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.

An infrared study of the nitro—nitrito linkage isomerization in solid nitro- and nitritopentamminecobalt(III) chloride

NASA Astrophysics Data System (ADS)

Heyns, A. M.; de Waal, D.

1989-01-01

The photochemical isomerization reaction of [Co(NH 3) 5NO 2]Cl 2 to [Co(NH 3) 5ONO]Cl 2 has been studied in the solid state by means of i.r. spectroscopy. The reaction is first order with k = 2.53±0.05 × 10 -4s -1 and is much faster ( t1/2=49min) than the well-known spontaneous nitrito → nitro isomerization ( t1/2 = 6 days). The i.r. bands of both the NH 3 and ONO - -groups in the range 4000-50 cm -1 indicate minor differences between the structures of freshly and photochemically prepared [Co(NH 3) 5ONO]Cl 2. The far i.r. spectra indicate the disorder existing in the intermediate products during the isomerization processes.

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.

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

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.

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

PubMed

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

2009-05-13

We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal-acid mixtures designed to maintain alkane-alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activation barriers increased with increasing DPE, as also shown for alkanol dehydration reactions. These trends are consistent with thermochemical analyses of the transition states involved in isomerization and elimination steps. For all reactions, barriers increased by less than the concomitant increase in DPE upon changes in composition, because electrostatic stabilization of ion-pairs at the relevant transition states becomes more effective for weaker acids, as a result of their higher charge density at the anionic conjugate base. Alkoxide isomerization barriers were more sensitive to DPE than for elimination from H-bonded alkanols, the step that limits 2-butanol and 1-butanol dehydration rates; the latter two reactions showed similar DPE sensitivities, despite significant differences in their rates and activation barriers, indicating that slower reactions are not necessarily more sensitive to acid strength, but instead reflect the involvement of more unstable organic cations at their transition states. These compensating effects from electrostatic stabilization depend on how similar the charge density in these organic cations is to that in the proton removed. Cations with more localized charge favor strong electrostatic interactions with anions and form more stable ionic structures than do cations with more diffuse charges. Ion-pairs at elimination transition states contain cations with higher local charge density at the sp(2) carbon than for isomerization transition states; as a result, these ion-pairs recover a larger fraction of the deprotonation energy, and, consequently, their reactions become less sensitive to acid strength. These concepts lead us to conclude that the energetic difficulty of a catalytic reaction, imposed by gas-phase reactant proton affinities in transition state analogues, does not determine its sensitivity to the acid strength of solid catalysts.

Activation and thermodynamic parameter study of the heteronuclear C=O···H-N hydrogen bonding of diphenylurethane isomeric structures by FT-IR spectroscopy using the regularized inversion of an eigenvalue problem.

PubMed

Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

2012-08-02

The doublet of the ν(C=O) carbonyl band in isomeric urethane systems has been extensively discussed in qualitative terms on the basis of FT-IR spectroscopy of the macromolecular structures. Recently, a reaction extent model was proposed as an inverse kinetic problem for the synthesis of diphenylurethane for which hydrogen-bonded and non-hydrogen-bonded C=O functionalities were identified. In this article, the heteronuclear C=O···H-N hydrogen bonding in the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol was investigated via FT-IR spectroscopy, using a methodology of regularization for the inverse reaction extent model through an eigenvalue problem. The kinetic and thermodynamic parameters of this system were derived directly from the spectroscopic data. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied. The study determined the enthalpy (ΔH = 15.25 kJ/mol), entropy (TΔS = 14.61 kJ/mol), and free energy (ΔG = 0.6 kJ/mol) of heteronuclear C=O···H-N hydrogen bonding by FT-IR spectroscopy through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S, and δΔ(‡)G) at equilibrium in the chemical reaction system. The parameters obtained in this study may contribute toward a better understanding of the properties of, and interactions in, supramolecular systems, such as the switching behavior of hydrogen bonding.

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

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

Conformational study of the hydroxyproline-O-glycosidic linkage: sugar-peptide orientation and prolyl amide isomerization in (α/β)-galactosylated 4(R/S)-hydroxyproline.

PubMed

Naziga, Emmanuel B; Schweizer, Frank; Wetmore, Stacey D

2012-01-19

Glycosylation is a frequent post-translational modification of proteins that has been shown to influence protein structure and function. Glycosylation of hydroxyproline occurs widely in plants, but is absent in humans and animals. Previous experimental studies on model amides have indicated that α/β-galactosylation of 4R-hydroxyproline (Hyp) has no measurable effect on prolyl amide isomerization, while a 7% increase in the trans isomer population, as well as a 25-50% increase in the isomerization rate, was observed for the 4S stereoisomer (hyp). In this work, molecular dynamics simulations in explicit water and implicit solvent DFT optimizations are used to examine the structure of the hydroxyproline-O-galactosyl linkage and the effect of glycosylation on the structure and cis/trans isomerization of the peptide backbone. The calculations show two major minima with respect to the glycosidic linkage in all compounds. The C(γ)-exo puckering observed in 4R compounds projects the sugar away from the peptide backbone, while a twisted C(γ)-endo/C(β)-exo pucker in the 4S compounds brings the peptide and sugar rings together and leads to an intramolecular hydrogen-bonding interaction that is sometimes bridged by a water molecule. This hydrogen bond changes the conformation of the peptide backbone, inducing a favorable n → π* interaction between the oxygen lone pair from the prolyl N-terminal amide and the C═O, which explains the observed increase in trans isomer population in α/β-galactosylated 4S-hydroxyproline. Our results provide the first molecular level information about this important glycosidic linkage, as well as provide an explanation for the previously observed increase in trans isomer population in 4S-hyp compounds. Moreover, this study provides evidence that sugar-mediated long-range hydrogen bonding between hydroxyl groups and the carbonyl peptide backbone can modify the properties of N-terminal prolyl cis/trans isomerization in peptides.

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.

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.

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.

Characterization of Isomeric Glycans by Reversed Phase Liquid Chromatography-Electronic Excitation Dissociation Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Tang, Yang; Wei, Juan; Costello, Catherine E.; Lin, Cheng

2018-04-01

The occurrence of numerous structural isomers in glycans from biological sources presents a severe challenge for structural glycomics. The subtle differences among isomeric structures demand analytical methods that can provide structural details while working efficiently with on-line glycan separation methods. Although liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool for mixture analysis, the commonly utilized collision-induced dissociation (CID) method often does not generate a sufficient number of fragments at the MS2 level for comprehensive structural characterization. Here, we studied the electronic excitation dissociation (EED) behaviors of metal-adducted, permethylated glycans, and identified key spectral features that could facilitate both topology and linkage determinations. We developed an EED-based, nanoscale, reversed phase (RP)LC-MS/MS platform, and demonstrated its ability to achieve complete structural elucidation of up to five structural isomers in a single LC-MS/MS analysis. [Figure not available: see fulltext.

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.

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.

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).

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

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.

Survey of conformational isomerism in (E)-2-[(4-bromophenylimino)methyl]-5-(diethylamino)phenol compound from structural and thermochemical points of view.

PubMed

Albayrak, Çiğdem; Kaştaş, Gökhan; Odabaşoğlu, Mustafa; Frank, René

2012-09-01

In this study, (E)-2-[(4-bromophenylimino)methyl]-5-(diethylamino)phenol compound was investigated by mainly focusing on conformational isomerism. For this purpose, molecular structure and spectroscopic properties of the compound were experimentally characterized by X-ray diffraction, FT-IR and UV-Vis spectroscopic techniques, and computationally by DFT method. The X-ray diffraction analysis of the compound shows the formation of two conformers (anti and eclipsed) related to the ethyl groups of the compound. The two conformers are connected to each other by non-covalent C-H⋯Br and C-H⋯π interactions. The combination of these interactions is resulted in fused R(2)(2)(10) and R(2)(4)(20) synthons which are responsible for the tape structure of crystal packing arrangement. The X-ray diffraction and FT-IR analyses also reveal the existence of enol form in the solid state. From thermochemical point of view, the computational investigation of isomerism includes three studies: the calculation of (a) the rate constants for transmission from anti or eclipsed conformations to transition state by using Eyring equation, (b) the activation energy needed for isomerism by using Arrhenius equation, (c) the equilibrium constant from anti conformer to eclipsed conformer by using the equation including the change in Gibbs free energy. The dependence of tautomerism on solvent types was studied on the basis of UV-Vis spectra recorded in different organic solvents. The results showed that the compound exists in enol form in all solvents except ethyl alcohol. Copyright © 2012 Elsevier B.V. All rights reserved.

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.

Identification of Isomeric N-Glycan Structures by Mass Spectrometry with 157 nm Laser-Induced Photofragmentation

PubMed Central

Devakumar, Arugadoss; Mechref, Yehia; Kang, Pilsoo; Novotny, Milos V.; Reilly, James P.

2008-01-01

Characterization of structural isomers has become increasingly important and extremely challenging in glycobiology. This communication demonstrates the capability of ion-trap mass spectrometry in conjunction with 157 nm photofragmentation to identify different structural isomers of permethylated N-glycans derived from ovalbumin without chromatographic separation. The results are compared with CID experiments. Photodissociation generates extensive cross-ring fragment ions as well as diagnostic glycosidic product ions that are not usually observed in CID MS/MS experiments. The detection of these product ions aids in characterizing indigenous glycan isomers. The ion-trap facilitates MSn experiments on the diagnostic glycosidic fragments and cross-ring product ions generated through photofragmentation, thus allowing unambiguous assignment of all of the isomeric structures associated with the model glycoprotein utilized in this study. Photofragmentation is demonstrated to be a powerful technique for the structural characterization of glycans. PMID:18487060

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.

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.

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)

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.

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

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

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.

Application of Δ- and λ-isomerism of octahedral metal complexes for inducing chiral nematic phases.

PubMed

Sato, Hisako; Yamagishi, Akihiko

2009-11-20

The Delta- and Lambda-isomerism of octahedral metal complexes is employed as a source of chirality for inducing chiral nematic phases. By applying a wide range of chiral metal complexes as a dopant, it has been found that tris(beta-diketonato)metal(III) complexes exhibit an extremely high value of helical twisting power. The mechanism of induction of the chiral nematic phase is postulated on the basis of a surface chirality model. The strategy for designing an efficient dopant is described, together with the results using a number of examples of Co(III), Cr(III) and Ru(III) complexes with C(2) symmetry. The development of photo-responsive dopants to achieve the photo-induced structural change of liquid crystal by use of photo-isomerization of chiral metal complexes is also described.

Application of Δ- and Λ-Isomerism of Octahedral Metal Complexes for Inducing Chiral Nematic Phases

PubMed Central

Sato, Hisako; Yamagishi, Akihiko

2009-01-01

The Δ- and Λ-isomerism of octahedral metal complexes is employed as a source of chirality for inducing chiral nematic phases. By applying a wide range of chiral metal complexes as a dopant, it has been found that tris(β-diketonato)metal(III) complexes exhibit an extremely high value of helical twisting power. The mechanism of induction of the chiral nematic phase is postulated on the basis of a surface chirality model. The strategy for designing an efficient dopant is described, together with the results using a number of examples of Co(III), Cr(III) and Ru(III) complexes with C2 symmetry. The development of photo-responsive dopants to achieve the photo-induced structural change of liquid crystal by use of photo-isomerization of chiral metal complexes is also described. PMID:20057959

Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change*s

PubMed Central

Li, Yi-Ching; Chiang, Chia-Wang; Yeh, Hui-Chun; Hsu, Pei-Yung; Whitby, Frank G.; Wang, Lee-Ho; Chan, Nei-Li

2008-01-01

Prostacyclin synthase (PGIS) is a cytochrome P450 (P450) enzyme that catalyzes production of prostacyclin from prostaglandin H2. PGIS is unusual in that it catalyzes an isomerization rather than a monooxygenation, which is typical of P450 enzymes. To understand the structural basis for prostacyclin biosynthesis in greater detail, we have determined the crystal structures of ligand-free, inhibitor (minoxidil)-bound and substrate analog U51605-bound PGIS. These structures demonstrate a stereo-specific substrate binding and suggest features of the enzyme that facilitate isomerization. Unlike most microsomal P450s, where large substrate-induced conformational changes take place at the distal side of the heme, conformational changes in PGIS are observed at the proximal side and in the heme itself. The conserved and extensive heme propionate-protein interactions seen in all other P450s, which are largely absent in the ligand-free PGIS, are recovered upon U51605 binding accompanied by water exclusion from the active site. In contrast, when minoxidil binds, the propionate-protein interactions are not recovered and water molecules are largely retained. These findings suggest that PGIS represents a divergent evolution of the P450 family, in which a heme barrier has evolved to ensure strict binding specificity for prostaglandin H2, leading to a radical-mediated isomerization with high product fidelity. The U51605-bound structure also provides a view of the substrate entrance and product exit channels. PMID:18032380

Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

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

Alsanousi, Nesreen; Sugiki, Toshihiko, E-mail: sugiki@protein.osaka-u.ac.jp; Furuita, Kyoko

Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant.more » In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and inhibitory activity.« 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

Structural analysis of isomeric chondroitin sulfate oligosaccharides using regioselective 6-O-desulfation method and tandem mass spectrometry.

PubMed

Chen, Shu-Ting; Her, Guor-Rong

2014-09-16

A strategy based on a regioselective 6-O-desulfation reaction and negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)) was developed for the structural delineation of isomeric chondroitin sulfate oligosaccharides. Product ions resulting from the glycosidic cleavage provided information about the number of sulfate groups in each sugar residue. After the regioselective 6-O-desulfation reaction, the number of sulfate groups on each residue was obtained using a tandem mass spectrometry analysis of the reaction product. The sulfation pattern could be obtained based on the product ions of analytes before and after the desulfation reaction. The strategy was demonstrated using a series of tetrasaccharides prepared from shark cartilage chondroitin sulfate D. Among the 12 identified tetrasaccharides, six structures had not been reported before. Copyright © 2014 Elsevier B.V. All rights reserved.

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

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.

Isomeric oxydiphthalic anhydride polyimides

NASA Technical Reports Server (NTRS)

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

1988-01-01

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

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.

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.

Catalyst-Directed Diastereoselective Isomerization of Allylic Alcohols for the Stereoselective Construction of C(20) in Steroid Side Chains: Scope and Topological Diversification.

PubMed

Li, Houhua; Mazet, Clément

2015-08-26

The stereoselective construction of C20 in steroidal derivatives by a highly diastereoselective Ir-catalyzed isomerization of primary allylic alcohols is reported. A key aspect of this strategy is a straightforward access to geometrically pure steroidal enol tosylate and enol triflate intermediates for subsequent high yielding stereoretentive Negishi cross-coupling reactions to allow structural diversity to be introduced. A range of allylic alcohols participates in the diastereoselective isomerization under the optimized reaction conditions. Electron-rich and electron-poor aryl or heteroaryl substituents are particularly well-tolerated, and the stereospecific nature of the reaction provides indifferently access to the natural C20-(R) and unnatural C20-(S) configurations. Alkyl containing substrates are more challenging as they affect regioselectivity of iridium-hydride insertion. A rationale for the high diastereoselectivities observed is proposed for aryl containing precursors. The scope of our method is further highlighted through topological diversification in the side chain and within the polycyclic domain of advanced and complex steroidal architectures. These findings have the potential to greatly simplify access to epimeric structural analogues of important steroid scaffolds for applications in biological, pharmaceutical, and medical sciences.

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

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.

Surface chemistry and catalytic performance of amorphous NiB/Hβ catalyst for n-hexane isomerization

NASA Astrophysics Data System (ADS)

Chen, Jinshe; Cai, Tingting; Jing, Xiaohui; Zhu, Lijun; Zhou, Yulu; Xiang, Yuzhi; Xia, Daohong

2016-12-01

The amorphous NiB nanoparticles were synthesized and a novel type of NiB/Hβ catalyst was prepared for the isomerization of n-hexane. The optimum preparation conditions were investigated and the effect of preparation conditions on the surface chemistry information of catalysts was characterized by XRD, N2 sorption studies, XPS, TPD and other related means. It was demonstrated that the loading amounts of NiB have effect on textural properties and the acid properties of surface. The loading amounts of NiB were also related to the amount of strong Lewis acid sites and the ratios of weak acid to strong acid of samples. Meanwhile, calcination temperatures of samples were closely associated with the structure of active components that function as metal centers. When the loading amount of NiB was 5 wt.% and calcination temperature was 200 °C, the catalyst had proper surface acidity sites and metal active sites to provide suitable synergistic effects. The mechanism for n-hexane isomerization was also investigated and the existence of unique structure of Bsbnd Nisbnd H was proved, which could provide good hydrogenation-dehydrogenation functions.

Access to Different Isomeric Dibenzoxazepinones through Copper-Catalyzed C-H Etherification and C-N Bond Construction with Controllable Smiles Rearrangement.

PubMed

Zhou, Yunfei; Zhu, Jianming; Li, Bo; Zhang, Yong; Feng, Jia; Hall, Adrian; Shi, Jiye; Zhu, Weiliang

2016-02-05

An efficient new way to access two regio-isomeric dibenzoxazepinones is reported from 8-aminoquinoline benzamides and 2-bromophenols. Through choice of conditions, the reaction proceeds either through a sequential C-H etherification and subsequent Goldberg reaction, both controlled by the aminoquinoline group and Cu(I), or via a C-H etherification and subsequent Smiles rearrangement promoted by Cu(II) and t-BuOK. The 8-aminoquinoline moiety, e.g., 8-amino-5-methoxyquinoline, is readily removable from the structures of dibenzoxazepinones under moderate conditions.

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.

The distorted tropane of scopoline.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Basterretxea, Francisco J; Fernández, José A; Castaño, Fernando

2013-06-24

The structural isomerization of scopine into scopoline (oscine) has been observed in a supersonic jet expansion using microwave spectroscopy. The rotational spectrum evidences a single structure in the gas phase, providing a first description of the (three-ring) structurally distorted tropane in scopoline. The absence of rotational signatures of any scopine conformation suggests a practically quantitative isomerization at the vaporization temperatures of the experiment (ca. 90 °C). The determined rotational parameters of scopoline reveal the structural consequences of the intramolecular cyclation of scopine, which breaks the original epoxy group and creates a new ether bridge and a 7β-hydroxytropane configuration. The hydroxy group further stabilizes the molecule by an O-H⋅⋅⋅N intramolecular hydrogen bond, which, in turn, forces the N-methyl group to the less stable axial form. Supporting ab initio (MP2) and DFT (B3LYP, M06-2X) calculations are included. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Platinum-mordenite catalysts for n-Hexane isomerization: Characterization by X-ray absorption spectroscopy and chemical probes

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

Otten, M.M.; Clayton, M.J.; Lamb, H.H.

Platinum-mordenite (Pt-MOR) catalysts were prepared from NH{sub 4}-MOR by ion exchange with (Pt{sup II}(NH{sub 3}){sub 4})(OH){sub 2}, calcination in O{sub 2} at 350{degrees}C, and reduction in H{sub 2} at 350{degrees}C. The resultant Pt-H-MOR was active for n-hexane isomerization and hydrocracking via bifunctional catalysis at 240-300{degrees}C and 1 atm. The observed activation energies for C{sub 6} branched-isomer formation are unusually low, suggesting that the isomerization rates were controlled by pore diffusion. A Pt-KH-MOR catalyst was prepared by ion exchange with aqueous KNO{sub 3} and re-reduction at 350{degrees}C; elemental analysis evidenced 90% exchange of protons for K{sup +} ions. The product distributionmore » and observed activation energies for C{sub 6} branched-isomer formation over Pt-KH-MOR are consistent with n-hexane isomerization via bifunctional catalysis. Hydrocracking was strongly suppressed, and light hydrocarbons were formed primarily by Pt-catalyzed hydrogenolysis. From in-situ extended X-ray absorption fine structure spectroscopy and H{sub 2} temperature-programmed desorption, we conclude that the Pt-MOR catalysts consist of small Pt clusters hosted within the mordenite crystals. The PtL{sub III}X-ray absorption near-edge structure (XANES) spectra of Pt-H-MOR and Pt-KH-MOR are closely similar, suggesting that the electronic structure of the Pt clusters is unaffected by mordenite acid-base chemistry. The infrared spectrum of CO adsorbed on Pt-H-MOR contains an intense band at 2084 cm{sup -1}, which is assigned to linear CO moieties on Pt clusters. The infrared spectrum of CO adsorbed on Pt-KH-MOR evidences a red shift of the linear CO band, which the authors suggest is due to electrostatic interactions between carbonyl O atoms and nearby K{sup +} ions. 45 refs., 9 figs., 6 tabs.« less

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.

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.

Synthetic Biology of Proteins: Tuning GFPs Folding and Stability with Fluoroproline

PubMed Central

Steiner, Thomas; Hess, Petra; Bae, Jae Hyun; Wiltschi, Birgit; Moroder, Luis; Budisa, Nediljko

2008-01-01

Background Proline residues affect protein folding and stability via cis/trans isomerization of peptide bonds and by the Cγ-exo or -endo puckering of their pyrrolidine rings. Peptide bond conformation as well as puckering propensity can be manipulated by proper choice of ring substituents, e.g. Cγ-fluorination. Synthetic chemistry has routinely exploited ring-substituted proline analogs in order to change, modulate or control folding and stability of peptides. Methodology/Principal Findings In order to transmit this synthetic strategy to complex proteins, the ten proline residues of enhanced green fluorescent protein (EGFP) were globally replaced by (4R)- and (4S)-fluoroprolines (FPro). By this approach, we expected to affect the cis/trans peptidyl-proline bond isomerization and pyrrolidine ring puckering, which are responsible for the slow folding of this protein. Expression of both protein variants occurred at levels comparable to the parent protein, but the (4R)-FPro-EGFP resulted in irreversibly unfolded inclusion bodies, whereas the (4S)-FPro-EGFP led to a soluble fluorescent protein. Upon thermal denaturation, refolding of this variant occurs at significantly higher rates than the parent EGFP. Comparative inspection of the X-ray structures of EGFP and (4S)-FPro-EGFP allowed to correlate the significantly improved refolding with the Cγ-endo puckering of the pyrrolidine rings, which is favored by 4S-fluorination, and to lesser extents with the cis/trans isomerization of the prolines. Conclusions/Significance We discovered that the folding rates and stability of GFP are affected to a lesser extent by cis/trans isomerization of the proline bonds than by the puckering of pyrrolidine rings. In the Cγ-endo conformation the fluorine atoms are positioned in the structural context of the GFP such that a network of favorable local interactions is established. From these results the combined use of synthetic amino acids along with detailed structural knowledge and existing protein engineering methods can be envisioned as a promising strategy for the design of complex tailor-made proteins and even cellular structures of superior properties compared to the native forms. PMID:18301757

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.

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.

Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-acetyltransferase from Shewanella denitrificans¶

PubMed Central

Chantigian, Daniel P.; Thoden, James B.; Holden, Hazel M.

2014-01-01

Unusual N-acetylated sugars have been observed on the O-antigens of some Gram-negative bacteria and on the S-layers of both Gram-positive and Gram-negative bacteria. One such sugar is 3-acetamido-3,6-dideoxy-α-d-galactose or Fuc3NAc. The pathway for its production requires five enzymes with the first step involving the attachment of dTMP to glucose-1-phosphate. Here we report a structural and biochemical characterization of a bifunctional enzyme from Shewanella denitificans thought to be involved in the biosynthesis of dTDP-Fuc3NAc. On the basis of a bioinformatics analysis, the enzyme, hereafter referred to as FdtD, has been postulated to catalyze the third and fifth steps in the pathway, namely a 3,4-keto isomerization and an N-acetyltransferase reaction. For the X-ray analysis reported here, the enzyme was crystallized in the presence of dTDP and CoA. The crystal structure shows that FdtD adopts a hexameric quaternary structure with 322 symmetry. Each subunit of the hexamer folds into two distinct domains connected by a flexible loop. The N-terminal domain adopts a left-handed β-helix motif and is responsible for the N-acetylation reaction. The C-terminal domain folds into an antiparallel flattened β-barrel that harbors the active site responsible for the isomerization reaction. Biochemical assays verify the two proposed catalytic activities of the enzyme and reveal that the 3,4-keto isomerization event leads to inversion of configuration about the hexose C-4' carbon. PMID:24128043

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.

Ion mobility studies of PdC{sub n}{sup +} clusters: Where are the fullerenes?

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

Shelimov, K.B.; Jarrold, M.F.

1995-12-14

Gas-phase ion mobility measurements have been used to study the structures and isomerization of PdC{sub n}{sup +} (n = 10-60) clusters. Non-fullerene isomers of PdC{sub n}{sup +} clusters are similar to those of C{sub n}{sup +} and MC{sub n}{sup +} (M = La and Nb) clusters, and include metal-containing mono- and bicyclic rings and graphite sheets. Neither endohedral nor nonendohedral PdC{sub n} {sup +} fullerene isomers are detected. When collisionally heated, PdC{sub n}{sup +} clusters efficiently convert into fullerenes, but the exothermicity of this process results in the loss of the Pd atom and the formation of a pure carbonmore » cluster cation. PdC{sub n}{sup +} bicyclic rings with an odd number of carbon atoms efficiently isomerize into monocyclic rings, while no evidence is found for this isomerization process for bicyclic rings with an even number of carbon atoms. 18 refs., 4 figs.« less

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

Linkage and Anomeric Differentiation in Trisaccharides by Sequential Fragmentation and Variable-Wavelength Infrared Photodissociation

NASA Astrophysics Data System (ADS)

Tan, Yanglan; Polfer, Nicolas C.

2015-02-01

Carbohydrates and their derivatives play important roles in biological systems, but their isomeric heterogeneity also presents a considerable challenge for analytical techniques. Here, a stepwise approach using infrared multiple-photon dissociation (IRMPD) via a tunable CO2 laser (9.2-10.7 μm) was employed to characterize isomeric variants of glucose-based trisaccharides. After the deprotonated trisaccharides were trapped and fragmented to disaccharide C2 fragments in a Fourier transform ion cyclotron resonance (FTICR) cell, a further variable-wavelength infrared irradiation of the C2 ion produced wavelength-dependent dissociation patterns that are represented as heat maps. The photodissociation patterns of these C2 fragments are shown to be strikingly similar to the photodissociation patterns of disaccharides with identical glycosidic bonds. Conversely, the photodissociation patterns of different glycosidic linkages exhibit considerable differences. On the basis of these results, the linkage position and anomericity of glycosidic bonds of disaccharide units in trisaccharides can be systematically differentiated and identified, providing a promising approach to characterize the structures of isomeric oligosaccharides.

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.

Structure and Activity of the Peptidyl-Prolyl Isomerase Domain from the Histone Chaperone Fpr4 toward Histone H3 Proline Isomerization*

PubMed Central

Monneau, Yoan R.; Soufari, Heddy; Nelson, Christopher J.; Mackereth, Cameron D.

2013-01-01

The FK506-binding protein (FKBP) family of peptidyl-prolyl isomerases (PPIases) is characterized by a common catalytic domain that binds to the inhibitors FK506 and rapamycin. As one of four FKBPs within the yeast Saccharomyces cerevisiae, Fpr4 has been described as a histone chaperone, and is in addition implicated in epigenetic function in part due to its mediation of cis-trans conversion of proline residues within histone tails. To better understand the molecular details of this activity, we have determined the solution structure of the Fpr4 C-terminal PPIase domain by using NMR spectroscopy. This canonical FKBP domain actively increases the rate of isomerization of three decapeptides derived from the N terminus of yeast histone H3, whereas maintaining intrinsic cis and trans populations. Observation of the uncatalyzed and Fpr4-catalyzed isomerization rates at equilibrium demonstrate Pro16 and Pro30 of histone H3 as the major proline targets of Fpr4, with little activity shown against Pro38. This alternate ranking of the three target prolines, as compared with affinity determination or the classical chymotrypsin-based fluorescent assay, reveals the mechanistic importance of substrate residues C-terminal to the peptidyl-prolyl bond. PMID:23888048

mer and fac isomerism in tris chelate diimine metal complexes.

PubMed

Dabb, Serin L; Fletcher, Nicholas C

2015-03-14

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

Accelerating the design of solar thermal fuel materials through high throughput simulations.

PubMed

Liu, Yun; Grossman, Jeffrey C

2014-12-10

Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastable structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.

Profiling of the molecular weight and structural isomer abundance of macroalgae-derived phlorotannins.

PubMed

Heffernan, Natalie; Brunton, Nigel P; FitzGerald, Richard J; Smyth, Thomas J

2015-01-16

Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4-12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds.

Profiling of the Molecular Weight and Structural Isomer Abundance of Macroalgae-Derived Phlorotannins

PubMed Central

Heffernan, Natalie; Brunton, Nigel P.; FitzGerald, Richard J.; Smyth, Thomas J.

2015-01-01

Phlorotannins are a group of complex polymers of phloroglucinol (1,3,5-trihydroxybenzene) unique to macroalgae. These phenolic compounds are integral structural components of the cell wall in brown algae, but also play many secondary ecological roles such as protection from UV radiation and defense against grazing. This study employed Ultra Performance Liquid Chromatography (UPLC) with tandem mass spectrometry to investigate isomeric complexity and observed differences in phlorotannins derived from macroalgae harvested off the Irish coast (Fucus serratus, Fucus vesiculosus, Himanthalia elongata and Cystoseira nodicaulis). Antioxidant activity and total phenolic content assays were used as an index for producing phlorotannin fractions, enriched using molecular weight cut-off dialysis with subsequent flash chromatography to profile phlorotannin isomers in these macroalgae. These fractions were profiled using UPLC-MS with multiple reaction monitoring (MRM) and the level of isomerization for specific molecular weight phlorotannins between 3 and 16 monomers were determined. The majority of the low molecular weight (LMW) phlorotannins were found to have a molecular weight range equivalent to 4–12 monomers of phloroglucinol. The level of isomerization within the individual macroalgal species differed, resulting in substantially different numbers of phlorotannin isomers for particular molecular weights. F. vesiculosus had the highest number of isomers of 61 at one specific molecular mass, corresponding to 12 phloroglucinol units (PGUs). These results highlight the complex nature of these extracts and emphasize the challenges involved in structural elucidation of these compounds. PMID:25603345

[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.

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

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

Hu, Bin; School of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, 330063; Geng, Jiao

2014-07-01

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

Analysis of isomeric ratios for medium-mass nuclei

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

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

Values of the isomeric ratios for product nuclei originating from simple charge-exchange reactions were analyzed. The cross sections for the formation of product nuclei in ground and isomeric states were calculated with the aid of the TALYS 1.4 and EMPIRE 3.2 codes. The calculated values of the isomeric ratios were compared with their experimental counterparts taken from the EXFOR database. For the {sup 86,87}Y, {sup 94,95,96,99}Tc, and {sup 44}Sc nuclei, the experimental values of the isomeric ratios exceed the respective calculated values. The nuclei in question feature weak deformations and have high-spin yrast lines and rotational bands. The possible reasonmore » behind the discrepancy between theoretical and experimental isomeric ratios is that the decay of yrast states leads with a high probability to the formation of isomeric states of detected product nuclei.« less

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.

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

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

PubMed

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

2015-12-01

The bilirubin (BR) photo-conversion in the human body is a protein-dependent process; an effective photo-isomerization of the potentially neurotoxic Z,Z-BR as well as its oxidation to biliverdin in the antioxidant redox cycle is possible only when BR is bound on serum albumin. We present a novel analytical concept in the study of linear tetrapyrroles metabolic processes based on an in-depth mapping of binding sites in the structure of human serum albumin (HSA). A combination of fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular modeling methods was used for recognition of the binding site for BR, its derivatives (mesobilirubin and bilirubin ditaurate), and the products of the photo-isomerization and oxidation (lumirubin, biliverdin, and xanthobilirubic acid) on HSA. The CD spectra and fluorescent quenching of the Trp-HSA were used to calculate the binding constants. The results of the CD displacement experiments performed with hemin were interpreted together with the findings of molecular docking performed on the pigment-HSA complexes. We estimated that Z,Z-BR and its metabolic products bind on two independent binding sites. Our findings support the existence of a reversible antioxidant redox cycle for BR and explain an additional pathway of the photo-isomerization process (increase of HSA binding capacity; the excess free [unbound] BR can be converted and also bound to HSA). Copyright © 2015 Elsevier Inc. All rights reserved.

Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.

PubMed

Manjasetty, Babu A; Chance, Mark R

2006-07-07

Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 A resolution. The subunit structure of ECAI is organised into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.

Influence of C-H···O Hydrogen Bonds on Macroscopic Properties of Supramolecular Assembly.

PubMed

Ji, Wei; Liu, Guofeng; Li, Zijian; Feng, Chuanliang

2016-03-02

For CH···O hydrogen bonds in assembled structures and the applications, one of the critical issues is how molecular spatial structures affect their interaction modes as well as how to translate the different modes into the macroscopic properties of materials. Herein, coumarin-derived isomeric hydrogelators with different spatial structures are synthesized, where only nitrogen atoms locate at the ortho, meso, or para position in the pyridine ring. The gelators can self-assemble into single crystals and nanofibrous networks through CH···O interactions, which are greatly influenced by nitrogen spatial positions in the pyridine ring, leading to the different self-assembly mechanisms, packing modes, and properties of the nanofibrous networks. Typically, different cell proliferation rates are obtained on the different CH···O bonds driving nanofibrous structures, implying that tiny variation of the stereo-position of nitrogen atoms can be sensitively detected by cells. The study paves a novel way to investigate the influence of isomeric molecular assembly on macroscopic properties and functions of materials.

Structure-property relationships in halogenbenzoic acids: Thermodynamics of sublimation, fusion, vaporization and solubility.

PubMed

Zherikova, Kseniya V; Svetlov, Aleksey A; Kuratieva, Natalia V; Verevkin, Sergey P

2016-10-01

Temperature dependences of vapor pressures for 2-, 3-, and 4-bromobenzoic acid, as well as for five isomeric bromo-methylbenzoic acids were studied by the transpiration method. Melting temperatures and enthalpies of fusion for all isomeric bromo-methylbenzoic acids and 4-bromobenzoic acid were measured with a DSC. The molar enthalpies of sublimation and vaporization were derived. These data together with results available in the literature were collected and checked for internal consistency using a group-additivity procedure and results from X-ray structural diffraction studies. Specific (hydrogen bonding) interactions in the liquid and in the crystal phase of halogenbenzoic acids were quantified based on experimental values of vaporization and sublimation enthalpies. Structure-property correlations of solubilities of halogenobenzoic acids with sublimation pressures and sublimation enthalpies were developed and solubilities of bromo-benzoic acids were estimated. These new results resolve much of the ambiguity in the available thermochemical and solubility data on bromobenzoic acids. The approach based on structure property correlations can be applied for the assessment of water solubility of sparingly soluble drugs. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Thermal Isomerization of Hydroxyazobenzenes as a Platform for Vapor Sensing

PubMed Central

2018-01-01

Photoisomerization of azobenzene derivatives is a versatile tool for devising light-responsive materials for a broad range of applications in photonics, robotics, microfabrication, and biomaterials science. Some applications rely on fast isomerization kinetics, while for others, bistable azobenzenes are preferred. However, solid-state materials where the isomerization kinetics depends on the environmental conditions have been largely overlooked. Herein, an approach to utilize the environmental sensitivity of isomerization kinetics is developed. It is demonstrated that thin polymer films containing hydroxyazobenzenes offer a conceptually novel platform for sensing hydrogen-bonding vapors in the environment. The concept is based on accelerating the thermal cis–trans isomerization rate through hydrogen-bond-catalyzed changes in the thermal isomerization pathway, which allows for devising a relative humidity sensor with high sensitivity and quick response to relative humidity changes. The approach is also applicable for detecting other hydrogen-bonding vapors such as methanol and ethanol. Employing isomerization kinetics of azobenzenes for vapor sensing opens new intriguing possibilities for using azobenzene molecules in the future. PMID:29607244

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

Infrared Lasers in Chemistry.

ERIC Educational Resources Information Center

John, Phillip

1982-01-01

Selected infrared laser chemistry topics are discussed including carbon dioxide lasers, infrared quanta and molecules, laser-induced chemistry, structural isomerization (laser purification, sensitized reactions, and dielectric breakdown), and fundamental principles of laser isotope separation, focusing on uranium isotope separation. (JN)

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.

Topologically identical, but geometrically isomeric layers in hydrous α-, β-Rb[UO2(AsO3OH)(AsO2(OH)2)]·H2O and anhydrous Rb[UO2(AsO3OH)(AsO2(OH)2)

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

Yu, Na; Klepov, Vladislav V.; Villa, Eric M.

The hydrothermal reaction of uranyl nitrate with rubidium nitrate and arsenic (III) oxide results in the formation of polymorphic α- and β-Rb[UO2(AsO3OH)(AsO2(OH)2)]·H2O (α-, β-RbUAs) and the anhydrous phase Rb[UO2(AsO3OH)(AsO2(OH)2)] (RbUAs). These phases were structurally, chemically and spectroscopically characterized. The structures of all three compounds are based upon topologically identical, but geometrically isomeric layers. The layers are linked with each other by means of the Rb cations and hydrogen bonding. Dehydration experiments demonstrate that water deintercalation from hydrous α- and β-RbUAs yields anhydrous RbUAs via topotactic reactions.

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA).

PubMed

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T; Marzilli, Luigi G

2012-09-01

The reaction of an aminopolycarboxylate ligand, as partic- N - m onoacetic a cid (ASMA), with [Re(CO) 3 (H 2 O) 3 ] + was examined. The tridentate coordination of ASMA to this Re I tricarbonyl precursor yielded fac -Re(CO) 3 (ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the Tc I tricarbonyl complex, which yields fac - 99m Tc(CO) 3 (ASMA) under similar conditions. The formation, structure, and isomerization of fac -Re(CO) 3 (ASMA) products were characterized by HPLC, 1 H NMR spectroscopy, and X-ray crystallography. The two major fac -Re(CO) 3 (ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac -Re(CO) 3 (ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99m Tc(CO) 3 (ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99m Tc radiopharmaceuticals.

Synthesis and characterization of fac-Re(CO)3-aspartic-N-monoacetic acid, a structural analogue of a potential new renal tracer, fac-99mTc(CO)3(ASMA)

PubMed Central

Klenc, Jeffrey; Lipowska, Malgorzata; Taylor, Andrew T.; Marzilli, Luigi G.

2013-01-01

The reaction of an aminopolycarboxylate ligand, aspartic-N-monoacetic acid (ASMA), with [Re(CO)3(H2O)3]+ was examined. The tridentate coordination of ASMA to this ReI tricarbonyl precursor yielded fac-Re(CO)3(ASMA) as a mixture of diastereomers. The chemistry is analogous to that of the TcI tricarbonyl complex, which yields fac-99mTc(CO)3(ASMA) under similar conditions. The formation, structure, and isomerization of fac-Re(CO)3(ASMA) products were characterized by HPLC, 1H NMR spectroscopy, and X-ray crystallography. The two major fac-Re(CO)3(ASMA) diastereomeric products each have a linear ONO coordination mode with two adjacent five-membered chelate rings, but they differ in the endo or exo orientation of the uncoordinated acetate group, in agreement with expectations based on previous studies. Conditions have been identified for the expedient isomerization of fac-Re(CO)3(ASMA) to a mixture consisting primarily of one major product. Because different isomeric species typically have different pharmacokinetic characteristics, these conditions may provide for the practical isolation of a single 99mTc(CO)3(ASMA) species, thus allowing the isolation of the isomer that has optimal imaging and pharmacokinetic characteristics. This information will aid in the design of future 99mTc radiopharmaceuticals. PMID:24273448

Relationship between surface property and catalytic application of amorphous NiP/Hβ catalyst for n-hexane isomerization

NASA Astrophysics Data System (ADS)

Chen, Jinshe; Duan, Zunbin; Song, Zhaoyang; Zhu, Lijun; Zhou, Yulu; Xiang, Yuzhi; Xia, Daohong

2017-12-01

The amorphous NiP nanoparticles were synthesized and a novel amorphous NiP/Hβ catalyst was prepared successfully further. Due to the superior surface property of amorphous NiP/Hβ catalyst, it exhibited good catalytic application for n-hexane isomerization. The catalytic activity of amorphous NiP/Hβ catalyst was close to that of the prepared Pt/Hβ sample, and better than that of commercial catalyst and crystalline Ni2P/Hβ catalyst. What's more, the amorphous NiP/Hβ catalyst shows high resistance to different sulfur compounds and water on account of its unique surface property. The effect of loading amounts on surface property and catalytic performance was investigated, and the structure-function relationship among them was studied ulteriorly. The results demonstrate that loading amounts have effect on textural property and surface acid property, which further affect the catalytic performance. The 10 wt.% NiP/Hβ sample has appropriate pore structure and acid property with uniformly dispersed NiP nanoparticles on surface, which is helpful for providing suitable synergistic effect. The effects of reaction conditions on surface reactions and the mechanism for n-hexane isomerization were investigated further. Based on these results, the amorphous NiP/Hβ catalyst with superior surface property probably pavesa way to overcome the drawbacks of traditional noble metal catalyst, which shows good catalytic application prospects.

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.

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.

Glucose transformation to 5-hydroxymethylfurfural in acidic ionic liquid: A quantum mechanical study.

PubMed

Arifin; Puripat, Maneeporn; Yokogawa, Daisuke; Parasuk, Vudhichai; Irle, Stephan

2016-01-30

Isomerization and transformation of glucose and fructose to 5-hydroxymethylfurfural (HMF) in both ionic liquids (ILs) and water has been studied by the reference interaction site model self-consistent field spatial electron density distribution (RISM-SCF-SEDD) method coupled with ab initio electronic structure theory, namely coupled cluster single, double, and perturbative triple excitation (CCSD(T)). Glucose isomerization to fructose has been investigated via cyclic and open chain mechanisms. In water, the calculations support the cyclic mechanism of glucose isomerization; with the predicted activation free energy is 23.8 kcal mol(-1) at experimental condition. Conversely, open ring mechanism is more favorable in ILs with the energy barrier is 32.4 kcal mol(-1) . Moreover, the transformation of fructose into HMF via cyclic mechanism is reasonable; the calculated activation barriers are 16.0 and 21.5 kcal mol(-1) in aqueous and ILs solutions, respectively. The solvent effects of ILs could be explained by the decomposition of free energies and radial distribution functions of solute-solvent that are produced by RISM-SCF-SEDD. © 2015 Wiley Periodicals, Inc.

Isomeric organic semiconductors containing fused-thiophene cores: molecular packing and charge transport.

PubMed

Dang, Dongfeng; Zhou, Pei; Wu, Yong; Xu, Yanzi; Zhi, Ying; Zhu, Weiguo

2018-05-16

Isomeric TF1 and TF2 with highly fused thiophene cores were designed and synthesized here, in which a highly planar molecular structure was obtained for TF1 with the face-to-face sulfur atoms in the lateral region and a twisted molecular backbone was observed for TF2 with the back-to-back sulfur atoms. It is worth noting that different intermolecular interactions dominated in TF1 and TF2 caused by their isomeric thiophene cores, in which strong π-π stacking was achieved for TF1, whereas sulphur-involved nonbonding intermolecular interactions dominated in TF2, leading to the different fluorescence behaviors and also the altered liquid crystalline phases. Finally, typical P-type charge transport behaviors were achieved in both TF1- and TF2-based solution-processed OFETs. Also owing to the much ordered molecular packing in TF1, a higher charge carrier mobility of 3.7 × 10-3 cm2 V-1 s-1 was achieved for TF1-based OFETs compared to TF2-based OFETs.

Reaction of Pentanol isomers with OH radical – A theoretical perspective

NASA Astrophysics Data System (ADS)

Aazaad, Basheer; Lakshmipathi, Senthilkumar

2018-05-01

The stability of all the three isomeric forms of Pentanol has been examined with relative energy analysis. Even though 2-Pentanol is predicted to be most stable isomeric form, all the three isomeric forms undergo hydrogen atom abstraction reaction with OH radical. Among the proposed 18 different hydrogen atom abstraction reaction, the abstraction from CH2 and CH functional group is found to be a favourable reactive site with low energy barrier in M06-2X/6-311+G(d,p) level of theory. Wiberg bond order analysis shows all the abstraction reactions are concreted but not synchronic in nature. Using force analysis, the calculated work done of individual reaction regions illustrates that structural rearrangements drive the reaction with higher contribution to the energy barrier. The rate constant calculated at M06-2X method for the most favourable reaction is well matched with available experimental data. Using the reported atmospheric OH concentration (1 × 106 molecules/cm3), the life time of 1-Pentanol, 2-Pentanol and 3-Pentanol has calculated to be 18.66, 0.36 and 2.86 days, respectively.

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

Accelerating the Design of Solar Thermal Fuel Materials through High Throughput Simulations

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

Liu, Y; Grossman, JC

2014-12-01

Solar thermal fuels (STF) store the energy of sunlight, which can then be released later in the form of heat, offering an emission-free and renewable solution for both solar energy conversion and storage. However, this approach is currently limited by the lack of low-cost materials with high energy density and high stability. In this Letter, we present an ab initio high-throughput computational approach to accelerate the design process and allow for searches over a broad class of materials. The high-throughput screening platform we have developed can run through large numbers of molecules composed of earth-abundant elements and identifies possible metastablemore » structures of a given material. Corresponding isomerization enthalpies associated with the metastable structures are then computed. Using this high-throughput simulation approach, we have discovered molecular structures with high isomerization enthalpies that have the potential to be new candidates for high-energy density STF. We have also discovered physical principles to guide further STF materials design through structural analysis. More broadly, our results illustrate the potential of using high-throughput ab initio simulations to design materials that undergo targeted structural transitions.« less

Atmospheric pressure chemical ionization studies of non-polar isomeric hydrocarbons using ion mobility spectrometry and mass spectrometry with different ionization techniques

NASA Technical Reports Server (NTRS)

Borsdorf, H.; Nazarov, E. G.; Eiceman, G. A.

2002-01-01

The ionization pathways were determined for sets of isomeric non-polar hydrocarbons (structural isomers, cis/trans isomers) using ion mobility spectrometry and mass spectrometry with different techniques of atmospheric pressure chemical ionization to assess the influence of structural features on ion formation. Depending on the structural features, different ions were observed using mass spectrometry. Unsaturated hydrocarbons formed mostly [M - 1]+ and [(M - 1)2H]+ ions while mainly [M - 3]+ and [(M - 3)H2O]+ ions were found for saturated cis/trans isomers using photoionization and 63Ni ionization. These ionization methods and corona discharge ionization were used for ion mobility measurements of these compounds. Different ions were detected for compounds with different structural features. 63Ni ionization and photoionization provide comparable ions for every set of isomers. The product ions formed can be clearly attributed to the structures identified. However, differences in relative abundance of product ions were found. Although corona discharge ionization permits the most sensitive detection of non-polar hydrocarbons, the spectra detected are complex and differ from those obtained with 63Ni ionization and photoionization. c. 2002 American Society for Mass Spectrometry.

ANALYSIS OF GLYCANS DERIVED FROM GLYCOCONJUGATES BY CAPILLARY ELECTROPHORESIS-MASS SPECTROMETRY

PubMed Central

Mechref, Yehia

2012-01-01

The high structural variation of glycan derived from glycoconjugates, which substantially increases with the molecular size of a protein, contributes to the complexity of glycosylation patterns commonly associated with glycoconjugates. In the case of glycoproteins, such variation originates from the multiple glycosylation sites of proteins and the number of glycan structures associated with each site (microheterogeneity). The ability to comprehensively characterize highly complex mixture of glycans has been analytically stimulating and challenging. Although the most powerful mass spectrometric (MS) and tandem MS techniques are capable of providing a wealth of structural information, they are still not able to readily identify isomeric glycan structures without high order tandem MS (MSn). The analysis of isomeric glycan structures has been attained using several separation methods, including high-pH anion exchange chromatography (HPAEC), hydrophilic interaction chromatography (HILIC) and gas chromatography (GC). However, capillary electrophoresis (CE) and microfluidics capillary electrophoresis (MCE) offer high separation efficiency and resolutions, allowing the separation of closely related glycan structures. Therefore, interfacing CE and MCE to MS is a powerful analytical approach, allowing potentially comprehensive and sensitive analysis of complex glycan samples. This review describes and discusses the utility of different CE and MCE approaches in the structural characterization of glycoproteins and the feasibility of interfacing these approaches to mass spectrometry. PMID:22180203

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.

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.

Preclinical Evaluation of the Synthetic Adjuvant SQS-21 and its Constituent Isomeric Saponins

PubMed Central

Ragupathi, Govind; Damani, Payal; Deng, Kai; Adams, Michelle M.; Hang, Jianfeng; George, Constantine; Livingston, Philip O.; Gin, David Y.

2010-01-01

The saponin fraction QS-21 from Quillaja saponaria has been demonstrated to be a potent immunological adjuvant when mixed with keyhole limpet hemocyanin conjugate vaccines, as well as with other classes of subunit antigen vaccines. QS-21 adjuvant is composed of two isomers that include the apiose and xylose forms in a ratio of 65:35, respectively. The chemical syntheses of these two isomers in pure form have recently been disclosed. Herein we describe detailed in vivo immunological evaluations of these synthetic QS-21 isomeric constituents, employing the GD3-KLH melanoma antigen. With this vaccine construct, high antibody titers against GD3 ganglioside and KLH were elicited when GD3-KLH was co-administered with adjuvant, either as the individual separate synthetic QS-21 isomers (SQS-21-Api or SQS-21-Xyl), or as its reconstituted 65:35 isomeric mixture (SQS-21). These antibody titer levels were comparable to that elicited by vaccinations employing naturally derived QS-21 (PQS-21). Moreover, toxicities of the synthetic saponin adjuvants were also found to be comparable to that of naturally derived PQS-21. These findings demonstrate unequivocally that the adjuvant activity of QS-21 resides in these two principal isomeric forms, and not in trace contaminants within the natural extracts. This lays the foundation for future exploration of structure-function correlations to enable the discovery of novel saponins with increased potency, enhanced stability, and attenuated toxicity. PMID:20450868

Isomer-specific profiling of N-glycans derived from human serum for potential biomarker discovery in pancreatic cancer.

PubMed

Liu, Yufei; Wang, Chang; Wang, Ran; Wu, Yike; Zhang, Liang; Liu, Bi-Feng; Cheng, Liming; Liu, Xin

2018-06-15

Glycosylation is one of the most important post-translational modifications of protein. Recently, global profiling of human serum glycomics has become a noninvasive method for cancer-related biomarker discovery and many studies have focused on compositional glycan profiling. In contrast, structure-specific glycan profiling may provide more potential biomarkers with higher specificity than compositional profiling. In this work, N-glycans released from human serum were neutralized with methylamine and reduced by ammonia-borane complex prior to profiling using nanoLC-ESI-MS with porous graphitized carbon (PGC) and relative abundances of over 280 isomers were compared between pancreatic cancer (PC) cases (n = 32) and healthy controls (n = 32). Statistical analysis identified 25 specific-isomeric biomarkers with significant differences (p-value < 0.05). ROC and PCA analysis were performed to assess the potential biomarkers which were identified as being significantly altered in cancer. The AUCs of the significantly changed specific-isomers were ranging from 0.712 to 0.949. In addition, with the combination of all potential biomarkers, a higher AUC of 0.976 with sensitivity (93.5%) and specificity (90.6%) was obtained. Overall, the proposed strategy coupled to relative quantitative analysis of isomeric glycans make it possible to discover new biomarkers for the diagnosis of PC. Pancreatic cancer (PC) has a poor prognosis with a five-year survival rate <5%. Therefore, a strategy for accurate diagnosis of PC is indeed required. In this paper, a dual-derivatized strategy for structure-specific glycan profiling has been used and according to our best knowledge, this is the first application of this strategy for PC biomarker discovery, in which the separation, identification and relative quantification of isomeric glycans can be simultaneously obtained. In addition, by in-depth analysis of isomeric glycans, the full description of the stereo- and region- diversity of glycans can also be achieved, which might provide more potential information for PC biomarker discovery. Copyright © 2018 Elsevier B.V. All rights reserved.

Positionally isomeric organic gelators: structure-gelation study, racemic versus enantiomeric gelators, and solvation effects.

PubMed

Caplar, Vesna; Frkanec, Leo; Sijaković Vujicić, Natasa; Zinić, Mladen

2010-03-08

Low molecular weight gelator molecules consisting of aliphatic acid, amino acid (phenylglycine), and omega-aminoaliphatic acid units have been designed. By varying the number of methylene units in the aliphatic and omega-aminoaliphatic acid chains, as defined by descriptors m and n, respectively, a series of positionally isomeric gelators having different positions of the peptidic hydrogen-bonding unit within the gelator molecule has been obtained. The gelation properties of the positional isomers have been determined in relation to a defined set of twenty solvents of different structure and polarity and analyzed in terms of gelator versatility (G(ver)) and effectiveness (G(eff)). The results of gelation tests have shown that simple synthetic optimizations of a "lead gelator molecule" by variation of m and n, end-group polarity (carboxylic acid versus sodium carboxylate), and stereochemistry (racemate versus optically pure form) allowed the identification of gelators with tremendously improved versatility (G(ver)) and effectiveness (G(eff)). Dramatic differences in G(eff) values of up to 70 times could be observed between pure racemate/enantiomer pairs of some gelators, which were manifested even in the gelation of very similar solvents such as isomeric xylenes. The combined results of spectroscopic ((1)H NMR, FTIR), electron microscopy (TEM), and X-ray diffraction studies suggest similar organization of the positionally isomeric gelators at the molecular level, comprising parallel beta-sheet hydrogen-bonded primary assemblies that form inversed bilayers at a higher organizational level. Differential scanning calorimetry (DSC) studies of selected enantiomer/racemate gelator pairs and their o- and p-xylene gels revealed the simultaneous presence of different polymorphs in the racemate gels. The increased gelation effectiveness of the racemate compared to that of the single enantiomer is most likely a consequence of its spontaneous resolution into enantiomeric bilayers and their subsequent organization into polymorphic aggregates of different energy. The latter determine the gel fiber thickness and solvent immobilization capacity of the formed gel network.

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).

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.

Structure of H/ACA RNP protein Nhp2p reveals cis/trans isomerization of a conserved proline at the RNA and Nop10 binding interface

PubMed Central

Koo, Bon-Kyung; Park, Chin-Ju; Fernandez, Cesar F.; Chim, Nicholas; Ding, Yi; Chanfreau, Guillaume; Feigon, Juli

2011-01-01

H/ACA small nucleolar and Cajal body ribonucleoproteins (RNPs) function in site-specific pseudouridylation of eukaryotic rRNA and snRNA, rRNA processing, and vertebrate telomerase biogenesis. Nhp2, one of four essential protein components of eukaryotic H/ACA RNPs, forms a core trimer with the pseudouridylase Cbf5 and Nop10 that specifically binds to H/ACA RNAs. Crystal structures of archaeal H/ACA RNPs have revealed how the protein components interact with each other and with the H/ACA RNA. However, in place of Nhp2p, archaeal H/ACA RNPs contain L7Ae, which binds specifically to an RNA K-loop motif absent in eukaryotic H/ACA RNPs, while Nhp2 binds a broader range of RNA structures. We report solution NMR studies of S. cerevisiae Nhp2 (Nhp2p), which reveal that Nhp2p exhibits two major conformations in solution due to cis/trans isomerization of the evolutionarily conserved Pro83. The equivalent proline is in the cis conformation in all reported structures of L7Ae and other homologous proteins. Nhp2p has the expected α-β-α fold, but the solution structures of the major conformation of Nhp2p with trans Pro83 and of Nhp2p-S82W with cis Pro83 reveal that Pro83 cis/trans isomerization affects the positions of numerous residues at the Nop10- and RNA-binding interface. An S82W substitution, which stabilizes the cis conformation, also stabilizes the association of Nhp2p with H/ACA snoRNPs in vivo. We propose that Pro83 plays a key role in the assembly of the eukaryotic H/ACA RNP, with the cis conformation locking in a stable Cbf5-Nop10-Nhp2 ternary complex and positioning the protein backbone to interact with the H/ACA RNA. PMID:21708174

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.

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.

Determination of the conformation of 2-hydroxy- and 2-aminobenzoic acid dimers using 13C NMR and density functional theory/natural bond order analysis: the central importance of the carboxylic acid carbon.

PubMed

Burnette, Ronald R; Weinhold, Frank

2006-07-20

The 13C chemical shift for the carboxylic acid carbon provides a powerful diagnostic probe to determine the preferred isomeric dimer structures of benzoic acid derivatives undergoing intra- and intermolecular H-bonding in the gas, solution and crystalline phases. We have employed hybrid density functional calculations and natural bond orbital analysis to elucidate the electronic origins of the observed 13C shieldings and their relationship to isomeric stability. We find that delocalizing interactions from the carbonyl oxygen lone pairs (nO) into vicinal carbon-oxygen and carbon-carbon antibonds (sigmaCO*,sigmaCC*) make critical contributions to the 13C shieldings, and these nO --> sigmaCO*, nO --> sigmaCC* interactions are in turn sensitive to the intramolecular interactions that dictate dimer structure and stability. The carboxyl carbon atom can thus serve as a useful detector of subtle structural and conformational features in this pharmacologically important class of carboxylic acid interactions.

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.

Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-10-25

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65.

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.

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.

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.

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.

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.

Structural Explanation for Allolactose (lac Operon Inducer) Synthesis by lacZ β-Galactosidase and the Evolutionary Relationship between Allolactose Synthesis and the lac Repressor

PubMed Central

Wheatley, Robert W.; Lo, Summie; Jancewicz, Larisa J.; Dugdale, Megan L.; Huber, Reuben E.

2013-01-01

β-Galactosidase (lacZ) has bifunctional activity. It hydrolyzes lactose to galactose and glucose and catalyzes the intramolecular isomerization of lactose to allolactose, the lac operon inducer. β-Galactosidase promotes the isomerization by means of an acceptor site that binds glucose after its cleavage from lactose and thus delays its exit from the site. However, because of its relatively low affinity for glucose, details of this site have remained elusive. We present structural data mapping the glucose site based on a substituted enzyme (G794A-β-galactosidase) that traps allolactose. Various lines of evidence indicate that the glucose of the trapped allolactose is in the acceptor position. The evidence includes structures with Bis-Tris (2,2-bis(hydroxymethyl)-2,2′,2″-nitrilotriethanol) and l-ribose in the site and kinetic binding studies with substituted β-galactosidases. The site is composed of Asn-102, His-418, Lys-517, Ser-796, Glu-797, and Trp-999. Ser-796 and Glu-797 are part of a loop (residues 795–803) that closes over the active site. This loop appears essential for the bifunctional nature of the enzyme because it helps form the glucose binding site. In addition, because the loop is mobile, glucose binding is transient, allowing the release of some glucose. Bioinformatics studies showed that the residues important for interacting with glucose are only conserved in a subset of related enzymes. Thus, intramolecular isomerization is not a universal feature of β-galactosidases. Genomic analyses indicated that lac repressors were co-selected only within the conserved subset. This shows that the glucose binding site of β-galactosidase played an important role in lac operon evolution. PMID:23486479

LC-MS/MS Analysis of Permethylated Free Oligosaccharides and N-glycans Derived from Human, Bovine, and Goat Milk Samples

PubMed Central

Dong, Xue; Zhou, Shiyue; Mechref, Yehia

2016-01-01

Oligosaccharides in milk not only provide nutrition to the infants, but also have significant immune biofunctions such as inhibition of pathogen binding to the host cell. The main component in milk oligosaccharides is free oligosaccharides. Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. In this study, we investigated the permethylated free oligosaccharides and N-glycans extracted from bovine, goat and human milk using LC-MS/MS. Quantitation profiles of free oligosaccharides and N-glycans were reported. The number of free oligosaccharides observed in bovine, goat and human milk samples (without isomeric consideration) were 11, 8 and 11 respectively. Human milk had more complex free oligosaccharides structures than the other two milk samples. Totally 58, 21, and 43 N-glycan structures (without isomeric consideration) were associated with whey proteins extracted from bovine, goat and human milk samples, respectively. Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. Also, the isomeric glycans in milk samples were determined by PGC LC at elevated temperatures. For example, separation of human milk free oligosaccharide Gal-GlcNAc-(Fuc)-Gal-Glc and Gal-GlcNAc-Gal-Glc-Fuc isomers was achieved using PGC column. Permethylation of the glycan structures facilitated the interpretation of tandem MS. For example, internal cleavage and glycosidic bond cleavage are readily distinguished in the tandem mass spectra of permethylated glycans. This feature resulted in the identification of several isomers. PMID:26959529

The structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa.

PubMed

Kimber, Matthew S; Martin, Fernando; Lu, Yingjie; Houston, Simon; Vedadi, Masoud; Dharamsi, Akil; Fiebig, Klaus M; Schmid, Molly; Rock, Charles O

2004-12-10

Type II fatty acid biosynthesis systems are essential for membrane formation in bacteria, making the constituent proteins of this pathway attractive targets for antibacterial drug discovery. The third step in the elongation cycle of the type II fatty acid biosynthesis is catalyzed by beta-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase. There are two isoforms. FabZ, which catalyzes the dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP, is a universally expressed component of the bacterial type II system. FabA, the second isoform, as has more limited distribution in nature and, in addition to dehydration, also carries out the isomerization of trans-2- to cis-3-decenoyl-ACP as an essential step in unsaturated fatty acid biosynthesis. We report the structure of FabZ from the important human pathogen Pseudomonas aeruginosa at 2.5 A of resolution. PaFabZ is a hexamer (trimer of dimers) with the His/Glu catalytic dyad located within a deep, narrow tunnel formed at the dimer interface. Site-directed mutagenesis experiments showed that the obvious differences in the active site residues that distinguish the FabA and FabZ subfamilies of dehydratases do not account for the unique ability of FabA to catalyze isomerization. Because the catalytic machinery of the two enzymes is practically indistinguishable, the structural differences observed in the shape of the substrate binding channels of FabA and FabZ lead us to hypothesize that the different shapes of the tunnels control the conformation and positioning of the bound substrate, allowing FabA, but not FabZ, to catalyze the isomerization reaction.

A Mechanistic and Structural Analysis of the Inhibition of the 90-kDa Heat Shock Protein by the Benzoquinone and Hydroquinone AnsamycinsS⃞

PubMed Central

Reigan, Philip; Siegel, David; Guo, Wenchang

2011-01-01

The benzoquinone ansamycins inhibit the ATPase activity of the 90-kDa heat shock protein (Hsp90), disrupting the function of numerous client proteins involved in oncogenesis. In this study, we examine the role of NAD(P)H:quinone oxidoreductase 1 (NQO1) in the metabolism of trans- and cis-amide isomers of the benzoquinone ansamycins and their mechanism of Hsp90 inhibition. Inhibition of purified human Hsp90 by a series of benzoquinone ansamycins was examined in the presence and absence of NQO1, and their relative rate of NQO1-mediated reduction was determined. Computational-based molecular docking simulations indicated that the trans- but not the cis-amide isomers of the benzoquinone ansamycins could be accommodated by the NQO1 active site, and the ranking order of binding energies correlated with the relative reduction rate using purified human NQO1. The trans-cis isomerization of the benzoquinone ansamycins in Hsp90 inhibition has been disputed in recent reports. Previous computational studies have used the closed or cocrystallized Hsp90 structures in an attempt to explore this isomerization step; however, we have successfully docked both the trans- and cis-amide isomers of the benzoquinone ansamycins into the open Hsp90 structure. The results of these studies indicate that both trans- and cis-amide isomers of the hydroquinone ansamycins exhibited increased binding affinity for Hsp90 relative to their parent quinones. Our data support a mechanism in which trans- rather than cis-amide forms of benzoquinone ansamycins are metabolized by NQO1 to hydroquinone ansamycins and that Hsp90-mediated trans-cis isomerization via tautomerization plays an important role in subsequent Hsp90 inhibition. PMID:21285336

LC-MS/MS analysis of permethylated free oligosaccharides and N-glycans derived from human, bovine, and goat milk samples.

PubMed

Dong, Xue; Zhou, Shiyue; Mechref, Yehia

2016-06-01

Oligosaccharides in milk not only provide nutrition to the infants but also have significant immune biofunctions such as inhibition of pathogen binding to the host cell. The main component in milk oligosaccharides is free oligosaccharides. Since the proteins in milk are highly glycosylated, N-glycans in milk also play an import role. In this study, we investigated the permethylated free oligosaccharides and N-glycans extracted from bovine, goat, and human milks using LC-MS/MS. Quantitation profiles of free oligosaccharides and N-glycans were reported. The number of free oligosaccharides observed in bovine, goat, and human milk samples (without isomeric consideration) were 11, 8, and 11, respectively. Human milk had more complex free oligosaccharides structures than the other two milk samples. Totally 58, 21, and 43 N-glycan structures (without isomeric consideration) were associated with whey proteins extracted from bovine, goat, and human milk samples, respectively. Bovine milk free oligosaccharides and N-glycans from whey proteins were highly sialylated and to a lesser extend fucosylated. Goat and human milk free oligosaccharides and N-glycans from whey proteins were both highly fucosylated. Also, the isomeric glycans in milk samples were determined by porous graphitic carbon LC at elevated temperatures. For example, separation of human milk free oligosaccharide Gal-GlcNAc-(Fuc)-Gal-Glc and Gal-GlcNAc-Gal-Glc-Fuc isomers was achieved using porous graphitic carbon column. Permethylation of the glycan structures facilitated the interpretation of MS/MS. For example, internal cleavage and glycosidic bond cleavage are readily distinguished in the tandem mass spectra of permethylated glycans. This feature resulted in the identification of several isomers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Liquid chromatography fractionation with gas chromatography/mass spectrometry and preparative gas chromatography-nuclear magnetic resonance analysis of selected nonylphenol polyethoxylates.

PubMed

Wu, Ze-ying; Rühle, Christian P G; Marriott, Philip J

2011-07-01

Commercial nonylphenol polyethoxylates, designated as NPnEOs, where n is the number of ethoxy groups, comprise a range of ethoxylate groups. According to the starting material nonylphenol, they may also be composed of a complex mix of isomeric nonyl substituents. In order to study more fully the heterogeneity arising from both the ethoxylate and nonyl groups, a mixture of NPnEOs is first fractionated by normal phase liquid chromatography (NPLC) into separate fractions comprising individual ethoxymers, n. Preparative collection of each early elution ethoxymer fraction allows further separation of different isomeric nonyl group components by using analytical gas chromatography/mass spectrometry (GC/MS). The nonyl isomers are not resolved in the NPLC method. The distribution of the isomeric nonyl side chain of different ethoxymers bears close resemblance with each other, and also with the original nonylphenol starting material, although separation efficiency of the nonyl isomers for each ethoxymer decreases with increasing ethoxymer number. Mass spectrometry of the separated isomers display close similarity for presumed equivalent isomers in each fraction, based on elution order of the nonyl isomers. This suggests that each corresponding peak has the same isomer structure. Mass spectra are interpreted based on branching within the nonyl side chain. Preparative GC coupled with MS and nuclear magnetic resonance spectroscopy elucidated the molecular structure of one of the resolved isomers as 4-(1,3-dimethyl-1-propyl-butyl)-phenol diethoxylate. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

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.

Qualitative Aspects of UV-Vis Spectrophotometry of Beta-Carotene and Lycopene.

ERIC Educational Resources Information Center

Tan, Barrie; Soderstrom, David N.

1989-01-01

Explores the structural behavior of polyenic pi systems such as isomerization and conjugation. Uses the simultaneous spectrophotometric analysis of a beta-carotene and lycopene mixture. Presents an empirical method to determine the number of double bonds in the polyenic carotenoid. (MVL)

Polymer Nomenclature--or What's in a Name?

ERIC Educational Resources Information Center

Carraher, Charles, E., Jr.; And Others

1987-01-01

Discusses the diversity of names used for various types of polymeric materials. Concentrates on the naming of linear organic polymers. Delineates these polymers by discussing common names, source-based names, characteristic group names, and structure-based names. Introduces the specifications of tacticity and geometric isomerism. (TW)

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.

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.

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.

Dynamics of liquids, molecules, and proteins measured with ultrafast 2D IR vibrational echo chemical exchange spectroscopy.

PubMed

Fayer, M D

2009-01-01

A wide variety of molecular systems undergo fast structural changes under thermal equilibrium conditions. Such transformations are involved in a vast array of chemical problems. Experimentally measuring equilibrium dynamics is a challenging problem that is at the forefront of chemical research. This review describes ultrafast 2D IR vibrational echo chemical exchange experiments and applies them to several types of molecular systems. The formation and dissociation of organic solute-solvent complexes are directly observed. The dissociation times of 13 complexes, ranging from 4 ps to 140 ps, are shown to obey a relationship that depends on the complex's formation enthalpy. The rate of rotational gauche-trans isomerization around a carbon-carbon single bond is determined for a substituted ethane at room temperature in a low viscosity solvent. The results are used to obtain an approximate isomerization rate for ethane. Finally, the time dependence of a well-defined single structural transformation of a protein is measured.

Structure, isomerism, and vibrational assignment of aluminumtrifluoroacetylacetonate. An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Afzali, R.; Vakili, M.; Boluri, E.; Tayyari, S. F.; Nekoei, A.-R.; Hakimi-Tabar, M.; Darugar, V.

2018-02-01

An interpretation of the experimental IR and Raman spectra of Aluminum (III) trifluoroacetylacetonate (Al(TFAA)3) complex, which were synthesized by us, is first reported here. The charge distribution, isomerism, strength of metal-oxygen binding and vibrational spectral properties for this complex structure were theoretically investigated through population analysis, geometry optimization and harmonic frequency calculations, performed at B3LYP/6-311G* level of theory. In the population analysis, two different approaches reffered to as ;Atoms in molecules (AIM);, and ;Natural Bond Orbital (NBO); were used. According to the calculation resuls, the energy difference between the cis and trans isomers of Al(TFAA)3 is very small and indicates that both isomers coexist in the sample in comparable proportions. Comparison of the calculated frequency and intensity data with the observed IR and Raman spectra of the complex has supported this conclusion. On the other hand, comparison of the structural and vibrational spectral data of Al(TFAA)3, which were experimentally measured and calculated at B3LYP/6-311G* level, with the corresponding data of Aluminum acetylacetonate (Al(AA)3) has revealed the effects of CF3 substitution on the structural and vibrational spectral data associated with the CH3 groups in the complex structure.

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.

Synthesis, crystal structure and photo physical properties of isomeric fluorinated s-shaped polyaromatic dibenzo[c,l]chrysene derivatives

NASA Astrophysics Data System (ADS)

Moriguchi, Tetsuji; Tabuchi, Daichi; Yakeya, Daisuke; Tsuge, Akihiko; Jalli, Venkataprasad; Yoza, Kenji

2018-01-01

Two s-shaped fluorinated isomeric polyaromatic dibenzo[c,l]chrysene derivatives have been synthesized by a two step process using the Wittig, Heck and iodine promoted cyclization reactions. These cyclized compounds were characterized by 1H NMR and EI-MS. Further, absolute configurations of isomeric 4a and 4b were determined by X-ray diffraction analysis. Compound 4a crystallized under monoclinic system with space group P21/c and compound 4b crystallized under monoclinic system with space group Cc. They have good solubility in common organic solvents such as dichloromethane, chloroform and THF. Photophysical properties of 4a and 4b were evaluated by using UV-Visible and Fluorescence spectrophotometer. Compounds 4a and 4b showed strong absorption maximum wavelength at 317 nm. The emission spectra of 4a and 4b displayed sharp peaks in the visible region from 417 to 441 nm. The shape of the UV-Visible and Fluorescence spectra of 4a and 4b looks almost identical. But compound 4a exhibited better fluorescence intensity than compound 4b. This difference may be due to the difference in the configuration of compounds 4a and 4b.

Indexing molecules with chemical graph identifiers.

PubMed

Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

2011-09-01

Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. Copyright © 2011 Wiley Periodicals, Inc.

Separation and Identification of Isomeric Glycopeptides by High Field Asymmetric Waveform Ion Mobility Spectrometry

PubMed Central

2012-01-01

The analysis of intact glycopeptides by mass spectrometry is challenging due to the numerous possibilities for isomerization, both within the attached glycan and the location of the modification on the peptide backbone. Here, we demonstrate that high field asymmetric wave ion mobility spectrometry (FAIMS), also known as differential ion mobility, is able to separate isomeric O-linked glycopeptides that have identical sequences but differing sites of glycosylation. Two glycopeptides from the glycoprotein mucin 5AC, GT(GalNAc)TPSPVPTTSTTSAP and GTTPSPVPTTST(GalNAc)TSAP (where GalNAc is O-linked N-acetylgalactosamine), were shown to coelute following reversed-phase liquid chromatography. However, FAIMS analysis of the glycopeptides revealed that the compensation voltage ranges in which the peptides were transmitted differed. Thus, it is possible at certain compensation voltages to completely separate the glycopeptides. Separation of the glycopeptides was confirmed by unique reporter ions produced by supplemental activation electron transfer dissociation mass spectrometry. These fragments also enable localization of the site of glycosylation. The results suggest that glycan position plays a key role in determining gas-phase glycopeptide structure and have implications for the application of FAIMS in glycoproteomics. PMID:22280549

Influence of lithium cations on prolyl peptide bonds.

PubMed

Kunz, Claudia; Jahreis, Günther; Günther, Robert; Berger, Stefan; Fischer, Gunter; Hofmann, Hans-Jörg

2012-06-01

The influence of lithium cations on the cis/trans isomerization of prolyl peptide bonds was investigated in a quantitative manner in trifluoroethanol (TFE) and acetonitrile, employing NMR techniques. The focus was on various environmental and structural aspects, such as lithium cation and water concentrations, the type of the partner amino acid in the prolyl peptide bond, and the peptide sequence length. Comparison of the thermodynamic parameters of the isomerization in LiCl/TFE and TFE shows a lithium cation concentration dependence of the cis/trans ratio, which saturates at cation concentrations >200 mM. A pronounced increase in the cis isomer content in the presence of lithium cations occurs with the exception of peptides with Gly-Pro and Asp-Pro moieties. The cation effect appears already at the dipeptide level. The salt concentration can considerably be reduced in solvents with a lower number of nucleophilic centers like acetonitrile. The lithium cation effect decreases with small amounts of water and disappears at a water concentration of about 5%. The isomerization kinetics under the influence of lithium cations suggests a weak cation interaction with the carbonyl oxygen of the peptide bond. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.

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

Thermal decomposition and isomerization of cis-permethrin and beta-cypermethrin in the solid phase.

PubMed

González Audino, Paola; Licastro, Susana A; Zerba, Eduardo

2002-02-01

The stability to heart of cis-permethrin and beta-cypermethrin in the solid phase was studied and the decomposition products identified. Samples heated at 210 degrees C in an oven in the dark showed that, in the absence of potassium chlorate (the salt present in smoke-generating formulations of these pyrethroids), cis-permethrin was not isomerized, although in the presence of that salt, decomposition was greater and thermal isomerization occurred. Other salts of the type KXO3 or NaXO3, with X being halogen or nitrogen, also led to a considerable thermal isomerization. Heating the insecticides in solution in the presence of potassium chlorate did not produce isomerization in any of the solvents assayed. Salt-catalysed thermal cis-trans isomerization was also found for other pyrethroids derived from permethrinic or deltamethrinic acid but not for those derived from chrysanthemic acid. The main thermal degradation processes of cis-permethrin and beta-cypermethrin decomposition when potassium chlorate was present were cyclopropane isomerization, ester cleavage and subsequent oxidation of the resulting products. Permethrinic acid, 3-phenoxybenzyle chloride, alcohol, aldehyde and acid were identified in both cases, as well as 3-phenoxybenzyl cyanide from beta-cypermethrin. A similar decomposition pattern occurred after combustion of pyrethroid fumigant formulations.

Characterization of Nα-Fmoc-protected dipeptide isomers by electrospray ionization tandem mass spectrometry (ESI-MS(n)): effect of protecting group on fragmentation of dipeptides.

PubMed

Ramesh, M; Raju, B; Srinivas, R; Sureshbabu, V V; Vishwanatha, T M; Hemantha, H P

2011-07-30

A series of positional isomeric pairs of Fmoc-protected dipeptides, Fmoc-Gly-Xxx-OY/Fmoc-Xxx-Gly-OY (Xxx=Ala, Val, Leu, Phe) and Fmoc-Ala-Xxx-OY/Fmoc-Xxx-Ala-OY (Xxx=Leu, Phe) (Fmoc=[(9-fluorenylmethyl)oxy]carbonyl) and Y=CH(3)/H), have been characterized and differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-IT-MS(n)). In contrast to the behavior of reported unprotected dipeptide isomers which mainly produce y(1)(+) and/or a(1)(+) ions, the protonated Fmoc-Xxx-Gly-OY, Fmoc-Ala-Xxx-OY and Fmoc-Xxx-Ala-OY yield significant b(1)(+) ions. These ions are formed, presumably with stable protonated aziridinone structures. However, the peptides with Gly- at the N-terminus do not form b(1)(+) ions. The [M+H](+) ions of all the peptides undergo a McLafferty-type rearrangement followed by loss of CO(2) to form [M+H-Fmoc+H](+). The MS(3) collision-induced dissociation (CID) of these ions helps distinguish the pairs of isomeric dipeptides studied in this work. Further, negative ion MS(3) CID has also been found to be useful for differentiating these isomeric peptide acids. The MS(3) of [M-H-Fmoc+H](-) of isomeric peptide acids produce c(1)(-), z(1)(-) and y(1)(-) ions. Thus the present study of Fmoc-protected peptides provides additional information on mass spectral characterization of the dipeptides and distinguishes the positional isomers. Copyright © 2011 John Wiley & Sons, Ltd.

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

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

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.

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

NASA Astrophysics Data System (ADS)

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

2014-07-01

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

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

PubMed

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

2014-07-01

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

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.

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

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)

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

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

Zhou, Meng; Tian, Shubo; Zeng, Chenjie

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

Ultrafast Relaxation Dynamics of Au 38 (SC 2 H 4 Ph) 24 Nanoclusters and Effects of Structural Isomerism

DOE PAGES

Zhou, Meng; Tian, Shubo; Zeng, Chenjie; ...

2016-12-22

Structural isomerism in nanoparticles has recently emerged as a new topic and stimulated research interest because the atomic structures of ultrasmall nanoparticles may have great impact on their fundamental properties and applications. We report the correlation between ultrafast relaxation dynamics and atomic structures of two isomers of thiolate-protected Au 38(SC 2H 4Ph) 24. The bi-icosahedral Au 38 (denoted as Au 38Q) with a Au 23 inner core in its atomic structure shows rapid decay (1.5 ps) followed by nanosecond relaxation to the ground state, whereas its structural isomer (Au 38T) exhibits similar relaxation processes, but the rapid decay is acceleratedmore » by ~50% (1.0 ps). The picosecond relaxations in both cases can be assigned to core–shell charge transfer or electronic rearrangement within the metal core. The acceleration of the fast decay in Au38T is ascribed to its unique core structure, which is made up of a mono-icosahedral Au 13 capped by a Au 12 tri-tetrahedron by sharing two atoms. Interestingly, coherent phonon emissions (25 cm –1 for Au 38Q, 27 and 60 cm –1 for Au 38T) are observed in both isomers with pumping in the NIR region. These results illustrate for the first time the importance of atomic structures in the photophysics of same sized gold nanoclusters.« less

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

Regular square planer bis-(4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione)/copper(II) complex: Trans/cis-DFT isomerization, crystal structure, thermal, solvatochromism, hirshfeld surface and DNA-binding analysis

NASA Astrophysics Data System (ADS)

Hema, M. K.; Karthik, C. S.; Warad, Ismail; Lokanath, N. K.; Zarrouk, Abdelkader; Kumara, Karthik; Pampa, K. J.; Mallu, P.

2018-04-01

Trans-[Cu(O∩O)2] complex, O∩O = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione was reported with high potential toward CT-DNA binder. The solved XRD-structure of complex indicated a perfect regular square-planer geometry around the Cu(II) center. The trans/cis-DFT-isomerization calculation supported the XRD seen in reflecting the trans-isomer as the kinetic-favor isomer. The desired complex structure was also characterized by conductivity measurement, CHN-elemental analyses, MS, EDX, SEM, UV-Vis., FT-IR, HAS and TG/DTG. The Solvatochromism behavior of the complex was evaluated using four different polar solvents. MPE and Hirshfeld surface analysis (HSA) come to an agreement that fluoride and thiophene protons atoms are with suitable electro-potential environment to form non-classical H-bonds of type CThsbnd H⋯F. The DNA-binding properties were investigated by viscosity tests and spectrometric titrations, the results revealed the complex as strong calf-thymus DNA binder. High intrinsic-binding constants value ∼1.8 × 105 was collected.

Photodissociation of conformer-selected ubiquitin ions reveals site-specific cis/trans isomerization of proline peptide bonds.

PubMed

Warnke, Stephan; Baldauf, Carsten; Bowers, Michael T; Pagel, Kevin; von Helden, Gert

2014-07-23

Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequence, which can lead to a very high sequence coverage as required in typical top-down proteomics applications. However, in the gas phase, proteins can adopt a multitude of distinct and sometimes coexisting conformations, and it is not clear how this three-dimensional structure affects the UVPD fragmentation behavior. Using ion mobility-UVPD-mass spectrometry in conjunction with molecular dynamics simulations, we provide the first experimental evidence that UVPD is sensitive to the higher order structure of gas-phase proteins. Distinct UVPD spectra were obtained for different extended conformations of 11(+) ubiquitin ions. Assignment of the fragments showed that the majority of differences arise from cis/trans isomerization of one particular proline peptide bond. Seen from a broader perspective, these data highlight the potential of UVPD to be used for the structural analysis of proteins in the gas phase.

On the Origin of the Methyl Radical Loss from Deprotonated Ferulic and Isoferulic Acids: Electronic Excitation of a Transient Structure

NASA Astrophysics Data System (ADS)

Zhang, Xiaoping; Li, Fei; Lv, Huiqing; Wu, Yanqing; Bian, Gaofeng; Jiang, Kezhi

2013-06-01

Formation of radical fragments from even-electron ions is an exception to the "even-electron rule". In this work, ferulic acid (FA) and isoferulic acid (IFA) were used as the model compounds to probe the fragmentation mechanisms and the isomeric effects on homolytic cleavage. Elimination of methyl radical and CO2 are the two competing reactions observed in the CID-MS of [FA - H]- and [IFA - H]-, of which losing methyl radical violates the "even-electron rule". The relative intensity of their product ions is significantly different, and thereby the two isomeric compounds can be differentiated by tandem MS. Theoretical calculations indicate that both the singlet-triplet gap and the excitation energy decrease in the transient structures, as the breaking C-O bond is lengthened. The methyl radical elimination has been rationalized as the intramolecular electronic excitation of a transient structure with an elongating C-O bond. The potential energy diagrams, completed by the addition of the energy barrier of the radical elimination, have provided a reasonable explanation of the different CID-MS behaviors of [FA - H]- and [IFA - H]-.

Identification and structural characterization of O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate in yeast methionine initiator tRNA.

PubMed Central

Keith, G; Glasser, A L; Desgrès, J; Kuo, K C; Gehrke, C W

1990-01-01

We report in this paper on the complete structure determination of the modified nucleotide A*, now called Ar(p), that was previously identified in yeast methionine initiator tRNA as an isomeric form of O-ribosyl-adenosine bearing an additional phosphoryl-monoester group on its ribose2 moiety. By using the chemical procedure of periodate oxidation and subsequent beta-elimination with cyclohexylamine on mono- and dinucleotides containing Ar(p), we characterized the location of the phosphate group on the C-5" of the ribose2 moiety, and the linkage between the two riboses as a (1"----2')-glycosidic bond. Since the structural difference between phosphatase treated Ar(p) and authentic O-alpha-ribosyl-(1"----2')-adenosine from poly(ADP-Ribose) was previously assigned to an isomeric difference in the ribose2-ribose1 linkage, the (1"----2')-glycosidic bond of Ar(p) was deduced to have a beta-spatial configuration. Thus, final chemical structure for Ar(p) at the position 64 in yeast initiator tRNA(Met) has been established as O-beta-ribosyl-(1"----2')-adenosine-5"-phosphate. This nucleotide is linked by a 3',5'-phosphodiester bond to G at the position 65. PMID:2235481

Quantitative structure-retention relationship studies for taxanes including epimers and isomeric metabolites in ultra fast liquid chromatography.

PubMed

Dong, Pei-Pei; Ge, Guang-Bo; Zhang, Yan-Yan; Ai, Chun-Zhi; Li, Guo-Hui; Zhu, Liang-Liang; Luan, Hong-Wei; Liu, Xing-Bao; Yang, Ling

2009-10-16

Seven pairs of epimers and one pair of isomeric metabolites of taxanes, each pair of which have similar structures but different retention behaviors, together with additional 13 taxanes with different substitutions were chosen to investigate the quantitative structure-retention relationship (QSRR) of taxanes in ultra fast liquid chromatography (UFLC). Monte Carlo variable selection (MCVS) method was adopted to choose descriptors. The selected four descriptors were used to build QSRR model with multi-linear regression (MLR) and artificial neural network (ANN) modeling techniques. Both linear and nonlinear models show good predictive ability, of which ANN model was better with the determination coefficient R(2) for training, validation and test set being 0.9892, 0.9747 and 0.9840, respectively. The results of 100 times' leave-12-out cross validation showed the robustness of this model. All the isomers can be correctly differentiated by this model. According to the selected descriptors, the three dimensional structural information was critical for recognition of epimers. Hydrophobic interaction was the uppermost factor for retention in UFLC. Molecules' polarizability and polarity properties were also closely correlated with retention behaviors. This QSRR model will be useful for separation and identification of taxanes including epimers and metabolites from botanical or biological samples.

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.

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.

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.

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

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

Toufen, D. L., E-mail: dennis@if.usp.br; Federal Institute of Education, Science and Technology of São Paulo - IFSP, 07115-000 Guarulhos, São Paulo; Allegro, P. R. P.

2014-07-15

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

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.

Photochemistry of fac-[Re(CO)3(dcbH2)( trans-stpy)]+: New Insights on the Isomerization Mechanism of Coordinated Stilbene-like Ligands.

PubMed

Faustino, Leandro A; Hora Machado, Antonio Eduardo; Patrocinio, Antonio Otavio T

2018-03-05

In this work, a novel complex fac-[Re(CO) 3 (dcbH 2 )( trans-stpy)] + , (dcbH 2 = 4,4'-dicarboxylic acid-2,2'-bipyridine; trans-stpy = trans-4-styrylpyridine) was synthesized and characterized toward its spectroscopic, photochemical, and photophysical properties. The experimental data provide new insights on the mechanism of photochemical trans-to- cis isomerization of the stilbene-like ligand coordinated to Re(I) polypyridyl complexes. The new complex exhibits an unusual and strong dependence of the isomerization quantum yield (Φ t →c ) on the irradiation wavelength. Φ t →c was 0.81 ± 0.08 for irradiation at 365 nm and continuously decreased as the irradiation wavelength is shifted to the visible. At 405 nm irradiation Φ t →c is almost 2 orders of magnitude lower (0.010 ± 0.005) than that observed at 365 nm excitation. This behavior can be explained by the low-lying triplet metal-to-ligand charge-transfer excited state ( 3 MLCT) that hinders the triplet photoreaction mechanism under visible light absorption. Under UV irradiation, direct population of styrylpyridine-centered excited state ( 1 IL) leads to the occurrence of the photoisomerization via a singlet mechanism. Further experiments were performed with the complex immobilized on the surface of TiO 2 and Al 2 O 3 films. The nonoccurrence of isomerization at the oxide surfaces even under UV excitation evidences the role of energy gap between the 1 IL/ 1 MLCT states on the photochemical/photophysical processes. The results establish important relationships between the molecular structure and the photoelectrochemical behavior, which can further contribute to the development of solid-state molecular switches based on Re(I) polypyridyl complexes.

Optical Properties of the Organic Semiconductor Polyacetylene.

NASA Astrophysics Data System (ADS)

Feldblum, Avinoam Y.

Polyacetylene is the prototype conducting organic polymer. In its pristine form, it exhibits physical properties closely resembling those of a conventional inorganic semiconductor. When chemically or electrochemically doped, the polymer undergoes a semiconductor-metal transition. The nature of lightly doped polyacetylene, prior to the metallic transition, is not well understood. In addition, there still remain questions as to the nature of the pristine film itself. In this thesis, optical absorption experiments were performed in order to gain a clearer understanding of the electronic structure of polyacetylene. To attain this understanding, opto-electrochemical spectroscopy (OES), a new technique combining optical measurements with in situ electrochemical doping was developed. Optical absorption measurements were performed on cis-(CH)(,x) in order to examine doping induced isomerization. When doped to metallic levels followed by compensation or undoping, cis-(CH)(,x) isomerizes to trans-(CH)(,x). Using OES, one finds that with light doping, the main contribution to the midgap transition comes from the small trans content in the film. Electrochemical cycling shows isomerization beginning below y = 0.01 and repeated cycling to different concentrations indicate that the total isomerization depends on the value of the highest dopant level. These results suggest that upon light doping, the trans-(CH)(,x) dopes first, followed by enough cis-(CH)(,x) isomerizing to accomodate the injected charge. A quantitative study of the effects of doping on the absorption coefficient of trans-(CH)(,x) was carried out using OES. Upon doping, the interband absorption uniformly decreases over an extremely wide range. A strong absorbtion appeared at mid-gap; its oscillator strength increasing linearly with dopant concentration. A weak shoulder is observed on the interband edge which grows at low concentrations and then decreases to zero by 4%. These results agree with the predictions of the soliton model--the midgap absorption is identified as a soliton level and the shoulder as a transition between localized polaron levels. The pressure dependence of the photoabsorption of cis- and trans-(CH)(,x) has been measured. In both cases the bandedge shifted to a lower energy, and the value of the peak absorption coefficient decreased. These results suggest that the observed bandwidth is due primarily to the transverse transfer integral.

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.

PubMed

Vdovenko, Sergey I; Gerus, Igor I; Pagacz-Kostrzewa, Magdalena; Wierzejewska, Maria; Zhuk, Yuri I; Kukhar, Valery P

2018-06-15

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 F 3 C-COCHCHNH(CH 3 ) (1) in Ar-matrix exposed to UV-radiation (λ=340nm) 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 F 3 C-CO-C(CH 3 )CH-NH(CH 3 ) (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. Copyright © 2018 Elsevier B.V. All rights reserved.

Microwave discharge electrodeless lamps (MDEL). Part VII. Photo-isomerization of trans-urocanic acid in aqueous media driven by UV light from a novel Hg-free Dewar-like microwave discharge thermally-insulated electrodeless lamp (MDTIEL). Performance evaluation.

PubMed

Horikoshi, Satoshi; Sato, Tatsuro; Sakamoto, Kazutami; Abe, Masahiko; Serpone, Nick

2011-07-01

A novel mercury-free Dewar-like (double-walled structure) microwave discharge thermally-insulated electrodeless lamp (MDTIEL) was fabricated and its performance evaluated using the photo-isomerization of trans-urocanic acid (trans-UA) in aqueous media as a test process driven by the emitted UV light when ignited with microwave radiation. The photo-isomerization processes trans-UA → cis-UA and cis-UA → trans-UA were re-visited using light emitted from a conventional high-pressure Hg light source and examined for the influence of UV light irradiance and solution temperature; the temperature dependence of the trans → cis process displayed a negative activation energy, E(a) = -1.3 cal mol(-1). To control the photo-isomerization of urocanic acid from the heat usually dissipated by a microwave discharge electrodeless lamp (single-walled MDEL), it was necessary to suppress the microwave-initiated heat. For comparison, the gas-fill in the MDEL lamp, which typically consists of a mixture of Hg and Ar, was changed to the more eco-friendly N(2) gas in the novel MDTIEL device. The dynamics of the photo-isomerization of urocanic acid driven by the UV wavelengths of the N(2)-MDTIEL light source were compared to those from the more conventional single-walled N(2)-MDEL and Hg/Ar-MDEL light sources, and with those from the Hg lamp used to irradiate, via a fiber optic, the photoreactor located in the wave-guide of the microwave apparatus. The heating efficiency of a solution with the double-walled N(2)-MDTIEL was compared to the efficiency from the single-walled N(2)-MDEL device. Advantages of N(2)-MDTIEL are described from a comparison of the dynamics of the trans-UA → cis-UA process on the basis of unit surface area of the lamp and unit power consumption. The considerably lower temperature on the external surface of the N(2)-MDTIEL light source should make it attractive in carrying out photochemical reactions that may be heat-sensitive such as the photothermochromic urocanic acid system.

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.

Preformulation stability study of the EGFR inhibitor HKI-272 (Neratinib) and mechanism of degradation.

PubMed

Lu, Qinghong; Ku, Mannching Sherry

2012-03-01

The stability in solution of HKI-272 (Neratinib) was studied as a function of pH. The drug is most stable from pH 3 to 4, and degradation rate increases rapidly around pH 6 and appears to approach a maximum asymptotic limit in the range of pH 812. Pseudo first-order reaction kinetics was observed at all pH values. The structure of the major degradation product indicates that it is formed by a cascade of reactions within the dimethylamino crotonamide group of HKI-272. It is assumed that the rate-determining step is the initial isomerization from allyl amine to enamine functionality, followed by hydrolysis and subsequent cyclization to a stable lactam. The maximum change in degradation rate as a function of pH occurs at about pH 6, which corresponds closely to the theoretical pKa value of the dimethylamino group of HKI-272 when accounting for solvent/temperature effects. The observed relationship between pH and degradation rate is discussed, and a self-catalyzed mechanism for the allylamine-enamine isomerization reaction is proposed. The relevance of these findings to other allylamine drugs is discussed in terms of the relative stability of the allylic anion intermediate through which, the isomerization occurs.

Isolation and characterization of a 17-kDa FKBP-type peptidyl-prolyl cis/trans isomerase from Vibrio anguillarum.

PubMed

Jo, Geon-A; Lee, Jong Min; No, Gyuyou; Kang, Dong Seop; Kim, So-Hyun; Ahn, Sun-Hee; Kong, In-Soo

2015-06-01

Peptidyl-prolyl cis/trans isomerase (PPIase) catalyzes the isomerization of peptide bonds to achieve conformational changes in native folded proteins. An FKBP-type PPIase with an approximate molecular weight of 17kDa was isolated from Vibrio anguillarum O1 and named VaFKBP17. To investigate its biochemical properties, the ppi gene from V. anguillarum O1 was isolated and overexpressed in Escherichia coli. A protease-coupled assay for isomerization activity, using Succinyl-Ala-Phe-Pro-Phe-p nitroanilide as substrate, indicated that the activity of VaFKBP17 was highest at low temperature (5°C) and alkaline conditions (pH 10). The immunosuppressant FK506 inhibited the isomerization activity of VaFKBP17. The chaperone activity of VaFKBP17 was assessed using a citrate synthase thermal aggregation activity assay. To evaluate its ability to catalyze protein refolding, the effect of VaFKBP17 on inclusion bodies was investigated during a dilution process. In this assay, VaFKBP17 was able to assist protein refolding. These results provide evidence that VaFKBP17 possesses chaperone-like activity. The structural homology of VaFKBP17 relative to other known bacterial FKBPs was also examined. Copyright © 2015 Elsevier Inc. All rights reserved.

Accelerated photostability study of tretinoin and isotretinoin in liposome formulations.

PubMed

Ioele, G; Cione, E; Risoli, A; Genchi, G; Ragno, G

2005-04-11

The photodegradation of retinoic acids, tretinoin and isotretinoin, in ethanol and liposomes was studied. The light irradiation was performed according to the conditions suggested by the ICH Guideline for photostability testing by using a Xenon lamp within a wavelength range of 300-800 nm. The photodegradation process was monitored by UV spectrophotometry. In ethanol solution, tretinoin and isotretinoin undergo complete isomerization just within a few seconds of light exposure to give 13-cis and 9-cis isomers, respectively. The 13-cis isomer from tretinoin undergoes in turn a slow isomerization to the same 9-cis isomer. Both retinoic acids incorporated in liposome complexes showed an increased stability in comparison to the ethanol solutions. In particular for tretinoin, a residual concentration of 60% was still present after a light irradiance of 3470 kJ/m(2), by means of a 250 W/m(2) light power for 240 min, versus a residual value of just 8% measured at the same time in ethanol solution. Moreover, the isomerization rate in liposomes resulted reduced for isotretinoin and practically irrelevant for tretinoin. The degradation rate was found to be dependent on the drug concentration. The better stability of the tretinoin in liposome complex was supposed to be related to its higher incorporation value due to the linear structure of the molecule.

Simultaneous monitoring of oxidation, deamidation, isomerization, and glycosylation of monoclonal antibodies by liquid chromatography-mass spectrometry method with ultrafast tryptic digestion.

PubMed

Wang, Yi; Li, Xiaojuan; Liu, Yan-Hui; Richardson, Daisy; Li, Huijuan; Shameem, Mohammed; Yang, Xiaoyu

Monoclonal antibodies are subjected to a wide variety of post-translational modifications (PTMs) that cause structural heterogeneity. Characterization and control of these modifications or quality attributes are critical to ensure antibody quality and to define any potential effects on the ultimate safety and potency of antibody therapeutics. The biopharmaceutical industry currently uses numerous tools to analyze these quality attributes individually, which requires substantial time and resources. Here, we report a simple and ultrafast bottom-up liquid chromatography-mass spectrometry (uLC-MS) method with 5 min tryptic digestion to simultaneously analyze multiple modifications, including oxidation, deamidation, isomerization, glycation, glycosylation, and N-terminal pyro-glutamate formation, which can occur during antibody production in mammalian cell culture, during purification and/or on storage. Compared to commonly used preparation procedures, this uLC-MS method eliminates assay artifacts of falsely-increased Met oxidation, Asp isomerization, and Asn deamidation, a problem associated with long digestion times in conventional LC-MS methods. This simple, low artifact multi-attribute uLC-MS method can be used to quickly and accurately analyze samples at any stage of antibody drug development, in particular for clone and media selection during cell culture development.

Light-induced radical formation and isomerization of an aromatic thiol in solution followed by time-resolved x-ray absorption spectroscopy at the sulfur K-edge

DOE PAGES

Ochmann, Miguel; von Ahnen, Inga; Cordones, Amy A.; ...

2017-02-20

Here, we applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ~70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemicalmore » reaction pathways and transient products of sulfur-containing molecules in solution.« less

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.

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.

Light-induced radical formation and isomerization of an aromatic thiol in solution followed by time-resolved x-ray absorption spectroscopy at the sulfur K-edge

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

Ochmann, Miguel; von Ahnen, Inga; Cordones, Amy A.

Here, we applied time-resolved sulfur-1s absorption spectroscopy to a model aromatic thiol system as a promising method for tracking chemical reactions in solution. Sulfur-1s absorption spectroscopy allows tracking multiple sulfur species with a time resolution of ~70 ps at synchrotron radiation facilities. Experimental transient spectra combined with high-level electronic structure theory allow identification of a radical and two thione isomers, which are generated upon illumination with 267 nm radiation. Moreover, the regioselectivity of the thione isomerization is explained by the resulting radical frontier orbitals. This work demonstrates the usefulness and potential of time-resolved sulfur-1s absorption spectroscopy for tracking multiple chemicalmore » reaction pathways and transient products of sulfur-containing molecules in solution.« less

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

Stereoscopic Projection in Organic Chemistry: Bridging the Gap between Two and Three Dimensions.

ERIC Educational Resources Information Center

Rozzelle, Arlene A.; Rosenfeld, Stuart M.

1985-01-01

Shows how to make stereo slides of three-dimensional molecular models. The slides have been used to teach chirality, conformational isomerism, how models and two-dimensional representations embody selected aspects of structure, and fundamentals of using the specific model set required in a particular organic chemistry course. (JN)

Copper/H2O2-mediated oxidation of 2'-deoxyguanosine in the presence of 2-naphthol leads to the formation of two distinct isomeric adducts.

PubMed

Fleming, Aaron M; Kannan, Arunkumar; Muller, James G; Liao, Yi; Burrows, Cynthia J

2011-10-07

Exposure of cells to phenolic compounds through exogenous and endogenous sources can lead to deleterious effects via nucleobase modifications of DNA occurring under oxidative conditions. 2'-Deoxyguanosine (dG) is the most electron rich of the four canonical bases and includes many nucleophilic sites; it is also susceptible to oxidation with numerous reactive oxygen species. In these studies, dG was allowed to react with 2-naphthol in the presence of copper or iron salts yielding two principal isomeric products. Spectroscopic analysis and reactions with alkylated nucleosides support the assignment of compound 1a/1b as a pair of atropisomer N(2) adducts and compound 2a/2b as a diastereomeric mixture of tricyclic [4.3.3.0] adducts. Both products are the result of an overall four-electron oxidation process and consequently have the same masses, though drastically different structures, providing mechanistic insight into their formation. Thus, dG alkylation by 2-naphthol under oxidative conditions yields products whose structural properties are altered, leading to potentially mutagenic effects in genomic DNA.

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length

PubMed Central

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S.; Du, Yang; Nielsen, Anne K.; Byrne, Bernadette; Kobilka, Brian K.; Loland, Claus J.; Guan, Lan

2017-01-01

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile–lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. PMID:27981750

Structures of cycloserine and 2-oxazolidinone probed by X-ray photoelectron spectroscopy: theory and experiment.

PubMed

Ahmed, Marawan; Wang, Feng; Acres, Robert G; Prince, Kevin C

2014-05-22

The electronic structures and properties of 2-oxazolidinone and the related compound cycloserine (CS) have been investigated using theoretical calculations and core and valence photoelectron spectroscopy. Isomerization of the central oxazolidine heterocycle and the addition of an amino group yield cycloserine. Theory correctly predicts the C, N, and O 1s core spectra, and additionally, we report theoretical natural bond orbital (NBO) charges. The valence ionization energies are also in agreement with theory and previous measurements. Although the lowest binding energy part of the spectra of the two compounds shows superficial similarities, further analysis of the charge densities of the frontier orbitals indicates substantial reorganization of the wave functions as a result of isomerization. The highest occupied molecular orbital (HOMO) of CS shows leading carbonyl π character with contributions from other heavy (non-H) atoms in the molecule, while the HOMO of 2-oxazolidinone (OX2) has leading nitrogen, carbon, and oxygen pπ characters. The present study further theoretically predicts bond resonance effects of the compounds, evidence for which is provided by our experimental measurements and published crystallographic data.

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.

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.

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

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.

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.

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.

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.

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®

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.

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.

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.

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.

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

Masubuchi, Tsugunosuke; Iwasa, Takeshi; JST, ERATO, Nakajima Designer Nanocluster Assembly Project, 3-2-1 Sakado, Takatsu-ku, Kawasaki 213-0012

One end open V{sub n}Bz{sub n}{sup −} (n = 1–5; Bz = benzene) and both ends open V{sub n}Bz{sub n−1}{sup −} (n = 2–5) vanadium–benzene cluster anions were studied using anion photoelectron spectroscopy and density functional calculations. The smaller (n ≤ 3) V{sub n}Bz{sub n} and V{sub n}Bz{sub n−1} clusters and corresponding anions were found to have structural isomers, whereas full-sandwiched V{sub n}Bz{sub n+1} clusters preferred to form multiple-decker sandwich structures. Several isomeric V{sub 2}Bz{sub 2} structures were identified theoretically and the anion photoelectron spectra of V{sub 2}Bz{sub 2}{sup 0/−} were explained well by the coexistence of two isomeric structures:more » (1) a V{sub 2}-core structure sandwiched between benzene molecules and (2) an alternating sandwich structure with the spin state strongly dependent on the structure. The adiabatic electron affinity of both V{sub n}Bz{sub n} and V{sub n}Bz{sub n−1} was found to increase with the cluster size at larger sizes (n = 4 or 5) and approaches to that of V{sub n}Bz{sub n+1}. The evolution of the structural and electronic properties of V{sub n}Bz{sub m} and V{sub n}Bz{sub m}{sup −} (m = n and n − 1) with size is discussed in comparison with V{sub n}Bz{sub n+1} and V{sub n}Bz{sub n+1}{sup −}.« less

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy.

PubMed

Smith, S O; Lugtenburg, J; Mathies, R A

1985-01-01

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an efficient light-energy convertor. Important unresolved questions involve the mechanism by which the protein catalyzes deprotonation of the L550 intermediate and the mechanism of the thermal conversion of M412 back to BR568. Also, it has been shown that under conditions of high ionic strength and/or low light intensity two protons are pumped per photocycle (Kuschmitz & Hess, 1981). How might this be accomplished?(ABSTRACT TRUNCATED AT 400 WORDS)

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.

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

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)

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

Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore

DTIC Science & Technology

2015-11-03

al. Angew. Chem. Int. Ed. 2008, 47, 1668 –1671 Dehydrated gas-phase structures Barlow Correlation Experiment – Barrier energy in protein is ~1-1.2...eV, and inversely correlated with the absorption wavelength Theory – ~1-2eV Barlow R.B.; Birge R.R.; Kaplan E.; Tallent J.R. Nature 1993, 366, 64

A Classical Trajectory Study of the Dissociation and Isomerization of C2H5

DTIC Science & Technology

2013-01-01

modifications are possible but would be sensible only in the context of systematic ab initio calculations to provide the basis for such changes. As the... Ciudad , T.; Ramírez, R.; Schulte, J.; Böhm, M. C. Anharmonic Effects on the Structural and Vibrational Properties of the Ethyl Radical: A Path Integral

Ultrafast isomerization initiated by X-ray core ionization

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

Pronounced photosensitivity of molecular [Ru(bpy)2(OSO)]+ solutions based on two photoinduced linkage isomers.

PubMed

Dieckmann, Volker; Eicke, Sebastian; Rack, Jeffrey J; Woike, Theo; Imlau, Mirco

2009-08-17

Photosensitive properties of [Ru(bpy)(2)(OSO)] PF(6) dissolved in propylene carbonate originating from photoinduced linkage isomerism have been studied by temperature and exposure dependent transmission and UV/Vis absorption spectroscopy. An exceeding photochromic photosensitivity of S = (63 +/- 10) x 10(3) cm l J(-1) mol(-1) is determined. It is attributed to a maximum population of 100% molecules in the photoinduced isomers, a unique absorption cross section per molecule and a very low light exposure of Q(0) = (0.25 +/- 0.03) Ws cm(-2) for isomerism. Relaxation studies of O-bonded to S-bonded isomers at different temperatures verify the existence of two distinct structures of linkage isomers determined by the activation energies of E(A,1) = (0.76 +/- 0.08) eV and E(A,2) = (1.00 +/- 0.14) eV.

Dual Catalytic Activity of a Cytochrome P450 Controls Bifurcation at a Metabolic Branch Point of Alkaloid Biosynthesis in Rauwolfia serpentina

PubMed Central

Dang, Thu‐Thuy T.; Franke, Jakob; Tatsis, Evangelos

2017-01-01

Abstract Plants create tremendous chemical diversity from a single biosynthetic intermediate. In plant‐derived ajmalan alkaloid pathways, the biosynthetic intermediate vomilenine can be transformed into the anti‐arrhythmic compound ajmaline, or alternatively, can isomerize to form perakine, an alkaloid with a structurally distinct scaffold. Here we report the discovery and characterization of vinorine hydroxylase, a cytochrome P450 enzyme that hydroxylates vinorine to form vomilenine, which was found to exist as a mixture of rapidly interconverting epimers. Surprisingly, this cytochrome P450 also catalyzes the non‐oxidative isomerization of the ajmaline precursor vomilenine to perakine. This unusual dual catalytic activity of vinorine hydroxylase thereby provides a control mechanism for the bifurcation of these alkaloid pathway branches. This discovery highlights the unusual catalytic functionality that has evolved in plant pathways. PMID:28654178

Dual Catalytic Activity of a Cytochrome P450 Controls Bifurcation at a Metabolic Branch Point of Alkaloid Biosynthesis in Rauwolfia serpentina.

PubMed

Dang, Thu-Thuy T; Franke, Jakob; Tatsis, Evangelos; O'Connor, Sarah E

2017-08-01

Plants create tremendous chemical diversity from a single biosynthetic intermediate. In plant-derived ajmalan alkaloid pathways, the biosynthetic intermediate vomilenine can be transformed into the anti-arrhythmic compound ajmaline, or alternatively, can isomerize to form perakine, an alkaloid with a structurally distinct scaffold. Here we report the discovery and characterization of vinorine hydroxylase, a cytochrome P450 enzyme that hydroxylates vinorine to form vomilenine, which was found to exist as a mixture of rapidly interconverting epimers. Surprisingly, this cytochrome P450 also catalyzes the non-oxidative isomerization of the ajmaline precursor vomilenine to perakine. This unusual dual catalytic activity of vinorine hydroxylase thereby provides a control mechanism for the bifurcation of these alkaloid pathway branches. This discovery highlights the unusual catalytic functionality that has evolved in plant pathways. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface

NASA Astrophysics Data System (ADS)

Molla, Mijanur Rahaman; Rangadurai, Poornima; Antony, Lucas; Swaminathan, Subramani; de Pablo, Juan J.; Thayumanavan, S.

2018-06-01

Nature has engineered exquisitely responsive systems where molecular-scale information is transferred across an interface and propagated over long length scales. Such systems rely on multiple interacting, signalling and adaptable molecular and supramolecular networks that are built on dynamic, non-equilibrium structures. Comparable synthetic systems are still in their infancy. Here, we demonstrate that the light-induced actuation of a molecularly thin interfacial layer, assembled from a hydrophilic- azobenzene -hydrophobic diblock copolymer, can result in a reversible, long-lived perturbation of a robust glassy membrane across a range of over 500 chemical bonds. We show that the out-of-equilibrium actuation is caused by the photochemical trans-cis isomerization of the azo group, a single chemical functionality, in the middle of the interfacial layer. The principles proposed here are implemented in water-dispersed nanocapsules, and have implications for on-demand release of embedded cargo molecules.

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.

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.

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∘ .

Effect of SiO2/Al2O3 Ratio on Micro-Mesopore Formation for Pt/Beta-MCM-41 via NaOH Treatment and the Catalytic Performance in N-heptane Hydro isomerization

NASA Astrophysics Data System (ADS)

Gao, Li; Shi, Zhiyuan; Liu, Yingming; Zhao, Yuanshou; Liu, Qinghua; Xu, Chengguo; Bai, Peng; Yan, Zifeng

2018-01-01

Micro-mesoporous composite material Beta-MCM-41(BM) were hydrothermally synthesized by treating parent beta with molar SiO2/Al2O3 ratios of 12.5, 20 and 30 as precursors. The influence of SiO2/Al2O3 ratio of zeolite beta on effective micro-mesoporous composite formation was studied by investigating the crystallinity, morphology, chemical composition, acidity and textural property of Beta-MCM-41 through XRD, nitrogen adsorption, SEM, TEM, NH3-TPD, FTIR and Pyridine-FTIR. The catalytic performance was evaluated in terms of n-heptane hydro isomerization. The results demonstrated that Beta-MCM-41 supported Pt catalysts showed higher selectivity to isoheptanes than Pt/Beta. It was attributed to the superiorities of the pore structure and mesoporous accelerated the diffusion of larger molecules of isoheptanes.

Antifungal activity and isomerization of octadecyl p-coumarates from Ipomoea carnea subsp. fistulosa.

PubMed

Nidiry, Eugene Sebastian J; Ganeshan, Girija; Lokesha, Ankanahalli N

2011-12-01

Bioassay monitored HPLC assisted isolation and purification of the chief antifungal fraction of the leaves of Ipomoea carnea subsp. fistulosa (Convulvulaceae) were achieved using Colletotrichum gloeosporioides and Cladosporium cucumerinum as test organisms. The activity of the purified fraction was further confirmed by the dose dependent inhibition of the spore germination of Alternaria alternata and A. porri. The active fraction was identified as a mixture of (E)-octadecyl p-coumarate and (Z)-octadecyl p-coumarate. The two isomers were detected on an HPLC column with substantially different retention times, but once eluted from the column, one form was partly converted to the other in daylight. Conclusive evidence for the structures and their isomerization were obtained from the HPLC behavior, IR, UV, HRESIMS, CIMS and and NMR spectral data. Important 1H NMR and 13C NMR signals could be separately assigned for the isomers using 2D NMR techniques.

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.

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.

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

Photo-switching of a non-ionic azobenzene amphiphile in Langmuir and Langmuir-Blodgett films.

PubMed

Piosik, Emilia; Kotkowiak, Michał; Korbecka, Izabela; Galewski, Zbigniew; Martyński, Tomasz

2017-08-30

The concept of programmable and reconfigurable soft matter has emerged in science in the last few decades and can be realized by photoisomerization of azobenzene derivatives. This possibility results in great application potential of these compounds in optical storage devices, molecular junctions of electronic devices, command layers of liquid crystal displays or holographic gratings. In this paper, we present the results of a study on the organization and isomerization of the non-ionic and amphiphilic methyl 4-[(E)-2-[4-(nonyloxy)phenyl]diazen-1-yl]benzoate (LCA) in a 2D layer architecture of Langmuir and Langmuir-Blodgett (LB) films supported by spectroscopic studies on LCA chloroform solutions. Our investigation has shown a significantly different molecular organization of LCA depending on the ratio of trans and cis isomers in the monolayers. Taking advantage of a relatively low packing density and aggregation strength in the cis-LCA monolayer, we demonstrated the reversible isomerization in the LB film initially formed of LCA molecules in the cis form, while in the trans-LCA monolayer this effect was not observed. Our approach allows the formation of a switchable monolayer made of the amphiphilic LCA showing liquid crystalline properties without introducing an ionic group into the molecule structure, mixing with another compound or changing the subphase pH to provide free space for the molecules' isomerization.

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

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.

Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

DOEpatents

Sachtler, W.M.H.; Huang, Y.Y.

1998-07-28

Methods are disclosed for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physical sorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics. 17 figs.

Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

DOEpatents

Sachtler, Wolfgang M. H.; Huang, Yin-Yan

1998-01-01

Methods for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physisorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics.

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

PubMed Central

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

1995-01-01

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

Cis and Trans Isomerization in Cyclic Alkenes: A Topic for Discovery Using the Results of Molecular Modeling

ERIC Educational Resources Information Center

Barrows, Susan E.; Eberlein, Thomas H.

2004-01-01

Activities in which students explore the fundamental reasons behind the unusual instability of the trans isomers in medium-sized cycloalkenes by using the results of molecular modeling are described. Exercises have been proposed to explore the structures of cycloheptene and cyclooctene by Hehre and others which would be helpful to disabuse…

Total synthesis of (+)-antroquinonol and (+)-antroquinonol D.

PubMed

Sulake, Rohidas S; Chen, Chinpiao

2015-03-06

The first total synthesis of (+)-antroquinonol and (+)-antroquinonol D, two structurally unique quinonols with a sesquiterpene side chain, is described. The route features an iridium-catalyzed olefin isomerization-Claisen rearrangement reaction (ICR), lactonization, and Grubbs olefin metathesis. The requisite α,β-unsaturation was achieved via the selenylation/oxidation protocol and elimination of β-methoxy group to provide two natural products from a common intermediate.

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.

Structural and Acidic Properties of Niobia-Silica and Niobia-Alumina Aerogels

DTIC Science & Technology

1991-05-06

some weak Bronsted acidity. The silica aerogel supported niobia samples also had strong Lewis acidity as well as strong iv Bronsted acidity which was...NS25w or the silica aerogel supported niobia because of the formation of a distorted octahedral niobia-rigid silica interface. Isomerization of 1...67 2.1.2 Silica Aerogel .......................................................... 70 2.1.3 Alumina

Mapping heat exchange in an allosteric protein.

PubMed

Gupta, Shaweta; Auerbach, Anthony

2011-02-16

Nicotinic acetylcholine receptors (AChRs) are synaptic ion channels that spontaneously isomerize (i.e., gate) between resting and active conformations. We used single-molecule electrophysiology to measure the temperature dependencies of mouse neuromuscular AChR gating rate and equilibrium constants. From these we estimated free energy, enthalpy, and entropy changes caused by mutations of amino acids located between the transmitter binding sites and the middle of the membrane domain. The range of equilibrium enthalpy change (13.4 kcal/mol) was larger than for free energy change (5.5 kcal/mol at 25°C). For two residues, the slope of the rate-equilibrium free energy relationship (Φ) was approximately constant with temperature. Mutant cycle analysis showed that both free energies and enthalpies are additive for energetically independent mutations. We hypothesize that changes in energy associated with changes in structure mainly occur close to the site of the mutation, and, hence, that it is possible to make a residue-by-residue map of heat exchange in the AChR gating isomerization. The structural correlates of enthalpy changes are discussed for 12 different mutations in the protein. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG)

NASA Astrophysics Data System (ADS)

Masson, Antoine; Kamrath, Michael Z.; Perez, Marta A. S.; Glover, Matthew S.; Rothlisberger, U.; Clemmer, David E.; Rizzo, Thomas R.

2015-09-01

We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational families with collisional cross-sections of 93.8 and 96.8 Å2. After separation, each family is independently analyzed by acquiring the infrared predissociation spectrum of the H2-tagged molecules. The ion mobility and spectroscopic data combined with density functional theory (DFT) based molecular dynamics simulations confirm the presence of one major conformer per family, which arises from cis/ trans isomerization about the proline residue. We induce isomerization between the two conformers by using collisional activation in the drift tube and monitor the evolution of the ion distribution with ion mobility and infrared spectroscopy. While the cis-proline species is the preferred gas-phase structure, its relative population is smaller than that of the trans-proline species in the initial ion mobility drift distribution. This suggests that a portion of the trans-proline ion population is kinetically trapped as a higher energy conformer and may retain structural elements from solution.

Isomeric Detergent Comparison for Membrane Protein Stability: Importance of Inter-Alkyl-Chain Distance and Alkyl Chain Length.

PubMed

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S; Du, Yang; Nielsen, Anne K; Byrne, Bernadette; Kobilka, Brian K; Loland, Claus J; Guan, Lan; Chae, Pil Seok

2016-12-14

Membrane proteins encapsulated by detergent micelles are widely used for structural study. Because of their amphipathic property, detergents have the ability to maintain protein solubility and stability in an aqueous medium. However, conventional detergents have serious limitations in their scope and utility, particularly for eukaryotic membrane proteins and membrane protein complexes. Thus, a number of new agents have been devised; some have made significant contributions to membrane protein structural studies. However, few detergent design principles are available. In this study, we prepared meta and ortho isomers of the previously reported para-substituted xylene-linked maltoside amphiphiles (XMAs), along with alkyl chain-length variation. The isomeric XMAs were assessed with three membrane proteins, and the meta isomer with a C 12 alkyl chain was most effective at maintaining solubility/stability of the membrane proteins. We propose that interplay between the hydrophile-lipophile balance (HLB) and alkyl chain length is of central importance for high detergent efficacy. In addition, differences in inter-alkyl-chain distance between the isomers influence the ability of the detergents to stabilise membrane proteins. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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

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.

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)).

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.

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

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.

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.

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.

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

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.

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.

Synthesis, crystal structure and antimicrobial activities of two isomeric gold(I) complexes with nitrogen-containing heterocycle and triphenylphosphine ligands, [Au(L)(PPh3)] (HL = pyrazole and imidazole).

PubMed

Nomiya, K; Noguchi, R; Ohsawa, K; Tsuda, K; Oda, M

2000-03-01

Two isomeric gold(I)-triphenylphosphine complexes with nitrogen-containing heterocycles, [Au(L)(PPh3) (HL = pyrazole (1), imidazole (2)) were isolated as colorless cubic crystals for 1 and colorless plate crystals for 2, respectively. The crystal structures of 1 and 2 were determined by single-crystal X-ray diffraction. These complexes were also fully characterized by complete elemental analyses, thermogravimetric/differential thermal analyses (TG/DTA) and FT-IR in the solid state and by solution NMR (31P, 1H and 13C) spectroscopy and molecular weight measurements in acetone solution. These complexes consisted of a monomeric 2-coordinate AuNP core both in the solid state and in solution. The molecular structures of 1 and 2 were compared with those of related gold(I) complexes, [Au(1,2,3-triz)(PPh3)] (3, Htriz = triazole), [Au(1,2,4-triz)(PPh3)]2 (4) as a dimer through a gold(I)-gold(I) bond in the solid state, and [Au(tetz)(PPh3)] (5, Htetz = tetrazole). Selective and effective antimicrobial activities against two gram-positive bacteria (B. subtilis, S. aureus) and modest activities against one yeast (C. albicans) found in these gold(I) complexes 1-4 are noteworthy, in contrast to poor activities observed in the corresponding silver(I) complexes.

Triterpenes and flavonol glucuronides from Oenothera cheiranthifolia.

PubMed

Nakanishi, Tsutomu; Inatomi, Yuka; Murata, Hiroko; Ishida, Syun-Suke; Fujino, Yuri; Miura, Kanako; Yasuno, Yoshito; Inada, Akira; Lang, Frank A; Murata, Jin

2007-02-01

A new ursane-type triterpene, named as cheiranthic acid (1), was isolated from the MeOH extract of whole plants of Oenothera cheiranthifolia (Onagraceae) along with an isomeric pair of known oleanane- and ursane-type triterpenes (arjunolic acid and asiatic acid) and three flavonol glucuronide analogues (quercetin 3-O-glucuronide, its n-butyl ester, and myricetin 3-O-glucuronide). Their structures were elucidated based on spectroscopic evidence.

Rapid determination of the isomeric truxillines in illicit cocaine via capillary gas chromatography/flame ionization detection and their use and implication in the determination of cocaine origin and trafficking routes.

PubMed

Mallette, Jennifer R; Casale, John F

2014-10-17

The isomeric truxillines are a group of minor alkaloids present in all illicit cocaine samples. The relative amount of truxillines in cocaine is indicative of the variety of coca used for cocaine processing, and thus, is useful in source determination. Previously, the determination of isomeric truxillines in cocaine was performed with a gas chromatography/electron capture detection method. However, due to the tedious sample preparation as well as the expense and maintenance required of electron capture detectors, the protocol was converted to a gas chromatography/flame-ionization detection method. Ten truxilline isomers (alpha-, beta-, delta-, epsilon-, gamma-, omega, zeta-, peri-, neo-, and epi-) were quantified relative to a structurally related internal standard, 4',4″-dimethyl-α-truxillic acid dimethyl ester. The method was shown to have a linear response from 0.001 to 1.00 mg/mL and a lower detection limit of 0.001 mg/mL. In this method, the truxillines are directly reduced with lithium aluminum hydride and then acylated with heptafluorobutyric anhydride prior to analysis. The analysis of more than 100 cocaine hydrochloride samples is presented and compared to data obtained by the previous methodology. Authentic cocaine samples obtained from the source countries of Colombia, Bolivia, and Peru were also analyzed, and comparative data on more than 23,000 samples analyzed over the past 10 years with the previous methodology is presented. Published by Elsevier B.V.

Two-dimensional gas chromatography-online hydrogenation for improved characterization of petrochemical samples.

PubMed

Potgieter, H; Bekker, R; Govender, A; Rohwer, E

2016-05-06

The Fischer-Tropsch (FT) process produces a variety of hydrocarbons over a wide carbon number range and during subsequent product workup a large variety of synthetic fuels and chemicals are produced. The complexity of the product slate obtained from this process is well documented and the high temperature FT (HT-FT) process products are spread over gas, oil and water phases. The characterization of these phases is very challenging even when using comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOFMS). Despite the increase in separation power, peak co-elution still occurs when samples containing isomeric compounds are analysed by comprehensive two dimensional GC. The separation of isomeric compounds with the same double bond equivalents is especially difficult since these compounds elute in a similar position on the GC×GC chromatogram and have identical molecular masses and similar fragmentation patterns in their electron ionization (EI) mass spectra. On-line hydrogenation after GC×GC separation is a possible way to distinguish between these isomeric compounds since the number of rings and alkene double bonds can be determined from the mass spectra of the compounds before and after hydrogenation. This paper describes development of a GC×GC method with post column hydrogenation for the determination of the backbone of cyclic/olefinic structures enabling us to differentiate between classes like dienes and cyclic olefins in complex petrochemical streams. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

Use of Fibonacci numbers in lipidomics - Enumerating various classes of fatty acids.

PubMed

Schuster, Stefan; Fichtner, Maximilian; Sasso, Severin

2017-01-10

In lipid biochemistry, a fundamental question is how the potential number of fatty acids increases with their chain length. Here, we show that it grows according to the famous Fibonacci numbers when cis/trans isomerism is neglected. Since the ratio of two consecutive Fibonacci numbers tends to the Golden section, 1.618, organisms can increase fatty acid variability approximately by that factor per carbon atom invested. Moreover, we show that, under consideration of cis/trans isomerism and/or of modification by hydroxy and/or oxo groups, diversity can be described by generalized Fibonacci numbers (e.g. Pell numbers). For the sake of easy comprehension, we deliberately build the proof on the recursive definitions of these number series. Our results should be of interest for mass spectrometry, combinatorial chemistry, synthetic biology, patent applications, use of fatty acids as biomarkers and the theory of evolution. The recursive definition of Fibonacci numbers paves the way to construct all structural formulas of fatty acids in an automated way.

Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations

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

Erdmann, Ewa; Labuda, Marta; Aguirre, Nestor F.

We present a complete exploration of the different fragmentation mechanisms of furan (C 4H 4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H 2 loss processes (this last one was not yet explored). Our results are compared with the existing experimental and theoretical investigations for furan fragmentation. At low energies the first processes to appear are isomerization, which always implies the breakingmore » of one C–O bond and one or several hydrogen transfers; at intermediate energies the fragmentation of the molecular skeleton becomes the most relevant mechanism; and H/H 2 loss is the dominant processes at high energy. However, the three mechanisms are active in very wide energy ranges and, therefore, at most energies there is a competition among them.« less

Furan Fragmentation in the Gas Phase: New Insights from Statistical and Molecular Dynamics Calculations

DOE PAGES

Erdmann, Ewa; Labuda, Marta; Aguirre, Nestor F.; ...

2018-03-15

We present a complete exploration of the different fragmentation mechanisms of furan (C 4H 4O) operating at low and high energies. Three different theoretical approaches are combined to determine the structure of all possible reaction intermediates, many of them not described in previous studies, and a large number of pathways involving three types of fundamental elementary mechanisms: isomerization, fragmentation, and H/H 2 loss processes (this last one was not yet explored). Our results are compared with the existing experimental and theoretical investigations for furan fragmentation. At low energies the first processes to appear are isomerization, which always implies the breakingmore » of one C–O bond and one or several hydrogen transfers; at intermediate energies the fragmentation of the molecular skeleton becomes the most relevant mechanism; and H/H 2 loss is the dominant processes at high energy. However, the three mechanisms are active in very wide energy ranges and, therefore, at most energies there is a competition among them.« less

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.

Acylation of Chiral Alcohols: A Simple Procedure for Chiral GC Analysis.

PubMed

Oromí-Farrús, Mireia; Torres, Mercè; Canela, Ramon

2012-01-01

The use of iodine as a catalyst and either acetic or trifluoroacetic acid as a derivatizing reagent for determining the enantiomeric composition of acyclic and cyclic aliphatic chiral alcohols was investigated. Optimal conditions were selected according to the molar ratio of alcohol to acid, the reaction time, and the reaction temperature. Afterwards, chiral stability of chiral carbons was studied. Although no isomerization was observed when acetic acid was used, partial isomerization was detected with the trifluoroacetic acid. A series of chiral alcohols of a widely varying structural type were then derivatized with acetic acid using the optimal conditions. The resolution of the enantiomeric esters and the free chiral alcohols was measured using a capillary gas chromatograph equipped with a CP Chirasil-DEX CB column. The best resolutions were obtained with 2-pentyl acetates (α = 3.00) and 2-hexyl acetates (α = 1.95). This method provides a very simple and efficient experimental workup procedure for analyzing chiral alcohols by chiral-phase GC.

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.

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.

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

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.

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.

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.

Conversion of glucose to sorbose

DOEpatents

Davis, Mark E.; Gounder, Rajamani

2016-02-09

The present invention is directed to methods for preparing sorbose from glucose, said method comprising: (a) contacting the glucose with a silica-containing structure comprising a zeolite having a topology of a 12 membered-ring or larger, an ordered mesoporous silica material, or an amorphous silica, said structure containing Lewis acidic Ti.sup.4+ or Zr.sup.4+ or both Ti.sup.4+ and Zr.sup.4+ framework centers, said contacting conducted under reaction conditions sufficient to isomerize the glucose to sorbose. The sorbose may be (b) separated or isolated; or (c) converted to ascorbic acid.

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 .

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.

Applications of Second Harmonic and Sum Frequency Generation to Graphite and Silica Type Interfaces.

DTIC Science & Technology

1994-08-01

investigated. The ultrafast barrierless isomerization of an organic dye, Malachite Green, has also been probed with femtosecond time resolution, enabling the... Malachite Green, has also been probed with femtosecond time resolution, enabling the structure of water at various aqueous interfaces to be probed. In...6G at air/aqueous interface ....................................... 7 6. Time-resolved SHG of Malachite Green at air and silica/aqueous interfaces

Polyacetylene, (CH){sub x}, as an Emerging Material for Solar Cell Applications. Final Technical Report, March 19, 1979 - March 18, 1980

DOE R&D Accomplishments Database

Heeger, A. J.; MacDiarmid, A. G.

1980-06-05

Despite great theoretical and technological interest in polyacetylene, (CH){sub x}, the basic features of its band structure have not been unambiguously resolved. Since photoconductivity and optical absorption data have frequently been used to infer information on the band structure of semiconductors, such measurements were carried out on (CH){sub x}. The main results of an extensive study of the photoconductivity (..delta.. sigma{sub ph}) and absorption coefficient (..cap alpha..) in (CH){sub x} are presented. The absence of photoconductivity in cis-(CH){sub x}, despite the similarity in optical properties indicates that ..delta.. sigma/sub ph/ in trans-(CH){sub x} is induced by isomerization. It is found that isomerization generates states deep inside the gap that act as safe traps for minority carriers and thereby enhance the photoconductivity. Compensation of trans-(CH){sub x} with ammonia appears to decrease the number of safe traps, whereas acceptor doping increases their number. Thus, chemical doping can be used to control the photoconductive response. The energy of safe traps inside the gap is independent of the process used to generate them; indicative of an intrinsic localized defect level in trans-(CH){sub x}. A coherent picture based on the soliton model can explain these results, including the safe trapping.

LC-MS n Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

NASA Astrophysics Data System (ADS)

Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

2011-09-01

Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MS n . The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MS n fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MS n experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MS n methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications.

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores

PubMed Central

Shrestha, Prakash; Emura, Tomoko; Koirala, Deepak; Cui, Yunxi; Hidaka, Kumi; Maximuck, William J; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin

2016-01-01

DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10–35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as ‘mechanophores’ that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators. PMID:27387283

LC-MSn Analysis of Isomeric Chondroitin Sulfate Oligosaccharides Using a Chemical Derivatization Strategy

PubMed Central

Huang, Rongrong; Pomin, Vitor H.; Sharp, Joshua S.

2011-01-01

Improved methods for structural analyses of glycosaminoglycans (GAGs) are required to understand their functional roles in various biological processes. Major challenges in structural characterization of complex GAG oligosaccharides using liquid chromatography-mass spectrometry (LC-MS) include the accurate determination of the patterns of sulfation due to gas-phase losses of the sulfate groups upon collisional activation and inefficient on-line separation of positional sulfation isomers prior to MS/MS analyses. Here, a sequential chemical derivatization procedure including permethylation, desulfation, and acetylation was demonstrated to enable both on-line LC separation of isomeric mixtures of chondroitin sulfate (CS) oligosaccharides and accurate determination of sites of sulfation by MSn. The derivatized oligosaccharides have sulfate groups replaced with acetyl groups, which are sufficiently stable to survive MSn fragmentation and reflect the original sulfation patterns. A standard reversed-phase LC-MS system with a capillary C18 column was used for separation, and MSn experiments using collision-induced dissociation (CID) were performed. Our results indicate that the combination of this derivatization strategy and MSn methodology enables accurate identification of the sulfation isomers of CS hexasaccharides with either saturated or unsaturated nonreducing ends. Moreover, derivatized CS hexasaccharide isomer mixtures become separable by LC-MS method due to different positions of acetyl modifications. PMID:21953261

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.

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

Effect of humidity on solid-state isomerization of various kinds of lactose during grinding.

PubMed

Otsuka, M; Ohtani, H; Otsuka, K; Kaneniwa, N

1993-01-01

The effect of humidity on isomerization during grinding of alpha-monohydrate, alpha-anhydrate and beta-anhydrate of lactose was investigated. Samples were ground in an agate centrifugal ball mill at 270 rev min-1 at room temperature (21 degrees C) and at 5 and 60% relative humidity. Crystallinity of the ground lactose was measured by Hermans' method from the powder X-ray diffraction profiles. The alpha- and beta-lactose content of the ground lactose was measured by using angular rotation spectrophotometry. The crystalline lactose samples were transformed into noncrystalline solids by mechanical stress during grinding. After grinding, the adsorbed water content of all ground lactose samples increased, and the isomerized amount increased with increase of the water content during grinding at 5 and 60% relative humidity. The results suggest that the isomerization rate of alpha-monohydrate during grinding may depend on the crystallinity, but those of alpha- and beta-anhydrate depend on the content of adsorbed water.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Crystal structures and hydrogen bonding in the anhydrous tryptaminium salts of the isomeric (2,4-di­chloro­phen­oxy)acetic and (3,5-di­chloro­phen­oxy)acetic acids

PubMed Central

Smith, Graham; Lynch, Daniel E.

2015-01-01

The anhydrous salts of 2-(1H-indol-3-yl)ethanamine (tryptamine) with isomeric (2,4-di­chloro­phen­oxy)acetic acid (2,4-D) and (3,5-di­chloro­phen­oxy)acetic (3,5-D), both C10H13N2 +·C8H5Cl2O3 − [(I) and (II), respectively], have been determined and their one-dimensional hydrogen-bonded polymeric structures are described. In the crystal of (I), the aminium H atoms are involved in three separate inter-species N—H⋯O hydrogen-bonding inter­actions, two with carboxyl­ate O-atom acceptors and the third in an asymmetric three-centre bidentate carboxyl­ate O,O′ chelate [graph set R 1 2(4)]. The indole H atom forms an N—H⋯Ocarboxyl­ate hydrogen bond, extending the chain structure along the b-axis direction. In (II), two of the three aminium H atoms are also involved in N—H⋯Ocarboxyl­ate hydrogen bonds similar to (I) but with the third, a three-centre asymmetric inter­action with carboxyl­ate and phen­oxy O atoms is found [graph set R 1 2(5)]. The chain polymeric extension is also along b. There are no π–π ring inter­actions in either of the structures. The aminium side-chain conformations differ significantly between the two structures, reflecting the conformational ambivalence of the tryptaminium cation, as found also in the benzoate salts. PMID:26090147

Fragmentation Pathways of Lithiated Hexose Monosaccharides

NASA Astrophysics Data System (ADS)

Abutokaikah, Maha T.; Frye, Joseph W.; Tschampel, John; Rabus, Jordan M.; Bythell, Benjamin J.

2018-05-01

We characterize the primary fragmentation reactions of three isomeric lithiated D-hexose sugars (glucose, galactose, and mannose) utilizing tandem mass spectrometry, regiospecific labeling, and theory. We provide evidence that these three isomers populate similar fragmentation pathways to produce the abundant cross-ring cleavage peaks (0,2A1 and 0,3A1). These pathways are highly consistent with the prior literature (Hofmeister et al. J. Am. Chem. Soc. 113, 5964-5970, 1991, Bythell et al. J. Am. Soc. Mass Spectrom. 28, 688-703, 2017, Rabus et al. Phys. Chem. Chem. Phys. 19, 25643-25652, 2017) and the present labeling data. However, the structure-specific energetics and rate-determining steps of these reactions differ as a function of precursor sugar and anomeric configuration. The lowest energy water loss pathways involve loss of the anomeric oxygen to furnish B1 ions. For glucose and galactose, the lithiated α-anomers generate ketone structures at C2 in a concerted reaction involving a 1,2-migration of the C2-H to the anomeric carbon (C1). In contrast, the β-anomers are predicted to form 1,3-anhydroglucose/galactose B1 ion structures. Initiation of the water loss reactions from each anomeric configuration requires distinct reactive conformers, resulting in different product ion structures. Inversion of the stereochemistry at C2 has marked consequences. Both lithiated mannose forms expel water to form 1,2-anhydromannose B1 ions with the newly formed epoxide group above the ring. Additionally, provided water loss is not instantaneous, the α-anomer can also isomerize to generate a ketone structure at C2 in a concerted reaction involving a 1,2-migration of the C2-H to C1. This product is indistinguishable to that from α-glucose. The energetics and interplay of these pathways are discussed. [Figure not available: see fulltext.

Two isomeric lead(II) carboxylate-phosphonates: syntheses, crystal structures and characterizations

NASA Astrophysics Data System (ADS)

Lei, Chong; Mao, Jiang-Gao; Sun, Yan-Qiong

2004-07-01

Two isomeric layered lead(II) carboxylate-phosphonates of N-(phosphonomethyl)- N-methyl glycine ([MeN(CH 2CO 2H)(CH 2PO 3H 2)]=H 3L), namely, monoclinic Pb 3L 2·H 2O 1 and triclinic Pb 3L 2·H 2O 2, have been synthesized and structurally determined. Compound 1 synthesized by hydrothermal reaction at 150°C is monoclinic, space group C2/ c with a=19.9872(6), b=11.9333(1) and c=15.8399(4) Å, β=110.432(3)°, V=3540.3(1) Å 3, and Z=8. The structure of compound 1 features a <400> layer in which the lead(II) ions are bridged by both phosphonate and carboxylate groups. The lattice water molecules are located between the layers, forming hydrogen bonds with the non-coordinated carboxylate oxygen atoms. Compound 2 with a same empirical formula as compound 1 was synthesized by hydrothermal reaction at 170°C. It has a different layer structure from that of compound 1 due to the adoption of a different coordination mode for the ligand. It crystallizes in the triclinic system, space group P 1¯ with cell parameters of a=7.1370(6), b=11.522(1), c=11.950(1) Å, α=110.280(2), β=91.625(2), γ=95.614(2)°, V=915.3(1) Å 3 and Z=2. The structure of compound 2 features a <020> metal carboxylate-phosphonate double layer built from 1D lead(II) carboxylate chains interconnected with 1D lead(II) phosphonate double chains. XRD powder patterns of compounds 1 and 2 indicate that each compound exists as a single phase.

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.

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.

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.

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.

Post-translational amino acid racemization in the frog skin peptide deltorphin I in the secretion granules of cutaneous serous glands.

PubMed

Auvynet, Constance; Seddiki, Nabila; Dunia, Irene; Nicolas, Pierre; Amiche, Mohamed; Lacombe, Claire

2006-01-01

The dermal glands of the South American hylid frog Phyllomedusa bicolor synthesize and expel huge amounts of cationic, alpha-helical, 24- to 33-residue antimicrobial peptides, the dermaseptins B. These glands also produce a wide array of peptides that are similar to mammalian hormones and neuropeptides, including a heptapeptide opioid containing a D-amino acid, deltorphin I (Tyr-DAla-Phe-Asp-Val-Val-Gly NH2). Its biological activity is due to the racemization of L-Ala2 to D-Ala. The dermaseptins B and deltorphins are all derived from a single family of precursor polypeptides that have an N-terminal preprosequence that is remarkably well conserved, although the progenitor sequences giving rise to mature opioid or antimicrobial peptides are markedly different. Monoclonal and polyclonal antibodies were used to examine the cellular and ultrastructural distributions of deltorphin I and dermaseptin B in the serous glands by immunofluoresence confocal microscopy and immunogold-electron microscopy. Preprodeltorphin I and preprodermaseptins B are sorted into the regulated pathway of secretion, where they are processed to give the mature products. Deltorphin I, [l-Ala2]-deltorphin I and dermaseptin B are all stored together in secretion granules which accumulate in the cytoplasm of all serous glands. We conclude that the L- to D-amino acid isomerization of the deltorphin I occurs in the secretory granules as a post-translational event. Thus the specificity of isomerization depends on the presence of structural and/or conformational determinants in the peptide N-terminus surrounding the isomerization site.

Synthesis and isomerization of acridine substituted 1,3-thiazolidin-4-ones and 4-oxo-1,3-thiazolidin-5-ylidene acetates. An experimental and computational study

NASA Astrophysics Data System (ADS)

Bečka, Michal; Vilková, Mária; Šoral, Michal; Potočňák, Ivan; Breza, Martin; Béres, Tibor; Imrich, Ján

2018-02-01

Acridine thiosemicarbazones 3a-g, obtained through a two-step reaction between aromatic isothiocyanates and hydrazine followed by the treatment with acridin-9-carbaldehyde, in reaction with bifunctional reagents; methyl bromoacetate (MBA) and diethyl acetylenedicarboxylate (DEAD) afforded acridin-thiazolidinone derivatives 4a-g and 7a-f and not their regioisomers 6a-g and 9a-f. Derivatives 4a-g and 7a-f exhibit ZC2N6EN7C8 configuration. Upon standing in DMSO-d6 the thiazolidinones 4a-g and 7a-f spontaneously isomerized into ZC2N6ZN7C8 isomers 5a-g and 8a-f to give a mixture of the both stereoisomers. All compounds were fully characterized by multinuclear NMR, mass spectrometry (MS) and X-ray crystal structure of 4b is also described. X-ray diffraction study revealed that the representative compound 4b crystallized in the monoclinic crystal system with the C2/c space group and Z = 4. Intramolecular C1‧sbnd H1‧⋯N-7 hydrogen bond between the acridine proton H-1‧ and nitrogen N-7 of linker existed. This hydrogen bond is responsible for the E isomerism on C-8 atom which was observed in the NMR experiments. Quantum-chemical calculations and NOESY experiments confirmed ZC2N6ZN7C8 configuration of the transformed stereoisomers 5a-g and 8a-f.

LC-ESI-QTOF-MS based screening and identification of isomeric jujubogenin and pseudojujubogenin aglycones in Bacopa monnieri extract.

PubMed

Nuengchamnong, Nitra; Sookying, Sontaya; Ingkaninan, Kornkanok

2016-09-10

Bacopa monnieri (L.) Wettst. (Scrophulariaceae) is an Ayurvedic medicinal plant used as a memory enhancer. Its major chemical constituents are Bacopa saponins consisting of jujubogenin and pseudojujubogenin glycosides. These two aglycones are isomers different at the positions of prenyl substitution i.e., at C-23 for jujubogenin and at C-22 for pseudojujubogenin. In this study, we demonstrate the rapid and comprehensive characterization of saponin glycosides in B. monnieri using liquid chromatography with electrospray ionization quadrupole time-of-flight mass spectrometer (LC-ESI-QTOF-MS). This shows that ESI-QTOF-MS in positive-ion mode, jujubogenin and pseudojujubogenin glycosides could be discriminated by the peak abundance ratio of m/z 455 [Aglycone+H-H2O](+) to m/z of 473 [Aglycone+H](+). Furthermore, the sequence of sugar moieties can be observed. In a similar manner, the isomeric saponins; deoxyjujubogenin and deoxypseudojujubogenin glycosides can be distinguished using the m/z 437[Aglycone+H-H2O](+) and m/z 455[Aglycone+H](+) peak ratio. Use of the negative-ion mode with MS/MS fragmentation can provide information about the type of sugar linked to the aglycone i.e., at m/z 633 (aglycone+glucose) or at m/z 603 (aglycone+arabinose). With our method, 62 chemical constituents in B. monnieri including saponin glycosides, flavonoids, and alkaloids were identified. This is the first systematic study in structural characterization on isomeric saponins and other metabolites in B. monnieri using ESI-QTOF-MS. Copyright © 2016 Elsevier B.V. All rights reserved.

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

{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.

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.

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.

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.

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-...

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.

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.

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.

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.

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.

Mass Spectrometry Based Identification of Geometric Isomers during Metabolic Stability Study of a New Cytotoxic Sulfonamide Derivatives Supported by Quantitative Structure-Retention Relationships

PubMed Central

Belka, Mariusz; Hewelt-Belka, Weronika; Sławiński, Jarosław; Bączek, Tomasz

2014-01-01

A set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships were applied. Human liver microsomes were used as an in vitro model of metabolism. The biotransformation reactions were tracked by liquid chromatography assay and additionally, fragmentation mass spectra were recorded. In silico molecular modeling at a semi-empirical level was conducted as a starting point for molecular descriptor calculations. A quantitative structure-retention relationship model was built applying multiple linear regression based on selected three-dimensional descriptors. The studied compounds revealed high metabolic stability, with a tendency to form hydroxylated biotransformation products. However, significant chemical instability in conditions simulating human body fluids was noticed. According to literature and MS data geometrical isomerization was suggested. The developed in sillico model was able to describe the relationship between the geometry of isomer pairs and their chromatographic retention properties, thus it supported the hypothesis that the observed pairs of peaks are most likely geometric isomers. However, extensive structural investigations are needed to fully identify isomers’ geometry. An effort to describe MS fragmentation pathways of novel chemical structures is often not enough to propose structures of potent metabolites and products of other chemical reactions that can be observed in compound solutions at early drug discovery studies. The results indicate that the relatively non-expensive and not time- and labor-consuming in sillico approach could be a good supportive tool assisting the identification of cis-trans isomers based on retention data. This methodology can be helpful during the structural identification of biotransformation and degradation products of new chemical entities - potential new drugs. PMID:24893169

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

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.

Light-triggered Supramolecular Isomerism in a Self-catenated Zn(II)-organic Framework: Dynamic Photo-switching CO2 Uptake and Detection of Nitroaromatics.

PubMed

Song, Wei-Chao; Cui, Xun-Zhe; Liu, Zhong-Yi; Yang, En-Cui; Zhao, Xiao-Jun

2016-10-11

A self-catenated Zn(II)-organic framework formulated as [Zn 2 (3,3'-bpeab)(oba) 2 ]·DMF (1) exhibiting a six-connected 4 4 ·6 10 ·8 topology has been successfully synthesized through the mixed-ligand of kinked 3,3'-bis[2-(4-pyridyl)ethenyl]azobenzene (3,3'-bpeab) and 4,4'-oxybis-benzoic acid (H 2 oba) under solvothermal condition. UV light triggers isomerization of complex 1 in a single-crystal-to-single-crystal (SCSC) manner, giving rise to a conformational supramolecular isomer 1_UV through the pedal motion of photoresponsive double bonds. Dynamic photo-switching in the obtained light-responsive supramolecular isomers leads to instantly reversible CO 2 uptake. Furthermore, the ligand originated fluorescence emission of water-resistant complex 1 is selectively sensitive to 4-nitrotoluene (4-NT) owing to a higher quenching efficiency of the perilous explosive over other structurally similar nitroaromatics, prefiguring the potentials of 1 as a fluorescence sensor towards 4-NT in aquatic media.

Light-triggered Supramolecular Isomerism in a Self-catenated Zn(II)-organic Framework: Dynamic Photo-switching CO2 Uptake and Detection of Nitroaromatics

PubMed Central

Song, Wei-Chao; Cui, Xun-Zhe; Liu, Zhong-Yi; Yang, En-Cui; Zhao, Xiao-Jun

2016-01-01

A self-catenated Zn(II)-organic framework formulated as [Zn2(3,3′-bpeab)(oba)2]·DMF (1) exhibiting a six-connected 44·610·8 topology has been successfully synthesized through the mixed-ligand of kinked 3,3′-bis[2-(4-pyridyl)ethenyl]azobenzene (3,3′-bpeab) and 4,4′-oxybis-benzoic acid (H2oba) under solvothermal condition. UV light triggers isomerization of complex 1 in a single-crystal-to-single-crystal (SCSC) manner, giving rise to a conformational supramolecular isomer 1_UV through the pedal motion of photoresponsive double bonds. Dynamic photo-switching in the obtained light-responsive supramolecular isomers leads to instantly reversible CO2 uptake. Furthermore, the ligand originated fluorescence emission of water-resistant complex 1 is selectively sensitive to 4-nitrotoluene (4-NT) owing to a higher quenching efficiency of the perilous explosive over other structurally similar nitroaromatics, prefiguring the potentials of 1 as a fluorescence sensor towards 4-NT in aquatic media. PMID:27725711

Feeding-induced rearrangement of green leaf volatiles reduces moth oviposition

PubMed Central

Allmann, Silke; Späthe, Anna; Bisch-Knaden, Sonja; Kallenbach, Mario; Reinecke, Andreas; Sachse, Silke; Baldwin, Ian T; Hansson, Bill S

2013-01-01

The ability to decrypt volatile plant signals is essential if herbivorous insects are to optimize their choice of host plants for their offspring. Green leaf volatiles (GLVs) constitute a widespread group of defensive plant volatiles that convey a herbivory-specific message via their isomeric composition: feeding of the tobacco hornworm Manduca sexta converts (Z)-3- to (E)-2-GLVs thereby attracting predatory insects. Here we show that this isomer-coded message is monitored by ovipositing M. sexta females. We detected the isomeric shift in the host plant Datura wrightii and performed functional imaging in the primary olfactory center of M. sexta females with GLV structural isomers. We identified two isomer-specific regions responding to either (Z)-3- or (E)-2-hexenyl acetate. Field experiments demonstrated that ovipositing Manduca moths preferred (Z)-3-perfumed D. wrightii over (E)-2-perfumed plants. These results show that (E)-2-GLVs and/or specific (Z)-3/(E)-2-ratios provide information regarding host plant attack by conspecifics that ovipositing hawkmoths use for host plant selection. DOI: http://dx.doi.org/10.7554/eLife.00421.001 PMID:23682312

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Five chiral Cd(II) complexes with dual chiral components: Effect of positional isomerism, luminescence and SHG response

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

Cheng, Lin, E-mail: lcheng@seu.edu.cn; Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, Southeast University, Nanjing 211189; Wang, Jun

2015-01-15

Five chiral Cd(II) complexes with dual chiral components have been synthesized by using a series of (1R,2R)–N{sup 1},N{sup 2}-bis(pyridinylmethyl)cyclohexane-1,2-diamine ligands with different N-positions of pyridyl rings and Cd(NO{sub 3}){sub 2}. The circular dichroism (CD) spectra and second-harmonic generation (SHG) efficiency measurements confirmed that they are of structural chirality in the bulk samples. The luminescent properties indicated that they may have potential applications as optical materials. The formation of discrete mononuclear and binuclear complexes, and one-dimensional chains may be attributed to positional isomerism of the ligands. - Graphical abstract: Five chiral Cd(II) complexes with dual chiral components have been synthesized bymore » using a series of chiral ligands with different N-positions of pyridyl rings. - Highlights: • Five chiral Cd(II) complexes with dual chiral components have been synthesized. • CD spectra and SHG efficiency of the bulk samples have been measured. • The complexes display luminescent properties.« less

Isolation and spectral characterization of thermally generated multi-Z-isomers of lycopene and the theoretically preferred pathway to di-Z-isomers.

PubMed

Honda, Masaki; Kudo, Tatsuya; Kuwa, Takahiro; Higashiura, Takuma; Fukaya, Tetsuya; Inoue, Yoshinori; Kitamura, Chitoshi; Takehara, Munenori

2017-02-01

Lycopene has a large number of geometric isomers caused by E/Z isomerization at arbitrary sites within the 11 conjugated double bonds, offering varying characteristics related to features such as antioxidant capacity and bioavailability. However, the geometric structures of only a few lycopene Z-isomers have been thoroughly identified from natural sources. In this study, seven multi-Z-isomers of lycopene, (9Z,13'Z)-, (5Z,13Z,9'Z)-, (9Z,9'Z)-, (5Z,13'Z)-, (5Z,9'Z)-, (5Z,9Z,5'Z)-, and (5Z,9Z)-lycopene, were obtained from tomato samples by thermal isomerization, and then isolated by elaborate chromatography, and fully assigned using proton nuclear magnetic resonance. Moreover, the theoretically preferred pathway from (all-E)-lycopene to di-Z-isomers was examined with a computational approach using a Gaussian program. Fine-tuning of the HPLC separation conditions led to the discovery of novel multi-Z-isomers, and whose formation was supported by advanced theoretical calculations.

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.

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

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

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)

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.

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.

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.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate.

PubMed

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-10-28

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hnu approximately 2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hnu approximately 2.2 eV and above hnu approximately 4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

Excitation mechanism in the photoisomerization of a surface-bound azobenzene derivative: Role of the metallic substrate

NASA Astrophysics Data System (ADS)

Hagen, Sebastian; Kate, Peter; Leyssner, Felix; Nandi, Dhananjay; Wolf, Martin; Tegeder, Petra

2008-10-01

Two-photon photoemission spectroscopy is employed to elucidate the electronic structure and the excitation mechanism in the photoinduced isomerization of the molecular switch tetra-tert-butyl-azobenzene (TBA) adsorbed on Au(111). Our results demonstrate that the optical excitation and the mechanism of molecular switching at a metal surface is completely different compared to the corresponding process for the free molecule. In contrast to direct (intramolecular) excitation operative in the isomerization in the liquid phase, the conformational change in the surface-bound TBA is driven by a substrate-mediated charge transfer process. We find that photoexcitation above a threshold hν ≈2.2 eV leads to hole formation in the Au d-band followed by a hole transfer to the highest occupied molecular orbital of TBA. This transiently formed positive ion resonance subsequently results in a conformational change. The photon energy dependent photoisomerization cross section exhibit an unusual shape for a photochemical reaction of an adsorbate on a metal surface. It shows a thresholdlike behavior below hν ≈2.2 eV and above hν ≈4.4 eV. These thresholds correspond to the minimum energy required to create single or multiple hot holes in the Au d-bands, respectively. This study provides important new insights into the use of light to control the structure and function of molecular switches in direct contact with metal electrodes.

Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations

PubMed Central

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong

2015-01-01

The phenazine biosynthetic pathway is of considerable importance for the pharmaceutical industry. The pathway produces two products: phenazine-1,6-dicarboxylic acid and phenazine-1-carboxylic acid. PhzF is an isomerase that catalyzes trans-2,3-dihydro-3-hydroxyanthranilic acid isomerization and plays an essential role in the phenazine biosynthetic pathway. Although the PhzF crystal structure has been determined recently, an understanding of the detailed catalytic mechanism and the roles of key catalytic residues are still lacking. In this study, a computational strategy using a combination of molecular modeling, molecular dynamics simulations, and quantum mechanics/molecular mechanics simulations was used to elucidate these important issues. The Apo enzyme, enzyme–substrate complexes with negatively charged Glu45, enzyme–transition state analog inhibitor complexes with neutral Glu45, and enzyme–product complexes with negatively charged Glu45 structures were optimized and modeled using a 200 ns molecular dynamics simulation. Residues such as Gly73, His74, Asp208, Gly212, Ser213, and water, which play important roles in ligand binding and the isomerization reaction, were comprehensively investigated. Our results suggest that the Glu45 residue at the active site of PhzF acts as a general base/acid catalyst during proton transfer. This study provides new insights into the detailed catalytic mechanism of PhzF and the results have important implications for PhzF modification. PMID:26414009

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

Synthesis and NMR analysis of model compounds related to fucosylated chondroitin sulfates: GalNAc and Fuc(1 → 6)GalNAc derivatives.

PubMed

Vinnitskiy, Dmitry Z; Ustyuzhanina, Nadezhda E; Dmitrenok, Andrey S; Shashkov, Alexander S; Nifantiev, Nikolay E

2017-01-13

Unsubstituted and 6-O-α-L-fucosylated propyl 2-acetamido-2-deoxy-β-D-galactopyranosides and their selectively O-sulfated (both in GalNAc and Fuc units) derivatives were synthesized as model compounds representing the fragments of fucosylated chondroitin sulfates (FCS) from sea cucumbers. Per-O-acetylated 2-deoxy-2-N-phthalimido-D-glucopyranose was used as a key precursor for the preparation of all 2-acetamido-2-deoxy-D-galactopyranoside containing products. Attempts at 6-O-glycosylation of propyl 3-O-benzoyl-2-deoxy-2-N-phthalimido-D-galactoside by 2-O-benzyl-3,4-di-O-chloracetyl-L-fucosyl trichloracetimidate in the presence of TMSOTf gave a 1:1 mixture of the corresponding α- and β-isomeric disaccharides, while the use of structurally related fucosyl bromide donor with promotion by Bu 4 NBr led to the formation of desired α-isomeric disaccharide exclusively. Selective removal of orthogonal O-protections permitted subsequent O-sulfation both at the GalNAc and Fuc units. Further removal of blocking groups yielded the target products which were systematically studied by 1 H and 13 C NMR spectroscopy in order to determine the spectral effects of O-sulfation and α-L-fucosylation needed for the development of computer assisted structural analysis of natural FCS. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores.

PubMed

Shrestha, Prakash; Emura, Tomoko; Koirala, Deepak; Cui, Yunxi; Hidaka, Kumi; Maximuck, William J; Endo, Masayuki; Sugiyama, Hiroshi; Mao, Hanbin

2016-08-19

DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10-35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as 'mechanophores' that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interpolating moving least-squares methods for fitting potential energy surfaces: using classical trajectories to explore configuration space.

PubMed

Dawes, Richard; Passalacqua, Alessio; Wagner, Albert F; Sewell, Thomas D; Minkoff, Michael; Thompson, Donald L

2009-04-14

We develop two approaches for growing a fitted potential energy surface (PES) by the interpolating moving least-squares (IMLS) technique using classical trajectories. We illustrate both approaches by calculating nitrous acid (HONO) cis-->trans isomerization trajectories under the control of ab initio forces from low-level HF/cc-pVDZ electronic structure calculations. In this illustrative example, as few as 300 ab initio energy/gradient calculations are required to converge the isomerization rate constant at a fixed energy to approximately 10%. Neither approach requires any preliminary electronic structure calculations or initial approximate representation of the PES (beyond information required for trajectory initial conditions). Hessians are not required. Both approaches rely on the fitting error estimation properties of IMLS fits. The first approach, called IMLS-accelerated direct dynamics, propagates individual trajectories directly with no preliminary exploratory trajectories. The PES is grown "on the fly" with the computation of new ab initio data only when a fitting error estimate exceeds a prescribed tight tolerance. The second approach, called dynamics-driven IMLS fitting, uses relatively inexpensive exploratory trajectories to both determine and fit the dynamically accessible configuration space. Once exploratory trajectories no longer find configurations with fitting error estimates higher than the designated accuracy, the IMLS fit is considered to be complete and usable in classical trajectory calculations or other applications.

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.

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond

NASA Astrophysics Data System (ADS)

Samgina, Tatiana Yu; Kovalev, Sergey V.; Tolpina, Miriam D.; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T.

2018-05-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. [Figure not available: see fulltext.

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond.

PubMed

Samgina, Tatiana Yu; Kovalev, Sergey V; Tolpina, Miriam D; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T

2018-05-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS 3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops. Graphical Abstract ᅟ.

Purification and Quantification of an Isomeric Compound in a Mixture by Collisional Excitation in Multistage Mass Spectrometry Experiments.

PubMed

Jeanne Dit Fouque, Dany; Maroto, Alicia; Memboeuf, Antony

2016-11-15

The differentiation, characterization, and quantification of isomers and/or isobars in mixtures is a recurrent problem in mass spectrometry and more generally in analytical chemistry. Here we present a new strategy to assess the purity of a compound that is susceptible to be contaminated with another isomeric side-product in trace levels. Providing one of the isomers is available as pure sample, this new strategy allows the detection of isomeric contamination. This is done thanks to a "gas-phase collisional purification" inside an ion trap mass spectrometer paving the way for an improved analysis of at least similar samples. This strategy consists in using collision induced dissociation (CID) multistage mass spectrometry (MS 2 and MS 3 ) experiments and the survival yield (SY) technique. It has been successfully applied to mixtures of cyclic poly( L -lactide) (PLA) with increasing amounts of its linear topological isomer. Purification in gas phase of PLA mixtures was established based on SY curves obtained in MS 3 mode: all samples gave rise to the same SY curve corresponding then to the pure cyclic component. This new strategy was sensitive enough to detect traces of linear PLA (<3%) in a sample of cyclic PLA that was supposedly pure according to other characterization techniques ( 1 H NMR, MALDI-HRMS, and size-exclusion chromatography). Moreover, in this case, the presence of linear isomer was undetectable according to MS/MS or MS/MS/MS analysis only as fragment ions are also of the same m/z values. This type of approach could easily be implemented in hyphenated mass spectrometric techniques to improve the structural and quantitative analysis of complex samples.

Triphenylamine based reactive coloro/fluorimetric chemosensors: Structural isomerism and solvent dependent sensitivity and selectivity

NASA Astrophysics Data System (ADS)

Kundu, Anu; Anthony, Savarimuthu Philip

2018-01-01

Triphenyl amine based chemosensors, (2-(((2-(9H-carbazol-9-yl)phenyl)imino)methyl)-5-(diphenylamino)phenol (ortho-CPDP) and 2-(((4-(9H-carbazol-9-yl)phenyl)imino)methyl)-5-(diphenylamino)phenol (para-CPDP), showed solvent and isomerism dependent selective coloro/fluorometric sensing of multiple metal ions (Fe3 +, Al3 + and Zn2 +) with distinguishable responses. In CH3CN, ortho and para-CPDP selectively produced yellow color upon addition of Al3 + and Fe3 + that was slowly disappeared. The yellow color of ortho and para-CPDP in DMF was decolourised selectively by adding Al3 + and Fe3 +. Both ortho and para-CPDP in CH3CN showed nearly similar rate of decolourization for Fe3 + and Al3 +. However, the rate of decolourization of ortho and para-CPDP in DMF was different for Fe3 + (10 μM, 8 min) and Al3 + (5 × 10- 4 M, 40 min) ions. The limit of detection of para-CPDP for Fe3 + is 10 μM and Al3 + 500 μM. The mechanistic studies revealed the imine hydrolysis of ortho and para-CPDP in presence of Lewis acidic Fe3 + and Al3 +. The reactivity based sensing lead to high selectivity for Al3 + and Fe3 + ions. Further, para-CPDP exhibited selective fluorescence turn-on for Zn2 + in DMF (λmax = 513 nm) and detection limit of 6.0 μM. Thus, reactive chemosensors, ortho and para-CPDP, exhibited selective and distinguishable colorimetric sensing of Fe3 + and Al3 + ions and isomerism and solvent dependent fluorescence sensing of Zn2 +.

EThcD Discrimination of Isomeric Leucine/Isoleucine Residues in Sequencing of the Intact Skin Frog Peptides with Intramolecular Disulfide Bond

NASA Astrophysics Data System (ADS)

Samgina, Tatiana Yu; Kovalev, Sergey V.; Tolpina, Miriam D.; Trebse, Polonca; Torkar, Gregor; Lebedev, Albert T.

2018-01-01

Our scientific interests involve de novo sequencing of non-tryptic natural amphibian skin peptides including those with intramolecular S-S bond by means of exclusively mass spectrometry. Reliable discrimination of the isomeric leucine/isoleucine residues during peptide sequencing by means of mass spectrometry represents a bottleneck in the workflow for complete automation of the primary structure elucidation of these compounds. MS3 is capable of solving the problem. Earlier we demonstrated the advanced efficiency of ETD-HCD method to discriminate Leu/Ile in individual peptides by consecutive application of ETD to the polyprotonated peptides followed by HCD applied to the manually selected primary z-ions with the targeted isomeric residues at their N-termini and registration of the characteristic w-ions. Later this approach was extended to deal with several (4-7) broad band mass ranges, without special isolation of the primary z-ions. The present paper demonstrates an advanced version of this method when EThcD is applied in the whole mass range to a complex mixture of natural non-tryptic peptides without their separation and intermediate isolation of the targeted z-ions. The proposed EThcD method showed over 81% efficiency for the large natural peptides with intact disulfide ring, while the interfering process of radical site migration is suppressed. Due to higher speed and sensitivity, the proposed EThcD approach facilitates the analytical procedure and allows for the automation of the entire experiment and data processing. Moreover, in some cases it gives a chance to establish the nature of the residues in the intact intramolecular disulfide loops.

Isomerization Reaction of mer- to fac-Tris(2-phenylpyridinato-N,C2')Iridium(III) Monitored by Using Surface-Enhanced Raman Spectroscopy.

PubMed

Wu, Bo-Han; Huang, Min-Jie; Lai, Cheng-Chang; Cheng, Chien-Hong; Chen, I-Chia

2018-04-16

We developed a new method by enclosing the complex tris(2-phenylpyridinato-N,C2')Iridium(III), Ir(ppy) 3 with surfactant cetyltrimethylammonium bromide (CATB), coated with a thin layer of silica then bonded to the surface of silver nanoparticle. These samples were used to acquire surface-enhanced Raman scattering (SERS) spectra. The thickness of silica layer was controlled to have efficient phosphorescence quenching and Raman enhancement by metal nanoparticle. The SERS spectra of fac- and mer-Ir(ppy) 3 , recorded at 633 nm excitation, display distinct ring breathing mode features because the total symmetric vibrational bands were enhanced. This provides a convenient means to differentiate these isomers with great sensitivity and to study their isomerization process. A direct conversion reaction of mer- to fac- isomerization is identified with time constant 3.1 min when mer was irradiated with Xe light. Via thermal activation, under moderate conditions (pH 5.5 and 343 K), we observed an intermediate particularly with new bands 320/662 cm -1 after heating for 17.5 h, and then those bands disappeared to form fac-Ir(ppy) 3 . On the basis of DFT calculations, the intermediate is proposed to contain octahedral N-N Ir(ppy) 3 -HO-silica structure; band at 320 cm -1 is assigned to iridium oxygen stretching mode ν Ir-O of this intermediate. Under acidic conditions, pH 1-2 catalyzed by silanol in silica, byproduct with band at 353 cm -1 was observed. According to the SERS bands and the calculation, this byproduct is assigned to be iridium(III) siloxide, and the new band is assigned to ν Ir-O .

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.

Spontaneous translocation of antitumor oxaliplatin, its enantiomeric analogue, and Cisplatin from one strand to another in double-helical DNA.

PubMed

Malina, Jaroslav; Natile, Giovanni; Brabec, Viktor

2013-09-02

Oxaliplatin and cisplatin belong to the class of platinum-based anticancer agents. Formation of DNA adducts by these complexes and the consequences for its structure and function, is the mechanistic paradigm by which these drugs exert their antitumor activity. We show that employing short oligonucleotide duplexes containing single, site-specific 1,3-intrastrand cross-links of oxaliplatin, its enantiomeric analogue, or cisplatin and by using gel electrophoresis that under physiological conditions the coordination bonds between platinum and the N7 position of guanine residues involved in the cross-links of the Pt(II) complexes can be cleaved. This cleavage may lead to linkage isomerization reactions between these metallodrugs and double-helical DNA. For instance, approximately 25 % 1,3-intrastrand cross-links of the platinum complexes isomerized after 192 h (at 310 K in 200 mM NaClO4). Differential scanning calorimetry of duplexes containing single, site-specific cross-links of oxaliplatin, its enantiomeric analogue, and cisplatin reveals that one of the driving forces that leads to the lability of DNA cross-links of these metallodrugs is a difference between the thermodynamic destabilization induced by the cross-link and by the adduct into which it could isomerize. The rearrangements may proceed in the way that cross-links originally formed in one strand of the DNA can spontaneously translocate from one DNA strand to its complementary counterpart, which may evoke walking of the platinum complex on DNA molecule. In addition, the differences in the kinetics of the rearrangement reactions and the thermodynamic destabilization of DNA observed for adducts of oxaliplatin and its enantiomeric analogue confirm that the chirality at the carrier 1,2-diaminocyclohexane ligand can considerably affect structural and other physical properties of DNA adducts and consequently their biological effects. In aggregate, interesting generalization of the results described in this work might be that the migration of oxaliplatin, its enantiomeric analogue, or cisplatin from one strand to another in double-helical DNA controlled by energetic signatures of these agents might contribute to a better understanding of their cytotoxic and mutagenic potential. Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

Alignment and Imaging of the CS2 Dimer Inside Helium Nanodroplets

NASA Astrophysics Data System (ADS)

Pickering, James D.; Shepperson, Benjamin; Hübschmann, Bjarke A. K.; Thorning, Frederik; Stapelfeldt, Henrik

2018-03-01

The carbon disulphide (CS2) dimer is formed inside He nanodroplets and identified using fs laser-induced Coulomb explosion, by observing the CS2+ ion recoil velocity. It is then shown that a 160 ps moderately intense laser pulse can align the dimer in advantageous spatial orientations which allow us to determine the cross-shaped structure of the dimer by analysis of the correlations between the emission angles of the nascent CS2+ and S+ ions, following the explosion process. Our method will enable fs time-resolved structural imaging of weakly bound molecular complexes during conformational isomerization, including formation of exciplexes.

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).

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology.

PubMed

Chow, Sih Yao; Wang, Yung Lin; Hsieh, Yu Chiao; Lee, Guan Chiun; Liaw, Shwu Huey

2017-11-01

Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.

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.

Stereoselective Synthesis of Functionalized Bicyclic Scaffolds by Passerini 3-Center-2-Component Reactions of Cyclic Ketoacids.

PubMed

Cioc, Răzvan C; Estévez, Verónica; van der Niet, Daan J; Vande Velde, Christophe M L; Turrini, Nikolaus G; Hall, Mélanie; Faber, Kurt; Ruijter, Eelco; Orru, Romano V A

2017-03-03

We report the use of bifunctional starting materials (ketoacids) in a diastereoselective Passerini three-center-two-component reaction. Study of the reaction scope revealed the required structural features for stereoselectivity in the isocyanide addition. In this system, an interesting isomerization of the primary Passerini product - the α-carboxamido lactone - into an atypical product, an α-hydroxy imide, was found to occur under acidic conditions. Furthermore, enantioenriched Passerini products can be generated from an enantioenriched ketoacid obtained by chemoenzymatic synthesis.

Molecular structure of the lithium enolate of acetaldehyde

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

Lynch, T.J.; Newcomb, M.; Bergbreiter, D.E.

1980-11-21

Calculations of the structures of isomers of the lithium enolate of acetaldehyde done at the restricted Hartree-Fock level with the HONDO program on the CDC 7600 are reported. Using the standard 4-31 G basis set, these calculations produce excessively large bond angles, and this favors the most open of the three isomeric structures. Including the polarization functions on the carbons and oxygen and using the recent Dunning and Hayes (3s2p/2s) contraction indicates that the chirol enolates are the lowest energy structure. However, the differences of the various enolate structures are small and could be modified by solvent effects. These resultsmore » are proported to suggest that the enolates containing internal ligands may be prepared such that a new chirol center would exist by virtue of the counterion position. (BLM)« less

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.

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.

Hydro-isomerization of n-hexane on bi-functional catalyst: Effect of total and hydrogen partial pressures

NASA Astrophysics Data System (ADS)

Thoa, Dao Thi Kim; Loc, Luu Cam

2017-09-01

The effect of both total pressure and hydrogen partial pressure during n-hexane hydro-isomerization over platinum impregnated on HZSM-5 was studied. n-Hexane hydro-isomerization was conducted at atmospheric pressure and 0.7 MPa to observe the influence of total pressure. In order to see the effect of hydrogen partial pressure, the reaction was taken place at different partial pressure of hydrogen varied from 307 hPa to 718 hPa by dilution with nitrogen to keep the total pressure at 0.1 MPa. Physico-chemical characteristics of catalyst were determined by the methods of nitrogen physi-sorption BET, SEM, XRD, TEM, NH3-TPD, TPR, and Hydrogen Pulse Chemi-sorption. Activity of catalyst in the hydro-isomerization of n-hexane was studied in a micro-flow reactor in the temperature range of 225-325 °C; the molar ratio H2/ hydrocarbon: 5.92, concentration of n-hexane: 9.2 mol.%, GHSV 2698 h-1. The obtained catalyst expressed high acid density, good reducing property, high metal dispersion, and good balance between metallic and acidic sites. It is excellent contact for n-hexane hydro-isomerization. At 250 °C, n-hexane conversion and selectivity were as high as 59-76 % and 85-99 %, respectively. It was found that catalytic activity was promoted either by total pressure or hydrogen partial pressure. At total pressure of 0.7 MPa while hydrogen partial pressure of 718 hPa, catalyst produced 63 RON liquid product containing friendly environmental iso-paraffins which is superior blending stock for green gasoline. Hydrogen did not only preserve catalyst actives by depressing hydrocracking and removing coke precursors but also facilitated hydride transfer step in the bi-functional bi-molecular mechanism.

Crystal Structure and Substrate Specificity of D-Galactose-6-Phosphate Isomerase Complexed with Substrates

PubMed Central

Lee, Jung-Kul; Pan, Cheol-Ho

2013-01-01

D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26), which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD), catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi). Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays. PMID:24015281

Isolation and Spectroscopic Characterization of Reactive Species in Atmospheric and Interstellar Reactions

NASA Astrophysics Data System (ADS)

Relph, Rachael A.

2011-12-01

A critical element to the study of chemical reactions is the characterization of reaction intermediates. Methods have been developed to isolate these transient species in the gas phase and when combined with infrared spectroscopy have proven to be excellent tools for determining the structure and reactivity of key intermediates. The studies presented here exploit these technologies to better understand the chemistry of species involved in atmospheric and interstellar reactions. An excellent example of their utility is in the study of the formation of proton hydrates and HONO in the upper atmosphere by sequential addition of water molecules onto the nitrosonium ion. This reaction only proceeds to products after addition of the fourth water molecule, and isolation and characterization of the intermediate trihydrate, NO+(H 2O)3, shows that this species is formed in three isomeric forms, each with a different water network that controls the degree of bond formation between the nitrosonium ion and an activated water molecule. Many isomeric structures are also seen in the clustering reactions of acetylene which may be a mechanism for the formation of benzene cation in interstellar space. The spectroscopy of the trimer, (C2H2)3 + indicates that this species exists in two major isomer classes; covalent forms, one of which may be benzene, and an ion-molecule complex, comprised of a loosely bound acetylene on a dimer core. Interestingly, this dimer core is different from the cyclobutadiene-like structure observed in dimerized acetylene, and proves to be a robust species on the potential energy surface as it survives further clustering events. Two structural isomers of CO3 -and NO3 - are also investigated, and found to have drastically different infrared spectra which are analyzed in the context of their electronic structure. Isomers in these systems are prepared under different expansion conditions which accounts for their unique spectral signatures.

Left atrial isomerism in the adolescence: report of two cases.

PubMed

Liu, C Y; Chiu, I S; Chen, J J; Hung, C R; Lien, W P

1991-01-01

Atrial isomerism is very rare in adolescence. Two cases of left atrial isomerism are reported here in 2 females, aged 21 and 19 years. They had presented with cyanosis and dyspnea since childhood. High kilovoltage filter films showed a bilateral morphologically left bronchus. Cardiac catheterization in Case 1 revealed normal pulmonary artery pressure, severe subvalvular pulmonic stenosis, a double outlet right ventricle, a significant oxygen step-up at the atrial level and moderate systemic oxygen desaturation; while Case 2 disclosed pulmonary hypertension and mild systemic oxygen desaturation. Both cases had the following anatomical features: ipsilateral connection of pulmonary veins to the bilateral morphological left atrium; interrupted inferior vena cave with azygos or hemiazygos continuation; total anomalous hepatic venous return to the right-sided atrium; complete atrioventricular canal. The diagnoses were confirmed in both cases at surgical correction.

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.

Stability of lycopene during food processing and storage.

PubMed

Xianquan, S; Shi, J; Kakuda, Y; Yueming, J

2005-01-01

With an increasing understanding of the health benefit of lycopene, how to preserve lycopene during food processing and storage has caused much attention. Lycopene belongs to the carotenoid family and mostly exists in nature as the all-trans form. Heat, light, oxygen, and different food matrices are factors that have an effect on lycopene isomerization and autooxidation. Lycopene may isomerize to mono- or poly-cis forms with the presence of heat or oil or during dehydration. Reisomerization takes place during storage. After oxidation, the lycopene molecule split, which causes loss of color and off-flavor. The effects of heat, oxygen, light, and the presence of oil on the stability of lycopene are uniform in much of the literature; however, controversy still exists on some details, such as the conditions causing the occurrence of isomerization, the optimal moisture, and temperature for storage.

A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.

PubMed

Nosrati, Meisam; Berbasova, Tetyana; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H

2016-07-20

The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.

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.

Contra-Thermodynamic, Photocatalytic E→Z Isomerization of Styrenyl Boron Species: Vectors to Facilitate Exploration of Two-Dimensional Chemical Space.

PubMed

Molloy, John J; Metternich, Jan B; Daniliuc, Constantin G; Watson, Allan J B; Gilmour, Ryan

2018-03-12

Designing strategies to access stereodefined olefinic organoboron species is an important synthetic challenge. Despite significant advances, there is a striking paucity of routes to Z-α-substituted styrenyl organoborons. Herein, this strategic imbalance is redressed by exploiting the polarity of the C(sp 2 )-B bond to activate the neighboring π system, thus enabling a mild, traceless photocatalytic isomerization of readily accessible E-α-substituted styrenyl BPins to generate the corresponding Z-isomers with high fidelity. Preliminary validation of this contra-thermodynamic E→Z isomerization is demonstrated in a series of stereoretentive transformations to generate Z-configured trisubstituted alkenes, as well as in a concise synthesis of the anti-tumor agent Combretastatin A4. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins.

PubMed

Das, Sreetama; Bhadra, Pratiti; Ramakumar, Suryanarayanarao; Pal, Debnath

2017-08-04

cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomerization of cis-peptide to trans form for molecular activity. Hence we have incorporated both static (cis-peptide) and dynamics information to improve the prediction of protein molecular function. Our results show that cis-peptide information alone cannot detect functional matches in cases where cis-trans isomerization exists but 3D coordinates have been obtained for only the trans isomer or when the cis-peptide bond is incorrectly assigned as trans. On the contrary, use of dynamics information alone includes false-positive matches for cases where fragments with similar secondary structure show similar dynamics, but the proteins do not share a common function. Combining the two methods reduces errors while detecting the true matches, thereby enhancing the utility of our method in function annotation. A combined approach, therefore, opens up new avenues of improving existing automated function annotation methodologies.

Characteristics of the isomeric flavonoids apigenin and genistein binding to hemoglobin by spectroscopic methods

NASA Astrophysics Data System (ADS)

Yuan, Jiang-Lan; Liu, Hui; Kang, Xu; Lv, Zhong; Zou, Guo-Lin

2008-11-01

Apigenin (Ap) and genistein (Ge), a couple of isomeric flavonoids with extensive bioactivities, are the most common dietary ingredients. They have been widely investigated due to their potential therapeutic actions for some diseases. In our work, binding characteristics of Ap and Ge to hemoglobin (Hb) were analyzed with fluorescence spectroscopy, circular dichroism (CD) and UV-vis absorption spectroscopy. The results indicated that Ap and Ge caused strong fluorescence quenching of Hb by static quenching mechanism, but their quenching efficiency and mechanisms were different. The binding site n suggested that there was a single binding site in Hb for Ap and Ge. The results of synchronous fluorescence showed that the microenvironment around Tyr residues of Hb had a slight trend of polarity decreasing, but the polarity around Trp residues increased by adding Ap. Results of CD indicated that the Ap and Ge did not changed the secondary structure of Hb. According to the theory of Förster resonance energy transfer, the binding distance r between Trp 37 and Ap/Ge was predicted to be 3.4 nm and 3.32 nm, respectively. The affinity of Ge toward Hb was higher than that of Ap.

Electron Anisotropy as a Signature of Mode Specific Isomerization in Vinylidene

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

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

Holliday, Michael; Zhang, Fengli; Isern, Nancy G.

2014-04-01

Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerizationmore » reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.« less

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.

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

PubMed

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

2013-08-26

Bump the base: This study reports the discovery of the base-induced Z-to-E isomerization of exo-glycals bearing an electron-withdrawing group (EWG). The scope of this novel transformation regarding the carbohydrate unit is also discussed. After elucidating the mechanism, preparation of novel (E)-exo- glycals was performed (TBS = tert-butyldimethylsilyl). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Differential Selectivity of the Escherichia coli Cell Membrane Shifts the Equilibrium for the Enzyme-Catalyzed Isomerization of Galactose to Tagatose▿

PubMed Central

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-01-01

An Escherichia coli galactose kinase gene knockout (ΔgalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the ΔgalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37°C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A ΔmglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions. PMID:18263746

Differential selectivity of the Escherichia coli cell membrane shifts the equilibrium for the enzyme-catalyzed isomerization of galactose to tagatose.

PubMed

Kim, Jin-Ha; Lim, Byung-Chul; Yeom, Soo-Jin; Kim, Yeong-Su; Kim, Hye-Jung; Lee, Jung-Kul; Lee, Sook-Hee; Kim, Seon-Won; Oh, Deok-Kun

2008-04-01

An Escherichia coli galactose kinase gene knockout (DeltagalK) strain, which contains the l-arabinose isomerase gene (araA) to isomerize d-galactose to d-tagatose, showed a high conversion yield of tagatose compared with the original galK strain because galactose was not metabolized by endogenous galactose kinase. In whole cells of the DeltagalK strain, the isomerase-catalyzed reaction exhibited an equilibrium shift toward tagatose, producing a tagatose fraction of 68% at 37 degrees C, whereas the purified l-arabinose isomerase gave a tagatose equilibrium fraction of 36%. These equilibrium fractions are close to those predicted from the measured equilibrium constants of the isomerization reaction catalyzed in whole cells and by the purified enzyme. The equilibrium shift in these cells resulted from the higher uptake and lower release rates for galactose, which is a common sugar substrate, than for tagatose, which is a rare sugar product. A DeltamglB mutant had decreased uptake rates for galactose and tagatose, indicating that a methylgalactoside transport system, MglABC, is the primary contributing transporter for the sugars. In the present study, whole-cell conversion using differential selectivity of the cell membrane was proposed as a method for shifting the equilibrium in sugar isomerization reactions.

An efficient process for obtaining prebiotic oligosaccharides derived from lactulose using isomerized and purified whey permeate.

PubMed

Sabater, Carlos; Olano, Agustín; Prodanov, Marin; Montilla, Antonia; Corzo, Nieves

2017-12-01

One of the most promising uses of whey permeate (WP) is the synthesis of prebiotic oligosaccharides. Herein, commercial WP was submitted to chemical isomerization catalysed by sodium borate at an alkaline pH and subsequent purification using anion-exchange resins to remove boron. Subsequently, purified mixtures were used to synthesize prebiotic oligosaccharides using β-galactosidase from Bacillus circulans. Isomerization of concentrated WP (200 g L -1 lactose) gave rise to levels of lactulose up to 155.5 g L -1 after 30 min of reaction (molar ratio of boron/lactose, 1/1; pH 12; 70 °C). Boron was removed from the isomerized WP (IWP) using the combination of a strong acid (IR-120, H + ) and a weak base (IRA-743) anion-exchange resins, reducing its level to <1 ppm, without loss of lactulose. During the transglycosylation reaction of purified IWP (lactose/lactulose ratio, 1/2.4) maximum content of prebiotic compounds was achieved, i.e. 690 g kg -1 WP after 3 h of reaction. This study shows that combined chemical-enzymatic reactions together with the purification of IWP results in an efficient synthesis of prebiotic oligosaccharides. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Mechanisms of glucagon degradation at alkaline pH.

PubMed

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

2013-07-01

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. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

Kinetic and Thermodynamic Rationale for SAHA Being a Preferential Human HDAC8 Inhibitor as Compared to the Structurally Similar Ligand, TSA

PubMed Central

Singh, Raushan K.; Lall, Naveena; Leedahl, Travis S.; McGillivray, Abigail; Mandal, Tanmay; Haldar, Manas; Mallik, Sanku; Cook, Gregory; Srivastava, D.K.

2013-01-01

Of the different hydroxamate-based histone deacetylase (HDAC) inhibitors, Suberoylanilide hydroxamic acid (SAHA) has been approved by the FDA for treatment of T-cell lymphoma. Interestingly, a structurally similar inhibitor, Trichostatin A (TSA), which has a higher in vitro inhibitory-potency against HDAC8, reportedly shows a poor efficacy in clinical settings. In order to gain the molecular insight into the above discriminatory feature, we performed transient kinetic and isothermal titration calorimetric studies for the interaction of SAHA and TSA to the recombinant form of human HDAC8. The transient kinetic data revealed that the binding of both the inhibitors to the enzyme showed the biphasic profiles, which represented an initial encounter of enzyme with the inhibitor followed by the isomerization of the transient enzyme-inhibitor complexes. The temperature-dependent transient kinetic studies with the above inhibitors revealed that the bimolecular process is primarily dominated by favorable enthalpic changes, as opposed to the isomerization step; which is solely contributed by entropic changes. The standard binding-enthalpy (ΔH0) of SAHA, deduced from the transient kinetic as well as the isothermal titration calorimetric experiments, was 2–3 kcal/mol higher as compared to TSA. The experimental data presented herein suggests that SAHA serves as a preferential (target-specific/selective) HDAC8 inhibitor as compared to TSA. Arguments are presented that the detailed kinetic and thermodynamic studies may guide in the rational design of HDAC inhibitors as therapeutic agents. PMID:24079912

Photoelectron velocity-map imaging spectroscopic and theoretical study on the reactivity of the gold atom toward CH3SH, CH3OH, and H2O.

PubMed

Qin, Zhengbo; Cong, Ran; Wu, Xia; Liu, Zhiling; Xie, Hua; Tang, Zichao; Jiang, Ling; Fan, Hongjun

2013-07-21

Photoelectron velocity-map imaging spectroscopy has been used to study the reaction of the anionic gold atom with the HR (R = SCH3, OCH3, OH) molecules. The solvated [Au···HR](-) and inserted [HAuR](-) products have been experimentally observed for R = SCH3, whereas only solvated [Au⋯HR](-) products were found for R = OCH3 and OH. This significant difference in the photoelectron spectra suggests the different reactivity of the Au(-) toward the CH3SH, CH3OH, and H2O molecules. Second order Møller-Plesset perturbation theory and coupled-cluster single double triple excitation calculations have been performed to aid the structural assignment of the spectra and to explore the reaction mechanism. Activation energies for the isomerizations of the solvated structures to the inserted ones in the Au(-)∕Au + HR reactions (R = OCH3 and OH) are predicted to be much higher than those for the Au(-)∕Au + CH3SH reactions, supporting the experimental observation. Theoretical calculations provide the evidence that the intriguing [HAuSCH3](-) product may be formed by the attachment of the electron onto the neutral HAuSCH3 species or the isomerization from the anionic [Au···HSCH3](-) one. These findings should be helpful for understanding the feature that the thiols are able to form the staple motifs, whereas CH3OH and H2O are not.

Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1995-01-01

The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBrO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

Ab Initio Characterization of Triatomic Bromine Molecules of Potential Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee. Timothy J.

1995-01-01

The equilibrium structures, harmonic vibrational frequencies, quadratic force fields, dipole moments, and IR intensities of several triatomic bromine compounds of known or potential importance in stratospheric ozone depletion chemistry have been determined using the CCSD(T) electron correlation method in conjunction with a basis set of triple zeta double polarized (TZ2P) quality. Specifically, the molecules included in the present study are HOBr, HBrO, FOBr, FBrO, BrNO, BrON, Br2O, BrBrO, BrCN, BrNC, ClOBr, ClBrO, and BrClO. Very accurate isomeric energy differences have also been determined at the CCSD(T) level with atomic natural orbital basis sets that include through g-type functions. In most cases, the isomer with a normal neutral Lewis dot structure is the lowest energy form, with the single exception that FBRO is predicted to be 11.1 kcal/mol (0 K) lower in energy than FOBr. In all cases, however, the hypervalent isomer is more stable relative to the isomer with a normal Lewis dot structure as compared to the chlorine analogs. Consistent with this observation, the energy of the last three molecules given above increases in the order ClOBr less than ClBrO less than BrClO. The CCSD(T)/TZ2P geometries and vibrational frequencies are in good agreement with the available experimental data. Heats of formation are determined for all species using a combination of theoretical isomeric, homodesmic, and isodesmic reaction energies. The accuracy of these quantities is ultimately dependent on the reliability of the experimental heat of formation of HOBr.

Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations

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

Deng, Liulin; Webb, Ian K.; Garimella, Sandilya V. B.

Ion mobility (IM) separations have a broad range of analytical applications, but insufficient resolution limits many applications. Here we report on traveling wave (TW) ion mobility (IM) separations in a Serpentine Ultra-long Path with Extended Routing (SUPER) Structures for Lossless Ion Manipulations (SLIM) module in conjunction with mass spectrometry (MS). The extended routing utilized multiple passes was facilitated by the introduction of a lossless ion switch at the end of the ion path that either directed ions to the MS detector or to another pass through the serpentine separation region, providing theoretically unlimited TWIM path lengths. Ions were confined inmore » the SLIM by rf fields in conjunction with a DC guard bias, enabling essentially lossless TW transmission over greatly extended paths (e.g., ~1094 meters over 81 passes through the 13.5 m serpentine path). In this multi-pass SUPER TWIM provided resolution approximately proportional to the square root of the number of passes (or path length). More than 30-fold higher IM resolution for Agilent tuning mix m/z 622 and 922 ions (~340 vs. ~10) was achieved for 40 passes compared to commercially available drift tube IM and other TWIM-based platforms. An initial evaluation of the isomeric sugars Lacto-N-hexaose and Lacto-N-neohexaose showed the isomeric structures to be baseline resolved, and a new conformational feature for Lacto-N-neohexaose was revealed after 9 passes. The new SLIM SUPER high resolution TWIM platform has broad utility in conjunction with MS and is expected to enable a broad range of previously challenging or intractable separations.« less

Topologically identical, but geometrically isomeric layers in hydrous α-, β-Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O and anhydrous Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})

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

Yu, Na; Klepov, Vladislav V.; Villa, Eric M.

2014-07-01

The hydrothermal reaction of uranyl nitrate with rubidium nitrate and arsenic (III) oxide results in the formation of polymorphic α- and β-Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O (α-, β-RbUAs) and the anhydrous phase Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})] (RbUAs). These phases were structurally, chemically and spectroscopically characterized. The structures of all three compounds are based upon topologically identical, but geometrically isomeric layers. The layers are linked with each other by means of the Rb cations and hydrogen bonding. Dehydration experiments demonstrate that water deintercalation from hydrous α- and β-RbUAs yields anhydrous RbUAs via topotactic reactions. - Graphical abstract: Three differentmore » layer geometries observed in the structures of Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})] and α- and β- Rb[UO{sub 2}(AsO{sub 3}OH)(AsO{sub 2}(OH){sub 2})]·H{sub 2}O. Two different coordination environments of uranium polyhedra (types I and II) are shown schematically on the top of the figure. - Highlights: • Three new uranyl arsenates were synthesized from the hydrothermal reactions. • The phases consist of the topologically identical but geometrically different layers. • Topotactic transitions were observed in the processes of mono-hyrates dehydration.« less

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

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.

Broad Separation of Isomeric Lipids by High-Resolution Differential Ion Mobility Spectrometry with Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bowman, Andrew P.; Abzalimov, Rinat R.; Shvartsburg, Alexandre A.

2017-08-01

Maturation of metabolomics has brought a deeper appreciation for the importance of isomeric identity of lipids to their biological role, mirroring that for proteoforms in proteomics. However, full characterization of the lipid isomerism has been thwarted by paucity of rapid and effective analytical tools. A novel approach is ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) at high electric fields, which is more orthogonal to mass spectrometry. Here we broadly explore the power of FAIMS to separate lipid isomers, and find a 75% success rate across the four major types of glycero- and phospho- lipids ( sn, chain length, double bond position, and cis/ trans). The resolved isomers were identified using standards, and (for the first two types) tandem mass spectrometry. These results demonstrate the general merit of incorporating high-resolution FAIMS into lipidomic analyses.

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.

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

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.

d-Tagatose production by permeabilized and immobilized Lactobacillus plantarum using whey permeate.

PubMed

Jayamuthunagai, J; Srisowmeya, G; Chakravarthy, M; Gautam, P

2017-07-01

The aim of the work is to produce d-Tagatose by direct addition of alginate immobilized Lactobacillus plantarum cells to lactose hydrolysed whey permeate. The cells were untreated and immobilized (UIC), permeabilized and immobilized (PIC) and the relative activities were compared with purified l-arabinose isomerase (l-AI) for d-galactose isomerization. Successive lactose hydrolysis by β-galactosidase from Escherichia coli and d-galactose isomerization using l-AI from Lactobacillus plantarum was performed to investigate the in vivo production of d-tagatose in whey permeate. In whey permeate, maximum conversion of 38% and 33% (w/w) d-galactose isomerization by PIC and UIC has been obtained. 162mg/g and 141mg/g of d-tagatose production was recorded in a 48h reaction time at 50°C, pH 7.0 with 5mM Mn 2+ ion concentration in the initial substrate mixture. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mesoporous Aluminosilicate Catalysts for the Selective Isomerization of n-Hexane: The Roles of Surface Acidity and Platinum Metal.

PubMed

Musselwhite, Nathan; Na, Kyungsu; Sabyrov, Kairat; Alayoglu, Selim; Somorjai, Gabor A

2015-08-19

Several types of mesoporous aluminosilicates were synthesized and evaluated in the catalytic isomerization of n-hexane, both with and without Pt nanoparticles loaded into the mesopores. The materials investigated included mesoporous MFI and BEA type zeolites, MCF-17 mesoporous silica, and an aluminum modified MCF-17. The acidity of the materials was investigated through pyridine adsorption and Fourier Transform-Infrared Spectroscopy (FT-IR). It was found that the strong Brönsted acid sites in the micropores of the zeolite catalysts facilitated the cracking of hexane. However, the medium strength acid sites on the Al modified MCF-17 mesoporous silica greatly enhanced the isomerization reaction. Through the loading of different amounts of Pt into the mesopores of the Al modified MCF-17, the relationship between the metal nanoparticles and acidic sites on the support was revealed.

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

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data.

PubMed

Roy Choudhury, Amrita; Sikorska, Emilia; van den Boom, Johannes; Bayer, Peter; Popenda, Łukasz; Szutkowski, Kosma; Jurga, Stefan; Bonomi, Massimiliano; Sali, Andrej; Zhukov, Igor; Passamonti, Sabina; Novič, Marjana

2015-01-01

We present a 3D model of the four transmembrane (TM) helical regions of bilitranslocase (BTL), a structurally uncharacterized protein that transports organic anions across the cell membrane. The model was computed by considering helix-helix interactions as primary constraints, using Monte Carlo simulations. The interactions between the TM2 and TM3 segments have been confirmed by Förster resonance energy transfer (FRET) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy, increasing our confidence in the model. Several insights into the BTL transport mechanism were obtained by analyzing the model. For example, the observed cis-trans Leu-Pro peptide bond isomerization in the TM3 fragment may indicate a key conformational change during anion transport by BTL. Our structural model of BTL may facilitate further studies, including drug discovery.

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

NASA Astrophysics Data System (ADS)

Pietrucci, Fabio; Andreoni, Wanda

2011-08-01

Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

Two new isoarylbenzofuran diglucosides from the root bark of Morus alba.

PubMed

Park, Ji-Hae; Jung, Ye-Jin; Jung, Jae-Woo; Shrestha, Sabina; Han, Daeseok; Lim, Dong Wook; Baek, Nam-In

2015-01-01

Two new arylbenzofuran diglucopyranosides, (2″R)-(-)-moracin-O-5',3″-β-D-diglucopyranoside (1) and (2″R)-(-)-moracin-P-5',2″-β-d-diglucopyranoside (2), along with known arylbenzofurans, moracin M 6-β-D-glucopyranoside (3), and an isomeric mixture of R-(-)-moracin O (4) and R-(-)-moracin P (5), were isolated from the root bark of Morus alba L. The structure of the compounds was elucidated based on mass spectrometry, infrared, 1D and 2D nuclear magnetic resonance spectroscopic data.

Physangulidines A, B, and C: three new antiproliferative withanolides from Physalis angulata L.

PubMed

Jin, Zhuang; Mashuta, Mark S; Stolowich, Neal J; Vaisberg, Abraham J; Stivers, Nicole S; Bates, Paula J; Lewis, Walter H; Hammond, Gerald B

2012-03-02

Bioassay-directed fractionation of the whole plant of Physalis angulata L. afforded three new antiproliferative withanolides with an unusual carbon framework: physangulidines A (1), B (2), and C (3). Structures of the three isomeric withanolides were determined by a combination of HRMS, NMR spectroscopic, and X-ray crystallographic methods. Each has shown significant antiproliferative activity against DU145 prostate cancer cells. Physangulidine A (1) was further tested against a wide range of additional cancer cell lines and found to exhibit significant antiproliferative activity. © 2012 American Chemical Society

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.

Inhibitory effect of chalcone derivatives on recombinant human aldose reductase.

PubMed

Iwata, S; Nagata, N; Omae, A; Yamaguchi, S; Okada, Y; Shibata, S; Okuyama, T

1999-03-01

More than fifty chalcone derivatives were synthesized to examine structure-activity relationships against human aldose reductase. Certain 2',4'-dihydroxychalcone derivatives inhibited human aldose reductase activities, and 2',4',2, 4-tetrahydroxychalcone and 2',4',2-trihydroxychalcone showed potent inhibitory activity with IC50 values of 7.4x10(-9) M and 1.6x10(-7) M, respectively. On the other hand, cis-form chalcones, which were isomerized from the original trans-forms by irradiation of daylight in methanol solution, promoted the activity of human aldose reductase.

A liposomal model that mimics the cutaneous production of vitamin D3. Studies of the mechanism of the membrane-enhanced thermal isomerization of previtamin D3 to vitamin D3

NASA Technical Reports Server (NTRS)

Tian, X. Q.; Holick, M. F.

1999-01-01

We reported previously that the rate of previtamin D3 (preD3) <==> vitamin D3 isomerization was enhanced by about 10 times in the skin compared with that in organic solvents. To elucidate the mechanism by which the rate of this reaction is enhanced in the skin, we developed a liposomal model that mimicked the enhanced isomerization of preD3 to vitamin D3 that was described in human skin. Using this model we studied the effect of changing the polarity of preD3 as well as changing the chain length and the degree of saturation of liposomal phospholipids on the kinetics of preD3 <==> vitamin D3 isomerization. We found that a decrease in the hydrophilic interaction of the preD3 with liposomal phospholipids by an esterification of the 3beta-hydroxy of preD3 (previtamin D3-3beta-acetate) reduced the rate of the isomerization by 67%. The addition of a hydroxyl on C-25 of the hydrophobic side chain (25-hydroxyprevitamin D3), which decreased the hydrophobic interaction of preD3 with the phospholipids, reduced the rate by 87%. In contrast, in an isotropic n-hexane solution, there was little difference among the rates of the conversion of preD3, its 3beta-acetate, and 25-hydroxy derivatives to their corresponding vitamin D3 compounds. We also determined rate constants (k) of preD3 <==> vitamin D3 isomerization in liposomes containing phosphatidylcholines with different carbon chain lengths. The rates of the reaction were found to be enhanced as the number of carbons (Cn) in the hydrocarbon chain of the phospholipids increased from 10 to 18. In conclusion, these results support our hypothesis that amphipathic interactions between preD3 and membrane phospholipids stabilize preD3 in its "cholesterol like" cZc-conformer, the only conformer of preD3 that can convert to vitamin D3. The stronger these interactions were, the more preD3 was likely in its cZc conformation at any moment and the faster was the rate of its conversion to vitamin D3.

Left isomerism syndrome with total anomalous systemic connection.

PubMed

Vo, Anh Tuan; Cao, Khang Dang; Le, Khoi Minh; Nguyen, Dinh Hoang

2017-01-01

We present a case of left isomerism with total anomalous systemic venous connection where the inferior vena cava was absent and all other systemic veins connected abnormally to the left atrium. The right atrium was hypoplastic with an intact atrial septum. Blood flow to the lungs was through a large ventricular septal defect. The diagnosis was made with echocardiography, angiography, and computed tomography. Complete repair was performed successfully, and the 7-year-old patient had an uneventful recovery.

Voltammetric Characterization of Soluble Polyacetylene Derivatives Obtained from the Ring-Opening Metathesis Polymerization (ROMP) of Substituted Cyclooctatetraenes

DTIC Science & Technology

1993-01-15

emct ,t ,n electrochemical cis-trans isomerization on the first voltammetric sweep through either reductive or doping. Spectroelectrochemical studies...predominantly- cis poly-RCOT films was irreversible, and indicated the presence of an electrochemical cis-trans isomerization on the first voltammetric sweep ...electrochemical measurements were performed under N2(g) in a Vacuum Atmospheres dry box. Cyclic voltametry was performed using a 3-electrode configuration in a l

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.

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.

Crystal structures of isomeric 3,5-di-chloro-N-(2,3-di-methyl-phen-yl)benzene-sulfonamide, 3,5-di-chloro-N-(2,6-di-methyl-phen-yl)benzene-sulfonamide and 3,5-di-chloro-N-(3,5-di-methyl-phen-yl)benzene-sulfonamide.

PubMed

Shakuntala, K; Naveen, S; Lokanath, N K; Suchetan, P A

2017-05-01

The crystal structures of three isomeric compounds of formula C 14 H 13 Cl 2 NO 2 S, namely 3,5-di-chloro- N -(2,3-di-methyl-phen-yl)-benzene-sulfonamide (I), 3,5-di-chloro- N -(2,6-di-methyl-phen-yl)benzene-sulfonamide (II) and 3,5-di-chloro- N -(3,5-di-methyl-phen-yl)benzene-sulfonamide (III) are described. The mol-ecules of all the three compounds are U-shaped with the two aromatic rings inclined at 41.3 (6)° in (I), 42.1 (2)° in (II) and 54.4 (3)° in (III). The mol-ecular conformation of (II) is stabilized by intra-molecular C-H⋯O hydrogen bonds and C-H⋯π inter-actions. The crystal structure of (I) features N-H⋯O hydrogen-bonded R 2 2 (8) loops inter-connected via C (7) chains of C-H⋯O inter-actions, forming a three-dimensional architecture. The structure also features π-π inter-actions [ Cg ⋯ Cg = 3.6970 (14) Å]. In (II), N-H⋯O hydrogen-bonded R 2 2 (8) loops are inter-connected via π-π inter-actions [inter-centroid distance = 3.606 (3) Å] to form a one-dimensional architecture running parallel to the a axis. In (III), adjacent C (4) chains of N-H⋯O hydrogen-bonded mol-ecules running parallel to [010] are connected via C-H⋯π inter-actions, forming sheets parallel to the ab plane. Neighbouring sheets are linked via offset π-π inter-actions [inter-centroid distance = 3.8303 (16) Å] to form a three-dimensional architecture.

The Antineoplastic Effect of Nitric Oxide-Donating Acetylsalicylic Acid (NO-ASA) in Chronic Lymphocytic Leukemia (CLL) Cells is Highly Dependent on its Positional Isomerism.

PubMed

Gehrke, Iris; Razavi, Regina; Poll-Wolbeck, Simon Jonas; Berkessel, Albrecht; Hallek, Michael; Kreuzer, Karl-Anton

2011-10-01

Chronic Lymphocytic Leukemia (CLL) is not curable in patients that are not eligible for allogeneic stem cell transplantation. Therefore, new treatment options are highly desirable. Chemically modified nonsteroidal anti-inflammatory drugs (NSAIDs), such as nitric-oxide-donating acetylsalicylic acid (NO-ASA), have been described to possess antineoplastic capacity. Recently, we could demonstrate a potent apoptosis induction in primary CLL cells in vitro and tumor growth inhibition by para-NO-ASA in a xenograft mouse model. However, little is known about the impact of positional isomerism of NO-ASA on its antineoplastic capacity in CLL. Primary CLL cells were treated with the meta-or para-isomer of NO-ASA at varying concentrations and durations. Viability was assessed flow cytometrically by annexin V-FITC/PI staining and by CellTiter-Glo luminescence cell viability assay. Caspase and PARP cleavage as well as involvement of β-catenin/Lef-1 signaling was determined by immunoblotting. For caspase inhibition, BD™ ApoBlock was used. Nude mice were xenografted with JVM3 cells and treated with meta-NO-ASA, para-NO-ASA or vehicle control. The meta-isomer was entirely ineffective in inducing CLL cell apoptosis in concentrations up to 100 μM, while para-NO-ASA acted in the low micromolar range. meta-NO-ASA, in contrast to para-NO-ASA, did not alter caspase activity. While para-NO-ASA action involved inhibition of β-catenin/Lef-1 signaling, meta-NO-ASA did not show any impact on this signaling pathway. Further, meta-NO-ASA did not significantly reduce tumor growth in a CLL xenograft mouse model, while para-NO-ASA was highly potent. We conclude that positional isomerism is crucial for the antineoplastic effect of NO-ASA in CLL. It can be suggested that the para-isomer, but not the meta-isomer, generates a chemical structure which is essential for the neoplastic effect of NO-ASA.

The Antineoplastic Effect of Nitric Oxide-Donating Acetylsalicylic Acid (NO-ASA) in Chronic Lymphocytic Leukemia (CLL) Cells is Highly Dependent on its Positional Isomerism

PubMed Central

Gehrke, Iris; Razavi, Regina; Poll-Wolbeck, Simon Jonas; Berkessel, Albrecht; Hallek, Michael; Kreuzer, Karl-Anton

2011-01-01

Background: Chronic Lymphocytic Leukemia (CLL) is not curable in patients that are not eligible for allogeneic stem cell transplantation. Therefore, new treatment options are highly desirable. Chemically modified nonsteroidal anti-inflammatory drugs (NSAIDs), such as nitric-oxide-donating acetylsalicylic acid (NO-ASA), have been described to possess antineoplastic capacity. Recently, we could demonstrate a potent apoptosis induction in primary CLL cells in vitro and tumor growth inhibition by para-NO-ASA in a xenograft mouse model. However, little is known about the impact of positional isomerism of NO-ASA on its antineoplastic capacity in CLL. Methods: Primary CLL cells were treated with the meta-or para-isomer of NO-ASA at varying concentrations and durations. Viability was assessed flow cytometrically by annexin V-FITC/PI staining and by CellTiter-Glo luminescence cell viability assay. Caspase and PARP cleavage as well as involvement of β-catenin/Lef-1 signaling was determined by immunoblotting. For caspase inhibition, BD™ ApoBlock was used. Nude mice were xenografted with JVM3 cells and treated with meta-NO-ASA, para-NO-ASA or vehicle control. Results: The meta-isomer was entirely ineffective in inducing CLL cell apoptosis in concentrations up to 100 μM, while para-NO-ASA acted in the low micromolar range. meta-NO-ASA, in contrast to para-NO-ASA, did not alter caspase activity. While para-NO-ASA action involved inhibition of β-catenin/Lef-1 signaling, meta-NO-ASA did not show any impact on this signaling pathway. Further, meta-NO-ASA did not significantly reduce tumor growth in a CLL xenograft mouse model, while para-NO-ASA was highly potent. Conclusion: We conclude that positional isomerism is crucial for the antineoplastic effect of NO-ASA in CLL. It can be suggested that the para-isomer, but not the meta-isomer, generates a chemical structure which is essential for the neoplastic effect of NO-ASA. PMID:23556096

In situ {sup 13}C MAS NMR study of n-hexane conversion on Pt and Pd supported on basic materials. II. On the mechanism of isomerization and hydrocracking

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

Ivanova, I.I.; Seirvert, M.; Pasau-Claerbout, A.

{sup 13}C MAS NMR spectroscopy was performed in situ to investigate the mechanisms of n-hexane isomerization and hydrocracking on Pt and Pd supported on Al-stabilized magnesia (Pt/Mg(Al)O and Pd/Mg(Al)O), and Pt on KL zeolite (Pt/KL). All the catalysts had high metal dispersion, the metal particle sizes being 13, 11, and 18 {Angstrom}, respectively. n-Hexane 1-{sup 13}C was used for in situ label tracer experiments. {sup 13}C MAS NMR spectra were obtained during the time course of the reaction at 573 and 653 K. The NMR results were then quantified, and the reaction kinetics were studied. Identification of the primary andmore » secondary labeled reaction products led to the conclusion that both cyclic and bond-shift isomerization mechanisms operate on the three catalysts. In the case of Pt/Mg(Al)O, the cyclic mechanism accounts for 80% of the isomerization products. In the case of Pt/KL and Pd/Mg(Al)O, the contribution of bond-shift reactions increases due to restricted formation of the methylcyclopentane intermediate on the former and to suppressed hydrogenolysis of methylcyclopentane on the latter. A nonselective cyclic isomerization mechanism operates on magnesia catalysts, while on Pt/KL selective bisecondary bond rupturing occurs. Mechanistic pathways of bond-shift and hydrocracking reactions involve both 1,3- and 2,4-metallocyclobutane intermediates in the case of magnesia-supported catalysts, while in the case of the Pt/KL catalyst a 1,3-metallocyclobutane intermediate is preferentially formed. Only terminal scission occurs on Pt/KL. The Pd catalyst demonstrates enhanced activity in demethylation. The observed differences in the mechanistic pathways are explained on the basis of the specific properties of the metal and support. 64 refs., 14 figs., 6 tabs.« less

Dithiol amino acids can structurally shape and enhance the ligand-binding properties of polypeptides

NASA Astrophysics Data System (ADS)

Chen, Shiyu; Gopalakrishnan, Ranganath; Schaer, Tifany; Marger, Fabrice; Hovius, Ruud; Bertrand, Daniel; Pojer, Florence; Heinis, Christian

2014-11-01

The disulfide bonds that form between two cysteine residues are important in defining and rigidifying the structures of proteins and peptides. In polypeptides containing multiple cysteine residues, disulfide isomerization can lead to multiple products with different biological activities. Here, we describe the development of a dithiol amino acid (Dtaa) that can form two disulfide bridges at a single amino acid site. Application of Dtaas to a serine protease inhibitor and a nicotinic acetylcholine receptor inhibitor that contain disulfide constraints enhanced their inhibitory activities 40- and 7.6-fold, respectively. X-ray crystallographic and NMR structure analysis show that the peptide ligands containing Dtaas have retained their native tertiary structures. We furthermore show that replacement of two cysteines by Dtaas can avoid the formation of disulfide bond isomers. With these properties, Dtaas are likely to have broad application in the rational design or directed evolution of peptides and proteins with high activity and stability.

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

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.

Isomer-Specific Hydrogen Bonding as a Design Principle for Bidirectionally Quantitative and Redshifted Hemithioindigo Photoswitches.

PubMed

Zweig, Joshua E; Newhouse, Timothy R

2017-08-16

A new class of bidirectionally quantitative photoswitches based on the hemithioindigo (HTI) scaffold is reported. Incorporation of a pyrrole hydrogen-bond donor leads to a bathochromic shift allowing for quantitative bidirectional isomerization. Additionally, extending conjugation from the electron-rich pyrrole results in quantitative visible-light photoswitches, as well as photoswitches that isomerize with red and near-infrared light. The presence of the hydrogen bond leading to the observed redshift is supported by computational and spectroscopic evidence.

Hepatic venous connection to a persistent inferior caval vein in left isomerism.

PubMed

Guenthard, J; Carvalho, J S; Anderson, R H; Rigby, M L

1990-09-01

In 22 cases of left atrial isomerism studied at the Brompton Hospital, four cases were found to have an unusual arrangement of the abdominal vessels. There was persistence of an inferior caval vein, partially anomalous hepatic venous connection and additional continuation of part of the venous return from the lower body through the azygos venous system. This venous pattern had surgical implications in our index case, since redirection of the inferior caval venous return was necessary.

Synthesis of Triazole Derivatives of Levoglucosenone As Promising Anticancer Agents: Effective Exploration of the Chemical Space through retro-aza-Michael//aza-Michael Isomerizations.

PubMed

Tsai, Yi-Hsuan; Borini Etichetti, Carla M; Di Benedetto, Carolina; Girardini, Javier E; Martins, Felipe Terra; Spanevello, Rolando A; Suárez, Alejandra G; Sarotti, Ariel M

2018-04-06

The design and synthesis of biomass-derived triazoles and the in vitro evaluation as potential anticancer agents are described. The discovery of base-catalyzed retro-aza-Michael//aza-Michael isomerizations allowed the exploration of the chemical space by affording novel types of triazoles, difficult to obtain otherwise. Following this strategy, 2,4-disubstituted 1,2,3-triazoles could be efficiently obtained from the corresponding 1,4-disubstituted analogues.

Folded and unfolded conformations of the omega-3 polyunsaturated fatty acid family: ch(3)ch(2)[ch=chch(2)](b)[ch(2)](m)cooh: first principles study.

PubMed

Law, Jacqueline M S; Szori, Milan; Izsak, Robert; Penke, Botond; Csizmadia, Imre G; Viskolcz, Bela

2006-05-11

Polyunsaturated fatty acids (PUFA) like stearidonic acid (SDA;18:4 n-3) eicosapentaenoic acid (EPA; 20:5 n-3), and docosahexaenoic acid (DHA; 22:6 n-3) and its chain fragment models were studied at B3LYP/6-31G(d) levels of theory. Significant conformations for the cis and trans isomers were selected to obtained the thermodynamic functions (DeltaH, DeltaS, DeltaG) for the cis-trans isomerization and for folding using the B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d) level of theory. The structural analysis shows that there are significant differences in thermodynamic function of the trans- and cis-PUFAs. The trans-cis isomerization energy values reinforce the consistency and the relative accuracy of theoretical model calculations. The observed flexibility of naturally cis PUFAs could be explained by a very special "smooth basin" PES of the motif of sp(2)-sp(3)-sp(2) hybrid states as reported previously (J. Phys. Chem. A 2005, 109, 520-533). We assumed that intrinsic thermodynamic functions may describe this flexible folding process. The folding enthalpy as well as the folding entropy suggests that there is a new role of the cis-PUFAs in membranes: these cis isomers may have a strong influence on membrane stability and permeability. The average length of the cis helix and beta PUFA was approximated. The difference between the lengths of these two structures is approximately 10 A.

Fragmentation pathways of O-alkyl methylphosphonothionocyanidates in the gas phase: toward unambiguous structural characterization of chemicals in the Chemical Weapons Convention framework.

PubMed

Saeidian, Hamid; Babri, Mehran; Ashrafi, Davood; Sarabadani, Mansour; Naseri, Mohammad Taghi

2013-08-01

The electron-impact (EI) mass spectra of a series of O-alkyl methylphosphonothionocyanidates were studied for Chemical Weapons Convention (CWC) purposes. General EI fragmentation pathways were constructed and discussed, and collision-induced dissociation studies of the major EI ions were performed to confirm proposed fragment structures by analyzing fragment ions of deuterated analogs and by use of density functional theory (DFT) calculations. Thiono-thiolo rearrangement, McLafferty-type rearrangement, and a previously unknown intramolecular electrophilic aromatic substitution reaction were observed and confirmed. The study also focused on differentiation of isomeric compounds. Retention indices for all compounds, and an electrophilicity index for several compounds, are reported and interpreted.

Synthesis and application of pyridine-based ambipolar hosts: control of charge balance in organic light emitting devices (OLEDs) by chemical structure modification

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

Koech, Phillip K.; Polikarpov, Evgueni; Rainbolt, James E.

2010-11-05

Pyridine-based host materials were synthesized via Grignard metathesis of bromopyridines to provide the required organometallic reagent. The isomeric hosts (4-(9H-carbazol-9-yl)phenyl)(phenyl)(pyridin-3-yl)phosphine oxide (HM-A4), (5-(9H-carbazol-9-yl)pyridin-2-yl)diphenylphosphine oxide (HM-A5), and (5-(diphenylamino)pyridin-2-yl)diphenylphosphine oxide (HM-A6), (4-(diphenylamino)phenyl)(phenyl)(pyridin-3-yl)phosphine oxide (HM-A8) have similar frontier orbital energies. Organic light emitting devices (OLEDs) fabricated using the series of the host materials demonstrate that small structural modification of the host results in significant change in charge transporting ability.

Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB.

PubMed

Velázquez Escobar, Francisco; Buhrke, David; Fernandez Lopez, Maria; Shenkutie, Sintayehu Manaye; von Horsten, Silke; Essen, Lars-Oliver; Hughes, Jon; Hildebrandt, Peter

2017-05-01

The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr substates, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics. © 2017 Federation of European Biochemical Societies.

Probing peptide fragment ion structures by combining sustained off-resonance collision-induced dissociation and gas-phase H/D exchange (SORI-HDX) in Fourier transform ion-cyclotron resonance (FT-ICR) instruments.

PubMed

Somogyi, Arpád

2008-12-01

The usefulness of gas-phase H/D exchange is demonstrated to probe heterogeneous fragment and parent ion populations. Singly and multiply protonated peptides/proteins were fragmented by using sustained off-resonance irradiation collision-induced dissociation (SORI-CID). The fragments and the surviving precursor ions then all undergo H/D exchange in the gas-phase with either D(2)O or CD(3)OD under the same experimental conditions. Usually, 10 to 60 s of reaction time is adequate to monitor characteristic differences in the H/D exchange kinetic rates. These differences are then correlated to isomeric ion structures. The SORI-HDX method can be used to rapidly test fragment ion structures and provides useful insights into peptide fragmentation mechanisms.

Mapping reversible photoswitching of molecular-resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches.

PubMed

Cho, Duckhyung; Yang, Myungjae; Shin, Narae; Hong, Seunghun

2018-06-07

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular-resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans-to-cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans-to-cis and cis-to-trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general. © 2018 IOP Publishing Ltd.

Synchrotron Photoionization Mass Spectrometry Measurements of Kinetics and Product Formation in the Allyl Radical (H2CCHCH2)Self Reaction

NASA Technical Reports Server (NTRS)

Selby, Talitha M.; Melini, giovanni; Goulay, Fabien; Leone, Stephen R.; Fahr, Askar; Taatjes, Craig A.; Osborn, David L.

2008-01-01

Product channels for the self-reaction of the resonance-stabilized allyl radical, C3H5 + C3H5, have been studied with isomeric specificity at temperatures from 300-600 K and pressures from 1-6 Torr using time-resolved multiplexed photoionization mass spectrometry. Under these conditions 1,5-hexadiene was the only C6H10 product isomer detected. The lack of isomerization of the C6H10 product is in marked contrast to the C6H6 product in the related C3H3 + C3H3 reaction, and is due to the more saturated electronic structure of the C6H10 system. The disproportionation product channel, yielding allene + propene, was also detected, with an upper limit on the branching fraction relative to recombination of 0.03. Analysis of the allyl radical decay at 298 K yielded a total rate coefficient of (2.7 +/- 0.8) x 10(exp -11) cu cm/molecule/s, in good agreement with pre.vious experimental measurements using ultraviolet kinetic absorption spectroscopy and a recent theoretical determination using variable reaction coordinate transition state theory. This result provides independent indirect support for the literature value of the allyl radical ultraviolet absorption cross-section near 223 nm.

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.

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.

Understanding M-ligand bonding and mer-/fac-isomerism in tris(8-hydroxyquinolinate) metallic complexes.

PubMed

Lima, Carlos F R A C; Taveira, Ricardo J S; Costa, José C S; Fernandes, Ana M; Melo, André; Silva, Artur M S; Santos, Luís M N B F

2016-06-28

Tris(8-hydroxyquinolinate) metallic complexes, Mq3, are one of the most important classes of organic semiconductor materials. Herein, the nature of the chemical bond in Mq3 complexes and its implications on their molecular properties were investigated by a combined experimental and computational approach. Various Mq3 complexes, resulting from the alteration of the metal and substitution of the 8-hydroxyquinoline ligand in different positions, were prepared. The mer-/fac-isomerism in Mq3 was explored by FTIR and NMR spectroscopy, evidencing that, irrespective of the substituent, mer- and fac-are the most stable molecular configurations of Al(iii) and In(iii) complexes, respectively. The relative M-ligand bond dissociation energies were evaluated experimentally by electrospray ionization tandem mass spectrometry (ESI-MS-MS), showing a non-monotonous variation along the group (Al > In > Ga). The results reveal a strong covalent character in M-ligand bonding, which allows for through-ligand electron delocalization, and explain the preferred molecular structures of Mq3 complexes as resulting from the interplay between bonding and steric factors. The mer-isomer reduces intraligand repulsions, being preferred for smaller metals, while the fac-isomer is favoured for larger metals where stronger covalent M-ligand bonds can be formed due to more extensive through-ligand conjugation mediated by metal "d" orbitals.

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.

General and Facile Route to Isomerically Pure Tricyclic Peptides Based on Templated Tandem CLIPS/CuAAC Cyclizations.

PubMed

Richelle, Gaston J J; Ori, Sumeet; Hiemstra, Henk; van Maarseveen, Jan H; Timmerman, Peter

2018-01-08

We report a one-pot ligation/cyclization technology for the rapid and clean conversion of linear peptides into tricyclic peptides that is based on using tetravalent scaffolds containing two benzyl bromide and two alkyne moieties. These react via CLIPS/CuAAC reactions with cysteines and azides in the peptide. Flexibility in the scaffolds is key to the formation of isomerically pure products as the flexible scaffolds T4 1 and T4 2 mostly promote the formation of single isomeric tricycles while the rigid scaffolds T4 3 and T4 4 do not yield clean products. There seems to be no limitation to the number and types of amino acids present as 18 canonical amino acids were successfully implemented. We also observed that azides at the peptide termini and cysteine residues in the center gave better results than compounds with the functional groups placed the other way round. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Evidence for tunneling in base-catalyzed isomerization of glyceraldehyde to dihydroxyacetone by hydride shift under formose conditions.

PubMed

Cheng, Liang; Doubleday, Charles; Breslow, Ronald

2015-04-07

Hydrogen atom transfer reactions between the aldose and ketose are key mechanistic features in formose chemistry by which formaldehyde is converted to higher sugars under credible prebiotic conditions. For one of these transformations, we have investigated whether hydrogen tunneling makes a significant contribution to the mechanism by examining the deuterium kinetic isotope effect associated with the hydrogen transfer during the isomerization of glyceraldehyde to the corresponding dihydroxyacetone. To do this, we developed a quantitative HPLC assay that allowed us to measure the apparent large intrinsic kinetic isotope effect. From the Arrhenius plot of the kinetic isotope effect, the ratio of the preexponential factors AH/AD was 0.28 and the difference in activation energies Ea(D) - Ea(H) was 9.1 kJ·mol(-1). All these results imply a significant quantum-mechanical tunneling component in the isomerization mechanism. This is supported by multidimensional tunneling calculations using POLYRATE with small curvature tunneling.

A theoretical study on the mechanistic highlights behind the Brønsted-acid dependent mer-fac isomerization of homoleptic carbenic iridium complexes for PhOLEDs.

PubMed

Setzer, Tobias; Lennartz, Christian; Dreuw, Andreas

2017-06-06

Recently, a successful Brønsted-acid mediated geometric isomerization of the meridional homoleptic carbenic iridium(iii) complexes tris-(N-phenyl,N-methyl-benzimidazol-2-yl)iridium(iii) (1) and tris-(N-phenyl,N-benzyl-benzimidazol-2-yl)iridium(iii) (2) into their facial form has been reported. In the present work the pronounced acid-dependency of this particular isomerization procedure is revisited and additional mechanistic pathways are taken into account. Moreover, the acid-induced material decomposition is addressed. All calculations are carried out using density functional theory (DFT) while the environmental effects in solution are accounted for by the COSMO-RS model. The simulated results clearly reveal the outstanding importance of the complex interplay between acid strength, coordinating power of the corresponding base and the steric influence of the ligand system in contrast to the plain calculation of minimum energy pathways for selected complexes. Eventually, general rules to enhance the material-specific reaction yields are provided.

High-Resolution Mass Spectrometric Analysis of Secondary Organic Aerosol Produced by Ozonation of Limonene

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

Walser, Maggie L.; Dessiaterik, Yury; Laskin, Julia

2008-02-08

Secondary organic aerosol (SOA) particles formed from the ozone-initiated oxidation of limonene are characterized by high-resolution electrospray ionization mass spectrometry in both the positive and negative ion modes. The mass spectra reveal a large number of both monomeric (m/z < 300) and oligomeric (m/z > 300) products of oxidation. A combination of high resolving power (m/Δm ~60,000) and Kendrick mass defect analysis makes it possible to unambiguously determine the composition for hundreds of individual compounds in SOA samples. Van Krevelen analysis shows that the SOA compounds are heavily oxidized, with average O:C ratios of 0.43 and 0.50 determined from themore » positive and negative ion mode spectra, respectively. An extended reaction mechanism for the formation of the first generation SOA molecular components is proposed. The mechanism includes known isomerization and addition reactions of the carbonyl oxide intermediates generated during the ozonation of limonene, and numerous isomerization pathways for alkoxy radicals resulting from the decomposition of unstable carbonyl oxides. The isomerization reactions yield numerous products with a progressively increasing number of alcohol and carbonyl groups, whereas C-C bond scission reactions in alkoxy radicals shorten the carbon chain. Together these reactions yield a large number of isomeric products with broadly distributed masses. A qualitative agreement is found between the number and degree of oxidation of the predicted and measured reaction products in the monomer range.« less

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.

Escherichia coli arabinose isomerase and Staphylococcus aureus tagatose-6-phosphate isomerase: which is a better template for directed evolution of non-natural substrate isomerization?

PubMed

Kim, Hye Jung; Uhm, Tae Guk; Kim, Seong Bo; Kim, Pil

2010-06-01

Metallic and non-metallic isomerases can be used to produce commercially important monosaccharides. To determine which category of isomerase is more suitable as a template for directed evolution to improve enzymes for galactose isomerization, L-arabinose isomerase from Escherichia coli (ECAI; E.C. 5.3.1.4) and tagatose-6-phosphate isomerase from Staphylococcus aureus (SATI; E.C. 5.3.1.26) were chosen as models of a metallic and non-metallic isomerase, respectively. Random mutations were introduced into the genes encoding ECAI and SATI at the same rate, resulting in the generation of 515 mutants of each isomerase. The isomerization activity of each of the mutants toward a non-natural substrate (galactose) was then measured. With an average mutation rate of 0.2 mutations/kb, 47.5% of the mutated ECAIs showed an increase in activity compared with wild-type ECAI, and the remaining 52.5% showed a decrease in activity. Among the mutated SATIs, 58.6% showed an increase in activity, whereas 41.4% showed a decrease in activity. Mutant clones showing a significant change in relative activity were sequenced and specific increases in activity were measured. The maximum increase in activity achieved by mutation of ECAI was 130%, and that for SATI was 190%. Based on these results, the characteristics of the different isomerases are discussed in terms of their usefulness for directed evolution of non-natural substrate isomerization.

Synthesis and characterization of a symmetric bis(7-hydroxyflavylium) containing a methyl viologen bridge.

PubMed

Diniz, Ana M; Pinheiro, Carlos; Petrov, Vesselin; Parola, A Jorge; Pina, Fernando

2011-05-27

A symmetric bis(flavylium) constituted by two 7-hydroxyflavylium moieties linked by a methylviologen bridge was synthesized. The thermodynamic and kinetics of the network of chemical reactions involving bis(flavylium) and the model compound 7-hydroxy-4'-methylflavylium was completely characterized by means of direct and reverse pH jumps (stopped flow) and flash photolysis. Both compounds follow the usual pH-dependent network of chemical reactions of flavylium derivatives. The equilibrium species of the model compound are the flavylium cation (acidic species) and the trans-chalcone (basic species) with an apparent pK'(a)=2.85. In the case of the bis(flavylium) it was possible to characterize by (1)H NMR spectroscopy three species with different degrees of isomerization: all flavylium, flavylium-trans-chalcone, and all trans-chalcone. Representation of the time-dependent mole fraction distribution of these three forms after a pH jump from equilibrated solutions of all-flavylium cation (lower pH values) to higher pH values, shows that formation of trans-chalcone is not completely stochastic (two independent isomerizations), the isomerization of one flavylium showing a small influence on the isomerization of the other. The radical of the methyl viologen bridge is formed upon reduction of the bis(trans-chalcone) with dithionite. The system is reversible after addition of an oxidant in spite of the occurrence of some decomposition. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Potential energy surface of cyclooctatetraene

NASA Astrophysics Data System (ADS)

Andrés, José L.; Castaño, Obis; Morreale, Antonio; Palmeiro, Raul; Gomperts, Roberto

1998-01-01

We present a theoretical study of the cyclooctatetraene (COT) molecule. Seven COT structures are located on the singlet ground state potential energy surface. Four of them, which present D2d (tub), Cs (bicyclo[4.2.0]octa-2,4,7-triene or BOT), C2h (chair) and D4 (crown) symmetries are stable species, and the other three are transition state structures showing Cs, D4h, and D8h symmetry. We discuss the symmetry of wave functions for these stationary points. Geometries, energies, and harmonic vibrational frequencies of these structures, and energy gaps between singlet-triplet states and low-lying singlets are presented. For the planar D4h and D8h structures, Jahn-Teller and tunneling effects have also been discussed. Ring inversion, bond shifting and valence isomerization reactive channels from the tub COT conformer are discussed from the point of view of the corresponding transition state structures. Where possible, in order to lend support to this theoretical information comparisons with recent transition state spectroscopy data are made.

Complete structural characterization of ceramides as [M – H]− ions by multiple-stage linear ion trap mass spectrometry

PubMed Central

Hsu, Fong-Fu

2016-01-01

Ceramide is a huge lipid family consisting of diversified structures including various modifications in the fatty acyl chain and the long chain base (LCB). In this contribution, negative-ion ESI linear ion-trap multiple-stage mass spectrometric method (LIT MSn) towards complete structural determination of ceramides in ten major families characterized as the [M – H]− ions is described. Multiple sets of fragment ions reflecting the fatty acyl chain and LCB were observed in the CID MS2 spectrum, while the sequential MS3 and MS4 spectra contain structural information for locating the double bond and the functional groups, permitting realization of the fragmentation processes. Thereby, differentiation of ceramide molecules varied by chain length, the LCB (sphingosine, phytosphigosine, 6-hydroxy-sphingosine), and by the modification (α-hydroxy-, β-hydroxy-, ω-hydroxy-FA) can be achieved; and many isomeric structures in the biological specimen can be revealed in detail. PMID:27523779

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.

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.

Isomerization of α-pinene in the terpentin oil with TCA/Natural Zeolite using microwave irradiation

NASA Astrophysics Data System (ADS)

Wijayati, N.; Supartono; Kusumastuti, E.

2018-04-01

The catalytic potensial of trichloroacetic acid (TCA)//Natural Zeolite in the isomerization of α-pinene in the terpentin oil was investigated. The purpose of this study is to investigate the influence of the power of microvawe on activity and selectivity of catalyst. The main product were champhene, terpinene, limonene, p-cymene, and terpinolene. The highest selectivity was 28.26% with a conversion of 23.25%, whereas the higher conversion was 98.99% with selectivity of 16.90% at room temperature using power of microwave 640 W.

Relation of the Yield of the Isomeric Pair Te$sup 121$m, Te$sup 121$, Formed in the Nuclear Reaction, Sb$sup 121$(d,2n)Te$sup 121$. Report No. 61; RELACION DE LOS RENDIMENTOS DEL PAR ISOMERICO Te$sup 121$m, Te$sup 121$, FORMADO EN LA REACCION NUCLEAR Sb$sup 121$(d,2N)Te$sup 121$. INFORME NO. 61

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

Nassiff, S.J.; Abecasis, S.; Mocoroa, A.

1961-01-01

The effective cross sections of the isomeric pair, tellurium-121m- tellurium-121 in the reaction antimony121(d,2n)tellurium-121 were determined experimentally for deuteron energies from 9 to 28 Mev. (tr-auth)

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.

Experimental and theoretical IR and Raman spectra of picolinic, nicotinic and isonicotinic acids

NASA Astrophysics Data System (ADS)

Koczoń, P.; Dobrowolski, J. Cz.; Lewandowski, W.; Mazurek, A. P.

2003-07-01

The experimental and theoretical (B3PW91/6-311++G**) vibrational (IR and Raman) spectra of picolinic, nicotinic and isonicotinic acids (pyridine-2-, -3-, and -4-carboxylic acid, respectively) were studied. Three stable calculated structures were found for picolinic acid: the structure with intramolecular hydrogen COOH⋯N bond, and the two without hydrogen bond. For the nicotinic acid two stable theoretical structures differ in orientation of the COOH group with respect to the nitrogen atom, whereas for the isonicotinic acid only one form was stable. The theoretical vibrational spectra of the three acids were interpreted by means of potential energy distributions (PEDs) using VEDA 3 program. Next, selected experimental bands were assigned based on the scaled theoretical wavenumbers. Finally, the wavenumbers and intensities for the three isomeric acids were compared and discussed in terms of location of the carboxylic group.