomerization of the 11-cis isomer of the retinal chromophore to its all-trans isomer. This isomerization is known to occur through a conical intersection (CI) and the internal conversion through the CI is known to be vibrationally coherent. Recently measured two-dimensional electronic spectra (2DES) showed dramatic absorptive spectral features at early waiting times associated with the transition through the CI. The common two-state two-mode model Hamiltonian was unable to elucidate the origin of these features. To rationalize the source of these features, we employ a three-state three-mode model Hamiltonian where the hydrogen out-of plane (HOOP) mode and a higher-lying electronic state are included. The 2DES of the retinal chromophore in rhodopsin are calculated and compared with the experiment. Our analysis shows that the source of the observed features in the measured 2DES is the excited state absorption to a higher-lying electronic state and not the HOOP mode.

High-seniority states in spherical nuclei: Triple pair breaking in tin isotopes

NASA Astrophysics Data System (ADS)

Astier, Alain

2013-03-01

The 119-126Sn nuclei have been produced as fission fragments in two reactions induced by heavy ions: 12C+238U at 90 MeV bombarding energy, 18O+208Pb at 85 MeV. Their level schemes have been built from gamma rays detected using the Euroball array. High-spin states located above the long-lived isomeric states of the even- A and odd-A 120-126Sn nuclei have been identified. Moreover isomeric states lying around 4.5 MeV have been established in the even-A 120-126Sn from the delayed coincidences between the fission fragment detector SAPhIR and the Euroball array. All the states located above 3-MeV excitation energy are ascribed to several broken pairs of neutrons occupying the h11/2 orbit. The maximum value of angular momentum available in such a high-j shell, i.e. for mid-occupation and the breaking of the three neutron pairs (seniority v=6), has been identified.

Cyclam Derivatives with a Bis(phosphinate) or a Phosphinato-Phosphonate Pendant Arm: Ligands for Fast and Efficient Copper(II) Complexation for Nuclear Medical Applications.

PubMed

David, Tomáš; Kubíček, Vojtěch; Gutten, Ondrej; Lubal, Přemysl; Kotek, Jan; Pietzsch, Hans-Jürgen; Rulíšek, Lubomír; Hermann, Petr

2015-12-21

Cyclam derivatives bearing one geminal bis(phosphinic acid), -CH2PO2HCH2PO2H2 (H2L(1)), or phosphinic-phosphonic acid, -CH2PO2HCH2PO3H2 (H3L(2)), pendant arm were synthesized and studied as potential copper(II) chelators for nuclear medical applications. The ligands showed good selectivity for copper(II) over zinc(II) and nickel(II) ions (log KCuL = 25.8 and 27.7 for H2L(1) and H3L(2), respectively). Kinetic study revealed an unusual three-step complex formation mechanism. The initial equilibrium step leads to out-of-cage complexes with Cu(2+) bound by the phosphorus-containing pendant arm. These species quickly rearrange to an in-cage complex with cyclam conformation II, which isomerizes to another in-cage complex with cyclam conformation I. The first in-cage complex is quantitatively formed in seconds (pH ≈5, 25 °C, Cu:L = 1:1, cM ≈ 1 mM). At pH >12, I isomers undergo nitrogen atom inversion, leading to III isomers; the structure of the III-[Cu(HL(2))] complex in the solid state was confirmed by X-ray diffraction analysis. In an alkaline solution, interconversion of the I and III isomers is mutual, leading to the same equilibrium isomeric mixture; such behavior has been observed here for the first time for copper(II) complexes of cyclam derivatives. Quantum-chemical calculations showed small energetic differences between the isomeric complexes of H3L(2) compared with analogous data for isomeric complexes of cyclam derivatives with one or two methylphosphonic acid pendant arm(s). Acid-assisted dissociation proved the kinetic inertness of the complexes. Preliminary radiolabeling of H2L(1) and H3L(2) with (64)Cu was fast and efficient, even at room temperature, giving specific activities of around 70 GBq of (64)Cu per 1 μmol of the ligand (pH 6.2, 10 min, ca. 90 equiv of the ligand). These specific activities were much higher than those of H3nota and H4dota complexes prepared under identical conditions. The rare combination of simple ligand synthesis, very fast copper(II) complex formation, high thermodynamic stability, kinetic inertness, efficient radiolabeling, and expected low bone tissue affinity makes such ligands suitably predisposed to serve as chelators of copper radioisotopes in nuclear medicine.

Photoionization and trans-to-cis isomerization of β-cyclodextrin-encapsulated azobenzene induced by two-color two-laser-pulse excitation.

PubMed

Takeshita, Tatsuya; Hara, Michihiro

2018-03-15

Azobenzene (1) and the complex resulting from the incorporation of 1 with cyclodextrin (1/CD) are attractive for light-driven applications such as micromachining and chemical biology tools. The highly sensitive photoresponse of 1 is crucial for light-driven applications containing both 1 and 1/CD to reach their full potential. In this study, we investigated the photoionization and trans-to-cis isomerization of 1/CD induced by one- and two-color two-laser pulse excitation. Photoionization of 1/CD, which was induced by stepwise two-photon absorption, was observed using laser pulse excitation at 266nm. Additionally, simultaneous irradiation with 266 and 532nm laser pulses increased the trans-to-cis isomerization yield (Υ t→c ) by 27%. It was concluded that the increase in Υ t→c was caused by the occurrence of trans-to-cis isomerization in the higher-energy singlet state (S n ), which was reached by S 1 →S n transition induced by laser pulse excitation at 532nm. The results of this study are potentially applicable in light-driven applications such as micromachining and chemical biology tools. Copyright © 2018 Elsevier B.V. All rights reserved.

CH 3NO 2 decomposition/isomerization mechanism and product branching ratios: An ab initio chemical kinetic study

NASA Astrophysics Data System (ADS)

Zhu, R. S.; Lin, M. C.

2009-08-01

The low-lying energy pathways for the decomposition/isomerization of nitromethane (NM) have been investigated using different molecular orbital methods. Our results show that in addition to the commonly known CH 3 + NO 2 products formed by direct C-N bond breaking and the trans-CH 3ONO formed by nitro-nitrite isomerization, NM can also isomerize to cis-CH 3ONO via a very loose transition state (TS) lying 59.2 kcal/mol above CH 3NO 2 or 0.6 kcal/mol below the CH 3 + NO 2 asymptote predicted at the UCCSD(T)/CBS level of theory. Kinetic results indicate that in the energy range of 59 ± 1 kcal/mol, production of CH 3O + NO is dominant, whereas above the C-N bond breaking threshold, the formation of CH 3 + NO 2 sharply increases and becomes dominant. The k( E) values predicted at different energies clearly indicate that CH 3O + NO could be detected in an infrared multi-photon dissociation study, whereas in UV dissociation experiments with energies high above the C-N bond breaking threshold the CH 3 + NO 2 products are generated predominantly.

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

PubMed Central

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

2009-01-01

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

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

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

Justino, Licínia L. G., E-mail: liciniaj@ci.uc.pt; Reva, Igor; Fausto, Rui

2016-07-07

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 N{sub 2},more » Xe, and Ar matrices were fully assigned. Finally, the UV-induced photochemistry of the matrix isolated compound was investigated.« less

Is isomerism a risk factor for intestinal volvulus?

PubMed

Landisch, Rachel M; Loomba, Rohit S; Salazar, Jose H; Buelow, Matthew W; Frommelt, Michele; Anderson, Robert H; Wagner, Amy J

2018-03-06

Isomerism, or heterotaxy syndrome, affects many organ systems anatomically and functionally. Intestinal malrotation is common in patients with isomerism. Despite a low reported risk of volvulus, some physicians perform routine screening and prophylactic Ladd procedures on asymptomatic patients with isomerism who are found to have intestinal malrotation. The primary aim of this study was to determine if isomerism is an independent risk factor for volvulus. Kid's Inpatient Database data from 1997 to 2012 was utilized for this study. Characteristics of admissions with and without isomerism were compared with a particular focus on intestinal malrotation, volvulus, and Ladd procedure. A logistic regression was conducted to determine independent risk factors for volvulus with respect to isomerism. 15,962,403 inpatient admissions were included in the analysis, of which 7970 (0.05%) patients had isomerism, and 6 patients (0.1%) developed volvulus. Isomerism was associated with a 52-fold increase in the odds of intestinal malrotation by univariate analysis. Of 251 with isomerism and intestinal malrotation, only 2.4% experienced volvulus. Logistic regression demonstrated that isomerism was not an independent risk factor for volvulus. Isomerism is associated with an increased risk of intestinal malrotation but is not an independent risk factor for volvulus. Prognosis study. Level III. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Communication: Light driven remote control of microgels' size in the presence of photosensitive surfactant: Complete phase diagram

NASA Astrophysics Data System (ADS)

Schimka, Selina; Gordievskaya, Yulia D.; Lomadze, Nino; Lehmann, Maren; von Klitzing, Regine; Rumyantsev, Artem M.; Kramarenko, Elena Yu.; Santer, Svetlana

2017-07-01

Here we report on a light triggered remote control of microgel size in the presence of photosensitive surfactant. The hydrophobic tail of the cationic surfactant contains azobenzene group that undergoes a reversible photo-isomerization reaction from a trans- to a cis-state accompanied by a change in the hydrophobicity of the surfactant. We have investigated light assisted behaviour and the complex formation of the microgels with azobenzene containing surfactant over the broad concentrational range starting far below and exceeding several times of the critical micelle concentration (CMC). At small surfactant concentration in solution (far below CMC), the surfactant in the trans-state accommodates within the microgel causing its compaction, while the cis-isomer desorbs out of microgel resulting in its swelling. The process of the microgel size change can be described as swelling on UV irradiation (trans-cis isomerization) and shrinking on irradiation with blue light (cis-trans isomerization). However, at the surfactant concentrations larger than CMC, the opposite behaviour is observed: the microgel swells on blue irradiation and shrinks during exposure to UV light. We explain this behaviour theoretically taking into account isomer dependent micellization of surfactant within the microgels.

Structural Properties and UV-Visible Absorption Spectroscopy of Retinal-pyridyl-CN Re(I) Carbonyl Bipyridine Complex: A Theoretical Study.

PubMed

Eng, Julien; Daniel, Chantal

2015-10-29

The structural, electronic, and optical properties of the all-trans and five cis conformers of [Re(CO)3(bpy)(ret-pyr-CN)](+) (bpy = 2,2'-bipyridine; ret-pyr-CN = pyridyl-CN-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-2-n)-none-(2,4,6,8-tetraen) were studied in solvent by means of density functional theory (DFT) and time-dependent DFT. The isolated retinal-like chromophore ret-pyr-CN was investigated as well for comparison. By coordination to the complex the two lowest intraligand (IL) states localized on the retinal group are slightly red-shifted from 627 to 690 nm and from 415 to 450 nm, respectively. Several isomerization pathways are open upon irradiation of the Re(I) complex by visible light (400-450 nm), especially to two cis conformers corresponding to the isomerization of the two double bonds of the retinal-like ligand close to the pyridyl group linked to the Re(I) fragment. The metal-to-ligand charge transfer states localized either on the retinal group or on the bpy ligand should play a minor role in the isomerization process itself but could improve its efficiency via ultra-fast intersystem crossing.

Changes in Atmospheric Butanes and Pentanes and Their Isomeric Ratios in the Continental United States

NASA Astrophysics Data System (ADS)

Rossabi, Sam; Helmig, Detlev

2018-04-01

Nonmethane hydrocarbons have been used as tracers in research on emissions and atmospheric oxidation chemistry. This research investigates source region mixing ratio trends of the nonmethane hydrocarbons i-butane, n-butane, i-pentane, and n-pentane, and the (i/n) isomeric ratios of these compounds between 2001 and 2015. Data collected at Photochemical Assessment Monitoring Stations, mandated by the U.S. Environmental Protection Agency in ozone nonattainment areas, and data collected at Global Greenhouse Gas Reference Network sites within the National Oceanic and Atmospheric Administration network, and analyzed at the Institute of Arctic and Alpine Research at the University of Colorado-Boulder, were examined. Among all considered species, linear regression analyses on concentration time series had negative slopes at 81% of sites, indicating predominantly declining butane and pentane atmospheric concentrations. Mostly negative slopes (78% of sites) were found for the (i/n) butane and pentane isomeric ratios, including all six and seven statistically significant (i/n) butane and pentane trends, respectively. Over the 15 year investigation period and averaged over all sites, total relative changes were 30 and 45% for the (i/n) ratios of butanes and pentanes, respectively, with a relative increase in the prominence of the n-isomers. Most likely causes include changing isomeric ratios in gasoline sector emissions, and increasing influence of oil and natural gas industry emissions. Changes in concentrations and isomeric ratios depend on proximity of contributing emission sources to measurement sites.

Sequential picosecond isomerizations in a photochromic ruthenium sulfoxide complex triggered by pump-repump-probe spectroscopy.

PubMed

King, Albert W; Jin, Yuhuan; Engle, James T; Ziegler, Christopher J; Rack, Jeffrey J

2013-02-18

The complex [Ru(bpy)(2)(bpSO)](PF(6))(2), where bpy is 2,2'-bipydine and bpSO is 1,2-bis(phenylsulfinyl)ethane, exhibits three distinct isomers which are accessible upon metal-to-ligand charge-transfer (MLCT) irradiation. This complex and its parent, [Ru(bpy)(2)(bpte)](PF(6))(2), where bpte is 1,2-bis(phenylthio)ethane, have been synthesized and characterized by UV-visible spectroscopy, NMR, X-ray crystallography, and femtosecond transient absorption spectroscopy. A novel method of 2-color Pump-Repump-Probe spectroscopy has been employed to investigate all three isomers of the bis-sulfoxide complex. This method allows for observation of the isomerization dynamics of sequential isomerizations of each sulfoxide from MLCT irradiation of the S,S-bonded complex to ultimately form the O,O-bonded metastable complex. One-dimensional (1-D) and two-dimensional (2-D) (COSY, NOESY, and TOCSY) (1)H NMR data show the thioether and ground state S,S-bonded sulfoxide complexes to be rigorously C(2) symmetric and are consistent with the crystal structures. Transient absorption spectroscopy reveals that the S,S to S,O isomerization occurs with an observed time constant of 56.8 (±7.4) ps. The S,O to O,O isomerization time constant was found to be 59 (±4) ps by pump-repump-probe spectroscopy. The composite S,S- to O,O-isomer quantum yield is 0.42.

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

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

Changala, P. Bryan; Baraban, Joshua H.; Field, Robert W., E-mail: rwfield@mit.edu

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 tunnelingmore » 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.« less

Low-lying isomeric states in Ga80 from the β- decay of Zn80

NASA Astrophysics Data System (ADS)

Licǎ, R.; Mǎrginean, N.; GhiÅ£ǎ, D. G.; Mach, H.; Fraile, L. M.; Simpson, G. S.; Aprahamian, A.; Bernards, C.; Briz, J. A.; Bucher, B.; Chiara, C. J.; Dlouhý, Z.; Gheorghe, I.; Hoff, P.; Jolie, J.; Köster, U.; Kurcewicz, W.; Mǎrginean, R.; Olaizola, B.; Paziy, V.; Régis, J. M.; Rudigier, M.; Sava, T.; Stǎnoiu, M.; Stroe, L.; Walters, W. B.

2014-07-01

A new level scheme of Ga80 has been determined. This nucleus was populated following the β- decay of Zn80 at ISOLDE, CERN. The proposed level scheme is significantly different compared to the previously reported one and contains 26 levels up to 3.4 MeV in excitation energy. The present study establishes that the previously identified 1.9-s β--decaying 6- isomer is the ground state of Ga80 and the 1.3-s β--decaying 3- isomer lies at an excitation energy of 22.4 keV. A new isomeric level was identified at 707.8 keV and its half-life was measured to be 18.3(5) ns, allowing the 685.4-keV transition de-exciting this state to be assigned an M2 multipolarity. The newly measured spectroscopic observables are compared with shell-model calculations using the jj44bpn and JUN45 interactions.

Rotational band on a three-quasineutron isomer in 127Xe

NASA Astrophysics Data System (ADS)

Chakraborty, S.; Sharma, H. P.; Tiwary, S. S.; Majumder, C.; Banerjee, P.; Ganguly, S.; Rai, S.; Pragati, Modi, Swati; Arumugam, P.; Mayank, Kumar, S.; Palit, R.; Kumar, A.; Bhattacharjee, S. S.; Singh, R. P.; Muralithar, S.

2018-05-01

Excited states in 127Xe were populated via 122Sn(9Be,4 n γ ) fusion-evaporation reaction at Ebeam=48 MeV. A rotational band above an isomeric state at 2730.3 keV has been established. Jπ=23 /2+ has been assigned unambiguously to the bandhead. Structural features, configuration, and reduced hindrance factor per degree of K -forbiddenness (fν) have been discussed in the context of neighboring nuclei. Half-lives of 7 /2+ (t1 /2=37 ±1 ns) and 23 /2+ (t1 /2=28 ±1 ns) isomeric states have also been estimated and found to be consistent with the earlier reported values. The experimentally observed energy levels of the rotational band have been reproduced successfully by theoretical calculations carried out using the modified particle rotor model (MPRM) with β2˜0.22 and 15∘≲γ ≲22∘ .

A DFT and structural investigation of the conformations of Fischer carbene complexes

NASA Astrophysics Data System (ADS)

Landman, Marilé

2015-09-01

A set of different Fischer carbene complexes of group VI and VII metals, with varied heteroatom and heteroaromatic substituents on the carbene carbon atom, was studied. Density functional theory as well as single crystal diffraction techniques were employed to investigated the most stable conformation of these complexes. The complexes studied, [M(CO)4L{C(X)Z}], with L = PPh3 or CO, X = ethoxy (-OCH2CH3) or amino (-NH2 or NHCy) substituents as the heteroatom carbene substituents, Z = 2-furyl (-C4H3O), 2-thienyl (-C4H3S), 2-(N-methyl)pyrrolyl (-C4H3NCH3) as the second carbene substituent had their substituents varied systematically to give all the possible conformations of these complexes. The conformations of the complexes, in particular the relative orientations of the heteroatoms in the molecule (syn vs. anti), E/Z isomerism in the aminocarbene complexes and cis/trans isomerism in the ligand substituted complexes as well as various combinations of these aspects, were studied. In general, it was found that the most stable conformation theoretically as well as in the solid state for most of the complexes preferred the syn conformation. The Z-isomer is generally preferred over the E isomer while the cis is more predominant than the trans isomer. Using DFT and NBO calculations, explanations for the preferred conformations were explored. It was concluded that both steric and electronic factors influence the conformations of the carbene complexes, with the extent of contribution of these two factors varying for each of the different carbene substituents.

Creation of second-order nonlinear optical effects by photoisomerization of polar azo dyes in polymeric films: theoretical study of steady-state and transient properties

NASA Astrophysics Data System (ADS)

Sekkat, Zouheir; Knoll, Wolfgang

1995-10-01

It was shown recently that the application of a dc field across a polymer film containing polar azo dye chromophores at a temperature far below that of its glass transition leads to an appreciable polar order when the azo dyes undergo cis \\left-right-double-arrow trans isomerization. We present a detailed theoretical study of this phenomenon based on the enhanced mobility of the azo chromophores during the isomerization process. The equations representing this phenomenological theory are solved by recurrence relations of Legendre polynomials, and both the steady state and the dynamics are investigated. Analytical expressions are derived for the photoinduced polar order and its related anisotropy for both cis and trans molecular distributions.

Isomeric N-Annulated Perylene Diimide Dimers for Organic Solar Cells.

PubMed

Ma, Zetong; Fu, Huiting; Meng, Dong; Jiang, Wei; Sun, Yanming; Wang, Zhaohui

2018-04-16

Two isomeric N-annulated perylene diimide dimers, namely, p-BDNP and m-BDNP were designed and synthesized via geometric tuning. The distinct molecular geometry and packing arrangements of isomers with almost identical optical and electrochemical properties rendered us an in-depth understanding of the molecular structure-aggregation state-photovoltaic performance relationship. Blended with the commercially available donor PCE-10, p-BDNP and m-BDNP showed distinct differences in photovoltaic performance with power conversion efficiencies (PCEs) of 5.01 % and 4.15 %, respectively. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

One-Pot Isomerization–Cross Metathesis–Reduction (ICMR) Synthesis of Lipophilic Tetrapeptides

PubMed Central

2015-01-01

An efficient, versatile and rapid method toward homologue series of lipophilic tetrapeptide derivatives (herein, the opioid peptides H-TIPP-OH and H-DIPP-OH) is reported. High atom economy and a minimal number of synthetic steps resulted from a one-pot tandem isomerization-cross metathesis-reduction sequence (ICMR), applicable both in solution and solid phase methodology. The broadly applicable synthesis proceeds with short reaction times and simple work-up, as illustrated in this work for alkylated opioid tetrapeptides. PMID:24906051

Nudat 2

Science.gov Websites

modes), gamma rays (energy, intensity, multipolarity, coinc.) Nuclear Wallet Cards Search Latest Ground NuDat 2.7 Levels and Gammas Search Ground and excited states (energy, T1/2, spin/parity, decay and isomeric states properties Decay Radiation Search Radiation type, energy, intensity and dose

Peralkynylated buta-1,2,3-trienes: exceptionally low rotational barriers of cumulenic C=C bonds in the range of those of peptide C--N bonds.

PubMed

Auffrant, Audrey; Jaun, Bernhard; Jarowski, Peter D; Houk, Kendall N; Diederich, François

2004-06-21

A variety of 1,1,4,4-tetraal kynylbutatrienes and 1,4-dialkynylbutatrienes was synthezized by dimerization of the corresponding gem-dibromoolefins. Both (1)H and (13)C NMR spectroscopy indicated that the di- and tetraalkynylated butatrienes are formed as a mixture of cis and trans isomers. Variable temperature NMR studies evidenced a facile cis-trans isomerization, thus preventing the separation of these isomers by gravity or high-performance liquid chromatography (HPLC). For 1,1,4,4-tetraalkynylbutatrienes, the activation barrier deltaG( not equal ) was measured by magnetization transfer to be around 20 kcal mol(-1), in the range of the barrier for internal rotation about a peptide bond. Unlike the tetraalkynylated [3]cumulenes, 1,4-dialkynylbutatrienes are more difficult to isomerize and could, in one case, be obtained isomerically pure. Based on experimental data, the rotational barrier DeltaG( not equal ) for 1,4-dialkynylbutatrienes is estimated to be around 25 kcal mol(-1). The hypothesis of a stabilizing effect of the four alkynyl substituents on the proposed but-2-yne-1,4-diyl singlet diradical transition state of this cis-trans isomerization is further supported by a computational study.

Thermal decay of rhodopsin: role of hydrogen bonds in thermal isomerization of 11-cis retinal in the binding site and hydrolysis of protonated Schiff base.

PubMed

Liu, Jian; Liu, Monica Yun; Nguyen, Jennifer B; Bhagat, Aditi; Mooney, Victoria; Yan, Elsa C Y

2009-07-01

Although thermal stability of the G protein-coupled receptor rhodopsin is directly related to its extremely low dark noise level and has recently generated considerable interest, the chemistry behind the thermal decay process of rhodopsin has remained unclear. Using UV-vis spectroscopy and HPLC analysis, we have demonstrated that the thermal decay of rhodopsin involves both hydrolysis of the protonated Schiff base and thermal isomerization of 11-cis to all-trans retinal. Examining the unfolding of rhodopsin by circular dichroism spectroscopy and measuring the rate of thermal isomerization of 11-cis retinal in solution, we conclude that the observed thermal isomerization of 11-cis to all-trans retinal happens when 11-cis retinal is in the binding pocket of rhodopsin. Furthermore, we demonstrate that solvent deuterium isotope effects are involved in the thermal decay process by decreasing the rates of thermal isomerization and hydrolysis, suggesting that the rate-determining step of these processes involves breaking hydrogen bonds. These results provide insight into understanding the critical role of an extensive hydrogen-bonding network on stabilizing the inactive state of rhodopsin and contribute to our current understanding of the low dark noise level of rhodopsin, which enables this specialized protein to function as an extremely sensitive biological light detector. Because similar hydrogen-bonding networks have also been suggested by structural analysis of two other GPCRs, beta1 and beta2 adrenergic receptors, our results could reveal a general role of hydrogen bonds in facilitating GPCR function.

CP/MAS 13C NMR characterization of the isomeric states and intermolecular packing in tris(8-hydroxyquinoline) aluminum(III) (Alq3).

PubMed

Kaji, Hironori; Kusaka, Yasunari; Onoyama, Goro; Horii, Fumitaka

2006-04-05

The isomeric states and intermolecular packing of tris(8-hydroxyquinoline) aluminum(III) (Alq(3)) in the alpha-, gamma-, and delta-crystalline forms and in the amorphous state, which are important for understanding the light-emitting and electron-transport properties, have been analyzed by CP/MAS (13)C NMR. This simple NMR experiment shows that the isomeric state of alpha- and amorphous Alq(3) is meridional, whereas that of gamma- and delta-Alq(3) is facial. In the amorphous Alq(3), the inclusion of facial isomers has been under debate. Our experiments show that meridional isomers are dominant in the amorphous Alq(3), although the existence of facial isomers cannot be completely denied. The local structure of amorphous Alq(3) is similar to that of alpha-Alq(3) and is significantly different from those of gamma- and delta-Alq(3). Among these Alq(3) samples, the effect of intermolecular interaction is not found only for gamma-Alq(3). This finding can explain the good solvent solubility of gamma-Alq(3), compared with the other crystalline forms. It is also shown that the structures are locally disordered not only for amorphous Alq(3) but also for alpha-Alq(3), although clear X-ray diffraction peaks are observed for alpha-Alq(3). In contrast, the local structures of gamma- and delta-Alq(3) are well defined. A clear relation is found between the spectral patterns of CP/MAS (13)C NMR and the fluorescence wavelengths; the samples, which consist of facial isomers, show blue-shifted fluorescence compared with those of meridionals.

Alpha B- and βA3-crystallins containing d-aspartic acids exist in a monomeric state.

PubMed

Sakaue, Hiroaki; Takata, Takumi; Fujii, Norihiko; Sasaki, Hiroshi; Fujii, Noriko

2015-01-01

Crystallin stability and subunit-subunit interaction are essential for eye lens transparency. There are three types of crystallins in lens, designated as α-, β-, and γ-crystallins. Alpha-crystallin is a hetero-polymer of about 800kDa, consisting of 35-40 subunits of two different αA- and αB-subunits, each of 20kDa. The β/γ-crystallin superfamily comprises oligomeric β-crystallin (2-6 subunits) and monomeric γ-crystallin. Since lens proteins have very long half-lives, they undergo numerous post-translational modifications including racemization, isomerization, deamidation, oxidation, glycation, and truncation, which may decrease crystallin solubility and ultimately cause cataract formation. Racemization and isomerization of aspartyl (Asp) residues have been detected only in polymeric α- and oligomeric β-crystallin, while the situation in monomeric γ-crystallin has not been studied. Here, we investigated the racemization and isomerization of Asp in the γ-crystallin fraction of elderly donors. The results show that Asp residues of γS-, γD- and γC-crystallins were not racemized and isomerized. However, strikingly, we found that a portion of αB-crystallin and βA3-crystallin moved to the lower molecular weight fraction which is the same size of γ-crystallin. In those fractions, Asp-96 of αB-crystallin and Asp-37 of βA3-crystallin were highly inverted, which do not occur in the native lens higher molecular weight fraction. Our results indicate the possibility that the inversion of Asp residues may induce dissociation of αB- and βA3-crystallins from the polymeric and oligomeric states. This is the first report that stereoinversion of amino acids disturbs lens protein assembly in aged human lens. Copyright © 2014 Elsevier B.V. All rights reserved.

Short Lived Fission Product Yield Measurements in 235U, 238U and 239Pu

NASA Astrophysics Data System (ADS)

Silano, Jack; Tonchev, Anton; Tornow, Werner; Krishichayan, Fnu; Finch, Sean; Gooden, Matthew; Wilhelmy, Jerry

2017-09-01

Yields of short lived fission products (FPYs) with half lives of a few minutes to an hour contain a wealth of information about the fission process. Knowledge of short lived FPYs would contribute to existing data on longer lived FPY mass and charge distributions. Of particular interest are the relative yields between the ground states and isomeric states of FPYs since these isomeric ratios can be used to determine the angular momentum of the fragments. Over the past five years, a LLNL-TUNL-LANL collaboration has made precision measurements of FPYs from quasi-monoenergetic neutron induced fission of 235U, 238U and 239Pu. These efforts focused on longer lived FPYs, using a well characterized dual fission chamber and several days of neutron beam exposure. For the first time, this established technique will be applied to measuring short lived FPYs, with half lives of minutes to less than an hour. A feasibility study will be performed using irradiation times of < 1 hour, improving the sensitivity to short lived FPYs by limiting the buildup of long lived isotopes. Results from this exploratory study will be presented, and the implications for isomeric ratio measurements will be discussed. This work was performed under the auspices of US DOE by LLNL under Contract DE-AC52-07NA27344.

Prenatal diagnosis of left isomerism with normal heart: a case report

PubMed Central

De Paola, Nico; Ermito, Santina; Nahom, Antonella; Dinatale, Angela; Pappalardo, Elisa Maria; Carrara, Sabina; Cavaliere, Alessandro; Brizzi, Cristiana

2009-01-01

Objective: Left isomerism, also called polysplenia, is a laterality disturbance associated with with paired leftsidedness viscera and multiple small spleens. Left isomerism, heart congenital abnormalities and gastrointestinal malformation are strongly associated. Methods: We present a case of prenatal diagnosis of left isomerism in a fetus with a structurally normal heart. Conclusion: Left isomerism syndrone may coesist with a structurally normal heart. If prenatal left isomerism is suspected, even in presence of a normal heart, is mandatory to esclude sign of gastrointestinal abnormalities, as late poly hy dramnios, and cardiac rhytm disturbance during the pregnancy and neonatal age. PMID:22439041

Stalking Higher Energy Conformers on the Potential Energy Surface of Charged Species.

PubMed

Brites, Vincent; Cimas, Alvaro; Spezia, Riccardo; Sieffert, Nicolas; Lisy, James M; Gaigeot, Marie-Pierre

2015-03-10

Combined theoretical DFT-MD and RRKM methodologies and experimental spectroscopic infrared predissociation (IRPD) strategies to map potential energy surfaces (PES) of complex ionic clusters are presented, providing lowest and high energy conformers, thresholds to isomerization, and cluster formation pathways. We believe this association not only represents a significant advance in the field of mapping minima and transition states on the PES but also directly measures dynamical pathways for the formation of structural conformers and isomers. Pathways are unraveled over picosecond (DFT-MD) and microsecond (RRKM) time scales while changing the amount of internal energy is experimentally achieved by changing the loss channel for the IRPD measurements, thus directly probing different kinetic and isomerization pathways. Demonstration is provided for Li(+)(H2O)3,4 ionic clusters. Nonstatistical formation of these ionic clusters by both direct and cascade processes, involving isomerization processes that can lead to trapping of high energy conformers along the paths due to evaporative cooling, has been unraveled.

Metal-centred azaphosphatriptycene gear with a photo- and thermally driven mechanical switching function based on coordination isomerism.

PubMed

Ube, Hitoshi; Yasuda, Yoshihiro; Sato, Hiroyasu; Shionoya, Mitsuhiko

2017-02-08

Metal ions can serve as a centre of molecular motions due to their coordination geometry, reversible bonding nature and external stimuli responsiveness. Such essential features of metal ions have been utilized for metal-mediated molecular machines with the ability to motion switch via metallation/demetallation or coordination number variation at the metal centre; however, motion switching based on the change in coordination geometry remain largely unexplored. Herein, we report a Pt II -centred molecular gear that demonstrates control of rotor engagement and disengagement based on photo- and thermally driven cis-trans isomerization at the Pt II centre. This molecular rotary motion transmitter has been constructed from two coordinating azaphosphatriptycene rotators and one Pt II ion as a stator. Isomerization between an engaged cis-form and a disengaged trans-form is reversibly driven by ultraviolet irradiation and heating. Such a photo- and thermally triggered motional interconversion between engaged/disengaged states on a metal ion would provide a selector switch for more complex interlocking systems.

A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.

PubMed

Gustafson, Chelsea L; Parsley, Nicole C; Asimgil, Hande; Lee, Hsiau-Wei; Ahlbach, Christopher; Michael, Alicia K; Xu, Haiyan; Williams, Owen L; Davis, Tara L; Liu, Andrew C; Partch, Carrie L

2017-05-18

The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. Copyright © 2017 Elsevier Inc. All rights reserved.

Photochemistry of monodentate and bidentate carbonato complexes of rhodium (3). [applications to spacecraft fuel cells

NASA Technical Reports Server (NTRS)

Sheridan, P. S.

1980-01-01

A scheme for the photochemical fixation of water is proposed which involves a five-step reaction sequence; the first step involves the 2 electron reduction of a metal by a coordinated carbonate ligand, with corresponding oxidation of the carbonate to CO2 and O2. Ligand field photolysis of trans- (RH(en)2 H2O CO3) ClO4, and (Rh(en)2 CO3) CLO4 have been studied in the solid state and in aqueous solution at various pH values. Both salts are photoinert in the solid phase, but are quite photoreactive in aqueous solution. In solution, the monodentate ion undergoes efficient isomerization to a mixture of cis and trans - (Rh(en)2 H2O CO3)+, presumably with water exchange. A minor pH increase upon photolysis is evidence of inefficient carbonate (CO3 =) release, with formation of (Rh(en)2 (H2O)2)3+. In contrast, aqueous solutions of the bidentate carbonato complex undergo efficient pH decrease upon ligand field photolysis. Changes in the electronic spectrum (200-500 nm) and pH changes indicate that the desired redox is occurring. The pH increase is due to the aqueous behavior of CO2.

Survival of nature's rarest isotope {sup 180}Ta under stellar conditions

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

Mohr, P.; Kaeppeler, F.; Gallino, R.

2007-01-15

The nucleosynthesis of nature's rarest isotope {sup 180}Ta depends sensitively on the temperature of the astrophysical environment because of depopulation of the long-living isomeric state via intermediate states to the short-living ground state by thermal photons. Reaction rates for this transition have been measured in the laboratory. These ground state rates underestimate the stellar rates dramatically because under stellar conditions intermediate states are mainly populated by excitations from thermally excited states in {sup 180m}Ta. Full thermalization of {sup 180}Ta is already achieved for typical s-process temperatures around kT=25 keV. Consequently, for the survival of {sup 180}Ta in the s-process fastmore » convective mixing is required which has to transport freshly synthesized {sup 180}Ta to cooler regions. In supernova explosions {sup 180}Ta is synthesized by photon- or neutrino-induced reactions at temperatures above T{sub 9}=1 in thermal equilibrium; independent of the production mechanism, freeze-out from thermal equilibrium occurs at kT{approx_equal}40 keV, and only 35{+-}4% of the synthesized {sup 180}Ta survive in the isomeric state.« less

Rationalizing the role of structural motif and underlying electronic structure in the finite temperature behavior of atomic clusters

NASA Astrophysics Data System (ADS)

Susan, Anju; Joshi, Kavita

2014-04-01

Melting in finite size systems is an interesting but complex phenomenon. Many factors affect melting and owing to their interdependencies it is a challenging task to rationalize their roles in the phase transition. In this work, we demonstrate how structural motif of the ground state influences melting transition in small clusters. Here, we report a case with clusters of aluminum and gallium having same number of atoms, valence electrons, and similar structural motif of the ground state but drastically different melting temperatures. We have employed Born-Oppenheimer molecular dynamics to simulate the solid-like to liquid-like transition in these clusters. Our simulations have reproduced the experimental trends fairly well. Further, the detailed analysis of isomers has brought out the role of the ground state structure and underlying electronic structure in the finite temperature behavior of these clusters. For both clusters, isomers accessible before cluster melts have striking similarities and does have strong influence of the structural motif of the ground state. Further, the shape of the heat capacity curve is similar in both the cases but the transition is more spread over for Al36 which is consistent with the observed isomerization pattern. Our simulations also suggest a way to characterize transition region on the basis of accessibility of the ground state at a specific temperature.

How does the trans-cis photoisomerization of azobenzene take place in organic solvents?

PubMed

Tiberio, Giustiniano; Muccioli, Luca; Berardi, Roberto; Zannoni, Claudio

2010-04-06

The trans-cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the n, pi* isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion-inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans-cis photoisomerization quantum yield and decay times in various solvents (n-hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional-inversion pathway being the most important in solvents.

Potential energy surfaces and reaction dynamics of polyatomic molecules

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

Chang, Yan-Tyng

A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogenmore » atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.« less

Pressure-Induced Polymerization of Acetylene: Structure-Directed Stereoselectivity and a Possible Route to Graphane.

PubMed

Sun, Jiangman; Dong, Xiao; Wang, Yajie; Li, Kuo; Zheng, Haiyan; Wang, Lijuan; Cody, George D; Tulk, Christopher A; Molaison, Jamie J; Lin, Xiaohuan; Meng, Yufei; Jin, Changqing; Mao, Ho-Kwang

2017-06-01

Geometric isomerism in polyacetylene is a basic concept in chemistry textbooks. Polymerization to cis-isomer is kinetically preferred at low temperature, not only in the classic catalytic reaction in solution but also, unexpectedly, in the crystalline phase when it is driven by external pressure without a catalyst. Until now, no perfect reaction route has been proposed for this pressure-induced polymerization. Using in situ neutron diffraction and meta-dynamic simulation, we discovered that under high pressure, acetylene molecules react along a specific crystallographic direction that is perpendicular to those previously proposed. Following this route produces a pure cis-isomer and more surprisingly, predicts that graphane is the final product. Experimentally, polycyclic polymers with a layered structure were identified in the recovered product by solid-state nuclear magnetic resonance and neutron pair distribution functions, which indicates the possibility of synthesizing graphane under high pressure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dinuclear Cu(II) complexes of isomeric bis-(3-acetylacetonate)benzene ligands: synthesis, structure, and magnetic properties.

PubMed

Rancan, Marzio; Dolmella, Alessandro; Seraglia, Roberta; Orlandi, Simonetta; Quici, Silvio; Sorace, Lorenzo; Gatteschi, Dante; Armelao, Lidia

2012-05-07

Highly versatile coordinating ligands are designed and synthesized with two β-diketonate groups linked at the carbon 3 through a phenyl ring. The rigid aromatic spacer is introduced in the molecules to orient the two acetylacetone units along different angles and coordination vectors. The resulting para, meta, and ortho bis-(3-acetylacetonate)benzene ligands show efficient chelating properties toward Cu(II) ions. In the presence of 2,2'-bipyridine, they promptly react and yield three dimers, 1, 2, and 3, with the bis-acetylacetonate unit in bridging position between two metal centers. X-ray single crystal diffraction shows that the compounds form supramolecular chains in the solid state because of intermolecular interactions. Each of the dinuclear complexes shows a magnetic behavior which is determined by the combination of structural parameters and spin polarization effects. Notably, the para derivative (1) displays a moderate antiferromagnetic coupling (J = -3.3 cm(-1)) along a remarkably long Cu···Cu distance (12.30 Å).

Examination of the potential for adaptive chirality of the nitrogen chiral center in aza-aspartame.

PubMed

Bouayad-Gervais, Samir H; Lubell, William D

2013-11-28

The potential for dynamic chirality of an azapeptide nitrogen was examined by substitution of nitrogen for the α-carbon of the aspartate residue in the sweetener S,S-aspartame. Considering that S,S- and R,S-aspartame possess sweet and bitter tastes, respectively, a bitter-sweet taste of aza-aspartame 9 could be indicative of a low isomerization barrier for nitrogen chirality inter-conversion. Aza-aspartame 9 was synthesized by a combination of hydrazine and peptide chemistry. Crystallization of 9 indicated a R,S-configuration in the solid state; however, the aza-residue chiral center was considerably flattened relative to its natural amino acid counterpart. On tasting, the authors considered aza-aspartame 9 to be slightly bitter or tasteless. The lack of bitter sweet taste of aza-aspartame 9 may be due to flattening from sp2 hybridization in the urea as well as a high barrier for sp3 nitrogen inter-conversion, both of which may interfere with recognition by taste receptors.

Systems and methods for solar energy storage, transportation, and conversion utilizing photochemically active organometallic isomeric compounds and solid-state catalysts

DOEpatents

Vollhardt, K. Peter C.; Segalman, Rachel A; Majumdar, Arunava; Meier, Steven

2015-02-10

A system for converting solar energy to chemical energy, and, subsequently, to thermal energy includes a light-harvesting station, a storage station, and a thermal energy release station. The system may include additional stations for converting the released thermal energy to other energy forms, e.g., to electrical energy and mechanical work. At the light-harvesting station, a photochemically active first organometallic compound, e.g., a fulvalenyl diruthenium complex, is exposed to light and is photochemically converted to a second, higher-energy organometallic compound, which is then transported to a storage station. At the storage station, the high-energy organometallic compound is stored for a desired time and/or is transported to a desired location for thermal energy release. At the thermal energy release station, the high-energy organometallic compound is catalytically converted back to the photochemically active organometallic compound by an exothermic process, while the released thermal energy is captured for subsequent use.

Theory and Applications of Solid-State NMR Spectroscopy to Biomembrane Structure and Dynamics

NASA Astrophysics Data System (ADS)

Xu, Xiaolin

Solid-state Nuclear Magnetic Resonance (NMR) is one of the premiere biophysical methods that can be applied for addressing the structure and dynamics of biomolecules, including proteins, lipids, and nucleic acids. It illustrates the general problem of determining the average biomolecular structure, including the motional mean-square amplitudes and rates of the fluctuations. Lineshape and relaxtion studies give us a view into the molecular properties under different environments. To help the understanding of NMR theory, both lineshape and relaxation experiments are conducted with hexamethylbezene (HMB). This chemical compound with a simple structure serves as a perfect test molecule. Because of its highly symmetric structure, its motions are not very difficult to understand. The results for HMB set benchmarks for other more complicated systems like membrane proteins. After accumulating a large data set on HMB, we also proceed to develop a completely new method of data analysis, which yields the spectral densities in a body-fixed frame revealing internal motions of the system. Among the possible applications of solid-state NMR spectroscopy, we study the light activation mechanism of visual rhodopsin in lipid membranes. As a prototype of G-protein-coupled receptors, which are a large class of membrane proteins, the cofactor isomerization is triggered by photon absorption, and the local structural change is then propagated to a large-scale conformational change of the protein. Facilitation of the binding of transducin then passes along the visual signal to downstream effector proteins like transducin. To study this process, we introduce 2H labels into the rhodopsin chromophore retinal and the C-terminal peptide of transducin to probe the local structure and dynamics of these two hotspots of the rhodopsin activation process. In addition to the examination of local sites with solid-state 2H NMR spectroscopy, wide angle X-ray scattering (WAXS) provides us the chance of looking at the overall conformational changes through difference scattering profiles. Although the resolution of this method is not as high as NMR spectroscopy, which gives information on atomic scale, the early activation probing is possible because of the short duration of the optical pump and X-ray probe lasers. We can thus visualize the energy dissipation process by observing and comparing the difference scattering profiles at different times after the light activation moments.

[Tetralogy of Fallot associated with left atrial isomerism].

PubMed

Ferrín, L M; Atik, E; Aiello, V; Marcial, M B; Ebaid, M

1996-10-01

The association of tetralogy of Fallot with atrial isomerism has been rarely reported. Eight cases (five with left isomerism and three with right isomerism) are known. This paper reports two other cases of tetralogy of Fallot with left atrial isomerism. The syndrome's defects were disguised and without clinical expression because of the presence of the right ventricular outlet obstruction of tetralogy of Fallot. These diagnostic elements, not recognized in one of the patients previous to surgical correction of tetralogy of Fallot, were present: junctional rhythm, bronchial isomerism, partial anomalous pulmonary vein connection, agenesy of inferior vena cava and abdominal heterotaxy; their identification previous to surgical correction of tetralogy of Fallot, is necessary for an adequate surgical management.

Carotenoids, Fatty Acid Composition and Heat Stability of Supercritical Carbon Dioxide-Extracted-Oleoresins

PubMed Central

Longo, Cristiano; Leo, Lucia; Leone, Antonella

2012-01-01

The risk of chronic diseases has been shown to be inversely related to tomato intake and the lycopene levels in serum and tissue. Cis-isomers represent approximately 50%–80% of serum lycopene, while dietary lycopene maintains the isomeric ratio present in the plant sources with about 95% of all-trans-lycopene. Supercritical CO2 extraction (S-CO2) has been extensively developed to extract lycopene from tomato and tomato processing wastes, for food or pharmaceutical industries, also by using additional plant sources as co-matrices. We compared two S-CO2-extracted oleoresins (from tomato and tomato/hazelnut matrices), which showed an oil-solid bi-phasic appearance, a higher cis-lycopene content, and enhanced antioxidant ability compared with the traditional solvent extracts. Heat-treating, in the range of 60–100 °C, led to changes in the lycopene isomeric composition and to enhanced antioxidant activity in both types of oleoresins. The greater stability has been related to peculiar lycopene isomer composition and to the lipid environment. The results indicate these oleoresins are a good source of potentially healthful lycopene. PMID:22605975

Optical differential reflectance spectroscopy for photochromic molecules on solid surfaces

NASA Astrophysics Data System (ADS)

Nickel, Fabian; Bernien, Matthias; Lipowski, Uwe; Kuch, Wolfgang

2018-03-01

Optical reflectance of thin adsorbates on solid surfaces is able to reveal fundamental changes of molecular properties compared to bulk systems. The detection of very small changes in the optical reflectance required several technical improvements in the past decades. We present an experimental setup that is capable of high-quality measurements of submonolayers and ultrathin layers of photochromic molecules on surfaces as well as quantifying their isomerization kinetics. By using photomultipliers as detectors, an enhancement of the signal-to-noise ratio by a factor of three with a total reduction of light exposure on the sample by at least four orders of magnitude is achieved. The potential of the experimental setup is demonstrated by a characterization of the photoswitching and thermal switching of a spirooxazine derivate on a bismuth surface.

Isomer-delayed γ -ray spectroscopy of A =159 -164 midshell nuclei and the variation of K -forbidden E 1 transition hindrance factors

NASA Astrophysics Data System (ADS)

Patel, Z.; Walker, P. M.; Podolyák, Zs.; Regan, P. H.; Berry, T. A.; Söderström, P.-A.; Watanabe, H.; Ideguchi, E.; Simpson, G. S.; Nishimura, S.; Wu, Q.; Xu, F. R.; Browne, F.; Doornenbal, P.; Lorusso, G.; Rice, S.; Sinclair, L.; Sumikama, T.; Wu, J.; Xu, Z. Y.; Aoi, N.; Baba, H.; Bello Garrote, F. L.; Benzoni, G.; Daido, R.; Dombrádi, Zs.; Fang, Y.; Fukuda, N.; Gey, G.; Go, S.; Gottardo, A.; Inabe, N.; Isobe, T.; Kameda, D.; Kobayashi, K.; Kobayashi, M.; Komatsubara, T.; Kojouharov, I.; Kubo, T.; Kurz, N.; Kuti, I.; Li, Z.; Matsushita, M.; Michimasa, S.; Moon, C.-B.; Nishibata, H.; Nishizuka, I.; Odahara, A.; Şahin, E.; Sakurai, H.; Schaffner, H.; Suzuki, H.; Takeda, H.; Tanaka, M.; Taprogge, J.; Vajta, Zs.; Yagi, A.; Yokoyama, R.

2017-09-01

Excited states have been studied in 159Sm, 161Sm, 162Sm (Z =62 ), 163Eu (Z =63 ), and 164Gd (Z =64 ), populated by isomeric decay following 238U projectile fission at RIBF, RIKEN. The isomer half-lives range from 50 ns to 2.6 μ s . In comparison with other published data, revised interpretations are proposed for 159Sm and 163Eu. The first data for excited states in 161Sm are presented, where a 2.6-μ s isomer is assigned a three-quasiparticle, Kπ=17 /2- structure. The interpretation is supported by multi-quasiparticle Nilsson-BCS calculations, including the blocking of pairing correlations. A consistent set of reduced E 1 hindrance factors is obtained. Limited evidence is also reported for isomeric decay in 163Sm, 164Eu, and 165Eu.

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

Reversible photochromic system based on rhodamine B salicylaldehyde hydrazone metal complex.

PubMed

Li, Kai; Xiang, Yu; Wang, Xiaoyan; Li, Ji; Hu, Rongrong; Tong, Aijun; Tang, Ben Zhong

2014-01-29

Photochromic molecules are widely applied in chemistry, physics, biology, and materials science. Although a few photochromic systems have been developed before, their applications are still limited by complicated synthesis, low fatigue resistance, or incomplete light conversion. Rhodamine is a class of dyes with excellent optical properties including long-wavelength absorption, large absorption coefficient, and high photostability in its ring-open form. It is an ideal chromophore for the development of new photochromic systems. However, known photochromic rhodamine derivatives, such as amides, exhibit only millisecond lifetimes in their colored ring-open forms, making their application very limited and difficult. In this work, rhodamine B salicylaldehyde hydrazone metal complex was found to undergo intramolecular ring-open reactions upon UV irradiation, which led to a distinct color and fluorescence change both in solution and in solid matrix. The complex showed good fatigue resistance for the reversible photochromism and long lifetime for the ring-open state. Interestingly, the thermal bleaching rate was tunable by using different metal ions, temperatures, solvents, and chemical substitutions. It was proposed that UV light promoted isomerization of the rhodamine B derivative from enol-form to keto-form, which induced ring-opening of the rhodamine spirolactam in the complex to generate color. The photochromic system was successfully applied for photoprinting and UV strength measurement in the solid state. As compared to other reported photochromic molecules, the system in this study has its advantages of facile synthesis and tunable thermal bleaching rate, and also provides new insights into the development of photochromic materials based on metal complex and spirolactam-containing dyes.

Amino Acid Isomerization in the Production of l-Phenylalanine from d-Phenylalanine by Bacteria1

PubMed Central

Chibata, Ichiro; Tosa, Tetsuya; Sano, Ryujiro

1965-01-01

To establish an advantageous method for the production of l-amino acids, microbial isomerization of d- and dl-amino acids to l-amino acids was studied. Screening experiments on a number of microorganisms showed that cell suspensions of Pseudomonas fluorescens and P. miyamizu were capable of isomerizing d- and dl-phenylalanines to l-phenylalanine. Various conditions suitable for isomerization by these organisms were investigated. Cells grown in a medium containing d-phenylalanine showed highest isomerization activity, and almost completely converted d- or dl-phenylalanine into l-phenylalanine within 24 to 48 hr of incubation. Enzymatic studies on this isomerizing system suggested that the isomerization of d- or dl-phenylalanine is not catalyzed by a single enzyme, “amino acid isomerase,” but the conversion proceeds by a two step system as follows: d-pheylalanine is oxidized to phenylpyruvic acid by d-amino acid oxidase, and the acid is converted to l-phenylalanine by transamination or reductive amination. PMID:14339270

Ligand Rearrangements at Fe/S Cofactors: Slow Isomerization of a Biomimetic [2Fe-2S] Cluster.

PubMed

Bergner, Marie; Roy, Lisa; Dechert, Sebastian; Neese, Frank; Ye, Shengfa; Meyer, Franc

2017-04-18

Ligand exchange plays an important role in the biogenesis of Fe/S clusters, most prominently during cluster transfer from a scaffold protein to its target protein. Although in vivo and in vitro studies have provided some insight into this process, the microscopic details of the ligand exchange steps are mostly unknown. In this work, the kinetics of the ligand rearrangement in a biomimetic [2Fe-2S] cluster with mixed S/N capping ligands have been studied. Two geometrical isomers of the cluster are present in solution, and mechanistic insight into the isomerization process was obtained by variable-temperature 1 H NMR spectroscopy. Combined experimental and computational results reveal that this is an associative process that involves the coordination of a solvent molecule to one of the ferric ions. The cluster isomerizes at least two orders of magnitude faster in its protonated and mixed-valent states. These findings may contribute to a deeper understanding of cluster transfer and sensing processes occurring in Fe/S cluster biogenesis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toroidal high-spin isomers in the nucleus 304120

NASA Astrophysics Data System (ADS)

Staszczak, A.; Wong, Cheuk-Yin; Kosior, A.

2017-05-01

Background: Strongly deformed oblate superheavy nuclei form an intriguing region where the toroidal nuclear structures may bifurcate from the oblate spheroidal shape. The bifurcation may be facilitated when the nucleus is endowed with a large angular moment about the symmetry axis with I =Iz . The toroidal high-K isomeric states at their local energy minima can be theoretically predicted using the cranked self-consistent Skyrme-Hartree-Fock method. Purpose: We use the cranked Skyrme-Hartree-Fock method to predict the properties of the toroidal high-spin isomers in the superheavy nucleus 120304184. Method: Our method consists of three steps: First, we use the deformation-constrained Skyrme-Hartree-Fock-Bogoliubov approach to search for the nuclear density distributions with toroidal shapes. Next, using these toroidal distributions as starting configurations, we apply an additional cranking constraint of a large angular momentum I =Iz about the symmetry z axis and search for the energy minima of the system as a function of the deformation. In the last step, if a local energy minimum with I =Iz is found, we perform at this point the cranked symmetry- and deformation-unconstrained Skyrme-Hartree-Fock calculations to locate a stable toroidal high-spin isomeric state in free convergence. Results: We have theoretically located two toroidal high-spin isomeric states of 120304184 with an angular momentum I =Iz=81 ℏ (proton 2p-2h, neutron 4p-4h excitation) and I =Iz=208 ℏ (proton 5p-5h, neutron 8p-8h) at the quadrupole moment deformations Q20=-297.7 b and Q20=-300.8 b with energies 79.2 and 101.6 MeV above the spherical ground state, respectively. The nuclear density distributions of the toroidal high-spin isomers 120304184(Iz=81 ℏ and 208 ℏ ) have the maximum density close to the nuclear matter density, 0.16 fm-3, and a torus major to minor radius aspect ratio R /d =3.25 . Conclusions: We demonstrate that aligned angular momenta of Iz=81 ℏ and 208 ℏ arising from multiparticle-multihole excitations in the toroidal system of 120304184 can lead to high-spin isomeric states, even though the toroidal shape of 120304184 without spin is unstable. Toroidal energy minima without spin may be possible for superheavy nuclei with higher atomic numbers, Z ≳122 , as reported previously [7 A. Staszczak and C. Y. Wong, Acta Phys. Pol. B 40, 753 (2008)].

Toroidal high-spin isomers in the nucleus 120 304

DOE PAGES

Staszczak, A.; Wong, Cheuk-Yin; Kosior, A.

2017-05-22

Strongly deformed oblate superheavy nuclei form an intriguing region where the toroidal nuclear structures may bifurcate from the oblate spheroidal shape. The bifurcation may be facilitated when the nucleus is endowed with a large angular moment about the symmetry axis withmore » $$I=I_{z}$$. The toroidal high-$K$ isomeric states at their local energy minima can be theoretically predicted using the cranked self-consistent Skyrme-Hartree-Fock method. We use the cranked Skyrme-Hartree-Fock method to predict the properties of the toroidal high-spin isomers in the superheavy nucleus $$^{304}{120}_{184}$$. This method consists of three steps: first, we use the deformation-constrained Skyrme-Hartree-Fock-Bogoliubov approach to search for the nuclear density distributions with toroidal shapes. Next, using these toroidal distributions as starting configurations we apply an additional cranking constraint of a large angular momentum $$I=I_{z}$$ about the symmetry $z$-axis and search for the energy minima of the system as a function of the deformation. In the last step, if a local energy minimum with $$I=I_{z}$$ is found, we perform at this point the cranked symmetry- and deformation-unconstrained Skyrme-Hartree-Fock calculations to locate a stable toroidal high-spin isomeric state in free convergence. Furthemore, we have theoretically located two toroidal high-spin isomeric states of $$^{304}{120}_{184}$$ with an angular momentum $I$=$$I_z$$=81$$\\hbar$$ (proton 2p-2h, neutron 4p-4h excitation) and $I$=$$I_z$$=208$$\\hbar$$ (proton 5p-5h, neutron 8p-8h) at the quadrupole moment deformations $$Q_{20}=-297.7$$~b and $$Q_{20}=-300.8$$~b with energies 79.2 MeV and 101.6 MeV above the spherical ground state, respectively. The nuclear density distributions of the toroidal high-spin isomers $$^{304}{120}_{184}(I_z$$=81$$\\hbar$$ and 208$$\\hbar$$) have the maximum density close to the nuclear matter density, 0.16 fm$$^{-3}$$, and a torus major to minor radius aspect ratio $R/d=3.25$. Here, we demonstrate that aligned angular momenta of $$I_z$$=81$$\\hbar$$ and 208$$\\hbar$$ arising from multi-particle-multi-hole excitations in the toroidal system of $$^{304}{120}_{184}$$ can lead to high-spin isomeric states, even though the toroidal shape of $$^{304}120_{184}$$ without spin is unstable. Toroidal energy minima without spin may be possible for superheavy nuclei with higher atomic numbers, $$Z\\gtrsim$$122, as reported previously [A. Staszczak and C. Y. Wong,Acta Phys. Pol. B 40 , 753 (2008)].« less

Enhancement of the radiative transitions between the ground and the 3.5-EV isomer states in the hydrogen-like 229TH89+ ion

NASA Astrophysics Data System (ADS)

Karpeshin, F. F.; Wycech, S.; Band, I. M.; Trzhaskovskaya, M. B.; Pfützner, M.; Żylicz, J.

1998-12-01

Lifetimes for the M1 transitions from the isomeric 3.5 eV 3/2+ state to the ground state are predicted to be enhanced in the hydrogen-like 229Th89+ relative to the bare 229Th nucleus by several orders of magnitude. A possibility of experimental study of this phenomenon is discussed.

Regio- and conformational isomerization critical to design of efficient thermally-activated delayed fluorescence emitters

PubMed Central

Etherington, Marc K.; Franchello, Flavio; Gibson, Jamie; Northey, Thomas; Santos, Jose; Ward, Jonathan S.; Higginbotham, Heather F.; Data, Przemyslaw; Kurowska, Aleksandra; Dos Santos, Paloma Lays; Graves, David R.; Batsanov, Andrei S.; Dias, Fernando B.; Bryce, Martin R.; Penfold, Thomas J.; Monkman, Andrew P.

2017-01-01

Regio- and conformational isomerization are fundamental in chemistry, with profound effects upon physical properties, however their role in excited state properties is less developed. Here two regioisomers of bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide, a donor–acceptor–donor (D–A–D) thermally-activated delayed fluorescence (TADF) emitter, are studied. 2,8-bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide exhibits only one quasi-equatorial conformer on both donor sites, with charge-transfer (CT) emission close to the local triplet state leading to efficient TADF via spin-vibronic coupling. However, 3,7-bis(10H-phenothiazin-10-yl)dibenzo[b,d]thiophene-S,S-dioxide displays both a quasi-equatorial CT state and a higher-energy quasi-axial CT state. No TADF is observed in the quasi-axial CT emission. These two CT states link directly to the two folded conformers of phenothiazine. The presence of the low-lying local triplet state of the axial conformer also means that this quasi-axial CT is an effective loss pathway both photophysically and in devices. Importantly, donors or acceptors with more than one conformer have negative repercussions for TADF in organic light-emitting diodes. PMID:28406153

Cis-to- Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics.

PubMed

Muždalo, Anja; Saalfrank, Peter; Vreede, Jocelyne; Santer, Mark

2018-04-10

Azobenzene-based molecular photoswitches are becoming increasingly important for the development of photoresponsive, functional soft-matter material systems. Upon illumination with light, fast interconversion between a more stable trans and a metastable cis configuration can be established resulting in pronounced changes in conformation, dipole moment or hydrophobicity. A rational design of functional photosensitive molecules with embedded azo moieties requires a thorough understanding of isomerization mechanisms and rates, especially the thermally activated relaxation. For small azo derivatives considered in the gas phase or simple solvents, Eyring's classical transition state theory (TST) approach yields useful predictions for trends in activation energies or corresponding half-life times of the cis isomer. However, TST or improved theories cannot easily be applied when the azo moiety is part of a larger molecular complex or embedded into a heterogeneous environment, where a multitude of possible reaction pathways may exist. In these cases, only the sampling of an ensemble of dynamic reactive trajectories (transition path sampling, TPS) with explicit models of the environment may reveal the nature of the processes involved. In the present work we show how a TPS approach can conveniently be implemented for the phenomenon of relaxation-isomerization of azobenzenes starting with the simple examples of pure azobenzene and a push-pull derivative immersed in a polar (DMSO) and apolar (toluene) solvent. The latter are represented explicitly at a molecular mechanical (MM) and the azo moiety at a quantum mechanical (QM) level. We demonstrate for the push-pull azobenzene that path sampling in combination with the chosen QM/MM scheme produces the expected change in isomerization pathway from inversion to rotation in going from a low to a high permittivity (explicit) solvent model. We discuss the potential of the simulation procedure presented for comparative calculation of reaction rates and an improved understanding of activated states.

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)).

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

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-08-18

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. By and large, the main strength of the hybrid Minnesota density functionals is that the best ones provide verymore » 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). Finally, 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.« less

Multifaceted Quadruplet of Low-Lying Spin-Zero States in 66Ni: Emergence of Shape Isomerism in Light Nuclei

NASA Astrophysics Data System (ADS)

Leoni, S.; Fornal, B.; Mǎrginean, N.; Sferrazza, M.; Tsunoda, Y.; Otsuka, T.; Bocchi, G.; Crespi, F. C. L.; Bracco, A.; Aydin, S.; Boromiza, M.; Bucurescu, D.; Cieplicka-Oryǹczak, N.; Costache, C.; Cǎlinescu, S.; Florea, N.; GhiÅ£ǎ, D. G.; Glodariu, T.; Ionescu, A.; Iskra, Ł. W.; Krzysiek, M.; Mǎrginean, R.; Mihai, C.; Mihai, R. E.; Mitu, A.; NegreÅ£, A.; NiÅ£ǎ, C. R.; Olǎcel, A.; Oprea, A.; Pascu, S.; Petkov, P.; Petrone, C.; Porzio, G.; Şerban, A.; Sotty, C.; Stan, L.; Ştiru, I.; Stroe, L.; Şuvǎilǎ, R.; Toma, S.; Turturicǎ, A.; Ujeniuc, S.; Ur, C. A.

2017-04-01

A search for shape isomers in the 66Ni nucleus was performed, following old suggestions of various mean-field models and recent ones, based on state-of-the-art Monte Carlo shell model (MCSM), all considering 66Ni as the lightest nuclear system with shape isomerism. By employing the two-neutron transfer reaction induced by an 18O beam on a 64Ni target, at the sub-Coulomb barrier energy of 39 MeV, all three lowest-excited 0+ states in 66Ni were populated and their γ decay was observed by γ -coincidence technique. The 0+ states lifetimes were assessed with the plunger method, yielding for the 02+, 03+, and 04+ decay to the 21+ state the B (E 2 ) values of 4.3, 0.1, and 0.2 Weisskopf units (W.u.), respectively. MCSM calculations correctly predict the existence of all three excited 0+ states, pointing to the oblate, spherical, and prolate nature of the consecutive excitations. In addition, they account for the hindrance of the E 2 decay from the prolate 04+ to the spherical 21+ state, although overestimating its value. This result makes 66Ni a unique nuclear system, apart from U,238236 , in which a retarded γ transition from a 0+ deformed state to a spherical configuration is observed, resembling a shape-isomerlike behavior.

More SPECTRA! a Lot MORE! Better TOO! now What?

NASA Astrophysics Data System (ADS)

Field, Robert W.

2017-06-01

I have been a card-carrying spectroscopist for 52 years. I began my career studying spectroscopic perturbations in CS and CO. I eventually graduated to vibrational polyads in acetylene and Multichannel Quantum Defect Theory (MQDT) models for Rydberg states of CaF. My experimental arsenal evolved from atomic resonance lamps to finicky cw dye lasers to user-friendly Nd:YAG pumped dye lasers, ending up with Chirped Pulse Millimeter Waves, non-finicky solid state cw lasers, and death-defying dreams about Stimulated Raman Adiabatic Passage (STIRAP). It has become possible to record an enormous quantity of unimaginably high quality spectra quickly. Increases by factors of 10^{6} in spectral velocity have been claimed. Yet everything rests on assigning the spectrum. But the assignment game has changed. Instead of looking for patterns, we deal with meta-patterns. Our goal is to build a complex model that represents all of the energy levels and associates a multi-component eigenvector with each observed eigenstate. Eigenvectors can reveal what a molecule is thinking about doing when it grows up. Spectroscopy becomes a form of molecular psychoanalysis. A spectroscopist can observe the emergence and describe the mechanistic origin of new classes of large-amplitude intramolecular motions. This makes it possible to directly characterize things, such as transition states, which dogma has labeled "spectroscopically unobservable." Where is 21st century spectroscopy headed? I will discuss examples that include: spectroscopic perturbations of the S_{2} B^{3}Σ^{-}_{u} state, the SO_{2} C state with its unequal SO bond-lengths, and the transition state for trans-cis isomerization in the S_{1} state of acetylene.

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.

An integrated experimental and theoretical reaction path search: analyses of the multistage reaction of an ionized diethylether dimer involving isomerization, proton transfer, and dissociation.

PubMed

Matsuda, Yoshiyuki; Xie, Min; Fujii, Asuka

2018-05-30

An ionization-induced multistage reaction of an ionized diethylether (DEE) dimer involving isomerization, proton transfer, and dissociation is investigated by combining infrared (IR) spectroscopy, tandem mass spectrometry, and a theoretical reaction path search. The vertically-ionized DEE dimer isomerizes to a hydrogen-bonded cluster of protonated DEE and the [DEE-H] radical through barrierless intermolecular proton transfer from the CH bond of the ionized moiety. This isomerization process is confirmed by IR spectroscopy and the theoretical reaction path search. The multiple dissociation pathways following the isomerization are analyzed by tandem mass spectrometry. The isomerized cluster dissociates stepwise into a [protonated DEE-acetaldehyde (AA)] cluster, protonated DEE, and protonated AA. The structure of the fragment ion is also analyzed by IR spectroscopy. The reaction map of the multistage processes is revealed through a harmony of these experimental and theoretical methods.

National Nuclear Data Center

Science.gov Websites

reaction data Sigma Retrieval & Plotting Nuclear structure & decay Data Nuclear Science References Experimental Unevaluated Nuclear Data List Evaluated Nuclear Structure Data File NNDC databases Ground and isomeric states properties Nuclear structure & decay data journal Nuclear reaction model code Tools and

Confirmed assignments of isomeric dimethylbenzyl radicals generated by corona discharge.

PubMed

Yoon, Young Wook; Lee, Sang Kuk

2011-12-07

The controversial vibronic assignments of isomeric dimethylbenzyl radicals were clearly resolved by using different precursors. By employing corresponding dimethylbenzyl chlorides as precursors, we identified the origins of the vibronic bands of the dimethylbenzyl radicals generated by corona discharge of 1,2,4-trimethylbenzene. From the analysis of the spectra observed from the dimethylbenzyl chlorides in a corona excited supersonic expansion, we revised previous assignments of the 3,4-, 2,4-, and 2,5-dimethylbenzyl radicals. Spectroscopic data of electronic transition and vibrational mode frequencies in the ground electronic state of each isomer were accurately determined by comparing them with those obtained by an ab initio calculation and with the known vibrational data of 1,2,4-trimethylbenzene. © 2011 American Institute of Physics

Qualification of a Quantitative Method for Monitoring Aspartate Isomerization of a Monoclonal Antibody by Focused Peptide Mapping.

PubMed

Cao, Mingyan; Mo, Wenjun David; Shannon, Anthony; Wei, Ziping; Washabaugh, Michael; Cash, Patricia

Aspartate (Asp) isomerization is a common post-translational modification of recombinant therapeutic proteins that can occur during manufacturing, storage, or administration. Asp isomerization in the complementarity-determining regions of a monoclonal antibody may affect the target binding and thus a sufficiently robust quality control method for routine monitoring is desirable. In this work, we utilized a liquid chromatography-mass spectrometry (LC/MS)-based approach to identify the Asp isomerization in the complementarity-determining regions of a therapeutic monoclonal antibody. To quantitate the site-specific Asp isomerization of the monoclonal antibody, a UV detection-based quantitation assay utilizing the same LC platform was developed. The assay was qualified and implemented for routine monitoring of this product-specific modification. Compared with existing methods, this analytical paradigm is applicable to identify Asp isomerization (or other modifications) and subsequently develop a rapid, sufficiently robust quality control method for routine site-specific monitoring and quantitation to ensure product quality. This approach first identifies and locates a product-related impurity (a critical quality attribute) caused by isomerization, deamidation, oxidation, or other post-translational modifications, and then utilizes synthetic peptides and MS to assist the development of a LC-UV-based chromatographic method that separates and quantifies the product-related impurities by UV peaks. The established LC-UV method has acceptable peak specificity, precision, linearity, and accuracy; it can be validated and used in a good manufacturing practice environment for lot release and stability testing. Aspartate isomerization is a common post-translational modification of recombinant proteins during manufacture process and storage. Isomerization in the complementarity-determining regions (CDRs) of a monoclonal antibody A (mAb-A) has been detected and has been shown to have impact on the binding affinity to the antigen. In this work, we utilized a mass spectrometry-based peptide mapping approach to detect and quantitate the Asp isomerization in the CDRs of mAb-A. To routinely monitor the CDR isomerization of mAb-A, a focused peptide mapping method utilizing reversed phase chromatographic separation and UV detection has been developed and qualified. This approach is generally applicable to monitor isomerization and other post-translational modifications of proteins in a specific and high-throughput mode to ensure product quality. © PDA, Inc. 2016.

Designed catalysts from Pt nanoparticles supported on macroporous oxides for selective isomerization of n-hexane.

PubMed

An, Kwangjin; Alayoglu, Selim; Musselwhite, Nathan; Na, Kyungsu; Somorjai, Gabor A

2014-05-14

Selective isomerization toward branched hydrocarbons is an important catalytic process in oil refining to obtain high-octane gasoline with minimal content of aromatic compounds. Colloidal Pt nanoparticles with controlled sizes of 1.7, 2.7, and 5.5 nm were deposited onto ordered macroporous oxides of SiO2, Al2O3, TiO2, Nb2O5, Ta2O5, and ZrO2 to investigate Pt size- and support-dependent catalytic selectivity in n-hexane isomerization. Among the macroporous oxides, Nb2O5 and Ta2O5 exhibited the highest product selectivity, yielding predominantly branched C6 isomers, including 2- or 3-methylpentane, as desired products of n-hexane isomerization (140 Torr n-hexane and 620 Torr H2 at 360 °C). In situ characterizations including X-ray diffraction and ambient-pressure X-ray photoelectron spectroscopy showed that the crystal structures of the oxides in Pt/oxide catalysts were not changed during the reaction and oxidation states of Nb2O5 were maintained under both H2 and O2 conditions. Fourier transform infrared spectra of pyridine adsorbed on the oxides showed that Lewis sites were the dominant acidic site of the oxides. Macroporous Nb2O5 and Ta2O5 were identified to play key roles in the selective isomerization by charge transfer at Pt-oxide interfaces. The selectivity was revealed to be Pt size-dependent, with improved isomer production as Pt sizes increased from 1.7 to 5.5 nm. When 5.5 nm Pt nanoparticles were supported on Nb2O5 or Ta2O5, the selectivity toward branched C6 isomers was further increased, reaching ca. 97% with a minimum content of benzene, due to the combined effects of the Pt size and the strong metal-support interaction.

Thermal E/ Z Isomerization in First Generation Molecular Motors.

PubMed

Kuwahara, Shunsuke; Suzuki, Yuri; Sugita, Naoya; Ikeda, Mari; Nagatsugi, Fumi; Harada, Nobuyuki; Habata, Yoichi

2018-04-20

Determination of a thermal E/ Z isomerization barrier of first generation molecular motors is reported. Stable ( E)-1a directly converts to stable ( Z)-1c without photochemical E/ Z isomerization. The activation Gibbs energy of the isomerization was determined to be 123 kJ mol -1 by circular dichroism spectral changes. Density functional theory calculations show that ( Z)-1c is ∼11.4 kJ mol -1 more stable than ( E)-1a.

E2 transition probabilities for decays of isomers observed in neutron-rich odd Sn isotopes

DOE PAGES

Iskra, Ł. W.; Broda, R.; Janssens, R. V.F.; ...

2015-01-01

High-spin states were investigated with gamma coincidence techniques in neutron-rich Sn isotopes produced in fission processes following ⁴⁸Ca + ²⁰⁸Pb, ⁴⁸Ca + ²³⁸U, and ⁶⁴Ni + ²³⁸U reactions. By exploiting delayed and cross-coincidence techniques, level schemes have been delineated in odd ¹¹⁹⁻¹²⁵Sn isotopes. Particular attention was paid to the occurrence of 19/2⁺ and 23/2⁺ isomeric states for which the available information has now been significantly extended. Reduced transition probabilities, B(E2), extracted from the measured half-lives and the established details of the isomeric decays exhibit a striking regularity. This behavior was compared with the previously observed regularity of the B(E2) amplitudesmore » for the seniority ν = 2 and 3, 10⁺ and 27/2⁻ isomers in even- and odd-Sn isotopes, respectively.« less

Conjecture: imines as unidirectional photodriven molecular motors-motional and constitutional dynamic devices.

PubMed

Lehn, Jean-Marie

2006-08-07

Compounds containing the C==N group, such as imines and their derivatives, may undergo syn-anti isomerization by two different routes: 1) photochemically, by out-of-plane rotation around the carbon-nitrogen double bond through a "perpendicular" form, and 2) thermally, by in-plane nitrogen inversion through a "linear" transition state. When the two interconversions occur in sequence, a full, closed process is accomplished, restoring the initial state of the system along two different steps. In a chiral imine-type compound, for example, with an asymmetric center next to the C==N function, photoinduced rotation may be expected to occur in one sense in preference to the opposite one. Thus, photoisomerization followed by thermal isomerization in a chiral imine compound generates unidirectional molecular motion. Generally, imine-type compounds represent unidirectional molecular photomotors converting light energy into mechanical motion. As they are also able to undergo exchange of the carbonyl and amine partners, they present constitutional dynamics. Thus, imine-type compounds are double dynamic, motional, and constitutional devices.

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

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

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

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 verifiedmore » 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.« less

Identification of four rotamers of m-methoxystyrene by resonant two-photon ionization and mass analyzed threshold ionization spectroscopy

NASA Astrophysics Data System (ADS)

Xu, Yanqi; Tzeng, Sheng Yuan; Shivatare, Vidya; Takahashi, Kaito; Zhang, Bing; Tzeng, Wen Bih

2015-03-01

We report the vibronic and cation spectra of four rotamers of m-methoxystyrene, recorded by using the two-color resonant two-photon ionization and mass-analyzed threshold ionization techniques. The excitation energies of the S1← S0 electronic transition are found to be 32 767, 32 907, 33 222, and 33 281 cm-1, and the corresponding adiabatic ionization energies are 65 391, 64 977, 65 114, and 64 525 cm-1 for these isomeric species. Most of the observed active vibrations in the electronically excited S1 and cationic ground D0 states involve in-plane ring deformation and substituent-sensitive bending motions. It is found that the relative orientation of the methoxyl with respect to the vinyl group does not influence the vibrational frequencies of the ring-substituent bending modes. The two dimensional potential energy surface calculations support our experimental finding that the isomerization is restricted in the S1 and D0 states.

Double Molecular Photoswitch Driven by Light and Collisions

NASA Astrophysics Data System (ADS)

Bull, James N.; Scholz, Michael S.; Carrascosa, Eduardo; da Silva, Gabriel; Bieske, Evan J.

2018-06-01

The shapes of many molecules can be transformed by light or heat. Here we investigate collision- and photon-induced interconversions of E E , E Z , and Z Z isomers of the isolated Congo red (CR) dianion, a double molecular switch containing two - N ═ N - azo groups, each of which can have the E or Z configuration. We find that collisional activation of CR dianions drives a one-way Z Z →E Z →E E cascade towards the lowest-energy isomer, whereas the absorption of a single photon over the 270-600 nm range can switch either azo group from E to Z or Z to E , driving the CR dianion to lower- or higher-energy forms. The experimental results, which are interpreted with the aid of calculated statistical isomerization rates, indicate that photoisomerization of CR in the gas phase involves a passage through conical intersection seams linking the excited and ground state potential energy surfaces rather than through isomerization on the ground state potential energy surface following internal conversion.

Application of cinchona-sulfonate-based chiral zwitterionic ion exchangers for the separation of proline-containing dipeptide rotamers and determination of on-column isomerization parameters from dynamic elution profiles.

PubMed

Wernisch, Stefanie; Trapp, Oliver; Lindner, Wolfgang

2013-09-17

The interconversion of cis and trans isomers of dipeptides containing C-terminal proline was studied by dynamic chromatography on zwitterionic chiral stationary phases at temperatures ranging from -15°C to +45°C The cis-trans isomers could be separated below 0°C and above 0-10°C plateau formation and peak coalescence phenomena occurred, which is characteristic for a dynamic process at the time-scale of partitioning. At and above room temperature, full coalescence was observed, which allowed separations of enantiomers without interference from interconversion effects. Analysis of the dynamic elution profiles of the interconverting peptides allowed the determination of isomerization rate constants and thermodynamic activation parameters (isomerization enthalpy, entropy and activation energy). In accordance with established results, isomerization rates and thermodynamic parameters were found to depend on the nature of the N-terminal amino acid. Isomerization barriers were only slightly lower than values determined with other methods but significant differences in the relative contributions of the activation enthalpy and entropy as well as isomerization rates pointed toward selector-moderated isomerization dynamics. Copyright © 2013 Elsevier B.V. All rights reserved.

Methods for suppressing isomerization of olefin metathesis products

DOEpatents

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.

Configurational Isomerism in Polyoxovanadates.

PubMed

Mahnke, Lisa K; Kondinski, Aleksandar; Warzok, Ulrike; Näther, Christian; van Leusen, Jan; Schalley, Christoph A; Monakhov, Kirill Yu; Kögerler, Paul; Bensch, Wolfgang

2018-03-05

A water-soluble derivative of the polyoxovanadate {V 15 E 6 O 42 } (E=semimetal) archetype enables the study of cluster shell rearrangements driven by supramolecular interactions. A reaction unique to E=Sb, induced exclusively by ligand metathesis in peripheral [Ni(ethylenediamine) 3 ] 2+ counterions, results in the formation of the metastable α 1 * configurational isomer of the {V 14 Sb 8 O 42 } cluster type. Contrary to all other polyoxovanadate shell architectures, this isomer comprises an inward-oriented vanadyl group and is ca. 50 and 12 kJ mol -1 higher in energy than the previously isolated α and β isomers, respectively. We discuss this unexpected reaction in light of supramolecular Sb-O⋅⋅⋅V and Sb-O⋅⋅⋅Sb contacts manifested in {V 14 Sb 8 O 42 } 2 dimers detected in the solid state. ESI MS experiments confirm the stability of these dimers also in solution and in the gas phase. DFT calculations indicate that other, as of yet elusive isomers of {V 14 Sb 8 }, might be accessible as well. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

THE EFFECT OF PRESSURE ON THE OXIDATION STATE OF IRON, IV. THIOCYANATE AND ISOTHIOCYANATE LIGANDS*

PubMed Central

Fung, S. C.; Drickamer, H. G.

1969-01-01

The effect of pressure on the Mössbauer resonance spectra of Fe(III) with thiocyanate (M-SCN) and isothiocyanate (M-NCS) ligands has been studied. Fe(NCS)3·6H2O, which has the isothiocyanate structure, reduces with increasing pressure, reversibly, and with a pressure dependence for the conversion very similar to that shown by a wide variety of ionic ferric compounds. K3Fe(SCN)6 has the thiocyanate structure. At low pressures, it exhibits a significantly larger reduction than the Fe(NCS)3. With increasing pressure the thiocyanate complexes isomerize, each complex apparently exhibiting about the same degree of conversion at a given pressure. At 150 kb the isomerization is essentially complete. The reduction of the Fe(III) to Fe(II) is reversible but the isomerization is not, and the sample, when powdered and reloaded in the high-pressure cell, exhibits the isomer shift, quadrupole splitting, and Fe(III) to Fe(II) conversion characteristic of an isothiocyanate. Heating the thiocyanate to 110°C at 5 kb yields a mixture of thiocyanate and isothiocyanate that converts with pressure completely to the isothiocyanate. PMID:16591728

Azobenzene as a photoregulator covalently attached to RNA: a quantum mechanics/molecular mechanics-surface hopping dynamics study.

PubMed

Mondal, Padmabati; Granucci, Giovanni; Rastädter, Dominique; Persico, Maurizio; Burghardt, Irene

2018-05-28

The photoregulation of nucleic acids by azobenzene photoswitches has recently attracted considerable interest in the context of emerging biotechnological applications. To understand the mechanism of photoinduced isomerisation and conformational control in these complex biological environments, we employ a Quantum Mechanics/Molecular Mechanics (QM/MM) approach in conjunction with nonadiabatic Surface Hopping (SH) dynamics. Two representative RNA-azobenzene complexes are investigated, both of which contain the azobenzene chromophore covalently attached to an RNA double strand via a β-deoxyribose linker. Due to the pronounced constraints of the local RNA environment, it is found that trans -to- cis isomerization is slowed down to a time scale of ∼10-15 picoseconds, in contrast to 500 femtoseconds in vacuo , with a quantum yield reduced by a factor of two. By contrast, cis -to- trans isomerization remains in a sub-picosecond regime. A volume-conserving isomerization mechanism is found, similarly to the pedal-like mechanism previously identified for azobenzene in solution phase. Strikingly, the chiral RNA environment induces opposite right-handed and left-handed helicities of the ground-state cis -azobenzene chromophore in the two RNA-azobenzene complexes, along with an almost completely chirality conserving photochemical pathway for these helical enantiomers.

Revisiting the polytopal rearrangements in penta-coordinate d7-metallocomplexes: modified Berry pseudorotation, octahedral switch, and butterfly isomerization.

PubMed

Asatryan, Rubik; Ruckenstein, Eli; Hachmann, Johannes

2017-08-01

This paper provides a first-principles theoretical investigation of the polytopal rearrangements and fluxional behavior of five-coordinate d 7 -transition metal complexes. Our work is primarily based on a potential energy surface analysis of the iron tetracarbonyl hydride radical HFe˙(CO) 4 . We demonstrate the existence of distorted coordination geometries in this prototypical system and, for the first time, introduce three general rearrangement mechanisms, which account for the non-ideal coordination. The first of these mechanisms constitutes a modified version of the Berry pseudorotation via a square-based pyramidal C 4v transition state that connects two chemically identical edge-bridged tetrahedral stereoisomers of C 2v symmetry. It differs from the classical Berry mechanism, which involves two regular D 3h equilibrium structures and a C 4v transition state. The second mechanism is related to the famous "tetrahedral jump" hypothesis, postulated by Muetterties for a number of d 6 HML 4 and H 2 ML 4 complexes. Here, our study suggests two fluxional rearrangement pathways via distinct types of C 2v transition states. Both pathways of this mechanism can be described as a single-ligand migration to a vacant position of an "octahedron", thus interchanging (switching) the apical and basal ligands of the initial quasi-square pyramidal isomer, which is considered as an idealized octahedron with a vacancy. Accordingly, we call this mechanism "octahedral switch". The third mechanism follows a butterfly-type isomerization featuring a key-angle deformation, and we thus call it "butterfly isomerization". It connects the quasi-square pyramidal and edge-bridged tetrahedral isomers of HFe˙(CO) 4 through a distorted edge-bridged tetrahedral transition state of C s symmetry. Our paper discusses the overall features of the isomers and rearrangement mechanisms as well as their implications. We rationalize the existence of each stationary point through an electronic structure analysis and argue their relevance for isolobal analogues of HFe˙(CO) 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.

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations.

PubMed

Velazquez, Hector A; Hamelberg, Donald

2015-02-21

Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

Dynamical role of phosphorylation on serine/threonine-proline Pin1 substrates from constant force molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Velazquez, Hector A.; Hamelberg, Donald

2015-02-01

Cis-trans isomerization of peptidyl-prolyl bonds of the protein backbone plays an important role in numerous biological processes. Cis-trans isomerization can be the rate-limiting step due its extremely slow dynamics, compared to the millisecond time scale of many processes, and is catalyzed by a widely studied family of peptidyl-prolyl cis-trans isomerase enzymes. Also, mechanical forces along the peptide chain can speed up the rate of isomerization, resulting in "mechanical catalysis," and have been used to study peptidyl-prolyl cis-trans isomerization and other mechanical properties of proteins. Here, we use constant force molecular dynamics simulations to study the dynamical effects of phosphorylation on serine/threonine-proline protein motifs that are involved in the function of many proteins and have been implicated in many aberrant biological processes. We show that the rate of cis-trans isomerization is slowed down by phosphorylation, in excellent agreement with experiments. We use a well-grounded theory to describe the force dependent rate of isomerization. The calculated rates at zero force are also in excellent agreement with experimentally measured rates, providing additional validation of the models and force field parameters. Our results suggest that the slowdown in the rate upon phosphorylation is mainly due to an increase in the friction along the peptidyl-prolyl bond angle during isomerization. Our results provide a microscopic description of the dynamical effects of post-translational phosphorylation on cis-trans isomerization and insights into the properties of proteins under tension.

Prediction of nonlinear optical properties of organic materials. General theoretical considerations

NASA Technical Reports Server (NTRS)

Cardelino, B.; Moore, C.; Zutaut, S.

1993-01-01

The prediction of nonlinear optical properties of organic materials is geared to assist materials scientists in the selection of good candidate molecules. A brief summary of the quantum mechanical methods used for estimating hyperpolarizabilities will be presented. The advantages and limitations of each technique will be discussed. Particular attention will be given to the finite-field method for calculating first and second order hyperpolarizabilities, since this method is better suited for large molecules. Corrections for dynamic fields and bulk effects will be discussed in detail, focusing on solvent effects, conformational isomerization, core effects, dispersion, and hydrogen bonding. Several results will be compared with data obtained from third-harmonic-generation (THG) and dc-induced second harmonic generation (EFISH) measurements. These comparisons will demonstrate the qualitative ability of the method to predict the relative strengths of hyperpolarizabilities of a class of compounds. The future application of molecular mechanics, as well as other techniques, in the study of bulk properties and solid state defects will be addressed. The relationship between large values for nonlinear optical properties and large conjugation lengths is well known, and is particularly important for third-order processes. For this reason, the materials with the largest observed nonresonant third-order properties are conjugated polymers. An example of this type of polymer is polydiacetylene. One of the problems in dealing with polydiacetylene is that substituents which may enhance its nonlinear properties may ultimately prevent it from polymerizing. A model which attempts to predict the likelihood of solid-state polymerization is considered, along with the implications of the assumptions that are used. Calculations of the third-order optical properties and their relationship to first-order properties and energy gaps will be discussed. The relationship between monomeric and polymeric third-order optical properties will also be considered.

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

Gurgi, L. A.; Regan, P. H.; Söderström, P. -A.

In-flight fission of a 345 MeV per nucleon 238U primary beam on a 2 mm thick 9Be target has been used to produce and study the decays of a range of neutron-rich nuclei centred around the doubly mid-shell nucleus 170Dy at the RIBF Facility, RIKEN, Japan. The produced secondary fragments of interest were identified event-by-event using the BigRIPS separator. The fragments were implanted into the WAS3ABI position sensitive silicon active stopper which allowed pixelated correlations between implants and their subsequent β-decay. Discrete γ-ray transitions emitted following decays from either metastable states or excited states populated following beta decay were identifiedmore » using the 84 coaxial high-purity germanium (HPGe) detectors of the EURICA spectrometer, which was complemented by 18 additional cerium-doped lanthanum bromide (LaBr3) fast-timing scintillation detectors from the FATIMA collaboration. This paper presents the internal decay of a metastable isomeric excited state in the odd-odd nucleus 168Tb, which corresponds to a single proton-neutron hole configuration in the valence maximum nucleus 170Dy. These data represent the first information on excited states in this nucleus, which is the most neutron-rich odd-odd isotope of terbium (Z=65) studied to date. Nilsson configurations associated with an axially symmetric, prolate-deformed nucleus are proposed for the 168Tb ground state the observed isomeric state by comparison with Blocked BCS-Nilsson calculations.« less

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

Gurgi, L. A.; Regan, P. H.; Söderström, P. -A.

In-flight fission of a 345 MeV per nucleon 238U primary beam on a 2 mm thick 9Be target has been used to produce and study the decays of a range of neutron-rich nuclei centred around the doubly mid-shell nucleus 170Dy at the RIBF Facility, RIKEN, Japan. The produced secondary fragments of interest were identified event-by-event using the BigRIPS separator. The fragments were implanted into the WAS3ABI position sensitive silicon active stopper which allowed pixelated correlations between implants and their subsequent β-decay. Discrete γ-ray transitions emitted following decays from either metastable states or excited states populated following beta decay were identifiedmore » using the 84 coaxial high-purity germanium (HPGe) detectors of the EURICA spectrometer, which was complemented by 18 additional cerium-doped lanthanum bromide (LaBr 3) fast-timing scintillation detectors from the FATIMA collaboration. This paper presents the internal decay of a metastable isomeric excited state in the odd-odd nucleus 168Tb, which corresponds to a single proton-neutron hole configuration in the valence maximum nucleus 170Dy. These data represent the first information on excited states in this nucleus, which is the most neutron-rich odd-odd isotope of terbium (Z = 65) studied to date. Here, Nilsson configurations associated with an axially symmetric, prolate-deformed nucleus are proposed for the 168Tb ground state the observed isomeric state by comparison with Blocked BCS-Nilsson calculations.« less

Mean-field studies of time reversal breaking states in super-heavy nuclei with the Gogny force

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

Robledo, L. M., E-mail: luis.robledo@uam.es

2015-10-15

Recent progress on the description of time reversal breaking (odd mass and multi-quasiparticle excitation) states in super-heavy nuclei within a mean field framework and using several flavors of the Gogny interaction is reported. The study includes ground and excited states in selected odd mass isotopes of nobelium and mendelevium as well as high K isomeric states in {sup 254}No. These are two and four-quasiparticle excitations that are treated in the same self-consistent HFB plus blocking framework as the odd mass states.

Metalloenzyme-like catalyzed isomerizations of sugars by Lewis acid zeolites

PubMed Central

Bermejo-Deval, Ricardo; Assary, Rajeev S.; Nikolla, Eranda; Moliner, Manuel; Román-Leshkov, Yuriy; Hwang, Son-Jong; Palsdottir, Arna; Silverman, Dorothy; Lobo, Raul F.; Curtiss, Larry A.; Davis, Mark E.

2012-01-01

Isomerization of sugars is used in a variety of industrially relevant processes and in glycolysis. Here, we show that hydrophobic zeolite beta with framework tin or titanium Lewis acid centers isomerizes sugars, e.g., glucose, via reaction pathways that are analogous to those of metalloenzymes. Specifically, experimental and theoretical investigations reveal that glucose partitions into the zeolite in the pyranose form, ring opens to the acyclic form in the presence of the Lewis acid center, isomerizes into the acyclic form of fructose, and finally ring closes to yield the furanose product. The zeolite catalysts provide processing advantages over metalloenzymes such as an ability to work at higher temperatures and in acidic conditions that allow for the isomerization reaction to be coupled with other important conversions. PMID:22665778

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

NASA Astrophysics Data System (ADS)

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

2014-06-01

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

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

PubMed

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

2014-06-28

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

Full-dimensional quantum mechanics calculations for the spectroscopic characterization of the isomerization transition states of HOCO/DOCO systems.

PubMed

Ma, Dandan; Ren, Haisheng; Ma, Jianyi

2018-02-14

Full-dimensional quantum mechanics calculations were performed to determine the vibrational energy levels of HOCO and DOCO based on an accurate potential energy surface. Almost all of the vibrational energy levels up to 3500 cm -1 from the vibrational ground state were assigned, and the calculated energy levels in this work are well in agreement with the reported results by Bowman. The corresponding full dimensional wavefunctions present some special features. When the energy level approaches the barrier height, the trans-HOCO and cis-HOCO states strongly couple through tunneling interactions, and the tunneling interaction and Fermi resonance were observed in the DOCO system. The energy level patterns of trans-HOCO, cis-HOCO and trans-DOCO provide a reasonable fitted barrier height using the fitting formula of Field et al., however, a discrepancy exists for the cis-DOCO species which is considered as a random event. Our full-dimensional calculations give positive evidence for the accuracy of the spectroscopic characterization model of the isomerization transition state reported by Field et al., which was developed from one-dimensional model systems. Furthermore, the special case of cis-DOCO in this work means that the isotopic substitution can solve the problem of the accidental failure of Field's spectroscopic characterization model.

Ion mobility studies of carbohydrates as group I adducts: isomer specific collisional cross section dependence on metal ion radius.

PubMed

Huang, Yuting; Dodds, Eric D

2013-10-15

Carbohydrates play numerous critical roles in biological systems. Characterization of oligosaccharide structures is essential to a complete understanding of their functions in biological processes; nevertheless, their structural determination remains challenging in part due to isomerism. Ion mobility spectrometry provides the means to resolve gas phase ions on the basis of their shape-to-charge ratios, thus providing significant potential for separation and differentiation of carbohydrate isomers. Here, we report on the determination of collisional cross sections for four groups of isomeric carbohydrates (including five isomeric disaccharides, four isomeric trisaccharides, two isomeric pentasaccharides, and two isomeric hexasaccharides) as their group I metal ion adducts (i.e., [M + Li](+), [M + Na](+), [M + K](+), [M + Rb](+), and [M + Cs](+)). In all, 65 collisional cross sections were measured, the great majority of which have not been previously reported. As anticipated, the collisional cross sections of the carbohydrate metal ion adducts generally increase with increasing metal ion radius; however, the collisional cross sections were found to scale with the group I cation size in isomer specific manners. Such measurements are of substantial analytical value, as they illustrate how the selection of charge carrier influences carbohydrate ion mobility determinations. For example, certain pairs of isomeric carbohydrates assume unique collisional cross sections upon binding one metal ion, but not another. On the whole, these data suggest a role for the charge carrier as a probe of carbohydrate structure and thus have significant implications for the continued development and application of ion mobility spectrometry for the distinction and resolution of isomeric carbohydrates.

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.

{gamma}-vibrational states in superheavy nuclei

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

Sun Yang; Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000; Joint Institute for Nuclear Astrophysics, University of Notre Dame, Notre Dame, Indiana 46556

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.

Single crystal structures and theoretical calculations of uranium endohedral metallofullerenes (U@C2n , 2n = 74, 82) show cage isomer dependent oxidation states for U.

PubMed

Cai, Wenting; Morales-Martínez, Roser; Zhang, Xingxing; Najera, Daniel; Romero, Elkin L; Metta-Magaña, Alejandro; Rodríguez-Fortea, Antonio; Fortier, Skye; Chen, Ning; Poblet, Josep M; Echegoyen, Luis

2017-08-01

Charge transfer is a general phenomenon observed for all endohedral mono-metallofullerenes. Since the detection of the first endohedral metallofullerene (EMF), La@C 82 , in 1991, it has always been observed that the oxidation state of a given encapsulated metal is always the same, regardless of the cage size. No crystallographic data exist for any early actinide endohedrals and little is known about the oxidation states for the few compounds that have been reported. Here we report the X-ray structures of three uranium metallofullerenes, U@ D 3h -C 74 , U@ C 2 (5)-C 82 and U@ C 2v (9)-C 82 , and provide theoretical evidence for cage isomer dependent charge transfer states for U. Results from DFT calculations show that U@ D 3h -C 74 and U@ C 2 (5)-C 82 have tetravalent electronic configurations corresponding to U 4+ @ D 3h -C 74 4- and U 4+ @ C 2 (5)-C 82 4- . Surprisingly, the isomeric U@ C 2v (9)-C 82 has a trivalent electronic configuration corresponding to U 3+ @ C 2v (9)-C 82 3- . These are the first X-ray crystallographic structures of uranium EMFs and this is first observation of metal oxidation state dependence on carbon cage isomerism for mono-EMFs.

Reactions of atomic oxygen with the chlorate ion and the perchlorate ion

NASA Astrophysics Data System (ADS)

Anan'ev, Vladimir; Miklin, Mikhail; Kriger, Ludmila

2014-06-01

The reactions of the chlorate ion with atomic oxygen formed under photolysis of the nitrate ion introduced to potassium chlorate crystal by co-crystallization were studied by optical and infrared absorption spectroscopy. The perchlorate ion was found to form in solids as product of addition reaction of singlet atomic oxygen, formed under dissociation of the peroxynitrite ion - the product of isomerization of the excited nitrate ion. Triplet atomic oxygen does not react with the chlorate ion. The atomic oxygen formed under photolysis of the nitrate ion introduced to potassium perchlorate crystal by co-crystallization does not react with the perchlorate ion.

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

PubMed

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

2014-12-03

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

Overtone-induced dissociation and isomerization dynamics of the hydroxymethyl radical (CH2OH and CD2OH). I. A theoretical study

NASA Astrophysics Data System (ADS)

Kamarchik, E.; Rodrigo, C.; Bowman, J. M.; Reisler, H.; Krylov, A. I.

2012-02-01

The dissociation of the hydroxymethyl radical, CH2OH, and its isotopolog, CD2OH, following the excitation of high OH stretch overtones is studied by quasi-classical molecular dynamics calculations using a global potential energy surface (PES) fitted to ab initio calculations. The PES includes CH2OH and CH3O minima, dissociation products, and all relevant barriers. Its analysis shows that the transition states for OH bond fission and isomerization are both very close in energy to the excited vibrational levels reached in recent experiments and involve significant geometry changes relative to the CH2OH equilibrium structure. The energies of key stationary points are refined using high-level electronic structure calculations. Vibrational energies and wavefunctions are computed by coupled anharmonic vibrational calculations. They show that high OH-stretch overtones are mixed with other modes. Consequently, trajectory calculations carried out at energies about ˜3000 cm-1 above the barriers reveal that despite initial excitation of the OH stretch, the direct OH bond fission is relatively slow (10 ps) and a considerable fraction of the radicals undergoes isomerization to the methoxy radical. The computed dissociation energies are: D0(CH2OH → CH2O + H) = 10 188 cm-1, D0(CD2OH → CD2O + H) = 10 167 cm-1, D0(CD2OH → CHDO + D) = 10 787 cm-1. All are in excellent agreement with the experimental results. For CH2OH, the barriers for the direct OH bond fission and isomerization are: 14 205 and 13 839 cm-1, respectively.

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

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

Gromov, Evgeniy V., E-mail: evgeniy.gromov@pci.uni-heidelberg.de

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 theirmore » 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.« less

Identification of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid in Pseudomonas sp. strain E-3.

PubMed

Okuyama, H; Enari, D; Shibahara, A; Yamamoto, K; Morita, N

1996-06-01

A cell-free extract of Pseudomonas sp. strain E-3 catalyzed the conversion of 9-cis-hexadecenoic acid [16:1(9c)] to 9-trans-hexadecenoic acid [16:1(9t)] in the free acid form and when 16:1(9c) was esterified to phosphatidylethanolamine (PE). The cytosolic fraction catalyzed the isomerizations of free 16:1(9c) by itself and of 16:1(9c) esterified to PE in the presence of the membrane fraction. Tracer experiments using [2,2-2H2]16:1(9c) demonstrated that the isomerization of free 16:1(9c) occurred independently of the isomerization of 16:1(9c) esterified to PE, indicating that this bacterium has two types of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid.

Systematic features in the structure of doubly odd nuclei around A~=80 mass region: Band structure in 76Rb

NASA Astrophysics Data System (ADS)

García Bermúdez, G.; Baktash, C.; Lister, C. J.; Cardona, M. A.

1988-08-01

Multiple-particle γ-ray coincidence techniques have been used to establish the high spin structure of 76Rb. Two ΔI=1 bands were found built on the Iπ=1- ground state and on the Iπ=(4+) isomeric state at 316.8 keV energy. Systematic of positive parity bands seen in the Br-Kr-Rb isotones with N=39 and 41 is discussed.

Isomerization of one molecule observed through tip enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

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

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

Properties of γ -decaying isomers and isomeric ratios in the 100Sn region

NASA Astrophysics Data System (ADS)

Park, J.; Krücken, R.; Lubos, D.; Gernhäuser, R.; Lewitowicz, M.; Nishimura, S.; Ahn, D. S.; Baba, H.; Blank, B.; Blazhev, A.; Boutachkov, P.; Browne, F.; Čeliković, I.; de France, G.; Doornenbal, P.; Faestermann, T.; Fang, Y.; Fukuda, N.; Giovinazzo, J.; Goel, N.; Górska, M.; Grawe, H.; Ilieva, S.; Inabe, N.; Isobe, T.; Jungclaus, A.; Kameda, D.; Kim, G. D.; Kim, Y.-K.; Kojouharov, I.; Kubo, T.; Kurz, N.; Lorusso, G.; Moschner, K.; Murai, D.; Nishizuka, I.; Patel, Z.; Rajabali, M. M.; Rice, S.; Sakurai, H.; Schaffner, H.; Shimizu, Y.; Sinclair, L.; Söderström, P.-A.; Steiger, K.; Sumikama, T.; Suzuki, H.; Takeda, H.; Wang, Z.; Watanabe, H.; Wu, J.; Xu, Z. Y.

2017-10-01

Half-lives and energies of γ rays emitted in the decay of isomeric states of nuclei in the vicinity of the doubly magic 100Sn were measured in a decay spectroscopy experiment at Rikagaku Kenkyusho (The Institute of Physical and Chemical Research) of Japan Nishina Center. The measured half-lives, some with improved precision, are consistent with literature values. Three new results include a 55-keV E 2 γ ray from a new (4+) isomer with T1 /2=0.23 (6 ) μ s in 92Rh, a 44-keV E 2 γ ray from the (15+) isomer in 96Ag, and T1 /2(6+) =13 (2 ) ns in 98Cd. Shell-model calculations of electromagnetic transition strengths in the (p1 /2,g9 /2) model space agree with the experimental results. In addition, experimental isomeric ratios were compared to the theoretical predictions derived with an abrasion-ablation model and the sharp cutoff model. The results agreed within a factor of 2 for most isomers. From the nonobservation of time-delayed γ rays in 100Sn, new constraints on the T1 /2, γ -ray energy, and internal conversion coefficients are proposed for the hypothetical isomer in 100Sn.

Mechanistic consideration of the photochemical transformation of domoic acid (algal toxin) in DOM-Rich brackish water.

PubMed

Jin, Hangxing; Lian, Lushi; Zhou, Huaxi; Yan, Shuwen; Song, Weihua

2018-06-14

Domoic acid (DA) is a neurotoxin generated by several diatom species in harmful algae blooms (HABs). We report the photo-induced transformation products (TPs) and degradation mechanisms of DA in dissolved organic matter (DOM)-rich freshwater and brackish water. High-resolution quadrupole time-of-flight mass spectrometry (QTOF-MS) and the multivariate statistical strategy orthogonal partial least-squares discriminant analysis (OPLS-DA) identified 36 and 23 potential TPs in DOM-rich freshwater and brackish water, respectively. The main reactive sites of DA are the conjugated double bond and proline ring. Isomerization is the predominant transformation pathway induced by excited-state triplet DOM ( 3 DOM ∗ ). The second-order rate constant of the isomerization reaction was measured as (3.8 ± 0.2) × 10 8  M -1  s -1 . The inverse correlation between the dissolved oxygen (DO) concentration and the rate of photo-induced DA isomerization was revealed. Furthermore, under halide-present conditions, halide radicals are mainly responsible for the differentiation of products by quenching hydroxyl radicals and generating unique organic peroxide products. Our results indicated that halide radicals could be important in the photochemical transformation of organic contaminants in high saline environments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Electronic energy transfer in bimetallic Ru-Os complexes containing the 3,5-bis(pyridin-2-yl)-1,2,4-triazolate bridging ligand

NASA Astrophysics Data System (ADS)

De Cola, Luisa; Barigelletti, Francesco; Balzani, Vincenzo; Hage, Ronald; Haasnoot, Jaap G.; Reedijk, Jan; Vos, Johannes G.

1991-04-01

The luminescence and photochemical properties of the two isomeric heterobimetallic [(bpy) 2Ru(bpt)Os(bpy) 2] 3+ and [(bpy) 2Os(bpt)Ru(bpy) 2] 3+ complexes have been investigated (bpy=2,2'-pyridine; bpt -=3,5-bis(pyridin-2-yl)-1,2,4-triazolate ion). The properties of the two isomeric compounds are compared with those of the corresponding dinuclear homometallic inert and exhibit luminescence only from the Os-based component. Excitation in the Ru-based component is followed by ≈ 100% efficient energy transfer to the Os-based component. The energy-transfer mechanism is briefly discussed. The one-electron oxidation products (which contain Os in the 3+ oxidation state) are not luminescent because of the presence of a low-energy intervalence transfer level.

Matrix-specific distribution and diastereomeric profiles of hexabromocyclododecane (HBCD) in a multimedia environment: Air, soil, sludge, sediment, and fish.

PubMed

Jo, Hyeyeong; Son, Min-Hui; Seo, Sung-Hee; Chang, Yoon-Seok

2017-07-01

Hexabromocyclododecane (HBCD) contamination and its diastereomeric profile were investigated in a multi-media environment along a river at the local scale in air, soil, sludge, sediment, and fish samples. The spatial distribution of HBCD in each matrix showed a different result. The highest concentrations of HBCD in air and soil were detected near a general industrial complex; in the sediment and sludge samples, they were detected in the down-stream region (i.e., urban area). Each matrix showed the specific distribution patterns of HBCD diastereomers, suggesting continuous inputs of contaminants, different physicochemical properties, or isomerizations. The particle phases in air, sludge, and fish matrices were dominated by α-HBCD, owing to HBCD's various isomerization processes and different degradation rate in the environment, and metabolic capabilities of the fish; in contrast, the sediment and soil matrices were dominated by γ-HBCD because of the major composition of the technical mixtures and the strong adsorption onto solid particles. Based on these results, the prevalent and matrix-specific distribution of HBCD diastereomers suggested that more careful consideration should be given to the characteristics of the matrices and their effects on the potential influence of HBCD at the diastereomeric level. Copyright © 2017 Elsevier Ltd. All rights reserved.

Activation cross section and isomeric cross section ratio for the 76Ge(n,2n)75m,gGe process

NASA Astrophysics Data System (ADS)

Luo, Junhua; Jiang, Li; Wang, Xinxing

2018-04-01

We measured neutron-induced reaction cross sections for the 76Ge(n,2n)75m,gGe reactions and their isomeric cross section ratios σm/σg at three neutron energies between 13 and 15MeV by an activation and off-line γ-ray spectrometric technique using the K-400 Neutron Generator at the Chinese Academy of Engineering Physics (CAEP). Ge samples and Nb monitor foils were activated together to determine the reaction cross section and the incident neutron flux. The monoenergetic neutron beams were formed via the 3H( d, n)4He reaction. The pure cross section of the ground state was derived from the absolute cross section of the metastable state and the residual nuclear decay analysis. The cross sections were also calculated using the nuclear model code TALYS-1.8 with different level density options at neutron energies varying from the reaction threshold to 20MeV. Results are discussed and compared with the corresponding literature data.

197Au(n ,2 n ) reaction cross section in the 15-21 MeV energy range

NASA Astrophysics Data System (ADS)

Kalamara, A.; Vlastou, R.; Kokkoris, M.; Nicolis, N. G.; Patronis, N.; Serris, M.; Michalopoulou, V.; Stamatopoulos, A.; Lagoyannis, A.; Harissopulos, S.

2018-03-01

The cross section of the 197Au(n ,2 n )196Au reaction has been determined at six energies ranging from 15.3-20.9 MeV by means of the activation technique, relative to the 27Al(n ,α )24Na reaction. Quasimonoenergetic neutron beams were produced via the 3H(d ,n )4He reaction at the 5.5 MV Tandem T11/25 accelerator laboratory of NCSR "Demokritos". After the irradiations, the induced γ -ray activity of the target and reference foils was measured with high-resolution HPGe detectors. The cross section for the high spin isomeric state (12-) was determined along with the sum of the ground (2-), the first (5+), and second (12-) isomeric states. Theoretical calculations were carried out with the codes empire 3.2.2 and talys 1.8. Optimum input parameters were chosen in such a way as to simultaneously reproduce several experimental reaction channel cross sections in a satisfactory way, namely the (n ,elastic ), (n ,2 n ), (n ,3 n ), (n ,p ), (n ,α ), and (n ,total) ones.

Isomerization of glucose into fructose by environmentally friendly Fe/β zeolite catalysts.

PubMed

Xu, Siquan; Zhang, Lei; Xiao, Kehao; Xia, Haian

2017-06-29

Herein, the environmentally friendly Fe/β zeolite for glucose isomerization to fructose in aqueous media was reported for the first time. The effects of various reaction conditions including reaction temperature, reaction time, catalyst dosage, etc. on the isomerization reaction over Fe/β zeolite were studied in detail. Under the optimized conditions, yield of fructose higher than 20% were obtained. Moreover, the Fe/β zeolite catalysts were stable and remained constant catalytic activity after five consecutive runs. The possible active Fe species for isomerization of glucose in Fe/β zeolite is also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Olsen, Seth; Smith, Sean C.

2006-07-01

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

Isomer spectroscopy of neutron-rich 168Tb 103

DOE PAGES

Gurgi, L. A.; Regan, P. H.; Söderström, P. -A.; ...

2016-12-29

In-flight fission of a 345 MeV per nucleon 238U primary beam on a 2 mm thick 9Be target has been used to produce and study the decays of a range of neutron-rich nuclei centred around the doubly mid-shell nucleus 170Dy at the RIBF Facility, RIKEN, Japan. The produced secondary fragments of interest were identified event-by-event using the BigRIPS separator. The fragments were implanted into the WAS3ABI position sensitive silicon active stopper which allowed pixelated correlations between implants and their subsequent β-decay. Discrete γ-ray transitions emitted following decays from either metastable states or excited states populated following beta decay were identifiedmore » using the 84 coaxial high-purity germanium (HPGe) detectors of the EURICA spectrometer, which was complemented by 18 additional cerium-doped lanthanum bromide (LaBr 3) fast-timing scintillation detectors from the FATIMA collaboration. This paper presents the internal decay of a metastable isomeric excited state in the odd-odd nucleus 168Tb, which corresponds to a single proton-neutron hole configuration in the valence maximum nucleus 170Dy. These data represent the first information on excited states in this nucleus, which is the most neutron-rich odd-odd isotope of terbium (Z = 65) studied to date. Here, Nilsson configurations associated with an axially symmetric, prolate-deformed nucleus are proposed for the 168Tb ground state the observed isomeric state by comparison with Blocked BCS-Nilsson calculations.« less

Isomer spectroscopy of neutron-rich 168Tb103

NASA Astrophysics Data System (ADS)

Gurgi, L. A.; Regan, P. H.; Söderström, P.-A.; Watanabe, H.; Walker, P. M.; Podolyák, Zs.; Nishimura, S.; Berry, T. A.; Doornenbal, P.; Lorusso, G.; Isobe, T.; Baba, H.; Xu, Z. Y.; Sakurai, H.; Sumikama, T.; Catford, W. N.; Bruce, A. M.; Browne, F.; Lane, G. J.; Kondev, F. G.; Odahara, A.; Wu, J.; Liu, H. L.; Xu, F. R.; Korkulu, Z.; Lee, P.; Liu, J. J.; Phong, V. H.; Yag, A.; Zhang, G. X.; Alharbi, T.; Carroll, R. J.; Chae, K. Y.; Dombradi, Zs.; Estrade, A.; Fukuda, N.; Griffin, C.; Ideguchi, E.; Inabe, N.; Kanaoka, H.; Kojouharov, I.; Kubo, T.; Kubono, S.; Kurz, N.; Kuti, I.; Lalkovski, S.; Lee, E. J.; Lee, C. S.; Lotay, G.; Moon, C.-B.; Nishizuka, I.; Nita, C. R.; Patel, Z.; Roberts, O. J.; Schaffner, H.; Shand, C. M.; Suzuki, H.; Takeda, H.; Terashima, S.; Vajta, Zs.; Yoshida, S.; Valiente-Dòbon, J. J.

2017-11-01

In-flight fission of a 345 MeV per nucleon 238U primary beam on a 2 mm thick 9Be target has been used to produce and study the decays of a range of neutron-rich nuclei centred around the doubly mid-shell nucleus 170Dy at the RIBF Facility, RIKEN, Japan. The produced secondary fragments of interest were identified event-by-event using the BigRIPS separator. The fragments were implanted into the WAS3ABI position sensitive silicon active stopper which allowed pixelated correlations between implants and their subsequent β-decay. Discrete γ-ray transitions emitted following decays from either metastable states or excited states populated following beta decay were identified using the 84 coaxial high-purity germanium (HPGe) detectors of the EURICA spectrometer, which was complemented by 18 additional cerium-doped lanthanum bromide (LaBr3) fast-timing scintillation detectors from the FATIMA collaboration. This paper presents the internal decay of a metastable isomeric excited state in the odd-odd nucleus 168Tb, which corresponds to a single proton-neutron hole configuration in the valence maximum nucleus 170Dy. These data represent the first information on excited states in this nucleus, which is the most neutron-rich odd-odd isotope of terbium (Z=65) studied to date. Nilsson configurations associated with an axially symmetric, prolate-deformed nucleus are proposed for the 168Tb ground state the observed isomeric state by comparison with Blocked BCS-Nilsson calculations.

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.

Is an Appreciation of Isomerism the Key to Unlocking the Mysteries of the Cardiac Findings in Heterotaxy?

PubMed

Anderson, Robert H; Spicer, Diane E; Loomba, Rohit

2018-02-06

Pediatric cardiologists treating patients with severe congenital cardiac defects define "visceral heterotaxy" on the basis of isomerism of the atrial appendages. The isomeric features represent an obvious manifestation of disruption of left-right asymmetry during embryonic development. Thus, there are two subsets of individuals within the overall syndrome, with features of either right or left isomerism. Within the heart, it is only the atrial appendages that are truly isomeric. The remainder of the cardiac components shows variable morphology, as does the arrangement of the remaining body organs. Order is provided in this potentially chaotic arrangement simply by describing the specific features of each of the systems. These features as defined by clinicians, however, seem less well recognized by those investigating the developmental origins of the disruption of symmetry. Developmental biologists place much greater emphasis on ventricular looping. Although the direction of the loop can certainly be interpreted as representing an example of asymmetry, it is not comparable to the isomeric features that underscore the clinical syndromes. This is because, thus far, there is no evidence of ventricular isomerism, with the ventricles distinguished one from the other on the basis of their disparate anatomical features. In similar fashion, some consider transposition to represent abnormal lateralization, but again, clinical diagnosis depends on recognition of the lateralized features. In this review, therefore, we discuss the key questions that currently underscore the mismatch in the approaches to "lateralization" as taken by clinicians and developmental biologists.

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

PubMed Central

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

2015-01-01

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

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methods for suppressing isomerization of olefin metathesis products

DOEpatents

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.

Isomerization of 7-oxabenzonorbornadienes into naphthols catalyzed by [RuCl(2)(CO)(3)](2).

PubMed

Ballantine, Melissa; Menard, Michelle L; Tam, William

2009-10-02

Ruthenium-catalyzed isomerization of 7-oxanorbornadienes into naphthols was investigated. Among the various ruthenium catalysts tested, [RuCl(2)(CO)(3)](2) gave the highest yields in the isomerization, and various substituted naphthols were synthesized in moderate to excellent yields. Both symmetrical and unsymmetrical 7-oxanorbornadienes were employed in the study, and moderate to excellent regioselectivities were observed.

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

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

Gounder, Rajamani; Davis, Mark E.

Pure-silica zeolite beta containing Lewis acidic framework Ti 4+ 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 C5more » 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-mediated rearrangement of glucose to sorbose does not appear to have a metalloenzyme analog.« less

Scope and mechanism in palladium-catalyzed isomerizations of highly substituted allylic, homoallylic, and alkenyl alcohols.

PubMed

Larionov, Evgeny; Lin, Luqing; Guénée, Laure; Mazet, Clément

2014-12-03

Herein we report the palladium-catalyzed isomerization of highly substituted allylic alcohols and alkenyl alcohols by means of a single catalytic system. The operationally simple reaction protocol is applicable to a broad range of substrates and displays a wide functional group tolerance, and the products are usually isolated in high chemical yield. Experimental and computational mechanistic investigations provide complementary and converging evidence for a chain-walking process consisting of repeated migratory insertion/β-H elimination sequences. Interestingly, the catalyst does not dissociate from the substrate in the isomerization of allylic alcohols, whereas it disengages during the isomerization of alkenyl alcohols when additional substituents are present on the alkyl chain.

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

PubMed Central

Loppnow, G R; Mathies, R A

1988-01-01

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

The molecular mechanism of excitation in visual transduction and bacteriorhodopsin

PubMed Central

Lewis, Aaron

1978-01-01

An electronic theory of excitation is proposed and described in terms of a three-dimensional excited/ground-state energy surface which elucidates the photochemical and excited-state dynamics of rhodopsins. In this theory the primary action of light is to produce significant electron redistribution in the retinal, thereby generating new interactions that vibrationally excite and perturb the ground-state protein conformation. Thus, light energy causes charge redistribution in the retinal and induces transient charge-density assisted bond rearrangements (such as proton translocation) in the protein structure which is stabilized by subsequent retinal structural alteration. In this theory the isoprenoid chain of the retinal is considered a structurally pliable molecular entity that can generate charge redistributions and can be subsequently achieve intermediate conformations or various isomeric states to minimize the energy of the new protein structure generated by light. Thus, the 11-cis to all trans isomerization of the retinylidene chromophore is not considered a primary mechanism of excitation. An alternate biological role for this molecular process (which is eventually completed in all photoreceptors but not in bacterial rhodopsins) is to provide the irreversibility needed for effective quantum detection on the time scale of a neural response. Finally, it will be demonstrated that this mechanism, which readily accounts for the photophysical and photochemical data, can also be restated in terms of the Monod, Wyman, and Changeux terminology suggesting that aggregates of these pigments may function allosterically. PMID:273216

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

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

Isegawa, Miho; Liu, Fengyi; Morokuma, Keiji

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. Importantmore » 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.« less

Promotion or suppression of glucose isomerization in subcritical aqueous straight- and branched-chain alcohols.

PubMed

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

2015-01-01

The influence of water-miscible alcohols (methanol, 1-propanol, 2-propanol, and t-butyl alcohol) on the isomerization of glucose to fructose and mannose was investigated under subcritical aqueous conditions (180-200 °C). Primary and secondary alcohols promoted the conversion and isomerization of glucose to afford fructose and mannose with high and low selectivity, respectively. On the other hand, the decomposition (side-reaction) of glucose was suppressed in the presence of the primary and secondary alcohols compared with that in subcritical water. The yield of fructose increased with increasing concentration of the primary and secondary alcohols, and the species of the primary and secondary alcohols tested had little effect on the isomerization behavior of glucose. In contrast, the isomerization of glucose was suppressed in subcritical aqueous t-butyl alcohol. Both the conversion of glucose and the yield of fructose decreased with increasing concentration of t-butyl alcohol. In addition, mannose was not detected in reactions using subcritical aqueous t-butyl alcohol.

Isomerization of sugars

DOEpatents

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.

Isomer Shift and Magnetic Moment of the Long-Lived 1/2^{+} Isomer in _{30}^{79}Zn_{49}: Signature of Shape Coexistence near ^{78}Ni.

PubMed

Yang, X F; Wraith, C; Xie, L; Babcock, C; Billowes, J; Bissell, M L; Blaum, K; Cheal, B; Flanagan, K T; Garcia Ruiz, R F; Gins, W; Gorges, C; Grob, L K; Heylen, H; Kaufmann, S; Kowalska, M; Kraemer, J; Malbrunot-Ettenauer, S; Neugart, R; Neyens, G; Nörtershäuser, W; Papuga, J; Sánchez, R; Yordanov, D T

2016-05-06

Collinear laser spectroscopy is performed on the _{30}^{79}Zn_{49} isotope at ISOLDE-CERN. The existence of a long-lived isomer with a few hundred milliseconds half-life is confirmed, and the nuclear spins and moments of the ground and isomeric states in ^{79}Zn as well as the isomer shift are measured. From the observed hyperfine structures, spins I=9/2 and I=1/2 are firmly assigned to the ground and isomeric states. The magnetic moment μ (^{79}Zn)=-1.1866(10)μ_{N}, confirms the spin-parity 9/2^{+} with a νg_{9/2}^{-1} shell-model configuration, in excellent agreement with the prediction from large scale shell-model theories. The magnetic moment μ (^{79m}Zn)=-1.0180(12)μ_{N} supports a positive parity for the isomer, with a wave function dominated by a 2h-1p neutron excitation across the N=50 shell gap. The large isomer shift reveals an increase of the intruder isomer mean square charge radius with respect to that of the ground state, δ⟨r_{c}^{2}⟩^{79,79m}=+0.204(6)  fm^{2}, providing first evidence of shape coexistence.

Dynamic Electron Correlation Effects on the Ground State Potential Energy Surface of a Retinal Chromophore Model.

PubMed

Gozem, Samer; Huntress, Mark; Schapiro, Igor; Lindh, Roland; Granovsky, Alexander A; Angeli, Celestino; Olivucci, Massimo

2012-11-13

The ground state potential energy surface of the retinal chromophore of visual pigments (e.g., bovine rhodopsin) features a low-lying conical intersection surrounded by regions with variable charge-transfer and diradical electronic structures. This implies that dynamic electron correlation may have a large effect on the shape of the force fields driving its reactivity. To investigate this effect, we focus on mapping the potential energy for three paths located along the ground state CASSCF potential energy surface of the penta-2,4-dieniminium cation taken as a minimal model of the retinal chromophore. The first path spans the bond length alternation coordinate and intercepts a conical intersection point. The other two are minimum energy paths along two distinct but kinetically competitive thermal isomerization coordinates. We show that the effect of introducing the missing dynamic electron correlation variationally (with MRCISD) and perturbatively (with the CASPT2, NEVPT2, and XMCQDPT2 methods) leads, invariably, to a stabilization of the regions with charge transfer character and to a significant reshaping of the reference CASSCF potential energy surface and suggesting a change in the dominating isomerization mechanism. The possible impact of such a correction on the photoisomerization of the retinal chromophore is discussed.

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. Copyright © 2012. Published by Elsevier B.V.

Smart window using a thermally and optically switchable liquid crystal cell

NASA Astrophysics Data System (ADS)

Oh, Seung-Won; Kim, Sang-Hyeok; Baek, Jong-Min; Yoon, Tae-Hoon

2018-02-01

Light shutter technologies that can control optical transparency have been studied extensively for developing curtain-free smart windows. We introduce thermally and optically switchable light shutters using LCs doped with push-pull azobenzene, which is known to speed up thermal relaxation. The liquid crystal light shutter can be switched between translucent and transparent states or transparent and opaque states by phase transition through changing temperature or photo-isomerization of doped azobenzene. The liquid crystal light shutter can be used for privacy windows with an initial translucent state or energy-saving windows with an initial transparent state.

Prenatal diagnosis of atrial isomerism in the Korean population

PubMed Central

Lee, Mi-Young; Shim, Jae-Yoon; Lee, Pil-Ryang; Lee, Byong Sop; Kim, Ellen Ai-Rhan; Kim, Young-Hwue; Park, Jeong-Jun; Yun, Tae-Jin; Kim, Ahm

2014-01-01

Objective To report our experiences in the prenatal diagnosis of atrial isomerism and postnatal outcomes. Methods A total of 80 fetuses prenatally diagnosed with atrial isomerism were retrospectively analyzed between 1999 and 2011 at a single institution. Results Of 43 fetuses with prenatally diagnosed right atrial isomerism (RAI), 40 cases were analyzed. The diagnostic accuracy was 93%. The main intracardiac anomalies in RAI were atrioventricular septal defect (AVSD), abnormal pulmonary venous connection, bilateral superior vena cava (BSVC), and pulmonary atresia. Among 28 live births, three infants were lost to follow up, and the overall survival rate was 60%. Of 37 fetuses with prenatally diagnosed left atrial isomerism (LAI), 35 were evaluated. The diagnostic accuracy was 97%. The main intracardiac anomalies in LAI were ventricular septal defect, BSVC, AVSD, double outlet right ventricle, and bradyarrhythmia. Among seven patients with bradyarrhythmia, only one showed a complete atrioventricular block. All fetuses had an interrupted inferior vena cava with azygous continuation. The overall survival rate was 90%. Conclusion Our study confirms the previous findings of fetal atrial isomerism. We also demonstrates a much lower prevalence of AVSD and complete heart block in LAI and a better survival rate in RAI. Although the postnatal outcomes for RAI were worse than those for LAI, successful postnatal surgery with active management improved the survival rate. PMID:24883290

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

PubMed

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

2012-09-01

A high-performance liquid chromatographic (HPLC) analysis system for isomeric astaxanthin was developed. The separation system consisted of a C(30) column and an elution system of methanol/MTBE/water/dichloromethane (77:13:8:2, v/v/v/v). Using the combination of HPLC diode array detector and HPLC atmospheric pressure chemical ionization mass spectrometry, 11 geometrical isomers and 4 epoxides of astaxanthin were successfully identified. Referred to crystal, only isomerization with different degrees was found for solvent dissolving and iodine catalysis, while melting of astaxanthin caused isomerization, slight oxidation, and more noticeable polymerization confirmed by gel permeation chromatography. Chemical changes in isomeric samples all caused a decrease in UV content. The vibrational spectra (infrared and Raman) showed that epoxide was the only new functional group generated for melting. Changes of several key bands and formations of new bands were found in iodine catalysis and melting samples because of isomerization. Practical Application:  Eleven geometrical isomers and 4 epoxides, which were normally generated for solvent dissolving, iodine catalysis, and melting of astaxanthin, have been identified by C(30) -HPLC-MS technology. Furthermore, different samples were measured by gel permeation chromatography, UV, infrared, and Raman, based on the analysis of messages, the effect of each processing was well understood. © 2012 Institute of Food Technologists®

Effect of pH on simultaneous saccharification and isomerization by glucoamylase and glucose isomerase.

PubMed

Mishra, Abha; Debnath Das, Meera

2002-01-01

pH and temperature play critical roles in multistep enzymatic conversions. In such conversions, the optimal pH for individual steps differs greatly. In this article, we describe the production of glucoamylase (from Aspergillus oryzae MTCC152 in solid-state fermentation) and glucose isomerase (from Streptomyces griseus NCIM2020 in submerged fermentation), used in industries for producing high-fructose syrup. Optimum pH for glucoamylase was found to be 5.0. For glucose isomerase, the optimum pH ranged between 7.0 and 8.5, depending on the type of buffer used. Optimum temperature for glucoamylase and glucose isomerase was 50 and 60 degrees C, respectively. When both the enzymatic conversions were performed simultaneously at a compromised pH of 6.5, both the enzymes showed lowered activity. We also studied the kinetics at different pHs, which allows the two-step reaction to take place simultaneously. This was done by separating two steps by a thin layer of urease. Ammonia generated by the hydrolysis of urea consumed the hydrogen ions, thereby allowing optimal activity of glucose isomerase at an acidic pH of 5.0.

Radiation-induced transformations of isolated CH3CN molecules in noble gas matrices

NASA Astrophysics Data System (ADS)

Kameneva, Svetlana V.; Volosatova, Anastasia D.; Feldman, Vladimir I.

2017-12-01

The transformations of isolated CH3CN molecules in various solid noble-gas matrices (Ne, Ar, Kr, and Xe) under the action of X-ray irradiation at 5 K were investigated by FTIR spectroscopy. The main products are CH3NC, CH2CNH and CH2NCH molecular isomers as well as CH2CN and CH2NC radicals. The matrix has a strong effect on the distribution of reaction channels. In particular, the highest relative yield of keteneimine (CH2CNH) was found in Ne matrix, whereas the formation of CH3NC predominates in xenon. It was explained by differences in the matrix ionization energy (IE) resulting in different distributions of hot ionic reactions. The reactions of neutral excited states are mainly involved in Xe matrix with low IE, while the isomerization of the primary acetonitrile positive ions may be quite effective in Ne and Ar. Annealing of the irradiated samples results in mobilization of trapped hydrogen atoms followed by their reactions with radicals to yield parent molecule and its isomers. The scheme of the radiation-induced processes and its implications for the acetonitrile chemistry in cosmic ices are discussed.

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.

Sensitivity of the nuclear deformability and fission barriers to the equation of state

NASA Astrophysics Data System (ADS)

Seif, W. M.; Anwer, Hisham

2018-07-01

The model-dependent analysis of the fission data impacts the extracted fission-related quantities, which are not directly observables, such as the super- and hyperdeformed isomeric states and their energies. We investigated the model dependence of the deformability of a nucleus and its fission barriers on the nuclear equation of state. Within the microscopic-macroscopic model based on a large number of Skyrme nucleon-nucleon interactions, the total energy surfaces and the double-humped fission barrier of 230Th are calculated in a multidimensional deformation space. In addition to the ground-state (GS) and the superdeformed (SD) minima, all the investigated forces yielded a hyperdeformed (HD) minimum. The contour map of the shell-plus-pairing energy clearly displayed the three minima. We found that the GS binding energy and the deformation energy of the different deformation modes along the fission path increase with the incompressibility coefficient K0, while the fission barrier heights and the excitation energies of the SD and HD modes decrease with it. Conversely, the surface-energy coefficient asurf, the symmetry-energy, and its density-slope parameter decrease the GS energy and the deformation energies, but increase the fission barrier heights and the excitation energies. The obtained deformation parameters of the different deformation modes exhibit almost independence on K0, and on the symmetry-energy and its density-slope. The principle deformation parameters of the SD and HD isomeric states tend to decrease with asurf.

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

PubMed

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

2013-08-26

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

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.

Gold-Catalyzed Solid-Phase Synthesis of 3,4-Dihydropyrazin-2(1H)-ones: Relevant Pharmacophores and Peptide Backbone Constraints.

PubMed

Přibylka, Adam; Krchňák, Viktor

2017-11-13

Here, we report the efficient solid-phase synthesis of N-propargyl peptides using Fmoc-amino acids and propargyl alcohol as key building blocks. Gold-catalyzed nucleophilic addition to the triple bond induced C-N bond formation, which triggered intramolecular cyclization, yielding 1,3,4-trisubstituted-5-methyl-3,4-dihydropyrazin-2(1H)-ones. Conformations of acyclic and constrained peptides were compared using a two-step conformer distribution analysis at the molecular mechanics level and density functional theory. The results indicated that the incorporation of heterocyclic molecular scaffold into a short peptide sequence adopted extended conformation of peptide chain. The amide bond adjacent to the constraint did not show significant preference for either cis or trans isomerism. Prepared model compounds demonstrate a proof of concept for gold-catalyzed polymer-supported synthesis of variously substituted 3,4-dihydropyrazin-2(1H)-ones for applications in drug discovery and peptide backbone constraints.

Method For Reactivating Solid Catalysts Used For Alklation Reactions

DOEpatents

Ginosar, Daniel M.; Thompson, David N.; Coates, Kyle; Zalewski, David J.; Fox, Robert V.

2005-05-03

A method for reactivating a solid alkylation catalyst is provided which can be performed within a reactor that contains the alkylation catalyst or outside the reactor. Effective catalyst reactivation is achieved whether the catalyst is completely deactivated or partially deactivated. A fluid reactivating agent is employed to dissolve catalyst fouling agents and also to react with such agents and carry away the reaction products. The deactivated catalyst is contacted with the fluid reactivating agent under pressure and temperature conditions such that the fluid reactivating agent is dense enough to effectively dissolve the fouling agents and any reaction products of the fouling agents and the reactivating agent. Useful pressures and temperatures for reactivation include near-critical, critical, and supercritical pressures and temperatures for the reactivating agent. The fluid reactivating agent can include, for example, a branched paraffin containing at least one tertiary carbon atom, or a compound that can be isomerized to a molecule containing at least one tertiary carbon atom.

Method for reactivating solid catalysts used in alkylation reactions

DOEpatents

Ginosar, Daniel M.; Thompson, David N.; Coates, Kyle; Zalewski, David J.; Fox, Robert V.

2003-06-17

A method for reactivating a solid alkylation catalyst is provided which can be performed within a reactor that contains the alkylation catalyst or outside the reactor. Effective catalyst reactivation is achieved whether the catalyst is completely deactivated or partially deactivated. A fluid reactivating agent is employed to dissolve catalyst fouling agents and also to react with such agents and carry away the reaction products. The deactivated catalyst is contacted with the fluid reactivating agent under pressure and temperature conditions such that the fluid reactivating agent is dense enough to effectively dissolve the fouling agents and any reaction products of the fouling agents and the reactivating agent. Useful pressures and temperatures for reactivation include near-critical, critical, and supercritical pressures and temperatures for the reactivating agent. The fluid reactivating agent can include, for example, a branched paraffin containing at least one tertiary carbon atom, or a compound that can be isomerized to a molecule containing at least one tertiary carbon atom.

Influence of methyl functional groups on the stability of cubane carbon cage

NASA Astrophysics Data System (ADS)

Katin, Konstantin P.; Prudkovskiy, Vladimir S.; Maslov, Mikhail M.

2016-07-01

We present a quantum-chemical study to elucidate the structure, energetics and stability of isolated polymethylcubane molecules C8H8-q(CH3)q. The results obtained by means of originally developed nonorthogonal tight-binding approach are in good agreement with the existed experimental data for solid octamethylcubane C8(CH3)8. The isomerization mechanisms for polymethylcubane family are studied in detail and the minimum energy barriers' heights preventing the decomposition are calculated. The temperature dependence of octamethylcubane molecule lifetime to the decomposition moment was determined by direct molecular dynamics simulation. It is shown that methyl groups destabilize the cubic carbon cage, but less than nitro groups.

A new chemical tool for absinthe producers, quantification of α/β-thujone and the bitter components in Artemisia absinthium.

PubMed

Bach, Benoit; Cleroux, Marilyn; Saillen, Mayra; Schönenberger, Patrik; Burgos, Stephane; Ducruet, Julien; Vallat, Armelle

2016-12-15

The concentrations of α/β-thujone and the bitter components of Artemisia absinthium were quantified from alcoholic wormwood extracts during four phenological stages of their harvest period. A solid-phase micro-extraction method coupled to gas chromatography-mass spectrometry was used to determine the concentration of the two isomeric forms of thujone. In parallel, the combination of ultra-high pressure liquid chromatography and high resolution mass spectrometry allowed to quantify the compounds absinthin, artemisetin and dihydro-epi-deoxyarteannuin B. This present study aimed at helping absinthe producers to determine the best harvesting period. Copyright © 2016 Elsevier Ltd. All rights reserved.

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein

PubMed Central

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

2017-01-01

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes following photon absorption. The initial step is often the photo-isomerization of a conjugated chromophore. Isomerization occurs on ultrafast timescales, 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 PYP microcrystals over the time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction. PMID:27151871

‘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.

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)

1,2-Fluorine Radical Rearrangements: Isomerization Events in Perfluorinated Radicals.

PubMed

Van Hoomissen, Daniel J; Vyas, Shubham

2017-11-16

Devising effective degradation technologies for perfluoroalkyl substances (PFASs) is an active area of research, where the molecular mechanisms involving both oxidative and reductive pathways are still elusive. One commonly neglected pathway in PFAS degradation is fluorine atom migration in perfluoroalkyl radicals, which was largely assumed to be implausible because of the high C-F bond strength. Using density functional theory calculations, it was demonstrated that 1,2-F atom migrations are thermodynamically favored when the fluorine atom migrated from a less branched carbon center to a more branched carbon center. Activation barriers for these rearrangements were within 19-29 kcal/mol, which are possible to easily overcome at elevated temperatures or in photochemically activated species in the gas or aqueous phase. It was also found that the activation barriers for the 1,2-F atom migration are lowered as much as by 10 kcal/mol when common oxidative degradation products such as HF assisted the rearrangements or if the resulting radical center was stabilized by vicinal π-bonds. Natural bond orbital analyses showed that fluorine moves as a radical in a noncharge-separated state. These findings add an important reaction to the existing knowledge of mechanisms for PFAS degradation and highlights the fact that 1,2-F atom shifts may be a small channel for isomerization of these compounds, but upon availability of mineralization products, this isomerization process could become more prominent.

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.

Efficient assembly of polysubstituted pyrroles via a (3 + 2) cycloaddition/skeletal rearrangement/redox isomerization cascade reaction.

PubMed

Yu, Yuanyuan; Wang, Chunyu; He, Xinze; Yao, Xiaotong; Zu, Liansuo

2014-07-03

An unprecedented cascade strategy, used in conjunction with a redox isomerization, for the synthesis of 3-allyl pyrroles is reported. In a single step, readily accessible simple starting materials are transformed into highly substituted pyrroles with high efficiency. The products obtained contain allyl substituents, which can be readily elaborated to other useful functional groups. The reaction proceeds through an unusual (3 + 2) cycloaddition/skeletal rearrangement/redox isomerization pathway.

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.

CIS-TRANS ISOMERS OF VITAMIN A AND RETINENE IN THE RHODOPSIN SYSTEM

PubMed Central

Hubbard, Ruth; Wald, George

1952-01-01

Vitamin A and retinene, the carotenoid precursors of rhodopsin, occur in a variety of molecular shapes, cis-trans isomers of one another. For the synthesis of rhodopsin a specific cis isomer of vitamin A is needed. Ordinary crystalline vitamin A, as also the commercial synthetic product, both primarily all-trans, are ineffective. The main site of isomer specificity is the coupling of retinene with opsin. It is this reaction that requires a specific cis isomer of retinene. The oxidation of vitamin A to retinene by the alcohol dehydrogenase-cozymase system displays only a low degree of isomer specificity. Five isomers of retinene have been isolated in crystalline condition: all-trans; three apparently mono-cis forms, neoretinenes a and b and isoretinene a; and one apparently di-cis isomer, isoretinene b. Neoretinenes a and b were first isolated in our laboratory, and isoretinenes a and b in the Organic Research Laboratory of Distillation Products Industries. Each of these substances is converted to an equilibrium mixture of stereoisomers on simple exposure to light. For this reaction, light is required which retinene can absorb; i.e., blue, violet, or ultraviolet light. Yellow, orange, or red light has little effect. The single geometrical isomers of retinene must therefore be protected from low wave length radiation if their isomerization is to be avoided. By incubation with opsin in the dark, the capacity of each of the retinene isomers to synthesize rhodopsin was examined. All-trans retinene and neoretinene a are inactive. Neoretinene b yields rhodopsin indistinguishable from that extracted from the dark-adapted retina (λmax· 500 mµ). Isoretinene a yields a similar light-sensitive pigment, isorhodopsin, the absorption spectrum of which is displaced toward shorter wave lengths (λmax· 487 mµ). Isoretinene b appears to be inactive, but isomerizes preferentially to isoretinene a, which in the presence of opsin is removed to form isorhodopsin before the isomerization can go further. The synthesis of rhodopsin in solution follows the course of a bimolecular reaction, as though one molecule of neoretinene b combines with one of opsin. The synthesis of isorhodopsin displays similar kinetics. The bleaching of rhodopsin, whether by chemical means or by exposure to yellow or orange (i.e., non-isomerizing) light, yields primarily or exclusively all-trans retinene. The same appears to be true of isorhodopsin. The process of bleaching is therefore intrinsically irreversible. The all-trans retinene which results must be isomerized to active configurations before rhodopsin or isorhodopsin can be regenerated. A cycle of isomerization is therefore an integral part of the rhodopsin system. The all-trans retinene which emerges from the bleaching of rhodopsin must be isomerized to neoretinene b before it can go back; or if first reduced to all-trans vitamin A, this must be isomerized to neovitamin Ab before it can regenerate rhodopsin. The retina obtains new supplies of the neo-b isomer: (a) by the isomerization of all-trans retinene in the eye by blue or violet light; (b) by exchanging all-trans vitamin A for new neovitamin Ab from the blood circulation; and (c) the eye tissues may contain enzymes which catalyze the isomerization of retinene and vitamin A in situ. When the all-trans retinene which results from bleaching rhodopsin in orange or yellow light is exposed to blue or violet light, its isomerization is accompanied by a fall in extinction and a shift of absorption spectrum about 5 mµ toward shorter wave lengths. This is a second photochemical step in the bleaching of rhodopsin. It converts the inactive, all-trans isomer of retinene into a mixture of isomers, from which mixtures of rhodopsin and isorhodopsin can be regenerated. Isorhodopsin, however, is an artefact. There is no evidence that it occurs in the retina; nor has isovitamin Aa or b yet been identified in vivo. In rhodopsin and isorhodopsin, the prosthetic groups appear to retain the cis configurations characteristic of their retinene precursors. In accord with this view, the β-bands in the absorption spectra of both pigments appear to be cis peaks. The conversion to the all-trans configuration occurs during the process of bleaching. The possibility is discussed that rhodopsin may represent a halochromic complex of a retinyl ion with opsin. The increased resonance associated with the ionic state of retinene might then be responsible both for the color of rhodopsin and for the tendency of retinene to assume the all-trans configuration on its release from the complex. A distinction must be made between the immediate precursor of rhodopsin, neovitamin Ab, and the vitamin A which must be fed in order that rhodopsin be synthesized in vivo. Since vitamin A isomerizes in the body, it is probable that any geometrical isomer can fulfill all the nutritional needs for this vitamin. PMID:13011282

How does the isomerization rate affect the photoisomerization-induced transport properties of a doped molecular glass-former?

NASA Astrophysics Data System (ADS)

Accary, J.-B.; Teboul, V.

2013-07-01

We investigate the effect of the isomerization rate f on the microscopic mechanisms at the origin of the massive mass transport found in glass-formers doped with isomerizing azobenzene molecules that result in surface relief gratings formation. To this end we simulate the isomerization of dispersed probe molecules embedded into a molecular host glass-former. The host diffusion coefficient first increases linearly with f and then saturates. The saturated value of the diffusion coefficient and of the viscosity does not depend on f but increases with temperature while the linear response for these transport coefficients depends only slightly on the temperature. We interpret this saturation as arising from the appearance of increasingly soft regions around the probes for high isomerization rates, a result in qualitative agreement with experiments. These two different physical behaviors, linear response and saturation, are reminiscent of the two different unexplained mass transport mechanisms observed for small or large light intensities (for small intensities the molecules move towards the dark regions while for large intensities they move towards the illuminated regions).

Sol-gel technique for the preparation of beta-cyclodextrin derivative stationary phase in open-tubular capillary electrochromatography.

PubMed

Wang, Y; Zeng, Z; Guan, N; Cheng, J

2001-07-01

A novel open-tubular capillary electrochromatography (OT-CEC) column coated with 2,6-dibutyl-beta-cyclodextrin (DB-beta-CD) was prepared using sol-gel technique. In the sol-gel approach, owing to the three-dimensional network of sol-gel and the strong chemical bond between the stationary phase and the surface of capillary columns, good chromatographic characteristics and unique selectivity in separating isomers were shown. We achieved high efficiencies of 5-14 x 10(4) plates/m for the isomeric nitrophenols using the sol-gel-derived DB-beta-CD columns. The migration time reproducibility of the separation of the isomeric nitrophenols was better than 2.2% over five runs and 4.5% from column to column. These sol-gel-coated DB-beta-CD columns have shown improved separations of isomeric aminophenols, isomeric dihydroxybenzenes and isomeric nitrophenols, in comparison with the sol-gel matrix capillary column. The influences of buffer pH and methanol solvent on separation were investigated. The chiral resolution of enantiomers such as ibuprofen and binaphthol was explored primarily.

Organic photochemical storage of solar energy. Progress report, February 1, 1979-January 31, 1980

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

Jones, G. II

1980-02-01

Study of valence isomerization of organic compounds has focused on two mechanisms of photosensitization involving either electron donor-acceptor interaction or energy transfer. The quenching of fluorescent sensitizers by isomerizable substrates results in the formation of excited complexes. These sensitizer-substrate pairs are highly polarized, leading to changes in bond order for the substrates. For several substrates such as quadricyclene, hexamethyldewarbenzene, and a nonbornadiene derivative, this perturbation results in efficient valence isomerization. Isomerization observed on irradiation of charge transfer complexes of isomerizable substrates is consistent with a similar exciplex - template mechanism. The energy transfer mechanism of photosensitization has been studied bymore » measuring the temperature dependence of quantum yield for isomerization of dimethyl norbornadiene-2,3-dicarboxylate sensitized by benzanthrone. From temperature and quencher concentration profiles quenching constants have been obtained which are consistent with an endoergic triplet energy transfer mechanism. The thermal upconversion of the low energy triplet of benzanthrone results in a threefold increase in isomerization quantum yield over a 90/sup 0/ temperature range.« less

Purification, crystallization and preliminary crystallographic analysis of the SH2 domain of IL-2-inducible T-cell kinase.

PubMed

Joseph, Raji E; Ginder, Nathaniel D; Hoy, Julie A; Nix, Jay C; Honzatko, Richard B; Andreotti, Amy H

2011-02-01

Proline is a unique amino acid owing to the relatively small energy difference between the cis and trans conformations of its peptide bond. The X-Pro imide bond readily undergoes cis-trans isomerization in the context of short peptides as well as some proteins. However, the direct detection of cis-trans proline isomerization in folded proteins is technically challenging. NMR spectroscopy is well suited to the direct detection of proline isomerization in folded proteins. It is less clear how well X-ray crystallography can reveal this conformational exchange event in folded proteins. Conformational heterogeneity owing to cis-trans proline isomerization in the Src homology 2 (SH2) domain of the IL-2-inducible T-cell kinase (ITK) has been extensively characterized by NMR. Using the ITK SH2 domain as a test system, an attempt was made to determine whether proline isomerization could be detected in a crystal structure of the ITK SH2 domain. As a first step towards this goal, the purification, crystallization and preliminary characterization of the ITK SH2 domain are described.

NUBASE2012 Evaluation of Nuclear Properties

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

Wang, M., E-mail: wangm@impcas.ac.cn; CSNSM-Orsay, MPI-K, D-69117 Heidelberg; Audi, G.

NUBASE is a database containing the recommended values for the main properties of all known nuclides in their ground and excited isomeric states. Since the publication of the first version in 1997, NUBASE has been widely used in the nuclear science community. The latest version (NUBASE2012) was published in December 2012. Two specific examples are given to illustrate the evaluation policy of NUBASE2012.

Proof of the Feasibility of Coherent and Incoherent Schemes for Pumping a Gamma-Ray Laser

DTIC Science & Technology

1993-08-31

Eq. (1) as functions of the It was the purpose of the work reported here to exam . end-point energies of the irradiating spectra showed very ine the...34 lTam isomeric populations into freely radiating states. Reported values (Collins et al. 1990) are summarized in table I ard shown schematically in figure

Crystallization of Stretched Polyimides: A Structure-Property Study

NASA Technical Reports Server (NTRS)

Hinkley, Jeffrey A.; Dezern, James F.

2002-01-01

A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

On Closed Shells in Nuclei. II

DOE R&D Accomplishments Database

Mayer, M. G.

1949-04-01

Discussion on the use of spins and magnetic moments of the even-odd nuclei by Feenberg and Nordheim to determine the angular momentum of the eigenfunction of the odd particle; discussion of prevalence of isomerism in certain regions of the isotope chart; tabulated data on levels of square well potential, spectroscopic levels, spin term, number of states, shells and known spins and orbital assignments.

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.

Proline Can Have Opposite Effects on Fast and Slow Protein Folding Phases

PubMed Central

Osváth, Szabolcs; Gruebele, Martin

2003-01-01

Proline isomerization is well known to cause additional slow phases during protein refolding. We address a new question: does the presence of prolines significantly affect the very fast kinetics that lead to the formation of folding intermediates? We examined both the very slow (10–100 min) and very fast (4 μs–2.5 ms) folding kinetics of the two-domain enzyme yeast phosphoglycerate kinase by temperature-jump relaxation. Phosphoglycerate kinase contains a conserved cis-proline in position 204, in addition to several trans-prolines. Native cis-prolines have the largest effect on folding kinetics because the unfolded state favors trans isomerization, so we compared the kinetics of a P204H mutant with the wild-type as a proof of principle. The presence of Pro-204 causes an additional slow phase upon refolding from the cold denatured state, as reported in the literature. Contrary to this, the fast folding events are sped up in the presence of the cis-proline, probably by restriction of the conformational space accessible to the molecule. The wild-type and Pro204His mutant would be excellent models for off-lattice simulations probing the effects of conformational restriction on short timescales. PMID:12885665

Kinetics of autocatalysis in small systems

NASA Astrophysics Data System (ADS)

Arslan, Erdem; Laurenzi, Ian J.

2008-01-01

Autocatalysis is a ubiquitous chemical process that drives a plethora of biological phenomena, including the self-propagation of prions etiological to the Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. To explain the dynamics of these systems, we have solved the chemical master equation for the irreversible autocatalytic reaction A +B→2A. This solution comprises the first closed form expression describing the probabilistic time evolution of the populations of autocatalytic and noncatalytic molecules from an arbitrary initial state. Grand probability distributions are likewise presented for autocatalysis in the equilibrium limit (A+B⇌2A), allowing for the first mechanistic comparison of this process with chemical isomerization (B⇌A) in small systems. Although the average population of autocatalytic (i.e., prion) molecules largely conforms to the predictions of the classical "rate law" approach in time and the law of mass action at equilibrium, thermodynamic differences between the entropies of isomerization and autocatalysis are revealed, suggesting a "mechanism dependence" of state variables for chemical reaction processes. These results demonstrate the importance of chemical mechanism and molecularity in the development of stochastic processes for chemical systems and the relationship between the stochastic approach to chemical kinetics and nonequilibrium thermodynamics.

Theoretical investigation on the potential energy surface for the reactions of B, Al and Ga with NO

NASA Astrophysics Data System (ADS)

Zhang, Luning; Zhou, Mingfei

2000-06-01

The structures, binding energies and vibrational frequencies of various MNO structural isomers (M=B, Al and Ga) in their ground triplet states have been determined using the density functional (B3LYP, BP86 and B3PW91) and MP2 methods. The potential energy surfaces of the M+NO reactions have been developed at the B3LYP/6-311+G(d) level of theory, and transition states on the isomerization potential energy surfaces have been characterized. Our calculation results show that four BNO isomers, namely, nitrosyl BNO, isonitrosyl BON, side-bonded B- η2-NO and the inserted NBO molecules are stationary points, while for Al and Ga, only the MNO (nitrosyl), MON (isonitrosyl) and the OMN (insertion) molecules are local minimum. The B+NO reaction products are more strongly bonded compared to the Al and Ga+NO systems due to strong covalent bonding. The interactions of B, Al and Ga atoms with NO to generate nitrosyl and isonitrosyl addition molecules are barrierless, but subsequent isomerization reactions to form the side-bonded molecules and the inserted products require activation energy.

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

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

Auranen, K.; Uusitalo, J.; Juutinen, S.

A newly observed isomeric intruder ½ + state [T ½=3.5(6)ms] is identified in 203At using a gas-filled recoil separator and fusion-evaporation reactions. The isomer is depopulated through a cascade of E3 and mixed M1/E2 transitions to the 9/2 – ground state, and it is suggested to originate from the π(s ½) –1 configuration. In addition, the structures above the ½ + state in 203At and 197At are studied using in-beam γ-ray spectroscopy, recoil-decay tagging, and recoil-isomer decay tagging methods. As a result, the ½ + state is fed from 3/2 + and 5/2 + states, and the origin of thesemore » states are discussed.« less

Solution NMR study of environmental effects on substrate seating in human heme oxygenase: influence of polypeptide truncation, substrate modification and axial ligand.

PubMed

Zhu, Wenfeng; Li, Yiming; Wang, Jinling; Ortiz de Montellano, Paul R; La Mar, Gerd N

2006-01-01

Solution proton NMR has been used here to show that, as either the high-spin ferric, protohemin (PH) substrate complex at neutral pH, or the low-spin ferric, cyanide-inhibited PH substrate complex, the active site electronic and molecular structure of the 233- and 265-residue recombinant constructs of human heme oxygenase-1, hHO, are essentially indistinguishable. It is shown, moreover, that the equilibrium PH orientational isomerism about the alpha,gamma-meso axis is 1:1 in the water-ligated, resting-state complex, but changes to a 4:1 equilibrium ratio as the cyanide-inhibited complex, with the minor species in solution corresponding to the only one found in crystals. The introduction of significant PH orientational preference in the cyanide over the aquo complex is rationalized by the crystallographic observation for the same H2O and CN ligated complexes of rat heme oxygenase (rHO), where the steric tilt of the Fe-CN unit resulted in a approximately 1 A transition of PH into the hydrophobic interior, and stronger interaction of the vinyls with the HO matrix [M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukugama, Biochemistry 42 (2003) 9898-9905]. 1H NMR spectra of the cyanide-inhibited PH complex are the most used, and most useful, for determining the distribution of orientational isomerism for PH in complexes of HO. Hence, it is imperative that the time-course of the spectra after sample preparation be considered in order to reach conclusions that relate isomeric seating of the heme with variable isomeric biliverdin products. The natural orientational isomerism of PH leads to spectral congestion that has prompted the use of a synthetic, twofold symmetric substrate, 2,4-dimethyldeuterohemin, DMDH. While the hyperfine shift pattern for non-ligated residues are very similar and are consistent with largely conserved molecular structure with the alternate substrates, the steric tilt of the Fe-CN vector towards the protein interior, as determined by the orientation of the major magnetic axes, is 2 degrees smaller for DMDH than PH, and is rationalized by the substrate translating even further into the hydrophobic interior in the cyanide complex when the bulky vinyl groups are replaced by methyl groups.

Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde‡, ¶

PubMed Central

Toteva, Maria M.; Silvaggi, Nicholas R.; Allen, Karen N.; Richard, John P.

2011-01-01

D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D2O was monitored by 1H NMR spectroscopy and kcat/Km = 0.034 M−1 s−1 was determined for this isomerization at pD 7.0. This is similar to kcat/Km = 0.017 M−1 s−1 for the TIM-catalyzed carbon deprotonation reaction of DGA in D2O at pD 7.0 [Amyes, T. L.; O’Donoghue, A. C. and Richard J. P. (2001) J. Am. Chem. Soc. 123, 11325–11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (kcat/Km = 490 M−1 s−1) than for the TIM-catalyzed isomerization of DGAP (kcat/Km = 9.6 x 106 M−1 s−1) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219–410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI-catalyzed isomerization of DGA in D2O at pD 7.0 gives a 90% yield of [1-1H]-DHA and a 10% yield of [1-2H]-DHA, the product of isomerization with deuterium incorporation from solvent D2O. By comparison, the transfer of 3H from labeled hexose substrate to solvent is observed only once in every 109 turnovers for the XI-catalyzed isomerization of [2-3H]-glucose in H2O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), Biochemistry 33, 1481–1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI•sugar complexes. PMID:21995300

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.; Morillon, B.; Romain, P.; Jandel, M.; Kawano, T.; Vieira, D. J.; Bond, E. M.; Bredeweg, T. A.; Couture, A. J.; Haight, R. C.; Keksis, A. L.; Rundberg, R. S.; Ullmann, J. L.

2017-09-01

The isomeric ratios for the neutron capture reaction 176Lu(n,γ) to the Jπ = 5/2-, 761.7 keV, T1/2 = 32.8 ns and the Jπ = 15/2+, 1356.9 keV, T1/2 = 11.1 ns levels of 177Lu, have been measured for the first time with the Detector for Advanced Neutron Capture Experiments (DANCE) at the Los Alamos National Laboratory. These measured isomeric ratios are compared with TALYS calculations.

Initial decomposition mechanism for the energy release from electronically excited energetic materials: FOX-7 (1,1-diamino-2,2-dinitroethene, C{sub 2}H{sub 4}N{sub 4}O{sub 4})

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

Yuan, Bing; Yu, Zijun; Bernstein, Elliot R., E-mail: erb@lamar.Colostate.edu

Decomposition of the energetic material FOX-7 (1,1-diamino-2,2-dinitroethylene, C{sub 2}H{sub 4}N{sub 4}O{sub 4}) is investigated both theoretically and experimentally. The NO molecule is observed as an initial decomposition product subsequent to electronic excitation. The observed NO product is rotationally cold (<35 K) and vibrationally hot (2800 K). The initial decomposition mechanism is explored at the complete active space self-consistent field (CASSCF) level. Potential energy surface calculations at the CASSCF(12,8)/6-31G(d) level illustrate that conical intersections play an essential role in the decomposition mechanism. Electronically excited S{sub 2} FOX-7 can radiationlessly relax to lower electronic states through (S{sub 2}/S{sub 1}){sub CI} and (S{submore » 1}/S{sub 0}){sub CI} conical intersections and undergo a nitro-nitrite isomerization to generate NO product on the S{sub 0} state. The theoretically predicted mechanism is consistent with the experimental results. As FOX-7 decomposes on the ground electronic state, thus, the vibrational energy of the NO product from FOX-7 is high. The observed rotational energy distribution for NO is consistent with the final transition state structure on the S{sub 0} state. Ground state FOX-7 decomposition agrees with previous work: the nitro-nitrite isomerization has the lowest average energy barrier, the C–NH{sub 2} bond cleavage is unlikely under the given excitation conditions, and HONO formation on the ground state surface is energy accessible but not the main process.« less

Nuclear Data Sheets for A = 26

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

Basunia, M.S.; Hurst, A.M.

2016-05-15

Evaluated spectroscopic data and level schemes from radioactive decay and nuclear reaction studies are presented for {sup 26}O, {sup 26}F, {sup 26}Ne, {sup 26}Na, {sup 26}Mg, {sup 26}Al, {sup 26}Si, {sup 26}P, and {sup 26}S. This evaluation for A = 26 supersedes the earlier one by P. M. Endt (1998En04) and updates for some nuclides in ENSDF. Highlights of this evaluation are the following: This evaluation includes search results for {sup 26}S nuclide and its proton–decay mode (2011Fo08). An isomeric state (2.2 ms) in {sup 26}F has been discovered by 2013Le03. The state is proposed at 643.4 keV 1 frommore » γ–ray measurements. Internal-transition and beta-decay branches for the state are also determined. New excited levels in {sup 26}Ne have been identified from {sup 26}F β{sup −} decay (2.2 ms). For some {sup 26}Si resonance states conflicting spin-parity assignments exist in the literature. These are identified by footnotes. 2015Do07 ({sup 3}He,nγ) propose the first 0+ state above proton separation energy at an excitation energy of 5890 keV and suggested for additional independent measurements to confirm or refute the existence of 5946 keV 4. 2016Ch09 consider 5946 keV level as a distinct excited state in their reanalysis of the literature data with possible spin-parity assignment of 0+ or 4+ This evaluation also includes discovery of an isomeric state, at 164.1 keV 1, in {sup 26}P by 2014NiZZ.« less

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

NASA Astrophysics Data System (ADS)

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

2016-05-01

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

Activation energy of light induced isomerization of resveratrol.

PubMed

Figueiras, Teresa Sofia; Neves-Petersen, Maria Teresa; Petersen, Steffen B

2011-09-01

Isomerization of trans-stilbenes is known to be induced by light. The two isomers have distinct absorption, fluorescence excitation and emission spectra. Resveratrol, 3,4',5-trihydroxystilbene, is a member of the stilbene family. The interest of the scientific community in resveratrol has increased over the last years due to its biomedical properties. Whereas there is a growing confidence that trans-resveratrol is non-toxic, very little is known about the pharmacology of cis-resveratrol. Of this very reason there is considerable interest in knowing the energetics of the trans-cis conversion. Cis-resveratrol is characterized by a large fluorescence quantum yield when compared to trans-resveratrol. In the present paper we report a detailed analysis of the spectral changes induced in trans-resveratrol upon 260 nm excitation for different time periods. Spectral changes have been monitored with UV-visible absorption and steady-state fluorescence spectroscopy at pH 4 at 20, 25, 30, 35, 40, 45 and 50 °C. Continuous 260 nm excitation induces a blue shift in the absorption and fluorescence excitation spectra of resveratrol and a 14 nm blue shift in its fluorescence emission. The photoisomerization yield is reported as a function of 260 nm excitation time. 330 min continuous excitation led to ~60% isomerization yield. The kinetics of trans-cis isomerization has been monitored following the increase in fluorescence quantum yield upon continuous 260 nm excitation of trans-resveratrol. The study was carried out at the above mentioned temperatures in order to obtain the Arrhenius activation energy of photoisomerization. Activation energy and pre-exponential factor were 3.7 ± 0.3 kcal.mol(-1) and 10.6 ± 1.6 s(-1), respectively. The activation energy is comparable with previously reported values for the photoisomerization of other stilbenes.

Nonradiative inter- and intramolecular energy transfer from the aromatic donor anisole to a synthesized photoswitchable acceptor system.

PubMed

Bardhan, Munmun; Bhattacharya, Sudeshna; Misra, Tapas; Mukhopadhyay, Rupa; De, Asish; Chowdhury, Joydeep; Ganguly, Tapan

2010-02-01

We report steady state and time resolved fluorescence measurements on acetonitrile (ACN) solutions of the model compounds, energy donor anisole (A) and a photoswitchable acceptor N,N'-1,2-phenylene di-p-tosylamide (B) and the multichromophore (M) where A and B are connected by a spacer containing both rigid triple (acetylenic) and flexible methylene bonds. Both steady state and time correlated single photon counting measurements demonstrate that though intermolecular energy transfer, of Forster type, between the donor and acceptor moieties occurs with rate 10(8)s(-1) but when these two reacting components are linked by a spacer (multichromophore, M) the observed transfer rate ( approximately 10(11)s(-1)) enhances. This seemingly indicates that the imposition of the spacer by inserting a triple bond may facilitate in the propagation of electronic excitation energy through bond. The time resolved fluorescence measurements along with the theoretical predictions using Configuration interaction singles (CIS) method by using 6-31G (d,p) basis set, implemented in the Gaussian package indicate the formations of the two excited conformers of B. The experimental findings made from the steady state and time resolved fluorescence measurements demonstrate that, though two different isomeric species of the acceptor B are formed in the excited singlet states, the prevailing singlet-singlet nonradiative energy transfer route was found from the donor A to the relatively longer-lived isomeric species of B. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy.

PubMed

Groma, Géza I; Colonna, Anne; Martin, Jean-Louis; Vos, Marten H

2011-03-16

The primary energetic processes driving the functional proton pump of bacteriorhodopsin take place in the form of complex molecular dynamic events after excitation of the retinal chromophore into the Franck-Condon state. These early events include a strong electronic polarization, skeletal stretching, and all-trans-to-13-cis isomerization upon formation of the J intermediate. The effectiveness of the photoreaction is ensured by a conical intersection between the electronic excited and ground states, providing highly nonadiabatic coupling to nuclear motions. Here, we study real-time vibrational coherences associated with these motions by analyzing light-induced infrared emission from oriented purple membranes in the 750-1400 cm(-)(1) region. The experimental technique applied is based on second-order femtosecond difference frequency generation on macroscopically ordered samples that also yield information on phase and direction of the underlying motions. Concerted use of several analysis methods resulted in the isolation and characterization of seven different vibrational modes, assigned as C-C stretches, out-of-plane methyl rocks, and hydrogen out-of-plane wags, whereas no in-plane H rock was found. Based on their lifetimes and several other criteria, we deduce that the majority of the observed modes take place on the potential energy surface of the excited electronic state. In particular, the direction sensitivity provides experimental evidence for large intermediate distortions of the retinal plane during the excited-state isomerization process. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular and excited state properties of isomeric scarlet disperse dyes

NASA Astrophysics Data System (ADS)

Lim, Jihye; Szymczyk, Malgorzata; Mehraban, Nahid; Ding, Yi; Parrillo-Chapman, Lisa; El-Shafei, Ahmed; Freeman, Harold S.

2018-06-01

This work was part of an investigation aimed at characterizing the molecular and excited state properties of currently available disperse dyes developed to provide stability to extensive sunlight exposures when adsorbed on poly(ethylene terephthalate) (PET) fibers. Having completed the characterization of yellow, magenta, and cyan disperse dyes for PET-based fabrics used outdoors, our attention turned to the colors designed to enhance the color gamut of a standard 4-member (cyan/yellow/magenta/black) color set. The present study pertained specifically to the characterization of commercially available scarlet dyes. In this regard, HPLC analysis showed that a scarlet product used for PET coloration was mainly a 70/30 mixture of dyes, and the use of HRMS and single crystal X-ray diffraction analyses indicated that these two dyes were azo compounds derived from isomeric pyridine-based couplers which differed in the location of the primary amino (sbnd NH2) and anilino (sbnd NHPh) groups attached to the pyridine ring. One dye structure has the sbnd NHPh group para to the azo group (Sc2), while the other has that group in the ortho position (Sc3). The presence of either ortho substituent provides photostabilization through intramolecular H-bonding with the azo moiety. Further, results from molecular modeling studies showed that the lower excited state oxidation potential of Sc3 relative to that of Sc2 allows Sc3 to function as an energy quencher for the excited state of Sc2 - through thermodynamically favorable electron transfer.

Electronic structure and photochemistry of squaraine dyes: basic theoretical analysis and direct detection of the photoisomer of a symmetrical squarylium cyanine.

PubMed

Momicchioli, Fabio; Tatikolov, Aleksandr S; Vanossi, Davide; Ponterini, Glauco

2004-04-01

The photoisomerization kinetics of a squaraine dye has been the object both of experimental investigation and of interpretation in the framework of a qualitative theoretical model formulated by the aid of simple HMO calculations and orbital symmetry considerations. Such a model has first confirmed that the electronic structure and the spectroscopic properties of symmetrical squaraines are related to those of the parent cyanines, with ketocyanines as intermediate systems. Extension of the approach to structures twisted by 90[degree] about a polymethine bond has then provided insight into the electronic aspects and the mechanism of the photoisomerization of the squaraine under study. The reaction, previously indirectly investigated by fluorescence analysis, has been directly monitored by laser flash photolysis. These experiments indicate that, while photoisomerization is likely the main radiationless decay route from the spectroscopic minimum of the lowest excited singlet state (S(1)), the cis photoisomer is produced with only a 1% yield, likely because of an unfavourable cis/trans branching ratio from the perpendicular minimum of the S(1)-state potential energy surface. In contrast with what found for symmetrical cyanines, an increase in the solvent polarity was found to accelerate both the direct, excited-state reaction and, to a much larger extent, the ground-state back-isomerization. Such observations are consistent with predictions of the theoretical model and provide a clue for the identification of the isomerization coordinate.

A solid-state hybrid density functional theory study of Prussian blue analogues and related chlorides at pressure

NASA Astrophysics Data System (ADS)

Middlemiss, Derek S.; Lawton, Lorreta M.; Wilson, Chick C.

2008-08-01

The variations with pressure in the structural, electronic and magnetic properties of a series of Prussian blue analogues (PBAs) KIMII[CrIII(CN)6] (M = VII, MnII and NiII) and associated isomorphous chlorides KIMIICrIIICl6 are investigated within a series of solid-state hybrid density functional calculations. The sensitivity of the computed properties to the choice of Hamiltonian is tested by application of functionals containing 35%, 65% and 100% admixtures of Fock exchange. Magnetic coupling constants (J) are obtained at a range of cell volumes (V), with fits of the Bloch relationship (J \\propto V^{-\\varepsilon } , ɛ typically 3-4) yielding exponents ɛ in the ranges 5.16-6.34, 8.48-12.07 and 4.00-4.51 for the antiferromagnetic (AF) VIICrIII-, ferrimagnetic (FI) MnIICrIII- and ferromagnetic (FO) NiIICrIII PBAs, respectively; and 3.33-4.99, 1.86-3.09 and 1.65-3.28 for the AF VIICrIII-, FO MnIICrIII- and FO NiIICrIII chlorides, respectively. The MnIICrIII PBA range encloses the high values ɛ~9-10 obtained in a recent joint experimental and theoretical study, and it is suggested that this strong magnetostructural effect arises due to the presence of competing AF and FO interactions in this material. Estimates of the spin ordering temperatures derived from the combination of the 35%-functional couplings with a mean field approach are in good agreement with experiment in the VIICrIII and NiIICrIII PBAs, but are too low in the MnIICrIII system. The variations with pressure in the structural parameters, charges and spin moments are also detailed, the PBA and chloride energy-volume data yielding bulk moduli in the ranges 39-53 and 36-50 GPa, respectively. Finally, the energies governing CN- ligand isomerization are estimated and successfully interpreted in terms of a simple crystal field stabilization model.

The Origins and Evolution of Molecules in Icy Solids

NASA Technical Reports Server (NTRS)

Hudson, Reggie L.; Moore, Marla H.

2010-01-01

Astronomical observations of the past few decades have revealed the existence of a variety of molecules in extraterrestrial ices. These molecules include H2O, CO, and CO2, and organics such as CH4, CH30H, and C2H6. Some ices are dominated by polar molecules, while non-polar species appear to dominate others. Observations, mainly in the radio and IR regions, have allowed the inference of other solid-phase molecules whose formation remains difficult to explain by gas-phase chemistry alone. Several laboratory research groups have reported on extensive experiments on the solid-phase reaction chemistry of icy materials, generally as initiated by either ionizing radiation or vacuum-UV photons. These experiments not only permit molecular identifications to be made from astronomical observations, but also allow predictions of yet unidentified molecules. This laboratory approach has evolved over more than 30 years with much of the earliest work focusing on complex mixtures thought to represent either cometary or interstellar ices. Although those early experiments documented a rich solid-state photo- and radiation chemistry, they revealed few details of reactions for particular molecules, partly due to the multi-component nature of the samples. Since then, model systems have been examined that allow the chemistry of individual species and specific reactions to be probed. Reactions involving most of the smaller astronomical molecules have now been studied and specific processes identified. Current laboratory work suggests that a variety of reactions occur in extraterrestrial ices, including acid-base processes, radical dimerizations, proton transfers, oxidations, reductions, and isomerizations. This workshop presentation will focus on chemical reactions relevant to solar system and interstellar ices. While most of the work will be drawn from that to which the speaker has contributed, results from other laboratories also will be included. Suggestions for future studies will be made, with an emphasis on some present deficiencies. The speaker's work has been generously supported by these NASA research programs: Cassini Data Analysis, Exobiology, Mars Fundamental Research, Outer Planets Research, Planetary Atmospheres, Planetary Geology and Geophysics, and the NASA Astrobiology Institute.

Photoisomerization among ring-open merocyanines. I. Reaction dynamics and wave-packet oscillations induced by tunable femtosecond pulses.

PubMed

Ruetzel, Stefan; Diekmann, Meike; Nuernberger, Patrick; Walter, Christof; Engels, Bernd; Brixner, Tobias

2014-06-14

Upon ultraviolet excitation, photochromic spiropyran compounds can be converted by a ring-opening reaction into merocyanine molecules, which in turn can form several isomers differing by cis and trans configurations in the methine bridge. Whereas the spiropyran-merocyanine conversion reaction of the nitro-substituted indolinobenzopyran 6-nitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-indoline] (6-nitro BIPS) has been studied extensively in theory and experiments, little is known about photoisomerization among the merocyanine isomers. In this article, we employ femtosecond transient absorption spectroscopy with variable excitation wavelengths to investigate the excited-state dynamics of the merocyanine in acetonitrile at room temperature, where exclusively the trans-trans-cis (TTC) and trans-trans-trans (TTT) isomers contribute. No photochemical ring-closure pathways exist for the two isomers. Instead, we found that (18±4)% of excited TTC isomers undergo an ultrafast excited-state cis→trans photoisomerization to TTT within 200 fs, while the excited-state lifetime of TTC molecules that do not isomerize is 35 ps. No photoisomerization was detected for the TTT isomer, which relaxes to the ground state with a lifetime of roughly 160 ps. Moreover, signal oscillations at 170 cm(-1) and 360 cm(-1) were observed, which can be ascribed to excited-state wave-packet dynamics occurring in the course of the TTC→TTT isomerization. The results of high-level time-dependent density functional theory in conjunction with polarizable continuum models are presented in the subsequent article [C. Walter, S. Ruetzel, M. Diekmann, P. Nuernberger, T. Brixner, and B. Engels, J. Chem. Phys. 140, 224311 (2014)].

Characterization of a low-level unknown isomeric degradation product using an integrated online-offline top-down tandem mass spectrometry platform.

PubMed

Yu, Xiang; Warme, Christopher; Lee, Dinah; Zhang, Jing; Zhong, Wendy

2013-10-01

An integrated online-offline platform was developed combining automated online LC-MS fraction collection, continuous accumulation of selected ions (CASI), and offline top-down electron capture dissociation (ECD) tandem mass spectrometry experiments to identify a low-level, unknown isomeric degradant in a formulated drug product during an accelerated stability study. By identifying the diagnostic ions of the isoaspartic acid (isoAsp), the top-down ECD experiment showed that the Asp9 in exenatide was converted to isoAsp9 to form the unknown isomeric degradant. The platform described here provides an accurate, straightforward, and low limit of detection method for the analysis of Asp isomerization as well as other potential low-level degradants in therapeutic polypeptides and proteins. It is especially useful for unstable and time-sensitive degradants and impurities.

Quantification of in vivo site-specific Asp isomerization and Asn deamidation of mAbs in animal serum using IP-LC-MS.

PubMed

Mehl, John T; Sleczka, Bogdan G; Ciccimaro, Eugene F; Kozhich, Alexander T; Gilbertson, Deb G; Vuppugalla, Ragini; Huang, Christine S; Stevens, Brenda; Mo, Jingjie; Deyanova, Ekaterina G; Wang, Yun; Huang, Richard Yc; Chen, Guodong; Olah, Timothy V

2016-08-01

Isomerization of aspartic acid and deamidation of asparagine are two common amino acid modifications that are of particular concern if located within the complementarity-determining region of therapeutic antibodies. Questions arise as to the extent of modification occurring in circulation due to potential exposure of the therapeutic antibody to different pH regimes. To enable evaluation of site-specific isomerization and deamidation of human mAbs in vivo, immunoprecipitation (IP) has been combined with LC-MS providing selective enrichment, separation and detection of naive and modified forms of tryptic peptides comprising complementarity-determining region sequences. IP-LC-MS can be applied to simultaneously quantify in vivo drug concentrations and measure the extent of isomerization or deamidation in PK studies conducted during the drug discovery stage.

Isomerization of n-hexane and n-pentane mixture on Pt-alumina catalyst

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

Radhi, M.A.; Al-Mutawalli, F.S.; Al-Sammarie, E.A.

A mixture of n-hexane and n-penane (1:1) by volume was isomerized on commercial Pt-alumina catalyst in a continuously fixed-bed reactor at atmospheric pressure. The effect of temperature, LHSV, hydrogen/hyrocarbon molar ratio and chlorine concentration were studied. It was found that the yield of isohexanes and isopentane increases with increasing the chloride added up to 0.1 and 0.2 mole % CCl/sub 4/ respectively. The rate of isomerization became slower at higher concentrations. Isomerization activity of the catalyst increases with increasing temperature ranging between 350-400/sup 0/C. The yield of isomers decrease with increasing temperature above 400/sup 0/C. The relative conversion of n-hexanemore » in the mixture was found to be more than the conversion of pure n-hexane at the same conditions.« less

A viable method and configuration for fermenting biomass sugars to ethanol using native Saccharomyces cerevisiae.

PubMed

Yuan, Dawei; Rao, Kripa; Varanasi, Sasidhar; Relue, Patricia

2012-08-01

A system that incorporates a packed bed reactor for isomerization of xylose and a hollow fiber membrane fermentor (HFMF) for sugar fermentation by yeast was developed for facile recovery of the xylose isomerase enzyme pellets and reuse of the cartridge loaded with yeast. Fermentation of pre-isomerized poplar hydrolysate produced using ionic liquid pretreatment in HFMF resulted in ethanol yields equivalent to that of model sugar mixtures of xylose and glucose. By recirculating model sugar mixtures containing partially isomerized xylose through the packed bed and the HFMF connected in series, 39 g/l ethanol was produced within 10h with 86.4% xylose utilization. The modular nature of this configuration has the potential for easy scale-up of the simultaneous isomerization and fermentation process without significant capital costs. Copyright © 2012 Elsevier Ltd. All rights reserved.

Kinetics of enzymes with iso-mechanisms: analysis of product inhibition.

PubMed Central

Rebholz, K L; Northrop, D B

1993-01-01

Isomerizations of free enzyme can be detected in kinetic patterns of product inhibition when the isomerization is partially rate-limiting. The kinetic pattern is non-competitive, owing to binding of substrate and product to different forms of free enzyme. This adds an additional term to the rate equation, sometimes represented as KSP. Several kineticists have noted that, as the rate of isomerization becomes high in relation to catalytic turnover, the intercept effect will become small, KSP will approach infinity, and the pattern will look competitive. Britton [(1973) Biochem. J. 133, 255-261] asserted that KSP will also approach infinity when the rate of isomerization becomes low. This second assertion is incorrect and can be traced to the particular model and graphical representation used to examine KSP as a function of relative rate constants. The function portrayed as a parabola with two roots for KSP is, instead, a straight line with one root. The algebraic condition justifying the second root obtains in the limit of zero in the rate of reaction and thus is not experimentally relevant, and the appearance of competitive inhibition, based on KSP alone, is not valid. Using a more general model, new equations are derived and presented which provide direct calculations of the apparent rate constants for free enzyme isomerizations from product-inhibition data when the equilibrium of the isomerization is near 1, and useful limits for the rate constants when greater than or less than 1. PMID:7980736

Enhanced Deformation of Azobenzene-Modified Liquid Crystal Polymers under Dual Wavelength Exposure: A Photophysical Model

NASA Astrophysics Data System (ADS)

Liu, Ling; Onck, Patrick R.

2017-08-01

Azobenzene-embedded liquid crystal polymers can undergo mechanical deformation in response to ultraviolet (UV) light. The natural rodlike trans state azobenzene absorbs UV light and isomerizes to a bentlike cis state, which disturbs the order of the polymer network, leading to an anisotropic deformation. The current consensus is that the magnitude of the photoinduced deformation is related to the statistical building up of molecules in the cis state. However, a recent experimental study [Liu and Broer, Nat. Commun. 6 8334 (2015)., 10.1038/ncomms9334] shows that a drastic (fourfold) increase of the photoinduced deformation can be generated by exposing the samples simultaneously to 365 nm (UV) and 455 nm (visible) light. To elucidate the physical mechanism that drives this increase, we develop a two-light attenuation model and an optomechanical constitutive relation that not only accounts for the statistical accumulation of cis azobenzenes, but also for the dynamic trans-cis-trans oscillatory isomerization process. Our experimentally calibrated model predicts that the optimal single-wavelength exposure is 395 nm light, a pronounced shift towards the visible spectrum. In addition, we identify a range of optimal combinations of two-wavelength lights that generate a favorable response for a given amount of injected energy. Our model provides mechanistic insight into the different (multi)wavelength exposures used in experiments and, at the same time, opens new avenues towards enhanced, multiwavelength optomechanical behavior.

Single-molecule junction of an overcrowded ethylene with binary conductance states

NASA Astrophysics Data System (ADS)

Koike, Masato; Fujii, Shintaro; Cho, Haruna; Shoji, Yoshiaki; Nishino, Tomoaki; Fukushima, Takanori; Kiguchi, Manabu

2018-03-01

Overcrowded ethylene 1 shows mechanochromic behavior with contrasting color change between yellow and violet arising from its conformational isomerization, which should also be accompanied by the change in the electronic structure. Here, we report a single-molecule electronic study of 1 using scanning tunneling microcopy (STM) and STM-based break junction techniques. The single-molecule junction of 1 sandwiched by Au electrodes showed two distinct high- and low-conductance states with the conductance values of 0.003 and 0.0002 G 0. The high-conductance state is one order of magnitude more conductive than the low-conductance state. The two states can be ascribed to two conformational isomers of 1 in the junction.

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

2015-03-02

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fragmentation of Small Molecules by Photo-Double Ionization

NASA Astrophysics Data System (ADS)

Osipov, Timur

2008-05-01

Molecular structure, formation, breakup pathways and recombination formed the subject of many theoretical and experimental studies. Among molecular species like H2, CO, N2, O2 recently great attention has been paid to the dynamics of the fragmentations and rearrangements of C2H2 molecule. Nature's smallest stable hydrocarbon, the symmetric linear acetylene molecule, C2H2, is an important polyatomic system for the study of photo initiated processes. Important features of the intramolecular dynamics in neutral acetylene have been revealed over many years through numerous spectroscopic studies. More recently, the availability of synchrotron radiation and intense laser sources has lead to intriguing studies of the ionization, isomerization and breakup dynamics of acetylene ions. Of particular interest are the yields into the symmetric (CH^+/CH^+), deprotonation (HCC^+/H^+) and quasi-symmetric (HHC^+/C^+) channels, the latter involving isomerization from the neutral acetylene structure into the vinylidene configuration prior to breakup. One expects that the products of dissociation, their kinetic energy releases (KER) and the isomerization times will depend on the particular initial electronic states of the dication involved, but such detailed information has heretofore not been available. We will present the results of the experiment where the dication of acetylene is prepared by Auger decay following core-level X-ray photoionization. Cold Target Recoil Ion Momentum Spectroscopy technique was used to measure the corresponding 3d momentum vectors of Auger electrons and recoil ions in coincidence. We will show that this experimental approach, in combination with ab initio quantum mechanical calculations, can yield a comprehensive map of the two-body dissociation pathways including transition through different electronic energy surfaces, barriers to direct dissociation and the associated rearrangement channels. Work done in collaboration with T. Rescigno, T. Weber, S. Miyabe, M. Hertlein, B. Feinberg, M. Prior, and A. Belkacem, Lawrence Berkeley National Laboratory; T. Jahnke, O. Jagutzki, L. Schmidt, M. Sch"offler, L. Foucar, S. Sch"ossler, T. Havermeier, S. Voss, and R. D"orner, Institut fur Kernphysik, J. W. Goethe-Universitat Frankfurt am Main; A. Landers, Auburn University, Alabama; A. Alnaser, Kansas State University; and L. Cocke, Kansas State University.

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

PubMed

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

2016-06-06

Reaction of a zinc/zirconium heterobimetallic complex with 1,5-cyclooctadiene (1,5-COD) results in slow isomerization to 1,3-cyclooctadiene (1,3-COD), along with the formation of a new complex that includes a cyclooctyne ligand bridging two metal centers. While analogous magnesium/zirconium and aluminum/zirconium heterobimetallic complexes are competent for the catalytic isomerization of 1,5-COD to 1,3-COD, only in the case of the zinc species is the cyclooctyne adduct observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of pH on the cis- trans isomerization of Valine-Proline dipeptide: An integrated NMR and theoretical investigation

NASA Astrophysics Data System (ADS)

Ivanova, Galya; Yakimova, Boryana; Angelova, Silvia; Stoineva, Ivanka; Enchev, Venelin

2010-06-01

The pH influence on the cis- trans isomerization of the Valine-Proline dipeptide was investigated by means of NMR spectral techniques and quantum chemical calculations at different computational levels. It was found that the process of isomerization is strongly pH dependent. The trans-isomer of Val-Pro is the more abundant isomer when the amino group is protonated, while an approximately equal distribution between the cis and trans-isomers for the neutral and anion forms of the dipeptide was confirmed.

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

PubMed Central

Butler, Michael J.; White, Andrew J. P.

2016-01-01

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

Bioinspired Orientation of β-Substituents on Porphyrin Antenna Ligands Switches Ytterbium(III) NIR Emission with Thermosensitivity.

PubMed

Ning, Yingying; Ke, Xian-Sheng; Hu, Ji-Yun; Liu, Yi-Wei; Ma, Fang; Sun, Hao-Ling; Zhang, Jun-Long

2017-02-20

"Configurational isomerism" is an important approach found in naturally occurring chlorophylls to modulate light harvesting function without significant structural changes; however, this feature has been seldom applied in design of antenna ligands for lanthanide (Ln) sensitization. In this work, we introduced a bioinspired approach by orientation of β-dilactone moieties on porphyrinates, namely cis-/trans-porphodilactones, to modulate the energy transfer process from the lowest triplet excited state of the ligand (T 1 ) to the emitting level of ytterbium(III) ( 2 F 5/2 , Yb*). Interestingly, near-infrared (NIR) emission of Yb(III) could be switched "on" by the cis-porphodilactone ligand, while the trans-isomer renders Yb(III) emission "off" and the ratio of quantum yields is ∼8. Analysis of the structure-photophysical properties relationship suggests that the significant emission difference is correlated to the energy gaps between T 1 and Yb* (1152 cm -1 in the cis- vs -25 cm -1 in the trans-isomer). More interestingly, due to back energy transfer (BEnT), the Yb(III) complex of cis-porphodilactone exhibits NIR emission with high thermosensitivity (4.0%°C -1 in solution and 4.9%°C -1 in solid state), comparable to previously reported terbium (Tb) and europium (Eu) visible emitters, in contrast to the trivial emission changes of the trans-isomer and porphyrin and porpholactone analogues. This work opens up new access to design NIR emissive Ln complexes by bioinspired modification of antenna ligands.

Chemical Modeling for Predicting the Abundances of Certain Aldimines and Amines in Hot Cores

NASA Astrophysics Data System (ADS)

Sil, Milan; Gorai, Prasanta; Das, Ankan; Bhat, Bratati; Etim, Emmanuel E.; Chakrabarti, Sandip K.

2018-02-01

We consider six isomeric groups ({{CH}}3{{N}}, {{CH}}5{{N}}, {{{C}}}2{{{H}}}5{{N}}, {{{C}}}2{{{H}}}7{{N}}, {{{C}}}3{{{H}}}7{{N}}, and {{{C}}}3{{{H}}}9{{N}}) to review the presence of amines and aldimines within the interstellar medium (ISM). Each of these groups contains at least one aldimine or amine. Methanimine ({{CH}}2{NH}) from {{CH}}3{{N}} and methylamine ({{CH}}3{{NH}}2) from {{CH}}5{{N}} isomeric group were detected a few decades ago. Recently, the presence of ethanimine ({{CH}}3{CHNH}) from {{{C}}}2{{{H}}}5{{N}} isomeric group has been discovered in the ISM. This prompted us to investigate the possibility of detecting any aldimine or amine from the very next three isomeric groups in this sequence: {{{C}}}2{{{H}}}7{{N}}, {{{C}}}3{{{H}}}7{{N}}, and {{{C}}}3{{{H}}}9{{N}}. We employ high-level quantum chemical calculations to estimate accurate energies of all the species. According to enthalpies of formation, optimized energies, and expected intensity ratio, we found that ethylamine (precursor of glycine) from {{{C}}}2{{{H}}}7{{N}} isomeric group, (1Z)-1-propanimine from {{{C}}}3{{{H}}}7{{N}} isomeric group, and trimethylamine from {{{C}}}3{{{H}}}9{{N}} isomeric group are the most viable candidates for the future astronomical detection. Based on our quantum chemical calculations and from other approximations (from prevailing similar types of reactions), a complete set of reaction pathways to the synthesis of ethylamine and (1Z)-1-propanimine is prepared. Moreover, a large gas-grain chemical model is employed to study the presence of these species in the ISM. Our modeling results suggest that ethylamine and (1Z)-1-propanimine could efficiently be formed in hot-core regions and could be observed with present astronomical facilities. Radiative transfer modeling is also implemented to additionally aid their discovery in interstellar space.

Structure of ²⁰⁷Pb populated in ²⁰⁸Pb + ²⁰⁸Pb deep-inelastic collisions*

DOE PAGES

Shand, C. M.; Wilson, E.; Podolyák, Zs.; ...

2015-01-01

The yrast structure of 207Pb above the 13/2 + isomeric state has been investigated in deep-inelastic collisions of 208Pb and 208Pb at ATLAS, Argonne National Laboratory. New and previously observed transitions were measured using the Gammasphere detector array. The level scheme of 207Pb is presented up to ~ 6 MeV, built using coincidence and γ-ray intensity analyses. In addition, the spin and parity assignments of states were made, based on angular distributions and comparisons to shell model calculations.

Review of metastable states in heavy nuclei

DOE PAGES

Dracoulis, G. D.; Walker, P. M.; Kondev, F. G.

2016-05-31

Here, the structure of nuclear isomeric states is reviewed in the context of their role in contemporary nuclear physics research. Emphasis is given to high-spin isomers in heavy nuclei, with A ≳ 150. The possibility to exploit isomers to study some of the most exotic nuclei is a recurring theme. In spherical nuclei, the role of octupole collectivity is discussed in detail, while in deformed nuclei the limitations of the K quantum number are addressed. Isomer targets and isomer beams are considered, along with applications related to energy storage, astrophysics, medicine, and experimental advances.

Structure of ²⁰⁷Pb populated in ²⁰⁸Pb + ²⁰⁸Pb deep-inelastic collisions*

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

Shand, C. M.; Wilson, E.; Podolyák, Zs.

The yrast structure of 207Pb above the 13/2 + isomeric state has been investigated in deep-inelastic collisions of 208Pb and 208Pb at ATLAS, Argonne National Laboratory. New and previously observed transitions were measured using the Gammasphere detector array. The level scheme of 207Pb is presented up to ~ 6 MeV, built using coincidence and γ-ray intensity analyses. In addition, the spin and parity assignments of states were made, based on angular distributions and comparisons to shell model calculations.

Determination of the formation of dark state via depleted spontaneous emission in a complex solvated molecule.

PubMed

Guo, Xunmin; Wang, Sufan; Xia, Andong; Su, Hongmei

2007-07-05

We present a general two-color two-pulse femtosecond pump-dump approach to study the specific population transfer along the reaction coordinate through the higher vibrational energy levels of excited states of a complex solvated molecule via the depleted spontaneous emission. The time-dependent fluorescence depletion provides the correlated dynamical information between the monitored fluorescence state and the SEP "dumped" dark states, and therefore allow us to obtain the dynamics of the formation of the dark states corresponding to the ultrafast photoisomerization processes. The excited-state dynamics of LDS 751 have been investigated as a function of solvent viscosity and solvent polarity, where a cooperative two-step isomerization process is clearly identified within LDS 751 upon excitation.

Isomeric Character of the Lowest Observed 4+ State in 44S

NASA Astrophysics Data System (ADS)

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

2017-02-01

Previous experiments observed a 4+ state in the N =28 nucleus 44S and suggested that this state may exhibit a hindered E 2 -decay rate, inconsistent with being a member of the collective ground state band. We populate this state via two-proton knockout from a beam of exotic 46Ar projectiles and measure its lifetime using the recoil distance method with the GRETINA γ -ray spectrometer. The result, 76 (14 )stat(20 )syst ps , implies a hindered transition of B (E 2 ;4+→21+)=0.61 (19 ) single-particle or Weisskopf units strength and supports the interpretation of the 4+ state as a K =4 isomer, the first example of a high-K isomer in a nucleus of such low mass.

Measurement of excitation functions and analysis of isomeric population in some reactions induced by proton on natural indium at low energy

NASA Astrophysics Data System (ADS)

Muhammed Shan, P. T.; Musthafa, M. M.; Najmunnisa, T.; Mohamed Aslam, P.; Rajesh, K. K.; Hajara, K.; Surendran, P.; Nair, J. P.; Shanbagh, Anil; Ghugre, S.

2018-06-01

The excitation functions for reaction residues populated via 115In(p , p) 115 mIn, 115In(p , pn) 114 mIn, 115In(p , p 2 n) 113 mIn, 113In(p , p) 113 mIn, 115In(p , nα) 111 mCd, 115In(p , 3 n) 113Sn and 113In(p , n) 113Sn channels were measured over the proton energy range of 8-22 MeV using stacked foil activation technique. Theoretical analysis of the data were performed within the framework of two statistical model codes EMPIRE-3.2 and TALYS-1.8. Isomeric cross section ratio for isomeric pairs m,g 115In, m,g 114In, m,g 113In, 113Sn m,g and m,g 111Cd were determined for the first time. The dependence of isomeric cross section ratio on various factors are analysed.

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.

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

PubMed Central

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-01-01

Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

Steranes and triterpanes generated from kerogen pyrolysis in the absence and presence of minerals

NASA Technical Reports Server (NTRS)

Tannenbaum, E.; Ruth, E.; Kaplan, I. R.

1986-01-01

Changes in the degree of isomerization of steranes and triterpanes during kerogen pyrolysis in the absence or presence of minerals are described. Kerogen from a Monterey Formation diatomite core sample was pyrolyzed under reduced pressure at 300 C for 2-1000 hrs in the presence or absence of calcite, illite, and montmorillonite. It is observed that the extent of isomerization of biomakers in C-20 in 14 alpha(H), 17 alpha(H)-steranes, at C-22 in 17 alpha(H), 21 beta(H)-hopanes and of 17 beta(H), 21 beta(H)-hopanes correlates to early diagenetic stages in rock extracts from sedimentary basins, and faster isomerization for steranes and triterpanes in the bitumen then for those in the kerogen structure are detected. The effects of the minerals on the isomerization reactions are examined; calcite inhibits, and illite and montmorillonite catalyze the reactions.

A new fundamental type of conformational isomerism

NASA Astrophysics Data System (ADS)

Canfield, Peter J.; Blake, Iain M.; Cai, Zheng-Li; Luck, Ian J.; Krausz, Elmars; Kobayashi, Rika; Reimers, Jeffrey R.; Crossley, Maxwell J.

2018-06-01

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term `akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Isomeric ratios in photonuclear reactions of molybdenum isotopes induced by bremsstrahlung in the giant dipole resonance region

NASA Astrophysics Data System (ADS)

Thiep, Tran Duc; An, Truong Thi; Cuong, Phan Viet; Vinh, Nguyen The; Hue, Bui Minh; Belov, A. G.; Maslov, O. D.; Mishinsky, G. V.; Zhemenik, V. I.

2017-01-01

We have determined the isomeric ratios of isomeric pairs 97m,gNb, 95m,gNb and 91m,gMo produced in 98Mo(γ, p)97m,gNb, 96Mo(γ, p)95m,gNb and 92Mo(γ, n)91m,gMo photonuclear reactions in the giant dipole resonance (GDR) region by the activation method. The results were analyzed, discussed and compared with the similar data from literature to examine the role of excitation energy, neutron configuration, channel effect and direct and pre-equilibrium processes in (γ, p) photonuclear reactions. In this work the isomeric ratios for 97m,gNb from 14 to 19 MeV, for 195m,gNb from14 to 24 MeV except 20 and 23.5 MeV and for 91m,gMo at 14 and 15 MeV are the first time measurements.

Fermentation of biomass sugars to ethanol using native industrial yeast strains.

PubMed

Yuan, Dawei; Rao, Kripa; Relue, Patricia; Varanasi, Sasidhar

2011-02-01

In this paper, the feasibility of a technology for fermenting sugar mixtures representative of cellulosic biomass hydrolyzates with native industrial yeast strains is demonstrated. This paper explores the isomerization of xylose to xylulose using a bi-layered enzyme pellet system capable of sustaining a micro-environmental pH gradient. This ability allows for considerable flexibility in conducting the isomerization and fermentation steps. With this method, the isomerization and fermentation could be conducted sequentially, in fed-batch, or simultaneously to maximize utilization of both C5 and C6 sugars and ethanol yield. This system takes advantage of a pH-dependent complexation of xylulose with a supplemented additive to achieve up to 86% isomerization of xylose at fermentation conditions. Commercially-proven Saccharomyces cerevisiae strains from the corn-ethanol industry were used and shown to be very effective in implementation of the technology for ethanol production. Copyright © 2010 Elsevier Ltd. All rights reserved.

Framework fluxionality of organometallic oxides: synthesis, crystal structure, EXAFS, and DFT studies on [[Ru(eta6-arene)]4Mo4O16] complexes.

PubMed

Laurencin, Danielle; Garcia Fidalgo, Eva; Villanneau, Richard; Villain, Françoise; Herson, Patrick; Pacifico, Jessica; Stoeckli-Evans, Helen; Bénard, Marc; Rohmer, Marie-Madeleine; Süss-Fink, Georg; Proust, Anna

2004-01-05

Reactions of the molybdates Na(2)MoO4.2 H2O and (nBu(4)N)2[Mo2O7] with [[Ru(arene)Cl(2)](2)] (arene=C(6)H5CH3, 1,3,5-C6H3(CH3)(3), 1,2,4,5-C6H2(CH3)4) in water or organic solvents led to formation of the triple-cubane organometallic oxides [[Ru(eta(6)-arene)](4)Mo4O16], whose crystal and molecular structures were determined. Refluxing triple cubane [[Ru(eta(6)-C6H5CH3)](4)Mo4O16] in methanol caused partial isomerization to the windmill form. The two isomers of [[Ru(eta(6)-C6H5CH3)](4)Mo4O16] were characterized by Raman and Mo K-edge X-ray absorption spectroscopy (XAS), both in the solid-state and in solution. This triple-cubane isomer was also used as a spectroscopic model to account for isomerization of the p-cymene windmill [[Ru(eta(6)-1,4-CH3C6H4CH(CH3)2)](4)Mo4O16] in solution. Using both Raman and XAS techniques, we were then able to determine the ratio between the windmill and triple-cubane isomers in dichloromethane and in chloroform. Density functional calculations on [[Ru(eta(6)-arene)](4)Mo4O16] (arene=C6H6, C6H5CH3, 1,3,5-C6H3(CH3)3, 1,4-CH3C6H4CH(CH3)2, C6(CH3)6) suggest that the windmill form is intrinsically more stable, provided the complexes are assumed to be isolated. Intramolecular electrostatic interactions and steric bulk induced by substituted arenes were found to modulate but not to reverse the energy difference between the isomers. The stability of the triple-cubane isomers should therefore be accounted for by effects of the surroundings that induce a shift in the energy balance between both forms.

Rational design of a pH-insensitive cyan fluorescent protein CyPet2 based on the CyPet crystal structure.

PubMed

Liu, Rui; Hu, Xiao-Jian; Ding, Yu

2017-06-01

The emission spectrum of widely used CyPet is pH-sensitive. In order to synthesize a pH-insensitive cyan fluorescent protein by rational design, we solved the crystal structures of CyPet under different pH conditions. The indole group of the CyPet chromophore adopts a cis-coplanar conformation in acidic and neutral conditions, while it converts to trans-coplanar under basic conditions. His148 and Glu222 play a vital role in this isomerization. The pH-sensitive chromophore isomerization and change in the emission spectrum can be explained by the coexistence of several different fluorescent states. We trap the chromophore in the trans conformation by A167I mutation (CyPet2), which also prevents the multiconformation of the seventh β-strand. CyPet2 exhibits an unchanged emission spectral shape as a function of pH. © 2017 Federation of European Biochemical Societies.

Divergent Coordination Chemistry: Parallel Synthesis of [2×2] Iron(II) Grid-Complex Tauto-Conformers.

PubMed

Schäfer, Bernhard; Greisch, Jean-François; Faus, Isabelle; Bodenstein, Tilmann; Šalitroš, Ivan; Fuhr, Olaf; Fink, Karin; Schünemann, Volker; Kappes, Manfred M; Ruben, Mario

2016-08-26

The coordination of iron(II) ions by a homoditopic ligand L with two tridentate chelates leads to the tautomerism-driven emergence of complexity, with isomeric tetramers and trimers as the coordination products. The structures of the two dominant [Fe(II) 4 L4 ](8+) complexes were determined by X-ray diffraction, and the distinctness of the products was confirmed by ion-mobility mass spectrometry. Moreover, these two isomers display contrasting magnetic properties (Fe(II) spin crossover vs. a blocked Fe(II) high-spin state). These results demonstrate how the coordination of a metal ion to a ligand that can undergo tautomerization can increase, at a higher hierarchical level, complexity, here expressed by the formation of isomeric molecular assemblies with distinct physical properties. Such results are of importance for improving our understanding of the emergence of complexity in chemistry and biology. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Hydrophobic Hydration of Stimulus-Responsive Polyproteins Measured by Single Molecule Force Spectroscopy

NASA Astrophysics Data System (ADS)

Zauscher, Stefan

2007-03-01

We present a new procedure to reduce and analyze force-extension data obtained by single molecule force spectroscopy (SMFS). This approach allows, for the first time, to infer effects of solvent quality and minor changes in molecular architecture on molecular-elasticity of individual (bio)macromolecules. Specifically, we show how changes in the effective Kuhn segment length can be used to interpret the hydrophobic hydration behavior of elastin-like polypeptides (ELPs).Our results are intriguing as they suggest that SMFS in combination with our analysis procedure can be used to study the subtleties of polypeptide-water interactions on the single molecule level. We also report on the force-induced cis-trans isomerization of prolines, which are repeated every fifth residue in the main chain of ELPs. We present evidence for this mechanism by Monte Carlo simulations of the force-extension curves using an elastically coupled two-state system. Our results suggest that SMFS could be used to assay proline cis-trans isomerization in proteins and may thus have significant potential diagnostic utility.

Substitution and solvent effects in the chalcones isomerization barrier of flavylium photochromic systems.

PubMed

Roque, Ana; Lima, João Carlos; Parola, A Jorge; Pina, Fernando

2007-04-01

Useful application of photochromic compounds as optical memories implies the existence of a large kinetic barrier between the forms interconverted by light. In the case of flavylium salts, the ground state isomerization barrier between the photoisomerizable chalcone isomers is shown to correlate with the electron donating ability of the substituents, measured by their effects in the (1)H NMR chemical shifts of the aromatic protons. Substitution with electron donating groups in ring A lowers the barrier while substitution at ring B has the opposite effect. However, in water, the observed increase is higher than expected in the case of compound 4',9-dihydroxychalcone when compared with the analogous 4'-dimethylamino-9-hydroxychalcone, containing a better electron donating group in the same position. Our interpretation is that the water network is providing an efficient pathway to form tautomers. In acetonitrile, unlike water, the expected order is indeed observed: E(a)(4',9-dihydroxychalcone) = 60 kJ mol(-1) < E(a) (4'-dimethylamino-9-hydroxychalcone) = 69 kJ mol(-1).

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization.

PubMed

Li, Chun-Biu; Matsunaga, Yasuhiro; Toda, Mikito; Komatsuzaki, Tamiki

2005-11-08

By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well. We elucidate the global phase-space structure which gives rise to the non-Markovian dynamics or the dynamical correlation of sequential multisaddle chemical reactions. The phase-space structure relevant to the controllability of the product state in chemical reactions is also discussed.

Interaction of a Model Peptide with a Water--Bilayer System

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M. A.

1994-01-01

We discuss a molecular dynamics study of the alanine dipeptide at the interface between water and a glycerol-1-monooleate (GMO) bilayer. The dipeptide is interfacially active and incorporates into the bilayer without disrupting its structure. The interfacial region that is readily penetrated by the dipeptide spans the entire head group portion of the bilayer. The polar groups of the alanine dipeptide mostly remain well solvated by water and the oxygen atoms of GMO, and conformations of the dipeptide are characterized by (phi, psi) angles typical of alpha-helix and beta-sheet structures. When the molecule is deeper in the bilayer, the C(sub 7eq) state also becomes stable. The barrier to the isomerization reaction at the interface is lower than in bulk phases. After 7 ns of trajectories, the system is not fully equilibrated, due to slow collective motions involving GMO head groups. These result in decreased mobility and lower rates of isomerization of the dipeptide at the interface.

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.

Study of the 26Alm (d ,p )27Al Reaction and the Influence of the 26 0+ Isomer on the Destruction of 26Al in the Galaxy

NASA Astrophysics Data System (ADS)

Almaraz-Calderon, S.; Rehm, K. E.; Gerken, N.; Avila, M. L.; Kay, B. P.; Talwar, R.; Ayangeakaa, A. D.; Bottoni, S.; Chen, A. A.; Deibel, C. M.; Dickerson, C.; Hanselman, K.; Hoffman, C. R.; Jiang, C. L.; Kuvin, S. A.; Nusair, O.; Pardo, R. C.; Santiago-Gonzalez, D.; Sethi, J.; Ugalde, C.

2017-08-01

The existence of 26 (t1 /2=7.17 ×105 yr ) in the interstellar medium provides a direct confirmation of ongoing nucleosynthesis in the Galaxy. The presence of a low-lying 0+ isomer (26m ), however, severely complicates the astrophysical calculations. We present for the first time a study of the 26Al m(d ,p ) 27Al reaction using an isomeric 26Al beam. The selectivity of this reaction allowed the study of ℓ=0 transfers to T =1 /2 , and T =3 /2 states in 27Al. Mirror symmetry arguments were then used to constrain the 26Al m(p ,γ ) 27Si reaction rate and provide an experimentally determined upper limit of the rate for the destruction of isomeric 26Al via radiative proton capture reactions, which is expected to dominate the destruction path of 26Alm in asymptotic giant branch stars, classical novae, and core collapse supernovae.

Manipulation of small particles at solid liquid interface: light driven diffusioosmosis.

PubMed

Feldmann, David; Maduar, Salim R; Santer, Mark; Lomadze, Nino; Vinogradova, Olga I; Santer, Svetlana

2016-11-03

The strong adhesion of sub-micron sized particles to surfaces is a nuisance, both for removing contaminating colloids from surfaces and for conscious manipulation of particles to create and test novel micro/nano-scale assemblies. The obvious idea of using detergents to ease these processes suffers from a lack of control: the action of any conventional surface-modifying agent is immediate and global. With photosensitive azobenzene containing surfactants we overcome these limitations. Such photo-soaps contain optical switches (azobenzene molecules), which upon illumination with light of appropriate wavelength undergo reversible trans-cis photo-isomerization resulting in a subsequent change of the physico-chemical molecular properties. In this work we show that when a spatial gradient in the composition of trans- and cis- isomers is created near a solid-liquid interface, a substantial hydrodynamic flow can be initiated, the spatial extent of which can be set, e.g., by the shape of a laser spot. We propose the concept of light induced diffusioosmosis driving the flow, which can remove, gather or pattern a particle assembly at a solid-liquid interface. In other words, in addition to providing a soap we implement selectivity: particles are mobilized and moved at the time of illumination, and only across the illuminated area.

Application of a novel type impinging streams reactor in solid-liquid enzyme reactions and modeling of residence time distribution using GDB model.

PubMed

Fatourehchi, Niloufar; Sohrabi, Morteza; Dabir, Bahram; Royaee, Sayed Javid; Haji Malayeri, Adel

2014-02-05

Solid-liquid enzyme reactions constitute important processes in biochemical industries. The isomerization of d-glucose to d-fructose, using the immobilized glucose isomerase (Sweetzyme T), as a typical example of solid-liquid catalyzed reactions has been carried out in one stage and multi-stage novel type of impinging streams reactors. Response surface methodology was applied to determine the effects of certain pertinent parameters of the process namely axial velocity (A), feed concentration (B), nozzles' flow rates (C) and enzyme loading (D) on the performance of the apparatus. The results obtained from the conversion of glucose in this reactor were much higher than those expected in conventional reactors, while residence time was decreased dramatically. Residence time distribution (RTD) in a one-stage impinging streams reactor was investigated using colored solution as the tracer. The results showed that the flow pattern in the reactor was close to that in a continuous stirred tank reactor (CSTR). Based on the analysis of flow region in the reactor, gamma distribution model with bypass (GDB) was applied to study the RTD of the reactor. The results indicated that RTD in the impinging streams reactor could be described by the latter model. Copyright © 2013 Elsevier Inc. All rights reserved.

Manipulation of small particles at solid liquid interface: light driven diffusioosmosis

NASA Astrophysics Data System (ADS)

Feldmann, David; Maduar, Salim R.; Santer, Mark; Lomadze, Nino; Vinogradova, Olga I.; Santer, Svetlana

2016-11-01

The strong adhesion of sub-micron sized particles to surfaces is a nuisance, both for removing contaminating colloids from surfaces and for conscious manipulation of particles to create and test novel micro/nano-scale assemblies. The obvious idea of using detergents to ease these processes suffers from a lack of control: the action of any conventional surface-modifying agent is immediate and global. With photosensitive azobenzene containing surfactants we overcome these limitations. Such photo-soaps contain optical switches (azobenzene molecules), which upon illumination with light of appropriate wavelength undergo reversible trans-cis photo-isomerization resulting in a subsequent change of the physico-chemical molecular properties. In this work we show that when a spatial gradient in the composition of trans- and cis- isomers is created near a solid-liquid interface, a substantial hydrodynamic flow can be initiated, the spatial extent of which can be set, e.g., by the shape of a laser spot. We propose the concept of light induced diffusioosmosis driving the flow, which can remove, gather or pattern a particle assembly at a solid-liquid interface. In other words, in addition to providing a soap we implement selectivity: particles are mobilized and moved at the time of illumination, and only across the illuminated area.

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly

PubMed Central

Torbeev, Vladimir Yu.; Hilvert, Donald

2013-01-01

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m’s stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition—incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein—modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation. PMID:24262149

Both the cis-trans equilibrium and isomerization dynamics of a single proline amide modulate β2-microglobulin amyloid assembly.

PubMed

Torbeev, Vladimir Yu; Hilvert, Donald

2013-12-10

The human protein β2-microglobulin (β2m) aggregates as amyloid fibrils in patients undergoing long-term hemodialysis. Isomerization of Pro32 from its native cis to a nonnative trans conformation is thought to trigger β2m misfolding and subsequent amyloid assembly. To examine this hypothesis, we systematically varied the free-energy profile of proline cis-trans isomerization by replacing Pro32 with a series of 4-fluoroprolines via total chemical synthesis. We show that β2m's stability, (un)folding, and aggregation properties are all influenced by the rate and equilibrium of Pro32 cis-trans isomerization. As anticipated, the β2m monomer was either stabilized or destabilized by respective incorporation of (2S,4S)-fluoroproline, which favors the native cis amide bond, or the stereoisomeric (2S,4R)-fluoroproline, which disfavors this conformation. However, substitution of Pro32 with 4,4-difluoroproline, which has nearly the same cis-trans preference as proline but an enhanced isomerization rate, caused pronounced destabilization of the protein and increased oligomerization at neutral pH. More remarkably, these subtle alterations in chemical composition--incorporation of one or two fluorine atoms into a single proline residue in the 99 amino acid long protein--modulated the aggregation properties of β2m, inducing the formation of polymorphically distinct amyloid fibrils. These results highlight the importance of conformational dynamics for molecular assembly of an amyloid cross-β structure and provide insights into mechanistic aspects of Pro32 cis-trans isomerism in β2m aggregation.

Density functional theoretical study on enantiomerization of 2,2'-biphenol.

PubMed

Sahnoun, Riadh; Koseki, Shiro; Fujimura, Yuichi

2006-02-23

The S-R enantiomerization processes of 2,2'-biphenol (biphenol) have been investigated using density functional theory (DFT). Five isomers for biphenol were identified: I0, which is the most stable isomer; I1a and I1b, which are formed by a restricted rotation of one OH group; and I2a and I2b, which are formed by a restricted rotation of the two OH groups where a and b denote cis and trans configurations, respectively. Each isomer has R- and S-enantiomers. The energies relative to the most stable isomer I0 are 1.6, 3.3, 5.3, and 5.5 kcal mol(-1) for I1a, I1b, I2a, and I2b, respectively. The direct enantiomerization of I0, in which the phenol-ring rotation is considered to be the reaction coordinate while the OH rotations are frozen, is forbidden because of the repulsion between the two OH groups. The transition states for isomerizations of I0 to other isomers (I1a, I1b, I2a, or I2b) were calculated as well as those for the other direct enantiomerizations except for that of I0. From the viewpoint of the least number of the transition states and their low energy levels, the probable S-R enantiomerization of I0 is expressed as a sequential process of isomerization: I0,S --> I1a,S, a direct enantiomerization induced by one of the two OH rotations, I1a,S --> I1a,R, and another isomerization, I1a,R --> I0,R, that is, I0,S --> I1a,S --> I1a,R --> I0,R as the whole process. This process is effective in quantum control of the enantiomerization of biphenol and can be carried out by a sequence of a pump-dump IR laser-pulse scheme.

Remote control of soft nano-objects by light using azobenzene containing surfactants

NASA Astrophysics Data System (ADS)

Santer, Svetlana

2018-01-01

We review recent progress in the field of light responsive soft nano-objects. These are systems the shape, size, surface area and surface energy of which can be easily changed by low-intensity external irradiation. Here we shall specifically focus on microgels, DNA molecules, polymer brushes and colloidal particles. One convenient way to render these objects photosensitive is to couple them via ionic and/or hydrophobic interactions with azobenzene containing surfactants in a non-covalent way. The advantage of this strategy is that these surfactants can make any type of charged object light responsive without the need for possibly complicated (and irreversible) chemical conjugation. In the following, we will exclusively discuss only photosensitive surfactant systems. These contain a charged head and a hydrophobic tail into which an azobenzene group is incorporated, which can undergo reversible photo-isomerization from a trans- to a cis-configuration under UV illumination. These kinds of photo-isomerizations occur on a picosecond timescale and are fully reversible. The two isomers in general possess different polarity, i.e. the trans-state is less polar with a dipole moment of usually close to 0 Debye, while the cis-isomer has a dipole moment up to 3 Debye or more, depending on additional phenyl ring substituents. As part of the hydrophobic tail of a surfactant molecule, the photo-isomerization also changes the hydrophobicity of the molecule as a whole and hence its solubility, surface energy, and strength of interaction with other substances. Being a molecular actuator, which converts optical energy in to mechanical work, the azobenzene group in the shape of surfactant molecule can be utilized in order to actuate matter on larger time and length scale. In this paper we show several interesting examples, where azobenzene containing surfactants play the role of a transducer mediating between different states of size, shape, surface energy and spatial arrangement of various nanoscale soft-material systems.

Comparison of sugar molecule decomposition through glucose and fructose: a high-level quantum chemical study.

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

Assary, R. S.; Curtiss, L. A.; MSD)

Efficient chemical conversion of biomass is essential to produce sustainable energy and industrial chemicals. Industrial level conversion of glucose to useful chemicals, such as furfural, hydroxymethylfurfural, and levulinic acid, is a major step in the biomass conversion but is difficult because of the formation of undesired products and side reactions. To understand the molecular level reaction mechanisms involved in the decomposition of glucose and fructose, we have carried out high-level quantum chemical calculations [Gaussian-4 (G4) theory]. Selective 1,2-dehydration, keto-enol tautomerization, isomerization, retro-aldol condensation, and hydride shifts of glucose and fructose molecules were investigated. Detailed kinetic and thermodynamic analyses indicate that,more » for acyclic glucose and fructose molecules, the dehydration and isomerization require larger activation barriers compared to the retro-aldol reaction at 298 K in neutral medium. The retro-aldol reaction results in the formation of C2 and C4 species from glucose and C3 species from fructose. The formation of the most stable C3 species, dihydroxyacetone from fructose, is thermodynamically downhill. The 1,3-hydride shift leads to the cleavage of the C-C bond in the acyclic species; however, the enthalpy of activation is significantly higher (50-55 kcal/mol) than that of the retro-aldol reaction (38 kcal/mol) mainly because of the sterically hindered distorted four-membered transition state compared to the hexa-membered transition state in the retro-aldol reaction. Both tautomerization and dehydration are catalyzed by a water molecule in aqueous medium; however, water has little effect on the retro-aldol reaction. Isomerization of glucose to fructose and glyceraldehyde to dihydroxyacetone proceeds through hydride shifts that require an activation enthalpy of about 40 kcal/mol at 298 K in water medium. This investigation maps out accurate energetics of the decomposition of glucose and fructose molecules that is needed to help find more efficient catalysts for the conversion of hexose to useful chemicals.« less

Spectroscopic and computational studies of matrix-isolated iso-CHBr{sub 3}: Structure, properties, and photochemistry of iso-bromoform

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

George, Lisa; Kalume, Aimable; Wagner, James

Iso-polyhalomethanes are known reactive intermediates that play a pivotal role in the photochemistry of halomethanes in condensed phases. In this work, iso-bromoform (iso-CHBr{sub 3}) and its deuterated isotopomer were characterized by matrix isolation infrared and UV/visible spectroscopy, supported by ab initio and density functional theory calculations, to further probe the structure, spectroscopy, and photochemistry of this important intermediate. Selected wavelength laser irradiation of CHBr{sub 3} isolated in Ar or Ne matrices at {approx}5 K yielded iso-CHBr{sub 3}; the observed infrared and UV/visible absorptions are in excellent agreement with computational predictions, and the energies of various stationary points on the CHBr{submore » 3} potential energy surface were characterized computationally using high-level methods in combination with correlation consistent basis sets. These calculations show that, while the corresponding minima lie {approx}200 kJ/mol above the global CHBr{sub 3} minimum, the isomer is bound by some 60 kJ/mol in the gas phase with respect to the CHBr{sub 2}+ Br asymptote. The photochemistry of iso-CHBr{sub 3} was investigated by selected wavelength laser irradiation into the intense S{sub 0}{yields} S{sub 3} transition, which resulted in back photoisomerization to CHBr{sub 3}. Intrinsic reaction coordinate calculations confirmed the existence of a first-order saddle point connecting the two isomers, which lies energetically below the threshold of the radical channel. Subsequently, natural bond orbital analysis and natural resonance theory were used to characterize the important resonance structures of the isomer and related stationary points, which demonstrate that the isomerization transition state represents a crossover from dominantly covalent to dominantly ionic bonding. In condensed phases, the ion-pair dominated isomerization transition state structure is preferentially stabilized, so that the barrier to isomerization is lowered.« less

Effects of molecular and lattice structure on the thermal behaviours of some long chain length potassium(I) n-alkanoates

NASA Astrophysics Data System (ADS)

Nelson, Peter N.; Ellis, Henry A.; Taylor, Richard A.

2014-01-01

Lattice structures and thermal behaviours for some long chain potassium carboxylates (nc = 8-18, inclusive) are investigated using Fourier Transform Infrared spectroscopy, X-ray Powder Diffraction, Solid State spin decoupled 13C NMR spectroscopy, Differential Scanning Calorimetry and Thermogravimetry. The measurements show that the carboxyl groups are coordinated to potassium atoms via asymmetric chelating bidentate bonding, with extensive carboxyl intermolecular interactions to yield tetrahedral metal centers, irrespective of chain length. Furthermore, the hydrocarbon chains are crystallized in the fully extended all-trans configuration and are arranged as non-overlapping lamellar bilayer structures with closely packed methyl groups from opposite layers. Additionally, odd-even alternation, observed in density and methyl group chemical shift, is ascribed to the relative vertical distances between layers in the bilayer, that are not in the same plane. Therefore, for even chain homologues, where this distances is less than for odd chain adducts, more intimate packing is indicated. The phase sequences for all compounds show several reversible crystal-crystal transition associated with kinetically controlled gauche-trans isomerism of the polymethylene chains which undergo incomplete fusion when heated to the melt. The compounds degrade above 785 K to yield carbon dioxide, water, potassium oxide and an alkene.

Polarization-controlled optimal scatter suppression in transient absorption spectroscopy

PubMed Central

Malý, Pavel; Ravensbergen, Janneke; Kennis, John T. M.; van Grondelle, Rienk; Croce, Roberta; Mančal, Tomáš; van Oort, Bart

2017-01-01

Ultrafast transient absorption spectroscopy is a powerful technique to study fast photo-induced processes, such as electron, proton and energy transfer, isomerization and molecular dynamics, in a diverse range of samples, including solid state materials and proteins. Many such experiments suffer from signal distortion by scattered excitation light, in particular close to the excitation (pump) frequency. Scattered light can be effectively suppressed by a polarizer oriented perpendicular to the excitation polarization and positioned behind the sample in the optical path of the probe beam. However, this introduces anisotropic polarization contributions into the recorded signal. We present an approach based on setting specific polarizations of the pump and probe pulses, combined with a polarizer behind the sample. Together, this controls the signal-to-scatter ratio (SSR), while maintaining isotropic signal. We present SSR for the full range of polarizations and analytically derive the optimal configuration at angles of 40.5° between probe and pump and of 66.9° between polarizer and pump polarizations. This improves SSR by (or compared to polarizer parallel to probe). The calculations are validated by transient absorption experiments on the common fluorescent dye Rhodamine B. This approach provides a simple method to considerably improve the SSR in transient absorption spectroscopy. PMID:28262765

Confined-Pyrolysis as an Experimental Method for Hydrothermal Organic Synthesis

NASA Technical Reports Server (NTRS)

Leif, Roald N.; Simoneit, Bernd R. T.

1995-01-01

A closed pyrolysis system has been developed as a tool for studying the reactions of organic compounds under extreme hydrothermal conditions. Small high pressure stainless steel vessels in which the ratio of sediment or sample to water has been adjusted to eliminate the headspace at peak experimental conditions confines the organic components to the bulk solid matrix and eliminates the partitioning of the organic compounds away from the inorganic components during the experiment. Confined pyrolysis experiments were performed to simulate thermally driven catagenetic changes in sedimentary organic matter using a solids to water ratio of 3.4 to 1. The extent of alteration was measured by monitoring the steroid and triterpenoid biomarkers and polycyclic aromatic hydrocarbon distributions. These pyrolysis experiments duplicated the hydrothermal transformations observed in nature. Molecular probe experiments using alkadienes, alkenes and alkanes in H2O and D2O elucidated the isomerization and hydrogenation reactions of aliphatic and the competing oxidative reactions occurring under hydrothermal conditions. This confined pyrolysis technique is being applied to test experiments on organic synthesis of relevance to chemical evolution for the origin of life.

Observation of the 2+ isomer in 52Co

NASA Astrophysics Data System (ADS)

Orrigo, S. E. A.; Rubio, B.; Gelletly, W.; Blank, B.; Fujita, Y.; Giovinazzo, J.; Agramunt, J.; Algora, A.; Ascher, P.; Bilgier, B.; Cáceres, L.; Cakirli, R. B.; de France, G.; Ganioǧlu, E.; Gerbaux, M.; Grévy, S.; Kamalou, O.; Kozer, H. C.; Kucuk, L.; Kurtukian-Nieto, T.; Molina, F.; Popescu, L.; Rogers, A. M.; Susoy, G.; Stodel, C.; Suzuki, T.; Tamii, A.; Thomas, J. C.

2016-10-01

We report the first observation of the 2+ isomer in 52Co, produced in the β decay of the 0+, 52Ni ground state. We have observed three γ rays at 849, 1910, and 5185 keV characterizing the β de-excitation of the isomer. We have measured a half-life of 102(6) ms for the isomeric state. The Fermi and Gamow-Teller transition strengths for the β decay of Com52 to 52Fe have been determined. We also add new information on the β decay of the 6+, 52Co ground state, for which we have measured a half-life of 112(3) ms.

A: The Progression of a Catalytic Immune Response. B: Molecular Recognition of Anions by Silica Bound Sapphyrin

DTIC Science & Technology

1994-08-01

Diels - Alder reactions (58-60), Claisen rearrangements (43-45), olefin isomerization (73), a O-elimination (74), an asymmetric ketone reduction (54...phosphorothioate hapten3 ........ 19 Figure 5. Carboxylic acid hydrolysis .................... 21 Figure 6. Reaction coordinates for antibody catalyzed ...and catalyze the reaction. Thus, it is important to design transition analogs that closely mimic the transition state in every possible chemical

Toroidal high-spin isomers in light nuclei with N ≠ Z

NASA Astrophysics Data System (ADS)

Staszczak, A.; Wong, Cheuk-Yin

2015-11-01

The combined considerations of both the bulk liquid-drop-type behavior and the quantized aligned rotation with cranked Skyrme-Hartree-Fock approach revealed previously (Staszczak and Wong 2014 Phys. Lett. B 738 401) that even-even, N = Z, toroidal high-spin isomeric states have general occurrences for light nuclei with 28≤slant A≤slant 52. We find that in this mass region there are in addition N\

The use of dendrimers as high-performance shells for round-trip energy transfer: efficient trans-cis photoisomerization from an excited triplet state produced within a dendrimer shell.

PubMed

Miura, Yousuke; Momotake, Atsuya; Takeuchi, Keiichirou; Arai, Tatsuo

2011-01-01

A series of stilbene-cored poly(benzyl ether) dendrimers with benzophenone peripheries were synthesized and their photophysical and photochemical properties were studied. Fluorescence studies revealed that singlet-singlet energy transfer (SSET) from the stilbene core to the benzophenone units took place efficiently in dendrimers of all generations. Similarly, phosphorescence and time-resolved spectroscopic measurements indicated efficient triplet-triplet energy transfer (TTET) from the benzophenone periphery to the stilbene core. Upon excitation at 310 nm, the stilbene core isomerizes via an energy round trip within the dendrimer shell. The quantum yields for the energy round trip (Φ(ERT)), defined as the product of the quantum yields of SSET, intersystem crossing, and TTET (Φ(ERT) = Φ(SS)Φ(isc)Φ(TT)), were extremely high for all generations--99%, 95% and 94% for G1, G2, and G3, respectively--which means that the excitation energy of the dendrimer core was transferred to the dendrimer periphery and back to the core almost quantitatively. The quantum yield for photoisomerization of G1-G3 via an energy round trip was higher than for other stilbene-cored dendrimers, which mainly isomerize from the excited singlet state. Photostability in the dendrimers was also demonstrated and discussed.

Fission yield measurements at IGISOL

NASA Astrophysics Data System (ADS)

Lantz, M.; Al-Adili, A.; Gorelov, D.; Jokinen, A.; Kolhinen, V. S.; Mattera, A.; Moore, I.; Penttilä, H.; Pomp, S.; Prokofiev, A. V.; Rakopoulos, V.; Rinta-Antila, S.; Simutkin, V.; Solders, A.

2016-06-01

The fission product yields are an important characteristic of the fission process. In fundamental physics, knowledge of the yield distributions is needed to better understand the fission process. For nuclear energy applications good knowledge of neutroninduced fission-product yields is important for the safe and efficient operation of nuclear power plants. With the Ion Guide Isotope Separator On-Line (IGISOL) technique, products of nuclear reactions are stopped in a buffer gas and then extracted and separated by mass. Thanks to the high resolving power of the JYFLTRAP Penning trap, at University of Jyväskylä, fission products can be isobarically separated, making it possible to measure relative independent fission yields. In some cases it is even possible to resolve isomeric states from the ground state, permitting measurements of isomeric yield ratios. So far the reactions U(p,f) and Th(p,f) have been studied using the IGISOL-JYFLTRAP facility. Recently, a neutron converter target has been developed utilizing the Be(p,xn) reaction. We here present the IGISOL-technique for fission yield measurements and some of the results from the measurements on proton induced fission. We also present the development of the neutron converter target, the characterization of the neutron field and the first tests with neutron-induced fission.

Effective Ion Mobility Peak Width as a New Isomeric Descriptor for the Untargeted Analysis of Complex Mixtures Using Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Farenc, Mathilde; Paupy, Benoit; Marceau, Sabrina; Riches, Eleanor; Afonso, Carlos; Giusti, Pierre

2017-07-01

Ion mobility coupled with mass spectrometry was proven to be an efficient way to characterize complex mixtures such as petroleum samples. However, the identification of isomeric species is difficult owing to the molecular complexity of petroleum and no availability of standard molecules. This paper proposes a new simple indicator to estimate the isomeric content of highly complex mixtures. This indicator is based on the full width at half maximum (FWHM) of the extracted ion mobility peak measured in millisecond or square angstrom that is corrected for instrumental factors such as ion diffusion. This value can be easily obtained without precisely identifying the number of isomeric species under the ion mobility peaks. Considering the Boduszynski model, the ion mobility profile for a particular elemental composition is expected to be a continuum of various isomeric species. The drift time-dependent fragmentation profile was studied and confirmed this hypothesis, a continuous evolution of the fragmentation profile showing that the larger alkyl chain species were detected at higher drift time values. This new indicator was proven to be a fast and efficient method to compare vacuum gas oils for which no difference was found using other analytical techniques.

Role of F357 as an Oxygen Gate in the Oxidative Half-Reaction of Choline Oxidase.

PubMed

Salvi, Francesca; Rodriguez, Isela; Hamelberg, Donald; Gadda, Giovanni

2016-03-15

Choline oxidase from Arthrobacter globiformis catalyzes the oxidation of choline to glycine betaine by using oxygen as an electron acceptor. A partially rate limiting isomerization of the reduced wild-type enzyme during the reaction with oxygen was previously detected using solvent viscosity effects. In this study, we hypothesized that the side chains of M62 and F357, located at the entrance to the active site of choline oxidase, may be related to the slow isomerization detected. We engineered a double-variant enzyme M62A/F357A. The kinetic characterization of the double-variant enzyme showed a lack of the isomerization detected in wild-type choline oxidase, and a lack of saturation with an oxygen concentration as high as 1 mM, while most other kinetic parameters were similar to those of wild-type choline oxidase. The kinetic characterization of the single-variant enzymes established that only the side chain of F357 plays a role in the isomerization of choline oxidase in the oxidative half-reaction. Molecular dynamics studies suggest that the slow isomerization related to F357 is possibly due to the participation of the phenyl ring in a newly proposed gating mechanism for a narrow tunnel, assumed to regulate the access of oxygen to the reduced cofactor.

Isolation and characterization of (15Z)-lycopene thermally generated from a natural source

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

Takehara, Munenori, E-mail: takehara@mat.usp.ac.jp; Kuwa, Takahiro; Inoue, Yoshinori

(15Z)-Lycopene was prepared by thermal isomerization of (all-E)-lycopene derived from tomatoes, and isolated by using a series of chromatographies. The fine red crystalline powder of (15Z)-lycopene was obtained from 556 mg of (all-E)-lycopene with a yield of 0.6 mg (purity: reversed-phase HPLC, 97.2%; normal-phase HPLC, ≥99.9%), and {sup 1}H and {sup 13}C NMR spectra of the isomer were fully assigned. More refined computational analyses that considered differences in the energy levels of the conformers involved in isomerization have also determined the stabilities of (15Z)-lycopene and other geometric isomers, along with the activation energies during isomerization from the all-E form. The fine controlmore » of conditions for HPLC separation and an advanced theoretical insight into geometric isomerization have led to the discovery of the 15Z-isomer generated from a natural source. - Highlights: • (15Z)-lycopene, isomerized from the all-E form of a natural source, was purified. • The obtained (15Z)-lycopene was structurally identified by an NMR analysis. • A modified theoretical study accounted for the generation of the 15Z-isomer. • This study demonstrated the occurrence of the isomer from a natural origin.« less

New low-spin states of 122Xe observed via high-statistics β-decay of 122Cs

NASA Astrophysics Data System (ADS)

Jigmeddorj, B.; Garrett, P. E.; Andreoiu, C.; Ball, G. C.; Bruhn, T.; Cross, D. S.; Garnsworthy, A. B.; Hadinia, B.; Moukaddam, M.; Park, J.; Pore, J. L.; Radich, A. J.; Rajabali, M. M.; Rand, E. T.; Rizwan, U.; Svensson, C. E.; Voss, P.; Wang, Z. M.; Wood, J. L.; Yates, S. W.

2018-05-01

Excited states of 122Xe were studied via the β+/EC decay of 122Cs with the 8π γ-ray spectrometer at the TRIUMF-ISAC facility. Compton-suppressed HPGe detectors were used for measurements of γ-ray intensities, γγ coincidences, and γ-γ angular correlations. Two sets of data were collected to optimize the decays of the ground (21.2 s) and isomeric (3.7 min) states of 122Cs. The data collected have enabled the observation of about 505 new transitions and about 250 new levels, including 51 new low-spin states. Spin assignments have been made for 58 low-spin states based on the deduced β-decay feeding and γ-γ angular correlation analyses.

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

Pletnev, Sergei; Shcherbo, Dmitry; Chudakov, Dmitry M.

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. Inmore » 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.« less

Four-Coordinate Iron(II) Diaryl Compounds with Monodentate N-Heterocyclic Carbene Ligation: Synthesis, Characterization, and Their Tetrahedral-Square Planar Isomerization in Solution.

PubMed

Liu, Yuesheng; Luo, Lun; Xiao, Jie; Wang, Lei; Song, You; Qu, Jingping; Luo, Yi; Deng, Liang

2015-05-18

The salt elimination reactions of (IPr2Me2)2FeCl2 (IPr2Me2 = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene) with the corresponding aryl Grignard reagents afford [(IPr2Me2)2FeAr2] (Ar = Ph, 3; C6H4-p-Me, 4; C6H4-p-(t)Bu, 5; C6H3-3,5-(CF3)2, 6) in good yields. X-ray crystallographic studies revealed the presence of both tetrahedral and trans square planar isomers for 3 and 6 and the tetrahedral structures for 4 and 5. Magnetic susceptibility and (57)Fe Mössbauer spectrum measurements on the solid samples indicated the high-spin (S = 2) and intermediate-spin (S = 1) nature of the tetrahedral and square planar structures, respectively. Solution property studies, including solution magnetic susceptibility measurement, variable-temperature (1)H and (19)F NMR, and absorption spectroscopy, on 3-6, as well as an (57)Fe Mössbauer spectrum study on a frozen tetrahydrofuran solution of tetrahedral [(IPr2Me2)2(57)FePh2] suggest the coexistence of tetrahedral and trans square planar structures in solution phase. Density functional theory calculations on (IPr2Me2)2FePh2 disclosed that the tetrahedral and trans square planar isomers are close in energy and that the geometry isomerization can occur by spin-change-coupled geometric transformation on four-coordinate iron(II) center.

Observation of steric hindrance effect controlling crystal packing structures and physical properties in three new isomeric nitronyl nitroxide radicals

NASA Astrophysics Data System (ADS)

Zhao, Hai-Rong; Sun, Jia-Sen; Sui, Yun-Xia; Ren, Xiao-Ming; Yao, Bin-Qian; Shen, Lin-Jiang; Meng, Qing-Jin

2009-07-01

Three isomeric nitronyl nitroxide radical compounds, 2-[ n-( N-benzyl)pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide bromide ( n = 2, 3 and 4 for 1, 2 and 3, respectively), have been synthesized and structurally characterized. The influence of steric hindrance on the molecular packing structures and physical properties has been observed. In the radical 1, such steric hindrance leads to a folding conformation of the imidazoline and benzene rings and the intramolecular C-H…π interaction between the methyl group and the benzene ring. There is no such effect in 2 and 3. In crystal of 2, there are the intermolecular C-H…π between methyl groups and benzene ring and intermolecular π…π stacking interaction between pyridine and benzene rings. Crystal of 2 with a chiral space group P2 12 12 1 shows the SHG response about 0.4 times as that of urea. In crystal of 3, there are three symmetry-independent radical molecules, which form an unusually six-membered supramolecular ring via intermolecular O…π interactions. For the solid sample of 3, the X-band EPR exhibits an axially symmetric signal and magnetic susceptibility data suggest intermolecular antiferromagnetic (AFM) coupling interactions and very weak intermolecular ferromagnetic (FM) coupling interactions which is more likely caused by magnetic anisotropy, while measurements of both 1 and 2 show isotropic X-band EPR signals and simple Currie-Weiss magnetic behavior.

A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple† †Electronic supplementary information (ESI) available: Synthetic methods and characterization; fluorescence up-conversion data; additional computational details; Cartesian coordinates of key structures; photochemical isomerization data; data for the anion of I. See DOI: 10.1039/c7sc04091a

PubMed Central

Conyard, Jamie; Heisler, Ismael A.; Chan, Yohan; Bulman Page, Philip C.

2018-01-01

The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples. PMID:29675225

Photoregeneration of bovine rhodopsin from its signaling state.

PubMed

Arnis, S; Hofmann, K P

1995-07-25

In rhodopsin, 11-cis-retinal is bound by a protonated Schiff base and acts as a strong antagonist, which holds the receptor in its inactive ground state conformation. Light induces cis-/trans-retinal isomerization and a sequence of thermal transitions through intermediates. The active conformation that catalyzes GDP/GTP exchange in the G-protein (Gt) is generated from the metarhodopsin II intermediate (MII) and mediated by Schiff base proton translocation and proton uptake from the aqueous phase. In the stable nucleotide-free MII-Gt complex, any thermal transition of MII into other forms of rhodopsin is blocked. We have now studied how Gt affects flash-induced photochemical conversions of MII. Difference spectra from measured absorption changes show that MII photolyzes through two parallel pathways, with fast (1 ms) and slow (50 ms) kinetics (12 degrees C, pH 6). The slow pathway regenerates rhodopsin (9- or 11-cis) via Schiff base reprotonation and proton release. We infer a cis-isomerized early photoproduct (reverted meta, RM) preceding these thermal transitions. When MII is photolyzed in the MII-Gt complex, the slow absorption change is abolished, indicating that Gt blocks the completion of the regeneration process. This is due to the formation of a stable RM-Gt complex, as shown by successive photolysis of MII, RM, and ground state rhodopsin, and the application of GTP gamma S at different stages. The complex dissociates with GTP gamma S, and rhodopsin relaxes to the ground state. The results indicate that cis-retinal and Gt can bind to the receptor at the same time. We discuss the result that the protonations in the meta II state uncouple retinal geometry from Gt interaction.

Atrial isomerism: a surgical experience.

PubMed

Sinzobahamvya, N; Arenz, C; Brecher, A M; Urban, A E

1999-06-01

Most publications on atrial isomerism are autopsy or case reports. The authors review 41 consecutive children operated on from 1980 through to 1996 with emphasis on associated cardiac anomalies, surgical procedures and outcome. Left atrial isomerism was present in 23 patients. Interruption of the inferior vena cava (56%), atrio-ventricular septal defect (47%), common atrium (38%) and cor triatriatum sinistrum (30%) were the most common diagnoses. Biventricular repair was achieved in 17 children and total cavo-pulmonary connection in two. Three underwent staged palliation: modified Blalock-Taussig shunt for two and bidirectional Glenn anastomosis for one. The remainder received a cardiac pacemaker. One patient died early after repair. Two underwent reoperation to correct a regurgitant left atrio-ventricular valve: one of these, in another hospital, had peroperative death. Three died later. Actuarial survival rate after repair and total cavo-pulmonary connection that was stabilized after 2 years was 84%. In the 18 children with right atrial isomerism, pulmonary atresia or stenosis predominated (89%) with discordant ventriculo-arterial connection (72%), atrio-ventricular septal defect (72%), 'single' ventricle (55%) and extracardiac total anomalous pulmonary venous drainage (50%). Biventricular repair was achieved in two patients and complete Fontan circulation in eight. The other eight underwent various staged palliative procedures and correction of extracardiac total anomalous pulmonary venous drainage. Five patients died postoperatively: two in our unit after modified Blalock-Taussig shunt and total cavo-pulmonary connection, three in other hospitals after repair (n = 1) and Fontan (n = 2). Five died later. One was lost for review. Survival after repair and Fontan stabilized after 6 months at 49%. In conclusion, the cardiovascular malformations associated with left atrial isomerism can often be successfully corrected. Those accompanying right atrial isomerism usually preclude a biventricular repair, require staged palliation and carry a poor prognosis.

Nuclear model calculation and targetry recipe for production of 110mIn.

PubMed

Kakavand, T; Mirzaii, M; Eslami, M; Karimi, A

2015-10-01

(110m)In is potentially an important positron emitting that can be used in positron emission tomography. In this work, the excitation functions and production yields of (110)Cd(d, 2n), (111)Cd(d, 3n), (nat)Cd(d, xn), (110)Cd(p, n), (111)Cd(p, 2n), (112)Cd(p, 3n) and (nat)Cd(p, xn) reactions to produce the (110m)In were calculated using nuclear model code TALYS and compared with the experimental data. The yield of isomeric state production of (110)In was also compared with ground state production ones to reach the optimal energy range of projectile for the high yield production of metastable state. The results indicate that the (110)Cd(p, n)(110m)In is a high yield reaction with an isomeric ratio (σ(m)/σ(g)) of about 35 within the optimal incident energy range of 15-5 MeV. To make the target, cadmium was electroplated on a copper substrate in varying electroplating conditions such as PH, DC current density, temperature and time. A set of cold tests were also performed on the final sample under several thermal shocks to verify target resistance. The best electroplated cadmium target was irradiated with 15 MeV protons at current of 100 µA for one hour and the production yield of (110m)In and other byproducts were measured. Copyright © 2015 Elsevier Ltd. All rights reserved.

Enhanced Deformation of Azobenzene-Modified Liquid Crystal Polymers under Dual Wavelength Exposure: A Photophysical Model.

PubMed

Liu, Ling; Onck, Patrick R

2017-08-04

Azobenzene-embedded liquid crystal polymers can undergo mechanical deformation in response to ultraviolet (UV) light. The natural rodlike trans state azobenzene absorbs UV light and isomerizes to a bentlike cis state, which disturbs the order of the polymer network, leading to an anisotropic deformation. The current consensus is that the magnitude of the photoinduced deformation is related to the statistical building up of molecules in the cis state. However, a recent experimental study [Liu and Broer, Nat. Commun. 6 8334 (2015).NCAOBW2041-172310.1038/ncomms9334] shows that a drastic (fourfold) increase of the photoinduced deformation can be generated by exposing the samples simultaneously to 365 nm (UV) and 455 nm (visible) light. To elucidate the physical mechanism that drives this increase, we develop a two-light attenuation model and an optomechanical constitutive relation that not only accounts for the statistical accumulation of cis azobenzenes, but also for the dynamic trans-cis-trans oscillatory isomerization process. Our experimentally calibrated model predicts that the optimal single-wavelength exposure is 395 nm light, a pronounced shift towards the visible spectrum. In addition, we identify a range of optimal combinations of two-wavelength lights that generate a favorable response for a given amount of injected energy. Our model provides mechanistic insight into the different (multi)wavelength exposures used in experiments and, at the same time, opens new avenues towards enhanced, multiwavelength optomechanical behavior.

The energy and work of a ligand-gated ion channel

PubMed Central

Auerbach, Anthony

2015-01-01

Ligand-gated ion channels are allosteric membrane proteins that isomerize between C(losed) and O(pen) conformations. A difference in affinity for ligands in the two shapes influences the C↔O ‘gating’ equilibrium constant. The energies associated with adult-type mouse neuromuscular nicotinic acetylcholine receptor-channel (AChR) gating have been measured by using single-channel electrophysiology. Without ligands the free energy, enthalpy and entropy of gating are ΔG0=+8.4, ΔH0=+10.9 and ΔS0=+2.4 kcal/mol (−100 mV, 23 °C). Many mutations throughout the protein change ΔG0, including natural ones that cause disease. Agonists and most mutations change approximately independently the ground state energy difference, so it is possible to forecast and engineer AChR responses simply by combining perturbations. The free energy of the low↔high affinity change for the neurotransmitter at each of two functionally-equivalent binding sites is ΔGBACh=−5.1 kcal/mol. ΔGBACh is set mainly by interactions of ACh with just three binding site aromatic groups. For a series of structurally-related agonists there is a correlation between the energies of low- and high-affinity binding, which implies that gating commences with the formation of the low affinity complex. Brief, intermediate states in binding and gating have been detected. Several proposals for the nature of the gating transition state energy landscape and the isomerization mechanism are discussed. PMID:23357172

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

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

Skobelev, N. K., E-mail: skobelev@jinr.ru

2016-07-15

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 ({sup 6}Li) and radioactive ({sup 6}He) beams of the DRIBs accelerator complex at the Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, and in deuteron and {sup 3}He beams of the U-120M cyclotron at themore » 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 ({sup 6}Li and {sup 3}He) 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.« less

Analysis of the Properties of the Esters of Neopentyl Glycol,

DTIC Science & Technology

The esters of neopentyl glycol and monocarboxylic acids of normal and isomeric structure were synthesized. The esters are characterized by higher...indices of viscosity and solidification temperatures than the esters of the acids of isomeric structure. The esters of neopentyl glycol and industrial

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

Left cardiac isomerism in the Sonic hedgehog null mouse.

PubMed

Hildreth, Victoria; Webb, Sandra; Chaudhry, Bill; Peat, Jonathan D; Phillips, Helen M; Brown, Nigel; Anderson, Robert H; Henderson, Deborah J

2009-06-01

Sonic hedgehog (Shh) is a secreted morphogen necessary for the production of sidedness in the developing embryo. In this study, we describe the morphology of the atrial chambers and atrioventricular junctions of the Shh null mouse heart. We demonstrate that the essential phenotypic feature is isomerism of the left atrial appendages, in combination with an atrioventricular septal defect and a common atrioventricular junction. These malformations are known to be frequent in humans with left isomerism. To confirm the presence of left isomerism, we show that Pitx2c, a recognized determinant of morphological leftness, is expressed in the Shh null mutants on both the right and left sides of the inflow region, and on both sides of the solitary arterial trunk exiting from the heart. It has been established that derivatives of the second heart field expressing Isl1 are asymmetrically distributed in the developing normal heart. We now show that this population is reduced in the hearts from the Shh null mutants, likely contributing to the defects. To distinguish the consequences of reduced contributions from the second heart field from those of left-right patterning disturbance, we disrupted the movement of second heart field cells into the heart by expressing dominant-negative Rho kinase in the population of cells expressing Isl1. This resulted in absence of the vestibular spine, and presence of atrioventricular septal defects closely resembling those seen in the hearts from the Shh null mutants. The primary atrial septum, however, was well formed, and there was no evidence of isomerism of the atrial appendages, suggesting that these features do not relate to disruption of the contributions made by the second heart field. We demonstrate, therefore, that the Shh null mouse is a model of isomerism of the left atrial appendages, and show that the recognized associated malformations found at the venous pole of the heart in the setting of left isomerism are likely to arise from the loss of the effects of Shh in the establishment of laterality, combined with a reduced contribution made by cells derived from the second heart field.

Probing the mer- to fac-isomerization of tris-cyclometallated homo- and heteroleptic (C,N)3 iridium(III) complexes.

PubMed

McDonald, Aidan R; Lutz, Martin; von Chrzanowski, Lars S; van Klink, Gerard P M; Spek, Anthony L; van Koten, Gerard

2008-08-04

We have developed techniques which allow for covalent tethering, via a "hetero" cyclometallating ligand, of heteroleptic tris-cyclometallated iridium(III) complexes to polymeric supports (for application in light-emitting diode technologies). This involved the selective synthesis and thorough characterization of heteroleptic [Ir(C,N) 2(C',N')] tris-cyclometallated iridium(III) complexes. Furthermore, the synthesis and characterization of heteroleptic [Ir(C,N) 2OR] complexes is presented. Under standard thermal conditions for the synthesis of the facial ( fac) isomer of tris-cyclometallated complexes, it was not possible to synthesize pure heteroleptic complexes of the form [Ir(C,N) 2(C',N')]. Instead, a mixture of homo- and heteroleptic complexes was acquired. It was found that a stepwise procedure involving the synthesis of a pure meridonial ( mer) isomer followed by photochemical isomerization of this mer to the fac isomer was necessary to synthesize pure fac-[Ir(C,N) 2(C',N')] complexes. Under thermal isomerization conditions, the conversion of mer-[Ir(C,N) 2(C',N')] to fac-[Ir(C,N) 2(C',N')] was also not a clean reaction, with again a mixture of homo- and heteroleptic complexes acquired. An investigation into the thermal mer to fac isomerization of both homo- and heteroleptic tris-cyclometallated complexes is presented. It was found that the process is an alcohol-catalyzed reaction with the formation of an iridium alkoxide [Ir(C,N) 2OR] intermediate in the isomerization process. This catalyzed reaction can be carried out between 50 and 100 degrees C, the first such example of low-temperature mer-fac thermal isomerization. We have synthesized analogous complexes and have shown that they do indeed react so as to give fac-tris-cyclometallated products. A detailed explanation of the intermediates (and all of their stereoisomers, in particular when systems of the generic formula [M(a,b) 2(a',b')] are synthesized) formed in the mer to fac isomerization process is presented, including how the formed intermediates react further, and the stereoisomeric products they yield.

Compartmental and noncompartmental modeling of ¹³C-lycopene absorption, isomerization, and distribution kinetics in healthy adults.

PubMed

Moran, Nancy E; Cichon, Morgan J; Riedl, Kenneth M; Grainger, Elizabeth M; Schwartz, Steven J; Novotny, Janet A; Erdman, John W; Clinton, Steven K

2015-12-01

Lycopene, which is a red carotenoid in tomatoes, has been hypothesized to mediate disease-preventive effects associated with tomato consumption. Lycopene is consumed primarily as the all-trans geometric isomer in foods, whereas human plasma and tissues show greater proportions of cis isomers. With the use of compartmental modeling and stable isotope technology, we determined whether endogenous all-trans-to-cis-lycopene isomerization or isomeric-bioavailability differences underlie the greater proportion of lycopene cis isomers in human tissues than in tomato foods. Healthy men (n = 4) and women (n = 4) consumed (13)C-lycopene (10.2 mg; 82% all-trans and 18% cis), and plasma was collected over 28 d. Unlabeled and (13)C-labeled total lycopene and lycopene-isomer plasma concentrations, which were measured with the use of high-performance liquid chromatography-mass spectrometry, were fit to a 7-compartment model. Subjects absorbed a mean ± SEM of 23% ± 6% of the lycopene. The proportion of plasma cis-(13)C-lycopene isomers increased over time, and all-trans had a shorter half-life than that of cis isomers (5.3 ± 0.3 and 8.8 ± 0.6 d, respectively; P < 0.001) and an earlier time to reach maximal plasma concentration than that of cis isomers (28 ± 7 and 48 ± 9 h, respectively). A compartmental model that allowed for interindividual differences in cis- and all-trans-lycopene bioavailability and endogenous trans-to-cis-lycopene isomerization was predictive of plasma (13)C and unlabeled cis- and all-trans-lycopene concentrations. Although the bioavailability of cis (24.5% ± 6%) and all-trans (23.2% ± 8%) isomers did not differ, endogenous isomerization (0.97 ± 0.25 μmol/d in the fast-turnover tissue lycopene pool) drove tissue and plasma isomeric profiles. (13)C-Lycopene combined with physiologic compartmental modeling provides a strategy for following complex in vivo metabolic processes in humans and reveals that postabsorptive trans-to-cis-lycopene isomerization, and not the differential bioavailability of isomers, drives tissue and plasma enrichment of cis-lycopene. This trial was registered at clinicaltrials.gov as NCT01692340. © 2015 American Society for Nutrition.

Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

PubMed Central

Rubina, Marina; Sherrill, William M; Barkov, Alexey Yu

2014-01-01

Summary A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands. PMID:25161709

High-pressure liquid chromatographic determination of chlorphenesin carbamate and the beta-isomeric carbamate.

PubMed

Beyer, W F

1976-12-01

A high-pressure liquid chromatographic assay was developed for the determination of chlorphenesin carbamate and its beta-isomeric carbamate. A single 4-mm i.d. X 30-cm column, prepacked with 10 micrometer fully porous silica gel particles, is used with 3% methanol in 50% water-saturated butyl chloride as the mobile phase. The procedure separates chlorphenesin carbamate from several possible impurities in addition to the beta-isomeric carbamate. The assay was applied to bulk drug and compressed tablets. The relative standard deviations for the assays of chlorphenesin carbamate and the beta-isomer are approximately 1 and 2%, respectively.

Using Vibrations to Probe and Control Photoisomerization in Liquids

DTIC Science & Technology

2014-08-07

Aniline in Supercritical CO2 The influence that different solvent environments have on the reaction dynamics of molecules in solution is a long...vibrationally excited stilbene, of a biomimetic switch, an N- alkylated indanylidene pyrroline Schiff base (NAIP), and of a model com- pound for excited...supercritical carbon dioxide, scCO2. Monitor- ing the excited-state isomerization of salicylidene aniline has shown the role of viscosity on the course of

Quantification of isomerically summed hydrocarbon contributions to crude oil by carbon number, double bond equivalent, and aromaticity using gas chromatography with tunable vacuum ultraviolet ionization.

PubMed

Nowak, Jeremy A; Weber, Robert J; Goldstein, Allen H

2018-03-12

The ability to structurally characterize and isomerically quantify crude oil hydrocarbons relevant to refined fuels such as motor oil, diesel, and gasoline represents an extreme challenge for chromatographic and mass spectrometric techniques. This work incorporates two-dimensional gas chromatography coupled to a tunable vacuum ultraviolet soft photoionization source, the Chemical Dynamics Beamline 9.0.2 of the Advanced Light Source at the Lawrence Berkeley National Laboratory, with a time-of-flight mass spectrometer (GC × GC-VUV-TOF) to directly characterize and isomerically sum the contributions of aromatic and aliphatic species to hydrocarbon classes of four crude oils. When the VUV beam is tuned to 10.5 ± 0.2 eV, both aromatic and aliphatic crude oil hydrocarbons are ionized to reveal the complete chemical abundance of C 9 -C 30 hydrocarbons. When the VUV beam is tuned to 9.0 ± 0.2 eV only aromatic hydrocarbons are ionized, allowing separation of the aliphatic and aromatic fractions of the crude oil hydrocarbon chemical classes in an efficient manner while maintaining isomeric quantification. This technique provides an effective tool to determine the isomerically summed aromatic and aliphatic hydrocarbon compositions of crude oil, providing information that goes beyond typical GC × GC separations of the most dominant hydrocarbon isomers.

Adaptation of cone pigments found in green rods for scotopic vision through a single amino acid mutation

PubMed Central

Kojima, Keiichi; Matsutani, Yuki; Yamashita, Takahiro; Yanagawa, Masataka; Imamoto, Yasushi; Yamano, Yumiko; Wada, Akimori; Hisatomi, Osamu; Nishikawa, Kanto; Sakurai, Keisuke; Shichida, Yoshinori

2017-01-01

Most vertebrate retinas contain a single type of rod for scotopic vision and multiple types of cones for photopic and color vision. The retinas of certain amphibian species uniquely contain two types of rods: red rods, which express rhodopsin, and green rods, which express a blue-sensitive cone pigment (M1/SWS2 group). Spontaneous activation of rhodopsin induced by thermal isomerization of the retinal chromophore has been suggested to contribute to the rod’s background noise, which limits the visual threshold for scotopic vision. Therefore, rhodopsin must exhibit low thermal isomerization rate compared with cone visual pigments to adapt to scotopic condition. In this study, we determined whether amphibian blue-sensitive cone pigments in green rods exhibit low thermal isomerization rates to act as rhodopsin-like pigments for scotopic vision. Anura blue-sensitive cone pigments exhibit low thermal isomerization rates similar to rhodopsin, whereas Urodela pigments exhibit high rates like other vertebrate cone pigments present in cones. Furthermore, by mutational analysis, we identified a key amino acid residue, Thr47, that is responsible for the low thermal isomerization rates of Anura blue-sensitive cone pigments. These results strongly suggest that, through this mutation, anurans acquired special blue-sensitive cone pigments in their green rods, which could form the molecular basis for scotopic color vision with normal red rods containing green-sensitive rhodopsin. PMID:28484015

High Temperature Chemistry of Chlorinated Acenaphthylene. 3C Bay Acetylene Additions and Annealing by Five-Membered Ring Shifts.

PubMed

McIntosh, Grant J; Russell, Douglas K

2015-12-24

Experimental and theoretical results concerning the growth and isomerization of chlorinated acenaphthylene, C12H8, during the pyrolysis of chlorohydrocarbons are presented here. A fullerene subunit, C12H8, is a useful system to investigate regarding C60 formation. However, direct experimental observation of isomerization and annealing processes in particular are difficult to confirm due to the high symmetry of the parent molecule. Chlorination lowers the symmetry, essentially labeling carbon atoms, allowing growth and isomerization to be followed directly. Pyrolysis of dichloro- and trichloroethylene, and their copyrolyses with trichlorobenzenes, provides an efficient and general source of chlorinated acenaphthylenes in a range of degrees of chlorination and over a number of unique congeners. Analysis of congener yields as a function of reagents employed, guided by DFT/B3LYP/6-311G(d,p) level calculations, strongly suggests that C2 addition across three-carbon bays in naphthalene is a major driver of growth. Additionally, extremely facile five-membered ring shifts are operative, with chlorine promoting isomerization. Theoretical study of C16H10- and C18H10-based congeners indicate that this is a general phenomenon, and with chlorine also favoring internal cyclopentafused rings in addition to increased isomerization rates, this suggests halogen moieties may be an important feature for efficient fullerene growth.

Phosphorylation effects on cis/trans isomerization and the backbone conformation of serine-proline motifs: accelerated molecular dynamics analysis.

PubMed

Hamelberg, Donald; Shen, Tongye; McCammon, J Andrew

2005-02-16

The presence of serine/threonine-proline motifs in proteins provides a conformational switching mechanism of the backbone through the cis/trans isomerization of the peptidyl-prolyl (omega) bond. The reversible phosphorylation of the serine/threonine modulates this switching in regulatory proteins to alter signaling and transcription. However, the mechanism is not well understood. This is partly because cis/trans isomerization is a very slow process and, hence, difficult to study. We have used our accelerated molecular dynamics method to study the cis/trans proline isomerization, preferred backbone conformation of a serine-proline motif, and the effects of phosphorylation of the serine residue. We demonstrate that, unlike normal molecular dynamics, the accelerated molecular dynamics allows for the system to escape very easily from the trans isomer to cis isomer, and vice versa. Moreover, for both the unphosphorylated and phosphorylated peptides, the statistical thermodynamic properties are recaptured, and the results are consistent with experimental values. Isomerization of the proline omega bond is shown to be asymmetric and strongly dependent on the psi backbone angle before and after phosphorylation. The rates of escape decrease after phosphorylation. Also, the alpha-helical backbone conformation is more favored after phosphorylation. This accelerated molecular dynamics approach provides a general approach for enhancing the conformational transitions of molecular systems without having prior knowledge of the location of the minima and barriers on the potential-energy landscape.

Cardiolipin modulates allosterically peroxynitrite detoxification by horse heart cytochrome c

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

Ascenzi, Paolo, E-mail: ascenzi@uniroma3.it; Ciaccio, Chiara; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, I-70126 Bari

2011-01-07

Research highlights: {yields} Cardiolipin binding to cytochrome c. {yields} Cardiolipin-dependent peroxynitrite isomerization by cytochrome c. {yields} Cardiolipin-cytochrome c complex plays pro-apoptotic effects. {yields} Cardiolipin-cytochrome c complex plays anti-apoptotic effects. -- Abstract: Upon interaction with bovine heart cardiolipin (CL), horse heart cytochrome c (cytc) changes its tertiary structure disrupting the heme-Fe-Met80 distal bond, reduces drastically the midpoint potential out of the range required for its physiological role, binds CO and NO with high affinity, and displays peroxidase activity. Here, the effect of CL on peroxynitrite isomerization by ferric cytc (cytc-Fe(III)) is reported. In the absence of CL, hexa-coordinated cytc does notmore » catalyze peroxynitrite isomerization. In contrast, CL facilitates cytc-Fe(III)-mediated isomerization of peroxynitrite in a dose-dependent fashion inducing the penta-coordination of the heme-Fe(III)-atom. The value of the second order rate constant for CL-cytc-Fe(III)-mediated isomerization of peroxynitrite (k{sub on}) is (3.2 {+-} 0.4) x 10{sup 5} M{sup -1} s{sup -1}. The apparent dissociation equilibrium constant for CL binding to cytc-Fe(III) is (5.1 {+-} 0.8) x 10{sup -5} M. These results suggest that CL-cytc could play either pro-apoptotic or anti-apoptotic effects facilitating lipid peroxidation and scavenging of reactive nitrogen species, such as peroxynitrite, respectively.« less

Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations.

PubMed

Kim, Peter W; Rockwell, Nathan C; Freer, Lucy H; Chang, Che-Wei; Martin, Shelley S; Lagarias, J Clark; Larsen, Delmar S

2013-07-20

The ultrafast mechanisms underlying the initial photoisomerization (P r → Lumi-R) in the forward reaction of the cyanobacterial photoreceptor Cph1 were explored with multipulse pump-dump-probe transient spectroscopy. A recently postulated multi-population model was used to fit the transient pump-dump-probe and dump-induced depletion signals. We observed dump-induced depletion of the Lumi-R photoproduct, demonstrating that photoisomerization occurs via evolution on both the excited- and ground-state electronic surfaces. Excited-state equilibrium was not observed, as shown via the absence of a dump-induced excited-state "Le Châtelier redistribution" of excited-state populations. The importance of incorporating the inhomogeneous dynamics of Cph1 in interpreting measured transient data is discussed.

Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations

PubMed Central

Kim, Peter W.; Rockwell, Nathan C.; Freer, Lucy H.; Chang, Che-Wei; Martin, Shelley S.; Lagarias, J. Clark; Larsen, Delmar S.

2013-01-01

The ultrafast mechanisms underlying the initial photoisomerization (Pr → Lumi-R) in the forward reaction of the cyanobacterial photoreceptor Cph1 were explored with multipulse pump-dump-probe transient spectroscopy. A recently postulated multi-population model was used to fit the transient pump-dump-probe and dump-induced depletion signals. We observed dump-induced depletion of the Lumi-R photoproduct, demonstrating that photoisomerization occurs via evolution on both the excited- and ground-state electronic surfaces. Excited-state equilibrium was not observed, as shown via the absence of a dump-induced excited-state “Le Châtelier redistribution” of excited-state populations. The importance of incorporating the inhomogeneous dynamics of Cph1 in interpreting measured transient data is discussed. PMID:24143267

Excited-State Proton-Transfer-Induced Trapping Enhances the Fluorescence Emission of a Locked GFP Chromophore

PubMed Central

2016-01-01

The chemical locking of the central single bond in core chromophores of green fluorescent proteins (GFPs) influences their excited-state behavior in a distinct manner. Experimentally, it significantly enhances the fluorescence quantum yield of GFP chromophores with an ortho-hydroxyl group, while it has almost no effect on the photophysics of GFP chromophores with a para-hydroxyl group. To unravel the underlying physical reasons for this different behavior, we report static electronic structure calculations and nonadiabatic dynamics simulations on excited-state intramolecular proton transfer, cis–trans isomerization, and excited-state deactivation in a locked ortho-substituted GFP model chromophore (o-LHBI). On the basis of our previous and present results, we find that the S1 keto species is responsible for the fluorescence emission of the unlocked o-HBI and the locked o-LHBI species. Chemical locking does not change the parts of the S1 and S0 potential energy surfaces relevant to enol–keto tautomerization; hence, in both chromophores, there is an ultrafast excited-state intramolecular proton transfer that takes only 35 fs on average. However, the locking effectively hinders the S1 keto species from approaching the keto S1/S0 conical intersections so that most of trajectories are trapped in the S1 keto region for the entire 2 ps simulation time. Therefore, the fluorescence quantum yield of o-LHBI is enhanced compared with that of unlocked o-HBI, in which the S1 excited-state decay is efficient and ultrafast. In the case of the para-substituted GFP model chromophores p-HBI and p-LHBI, chemical locking hardly affects their efficient excited-state deactivation via cis–trans isomerization; thus, the fluorescence quantum yields in these chromophores remain very low. The insights gained from the present work may help to guide the design of new GFP chromophores with improved fluorescence emission and brightness. PMID:26744782

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...

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…

Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

PubMed

Lu, Xiao-Xia; Tang, Hau-San; Ko, Chi-Chiu; Wong, Jenny Ka-Yan; Zhu, Nianyong; Yam, Vivian Wing-Wah

2005-03-28

The anion-assisted shift of trans-cis isomerization equilibrium of a palladium(II) complex containing acetanilide functionalities brought about by allosteric hydrogen bonding interactions has been established by UV/Vis, 1H NMR, 31P NMR and ESI-MS studies.

Polymeric proanthocyanidins: Interflavanoid linkage isomerism in (epicatechin-4)-(epicatechin-4)-catechin procyanidins

Treesearch

Richard W. Hemingway; L. Yeap Foo; L. J. Porter

1981-01-01

Procyanidin trimers have been isolated from a variety of plants,1-3 but their structures remain unresolved. We have now isolated three configurational isomers of (epicatechin-4)-(epicatechin-4)-catechin from Pinus taeda L. (loblolly pine) phloem which exhibit isomerism of the interflavanoid linkages.

Trans influence on the rate of reductive elimination. Reductive elimination of amines from isomeric arylpalladium amides with unsymmetrical coordination spheres.

PubMed

Yamashita, Makoto; Cuevas Vicario, Jose V; Hartwig, John F

2003-12-31

To determine the trans effect on the rates of reductive eliminations from arylpalladium(II) amido complexes, the reactions of arylpalladium amido complexes bearing symmetrical and unsymmetrical DPPF (DPPF = bis(diphenylphosphino)ferrocene) derivatives were studied. THF solutions of LPd(Ar)(NMeAr') (L = DPPF, DPPF-OMe, DPPF-CF3, DPPF-OMe,Ph, DPPF-Ph,CF3, and DPPF-OMe,CF3; Ar = C6H4-4-CF3; Ar' = C6H4-4-CH3, Ph, and C6H4-4-OMe) underwent C-N bond forming reductive elimination at -15 C to form the corresponding N-methyldiarylamine in high yield. Complexes ligated by symmetrical DPPF derivatives with electron-withdrawing substituents on the DPPF aryl groups underwent reductive elimination faster than complexes ligated by symmetrical DPPF derivatives with electron-donating substituents on the ligand aryl groups. Studies of arylpalladium amido complexes containing unsymmetrical DPPF ligands revealed several trends. First, the complex with the weaker donor trans to nitrogen and the stronger donor trans to the palladium-bound aryl group underwent reductive elimination faster than the regioisomeric complex with the stronger donor trans to nitrogen and the weaker donor trans to the palladium-bound aryl group. Second, the effect of varying the substituents on the phosphorus donor trans to the nitrogen was larger than the effect of varying the substituents on the phosphorus donor trans to the palladium-bound aryl group. Third, the difference in rate between the isomeric arylpalladium amido complexes was similar in magnitude to the differences in rates resulting from conventional variation of substituents on the symmetric phosphine ligands. This result suggests that the geometry of the complex is equal in importance to the donating ability of the dative ligands. The ratio of the differences in rates of reaction of the isomeric complexes was similar to the relative populations of the two geometric isomers. This result and consideration of transition state geometries suggest that the reaction rates are controlled more by substituent effects on ground state stability than on transition state energies. In addition, variation of the aryl group at the amido nitrogen showed systematically that complexes with more electron-donating groups at nitrogen undergo faster reductive elimination than those with less electron-donating groups at nitrogen.

Nonradiative Decay Dynamics of METHYL-4-HYDROXYCINNAMATE and its Monohydrated Complex Revealed by Picosecond Pump-Probe Spectroscopy

NASA Astrophysics Data System (ADS)

Ebata, T.; Shimada, D.; Kusaka, R.; Inokuchi, Y.; Ehara, M.

2012-06-01

The lifetimes of methyl 4-hydroxycinnamate (OMpCA) and its mono-hydrated complex (OMpCA-H_2O) in the S_1 state have been measured by picosecond pump-probe spectroscopy in a supersonic beam. For OMpCA, the lifetime of the S_1 - S_0 origin is 8 - 9 ps. On the other hand, the lifetime of OMpCA-H_2O complex at the origin is 930 ps, which is 100 times longer than that. Furthermore, in the complex the S_1 lifetime shows rapid decrease at an energy of 200 cm-1 above the origin and becomes as short as 9 ps at 500 cm-1. Theoretical calculations with symmetry-adapted cluster-configuration interaction (SAC-CI) method suggest that in OMpCA, the trans - cis isomerization occurs smoothly without a barrier on the S_1surface, while in OMpCA-H_2O complex, there exists a barrier along the isomerization coordinate. The calculated barrier height of OMpCA-H_2O is in good agreement with that estimated from the lifetime measurements.

Cn(n=2-4): current status

NASA Astrophysics Data System (ADS)

Varandas, A. J. C.; Rocha, C. M. R.

2018-03-01

The major aspects of the C2, C3 and C4 elemental carbon clusters are surveyed. For C2, a brief analysis of its current status is presented. Regarding C3, the most recent results obtained in our group are reviewed with emphasis on modelling its potential energy surface which is particularly complicated due to the presence of multiple conical intersections. As for C4, the most stable isomeric forms of both triplet and singlet spin states and their possible interconversion pathways are examined afresh by means of accurate ab initio calculations. The main strategies for modelling the ground triplet C4 potential are also discussed. Starting from a truncated cluster expansion and a previously reported DMBE form for C3, an approximate four-body term is calibrated from the ab initio energies. The final six-dimensional global DMBE form so obtained reproduces all known topographical aspects while providing an accurate description of the C4 linear-rhombic isomerization pathway. It is therefore commended for both spectroscopic and reaction dynamics studies. This article is part of the theme issue `Modern theoretical chemistry'.

Study of the Al m 26 ( d , p ) Al 27 Reaction and the Influence of the Al 26 0 + Isomer on the Destruction of Al 26 in the Galaxy

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

Almaraz-Calderon, S.; Rehm, K. E.; Gerken, N.

The existence of 26Al (t 1/2 = 7.17 × 10 5 yr) in the interstellar medium provides a direct confirmation of ongoing nucleosynthesis in the Galaxy. The presence of a low-lying 0 + isomer ( 26Al m), however, severely complicates the astrophysical calculations. Here we present for the first time a study of the 26Al m (d, p) 27 Al reaction using an isomeric 26Al beam. The selectivity of this reaction allowed the study of ℓ = 0 transfers to T = 1/2, and T = 3/2 states in 27Al . Mirror symmetry arguments were then used to constrain themore » 26Al m (p,γ) 27Si reaction rate and provide an experimentally determined upper limit of the rate for the destruction of isomeric 26Al via radiative proton capture reactions, which is expected to dominate the destruction path of 26Al m in asymptotic giant branch stars, classical novae, and core collapse supernovae.« less

Dynamic coupling between coordinates in a model for biomolecular isomerization

NASA Astrophysics Data System (ADS)

Ma, Ao; Nag, Ambarish; Dinner, Aaron R.

2006-04-01

To understand a complex reaction, it is necessary to project the dynamics of the system onto a low-dimensional subspace of physically meaningful coordinates. We recently introduced an automatic method for identifying coordinates that relate closely to stable-state commitment probabilities and successfully applied it to a model for biomolecular isomerization, the C7eq→αR transition of the alanine dipeptide [A. Ma and A. R. Dinner, J. Phys. Chem. B 109, 6769 (2005)]. Here, we explore approximate means for estimating diffusion tensors for systems subject to restraints in one and two dimensions and then use the results together with an extension of Kramers theory for unimolecular reaction rates [A. Berezhkovskii and A. Szabo, J. Chem. Phys. 122, 014503 (2005)] to show explicitly that both the potential of mean force and the diffusion tensor are essential for describing the dynamics of the alanine dipeptide quantitatively. In particular, the signficance of off-diagonal elements of the diffusion tensor suggests that the coordinates of interest are coupled by the hydrodynamic-like response of the bath of remaining degrees of freedom.

Study of the Al m 26 ( d , p ) Al 27 Reaction and the Influence of the Al 26 0 + Isomer on the Destruction of Al 26 in the Galaxy

DOE PAGES

Almaraz-Calderon, S.; Rehm, K. E.; Gerken, N.; ...

2017-08-17

The existence of 26Al (t 1/2 = 7.17 × 10 5 yr) in the interstellar medium provides a direct confirmation of ongoing nucleosynthesis in the Galaxy. The presence of a low-lying 0 + isomer ( 26Al m), however, severely complicates the astrophysical calculations. Here we present for the first time a study of the 26Al m (d, p) 27 Al reaction using an isomeric 26Al beam. The selectivity of this reaction allowed the study of ℓ = 0 transfers to T = 1/2, and T = 3/2 states in 27Al . Mirror symmetry arguments were then used to constrain themore » 26Al m (p,γ) 27Si reaction rate and provide an experimentally determined upper limit of the rate for the destruction of isomeric 26Al via radiative proton capture reactions, which is expected to dominate the destruction path of 26Al m in asymptotic giant branch stars, classical novae, and core collapse supernovae.« less

Study of the ^{26}Al^{m}(d,p)^{27}Al Reaction and the Influence of the ^{26}Al 0^{+} Isomer on the Destruction of ^{26}Al in the Galaxy.

PubMed

Almaraz-Calderon, S; Rehm, K E; Gerken, N; Avila, M L; Kay, B P; Talwar, R; Ayangeakaa, A D; Bottoni, S; Chen, A A; Deibel, C M; Dickerson, C; Hanselman, K; Hoffman, C R; Jiang, C L; Kuvin, S A; Nusair, O; Pardo, R C; Santiago-Gonzalez, D; Sethi, J; Ugalde, C

2017-08-18

The existence of ^{26}Al (t_{1/2}=7.17×10^{5}  yr) in the interstellar medium provides a direct confirmation of ongoing nucleosynthesis in the Galaxy. The presence of a low-lying 0^{+} isomer (^{26}Al^{m}), however, severely complicates the astrophysical calculations. We present for the first time a study of the ^{26}Al^{m}(d,p)^{27}Al reaction using an isomeric ^{26}Al beam. The selectivity of this reaction allowed the study of ℓ=0 transfers to T=1/2, and T=3/2 states in ^{27}Al. Mirror symmetry arguments were then used to constrain the ^{26}Al^{m}(p,γ)^{27}Si reaction rate and provide an experimentally determined upper limit of the rate for the destruction of isomeric ^{26}Al via radiative proton capture reactions, which is expected to dominate the destruction path of ^{26}Al^{m} in asymptotic giant branch stars, classical novae, and core collapse supernovae.

First hyperpolarizability of isomers of pyridinium N-phenoxide betaine dye in solution using the ASEC-FEG method

NASA Astrophysics Data System (ADS)

Torres, E. M.; Georg, H. C.; Fonseca, T. L.; Castro, M. A.

2018-05-01

The linear and nonlinear properties of isomeric forms of pyridinium-N-phenoxide betaine dye were investigated in protic and aprotic solvents using atomistic simulations. We employed the sequential Quantum Mechanics/Molecular Mechanics (S-QM/MM) and the free energy gradient (FEG) methods to optimize the geometry of each isomer in chloroform, acetonitrile, methanol and water. The results show a complex dependence of the first hyperpolarizability with respect to the solvent nature and isomeric form, with a marked effect of conformational changes for para-betaine. Large contrasts of the first hyperpolarizability show a clear distinction between isomeric forms in solution that could be experimentally detected.

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.

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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determining the magnitude and direction of photoinduced ligand field switching in photochromic metal-organic complexes: molybdenum-tetracarbonyl spirooxazine complexes.

PubMed

Paquette, Michelle M; Patrick, Brian O; Frank, Natia L

2011-07-06

The ability to optically switch or tune the intrinsic properties of transition metals (e.g., redox potentials, emission/absorption energies, and spin states) with photochromic metal-ligand complexes is an important strategy for developing "smart" materials. We have described a methodology for using metal-carbonyl complexes as spectroscopic probes of ligand field changes associated with light-induced isomerization of photochromic ligands. Changes in ligand field between the ring-closed spirooxazine (SO) and ring-opened photomerocyanine (PMC) forms of photochromic azahomoadamantyl and indolyl phenanthroline-spirooxazine ligands are demonstrated through FT-IR, (13)C NMR, and computational studies of their molybdenum-tetracarbonyl complexes. The frontier molecular orbitals (MOs) of the SO and PMC forms differ considerably in both electron density distributions and energies. Of the multiple π* MOs in the SO and PMC forms of the ligands, the LUMO+1, a pseudo-b(1)-symmetry phenanthroline-based MO, mixes primarily with the Mo(CO)(4) fragment and provides the major pathway for Mo(d)→phen(π*) backbonding. The LUMO+1 is found to be 0.2-0.3 eV lower in energy in the SO form relative to the PMC form, suggesting that the SO form is a better π-acceptor. Light-induced isomerization of the photochromic ligands was therefore found to lead to changes in the energies of their frontier MOs, which in turn leads to changes in π-acceptor ability and ligand field strength. Ligand field changes associated with photoisomerizable ligands allow tuning of excited-state and ground-state energies that dictate energy/electron transfer, optical/electrical properties, and spin states of a metal center upon photoisomerization, positioning photochromic ligand-metal complexes as promising targets for smart materials.

Infrared Spectroscopy of 1-CHOLOROMETHYLALLYL and 1-METHYLALLYL Radicals Produced in a Solid Para-Hydrogen Matrix.

NASA Astrophysics Data System (ADS)

Bahou, Mohammed; Wu, Jen-Yu; Tanaka, Keiichi; Lee, Yuan-Pern

2012-06-01

The reaction of chlorine atoms with trans-1,3-butadiene in solid para-hydrogen (p-H_2) matrix has been studied using Fourier transform infrared spectroscopy. When a mixture of Cl_2, trans-1,3-butadiene and p-H_2 was deposited onto a cold target at 3 K and irradiated by UV light at 365 nm, new intense lines at 809.0, 962.1, 1240.6 cm-1 and several weaker ones appeared. The carrier of this spectrum was assigned to the 1-chloromethylallyl radical, - (CH_2CHCH)CH_2Cl, based on the anharmonic vibrational frequencies calculated with the DFT method, indicating that the addition of the Cl atom to trans-1,3-butadiene occurs primarily at the terminal carbon atom. This is in sharp contrast to the reaction of chlorine atoms with propene in a solid p-H_2 matrix in which the addition of Cl to the central carbon atom to produce selectively the 2-chloropropyl is favored due to the steric effects. The energy diagram calculated with B3PW91 method supports this selective reaction process because 1) the channel from trans-1,3-butadiene to 1-chloro-methylallyl is almost barrierless (0.4 kcal/mol), and 2) isomereization from 1-chloromethylally to the 2-chloro-3-buten-1-yl radical, CH_2CHCHClCH_2 - by migration of Cl atom from the terminal to the central C atom, hardly occur in the p-H_2 matrix because of the isomerization barrier height (18.8 kcal/mol). We also observed a second set of lines with intense ones at 781.6, 957.93, 1433.6 cm-1 and several weaker ones when the UV-irradiated Cl_2/trans-1,3-butadiene/p-H_2 matrix was further irradiated with infrared light from a globar source. These lines are assigned to the 1-methylallyl radical, - (CH_2CHCH)CH_3, produced from reaction of 1,3-butadiene with an H atom that was produced from the reaction of Cl atoms with IR-irradiated p-H_2, Cl + H_2^* → H + HCl. The energy diagram calculated at the G3//B3LYP level similarly supports the reaction process to form selectively 1-methylallyl in the p-H_2 matrix. J. C. Amicangelo and Y. P. Lee, J. Phys. Chem. Lett. 1, 1956 (2010). J. L. Millerngelo, J. Phys. Chem. A 108, 2268 (2004).

A Molecular Reaction Cycle with a Solvatochromic Merocyanine Dye: An Experiment in Photochemistry, Kinetics, and Catalysis.

ERIC Educational Resources Information Center

Abdel-Kader, M. H.; Steiner, U.

1983-01-01

Three experiments using merocyanine M suitable as an integrated laboratory experience for undergraduates are described. Experiments demonstrate: complete molecular cycle composed of photochemical, thermal, and protolytic reaction steps; kinetics of cis-trans isomerization of the dye; and mechanism of base catalysis for thermal isomerization of the…

Formation, isomerization, and derivatization of keggin tungstoaluminates.

Treesearch

Jennifer J. Cowan; Alan J. Bailey; Robert A. Heintz; Bao T. Do; Kenneth I. Hardcastle; Craig L. Hill; Ira A. Weinstock

2001-01-01

Trends in the stability of ¥á and ©¬-Keggin heteropolytungstates of the second-row main-group heteroatoms Al(III), Si(IV), and P(V) are elaborated by data that establish the roles of kinetic and thermodynamic control in the formation and isomerization of Keggin tungstoaluminates. Slow, room-temperature co-...

TAGS measurements of 100 Nb ground and isomeric states and 140 Cs for neutrino physics with the new DTAS detector

DOE PAGES

Guadilla, V.; Algora, A.; Tain, J. L.; ...

2017-09-13

In this work we report on total absorption γ -ray spectroscopy measurements of the β decay of fission products that are important contributors to the antineutrino spectrum. The experiment was performed at IGISOL as a part of a campaign of measurements with the new DTAS spectrometer. Preliminary results of the analysis of the β decay of 100Nb, 100mNb and 140Cs are presented.

A dynamics prediction of nitromethane → methyl nitrite isomerization in external electric field.

PubMed

Ren, Fu-de; Cao, Duan-lin; Shi, Wen-jing

2016-04-01

As a follow-up to our investigation into the effect of external electric field on the chemical bond strength, the effects of external electric field on the CH3NO2 → CH3ONO isomerization dynamics were investigated using the MP2/6-311++G(2d,p) and CCSD/6-311++G(2d,p) methods. The rate constants in the absence and presence of various field strengths were calculated. The results show that, when the field strength is larger than +0.0060 a.u. along the C-NO2 bond axis, the barriers of the isomerization are lower than the C-NO2 bond dissociation energies, leading to the preferences of the isomerization over the C-NO2 bond dissociation. In this case, the sensitivities are higher than that in no field. However, in the other fields, the C-NO2 bond scission is favored and the sensitivities are almost equal to that in no field. Several good linear correlations are found between the field strengths and the changes of the bond lengths or corresponding electron densities.

Regioselective cis-trans isomerization of arachidonic double bonds by thiyl radicals: the influence of phospholipid supramolecular organization.

PubMed

Ferreri, Carla; Samadi, Abdelouahid; Sassatelli, Fabio; Landi, Laura; Chatgilialoglu, Chryssostomos

2004-02-04

Trans unsaturated fatty acids in humans may be originated by two different contributions. The exogenous track is due to dietary supplementation of trans fats and the endogenous path deals with free-radical-catalyzed cis-trans isomerization of fatty acids. Arachidonic acid residue (5c,8c,11c,14c-20:4), which has only two out of the four double bonds deriving from the diet, was used to differentiate the two paths and to assess the importance of a radical reaction. A detailed study on the formation of trans phospholipids catalyzed by the HOCH2CH2S* radical was carried out on L-alpha-phosphatidylcholine from egg lecithin and 1-stearoyl-2-arachidonoyl-L-alpha-phosphatidylcholine (SAPC) in homogeneous solution or in large unilamellar vesicles (LUVET). Thiyl radicals were generated from the corresponding thiol by either gamma-irradiation or UV photolysis, and the reaction course was followed by GC, Ag/TLC, and 13C NMR analyses. The isomerization was found to be independent of cis double bond location (random process) in i-PrOH solution. In the case of vesicles, the supramolecular organization of lipids produced a dramatic change of the isomerization outcome: (i) in egg lecithin, the reactivity of arachidonate moieties is higher than that of oleate and linoleate residues, (ii) in the linoleate residues of egg lecithin, the 9t,12c-18:2 isomer prevailed on the 9c,12t-18:2 isomer (3:1 ratio), and (iii) a regioselective isomerization of SAPC arachidonate residues occurred in the 5 and 8 positions. This effect of "positional preference" indicates that thiyl radicals entering the hydrophobic region of the membrane bilayer start to isomerize polyunsaturated fatty acid residues having the double bonds nearest to the membrane surfaces. We propose that arachidonic acid and its trans isomers can function as biomarkers in membranes for distinguishing the two trans fatty acid-forming pathways.

Formation, isomerization, and derivatization of Keggin tungstoaluminates.

PubMed

Cowan, J J; Bailey, A J; Heintz, R A; Do, B T; Hardcastle, K I; Hill, C L; Weinstock, I A

2001-12-17

Trends in the stability of alpha- and beta-Keggin heteropolytungstates of the second-row main-group heteroatoms Al(III), Si(IV), and P(V) are elaborated by data that establish the roles of kinetic and thermodynamic control in the formation and isomerization of Keggin tungstoaluminates. Slow, room-temperature co-condensation of Al(III) and W(VI) (2:11 molar ratio) in water gives a pH 7 solution containing beta(1) and beta(2) isomers of [Al(AlOH(2))W(11)O(39)](6)(-) (beta(1)- and beta(2)-1). Partial equilibration of this kinetic product mixture by gentle heating (2 h at 100 degrees C) or, alternatively, co-condensation of Al(III) and W(VI) for 2.5 h at 100 degrees C both give mixtures of beta(2)-, beta(3)-, and alpha-1. Full equilibration, by prolonged heating (25 days at 100 degrees C), gives an isomerically pure solution of alpha-1, thus demonstrating that isomerization occurs in the direction beta(1) --> beta(2) --> beta(3) --> alpha. Furthermore, kinetically controlled conversions of 1 to H(5)[AlW(12)O(40)] (2)-achieved by heating pH 0-0.2 solutions of 1 for 5 days at 100 degrees C-occur with retention of isomeric integrity, such that alpha-1 is converted to alpha-2 (92%; 8% beta), while mixtures of beta(2)- and beta(3)-1 are converted to beta-2 (87%; 13% alpha). These data, when combined with previously reported observations (equilibria between alpha- and beta-2, kinetically controlled hydrolyses of alpha-2 to alpha-[AlW(11)O(39)](9)(-) (alpha-3) and of beta-2 to beta(2)-3, and equilibria between beta(3)- and alpha-3), provide a comprehensive picture regarding the roles of kinetic and thermodynamic control. Finally, a general method for preparation of the isomerically pure derivatives alpha-K(9)(-)(n)()[AlM(n)()(+)W(11)O(39)] (4), M(n)()(+) = Al(III), [V(IV)O](2+), [V(V)O](3+), Mn(II), Mn(III), Mn(IV), Co(II), and Co(III), is provided. The presence of Mn(IV) is confirmed by cyclic voltammetry, pK(a) values of the aquo ligands on 4 are determined by pH titration, and the isomeric structure of these derivatives is established by (27)Al, (51)V, and (183)W NMR and IR spectroscopies and X-ray crystallography.

Compartmental and noncompartmental modeling of 13C-lycopene absorption, isomerization, and distribution kinetics in healthy adults123

PubMed Central

Moran, Nancy E; Cichon, Morgan J; Riedl, Kenneth M; Grainger, Elizabeth M; Schwartz, Steven J; Novotny, Janet A; Erdman, John W; Clinton, Steven K

2015-01-01

Background: Lycopene, which is a red carotenoid in tomatoes, has been hypothesized to mediate disease-preventive effects associated with tomato consumption. Lycopene is consumed primarily as the all-trans geometric isomer in foods, whereas human plasma and tissues show greater proportions of cis isomers. Objective: With the use of compartmental modeling and stable isotope technology, we determined whether endogenous all-trans-to-cis-lycopene isomerization or isomeric-bioavailability differences underlie the greater proportion of lycopene cis isomers in human tissues than in tomato foods. Design: Healthy men (n = 4) and women (n = 4) consumed 13C-lycopene (10.2 mg; 82% all-trans and 18% cis), and plasma was collected over 28 d. Unlabeled and 13C-labeled total lycopene and lycopene-isomer plasma concentrations, which were measured with the use of high-performance liquid chromatography–mass spectrometry, were fit to a 7-compartment model. Results: Subjects absorbed a mean ± SEM of 23% ± 6% of the lycopene. The proportion of plasma cis-13C-lycopene isomers increased over time, and all-trans had a shorter half-life than that of cis isomers (5.3 ± 0.3 and 8.8 ± 0.6 d, respectively; P < 0.001) and an earlier time to reach maximal plasma concentration than that of cis isomers (28 ± 7 and 48 ± 9 h, respectively). A compartmental model that allowed for interindividual differences in cis- and all-trans-lycopene bioavailability and endogenous trans-to-cis-lycopene isomerization was predictive of plasma 13C and unlabeled cis- and all-trans-lycopene concentrations. Although the bioavailability of cis (24.5% ± 6%) and all-trans (23.2% ± 8%) isomers did not differ, endogenous isomerization (0.97 ± 0.25 μmol/d in the fast-turnover tissue lycopene pool) drove tissue and plasma isomeric profiles. Conclusion: 13C-Lycopene combined with physiologic compartmental modeling provides a strategy for following complex in vivo metabolic processes in humans and reveals that postabsorptive trans-to-cis-lycopene isomerization, and not the differential bioavailability of isomers, drives tissue and plasma enrichment of cis-lycopene. This trial was registered at clinicaltrials.gov as NCT01692340. PMID:26561629

Prompt fissionγ-ray characteristics from neutron-induced fission on 239Pu and the time-dependence of prompt-γray emission

NASA Astrophysics Data System (ADS)

Gatera, Angélique; Göök, Alf; Hambsch, Franz-Josef; Moens, André; Oberstedt, Andreas; Oberstedt, Stephan; Sibbens, Goedele; Vanleeuw, David; Vidali, Marzio

2018-03-01

Recent years have seen an increased interest in prompt fission γ-ray (PFG) measurements motivated by a high priority request of the OECD/NEA for high precision data, mainly for the nuclear fuel isotopes 235U and 239Pu. Our group has conducted a PFG measurement campaign using state-of-the-art lanthanum halide detectors for all the main actinides to a precision better than 3%. The experiments were performed in a coincidence setup between a fission trigger and γ-ray detectors. The time-of-flight technique was used to discriminate photons, traveling at the speed of light, and prompt fission neutrons. For a full rejection of all neutrons below 20 MeV, the PFG time window should not be wider than a few nanoseconds. This window includes most PFG, provided that no isomeric states were populated during the de-excitation process. When isomeric states are populated, PFGs can still be emitted up to 1 yus after the instant of fission or later. To study these γ-rays, the detector response to neutrons had to be determined and a correction had to be applied to the γ-ray spectra. The latest results for PFG characteristics from the reaction 239Pu(nth,f) will be presented, together with an analysis of PFGs emitted up to 200 ns after fission in the spontaneous fission of 252Cf as well as for thermal-neutron induced fission on 235U and 239Pu. The results are compared with calculations in the framework of the Hauser-Feshbach Monte Carlo code CGMF and FIFRELIN.

Influence of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage.

PubMed

Baker, Joseph L; Furbish, Jeffrey; Lindberg, Gerrick E

2015-11-01

We examine the effect of the ionic liquid [C4mpy][Tf2N] on the structure of the miniprotein Trp-cage and contrast these results with the behavior of Trp-cage in water. We find the ionic liquid has a dramatic effect on Trp-cage, though many similarities with aqueous Trp-cage are observed. We assess Trp-cage folding by monitoring root mean square deviation from the crystallographic structure, radius of gyration, proline cis/trans isomerization state, protein secondary structure, amino acid contact formation and distance, and native and non-native contact formation. Starting from an unfolded configuration, Trp-cage folds in water at 298 K in less than 500 ns of simulation, but has very little mobility in the ionic liquid at the same temperature, which can be ascribed to the higher ionic liquid viscosity. At 365 K, the mobility of the ionic liquid is increased and initial stages of Trp-cage folding are observed, however Trp-cage does not reach the native folded state in 2 μs of simulation in the ionic liquid. Therefore, in addition to conventional molecular dynamics, we also employ scaled molecular dynamics to expedite sampling, and we demonstrate that Trp-cage in the ionic liquid does closely approach the aqueous folded state. Interestingly, while the reduced mobility of the ionic liquid is found to restrict Trp-cage motion, the ionic liquid does facilitate proline cis/trans isomerization events that are not seen in our aqueous simulations. Copyright © 2015 Elsevier Inc. All rights reserved.

Solid state 13C-NMR, infrared, X-ray powder diffraction and differential thermal studies of the homologous series of some mono-valent metal (Li, Na, K, Ag) n-alkanoates: A comparative study

NASA Astrophysics Data System (ADS)

Nelson, Peter N.; Ellis, Henry A.; White, Nicole A. S.

2015-06-01

A comparative study of the molecular packing, lattice structures and phase behaviors of the homologous series of some mono-valent metal carboxylates (Li, Na, K and Ag) is carried out via solid state FT-infrared and 13C-NMR spectroscopes, X-rays powder diffraction, density measurements, differential scanning calorimetry, polarizing light microscopy and variable temperature infrared spectroscopy. It is proposed that, for lithium, sodium and potassium carboxylates, metal-carboxyl coordination is via asymmetric chelating bidentate bonding with extensive intermolecular interactions to form tetrahedral metal centers, irrespective of chain length. However, for silver n-alkanoates, carboxyl moieties are bound to silver ions via syn-syn type bridging bidentate coordination to form dimeric units held together by extensive head group inter-molecular interactions. Furthermore, the fully extended hydrocarbon chains which are crystallized in the all-trans conformation are tilted at ca. 30°, 27°, 15° and 31° with respect to a normal to the metal plane, for lithium, sodium, silver and potassium carboxylates, respectively. All compounds are packed as lamellar bilayer structures, however, lithium compounds are crystallized in a triclinic crystal system whilst silver, sodium and potassium n-alkanoates are all monoclinic with possible P1 bravais lattice. Odd-even alternation observed in various physical features is associated with different inter-planar spacing between closely packed layers in the bilayer which are not in the same plane; a phenomenon controlled by lattice packing symmetry requirements. All compounds, except silver carboxylates, show partially reversibly first order pre-melting transitions; the number of which increases with increasing chain length. These transitions are associated, for the most part, with lamellar collapse followed by increased gauche-trans isomerism in the methylene group assembly, irrespective of chain length. It is proposed that the absence of mesomorphic transitions in their phase sequences is due to a lack of sufficient balance between attractive and repulsive electrostatic and van der Waals forces during phase change. The evidence presented in this study shows that phase behaviors of mono-valent metal carboxylates are controlled, mainly, by head group bonding.

Atmospheric Solid Analysis Probe Coupled to Ion Mobility Spectrometry-Mass Spectrometry, a Fast and Simple Method for Polyalphaolefin Characterization

NASA Astrophysics Data System (ADS)

Mendes Siqueira, Anna Luiza; Beaumesnil, Mathieu; Hubert-Roux, Marie; Loutelier-Bourhis, Corinne; Afonso, Carlos; Bai, Yang; Courtiade, Marion; Racaud, Amandine

2018-05-01

Polyalphaolefins (PAOs) are polymers produced from linear alpha olefins through catalytic oligomerization processes. The PAOs are known as synthetic high-performance base stock fluids used to improve the efficiency of many other synthetic products. In this study, we report the direct characterization of PAOs using atmospheric solid analysis probe (ASAP) coupled with ion mobility spectrometry-mass spectrometry (IMS-MS). We studied different PAOs grades exhibiting low- and high-viscosity index. Specific adjustments of the ASAP source parameters permitted the monitoring of ionization processes as three mechanisms could occur for these compounds: hydride abstraction, nitrogen addition, and/or the formation of [M-2H]+• ions. Several series of fragment ions were obtained, which allowed the identification of the alpha olefin used to synthesize the PAO. The use of the ion mobility separation dimension provides information on isomeric species. In addition, the drift time versus m/z plots permitted rapid comparison between PAO samples and to evidence their complexity. These 2D plots appear as fingerprints of PAO samples. To conclude, the resort to ASAP-IMS-MS provides a rapid characterization of the PAO samples in a direct analysis approach, without any sample preparation.

Odd-even chain packing, molecular and thermal models for some long chain sodium(I) n-alkanoates

NASA Astrophysics Data System (ADS)

Nelson, Peter N.; Ellis, Henry A.

2014-10-01

A homologous series of sodium(I) n-alkanoates, NaCnH2n-1O2, with chain lengths n = 8-18, inclusive, have been synthesized and their structural and thermal properties investigated via Fourier Transform Infrared and Solid State 13C NMR spectroscopies, X-ray powder diffraction, Thermogravimetry, Differential Scanning Calorimetry, Polarizing light microscopy and variable temperature Infrared spectroscopy. The measurements show that metal-carboxylate coordination is via asymmetric chelating bidentate bonding with extensive carboxyl group inter-molecular interactions in which four oxygen atoms are bonded tetrahedrally to a sodium atom. Furthermore, the compounds crystallize in a monoclinic crystal system with the hydrocarbon chains in the fully extended all-trans conformation, advancing along the c-axis. Moreover, the chains are packed as tilted (θ ∼ 63°), non-overlapping, tail-to-tail lamellar bilayers that are not in the same plane, within a lamellar. Though these compounds are nearly isostructural, there are subtle differences in the packing of the hydrocarbon chains in the crystal lattice, resulting in odd-even alternation in the terminal methyl group asymmetric stretching vibration and chemical shift. These differences arise from the relative vertical distances between hydrocarbon planes within the lamellar; such that, for odd-chain compounds, larger inter-planar distances result in less efficient packing in the crystal lattice and hence, lower inter-planar van der Waals interactions between hydrocarbon chains. Thermal traces, for all compounds, show several partially reversible solid-solid pre-melting transitions associated with different degrees of gauche conformers in the alkyl chains. The reversible gauche-trans isomerism, of the methylene groups, is kinetically controlled; hence, super-cooling of the melt and other transitions, are observed for all compounds. The kinetics of chain reversion follow the exponential law of nucleation, though complicated by competing processes. Thermogravimetric data show that all compounds decompose at temperatures in excess of 690 K; therefore, free radical thermal cracking of the hydrocarbon chains, in conjunction with decarboxylation is proposed for their non-oxidative degradation mechanism.

Rough energy landscapes in protein folding: dimeric E. coli Trp repressor folds through three parallel channels.

PubMed

Gloss, L M; Simler, B R; Matthews, C R

2001-10-05

The folding mechanism of the dimeric Escherichia coli Trp repressor (TR) is a kinetically complex process that involves three distinguishable stages of development. Following the formation of a partially folded, monomeric ensemble of species, within 5 ms, folding to the native dimer is controlled by three kinetic phases. The rate-limiting step in each phase is either a non-proline isomerization reaction or a dimerization reaction, depending on the final denaturant concentration. Two approaches have been employed to test the previously proposed folding mechanism of TR through three parallel channels: (1) unfolding double-jump experiments demonstrate that all three folding channels lead directly to native dimer; and (2) the differential stabilization of the transition state for the final step in folding and the native dimer, by the addition of salt, shows that all three channels involve isomerization of a dimeric species. A refined model for the folding of Trp repressor is presented, in which all three channels involve a rapid dimerization reaction between partially folded monomers followed by the isomerization of the dimeric intermediates to yield native dimer. The ensemble of partially folded monomers can be captured at equilibrium by low pH; one-dimensional proton NMR spectra at pH 2.5 demonstrate that monomers exist in two distinct, slowly interconverting conformations. These data provide a potential structural explanation for the three-channel folding mechanism of TR: random association of two different monomeric forms, which are distinguished by alternative packing modes of the core dimerization domain and the DNA-binding, helix-turn-helix, domain. One, perhaps both, of these packing modes contains non-native contacts. Copyright 2001 Academic Press.

Molecular dynamics analysis of transitions between rotational isomers in polymethylene

NASA Astrophysics Data System (ADS)

Zúñiga, Ignacio; Bahar, Ivet; Dodge, Robert; Mattice, Wayne L.

1991-10-01

Molecular dynamics trajectories have been computed and analyzed for linear chains, with sizes ranging from C10H22 to C100H202, and for cyclic C100H200. All hydrogen atoms are included discretely. All bond lengths, bond angles, and torsion angles are variable. Hazard plots show a tendency, at very short times, for correlations between rotational isomeric transitions at bond i and i±2, in much the same manner as in the Brownian dynamics simulations reported by Helfand and co-workers. This correlation of next nearest neighbor bonds in isolated polyethylene chains is much weaker than the correlation found for next nearest neighbor CH-CH2 bonds in poly(1,4-trans-butadiene) confined to the channel formed by crystalline perhydrotriphenylene [Dodge and Mattice, Macromolecules 24, 2709 (1991)]. Less than half of the rotational isomeric transitions observed in the entire trajectory for C50H102 can be described as strongly coupled next nearest neighbor transitions. If correlated motions are identified with successive transitions, which occur within a time interval of Δt≤1 ps, only 18% of the transitions occur through cooperative motion of bonds i and i±2. An analysis of the entire data set of 2482 rotational isomeric state transitions, observed in a 3.7 ns trajectory for C50H102 at 400 K, was performed using a formalism that treats the transitions at different bonds as being independent. On time scales of 0.1 ns or longer, the analysis based on independent bonds accounts reasonably well for the results from the molecular dynamics simulations. At shorter times the molecular dynamics simulation reveals a higher mobility than implied by the analysis assuming independent bonds, presumably due to the influence of correlations that are important at shorter times.

Brønsted acid-catalyzed decarboxylative redox amination: formation of N-alkylindoles from azomethine ylides by isomerization.

PubMed

Mao, Hui; Wang, Sichang; Yu, Peng; Lv, Huiqing; Xu, Runsheng; Pan, Yuanjiang

2011-02-18

A Brønsted acid-catalyzed decarboxylative redox amination involving aldehydes with 2-carboxyindoline for the synthesis of N-alkylindoles is described. The decarboxylative condensations of aldehydes with 2-carboxyindoline produce azomethine ylides in situ, which then transform into N-alkylindoles by isomerization. © 2011 American Chemical Society

[Isomeric derivatives of lupinine and epilupinine--organophosphorus inhibitors of cholinesterases].

PubMed

Basova, N E; Kormilitsyn, B N; Perchenok, A Iu; Rosengart, E V; Saakov, V S; Suvorov, A A

2012-01-01

The isomeric-structure analysis data of anticholinesterase action of organophosphorous inhibitors with similar structure help in the search of specific effectors and detection of differences in reactivity of various animals' enzymes. This study compared the data of efficacy in respect of 4 mammal and 5 arthropoda cholinesterase preparations for 26 quinolizidine inhibitors, which molecules contain both the isomeric unbranched and branched alkoxyl radicals in the phosphoryl group, and the epimeric lupinine and epilupinine derivatives in the leaving group. The changes in the alkoxyl radical structure of inhibitor molecules act on their efficacy only with respect to the mammal enzymes ("group" inhibitor specificity). The differences between lupinine and epilupinine derivatives were revealed. Highly specific inhibitors of different enzymes were detected among the tested compounds.

Results of a Direct Search Using Synchrotron Radiation for the Low-Energy 229Th Nuclear Isomeric Transition

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

Results of a Direct Search Using Synchrotron Radiation for the Low-Energy Th 229 Nuclear Isomeric Transition

DOE PAGES

Jeet, Justin; Schneider, Christian; Sullivan, Scott T.; ...

2015-06-23

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

Evidence for cis-trans isomerization of a double bond in the fatty acids of the psychrophilic bacterium Vibrio sp. strain ABE-1.

PubMed

Morita, N; Shibahara, A; Yamamoto, K; Shinkai, K; Kajimoto, G; Okuyama, H

1993-02-01

Vibrio sp. strain ABE-1 was grown in a medium that contained as its stable isotope tracer either [2,2-2H2]cis-9-hexadecenoic or [2,2-2H2]trans-9-hexadecenoic acid. Gas chromatographic-mass spectrometric analysis of the cis-9-hexadecenoic and trans-9-hexadecenoic acid fractions from the cells revealed the formation of an intracellularly isomerized 2,2-2H2-fatty acid which differed from the tracer only in the geometrical configuration of the double bond. This observation shows that cis-trans isomerization without a shift in double-bond position between these two geometric hexadecenoic acid isomers can occur in the cells.

Evidence for cis-trans isomerization of a double bond in the fatty acids of the psychrophilic bacterium Vibrio sp. strain ABE-1.

PubMed Central

Morita, N; Shibahara, A; Yamamoto, K; Shinkai, K; Kajimoto, G; Okuyama, H

1993-01-01

Vibrio sp. strain ABE-1 was grown in a medium that contained as its stable isotope tracer either [2,2-2H2]cis-9-hexadecenoic or [2,2-2H2]trans-9-hexadecenoic acid. Gas chromatographic-mass spectrometric analysis of the cis-9-hexadecenoic and trans-9-hexadecenoic acid fractions from the cells revealed the formation of an intracellularly isomerized 2,2-2H2-fatty acid which differed from the tracer only in the geometrical configuration of the double bond. This observation shows that cis-trans isomerization without a shift in double-bond position between these two geometric hexadecenoic acid isomers can occur in the cells. PMID:8423164

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.

β-decay spectroscopy for the r-process nucleosynthesis

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

Nishimura, Shunji; Collaboration: RIBF Decay Collaborations

2014-05-09

Series of decay spectroscopy experiments, utilizing of high-purity Ge detectors and double-sided silicon-strip detectors, have been conducted to harvest the decay properties of very exotic nuclei relevant to the r-process nucleosynthesis at the RIBF. The decay properties such as β-decay half-lives, low-lying states, β-delayed neutron emissions, isomeric states, and possibly Q{sub β} of the very neutron-rich nuclei are to be measured to give significant constraints in the uncertainties of nuclear properties for the r-process nucleosynthesis. Recent results of βγ spectroscopy study using in-flight fission of {sup 238}U-beam will be presented together with our future perspectives.

Fluorescence of carotenoids. Effect of oxygenation and cis/trans isomerization

NASA Astrophysics Data System (ADS)

Jørgensen, Kevin; Stapelfeldt, Henrik; Skibsted, Leif H.

1992-03-01

C 40 carotenoids fall, with respect to fluorescence in homogeneous solution, into two distinct groups depending on the presence of a CO group in the molecule. Excitation spectra agree with absorption spectra for the carbonyl derivatives astaxanthin and canthaxanthin. In contrast, zeaxanthin and isomers of β-carotene have a twentyfold increase in fluorescence quantum yield for excitation around 350 nm compared to excitation near the absorption maximum (at approximatively 430 nm). These differences are interpreted in terms of the role of non-emitting 1(n, π*) states related to the CO group in facilitating non-radiative deactivation of higher 1(π, π*) states.

Nuclear structure studies in the seaborgium region at SHIP

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

Antalic, S., E-mail: Stanislav.Antalic@fmph.uniba.sk; Andel, B.; Heßberger, F. P.

2015-10-15

New decay data for the isotopes {sup 259}Sg and {sup 255}Rf were obtained at the velocity filter SHIP using an α-decay spectroscopy measurement. Both isotopes were produced and studied via a one neutron evaporation channel in the compound fusion reaction {sup 54}Cr+{sup 208}Pb. New isomeric states were observed and the single-particle level systematics for isotones with 151 and 153 neutrons were extended. A change of the ground-state configuration for the heaviest N = 151 isotones was observed. Detailed Monte-Carlo simulation for the α decay of {sup 259}Sg applying the GEANT4 toolkit was performed and compared with experimental data.

Simple Quaternary Ammonium Ions R4N + ( R= nPr, nBu, nPen) as Versatile Structure Directors for the Synthesis of Zeolite-Like, Heterobimetallic Cyanide Frameworks

NASA Astrophysics Data System (ADS)

Poll, Eyck-Michael; Samba, Sabine; Dieter Fischer, R.; Olbrich, Falk; Davies, Nicola A.; Avalle, Paolo; Apperley, David C.; Harris, Robin K.

2000-06-01

The preparation of three new examples of water insoluble host/guest assemblies of the general composition: [(R4N)(Me3Sn)2M(CN)6·zH2O] (R=n-propyl or n-pentyl, M=Fe or Co, 0≤z≤2) from likewise polymeric super-Prussian-blue derivatives [(Me3Sn)3M(CN)6] and aqueous (R4N)X solutions are reported. According to combined single-crystal X-ray (3a and 3a*: R=nPr, M=Co, z=2; 5b: R=nPen, M=Fe, z=0.5), powder X-ray diffraction (XRD), and multinuclear (13C, 15N, 59Co, 119Sn) CPMAS solid-state magnetic resonance studies, 3a and 3a* contain cis- and trans-isomeric [Co(CN)4(CNSnMe3OH2)2]- building blocks, respectively, which are held together exclusively by Sn←OH2···NC-Co hydrogen bonds. In striking contrast, the building blocks of 5b and 5a are infinite [M-CN-Sn-NC] chains. In all these assemblies, also significant C-H···NC hydrogen bonds between the encapsulated R4N+ guest ion and exclusively terminal cyanide ligands of the host seem to play a notable auxiliary role.

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

Dracoulis, G. D.; Walker, P. M.; Kondev, F. G.

Here, the structure of nuclear isomeric states is reviewed in the context of their role in contemporary nuclear physics research. Emphasis is given to high-spin isomers in heavy nuclei, with A ≳ 150. The possibility to exploit isomers to study some of the most exotic nuclei is a recurring theme. In spherical nuclei, the role of octupole collectivity is discussed in detail, while in deformed nuclei the limitations of the K quantum number are addressed. Isomer targets and isomer beams are considered, along with applications related to energy storage, astrophysics, medicine, and experimental advances.

Optically-programmable nonlinear photonic component for dielectric-loaded plasmonic circuitry.

PubMed

Krasavin, Alexey V; Randhawa, Sukanya; Bouillard, Jean-Sebastien; Renger, Jan; Quidant, Romain; Zayats, Anatoly V

2011-12-05

We demonstrate both experimentally and numerically a compact and efficient, optically tuneable plasmonic component utilizing a surface plasmon polariton ring resonator with nonlinearity based on trans-cis isomerization in a polymer material. We observe more than 3-fold change between high and low transmission states of the device at milliwatt control powers (∼100 W/cm² by intensity), with the performance limited by switching speed of the material. Such plasmonic components can be employed in optically programmable and reconfigurable integrated photonic circuitry.

Thermal Chemistry of Cp*W(NO)(CH2CMe3)(H)(L) Complexes (L = Lewis Base).

PubMed

Fabulyak, Diana; Handford, Rex C; Holmes, Aaron S; Levesque, Taleah M; Wakeham, Russell J; Patrick, Brian O; Legzdins, Peter; Rosenfeld, Devon C

2017-01-03

The complexes trans-Cp*W(NO)(CH 2 CMe 3 )(H)(L) (Cp* = η 5 -C 5 Me 5 ) result from the treatment of Cp*W(NO)(CH 2 CMe 3 ) 2 in n-pentane with H 2 (∼1 atm) in the presence of a Lewis base, L. The designation of a particular geometrical isomer as cis or trans indicates the relative positions of the alkyl and hydrido ligands in the base of a four-legged piano-stool molecular structure. The thermal behavior of these complexes is markedly dependent on the nature of L. Some of them can be isolated at ambient temperatures [e.g., L = P(OMe) 3 , P(OPh) 3 , or P(OCH 2 ) 3 CMe]. Others undergo reductive elimination of CMe 4 via trans to cis isomerization to generate the 16e reactive intermediates Cp*W(NO)(L). These intermediates can intramolecularly activate a C-H bond of L to form 18e cis complexes that may convert to the thermodynamically more stable trans isomers [e.g., Cp*W(NO)(PPh 3 ) initially forms cis-Cp*W(NO)(H)(κ 2 -PPh 2 C 6 H 4 ) that upon being warmed in n-pentane at 80 °C isomerizes to trans-Cp*W(NO)(H)(κ 2 -PPh 2 C 6 H 4 )]. Alternatively, the Cp*W(NO)(L) intermediates can effect the intermolecular activation of a substrate R-H to form trans-Cp*W(NO)(R)(H)(L) complexes [e.g., L = P(OMe) 3 or P(OCH 2 ) 3 CMe; R-H = C 6 H 6 or Me 4 Si] probably via their cis isomers. These latter activations are also accompanied by the formation of some Cp*W(NO)(L) 2 disproportionation products. An added complication in the L = P(OMe) 3 system is that thermolysis of trans-Cp*W(NO)(CH 2 CMe 3 )(H)(P(OMe) 3 ) results in it undergoing an Arbuzov-like rearrangement and being converted mainly into [Cp*W(NO)(Me)(PO(OMe) 2 )] 2 , which exists as a mixture of two isomers. All new complexes have been characterized by conventional and spectroscopic methods, and the solid-state molecular structures of most of them have been established by single-crystal X-ray crystallographic analyses.

Carotenoid stability during production and storage of tomato juice made from tomatoes with diverse pigment profiles measured by infrared spectroscopy.

PubMed

Rubio-Diaz, Daniel E; Santos, Alejandra; Francis, David M; Rodriguez-Saona, Luis E

2010-08-11

Chemical changes in carotenoids and lipids were studied during production and storage of canned tomato juice using ATR infrared spectroscopy and HPLC. Samples from 10 groups of tomatoes with different carotenoid profiles were analyzed fresh, after hot-break and screening, after canning, and at five different time points during 1 year of storage. An apparent increase of carotenoids was observed after hot-break due to improved extraction efficiency. This increase was accompanied by some degree of lipid oxidation and carotenoid isomerization. Canning produced the most intense changes in the lipid profile with breakdown of triglycerides ( approximately 1743 cm(-1)), formation of fatty acids ( approximately 1712 cm(-1)), and degradation and isomerization of trans-carotenoids ( approximately 960 and approximately 3006 cm(-1)). Isomerization was corroborated by the relative increase of HPLC areas corresponding to carotenoid cis isomers. Canning reduced trans-lycopene, trans-delta-carotene, trans-beta-carotene, and trans-lutein by 30, 34, 43, and 67%, respectively. HPLC data indicate that canning causes a drastic reduction of tetra-cis-lycopene and promotes its isomerization to other geometric forms, including all-trans-lycopene. Infrared spectra of tomato juice lipid fractions correlated well with the number of days in storage (SECV < 11 days, r values > 0.99), demonstrating continuous degradation of lipids. Results demonstrated that individual carotenoids and their isomeric forms behave differently during production and storage of canned tomato juice. Information collected by infrared spectroscopy complemented well that of HPLC, providing marker bands to further the understanding of chemical changes taking place during processing and storage of tomato juice.

Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

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

Ligare, Marshall R.; Baker, Erin S.; Laskin, Julia

Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

Palladium Hydride Promoted Stereoselective Isomerization of Unactivated Di(exo)methylenes to Endocyclic Dienes

PubMed Central

2015-01-01

The exomethylenes of 2,6-disubstituted bicyclo[3.3.1]nonan-9-ones 2 are readily isomerized over a palladium catalyst under an atmosphere of hydrogen to predominantly form the isomer 3 with C2 symmetry with very little formation of the analogous product with Cs symmetry. A hydrogen source is essential to effect the rearrangement. PMID:24720691

Transient-Absorption Spectroscopy of Cis-Trans Isomerization of N,N-dimethyl-4,4'-Azodianiline with 3D-Printed Temperature-Controlled Sample Holder

ERIC Educational Resources Information Center

Kosenkov, Dmytro; Shaw, James; Zuczek, Jennifer; Kholod, Yana

2016-01-01

The laboratory unit demonstrates a project based approach to teaching physical chemistry laboratory where upper-division undergraduates carry out a transient-absorption experiment investigating the kinetics of cis-trans isomerization of N,N-dimethyl-4,4'-azodianiline. Students participate in modification of a standard flash-photolysis spectrometer…

Roaming Reactions and Roaming-Mediated Isomerization in the Decomposition of Energetic Materials

DTIC Science & Technology

2015-12-02

not   permit   effective   competition   between   isomerization  and  SBF  as  had  been  seen   for  nitromethane   in...vinylidene   is   formed   with   only   modest  rotational  excitation,  precluding   Coriolis -­‐induced  mixing  among  the

Europe Report, Science and Technology.

DTIC Science & Technology

1986-06-18

amylase, heat stable alpha-amylase and glucoamylase for processing starch as a substrate for 71 glucose and its isomerization to fructose using an...continuous column process under laboratory conditions. We have demonstrated that these preparations isomerize glucose syrups up to 42 percent, converting...food industry is the leading consumer of microbial enzymes devouring about 80 percent of the world production of enzymes -- glucose isomerase, alpha

The isomerization of allylrhodium intermediates in the rhodium-catalyzed nucleophilic allylation of cyclic imines.

PubMed

Hepburn, Hamish B; Lam, Hon Wai

2014-10-20

Allylrhodium species generated from potassium allyltrifluoroborates can undergo isomerization by 1,4-rhodium(I) migration to give more complex isomers, which then react with cyclic imines to provide products with up to three new stereochemical elements. High enantioselectivities are obtained using chiral diene-rhodium complexes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linkage isomerism in trimeric and polymeric 2,3-cis-procyanindins

Treesearch

Richard W. Hemingway; Lai Yeap Foo; Lawrence J. Porter

1982-01-01

Procyanindins polymers consist of chains of 5,7,3',4'-tetrahydroxyflavan-3-ol units linked by C(4)-C(6) or C(4)-C(8) bonds.1 Whereas the procyanidin-B group of dimers are known to exist as pairs of isomers with common flavan-3-ol units, but different interflavanoid linkages,2,3 the extent of such isomerism in...

Tandem isomerization-decarboxylation of unsaturated fatty acids to olefins via ruthenium metal-as-ligand catalysts

USDA-ARS?s Scientific Manuscript database

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...

Mechanisms of Glucagon Degradation at Alkaline pH

PubMed Central

Caputo, Nicholas; Castle, Jessica R.; Bergstrom, Colin P.; Carroll, Julie M.; Bakhtiani, Parkash A.; Jackson, Melanie A.; Roberts, Charles T.; David, Larry L.; Ward, W. Kenneth

2014-01-01

Glucagon is unstable and undergoes degradation and aggregation in aqueous solution. For this reason, its use in portable pumps for closed loop management of diabetes is limited to very short periods. In this study, we sought to identify the degradation mechanisms and the bioactivity of specific degradation products. We studied degradation in the alkaline range, a range at which aggregation is minimized. Native glucagon and analogs identical to glucagon degradation products were synthesized. To quantify biological activity in glucagon and in the degradation peptides, a protein kinase A-based bioassay was used. Aged, fresh, and modified peptides were analyzed by liquid chromatography with mass spectrometry (LCMS). Oxidation of glucagon at the Met residue was common but did not reduce bioactivity. Deamidation and isomerization were also common and were more prevalent at pH 10 than 9. The biological effects of deamidation and isomerization were unpredictable; deamidation at some sites did not reduce bioactivity. Deamidation of Gln 3, isomerization of Asp 9, and deamidation with isomerization at Asn 28 all caused marked potency loss. Studies with molecular-weight-cutoff membranes and LCMS revealed much greater fibrillation at pH 9 than 10. Further work is necessary to determine formulations of glucagon that minimize degradation and fibrillation. PMID:23651991

The concept of double inlet-double outlet right ventricle: a distinct congenital heart disease.

PubMed

Spadotto, Veronica; Frescura, Carla; Ho, Siew Yen; Thiene, Gaetano

The aim of this study was to estimate the incidence and to analyze the anatomy of double inlet-double outlet right ventricle complex and its associated cardiac anomalies in our autopsy series. Among the 1640 hearts with congenital heart disease of our Anatomical Collection, we reviewed the specimens with double inlet-double outlet right ventricle, according to the sequential-segmental analysis, identifying associated cardiac anomalies and examining lung histology to assess the presence of pulmonary vascular disease. We identified 14 hearts with double inlet-double outlet right ventricle (0.85%). Right atrial isomerism was observed in 10 hearts, situs solitus in 3 and left atrial isomerism in one. Regarding the mode of atrioventricular connection, all hearts but one had a common atrioventricular valve. Systemic or pulmonary venous abnormalities were noted in all patients with atrial isomerism. In nine patients a valvular or subvalvular pulmonary stenosis was present. Among the functionally "univentricular hearts", double inlet- double outlet right ventricle represents a peculiar entity, mostly in association with right atrial isomerism. Multiple cardiac anomalies are associated and may complicate surgical repair. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Geometrical isomerization of carotenoids mediated by cation radical/dication formation

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

Gao, G.; Wei, C.C.; Jeevarajan, A.S.

1996-03-28

Electrochemical oxidation of all-trans-canthaxanthin and {beta}-carotene in dichloromethane leads to significant trans-to-cis isomerization, with cis isomers accounting for about 40% of the products formed. The electrochemically generated isomers were separated by reverse-phase high-performance liquid chromatography and identified as 9-cis, 13-cis, 15-cis, and 9,13-di-cis isomers of the carotenoids by {sup 1}H-NMR spectroscopy and optical spectroscopy (Q ratio). The results of simultaneous bulk electrolysis and optical absorption spectroscopy indicate the following isomerization mechanism: the all-trans cation radicals and/or dications formed by electrochemical oxidation of all-trans-carotenoids can easily undergo geometrical isomerization to form cis cation radicals and/or dications. The latter are converted bymore » the comproportionation equilibrium to cation radicals which are then transformed to neutral cis-carotenoids by exchanging one electron with neutral carotenoids. AM1 molecular orbital calculations, which show that the energy barriers of configurational transformation from trans to cis are much lower in the cation radical and dication species than in the neutral molecule, strongly support the first step of this mechanism. 36 refs., 5 figs., 2 tabs.« less

Structure of the cyclic peptide [W8S]contryphan Vn: effect of the tryptophan/serine substitution on trans-cis proline isomerization.

PubMed

Nepravishta, Ridvan; Mandaliti, Walter; Melino, Sonia; Eliseo, Tommaso; Paci, Maurizio

2014-12-01

The structural characterization of [W8S]contryphan Vn, an analogue of Contryphan Vn with tryptophan 8 substituted with a serine residue (W8S), was performed by NMR spectroscopy, molecular dynamics simulations and fluorescence spectroscopy. Contryphan Vn, a bioactive cyclic peptide from the venom of the cone snail Conus ventricosus, contains an S-S bridge between two cysteines and a D-tryptophan. Like other Contryphans, [W8S]contryphan Vn has proline 7 isomerized trans, while the proline 4 has nearly equivalent populations of cis and trans configurations. The thermodynamic and kinetic parameters of the trans-cis isomerization of proline 4 were measured. The isomers of [W8S]contryphan Vn with proline 4 in cis and trans show structural differences. The absence of the salt bridge between the same Asp2 and Lys6, present in Contryphan Vn, may be attributed to the lack of the hydrophobic side chain of Trp8 where it likely protects the electrostatic interactions. These results may contribute to identifying, in these cyclic peptides, the structural determinants of the mechanism of proline trans-cis isomerization, this being also an important step in protein folding.

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.

a Study of the Role of Large-Amplitude Motions in Unimolecular Energy Transfer Using Molecular Beam Optothermal Spectroscopy.

NASA Astrophysics Data System (ADS)

Miller, Carl Cameron

1995-01-01

The role of molecular structure in energy transfer reactions in the ground and excited electronic states was explored using optothermal spectroscopy. In the ground state, the relationship between intramolecular van der Waals interactions and vibrational mode coupling was explored in a homologous series of disubstituted ethanes, including Gg^' -2-fluoroethanol, g-1,2-difluoroethane, g-1-chloro-2-fluoroethane, t-1-chloro-2-fluoroethane, and 1,1,2-trifluoroethane. This series of substituted ethanes varies in degree of van der Waals interactions that hinder internal rotation about the C-C bond. High resolution infrared molecular beam spectroscopy was used to determine the extent of vibrational mode coupling. Perturbations in the rotational structure of these molecules provided a measure of vibrational mode coupling. We have observed that the degree of intramolecular interaction, which is dependent on the van der Waals separation of the substituents and the shape of the potential well, correlates with the extent of vibrational mode coupling. The extent of vibrational mode coupling in this series of molecules did not correlate with the density of states available for coupling. Therefore, density of states alone is insufficient to explain the observed trend. In the excited electronic state, optothermal detection has been used to observe non-radiative relaxation channels in aniline, p-bromoaniline and trans-stilbene. p-Bromoaniline has no detectable fluorescence due to a heavy atom effect which increases the rate of intersystem crossing to the triplet state. An optothermal spectrum of p-bromoaniline was observed with the origin at 32625 cm^ {-1}. For trans-stilbene the differences between the laser excitation spectrum and the optothermal spectrum of the S_1 state clearly show the onset of isomerization at ~1250 cm^{-1} above the origin. Absolute quantum yields of fluorescence, Frank-Condon factors, non -radiative rates, and radiative rates have been obtained for a series of vibronic transitions. For low energy vibrational states there is good agreement between the current study and previous work. For vibrational energies above the barrier of isomerization predicted quantum yields do not agree with our experimental results.

Dinuclear (d(3)-d(3)) Diolate Complexes of Molybdenum and Tungsten. 2.(1) Derivatives of 2,2'-Methylenebis(6-tert-butyl-4-methylphenoxide). Direct Observation of the Conversion of Bridged to Chelate Isomers (M = Mo) and Reversible Carbon-Hydrogen Bond Oxidative Addition (M = W).

PubMed

Chisholm, Malcolm H.; Huang, Jui-Hsien; Huffman, John C.; Parkin, Ivan P.

1997-04-09

Hydrocarbon solutions of Mo(2)(NMe(2))(6) and 2,2'-methylenebis(6-tert-butyl-4-methylphenol) (>/=2 equiv), HO&ndblwave;CH(2)&ndblwave;OH, yield Mo(2)(NMe(2))(2)(O&ndblwave;CH(2)&ndblwave;O)(2), I, which exists in bridged Ib and chelated Ic isomers. These are formed under kinetic control, and recrystallization allows the separation of Ib (orange cubes) from Ic (yellow cubes) both of which have been crystallographically characterized. In each there is an ethane-like O(2)NMo&tbd1;MoO(2)N core with Mo-Mo = 2.2 Å (average). In Ib the two O&ndblwave;CH(2)&ndblwave;O ligands span the Mo&tbd1;Mo bond yielding a molecule of C(2) symmetry. In Ic the molecule has near-C(2) symmetry in the solid state, but in solution there is either rapid rotation about the M&tbd1;M bond or the anti-rotamer is preferred. In benzene-d(6), Ib and Ic do not interconvert at 110 degrees C over a period of days. However, the addition of pyridine or acetonitrile causes the isomerization of Ib to Ic, thereby establishing that Ic is the thermodynamic isomer. The rate of conversion of Ib to Ic has been shown to be dependent on the square of the concentration of added pyridine: k(obs) = k[py](2). From the temperature dependence of k(obs), we determine DeltaH() = 19 (+/-1) kcal/mol and DeltaS() = -25 (+/-3) eu for the pyridine-promoted isomerization of Ib to Ic. The related reaction involving W(2)(NMe(2))(6) and HO&ndblwave;CH(2)&ndblwave;OH (>/=2 equiv) in hydrocarbon solvents at room temperature and below yields a dark brown crystalline compound, wherein C-H activation has occurred at one of the O&ndblwave;CH(2)&ndblwave;O diolate ligands, W(2)(&mgr;-H)(&mgr;-NMe(2))(NMe(2))(eta(2)-O&ndblwave;CH(2)&ndblwave;O)(eta(3)-O&ndblwave;CH&ndblwave;O)(HNMe(2)), 2. The W-W distance in 2 is 2.495(1) Å, consistent with a (W=W)(8+) core. Heating 2 in the solid-state under a dynamic vacuum leads to the elimination of HNMe(2) and the formation of 3, W(2)(NMe(2))(2)(eta(2)-O&ndblwave;CH(2)&ndblwave;O)(2), an analog of Ic. In benzene-d(6) the equilibrium involving 2 and 3 + HNMe(2) has been observed by (1)H NMR spectroscopy. The addition of pyridine to hydrocarbon solutions of 3 yields W(2)(&mgr;-H)(&mgr;-NMe(2))(eta(2)-O&ndblwave;CH(2)&ndblwave;O)(&mgr;(3)-O&ndblwave;CH&ndblwave;O)(NMe(2))(py), 4, which has been shown by single-crystal X-ray crystallography to be an analogue of 2. Studies of the addition of PMe(3) to toluene-d(8) solutions of 3 at low temperatures reveal that adduct formation occurs prior to C-H oxidative addition. For the equilibrium involving 4 and 3 + py in benzene-d(6), DeltaH degrees = 14 (+/-1) kcal/mol and DeltaS degrees = 22 (+/-3) eu.

Triplet and ground state potential energy surfaces of 1,4-diphenyl-1,3-butadiene: theory and experiment.

PubMed

Saltiel, J; Dmitrenko, O; Pillai, Z S; Klima, R; Wang, S; Wharton, T; Huang, Z-N; van de Burgt, L J; Arranz, J

2008-05-01

Relative energies of the ground state isomers of 1,4-diphenyl-1,3-butadiene (DPB) are determined from the temperature dependence of equilibrium isomer compositions obtained with the use of diphenyl diselenide as catalyst. Temperature and concentration effects on photostationary states and isomerization quantum yields with biacetyl or fluorenone as triplet sensitizers with or without the presence of O(2), lead to significant modification of the proposed DPB triplet potential energy surface. Quantum yields for ct-DPB formation from tt-DPB increase with [tt-DPB] revealing a quantum chain process in the tt --> ct direction, as had been observed for the ct --> tt direction, and suggesting an energy minimum at the (3)ct* geometry. They confirm the presence of planar and twisted isomeric triplets in equilibrium (K), with energy transfer from planar or quasi-planar geometries (quantum chain events from tt and ct triplets) and unimolecular decay (k(d)) from twisted geometries. Starting from cc-DPB, varphi(cc-->tt) increases with increasing [cc-DPB] whereas varphi(cc-->ct) is relatively insensitive to concentration changes. The concentration and temperature dependencies of the decay rate constants of DPB triplets in cyclohexane are consistent with the mechanism deduced from the photoisomerization quantum yields. The experimental DeltaH between (3)tt-DPB* and (3)tp-DPB*, 2.7 kcal mol(-1), is compared with the calculated energy difference [DFT with B3LYP/6-31+G(d,p) basis set]. Use of the calculated DeltaS = 4.04 eu between the two triplets gives k(d) = (2.4-6.4) x 10(7) s(-1), close to 1.70 x 10(7) s(-1), the value for twisted stilbene triplet decay. Experimental and calculated relative energies of DPB isomers on the ground and triplet state surfaces agree and theory is relied upon to deduce structural characteristics of the equilibrated conformers in the DPB triplet state.

The role of tachysterol in vitamin D photosynthesis - a non-adiabatic molecular dynamics study

NASA Astrophysics Data System (ADS)

Cisneros, Cecilia; Thompson, Travis; Baluyot, Noel; Smith, Adam C.; Tapavicza, Enrico

To investigate the role of tachysterol in the photophysical/chemical regulation of vitamin D photosynthesis, we studied its electronic absorption properties and excited state dynamics using time-dependent density functional theory (TDDFT), coupled cluster theory (CC2), and non-adiabatic molecular dynamics. In excellent agreement with experiments, the simulated electronic spectrum shows a broad absorption band covering the spectra of the other vitamin D photoisomers. The broad band stems from the spectral overlap of four different ground state rotamers. After photoexcitation, the first excited singlet state (S1) decays within 882 fs. The S1 dynamics is characterized by a strong twisting of the central double bond. 96% of all trajectories relax without chemical transformation to the ground state. In 2.3 % of the trajectories we observed [1,5]-sigmatropic hydrogen shift forming the partly deconjugated toxisterol D1. 1.4 % previtamin D formation is observed via hula-twist double bond isomerization. We find a strong dependence between photoreactivity and dihedral angle conformation: hydrogen shift only occurs in cEc and cEt rotamers and double bond isomerization occurs mainly in cEc rotamers. Our study confirms the hypothesis that cEc rotamers are more prone to previtamin D formation than other isomers. We also observe the formation of a cyclobutene-toxisterol in the hot ground state (0.7 %). Due to its strong absorption and unreactive behavior, tachysterol acts mainly as a sun shield suppressing previtamin D formation. Tachysterol shows stronger toxisterol formation than previtamin D. Absorption of low energy UV light by the cEc rotamer can lead to previtamin D formation. Our study reinforces a recent hypothesis that tachysterol can act as a previtamin D source when only low energy ultraviolet light is available, as it is the case in winter or in the morning and evening hours of the day.

Emerging applications of spark plasma sintering in all solid-state lithium-ion batteries and beyond

NASA Astrophysics Data System (ADS)

Zhu, Hongzheng; Liu, Jian

2018-07-01

Solid-state batteries have received increasing attention due to their high safety aspect and high energy and power densities. However, the development of solid-state batteries is hindered by inferior solid-solid interfaces between the solid-state electrolyte and electrode, which cause high interfacial resistance, reduced Li-ion and electron transfer rate, and limited battery performance. Recently, spark plasma sintering (SPS) is emerging as a promising technique for fabricating solid-state electrolyte and electrode pellets with clean and intimate solid-solid interfaces. During the SPS process, the unique reaction mechanism through the combination of current, pressure and high heating rate allow the formation of desirable solid-solid interfaces between active material particles. Herein, this work focuses on the overview of the application of SPS for fabricating solid-state electrolyte and electrode in all solid-state Li-ion batteries, and beyond, such as solid-state Li-S and Na-ion batteries. The correlations among SPS parameters, interfacial resistance, and electrochemical properties of solid-state electrolytes and electrodes are discussed for different material systems. In the end, we point out future opportunities and challenges associated with SPS application in the hot area of solid-state batteries. It is expected that this timely review will stimulate more fundamental and applied research in the development of solid-state batteries by SPS.

Isomeric ratio measurements for the radiative neutron capture 176Lu(n ,γ ) at the LANL DANCE facility

NASA Astrophysics Data System (ADS)

Denis-Petit, D.; Roig, O.; Méot, V.; Morillon, B.; Romain, P.; Jandel, M.; Kawano, T.; Vieira, D. J.; Bond, E. M.; Bredeweg, T. A.; Couture, A. J.; Haight, R. C.; Keksis, A. L.; Rundberg, R. S.; Ullmann, J. L.

2016-11-01

The isomeric ratios for the neutron capture reaction 176Lu(n ,γ ) to the Jπ=5 /2- , 761.7 keV, T1 /2=32.8 ns and the Jπ=15 /2+ , 1356.9 keV, T1 /2=11.1 ns levels of 177Lu have been measured for the first time. The experiment was carried out with the Detector for Advanced Neutron Capture Experiments (DANCE) at the Los Alamos National Laboratory. Measured isomeric ratios are compared with talys calculations using different models for photon strength functions, level densities, and optical potentials. In order to reproduce the experimental γ -ray spectra, a low-energy resonance must be added in the photon strength function used in our Hauser-Feshbach calculations.

Photoisomerization of Trans Ortho-, Meta-, Para-Nitro Diarylbutadienes: A Case of Regioselectivity.

PubMed

Agnihotri, Harsha; Paramasivam, Mahalingavelar; Palakollu, Veerabhadraiah; Kanvah, Sriram

2015-11-01

A series of ortho-, meta- and para-substituted trans-nitro aryl (phenyl and pyridyl) butadienes have been synthesized and characterized. The effect of substitution and positional selectivity on their fluorescence and photoisomerization were systematically investigated. Among all dienes, meta- and para-nitro phenyl-substituted derivatives exhibit remarkable solvatochromic emission shifts due to intramolecular charge transfer. On the other hand, ortho derivatives undergo regioselective isomerization upon photoexcitation in contrast to inefficient isomerization of para and meta nitro-substituted dienes. Single crystal X-ray analysis revealed existence of intramolecular hydrogen bonding between the nitro group and the hydrogen of the proximal double bond. This restricts the rotation of the proximal double bond thereby allowing regioselective isomerization. The observations were also supported by NMR spectroscopic studies. © 2015 The American Society of Photobiology.

E/Z Isomers and Isomerization

NASA Astrophysics Data System (ADS)

Liaaen-Jensen, Synnøve; Lutnœes, Bjart Frode

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

Progress and prospect on failure mechanisms of solid-state lithium batteries

NASA Astrophysics Data System (ADS)

Ma, Jun; Chen, Bingbing; Wang, Longlong; Cui, Guanglei

2018-07-01

By replacing traditional liquid organic electrolyte with solid-state electrolyte, the solid-state lithium batteries powerfully come back to the energy storage field due to their eminent safety and energy density. In recent years, a variety of solid-state lithium batteries based on excellent solid-state electrolytes are developed. However, the performance degradation of solid-state lithium batteries during cycling and storing is still a serious challenge for practical application. Therefore, this review summarizes the research progress of solid-state lithium batteries from the perspectives of failure phenomena and failure mechanisms. Additionally, the development of methodologies on studying the failure mechanisms of solid-state lithium batteries is also reviewed. Moreover, some perspectives on the remaining questions for understanding the failure behaviors and achieving long cycle life, high safety and high energy density solid-state lithium batteries are presented. This review will help researchers to recognize the status of solid-state lithium batteries objectively and attract much more research interest in conquering the failure issues of solid-state lithium batteries.

Solid oxide fuel cells fueled with reducible oxides

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

Chuang, Steven S.; Fan, Liang Shih

A direct-electrochemical-oxidation fuel cell for generating electrical energy includes a cathode provided with an electrochemical-reduction catalyst that promotes formation of oxygen ions from an oxygen-containing source at the cathode, a solid-state reduced metal, a solid-state anode provided with an electrochemical-oxidation catalyst that promotes direct electrochemical oxidation of the solid-state reduced metal in the presence of the oxygen ions to produce electrical energy, and an electrolyte disposed to transmit the oxygen ions from the cathode to the solid-state anode. A method of operating a solid oxide fuel cell includes providing a direct-electrochemical-oxidation fuel cell comprising a solid-state reduced metal, oxidizing themore » solid-state reduced metal in the presence of oxygen ions through direct-electrochemical-oxidation to obtain a solid-state reducible metal oxide, and reducing the solid-state reducible metal oxide to obtain the solid-state reduced metal.« less

Niemann-Pick type C disease: a QM/MM study of conformational changes in cholesterol in the NPC1(NTD) and NPC2 binding pockets.

PubMed

Elghobashi-Meinhardt, Nadia

2014-10-21

Niemann-Pick Type C disease is characterized by disrupted lipid trafficking within the late endosomal (LE)/lysosomal (Lys) cellular compartments. Cholesterol transport within the LE/Lys is believed to take place via a concerted hand-off mechanism in which a small (131aa) soluble cholesterol binding protein, NPC2, transfers cholesterol to the N-terminal domain (NTD) of a larger (1278aa) membrane-bound protein, NPC1(NTD). The transfer is thought to occur through the formation of a stable intermediate complex NPC1(NTD)-NPC2, in which the sterol apertures of the two proteins align to allow passage of the cholesterol molecule. In the working model of the NPC1(NTD)-NPC2 complex, the sterol apertures are aligned, but the binding pockets are bent with respect to one another. In order for cholesterol to slide from one binding pocket to the other, a conformational change must occur in the proteins, in the ligand, or in both. Here, we investigate the possibility that the ligand undergoes a conformational change, or isomerization, to accommodate the bent transfer pathway. To understand what structural factors influence the isomerization rate, we calculate the energy barrier to cholesterol isomerization in both the NPC1(NTD) and NPC2 binding pockets. Here, we use a combined quantum mechanical/molecular mechanical (QM/MM) energy function to calculate the isomerization barrier within the native NPC1(NTD) and NPC2 binding pockets before protein-protein docking as well as in the binding pockets of the NPC1(NTD)-NPC2 complex after docking has occurred. The results indicate that cholesterol isomerization in the NPC2 binding pocket is energetically favorable, both before and after formation of the NPC1(NTD)-NPC2 complex. The NPC1(NTD) binding pocket is energetically unfavorable to conformational rearrangement of the hydrophobic ligand because it contains more water molecules near the ligand tail and amino acids with polar side chains. For three NPC1(NTD) mutants investigated, L175Q/L176Q, L175A/L176A, and E191A/Y192A, the isomerization barriers were all found to be higher than the barrier calculated in the NPC2 binding pocket. Our results indicate that cholesterol isomerization in the NPC2 binding pocket, either before or after docking, may ensure an efficient transfer of cholesterol to NPC1(NTD).

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Song, Jiangning; Burrage, Kevin; Yuan, Zheng; Huber, Thomas

2006-03-09

The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Special feature of kinetics of ZcE isomerization of β-N-methylaminovinyl trifluoromethyl ketone in Ar matrix exposed to UV radiation and spontaneous E ⇌ Z isomerization of α-methyl-β-N-methylaminovinyl trifluoromethyl ketone

NASA Astrophysics Data System (ADS)

Vdovenko, Sergey I.; Gerus, Igor I.; Pagacz-Kostrzewa, Magdalena; Wierzejewska, Maria; Zhuk, Yuri I.; Kukhar, Valery P.

2018-06-01

Although it is well known that reactivity of α,β-unsaturated enaminoketones is closely associated with spatial and electronic structure but until now little attention was devoted to quantitative investigation of interconversion of different stereoisomeric forms of enaminoketones. In present work we studied peculiarities of kinetics of Z ⇌ E isomerization of enaminoketone 4-(N-methylamino)-1,1,1-trifluorobut-3-en-2-one F3C-COsbnd CHdbnd CHsbnd NH(CH3) (1) in Ar-matrix exposed to UV-radiation (λ = 340 nm) with IR Fourier and 2D correlation spectroscopy and we found that Z-s-Z-s-trans isomer transforms primarily into two E-isomers, E-s-E-s-trans and E-s-Z-s-trans which further turn into the E-s-E-s-cis and E-s-Z-s-cis conformers all interconversion rate constants being comparable in magnitude. Along with this process long-term exposure to the UV-radiation results in proton transfer from nitrogen of methylamino group to carbonyl oxygen with simultaneous isomerization of 'cyclic' iminoenol form into 'linear'one. In solution of enaminoketone 4-(N-methylamino)-1,1,1-trifluoro-3-methylbut-3-en-2-one F3C-CO-C(CH3)dbnd CH-NH(CH3) (2) we observed reversed process, namely, spontaneous interconversion of the E-s-E-s-trans and E-s-Z-s-trans conformers into the Z-s-Z-trans isomer. It was found that rate constants of the dimeric forms of the E-s-E-s-trans and E-s-Z-s-trans conformers are higher than those of the monomers and are independent on total enaminoketone concentration. Addition of highly polar HMPA promotes proton transfer from nitrogen to oxygen in the Z-s-Z-s-trans isomer of 2 with subsequent isomerization into the linear imino-enol product but the rate constant of this transformation is ten-fold smaller than that for 1 in the Ar matrix exposed to UV radiation. Special feature of kinetics of Z ⇌ E isomerization of β-N-methylaminovinyl trifluoromethyl ketone in Ar matrix exposed to UV radiation and spontaneous E ⇌ Z isomerization of α-Methyl-, β-N-methylaminovinyl trifluoromethyl ketone. Sergey I. Vdovenko, Igor I. Gerus, Magdalena Pagacz-Kostrzewa, Maria Wierzejewska, Yuri I. Zhuk and Valery P. Kukhar.

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.

Monoquaternary neuromuscular blocking agents based on 1-tetralone and 1-indanone.

PubMed

Biggs, D F; Casy, A F; Chu, I; Coutts, R T

1976-04-01

The preparation of three isomeric 1-tetralone hydrozones 4 and three isomeric 1-indanone hydrozones 5 possessing a single quaternary ammonium center is described. Several of the compounds possessed significant neuromuscular blocking activity, and two approached suxamethonium in potency. 1H NMR evidence obtained from a study of the N,N-dimethylhydrozones indicated that the hydrazones adopted an E configuration in solution.

Fontan completion in patients with atrial isomerism and separate hepatic venous drainage.

PubMed

Nakata, Tomohiro; Fujimoto, Yoshifumi; Hirose, Keiichi; Osaki, Masaki; Tosaka, Yuko; Ide, Yujiro; Tachi, Maiko; Sakamoto, Kisaburo

2010-06-01

Fontan completion in patients with atrial isomerism, in which the inferior vena cava (IVC) and the hepatic vein (HV) drain separately, is technically challenging. Herein, we review our surgical approach to these patients. The medical records of 50 consecutive patients with atrial isomerism who underwent Fontan completion between 1998 and 2008 were reviewed retrospectively. Separate HV drainage was present in 17 patients. Patients with interrupted IVC were excluded. Patient characteristics were as follows: median age, 26 months (range 15-149); median weight, 9.6 kg (range 8.1-47.2); right atrial isomerism, 16 patients; and left atrial isomerism, one. The IVC and the separate HV at the level of diaphragm were contralateral in 16 patients, and ipsilateral in one. The surgical procedures for directing blood flow from the IVC and the separate HV to the pulmonary arteries were as follows: en bloc resection of the IVC and the HV and anastomosing these veins to an extracardiac conduit in 10 patients; connecting the IVC to the HV in a side-to-side fashion before anastomosing them to an extracardiac conduit in one; and lateral tunnel in another. When the IVC and the HV were widely separated by the vertebrae, we chose an intra-extracardiac conduit (intra-atrial septation) in four patients and an extracardiac conduit for the IVC and the right HV and lateral tunnel for the separate left HV in one. There was no mortality. Five re-operations were performed (pacemaker in two patients; one each of fenestration, release of outflow obstruction and ligation of collateral arteries). Sixteen patients underwent follow-up catheterisation, which revealed central venous pressure of 12.0 + or - 2.0 mmHg and arterial oxygen saturation of 92% + or - 6%. The mid-term results of the Fontan completion in patients with atrial isomerism and separate HV drainage were excellent. The distance between the IVC and the separate HV and the position of the vertebrae should be considered when choosing a surgical technique. Copyright 2010. Published by Elsevier B.V.

Patterns of Broken Patterns

NASA Astrophysics Data System (ADS)

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

2013-06-01

Spectroscopy - it is all about patterns. Some patterns look so indescribably complicated that, unlike pornography, you do not know one when you see one. It is tempting to say that, at high vibrational excitation, interactions among normal mode basis states are so strong and widespread that all patterns are obliterated. But this is not true. When normal mode frequencies are in near integer multiple ratios, polyads emerge. A polyad is a robust pattern often comprising many vibrational eigenstates. Each such pattern might span many hundreds of cm^{-1}, and it is inevitable that several unrelated polyad patterns overlap. When polyads overlap, it might seem impossible to disentangle them. However, the key to disentanglement is that polyads come in families in which successive generations are related by harmonic oscillator matrix element selection and scaling rules. Families of polyads are described by families of scaling-based effective Hamiltonian matrices, {H}^{{eff}}. No matter how complex and overlapped, the polyad {H}^{{eff}} serves as a magic decoder for picking out the polyad pattern. Sometimes the polyad patterns are systematically broken (a meta-pattern), owing to proximity to an isomerization barrier, as occurs in highly excited bending levels of the S_{1} state of HCCH, which encode the trans-cis minimum energy isomerization path. Quantum Chemists often dismiss {H}^{{eff}} models, precisely because they are models that do not express the full dimensionality of the complete Hamiltonian. But an {H}^{{eff}} explains rather than describes. Shunning {H}^{{eff}}s is like throwing out the baby with the bath water. Don't do it!

Photo-triggered destabilization of nanoscopic vehicles by dihydroindolizine for enhanced anticancer drug delivery in cervical carcinoma.

PubMed

Singh, Priya; Choudhury, Susobhan; Kulanthaivel, Senthilguru; Bagchi, Damayanti; Banerjee, Indranil; Ahmed, Saleh A; Pal, Samir Kumar

2018-02-01

The efficacy and toxicity of drugs depend not only on their potency but also on their ability to reach the target sites in preference to non-target sites. In this regards destabilization of delivery vehicles induced by light can be an effective strategy for enhancing drug delivery with spatial and temporal control. Herein we demonstrate that the photoinduced isomerization from closed (hydrophobic) to open isomeric form (hydrophilic) of a novel DHI encapsulated in liposome leads to potential light-controlled drug delivery vehicles. We have used steady state and picosecond resolved dynamics of a drug 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) incorporated in liposome to monitor the efficacy of destabilization of liposome in absence and presence UVA irradiation. Steady state and picosecond resolved polarization gated spectroscopy including the well-known strategy of solvation dynamics and Förster resonance energy transfer; reveal the possible mechanism out of various phenomena involved in destabilization of liposome. We have also investigated the therapeutic efficacy of doxorubicin (DOX) delivery from liposome to cervical cancer cell line HeLa. The FACS, confocal fluorescence microscopic and MTT assay studies reveal an enhanced cellular uptake of DOX leading to significant reduction in cell viability (∼40%) of HeLa followed by photoresponsive destabilization of liposome. Our studies successfully demonstrate that these DHI encapsulated liposomes have potential application as a smart photosensitive drug delivery system. Copyright © 2017 Elsevier B.V. All rights reserved.

Effects of proline cis-trans isomerization on TB domain secondary structure.

PubMed Central

Yuan, X.; Werner, J. M.; Knott, V.; Handford, P. A.; Campbell, I. D.; Downing, K.

1998-01-01

The transforming growth factor beta (TGF-beta) binding protein-like (TB) domain is found principally in proteins localized to extracellular matrix fibrils, including human fibrillin-1, the defective protein in the Marfan syndrome. Analysis of the nuclear magnetic resonance (NMR) data for the sixth TB module from human fibrillin-1 has revealed the existence of two stable conformers that differ in the isomerization states of two proline residues. Unusually, the two isoforms do not readily interconvert and are stable on the time scale of milliseconds. We have computed independent structures of the major and minor conformers of TB6 to assess how the domain fold adjusts to incorporate alternatively cis- or trans-prolines. Based on previous observations, it has been suggested that multiple conformers can only be accommodated in flexible regions of protein structure. In contrast, P22, which exists in trans in the major form and cis in the minor form of TB6, is in a rigid region of the domain, which is confirmed by backbone dynamics measurements. Overall, the structures of the major and minor conformers are similar. However, the secondary structure topologies of the two forms differ as a direct consequence of the changes in proline conformation. PMID:9792099

Optical Input/Electrical Output Memory Elements based on a Liquid Crystalline Azobenzene Polymer.

PubMed

Mosciatti, Thomas; Bonacchi, Sara; Gobbi, Marco; Ferlauto, Laura; Liscio, Fabiola; Giorgini, Loris; Orgiu, Emanuele; Samorì, Paolo

2016-03-01

Responsive polymer materials can change their properties when subjected to external stimuli. In this work, thin films of thermotropic poly(metha)acrylate/azobenzene polymers are explored as active layer in light-programmable, electrically readable memories. The memory effect is based on the reversible modifications of the film morphology induced by the photoisomerization of azobenzene mesogenic groups. When the film is in the liquid crystalline phase, the trans → cis isomerization induces a major surface reorganization on the mesoscopic scale that is characterized by a reduction in the effective thickness of the film. The film conductivity is measured in vertical two-terminal devices in which the polymer is sandwiched between a Au contact and a liquid compliant E-GaIn drop. We demonstrate that the trans → cis isomerization is accompanied by a reversible 100-fold change in the film conductance. In this way, the device can be set in a high- or low-resistance state by light irradiation at different wavelengths. This result paves the way toward the potential use of poly(metha)acrylate/azobenzene polymer films as active layer for optical input/electrical output memory elements.

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.

Photo-induced refractive index and topographical surface gratings in functionalized nanocarbon solid film

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

McGee, David J.; Ferrie, John; Plachy, Aljoscha

2015-11-02

We demonstrate that a single-walled carbon nanotube network noncovalently coupled with a pyrene-modified azo-benzene chromophore functions as a host matrix for a broad range of photo-orientation and photomechanical effects. The chromophore could be efficiently reoriented through repeated trans-cis-trans isomerization under linearly polarized 480 nm light, with Δn of 0.012 at 650 nm and fast characteristic rise-times of 0.12 s. Erasable phase diffraction gratings could also be written, with permanent surface relief gratings forming at sufficiently long irradiation times. In addition to demonstrating a mechanism for photo-manipulation of single-walled carbon nanotubes, these results show photo-orientation of chromophores in azo-functionalized single-walled carbon nanotube networks asmore » a path towards the photosensitive tuning of the electrostatic environment of the nanotube.« less

Hydrolysis of tRNA(sup Phe) on Suspensions of Amino Acids

NASA Technical Reports Server (NTRS)

Gao, Kui; Orgel, Leslie E.

2001-01-01

RNA is adsorbed strongly on suspensions of many moderately soluble organic solids. In some cases, the hydrolysis of tRNA(sup Phe) is greatly accelerated by adsorption, and the major sites of hydrolysis are changed from those that are important in homogeneous solution. Here we show that the hydrolysis is greatly accelerated by suspensions of aspartic acid and beta-glutamic acid but not by suspensions of alpha-glutamic acid, asparagine, or glutamine. The non-enzymatic hydrolysis of RNA has been studied extensively, especially because of its relevance to the mechanisms of action of ribozymes and to biotechnology and therapy. Many ribonucleases, ribozymes, and non-biological catalysts function via acid-base catalysis of an intramolecular transesterification mechanism in which the 2'-OH group attacks the adjacent phosphate group. The pentacoordinated phosphorane intermediate may collapse back to starting material, or yield isomerized or cleaved products.

Two novel cocrystals of lamotrigine with isomeric bipyridines and in situ monitoring of the cocrystallization.

PubMed

Du, Shichao; Wang, Yan; Wu, Songgu; Yu, Bo; Shi, Peng; Bian, Lin; Zhang, Dejiang; Hou, Jie; Wang, Jingkang; Gong, Junbo

2017-12-15

Crystal engineering strategy was applied to develop new solid forms of lamotrigine. Two novel cocrystals of lamotrigine forming with 4,4'-bipyridine (2:1) and 2,2'-bipyridine cocrystal (1:1.5) were successfully obtained by neat grinding and liquid assisted grinding. The novel cocrystals were fully characterized and confirmed by X-ray diffraction, thermal and spectroscopic analysis. DXRxi Raman microscope was also used to identify the cocrystals. The factors such as solvent and the structure of coformers which influenced the cocrystal formation were discussed. Furthermore, the novel cocrystals were both obtained by slurry crystallization. Process analytical technologies including focused beam reflectance measurement and attenuated total reflectance Fourier Transform Infrared were applied to investigate the cocrystallization process and the mechanism. HPLC analysis showed that the dissolution rate and the solubility of the two novel cocrystals were both improved. Copyright © 2017 Elsevier B.V. All rights reserved.

Need of a consistent and convenient nucleus identification in ENDF files for the automatic construction of the depletion chains

NASA Astrophysics Data System (ADS)

Mosca, Pietro; Mounier, Claude

2016-03-01

The automatic construction of evolution chains recently implemented in GALILEE system is based on the analysis of several ENDF files : the multigroup production cross sections present in the GENDF files processed by NJOY from the ENDF evaluation, the decay file and the fission product yields (FPY) file. In this context, this paper highlights the importance of the nucleus identification to properly interconnect the data mentioned above. The first part of the paper describes the present status of the nucleus identification among the several ENDF files focusing, in particular, on the use of the excited state number and of the isomeric state number. The second part reviews the problems encountered during the automatic construction of the depletion chains using recent ENDF data. The processing of the JEFF-3.1.1, ENDF/B-VII.0 (decay and FPY) and the JEFF-3.2 (production cross section) points out problems about the compliance or not of the nucleus identifiers with the ENDF-6 format and sometimes the inconsistencies among the various ENDF files. In addition, the analysis of EAF-2003 and EAF-2010 shows some incoherence between the ZA product identifier and the reaction identifier MT for the reactions (n, pα) and (n, 2np). As a main result of this work, our suggestion is to change the ENDF format using systematically the isomeric state number to identify the nuclei. This proposal is already compliant to a huge amount ENDF data that are not in agreement with the present ENDF format. This choice is the most convenient because, ultimately, it allows one to give human readable names to the nuclei of the depletion chains.

Allosteric Fine-Tuning of the Binding Pocket Dynamics in the ITK SH2 Domain by a Distal Molecular Switch: An Atomistic Perspective.

PubMed

Momin, Mohamed; Xin, Yao; Hamelberg, Donald

2017-06-29

Although the regulation of function of proteins by allosteric interactions has been identified in many subcellular processes, molecular switches are also known to induce long-range conformational changes in proteins. A less well understood molecular switch involving cis-trans isomerization of a peptidyl-prolyl bond could induce a conformational change directly to the backbone that is propagated to other parts of the protein. However, these switches are elusive and hard to identify because they are intrinsic to biomolecules that are inherently dynamic. Here, we explore the conformational dynamics and free energy landscape of the SH2 domain of interleukin-2-inducible T-cell or tyrosine kinase (ITK) to fully understand the conformational coupling between the distal cis-trans molecular switch and its binding pocket of the phosphotyrosine motif. We use multiple microsecond-long all-atom molecular dynamics simulations in explicit water for over a total of 60 μs. We show that cis-trans isomerization of the Asn286-Pro287 peptidyl-prolyl bond is directly coupled to the dynamics of the binding pocket of the phosphotyrosine motif, in agreement with previous NMR experiments. Unlike the cis state that is localized and less dynamic in a single free energy basin, the trans state samples two distinct conformations of the binding pocket-one that recognizes the phosphotyrosine motif and the other that is somewhat similar to that of the cis state. The results provide an atomic-level description of a less well understood allosteric regulation by a peptidyl-prolyl cis-trans molecular switch that could aid in the understanding of normal and aberrant subcellular processes and the identification of these elusive molecular switches in other proteins.

Nonradiative Decay Route of Cinnamate Derivatives Studied by Frequency and Time Domain Laser Spectroscopy in the Gas Phase, Matrix Isolation FTIR Spectroscopy and Quantum Chemical Calculations

NASA Astrophysics Data System (ADS)

Ebata, Takayuki

2017-06-01

The nonraddiative dececy route involving trans → cis photo-isomerization from the S_1 (ππ*) state has been investigated for several trans-cinnamate derivatives, which are known as sunscreen reagents. We examined two types of substitution effects. One is structural isomer such as ortho-, meta-, and para-hydroxy-methylcinnmate (o-, m-, p-HMC). The S_1 lifetime of p-HMC is less than 8 ps at zero-point level, and it undergoes rapid S_1 → ^1nπ* → T_1 decay via multiple conical intersections. Finally, the trans → cis isomerization proceeds in the T_1 state. On the other hand, both o- and m-HMC show very slow decay. Their S_1 lifetimes are in the order of 100 ps even at the excess energy of 2000-3000 \\wn. The other is the effect of the complexity of ester group in para-subsitituted species, such as para-methoxy-methyl, -ethyl and -2ethylhexyl cinnamate (p-MMC, p-MEC, p-M2EHC). p-MMC and p-MEC show sharp S_0 → S_1 (ππ*) vibronic bands, while p-M2EHC shows only broad structureless feature even under the jet-cooled condition. In addition, we found that the S_0 → ^1nπ* absorption appears at 1000 \\wn below the S_0 → S_1 (ππ*) transition in p-MEC and p-M2EHC, but not in p-MMC. Thus, the complexity of the ester group is very important for the appearance of the ^1nπ* state.

Isomeric yield ratios of 87m,gY from different nuclear reactions

NASA Astrophysics Data System (ADS)

Naik, H.; Kim, G. N.; Kim, K.; Zaman, M.; Sahid, M.; Yang, S.-C.; Lee, M. W.; Kang, Y. R.; Shin, S. G.; Cho, M.-H.; Goswami, A.; Song, T. Y.

2014-07-01

The independent isomeric yield ratios of 87m,gY produced from the 93Nb( γ, α2n) and natZr( γ, p xn) reactions with the end-point bremsstrahlung energy of 45-70 MeV have been determined by an off-line γ-ray spectrometric technique using 100 MeV electron linac at the Pohang accelerator laboratory, Korea. The isomeric yield ratios of 87m,gY were also determined from the natZr(p, αxn) and the 89Y(p,p2n) reactions with E P = 15-45 MeV as well as those from the 89Y( α, α2n) reaction with E α = 32-43 MeV using the MC-50 cyclotron at the Korea Institute of Radiological and Medical Science, Korea. The isomeric yield ratios of 87m,gY from the present work in the 93Nb( γ, α2n), natZr( γ, p xn), natZr(p, αxn), 89Y(p,p2n), and 89Y( α, α2n) reactions were compared with those of the literature data in the 85Rb( α, 2n), the 86,87,88Sr(d, xn), 89Y(n,3n), and the 89Y( γ, 2n) reactions to examine the role of target, projectiles, and ejectiles through compound nucleus excitation energy and input angular momentum. The isomeric yield ratios of 87m,gY in the above eleven reactions were also calculated using the computer code TALYS 1.4 and compared with the experimental data. The different behaviors between photon- and neutron-induced reactions and charged-particle-induced reactions are discussed from the viewpoint of compound and non-compound (pre-equilibrium) process.

Glutathione S-transferases act as isomerases in isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed Central

Chen, H; Juchau, M R

1997-01-01

A discovery that rapid enzymic isomerization of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) can be catalysed by purified hepatic glutathione S-transferases (GSTs; EC 2.5.1.18) from rat is now reported. Rates of cis-trans isomerization were determined quantitatively by HPLC. GST-catalysed reactions reached equilibrium rapidly, in marked contrast with uncatalysed or GSH-catalysed isomerizations. The GST-catalysed reaction exhibited substrate saturation kinetics with a Km of approx. 8 microM. The maximal velocity of the reaction and the catalytic efficiency of GSTs were determined. The initial rate of the reaction increased linearly as a function of enzyme concentration. Catalysis by GSTs was independent of the presence of GSH, indicating that GSTs act as GSH-independent isomerases as well as transferases. Incubation with guanidine (7-8 M) or heat-inactivation of GSTs (100 degrees C for 3 min) decreased isomerase activities by approx. 50% and 75% respectively. The same heat treatment did not significantly inhibit isomerization catalysed by GSH and apoferritin, indicating that the observed decrease in isomerase activity by heat inactivation was not primarily due to oxidation of protein thiol groups in the GSTs. The specific activity of GSTs was approx. 23- and 340-fold those of GSH and apoferritin respectively when comparisons were made on the basis of free thiol concentrations, indicating that free thiol in GSTs cannot account for the majority of observed isomerase activities and suggesting that specific conformations of GSTs are important for such activities. Complete inhibition of the reaction by low concentrations of N-ethylmaleimide (10 microM) demonstrated that intact protein thiols are required for the isomerase activities of GSTs. PMID:9581548

Glutathione S-transferases act as isomerases in isomerization of 13-cis-retinoic acid to all-trans-retinoic acid in vitro.

PubMed

Chen, H; Juchau, M R

1997-11-01

A discovery that rapid enzymic isomerization of 13-cis-retinoic acid (13-cRA) to all-trans-retinoic acid (t-RA) can be catalysed by purified hepatic glutathione S-transferases (GSTs; EC 2.5.1.18) from rat is now reported. Rates of cis-trans isomerization were determined quantitatively by HPLC. GST-catalysed reactions reached equilibrium rapidly, in marked contrast with uncatalysed or GSH-catalysed isomerizations. The GST-catalysed reaction exhibited substrate saturation kinetics with a Km of approx. 8 microM. The maximal velocity of the reaction and the catalytic efficiency of GSTs were determined. The initial rate of the reaction increased linearly as a function of enzyme concentration. Catalysis by GSTs was independent of the presence of GSH, indicating that GSTs act as GSH-independent isomerases as well as transferases. Incubation with guanidine (7-8 M) or heat-inactivation of GSTs (100 degrees C for 3 min) decreased isomerase activities by approx. 50% and 75% respectively. The same heat treatment did not significantly inhibit isomerization catalysed by GSH and apoferritin, indicating that the observed decrease in isomerase activity by heat inactivation was not primarily due to oxidation of protein thiol groups in the GSTs. The specific activity of GSTs was approx. 23- and 340-fold those of GSH and apoferritin respectively when comparisons were made on the basis of free thiol concentrations, indicating that free thiol in GSTs cannot account for the majority of observed isomerase activities and suggesting that specific conformations of GSTs are important for such activities. Complete inhibition of the reaction by low concentrations of N-ethylmaleimide (10 microM) demonstrated that intact protein thiols are required for the isomerase activities of GSTs.