Iodine-Catalyzed Isomerization of Dimethyl Muconate

Energy Technology Data Exchange (ETDEWEB)

Settle, Amy E [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Berstis, Laura R [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Zhang, Shuting [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Rorrer, Nicholas [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Hu, Haiming [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Richards, Ryan [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Beckham, Gregg T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Crowley, Michael F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Vardon, Derek R [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2018-04-12

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. Density 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. 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 biobased chemicals.

Selective stimulation of conformational conversions in free molecules

International Nuclear Information System (INIS)

Ismailzade, G.I.; Movsumov, I.Z.; Menzeleev, M.R.; Kazymova, S.B.

2014-01-01

Application of double-resonance (RF-MW, IR-MW, MW-MW) methods to enhance studies of unstable isomeric structures was discussed. The use of infrared pump radiation to excite conformational energy levels in order to stimulate selectively conformational conversions and to correct spectral line intensities of separate conformations was substantiated. (authors)

Formation, isomerization, and derivatization of keggin tungstoaluminates.

Science.gov (United States)

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-...

Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

DEFF Research Database (Denmark)

Toxvaerd, Søren

2001-01-01

Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

OpenAIRE

Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

2006-01-01

Dimethyl sulfite has three conformers of low energy, GG, GT and GG0, which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG0 conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ molK1, respectively, while the barriers associated with the GG0/GT and GT/GG isomerizations are 1.90 and 9.64 kJ molK1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonst...

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

Science.gov (United States)

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.

Peptide models of protein metastable binding sites: competitive kinetics of isomerization and hydrolysis.

Science.gov (United States)

Khan, S A; Sekulski, J M; Erickson, B W

1986-09-09

alpha 2-Macroglobulin and the complement components C3 and C4 each contain a metastable binding site that is essential for covalent attachment. Two cyclic peptides are useful models of these unusual protein sites. Five-membered lactam 1 (CH3CO-Gly-Cys-Gly-Glu-Glp-Asn-NH2) contains an internal residue of pyroglutamic acid (Glp). Fifteen-membered thiolactone 2 (CH3CO-Gly-Cys-Gly-Glu-Glu-Asn-NH2 15-thiolactone) contains a thiol ester bond between Cys-2 and Glu-5. These isomeric hexapeptides are spontaneously interconverted in water. Competing with the two isomerization reactions are three reactions involving hydrolysis of 1 and 2. These five processes were found to occur simultaneously under physiologic conditions (phosphate-buffered saline, pH 7.3, 37 degrees C). Best estimates of the five rate constants for these apparent first-order reactions were obtained by comparing the observed molar percentages of peptides 1-4 with those calculated from a set of exponential equations. Both isomerization reactions (ring expansion of 1 to 2, k1 = 6.4 X 10(-5) s-1; ring contraction of 2 to 1, k-1 = 69 X 10(-5) s-1) proceeded faster than any of the hydrolysis reactions: alpha-cleavage of 1 with fragmentation to form dipeptide 3 (k2 = 3.3 X 10(-5) s-1), gamma-cleavage of 1 with ring opening to yield mercapto acid 4 (k3 = 0.35 X 10(-5) s-1), and hydrolysis of 2 with ring opening to give 4 (k4 = 1.9 X 10(-5) s-1). The isomerization rate ratio (k1/k-1 = 10.9) agreed with the isomer ratio at equilibrium (1:2 = 11 starting from 1 and 10 starting from 2). The alpha/gamma regioselectivity ratio (k2/k3 = 9.7) for hydrolysis of the internal Glp residue of 1 was consistent with results for model tripeptides. Part of the chemistry of the protein metastable binding sites can be explained by similar isomerization and hydrolysis reactions.

Structural basis and kinetics of force-induced conformational changes of an αA domain-containing integrin.

Directory of Open Access Journals (Sweden)

Xue Xiang

Full Text Available Integrin α(Lβ₂ (lymphocyte function-associated antigen, LFA-1 bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1 when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 αA domain, determined by the position of its α₇-helix, have been suggested to correspond to three different affinity states for ligand binding.The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD simulations, that the αA domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its α₇-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the αA domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1.Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 αA domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction.

Kinetics of isomerization and inversion of aspartate 58 of αA-crystallin peptide mimics under physiological conditions.

Directory of Open Access Journals (Sweden)

Kenzo Aki

Full Text Available Although proteins consist exclusively of L-amino acids, we have reported that aspartyl (Asp 58 and Asp 151 residues of αA-crystallin of eye lenses from elderly cataract donors are highly inverted and isomerized to D-β, D-α and L-β-Asp residues through succinimide intermediates. Of these Asp isomers, large amounts of D-β- and L-β-isomers are present but the amount of D-α-isomer is not significant. The difference in abundance of the Asp isomers in the protein may be due to the rate constants for the formation of the isomers. However, the kinetics have not been well defined. Therefore, in this study, we synthesized a peptide corresponding to human αA-crystallin residues 55 to 65 (T(55VLD(58SGISEVR(65 and its isomers in which L-α-Asp at position 58 was replaced with L-β-, D-β- and D-α-Asp and determined the rate of isomerization and inversion of Asp residues under physiological conditions (37°C, pH7.4. The rate constant for dehydration from L-α-Asp peptide to L-succinimidyl peptide was 3 times higher than the rate constant for dehydration from L-β-Asp peptide to L-succinimidyl peptide. The rate constant for hydrolysis from L-succinimidyl peptide to L-β-Asp peptide was about 5 times higher than the rate constant for hydrolysis from L-succinimidyl peptide to L-α-Asp peptide. The rate constant for dehydration from L-α-Asp peptide to L-succinimidyl peptide was 2 times higher than the rate constant for dehydration from D-α-Asp peptide to D-succinimidyl peptide. The rate constants for hydrolysis from L-succinimidyl peptide to L-β-Asp peptide and for hydrolysis from D-succinimidyl peptide to D-β-Asp peptide were almost equal. Using these rate constants, we calculated the change in the abundance ratios of the 4 Asp isomers during a human lifespan. This result is consistent with the fact that isomerized Asp residues accumulate in proteins during the ageing process.

Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Science.gov (United States)

Min, Wei; Xie, X. Sunney; Bagchi, Biman

2009-08-01

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Kinetics of conformational changes of fibronectin adsorbed onto model surfaces.

Science.gov (United States)

Baujard-Lamotte, L; Noinville, S; Goubard, F; Marque, P; Pauthe, E

2008-05-01

Fibronectin (FN), a large glycoprotein found in body fluids and in the extracellular matrix, plays a key role in numerous cellular behaviours. We investigate FN adsorption onto hydrophilic bare silica and hydrophobic polystyrene (PS) surfaces using Fourier transform infrared spectroscopy-attenuated total reflection (FTIR-ATR) in aqueous medium. Adsorption kinetics using different bulk concentrations of FN were followed for 2h and the surface density of adsorbed FN and its time-dependent conformational changes were determined. When adsorption occurs onto the hydrophilic surface, FN molecules keep their native conformation independent of the adsorption conditions, but the amount of adsorbed FN increases with time and the bulk concentration. Although the protein surface density is the same on the hydrophobic PS surface, this has a strong impact on the average conformation of the adsorbed FN layer. Indeed, interfacial hydration changes induced by adsorption onto the hydrophobic surface lead to a decrease in unhydrated beta-sheet content and cause an increase in hydrated beta-strand and hydrated random domain content of adsorbed FN. This conformational change is mainly dependent on the bulk concentration. Indeed, at low bulk concentrations, the secondary structures of adsorbed FN molecules undergo strong unfolding, allowing an extended and hydrated conformation of the protein. At high bulk concentrations, the molecular packing reduces the unfolding of the stereoregular structures of the FN molecules, preventing stronger spreading of the protein.

Conformational Analysis of Contrast Media for X-Ray Diagnostic Radiology

International Nuclear Information System (INIS)

Solieman, A.H.M.

2010-01-01

The conformational analysis of iodinated non-ionic contrast agent, Iobitridol, was carried out using theoretical calculations to explore its conformational space, and to study different aspects connected with application of different search techniques. Monte Carlo (MC), random search (RS) and molecular dynamics (MD) based conformational search techniques were used to extract a reasonable-size sample that adequately represents and has an average behavior of the entire conformational ensemble.While MC is good for quick search for lowest energy conformer, RS is better in obtaining conformational sample that cover the whole conformational space and MD is the best for investigation of isomeric preferences inside the conformational ensemble at thermal equilibrium. Conformational analysis of the produced gas phase samples reveals that RS and MD methods could sufficiently present the 18 distinct isomeric classes that constitute the total conformational space of the Iobitridol. S samples of conformational space of Iobitridol are extensively studied, as it hypothetically cover the total conformational space. They are used to test the suitability of different methods (charge distribution methods, energy calculation methods) for Iobitridol molecular computations and internal structure forces (steric hindrance, resonance interaction), as well as dependences among the internal coordinates (dihedral angles correlations and coincidences). The atomic partial charge distribution is found to greatly affect the energy calculation for the molecular mechanics based conformational energy distributions. Further energy minimization of conformational sample by the quantum molecular orbital methods is crucial to obtain charge independent as well as energy balanced conformational sample.

Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

Directory of Open Access Journals (Sweden)

Tino Wolter

Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

Tetrazole acetic acid: Tautomers, conformers, and isomerization

Energy Technology Data Exchange (ETDEWEB)

Araujo-Andrade, C. [Unidad Académica de Física de la Universidad Autónoma de Zacatecas, Zacatecas (Mexico); Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal); Reva, I., E-mail: reva@qui.uc.pt; Fausto, R. [Department of Chemistry, University of Coimbra, 3004-535 Coimbra (Portugal)

2014-02-14

Monomers of (tetrazol-5-yl)-acetic acid (TAA) were obtained by sublimation of the crystalline compound and the resulting vapors were isolated in cryogenic nitrogen matrices at 13 K. The conformational and tautomeric composition of TAA in the matrix was characterized by infrared spectroscopy and vibrational calculations carried out at the B3LYP/6-311++G(d,p) level. TAA may adopt two tautomeric modifications, 1H- and 2H-, depending on the position of the annular hydrogen atom. Two-dimensional potential energy surfaces (PESs) of TAA were theoretically calculated at the MP2/6-311++G(d,p) level, for each tautomer. Four and six symmetry-unique minima were located on these PESs, for 1H- and 2H-TAA, respectively. The energetics of the detected minima was subsequently refined by calculations at the QCISD level. Two 1H- and three 2H-conformers fall within the 0–8 kJ mol{sup −1} energy range and should be appreciably populated at the sublimation temperature (∼330 K). Observation of only one conformer for each tautomer (1ccc and 2pcc) is explained in terms of calculated barriers to conformational rearrangements. All conformers with the cis O=COH moiety are separated by low barriers (less than 10 kJ mol{sup −1}) and collapse to the most stable 1ccc (1H-) and 2pcc (2H-) forms during deposition of the matrix. On the trans O=COH surfaces, the relative energies are very high (between 12 and 27 kJ mol{sup −1}). The trans forms are not thermally populated at the sublimation conditions and were not detected in matrices. One high-energy form in each tautomer, 1cct (1H-) and 2pct (2H-), was found to differ from the most stable form only by rotation of the OH group and separated from other forms by high barriers. This opened a perspective for their stabilization in a matrix. 1cct and 2pct were generated in the matrices selectively by means of narrow-band near-infrared (NIR) irradiations of the samples at 6920 and 6937 cm{sup −1}, where the first OH stretching overtone

Elucidation of structural isomers from the homogeneous rhodium-catalyzed isomerization of vegetable oils.

Science.gov (United States)

Andjelkovic, Dejan D; Min, Byungrok; Ahn, Dong; Larock, Richard C

2006-12-13

The structural isomers formed by the homogeneous rhodium-catalyzed isomerization of several vegetable oils have been elucidated. A detailed study of the isomerization of the model compound methyl linoleate has been performed to correlate the distribution of conjugated isomers, the reaction kinetics, and the mechanism of the reaction. It has been shown that [RhCl(C8H8)2]2 is a highly efficient and selective isomerization catalyst for the production of highly conjugated vegetable oils with a high conjugated linoleic acid (CLA) content, which is highly desirable in the food industry. The combined fraction of the two major CLA isomers [(9Z,11E)-CLA and (10E,12Z)-CLA] in the overall CLA mixture is in the range from 76.2% to 93.4%. The high efficiency and selectivity of this isomerization method along with the straightforward purification process render this approach highly promising for the preparation of conjugated oils and CLA. Proposed improvements in catalyst recovery and reusability will only make this method more appealing to the food, paint, coating, and polymer industries in the future.

Kinetic Dissection of the Pre-existing Conformational Equilibrium in the Trypsin Fold*

Science.gov (United States)

Vogt, Austin D.; Chakraborty, Pradipta; Di Cera, Enrico

2015-01-01

Structural biology has recently documented the conformational plasticity of the trypsin fold for both the protease and zymogen in terms of a pre-existing equilibrium between closed (E*) and open (E) forms of the active site region. How such plasticity is manifested in solution and affects ligand recognition by the protease and zymogen is poorly understood in quantitative terms. Here we dissect the E*-E equilibrium with stopped-flow kinetics in the presence of excess ligand or macromolecule. Using the clotting protease thrombin and its zymogen precursor prethrombin-2 as relevant models we resolve the relative distribution of the E* and E forms and the underlying kinetic rates for their interconversion. In the case of thrombin, the E* and E forms are distributed in a 1:4 ratio and interconvert on a time scale of 45 ms. In the case of prethrombin-2, the equilibrium is shifted strongly (10:1 ratio) in favor of the closed E* form and unfolds over a faster time scale of 4.5 ms. The distribution of E* and E forms observed for thrombin and prethrombin-2 indicates that zymogen activation is linked to a significant shift in the pre-existing equilibrium between closed and open conformations that facilitates ligand binding to the active site. These findings broaden our mechanistic understanding of how conformational transitions control ligand recognition by thrombin and its zymogen precursor prethrombin-2 and have direct relevance to other members of the trypsin fold. PMID:26216877

Conformational cooling and conformation selective aggregation in dimethyl sulfite isolated in solid rare gases

Science.gov (United States)

Borba, Ana; Gómez-Zavaglia, Andrea; Fausto, Rui

2006-08-01

Dimethyl sulfite has three conformers of low energy, GG, GT and GG', which have significant populations in the gas phase at room temperature. According to theoretical predictions, the GT and GG' conformers are higher in energy than the GG conformer by 0.83 and 1.18 kJ mol -1, respectively, while the barriers associated with the GG'→GT and GT→GG isomerizations are 1.90 and 9.64 kJ mol -1, respectively. Experimental data obtained for the compound isolated in solid argon, krypton and xenon demonstrated that the GG'→GT energy barrier is low enough to allow an extensive conversion of the GG' form into the GT conformer during deposition of the matrices, the extent of the conversion increasing along the series Arconformers could be trapped in both argon and krypton matrices, but, at a given temperature, the amount of GG' form trapped in krypton is considerably smaller than in argon, while the amount of GT form increases in relation to the most stable GG form. In addition, when xenon is used, no bands due to GG' are observed in the as-deposited spectra ( Tsubstrate≥10 K, the minimum substrate temperature accessible to our experimental set up), indicating that when the best relaxant gas is used the GG'→GT conversion during deposition of the matrix is complete even at 10 K. Annealing of the argon and krypton matrices shows that the increase of the temperature of the matrix first promotes the GG'→GT isomerization, and only at higher temperatures the GT→GG conversion starts to occur, in consonance with the relative energy barriers associated with these two processes. The results also indicate that dimethyl sulfite exhibits conformation selective aggregation, with the most stable form, which has the highest dipole moment, aggregating more easily than the remaining experimentally relevant conformers (GT and GG').

Compartmental and noncompartmental modeling of ¹³C-lycopene absorption, isomerization, and distribution kinetics in healthy adults.

Science.gov (United States)

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 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.

Compartmental and noncompartmental modeling of 13C-lycopene absorption, isomerization, and distribution kinetics in healthy adults123

Science.gov (United States)

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 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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Conformational isomerism of phenolic procyanidins: preferred conformations in organic solvents and water

Science.gov (United States)

Tsutomu Hatano; Richard W. Hemingway

1997-01-01

NMR studies of catechin-{4α→8)-epicatechin (I) and catechin-{4α→8)-catechin (2) provided complete assignment of the proton and carbon resonances for both the more extended and compact conformers in the free phenolic form. When 1 is in organic solvents, the more extended rotamer is preferred over the more compact rotamer (10:7), but...

Gas-Phase Hydrogen-Deuterium Exchange Labeling of Select Peptide Ion Conformer Types: a Per-Residue Kinetics Analysis.

Science.gov (United States)

Khakinejad, Mahdiar; Kondalaji, Samaneh Ghassabi; Tafreshian, Amirmahdi; Valentine, Stephen J

2015-07-01

The per-residue, gas-phase hydrogen deuterium exchange (HDX) kinetics for individual amino acid residues on selected ion conformer types of the model peptide KKDDDDDIIKIIK have been examined using ion mobility spectrometry (IMS) and HDX-tandem mass spectrometry (MS/MS) techniques. The [M + 4H](4+) ions exhibit two major conformer types with collision cross sections of 418 Å(2) and 446 Å(2); the [M + 3H](3+) ions also yield two different conformer types having collision cross sections of 340 Å(2) and 367 Å(2). Kinetics plots of HDX for individual amino acid residues reveal fast- and slow-exchanging hydrogens. The contributions of each amino acid residue to the overall conformer type rate constant have been estimated. For this peptide, N- and C-terminal K residues exhibit the greatest contributions for all ion conformer types. Interior D and I residues show decreased contributions. Several charge state trends are observed. On average, the D residues of the [M + 3H](3+) ions show faster HDX rate contributions compared with [M + 4H](4+) ions. In contrast the interior I8 and I9 residues show increased accessibility to exchange for the more elongated [M + 4H](4+) ion conformer type. The contribution of each residue to the overall uptake rate showed a good correlation with a residue hydrogen accessibility score model calculated using a distance from charge site and initial incorporation site for nominal structures obtained from molecular dynamic simulations (MDS).

{sup 13}C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)

Energy Technology Data Exchange (ETDEWEB)

Takeda, Mitsuhiro [Kumamoto University, Department of Structural BioImaging, Faculty of Life Sciences (Japan); Miyanoiri, Yohei [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Terauchi, Tsutomu [Tokyo Metropolitan University, Graduate School of Science and Engineering (Japan); Kainosho, Masatsune, E-mail: kainosho@tmu.ac.jp [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

2016-09-15

Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14–Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D {sup 13}C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically {sup 13}C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14–Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m{sub c14} and m{sub c38}). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 α-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for {sup 13}C relaxation dispersion experiments was obtained through the carbon line-shape profile. With respect to the m{sub c38} isomerization, the {sup 1}H-{sup 13}C signals at the β-position of the minor state were resolved from the major peaks and detected by exchange experiments at a low temperature.

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

Energy Technology Data Exchange (ETDEWEB)

Changala, P. Bryan, E-mail: bryan.changala@colorado.edu; Baraban, Joshua H.; Field, Robert W. [Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Stanton, John F. [Department of Chemistry and Biochemistry, Institute for Theoretical Chemistry, The University of Texas at Austin, Austin, Texas 78712 (United States); Merer, Anthony J. [Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1 (Canada)

2014-01-14

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

Einstein’s quadrupole formula from the kinetic-conformal Hořava theory

Science.gov (United States)

Bellorín, Jorge; Restuccia, Alvaro

We analyze the radiative and nonradiative linearized variables in a gravity theory within the family of the nonprojectable Hořava theories, the Hořava theory at the kinetic-conformal point. There is no extra mode in this formulation, the theory shares the same number of degrees of freedom with general relativity. The large-distance effective action, which is the one we consider, can be given in a generally-covariant form under asymptotically flat boundary conditions, the Einstein-aether theory under the condition of hypersurface orthogonality on the aether vector. In the linearized theory, we find that only the transverse-traceless tensorial modes obey a sourced wave equation, as in general relativity. The rest of variables are nonradiative. The result is gauge-independent at the level of the linearized theory. For the case of a weak source, we find that the leading mode in the far zone is exactly Einstein’s quadrupole formula of general relativity, if some coupling constants are properly identified. There are no monopoles nor dipoles in this formulation, in distinction to the nonprojectable Horava theory outside the kinetic-conformal point. We also discuss some constraints on the theory arising from the observational bounds on Lorentz-violating theories.

Modelling of tracer-kinetic results using xylene isomerization as an example

International Nuclear Information System (INIS)

Bauer, F.J.; Dermietzel, J.; Roesseler, M.; Koch, H.

1976-01-01

The analysis of results from differential or/and integral reactor experiments often admits the interpretation of a chemical reaction in several ways. In addition, the use of mathematical methods for the model selection and planning of experiments is rendered more difficult by great confidence intervals of the ascertained model parameters. The application of radioactively labelled molecules results in improving the knowledge of reaction mechanisms as well as the assessment of parameters obtained. This is shown on the basis of modelling the isomerization of xylene. (author)

Insights in the Rhodium-Catalyzed Tandem Isomerization-Hydroformylation of 10-Undecenitrile: Evidence for a Fast Isomerization Regime

Directory of Open Access Journals (Sweden)

Lucas Le Goanvic

2018-04-01

Full Text Available The tandem isomerization-hydroformylation of 10-undecenitrile (1 into the corresponding linear aldehyde (2 with a Rh-biphephos system was studied and the formation of internal olefin isomers (1-int-x was monitored over time. The existence of an “isomerization phenomenon” was evidenced, where fast isomerization of 1 into up to 70% of 1-int-x followed by fast back-isomerization of 1-int-x into 1 and, in turn, into 2 occurs. This fast dynamic isomerization regime is favored at high syngas pressure (40 bar and low biphephos-to-Rh ratio (5–10, and it is best observed at relatively high catalyst loadings ([1]0/[Rh] ≤ 3000. The latter regime is indeed evanescent, and gives place to a second stage in which isomerization of internal olefins (and eventual conversion into 2 proceeds much more slowly. The results are tentatively rationalized by the formation of an unstable species that promotes dynamic isomerization and which slowly vanishes or collapses into a Rh-biphephos species which is the one responsible for hydroformylation.

Is isomerism a risk factor for intestinal volvulus?

Science.gov (United States)

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.

Conformational Fluctuations in G-Protein-Coupled Receptors

Science.gov (United States)

Brown, Michael F.

2014-03-01

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

Quantum optimal control of ozone isomerization

International Nuclear Information System (INIS)

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

2004-01-01

We present a feasibility study of ozone isomerization based on a recent ab initio potential energy surface and a model Hamiltonian constructed by holding the bond lengths constant and using the valence angle as the isomerization coordinate. Optimal control theory is used to find an electric field that drives isomerization with a yield of 95% to the symmetric metastable triangular form of ozone. A frequency filter is applied as an additional spectral constraint limiting the field bandwidth. A post-facto analysis is performed showing a degree of inherent robustness of the isomerization yield to field noise

Isomeric Targets and Beams

International Nuclear Information System (INIS)

Oganesyan, Yu.Ts.; Karamyan, S.A.

1994-01-01

One of the main topics of modern nuclear physics is the investigation of exotic nuclei including hyper-nuclei, trans fermium elements, proton and neutron rich isotopes near drip lines as well as high-spin excited states and states with anomalous deformation. The isomerism of nuclei is closely related with such phenomena as the alignment of single-particle orbitals, the coexistence of various deformations and the manifestation of intruder-levels from neighbouring shells. The investigation of electromagnetic and nuclear interactions of isomers could give important information on their shell structure and its role in the mechanism of nuclear reactions. For such experiments one can either make isomeric targets (sufficiently long-lived) or use the methods of acceleration of isomeric nuclei. Recently, an exotic 16 + four-quasiparticle isomer of 178 Hf m 2 was produced in a micro weight quantity and the first nuclear reactions on it were successfully observed. The talk describes these experiments as well as new ideas for the continuation of the studies and some advantageous ways for the isomeric beams production by the method of direct acceleration or by the secondary beam method. 35 refs., 15 figs., 8 tabs

Lipid-protein interaction induced domains: Kinetics and conformational changes in multicomponent vesicles

Science.gov (United States)

Sreeja, K. K.; Sunil Kumar, P. B.

2018-04-01

The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated in the past. We show, using Monte Carlo simulations, that the affinity of proteins for specific lipids can hasten their aggregation kinetics. The lipid membrane is modeled as a dynamically triangulated surface with the proteins defined as in-plane fields at the vertices. We show that, even at low protein concentrations, strong lipid-protein interactions can result in large protein clusters indicating a route to lipid mediated signal amplification. At high protein concentrations, the domains form buds similar to that seen in lipid-lipid interaction induced phase separation. Protein interaction induced domain budding is suppressed when proteins act as anisotropic inclusions and exhibit nematic orientational order. The kinetics of protein clustering and resulting conformational changes are shown to be significantly different for the isotropic and anisotropic curvature inducing proteins.

Experimental grounds for nuclear shape isomerism

International Nuclear Information System (INIS)

Makarenko, V.E.

1995-11-01

Experimental data on fission isomeric states of actinide nuclei - half lives, energies, quantum numbers, decay branches and spectroscopic properties - are discussed. Quite a few results find their explanation in the framework of nuclear shape isomerism hypothesis being the in-thing for about thirty years. Others seem to be the hints to the quasiparticle nature of fission isomers. The problem could be solved by direct measurement of nuclear spin for isomeric states. (author). 44 refs, 1 tab

Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies.

Science.gov (United States)

Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah

2016-01-01

Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

Investigating the conformational stability of prion strains through a kinetic replication model.

Directory of Open Access Journals (Sweden)

Mattia Zampieri

2009-07-01

Full Text Available Prion proteins are known to misfold into a range of different aggregated forms, showing different phenotypic and pathological states. Understanding strain specificities is an important problem in the field of prion disease. Little is known about which PrP(Sc structural properties and molecular mechanisms determine prion replication, disease progression and strain phenotype. The aim of this work is to investigate, through a mathematical model, how the structural stability of different aggregated forms can influence the kinetics of prion replication. The model-based results suggest that prion strains with different conformational stability undergoing in vivo replication are characterizable in primis by means of different rates of breakage. A further role seems to be played by the aggregation rate (i.e. the rate at which a prion fibril grows. The kinetic variability introduced in the model by these two parameters allows us to reproduce the different characteristic features of the various strains (e.g., fibrils' mean length and is coherent with all experimental observations concerning strain-specific behavior.

Xylene isomerization

KAUST Repository

Bilaus, Rakan Sulaiman; Pinnau, Ingo

2016-01-01

at isomenzation conditions and producing an isomerized product comprising a higher proportion of p-xylene than in the feed mixture, wherein the catalyst comprises an acidic sulfonated catalytic membrane. Xylene isomenzation can also be coupled with a p

Nitrite-reductase and peroxynitrite isomerization activities of Methanosarcina acetivorans protoglobin.

Directory of Open Access Journals (Sweden)

Paolo Ascenzi

Full Text Available Within the globin superfamily, protoglobins (Pgb belong phylogenetically to the same cluster of two-domain globin-coupled sensors and single-domain sensor globins. Multiple functional roles have been postulated for Methanosarcina acetivorans Pgb (Ma-Pgb, since the detoxification of reactive nitrogen and oxygen species might co-exist with enzymatic activity(ies to facilitate the conversion of CO to methane. Here, the nitrite-reductase and peroxynitrite isomerization activities of the CysE20Ser mutant of Ma-Pgb (Ma-Pgb* are reported and analyzed in parallel with those of related heme-proteins. Kinetics of nitrite-reductase activity of ferrous Ma-Pgb* (Ma-Pgb*-Fe(II is biphasic and values of the second-order rate constant for the reduction of NO2- to NO and the concomitant formation of nitrosylated Ma-Pgb*-Fe(II (Ma-Pgb*-Fe(II-NO are k(app1= 9.6 ± 0.2 M(-1 s(-1 and k(app2 = 1.2 ± 0.1 M(-1 s(-1 (at pH 7.4 and 20 °C. The k(app1 and k(app2 values increase by about one order of magnitude for each pH unit decrease, between pH 8.3 and 6.2, indicating that the reaction requires one proton. On the other hand, kinetics of peroxynitrite isomerization catalyzed by ferric Ma-Pgb* (Ma-Pgb*-Fe(III is monophasic and values of the second order rate constant for peroxynitrite isomerization by Ma-Pgb*-Fe(III and of the first order rate constant for the spontaneous conversion of peroxynitrite to nitrate are h(app = 3.8 × 10(4 M(-1 s(-1 and h0 = 2.8 × 10(-1 s(-1 (at pH 7.4 and 20 °C. The pH-dependence of hon and h0 values reflects the acid-base equilibrium of peroxynitrite (pKa = 6.7 and 6.9, respectively; at 20 °C, indicating that HOONO is the species that reacts preferentially with the heme-Fe(III atom. These results highlight the potential role of Pgbs in the biosynthesis and scavenging of reactive nitrogen and oxygen species.

Experiments with neutron-rich isomeric beams

International Nuclear Information System (INIS)

Rykaczewski, K.; Lewitowicz, M.; Pfuetzner, 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

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

Science.gov (United States)

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

2016-09-12

Chiroptical molecular switches play an important role in responsive materials and dynamic molecular systems. Here we present the synthesis of four chiral overcrowded alkenes and the experimental and computational study of their photochemical and thermal behavior. By irradiation with UV light, metastable diastereoisomers with opposite helicity were generated through high yielding E-Z isomerizations. Kinetic studies on metastable 1-4 using CD spectroscopy and HPLC analysis revealed two pathways at higher temperatures for the thermal isomerization, namely a thermal E-Z isomerization (TEZI) and a thermal helix inversion (THI). These processes were also studied computationally whereby a new strategy was developed for calculating the TEZI barrier for second-generation overcrowded alkenes. To demonstrate that these overcrowded alkenes can be employed as bistable switches, photochromic cycling was performed, which showed that the alkenes display good selectivity and fatigue resistance over multiple irradiation cycles. In particular, switch 3 displayed the best performance in forward and backward photoswitching, while 1 excelled in thermal stability of the photogenerated metastable form. Overall, the alkenes studied showed a remarkable and unprecedented combination of switching properties including dynamic helicity, reversibility, selectivity, fatigue resistance, and thermal stability. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ti-Catalyzed Selective Isomerization of Terminal Mono-substituted Olefins

International Nuclear Information System (INIS)

Lee, Hyung Soo; Lee, Gab Yong

2005-01-01

The isomerization of olefins occurs either by a metal hydride addition-elimination or by a π-allyl metal hydride intermediate. HCo(CO) 4 , [(C 2 H 4 ) 2 RhCl] 2 , Ni[P(OEt) 3 ] 4 , and PtCl 2 (PPh 3 ) 2 -SnCl 2 are effective catalysts for isomerization of olefins via a metal hydride addition-elimination mechanism, 3,4 and Fe 3 (CO) 12 catalyzed isomerization of 3-ethyl-1-pentene and isomerization of 1-heptene catalyzed by (PhCN) 2 PdCl 2 occur via a π-allyl metal hydride mechanism. The cis/trans ratio of 2-butene obtained from isomerization of 1-butene by RhH(CO)(PPh 3 ) 3 has also been investigated. The skeletal isomerization of olefins catalyzed by (R 3 P) 2 NiCl 2 is developed such as conversion of cis-1,4-hexadiene to trans-2-methyl-1,3-pentadiene. Titanium complexes serve as an effective catalysts for a variety of reactions such as hydroalumination, hydroboration, and hydrogenation of unsaturated hydrocarbons. We have been interested in the selective reactions of unsaturated hydrocarbons by using titanium and zirconium compounds. The reagent system composed of LiAlH 4 /Cp 2 TiCl 2 ≤ 2 in the molar ratio promotes the isomerization of 1-octene, but the detailed reaction for isomerization of olefins has not been reported. We report here a selective isomerization of olefins with low valent titanium complex generated from Cp 2 TiCl 2 (Cp=cyclopentadienyl) and LiAlH 4

Theoretical and Spectroscopic investigations of conformations, rotational barriers and scaled vibrations of 2,3-dimethyl hexane

Directory of Open Access Journals (Sweden)

Aziz Aboulmouhajir

2017-01-01

Full Text Available The 2,3-dimethyl hexane conformational isomerism has been investigated in detail, based on HF, Post-HF and DFT calculations at different basis set. The effect of size of basis, ZPE, thermal contributions, electronic correlation and optimization methods on the conformational stability was discussed. The rotational barriers from the most stable conformer to the lowest energy secondary conformers and their correspondent inversion barriers at both HF and MP2 methods using 6-31G* basis set have also been approached. A normal mode calculation of the most and less-stable conformers using a scaled ab initio force field in terms of non-redundant local symmetry coordinates have been made to elucidate the conformational dependence of the vibrational spectra.

The conformally invariant Laplace-Beltrami operator and factor ordering

International Nuclear Information System (INIS)

Ryan, Michael P.; Turbiner, Alexander V.

2004-01-01

In quantum mechanics the kinetic energy term for a single particle is usually written in the form of the Laplace-Beltrami operator. This operator is a factor ordering of the classical kinetic energy. We investigate other relatively simple factor orderings and show that the only other solution for a conformally flat metric is the conformally invariant Laplace-Beltrami operator. For non-conformally-flat metrics this type of factor ordering fails, by just one term, to give the conformally invariant Laplace-Beltrami operator

Kinetics and mechanistic study of n-alkane hydroisomerization reaction on Pt-doped γ-alumina catalyst

Directory of Open Access Journals (Sweden)

Abhishek Dhar

2017-12-01

Full Text Available The catalysts γ-alumina (GA, the reference catalyst and Pt doped γ-alumina (PGA-s were synthesized using a simple sol-gel technique, in which at first preparation of porous base (GA, then impregnation of platinum salt over the base and finally reduction of platinum in the surface of the support were done. These catalysts prepared in different mole ratios of Pt:Al as 2:1, 1:1 and 1:2 are named as PGA-1, PGA-2 and PGA-3 respectively. The isomerization of n-alkanes (n-hexane, n-heptane and n-octane were investigated over the synthesized catalysts. The 2-methyl pentane (2-MP, 2,2-dimethyl pentane (2,2-DMP and 2,3-dimethyl hexane (2,3-DMH are the major products of respective isomerization of n-hexane, n-heptane and n-octane, besides a small amount of other branched isomers are also produced. The product distribution is comparable to that reported for Pt based other catalysts. The optimal mole ratios of Pt:Al is 1:1 (PGA-2 gives quite good catalytic activity for isomerization of n-alkane. Even through in reusability study, PGA-2 gives better performance than others. We have mainly focused on kinetic study, reaction mechanism behind isomerization and calculated the order of reactions and activation energies of the isomerization reactions in the present work. Keywords: Isomerization, n-alkanes, Catalyst, Reaction mechanism, Kinetics study, Activation energy

Transient-Absorption Spectroscopy of Cis-Trans Isomerization of N,N-dimethyl-4,4'-Azodianiline with 3D-Printed Temperature-Controlled Sample Holder

Science.gov (United States)

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…

Kinetics of the cooperative binding of glucose to dimeric yeast hexokinase P-I.

Science.gov (United States)

Hoggett, J G; Kellett, G L

1995-01-15

Kinetic studies of the cooperative binding of glucose to yeast hexokinase P-I at pH 6.5 have been carried out using the fluorescence temperature-jump technique. Three relaxation effects were observed: a fast low-amplitude effect which could only be resolved at low glucose concentrations (tau 1(-1) = 500-800 s-1), an intermediate effect (tau 2) which showed a linear dependence of reciprocal relaxation time on concentration, and a slow effect (tau 3) which showed a curved dependence on glucose concentration, increasing from approximately 28 s-1 at low concentrations to 250 s-1 at high levels. The findings are interpreted in terms of the concerted Monod-Wyman-Changeux mechanism, the two faster relaxations being assigned to binding to the R and T states, and the slow relaxation to isomerization between the states. Quantitative fitting of the kinetic data to the mechanism has been carried out using independent estimates of the equilibrium parameters of the model; these have been derived from equilibrium dialysis data and by determining the enhancement of the intrinsic ATPase activity of the enzyme by the non-phosphorylatable sugar lyxose, which switches the conformation of the enzyme to the active R state.

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

Science.gov (United States)

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.

Isomers chart; Table des isomeres

Energy Technology Data Exchange (ETDEWEB)

Dupont-Gautier, P; Chantelot, S; Moisson, N [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1967-07-01

The nuclear isomers are nuclides offering the same mass number and the same atomic number, but different energy levels. In the following chart the zero energy ground states are omitted and the metastable isomers, i.e. of non-zero energy, known and of measurable lifetime, are listed. The lower limit of this lifetime was set here to 0.1 x 10{sup -6} s. The various isomers were classified in increasing lifetimes. (authors) [French] Les isomeres nucleaires sont des nucleides presentant le meme nombre de masse et le meme numero atomique, mais des niveaux energetiques differents. Dans la table suivante, on a neglige les etats fondamentaux d'energie nulle et on a recense les isomeres metastables, c'est-a-dire d'energie non nulle, connus et de periode mesurable. La limite inferieure de cette periode a ete fixee ici a 0,1 x 10{sup -6} s. Les differents isomeres ont ete classes par periodes croissantes. (auteurs)

Isomers chart; Table des isomeres

Energy Technology Data Exchange (ETDEWEB)

Dupont-Gautier, P.; Chantelot, S.; Moisson, N. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1967-07-01

The nuclear isomers are nuclides offering the same mass number and the same atomic number, but different energy levels. In the following chart the zero energy ground states are omitted and the metastable isomers, i.e. of non-zero energy, known and of measurable lifetime, are listed. The lower limit of this lifetime was set here to 0.1 x 10{sup -6} s. The various isomers were classified in increasing lifetimes. (authors) [French] Les isomeres nucleaires sont des nucleides presentant le meme nombre de masse et le meme numero atomique, mais des niveaux energetiques differents. Dans la table suivante, on a neglige les etats fondamentaux d'energie nulle et on a recense les isomeres metastables, c'est-a-dire d'energie non nulle, connus et de periode mesurable. La limite inferieure de cette periode a ete fixee ici a 0,1 x 10{sup -6} s. Les differents isomeres ont ete classes par periodes croissantes. (auteurs)

Isotope exchange study of nickel xanthate in presence of aniline and isomeric toluidines

International Nuclear Information System (INIS)

Naidu, G.R.K.; Naidu, P.R.

1982-01-01

Isotopic exchange behaviour of nickel xanthate is studied in the presence of aniline and three isomeric toluidines at 18degC. The effect of base concentration is also studied on the exchange rate. The results show that the complex is labile in the kinetic sense in the presence of aniline meta and para toluidines. The rate of exchange increases with and para toluidines. The rate of exchange increases with increase in concentration of the base. The complex displays inert behaviour in the presence of o-toluidine and it is ascribed to dominant steric effect. (author)

Easy Synthesis of Two Positional Isomeric Tetrazole Libraries

NARCIS (Netherlands)

Wang, Yuanze; Patil, Pravin; Dömling, Alexander

2016-01-01

A fast and efficient synthesis of libraries of positional isomeric 1H-tetrazoles and 5H-tetrazoles, for the purpose of testing binding hypothesis of isomeric tetrazoles in fragment-based drug discovery, is described.

Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

Directory of Open Access Journals (Sweden)

David S. Kliger

2009-04-01

Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

Graphene oxide catalyzed cis-trans isomerization of azobenzene

Directory of Open Access Journals (Sweden)

Dongha Shin

2014-09-01

Full Text Available We report the fast cis-trans isomerization of an amine-substituted azobenzene catalyzed by graphene oxide (GO, where the amine functionality facilitates the charge transfer from azobenzene to graphene oxide in contrast to non-substituted azobenzene. This catalytic effect was not observed in stilbene analogues, which strongly supports the existence of different isomerization pathways between azobenzene and stilbene. The graphene oxide catalyzed isomerization is expected to be useful as a new photoisomerization based sensing platform complementary to GO-based fluorescence quenching methods.

Theoretical model based on the memory effect for the strange photoisomerization kinetics of diarylethene derivatives dispersed on polymer films

International Nuclear Information System (INIS)

Seki, Kazuhiko; Tachiya, M.

2007-01-01

In the present paper the authors present a theoretical model to explain the kinetics involving the induction period observed by Irie et al. [Nature (London) 420, 759 (2002)] for photoisomerization of diarylethene derivatives dispersed on polymer films at a single molecular level. In the model we assume that both ground state and excited state free energy landscapes which result from the interaction between the photochromic molecule and the surrounding polymer are rugged and have several local minima along the pathway to the critical point at which isomerization actually occurs. We assume that after one photoexcitation a fraction of the photochromic molecule moves to a new local minimum and stays there, although the other fraction returns to the original local minimum. The former effect is referred to as the memory effect. After repeated photoexcitations the photochromic molecule moves gradually from one local minimum to another in the pathway to the isomerization point. It finally reaches the isomerization point, where isomerization occurs. Their model successfully reproduces the kinetics of photoisomerization of diarylethene derivatives dispersed on polymer films observed experimentally

Induced quantum conformal gravity

International Nuclear Information System (INIS)

Novozhilov, Y.V.; Vassilevich, D.V.

1988-11-01

Quantum gravity is considered as induced by matter degrees of freedom and related to the symmetry breakdown in the low energy region of a non-Abelian gauge theory of fundamental fields. An effective action for quantum conformal gravity is derived where both the gravitational constant and conformal kinetic term are positive. Relation with induced classical gravity is established. (author). 15 refs

An automated and efficient conformation search of L-cysteine and L,L-cystine using the scaled hypersphere search method

Science.gov (United States)

Kishimoto, Naoki; Waizumi, Hiroki

2017-10-01

Stable conformers of L-cysteine and L,L-cystine were explored using an automated and efficient conformational searching method. The Gibbs energies of the stable conformers of L-cysteine and L,L-cystine were calculated with G4 and MP2 methods, respectively, at 450, 298.15, and 150 K. By assuming thermodynamic equilibrium and the barrier energies for the conformational isomerization pathways, the estimated ratios of the stable conformers of L-cysteine were compared with those determined by microwave spectroscopy in a previous study. Equilibrium structures of 1:1 and 2:1 cystine-Fe complexes were also calculated, and the energy of insertion of Fe into the disulfide bond was obtained.

Thermal E/ Z Isomerization in First Generation Molecular Motors.

Science.gov (United States)

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.

Designing bifunctional alkene isomerization catalysts using predictive modelling

NARCIS (Netherlands)

Landman, I.R.; Paulson, E.R.; Rheingold, A.L.; Grotjahn, D.B.; Rothenberg, G.

2017-01-01

Controlling the isomerization of alkenes is important for the manufacturing of fuel additives, fine-chemicals and pharmaceuticals. But even if isomerization seems to be a simple unimolecular process, the factors that govern catalyst performance are far from clear. Here we present a set of models

Biosynthesis of monoterpenes: Stereochemistry of the coupled isomerization and cyclization of geranyl pyrophosphate to camphane and isocamphane monoterpenes

International Nuclear Information System (INIS)

Croteau, R.; Gershenzon, J.; Wheeler, C.J.; Satterwhite, D.M.

1990-01-01

The conversion of geranyl pyrophosphate to (+)-bornyl pyrophosphate and (+)-camphene is considered to proceed by the initial isomerization of the substrate to (-)-(3R)-linalyl pyrophosphate and the subsequent cyclization of this bound intermediate. In the case of (-)-bornyl pyrophosphate and (-)-camphene, isomerization of the substrate to the (+)-(3S)-linalyl intermediate precedes cyclization. The geranyl and linalyl precursors were shown to be mutually competitive substrates (inhibitors) of the relevant cyclization enzymes isolated from Salvia officinalis (sage) and Tanacetum vulgare (tansy) by the mixed substrate analysis method, demonstrating that isomerization and cyclization take place at the same active site. Incubation of partially purified enzyme preparations with (3R)-[1Z-3H]linalyl pyrophosphate plus [1-14C]geranyl pyrophosphate gave rise to double-labeled (+)-bornyl pyrophosphate and (+)-camphene, whereas incubation of enzyme preparations catalyzing the antipodal cyclizations with (3S)-[1Z-3H]-linalyl pyrophosphate plus [1-14C]geranyl pyrophosphate yielded double-labeled (-)-bornyl pyrophosphate and (-)-camphene. Each product was then transformed to the corresponding (+)- or (-)-camphor without change in the 3H:14C isotope ratio, and the location of the tritium label was deduced in each case by stereoselective, base-catalyzed exchange of the exo-alpha-hydrogen of the derived ketone. The finding that the 1Z-3H of the linalyl precursor was positioned at the endo-alpha-hydrogen of the corresponding camphor in all cases, coupled to the previously demonstrated retention of configuration at C1 of the geranyl substrate in these transformations, confirmed the syn-isomerization of geranyl pyrophosphate to linalyl pyrophosphate and the cyclization of the latter via the anti,endo- conformer

Characterizing gamma fields using isomeric activation ratios

Science.gov (United States)

Venkataraman, Ramkumar; Fleming, Ronald F.

1994-12-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Alsanousi, Nesreen [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Sugiki, Toshihiko, E-mail: sugiki@protein.osaka-u.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kojima, Chojiro, E-mail: kojima-chojiro-xk@ynu.ac.jp [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)

2016-09-02

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

Essential role of conformational selection in ligand binding.

Science.gov (United States)

Vogt, Austin D; Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico

2014-02-01

Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and

Radiochemical study of isomerization of free butyl cations

International Nuclear Information System (INIS)

Sinotova, E.N.; Nefedov, V.D.; Skorokhodov, S.S.; Arkhipov, Yu.M.

1987-01-01

Ion-molecular reactions of free butyl cations, generated by nuclear chemical method, with carbon monoxide containing small quantities of ethanol vapors are studied. Carbon monoxide was used to fix instable butyl cations in the form of corresponding acyl ions. Ester of α-methyl-butyric acid appears to be the only product of free butyl cation interaction with carbon monoxide in the presence of ethanol vapors. That means, that up to the moment of butyl cation reaction with carbon monoxide, the primary butyl cations are almost completely isomerized into secondary in agreement with results of previous investigations. This allows one to study free butyl cation isomerization process according to ion-molecular reaction product isomeric composition

Evaluation of the performance of MP4-based procedures for a wide range of thermochemical and kinetic properties

Energy Technology Data Exchange (ETDEWEB)

Yu, Li-Juan; Wan, Wenchao; Karton, Amir, E-mail: amir.karton@uwa.edu.au

2016-11-30

We evaluate the performance of standard and modified MPn procedures for a wide set of thermochemical and kinetic properties, including atomization energies, structural isomerization energies, conformational energies, and reaction barrier heights. The reference data are obtained at the CCSD(T)/CBS level by means of the Wn thermochemical protocols. We find that none of the MPn-based procedures show acceptable performance for the challenging W4-11 and BH76 databases. For the other thermochemical/kinetic databases, the MP2.5 and MP3.5 procedures provide the most attractive accuracy-to-computational cost ratios. The MP2.5 procedure results in a weighted-total-root-mean-square deviation (WTRMSD) of 3.4 kJ/mol, whilst the computationally more expensive MP3.5 procedure results in a WTRMSD of 1.9 kJ/mol (the same WTRMSD obtained for the CCSD(T) method in conjunction with a triple-zeta basis set). We also assess the performance of the computationally economical CCSD(T)/CBS(MP2) method, which provides the best overall performance for all the considered databases, including W4-11 and BH76.

Isomeric states in 253No and 253Fm

International Nuclear Information System (INIS)

Antalic, S.; Kalaninova, Z.; Saro, S.; Venhart, M.; Hessberger, F.P.; Ackermann, D.; Heinz, S.; Kindler, B.; Khuyagbaatar, J.; Kojouharov, I.; Kuusiniemi, P.; Lommel, B.; Mann, R.; Sulignano, B.; Hofmann, S.; Leino, M.; Nishio, K.; Streicher, B.

2011-01-01

Nuclear structure and decay of isomeric states in 253 No were investigated. The isotope was produced by the reaction 48 Ca + 207 Pb. The excitation energy of the known single-particle isomeric state (5/2 + [622]) was measured by delayed coincidences between γ-rays and implanted evaporation residues and was placed into the level scheme. In addition, decay of a high-lying multi-quasiparticle isomer in 253 No was studied using e - -γ coincidence measurements. A rotational band populated by its de-excitation was identified in 253 No. A new isomeric state in 253 Fm was observed and a partial-level scheme for this isotope is suggested. In addition γ transitions from excited levels are reported for 253 Md. (orig.)

Xylene isomerization

KAUST Repository

Bilaus, Rakan Sulaiman

2016-06-23

A process for producing xylenes, in particular para-xylene that is less energy intensive than conventional processes is provided. In an embodiment the process comprises contacting a feed mixture in an isomenzation zone with a catalyst at isomenzation conditions and producing an isomerized product comprising a higher proportion of p-xylene than in the feed mixture, wherein the catalyst comprises an acidic sulfonated catalytic membrane. Xylene isomenzation can also be coupled with a p-xylene extraction process, where the raffinate (p-xylene deprived stream) from the extraction process is fed to an isomenzation reactor to produce p-xylene. In an embodiment, the process can comprise: a) providing a feed stream comprising a mixture of xylene isomers including p-xylene; b) extracting p-xylene from the feed stream using a separator to separate the feed stream into a p-xylene rich stream and a p-xylene deprived stream; and c) delivering the p-xylene deprived stream to an isomenzation unit, the isomenzation unit including an acidic sulfonated catalytic membrane, and using the isomenzation unit to produce an isomerized product comprising a higher proportion of p-xylene than in the p-xylene deprived stream delivered to the isomenzation unit. In any one or more aspects, the isomenzation unit can be operated at a temperature in the range of less than 350°, for example about 20°C to about 200°C.

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.

Science.gov (United States)

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.

Narrowband NIR-Induced In Situ Generation of the High-Energy Trans Conformer of Trichloroacetic Acid Isolated in Solid Nitrogen and its Spontaneous Decay by Tunneling to the Low-Energy Cis Conformer

Directory of Open Access Journals (Sweden)

R. F. G. Apóstolo

2015-12-01

Full Text Available The monomeric form of trichloroacetic acid (CCl3COOH; TCA was isolated in a cryogenic nitrogen matrix (15 K and the higher energy trans conformer (O=C–O–H dihedral: 180° was generated in situ by narrowband near-infrared selective excitation the 1st OH stretching overtone of the low-energy cis conformer (O=C–O–H dihedral: 0°. The spontaneous decay, by tunneling, of the generated high-energy conformer into the cis form was then evaluated and compared with those observed previously for the trans conformers of acetic and formic acids in identical experimental conditions. The much faster decay of the high-energy conformer of TCA compared to both formic and acetic acids (by ~35 and ca. 25 times, respectively was found to correlate well with the lower energy barrier for the trans→cis isomerization in the studied compound. The experimental studies received support from quantum chemistry calculations undertaken at the DFT(B3LYP/cc-pVDZ level of approximation, which allowed a detailed characterization of the potential energy surface of the molecule and the detailed assignment of the infrared spectra of the two conformers.

Theoretical study of isomerization and decomposition of propenal

International Nuclear Information System (INIS)

Chin, Chih-Hao; Lee, Shih-Huang

2011-01-01

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

Thermolysis of (1R,2R)-1,2-dideuteriocyclobutane. An application of vibrational circular dichroism to kinetic analysis

International Nuclear Information System (INIS)

Chickos, J.S.; Annamalai, A.; Keiderling, T.A.

1986-01-01

The relative rates of geometric isomerization to racemization have been studied for the title compound by using a combination of infrared (IR) and vibrational circular dichroism (VCD) spectroscopies, respectively. The results are interpreted with a kinetic and mechanistic scheme which parallels that used by Berson, Pedersen, and Carpenter on a similar study of chiral cyclopropane-d 2 thermolysis. Relative rates of isomerization to stereomutation of 1.5 +/- 0.4 were obtained which can be interpreted to be consistent with a mechanism best described by random methylene rotation in tetramethylene-d 2 . This is the first application of VCD to kinetic analysis, and the advantages of IR techniques over the more usually employed UV spectroscopies to this type of basic mechanistic problem are illustrated

Poly (3, 4-ethylendioxithiophene) (PEDOT) oxidation: activation energy and conformational energy

International Nuclear Information System (INIS)

Otero, T F; Romero, M C

2008-01-01

The oxidation kinetics of films of the conducting polymer PEDOT-C1O4 after electrochemical reduction by polarization at increasing cathodic potential was studied by potential steps. The response i/t presents a maximum at intermediate oxidation times. At the maximum the reaction occurs under chemical kinetic control following the expected current variations from the Chemical and Electrochemical Kinetics, when reactant concentrations or temperatures are changed. The obtained activation energy of the oxidation present two ranges as a function of the cathodic potential of prepolarization: constant values after prepolarization at low cathodic potentials and a lineal variation after prepolarization at increasing high cathodic potentials. According with the conformational relaxation model during electrochemical reduction the polymer shrinks, closes and packs the conformational structure. The activation energy for the subsequent oxidation includes two terms: the constant chemical activation energy and the conformational energy required to relax the packed polymeric structure. The conformational energy only appears after prepolarization at more cathodic potentials than the closing potential where more packed conformations were obtained. The conformational activation energy accounts the energetic requirements to relax and unfold the polymeric chains generating the required free volume to lodge balancing counterions; meanwhile the chemical activation energy accounts the energetic requirements for the electrochemical reaction to occur.

Isomerization of C[sub 4] alkenes

Science.gov (United States)

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.

Evaluation of excitation functions for isomeric levels in neutron reactions

International Nuclear Information System (INIS)

Grudzevich, O.T.; Zelenetskij, A.V.; Zolotarev, K.I.; Kornilov, N.V.; Pashchenko, A.B.

1993-07-01

The authors consider the use of theoretical models to describe experimental excitation functions for isomeric levels in neutron reactions and to predict the cross-sections when no experimental data are available. It is shown that, in many cases, experimental data can be described quite satisfactorily by calculations without adjustment of parameters. For threshold reactions at a neutron energy of ∼ 14 MeV the agreement between calculated and experimental isomeric ratios is ∼ 20%, and is determined mainly by errors in the experimental ratios. However, for some reactions there are considerable differences between experimental and calculated data, which are due, in the authors' opinion, to uncertainties in the schemes of the low-lying levels and of gamma transitions between levels and to the spin dependence of level density. The small isomeric ratio values R<0.1 are described with the lowest accuracy. A formula is suggested for the energy dependence of the isomeric ratio in the (n,γ) reaction. (author)

Glucose Isomerization by Enzymes and Chemo-catalysts: Status and Current Advances

DEFF Research Database (Denmark)

Li, Hu; Yang, Song; Saravanamurugan, Shunmugavel

2017-01-01

of isomerization of aldoses in terms of yields, catalysts, solvents, catalytic systems, etc., by both enzymatic and chemo-catalytic approaches. Among aldose ketose interconversion reactions, fructose production by glucose isomerization to make high-fructose corn syrup (HFCS) is an industrially important and large....../intermediate fructose. This review focuses on how both enzyme and chemo-catalysts are being useful for the isomerization of glucose to fructose. Specifically, development of Lewis acid containing zeolites for glucose isomerization is reviewed in detail, including mechanism, isotopic labeling, and computational studies....... biocatalytic process today, and a large number of studies have been reported on the process development. In parallel, also alternative chemo-catalytic systems have emerged, as enzymatic conversion has drawbacks, though they are typically more selective and produce fructose under mild reaction conditions...

High-spin μs isomeric states in 96 Ag

International Nuclear Information System (INIS)

Becerril, A. D.; Lorusso, G.; Amthor, A. M.; Brown, B. A.; Estrade, A.; Guess, C. J.; Hitt, G. W.; Meharchand, R.; Schatz, H.; Smith, K.; Zegers, R. G. T.; Baumann, T.; Bazin, D.; Ginter, T.; Hausmann, M.; Minamisono, K.; Portillo, M.; Stolz, A.; Berryman, J. S.; Crawford, H. L.

2011-01-01

The isomeric and β decays of the N=Z+2 nucleus 96 Ag were investigated at the National Superconducting Cyclotron Laboratory. A cascade of γ-ray transitions originating from the deexcitation of a microsecond isomer was observed for the first time and was found in coincidence with two previously known transitions with energies of 470 and 667 keV. The isomeric half-life was determined as 1.45(7) μs, more precise than previously reported. The existence of a second, longer-lived microsecond isomer, associated with a 743-keV γ transition, is also proposed here. Shell model results within the (p 3/2 p 1/2 f 5/2 g 9/2 ) model space, using the jj44b interaction, reproduced level energies and isomeric decay half-lives reasonably well.

Xylose Isomerization with Zeolites in a Two-Step Alcohol–Water Process

DEFF Research Database (Denmark)

Paniagua, Marta; Shunmugavel, Saravanamurugan; Melián Rodriguez, Mayra

2015-01-01

Isomerization of xylose to xylulose was efficiently catalyzed by large-pore zeolites in a two-step methanol–water process that enhanced the product yield significantly. The reaction pathway involves xylose isomerization to xylulose, which, in part, subsequently reacts with methanol to form methyl...

The development of isomerization catalysts for production of high-octane products

Energy Technology Data Exchange (ETDEWEB)

Pedrosa, A.M. Garrido; Melo, D.M.A.; Araujo, A.S. [Universidade Federal do Rio Grande do Norte, Natal, RN (Brazil). Dept. de Quimica; Souza, M.J.B.; Silva, A.O.S. [Universidade Federal do Rio Grande do Norte, Natal, RN (Brazil). Dept. de Engenharia Quimica

2004-07-01

In current petroleum industry, paraffins larger than C5 are used for catalytic reform. The catalytic reform is one of the most important processes for petroleum refine in reason of all reactions they drive to production of high-octane products. Reformate has high-octane products, but they contain 60% aromatics. Isomerization of C5- C7 can improve the octane number. The octane number of n-heptane is zero and increases after isomerization. For tri branched C7, the octane number reaches 113, which is higher than that of benzene. So, isomerization of C5-C7 is suggested to be a reasonable way to replace or partly replace the catalytic reforming process. It can decrease aromatics content with enhancement of octane number. Liquid acid catalysts were widely used in chemical industry in past decades. However, they face strong environmental challenges. The heavy corrosion of the reactor system is one of the main problems. Thus, solid acid catalysts are investigated for the isomerization reactions. The aim of this work is to develop a catalysts for the production of reformate products. Isomerization is catalyzed by metal-acid bifunctional catalysts. The metal components aid in hydrogenation, while the support, such as, zirconium, clays or zeolites, is the acidic component. (author)

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

Directory of Open Access Journals (Sweden)

Hongtao Zhu

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

Improving gasoline quality produced from MIDOR light naphtha isomerization unit

Directory of Open Access Journals (Sweden)

M.F. Mohamed

2017-03-01

Full Text Available Isomerization process became one of the best gasoline production sources, as it gives a high octane product while saving environment from pollution impacts. This paper presents a practical study that aims to improve the gasoline quality and economic income of an existing light naphtha isomerization unit used for octane improvement. The study included selecting the optimum combination of isomerization unit equipment that gives better product specifications for a specified feed. Eight scenarios were studied and simulated to predict the product specs. The original studied unit is MIDOR light naphtha isomerization unit at Alexandria-Egypt that recycles the unconverted hexane (C6. The other studied scenarios were adding fractionators for separating feed iso-pentanes, and recycling unconverted pentanes, hexanes and/or combinations of these fractionators. The results show a change in octane number of gasoline product for a specific feed. Once through process with no extra fractionators has lower octane number of 81 while that with de-iso-pentanizer–de-pentanizer and de-hexanizer produces gasoline with 92.3 octane number. Detailed economic study was done to calculate the return on investment “ROI” for each process option based on equipment, utilities, feed and product prices. Once through simple isomerization unit had the lowest ROI of 14.3% per year while the combination of De-iso-pentanizer with the De-hexanizer had the best ROI of 26.6% per year.

Isomerization Intermediates In Solution Phase Photochemistry Of Stilbenes

Science.gov (United States)

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.

cis–trans Isomerization of silybins A and B

Directory of Open Access Journals (Sweden)

Michaela Novotná

2014-05-01

Full Text Available Methods were developed and optimized for the preparation of the 2,3-cis- and the 10,11-cis-isomers of silybin by the Lewis acid catalyzed (BF3∙OEt2 isomerization of silybins A (1a and B (1b (trans-isomers. The absolute configuration of all optically pure compounds was determined by using NMR and comparing their electronic circular dichroism data with model compounds of known absolute configurations. Mechanisms for cis–trans-isomerization of silybin are proposed and supported by quantum mechanical calculations.

Left cardiac isomerism in the Sonic hedgehog null mouse.

Science.gov (United States)

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

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

DEFF Research Database (Denmark)

Petersen, Mette Terp; Nielsen, Thomas Eiland

2013-01-01

A series of 5-substituted 2-pyrrolidinones was synthesized through a one-pot ruthenium alkylidene-catalyzed tandem RCM/isomerization/nucleophilic addition sequence. The intermediates resulting from RCM/isomerization showed reactivity toward electrophiles in aldol condensation reactions which...

Synthesis, structure and isomerism of three-bridge exo-nido-osmacarborane clusters

International Nuclear Information System (INIS)

Kolomnikova, G.D.; Petrovskij, P.V.; Sorokin, P.V.; Dolgushin, F.M.; Yanovskij, A.I.; Chizhevskij, I.T.

2001-01-01

The structure and isomerism of exo-nido-osmacarboranes prepared by reaction between coordination-unsaturated complex OsCl 2 (PPh 3 ) 3 (Ph-phenyl) in benzene at 20 deg C and K + -salts of nido-dicarbaundecarborate anions were studied by the methods of 1 H and 11 B NMR (including usual and two-dimensional spectra) and X-ray diffraction analysis. It was ascertained that in the compounds prepared osmium-containing group is bound with nido-carborane ligand via three-center bonds, open pentagonal plane of carborane ligand being retained in the isomers. In it nature isomerism in the compounds mentioned is geometrical cis-trans-isomerism [ru

Ground-state kinetics of bistable redox-active donor-acceptor mechanically interlocked molecules.

Science.gov (United States)

Fahrenbach, Albert C; Bruns, Carson J; Li, Hao; Trabolsi, Ali; Coskun, Ali; Stoddart, J Fraser

2014-02-18

The ability to design and confer control over the kinetics of theprocesses involved in the mechanisms of artificial molecular machines is at the heart of the challenge to create ones that can carry out useful work on their environment, just as Nature is wont to do. As one of the more promising forerunners of prototypical artificial molecular machines, chemists have developed bistable redox-active donor-acceptor mechanically interlocked molecules (MIMs) over the past couple of decades. These bistable MIMs generally come in the form of [2]rotaxanes, molecular compounds that constitute a ring mechanically interlocked around a dumbbell-shaped component, or [2]catenanes, which are composed of two mechanically interlocked rings. As a result of their interlocked nature, bistable MIMs possess the inherent propensity to express controllable intramolecular, large-amplitude, and reversible motions in response to redox stimuli. In this Account, we rationalize the kinetic behavior in the ground state for a large assortment of these types of bistable MIMs, including both rotaxanes and catenanes. These structures have proven useful in a variety of applications ranging from drug delivery to molecular electronic devices. These bistable donor-acceptor MIMs can switch between two different isomeric states. The favored isomer, known as the ground-state co-conformation (GSCC) is in equilibrium with the less favored metastable state co-conformation (MSCC). The forward (kf) and backward (kb) rate constants associated with this ground-state equilibrium are intimately connected to each other through the ground-state distribution constant, KGS. Knowing the rate constants that govern the kinetics and bring about the equilibration between the MSCC and GSCC, allows researchers to understand the operation of these bistable MIMs in a device setting and apply them toward the construction of artificial molecular machines. The three biggest influences on the ground-state rate constants arise from

Relation between Protein Intrinsic Normal Mode Weights and Pre-Existing Conformer Populations.

Science.gov (United States)

Ozgur, Beytullah; Ozdemir, E Sila; Gursoy, Attila; Keskin, Ozlem

2017-04-20

Intrinsic fluctuations of a protein enable it to sample a large repertoire of conformers including the open and closed forms. These distinct forms of the protein called conformational substates pre-exist together in equilibrium as an ensemble independent from its ligands. The role of ligand might be simply to alter the equilibrium toward the most appropriate form for binding. Normal mode analysis is proved to be useful in identifying the directions of conformational changes between substates. In this study, we demonstrate that the ratios of normalized weights of a few normal modes driving the protein between its substates can give insights about the ratios of kinetic conversion rates of the substates, although a direct relation between the eigenvalues and kinetic conversion rates or populations of each substate could not be observed. The correlation between the normalized mode weight ratios and the kinetic rate ratios is around 83% on a set of 11 non-enzyme proteins and around 59% on a set of 17 enzymes. The results are suggestive that mode motions carry intrinsic relations with thermodynamics and kinetics of the proteins.

High-Pressure Limit Rate Rules for α-H Isomerization of Hydroperoxyalkylperoxy Radicals

KAUST Repository

Mohamed, Samah Y

2018-03-09

Hydroperoxyalkylperoxy (OOQOOH) radical isomerization is an important low-temperature chain branching reaction within the mechanism of hydrocarbon oxidation. This isomerization may proceed via the migration of the α-hydrogen to the hydroperoxide group. In this work, a combination of high level composite methods - CBS-QB3, G3 and G4 - is used to determine the high-pressure-limit rate parameters for the title reaction. Rate rules for H-migration reactions proceeding through 5-, 6-, 7- and 8-membered ring transitions states are determined. Migrations from primary, secondary and tertiary carbon sites to the peroxy group are considered. Chirality is also investigated by considering two diastereomers for reactants and transition states with two chiral centers. This is important since chirality may influence the energy barrier of the reaction as well as the rotational energy barriers of hindered rotors in chemical species and transition states. The effect of chirality and hydrogen bonding interactions in the investigated energies and rate constants is studied. The results show that while the energy difference between two diastereomers ranges from 0.1 - 3.2 kcal, chirality hardly affects the kinetics, except at low temperatures (atmospheric conditions) or when two chiral centers are present in the reactant. Regarding the effects of the peroxy group position and the H-migration ring size, it is found that in most cases, the 1,5 and 1,6 H-migration reactions have similar rates at low temperatures (below ~830K) since the 1,6 H-migration proceeds via a cyclohexane-like transition state similar to that of the 1,5 H-migration.

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

Science.gov (United States)

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.

Deconstructing field-induced ketene isomerization through Lagrangian descriptors.

Science.gov (United States)

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.

Rigid supersymmetry from conformal supergravity in five dimensions

International Nuclear Information System (INIS)

Pini, Alessandro; Rodriguez-Gomez, Diego; Schmude, Johannes

2015-01-01

We study the rigid limit of 5d conformal supergravity with minimal supersymmetry on Riemannian manifolds. The necessary and sufficient condition for the existence of a solution is the existence of a conformal Killing vector. Whenever a certain SU(2) curvature becomes abelian the backgrounds define a transversally holomorphic foliation. Subsequently we turn to the question under which circumstances these backgrounds admit a kinetic Yang-Mills term in the action of a vector multiplet. Here we find that the conformal Killing vector has to be Killing. We supplement the discussion with various appendices.

Isomerizations of the Nitromethane Radical Cation in the Gas Phase

DEFF Research Database (Denmark)

Egsgaard, Helge; Carlsen, Lars; Elbel, Susanne

1986-01-01

The concurrent isomerizations of the nitromethane radical cation to its aci-nitromethane and methylnitrite isomers, respectively, has been established based on metastable ion studies and collision activation mass spectrometry. The energy diagram for the ionized nitromethane/aci-nitromethane tauto......The concurrent isomerizations of the nitromethane radical cation to its aci-nitromethane and methylnitrite isomers, respectively, has been established based on metastable ion studies and collision activation mass spectrometry. The energy diagram for the ionized nitromethane...

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

Science.gov (United States)

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.

Conformational inversion-topomerization mechanism of ethylcyclohexyl isomers and its role in combustion kinetics

KAUST Repository

Bian, Huiting

2016-07-26

With the "strain-free" cyclic structure, cyclohexane and alkyl cyclohexanes (and their radicals) have various conformers (e.g. chair, boat, and twist etc.) by pseudorotation of the alkyl ring. Noting that different conformers will undergo different types of H-migration reactions, the mechanism of conformational change may impact the distribution of cyclohexyl and the branched cyclohexyl radical isomers during cyclohexane and alkyl cyclohexanes combustion. Consequently, it will influence the formation of subsequent decomposition products. In this work, the conformational inversion-topomerization mechanism and H-migration reactions for six ethylcyclohexyl radical isomers were systematically studied by ab initio calculations and the transition state theory. The updated sub-mechanism of these conformational changes is incorporated into an ethylcyclohexane pyrolysis model. By comparing the simulated results of the "complete" model including the sub-mechanism of conformational changes and the simplified model ignoring these processes, the effect of inversion-topomerization mechanism on the relative concentrations of various ethylcyclohexyl radicals and the formation of subsequent decomposition products were revealed. © 2016.

Excitation functions and isomeric ratios for the isomeric pair sup(106m)Ag and sup(106g)Ag in the 107Ag (d,t) reaction

International Nuclear Information System (INIS)

Lalli, M.E.; Wasilevsky de Lammirato, C.; Herreros, O.R.; Nassiff, S.J.

1976-09-01

Excitation functions and isomeric cross section ratios have been measured for the 107 Ag (d,t), reaction in which the isomeric pair sup(106m/106g)Ag is produced. Thick-target yields have been determined for different irradiation times and as a function of deuteron energy. Stacked silver foils with aluminium foils as monitors were bombarded with deuterons up to 27 MeV and the activities of products measured with a calibrated Ge(Li) counter. (author) [es

A detailed chemical kinetic model for pyrolysis of the lignin model compound chroman

Directory of Open Access Journals (Sweden)

James Bland

2013-12-01

Full Text Available The pyrolysis of woody biomass, including the lignin component, is emerging as a potential technology for the production of renewable fuels and commodity chemicals. Here we describe the construction and implementation of an elementary chemical kinetic model for pyrolysis of the lignin model compound chroman and its reaction intermediate ortho-quinone methide (o-QM. The model is developed using both experimental and theoretical data, and represents a hybrid approach to kinetic modeling that has the potential to provide molecular level insight into reaction pathways and intermediates while accurately describing reaction rates and product formation. The kinetic model developed here can replicate all known aspects of chroman pyrolysis, and provides new information on elementary reaction steps. Chroman pyrolysis is found to proceed via an initial retro-Diels–Alder reaction to form o-QM + ethene (C2H4, followed by dissociation of o-QM to the C6H6 isomers benzene and fulvene (+ CO. At temperatures of around 1000–1200 K and above fulvene rapidly isomerizes to benzene, where an activation energy of around 270 kJ mol-1 is required to reproduce experimental observations. A new G3SX level energy surface for the isomerization of fulvene to benzene supports this result. Our modeling also suggests that thermal decomposition of fulvene may be important at around 950 K and above. This study demonstrates that theoretical protocols can provide a significant contribution to the development of kinetic models for biomass pyrolysis by elucidating reaction mechanisms, intermediates, and products, and also by supplying realistic rate coefficients and thermochemical properties.

Exploring the free energy landscape: from dynamics to networks and back.

Directory of Open Access Journals (Sweden)

Diego Prada-Gracia

2009-06-01

Full Text Available Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.

Green Synthesis of Carvenone by Montmorillonite-Catalyzed Isomerization of 1,2-Limonene Oxide

DEFF Research Database (Denmark)

Nguyen, Thao-Tran Thi; Chau, Duy-Khiem Nguyen; Duus, Fritz

2013-01-01

Montmorillonite was considered as a good heterogeneous catalyst for the isomerization of 1,2-limonene oxide into car-venone under solvent-free condition. Both conventional heating and green activations were tested in this research. The microwave-assisted isomerization afforded carvenone in high...

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

Science.gov (United States)

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].

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

Science.gov (United States)

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

2018-04-10

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

Conformational Explosion: Understanding the Complexity of the Para-Dialkylbenzene Potential Energy Surfaces

Science.gov (United States)

Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

2017-06-01

This talk focuses on the single-conformation spectroscopy of small-chain para-dialkylbenzenes. This work builds on previous studies from our group on long-chain n-alkylbenzenes that identified the first folded structure in octylbenzene. The dialkylbenzenes are representative of a class of molecules that are common components of coal and aviation fuel and are known to be present in vehicle exhaust. We bring the molecules para-diethylbenzene, para-dipropylbenzene and para-dibutylbenzene into the gas phase and cool the molecules in a supersonic expansion. The jet-cooled molecules are then interrogated using laser-induced fluorescence excitation, fluorescence dip IR spectroscopy (FDIRS) and dispersed fluorescence. The LIF spectra in the S_{0}-S_{1} origin region show dramatic increases in the number of resolved transitions with increasing length of alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an 'egg carton' shape to the potential energy surface. We use a combination of electronic frequency shift and alkyl CH stretch infrared spectra to generate a consistent set of conformational assignments.

A comprehensive iso-octane combustion model with improved thermochemistry and chemical kinetics

KAUST Repository

Atef, Nour

2017-02-05

Iso-Octane (2,2,4-trimethylpentane) is a primary reference fuel and an important component of gasoline fuels. Moreover, it is a key component used in surrogates to study the ignition and burning characteristics of gasoline fuels. This paper presents an updated chemical kinetic model for iso-octane combustion. Specifically, the thermodynamic data and reaction kinetics of iso-octane have been re-assessed based on new thermodynamic group values and recently evaluated rate coefficients from the literature. The adopted rate coefficients were either experimentally measured or determined by analogy to theoretically calculated values. Furthermore, new alternative isomerization pathways for peroxy-alkyl hydroperoxide (ȮOQOOH) radicals were added to the reaction mechanism. The updated kinetic model was compared against new ignition delay data measured in rapid compression machines (RCM) and a high-pressure shock tube. These experiments were conducted at pressures of 20 and 40 atm, at equivalence ratios of 0.4 and 1.0, and at temperatures in the range of 632–1060 K. The updated model was further compared against shock tube ignition delay times, jet-stirred reactor oxidation speciation data, premixed laminar flame speeds, counterflow diffusion flame ignition, and shock tube pyrolysis speciation data available in the literature. Finally, the updated model was used to investigate the importance of alternative isomerization pathways in the low temperature oxidation of highly branched alkanes. When compared to available models in the literature, the present model represents the current state-of-the-art in fundamental thermochemistry and reaction kinetics of iso-octane; and thus provides the best prediction of wide ranging experimental data and fundamental insights into iso-octane combustion chemistry.

Trimethylphosphide isomerization in lanthanum ions presence

International Nuclear Information System (INIS)

Zacharias, M.A.; Massabni, A.M.G.

1984-01-01

The integration between the trimethilphosphide and the lanthanum ions carry to the formation of solid complexes in a relation of 6:1 where the ligand is the phosphonate what is resultant of the isomerization of trimetylphosphite. By the RMN -1 H and infra-red spectra the products were characterized. (L.M.J.) [pt

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

Science.gov (United States)

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

Kinetics of protein unfolding at interfaces

International Nuclear Information System (INIS)

Yano, Yohko F

2012-01-01

The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

Stability and isomerization reactions of phenyl cation C{sub 6}H{sub 5}{sup +} isomers

Energy Technology Data Exchange (ETDEWEB)

Shi, Dandan [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yang, Xue [College of Science, Jilin Institute of Chemical Technology, Jilin 132022 (China); Zhang, Xiaomei; Shan, Shimin [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Xu, Haifeng, E-mail: xuhf@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China); Yan, Bing, E-mail: yanbing@jlu.edu.cn [Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012 (China); Jilin Provincial Key Laboratory of Applied Atomic and Molecular Spectroscopy (Jilin University), Changchun 130012 (China)

2016-03-01

Highlights: • A total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations were obtained at density functional theory. • The stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers were performed. • The structures, frequencies, thermodynamic properties of isomers were summarized. • Ring to ring or chain isomerization pathways were investigated using IRC method. • Result shows reactions contain hydrogen transfer, bond broken and reconstruction. - Abstract: As a key polyatomic molecular cation that plays a pivotal role in growth of the polycyclic aromatic hydrocarbons, phenyl cation C{sub 6}H{sub 5}{sup +} exhibits various isomers and isomerization reactions. Investigation on the structure and stability of the isomers as well as the isomerization is important for better understanding the chemical reactions involving C{sub 6}H{sub 5}{sup +} cations. In this work, we have performed a theoretical study on the stability and isomerization reactions of C{sub 6}H{sub 5}{sup +} isomers at density functional theory B3LYP/6-311G (d, p) level. We have obtained a total of 60 isomers of C{sub 6}H{sub 5}{sup +} cations, most of which are reported for the first time. The geometries, vibrational frequencies, thermodynamic properties and stability of 28 out of 60 isomers have been summarized in detail. Different ring-to-ring and ring-to-chain isomerization pathways, which are connected via 28 transition states, have been investigated using the intrinsic reaction coordinate method. The results show that the isomerization reactions occur via hydrogen migration followed by bond-breaking and reconstruction.

Arbitrary spin conformal fields in (A)dS

International Nuclear Information System (INIS)

Metsaev, R.R.

2014-01-01

Totally symmetric arbitrary spin conformal fields in (A)dS space of even dimension greater than or equal to four are studied. Ordinary-derivative and gauge invariant Lagrangian formulation for such fields is obtained. Gauge symmetries are realized by using auxiliary fields and Stueckelberg fields. We demonstrate that Lagrangian of conformal field is decomposed into a sum of gauge invariant Lagrangians for massless, partial-massless, and massive fields. We obtain a mass spectrum of the partial-massless and massive fields and confirm the conjecture about the mass spectrum made in the earlier literature. In contrast to conformal fields in flat space, the kinetic terms of conformal fields in (A)dS space turn out to be diagonal with respect to fields entering the Lagrangian. Explicit form of conformal transformation which maps conformal field in flat space to conformal field in (A)dS space is obtained. Covariant Lorentz-like and de-Donder like gauge conditions leading to simple gauge-fixed Lagrangian of conformal fields are proposed. Using such gauge-fixed Lagrangian, which is invariant under global BRST transformations, we explain how the partition function of conformal field is obtained in the framework of our approach

Dehydrogenation and concurrent isomerization of n-butenes on mixed tin and antimony oxide catalysts

Energy Technology Data Exchange (ETDEWEB)

Irvine, E.A.; Taylor, D.

1978-01-01

The dehydrogenation and concurrent isomerization of n-butenes on mixed tin and antimony oxide catalysts which had been outgassed at 698/sup 0/K were carried out in the presence of oxygen at 474/sup 0/K, and the initial approximately zero-order rates of 1,3-butadiene formation and rates of isomerization were used as a measure of catalytic activity to construct activity patterns as a function of catalyst composition. A comparison of the patterns with those for the isomerization of 3,3-dimethyl-1-butene and for the selective oxidation of propane on the same catalysts indicated that the dehydrogenation of 1-butene involves a m-allyl intermediate, but isomerization occurs through carbonium ion formation. For the cis- and trans-isomers, both reactions apparently occurred via a common allyl (but not m-allyl) intermediate. Dehydrogenation to butadiene decreased in the order 1-butene > cis-2-butene trans-2-butene and was maximum at 10% antimony for 1-butene and 21% antimony for 2-butene. Isomerization was always slower than dehydrogenation and showed two maEima, at 21 (or 27%) and at 75% antimony.

Crystal structure of isomeric boron difluoride acetylnaphtholates

International Nuclear Information System (INIS)

Bukvetskij, B.V.; Fedorenko, E.V.; Mirochnik, A.G.; Karasev, V.E.

2006-01-01

Crystal structures of luminescent isomeric acetylnaphtholates of boron difluoride are investigated. Full X-ray structural analysis is done at 293 K. Coordinated of atoms, bond angles, bond lengths, interatomic distances are determined. Results of comparative evaluations of the isomers are represented [ru

Evaluation of isomeric excitation functions in neutron induced reactions

International Nuclear Information System (INIS)

Grudzevich, O.; Ignatyuk, A.; Zolotarev, K.

1992-01-01

The possibilities of isomer levels experimental excitation functions description with theoretical models are discussed. It is shown that the experimental data in many cases can be described by theoretical models quite well without parameter fitting. However, large discrepancies are observed for some reactions. In our opinion, these discrepancies are due to uncertainties of discrete level schemes, schemes of gamma-transitions between levels and spin dependence of level density. Small values of isomeric ratios (< 0.1) have been described with the largest errors. The simple formulae for energy dependence of isomeric ratio for (n,g) reaction has been proposed. (author). 53 refs, 10 figs, 8 tabs

Control of structural isomerism in noncovalent hydrogen-bonded assemblies using peripheral chiral information

NARCIS (Netherlands)

Prins, L.J.; Jolliffe, K.A.; Hulst, A.J.R.L.; Timmerman, P.; Reinhoudt, David

2000-01-01

The results of a systematic study of the structural isomerism in more than 30 noncovalent hydrogen-bonded assemblies are described. These dynamic assemblies, composed of three calix[4]arene dimelamines and six barbiturates/cyanurates, can be present in three isomeric forms with either D3, C3h, or Cs

Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting.

Science.gov (United States)

Pan, Lucy Yan; Salas-Solano, Oscar; Valliere-Douglass, John F

Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in C H 2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.

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

International Nuclear Information System (INIS)

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

2010-01-01

Neutron deficient isotopes of francium (Z=87, N∼121-123) as excited nuclei were produced in the fusion-evaporation reaction: 197 Au( 16 O, xn) 213-x Fr at 100 MeV. The γ rays from the residues were observed through the high sensitivity Germanium Clover detector array INGA. The decay of the high spin states and the isomeric states of the doubly-odd 208 Fr nuclei, identified from the known sequence of ground state transitions, were observed. The half-lives of the E γ =194(2) keV isomeric transition, known from earlier observations, was measured to be T 1/2 =233(18) ns. A second isomeric transition at E γ =383(2) keV and T 1/2 =33(7) ns was also found. The measured half-lives were compared with the corresponding single particle estimates, based on the level scheme obtained from the experiment.

Isomeric periodic mesoporous organosilicas with controllable properties

NARCIS (Netherlands)

Vercaemst, C.; Ide, I.; Friedrich, H.; de Jong, K.P.; Verpoort, F.; van der Voort, P.

2009-01-01

The synthesis procedure for isomeric periodic mesoporous organosilicas with E-configured ethenylene bridges was investigated using the homemade pure E-isomer of 1,2-bis(triethoxysilyl)ethene. The pH, aging temperature and the presence of cosolvents played a key role in obtaining well-ordered

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Isomeric rations study for the α + 70 Ge

International Nuclear Information System (INIS)

Hora Villano, M.H. da.

1984-12-01

Isomeric ratios for 73 Se F,I produced in the reaction α + 70 Ge with incidence laboratory energy ranging from 8 to 28 MeV, have been measured using off-line γ-ray spectroscopy. Relative formation cross-section for isomeric and ground states were obtained with NAT Ge targets. Compound nucleus statistical analyses were performed using computer codes Alice and Julian. Unlike to Alice code, the Julian code predictions agreed quite well with the experimental results. This agreement may be explained by the inclusion of the γ competition in the deexcitation channels of the compound nucleus and by the correct level density calculation of the emission probabilities in the Julian code. Finally angular momentum populations for isomers formations in the reaction 70 Ge(α, n) 73 have been determined. (author)

Possible evidence for shape isomeric γ-decay in μ- atoms of 238U

International Nuclear Information System (INIS)

Fromm, W.D.; Ortlepp, H.-G.; Polikanov, S.M.; Schmidt, U.; Zorin, G.N.; Arlt, R.; Musiol, G.

1977-01-01

A search for the γ-decay of the shape isomer in muonic 238 U excited by radiationless transitions has been performed. Seven delayed transitions in the energy region of 700 to 3200 keV have been observed with a large Ge(Li) detector. Two transitions with Esub(γ)=2215 and 3131 keV have been attributed to the decay of the shape isomeric state into levels in the first well. The isomeric shift of the second minimum Esub(II) approximately 600 keV in the presence of the muon and the decrease of the lifetime of the shape isomer to tau=12+-2 ns give arguments in favour of the connection of shape isomerism with large quadrupole deformations. (Auth.)

Low-lying isomeric levels in Cu75

Science.gov (United States)

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

2010-03-01

Isomeric low-lying states were identified and investigated in the Cu75 nucleus. Two states at 61.8(5)- and 128.3(7)-keV excitation energies with half-lives of 370(40)- and 170(15)-ns were assigned as Cu75m1 and Cu75m2, respectively. The measured half-lives combined with the recent spin assignment of the ground state allow one to deduce tentatively spin and parity of the two isomers and the dominant multipolarities of the isomeric transitions with respect to the systematics of the Cu isotopes. Shell-model calculations using an up-to-date effective interaction reproduce the evolution of the 1/2-, 3/2-, and 5/2- states for the neutron-rich odd-mass Cu isotopes when filling the νg9/2. The results indicate a significant change in the nuclear structure in this region, where a single-particle 5/2- state coexists with more and more collective 3/2- and 1/2- levels at low excitation energies.

Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3 and Ammonia (NH3 Donor-Acceptor Complex

Directory of Open Access Journals (Sweden)

Dulal C. Ghosh

2004-09-01

Full Text Available The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule

Multi-quasiparticle high-K isomeric states in deformed nuclei

Directory of Open Access Journals (Sweden)

Xu F. R.

2016-01-01

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

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

Science.gov (United States)

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.

Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

Science.gov (United States)

Suo, Zucai

2014-01-01

Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been done to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer (FRET) to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. PMID:24931550

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

New isomeric states in 152,154,156Nd produced by spontaneous fission of 252Cf

International Nuclear Information System (INIS)

Gautherin, C.; Houry, M.; Korten, W.; Le Coz, Y.; Lucas, R.; Phan, X.H.; Theisen, C.; Belier, G.; Girod, M.; Meot, V.; Peru, S.; Astier, A.; Ducroux, L.; Meyer, M.; Redon, N.

1998-01-01

Isomeric states have been observed in fission-fragments produced by spontaneous fission of 252 Cf. These states are found in neutron rich nuclei of different structure and deformations. About 50 isomeric nuclei have been observed using coincidences between γ-rays identified in EUROGAM II and fission fragments detected in photovoltaic cells (SAPhIR). Lifetimes in the range from 20 ns to 2μs have been measured. Presented calculations based on HFB+D1S force on new measured isomeric states in the 152,154,156 Nd show evidence for K-isomers. (orig.)

Proton affinity of diastereoisomers of modified prolines using the kinetic method and density functional theory calculations: role of the cis/trans substituent on the endo/exo ring conformation.

Science.gov (United States)

Mezzache, S; Pepe, C; Karoyan, P; Fournier, F; Tabet, J-C

2005-01-01

The proton affinity (PA) of cis/trans-3-prolinoleucines and cis/trans-3-prolinoglutamic acids have been studied by the kinetic method and density functional theory (DFT) calculations. Several conformations of the neutral and the protonated modified prolines, in particular the endo and exo ring conformations, were analyzed with respect to their contribution to the PA values. When the substituent is an alkyl, both the diastereoisomers have the same PA value. However, the PA values for the diastereoisomers are different when the substituted chain contains functional groups (e.g. a carboxyl group). This variation in PA values could be attributed to the existence of intramolecular hydrogen bonds. Copyright (c) 2005 John Wiley & Sons, Ltd.

Determination of the active site and mechanism for alkene isomerization in Cu(II) exchnaged Y-type zeolite

Energy Technology Data Exchange (ETDEWEB)

John, C S; Leach, H F

1977-01-01

An ESR study of 1-butene isomerization at 315/sup 0/-375/sup 0/C, 3,3-dimethyl-1-butene isomerization to 2,3-dimethyl-1- and -2-butene at 293/sup 0/K, and deuterium redistribution in 3,3-dideuteriopropene at 363/sup 0/-396/sup 0/K showed the presence of two copper(II) species in different environments, which reacted with the olefins at different rates. Although activation energies for the three reactions differed and only dideuteriopropene showed an induction period, a similar mechanism is proposed in all cases, involving preliminary reduction of copper(II), with the rates of reduction and isomerization differing from olefin to olefin. Apparently, the active site for the isomerization is a Broensted acid generated by the reduction, and the isomerization follows an associative (proton addition-elimination) mechanism with a carbonium ion intermediate. Spectra, graphs, diagram, and 12 references.

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

Science.gov (United States)

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).

Energetically Unfavorable Amide Conformations for N6-Acetyllysine Side Chains in Refined Protein Structures

Science.gov (United States)

Genshaft, Alexander; Moser, Joe-Ann S.; D'Antonio, Edward L.; Bowman, Christine M.; Christianson, David W.

2013-01-01

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular “switch” for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly-accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations. PMID:23401043

Preparing isomerically pure beams of short-lived nuclei at JYFLTRAP

Energy Technology Data Exchange (ETDEWEB)

Eronen, T. [Department of Physics, University of Jyvaeskylae, P.O. Box 35 (YFL), FIN-40014 (Finland)], E-mail: tommi.eronen@jyu.fi; Elomaa, V.-V.; Hager, U.; Hakala, J.; Jokinen, A.; Kankainen, A.; Rahaman, S.; Rissanen, J.; Weber, C.; Aystoe, J. [Department of Physics, University of Jyvaeskylae, P.O. Box 35 (YFL), FIN-40014 (Finland)

2008-10-15

A new procedure to prepare isomerically clean samples of short-lived ions with a mass resolving power of more than 1 x 10{sup 5} has been developed at the JYFLTRAP tandem Penning trap system. The method utilises a dipolar rf-excitation of the ion motion with separated oscillatory fields in the precision trap. During a subsequent retransfer to the purification trap, the contaminants are rejected and as a consequence, the remaining bunch is isomerically cleaned. This newly-developed method is suitable for very high-resolution cleaning and is at least a factor of five faster than the methods used so far in Penning trap mass spectrometry.

Conformational explosion: Understanding the complexity of short chain para-dialkylbenzene potential energy surfaces

Science.gov (United States)

Mishra, Piyush; Hewett, Daniel M.; Zwier, Timothy S.

2018-05-01

The single-conformation ultraviolet and infrared spectroscopy of three short-chain para-dialkylbenzenes (para-diethylbenzene, para-dipropylbenzene, and para-dibutylbenzene) is reported for the jet-cooled, isolated molecules. The present study builds off previous work on single-chain n-alkylbenzenes, where an anharmonic local mode Hamiltonian method was developed to account for stretch-bend Fermi resonance in the alkyl CH stretch region [D. P. Tabor et al., J. Chem. Phys. 144, 224310 (2016)]. The jet-cooled molecules are interrogated using laser-induced fluorescence (LIF) excitation, fluorescence dip infrared spectroscopy, and dispersed fluorescence. The LIF spectra in the S1 ← S0 origin region show a dramatic increase in the number of resolved transitions with increasing length of the alkyl chains, reflecting an explosion in the number of unique low-energy conformations formed when two independent alkyl chains are present. Since the barriers to isomerization of the alkyl chain are similar in size, this results in an "egg carton" shaped potential energy surface. A combination of electronic frequency shift and alkyl CH stretch infrared spectra is used to generate a consistent set of conformational assignments. Using these experimental techniques in conjunction with computational methods, subsets of origin transitions in the LIF excitation spectrum can be classified into different conformational families. Two conformations are resolved in para-diethylbenzene, seven in para-dipropylbenzene, and about nineteen in para-dibutylbenzene. These chains are largely independent of each other as there are no new single-chain conformations induced by the presence of a second chain. A cursory LIF excitation scan of para-dioctylbenzene shows a broad congested spectrum at frequencies consistent with interactions of alkyl chains with the phenyl π cloud.

Synthesis and Characterisation of Eight Isomeric Bis(2-pyridyloxynaphthalenes

Directory of Open Access Journals (Sweden)

Peter J. Steel

2006-09-01

Full Text Available Eight isomeric bis(2-pyridyloxynaphthalenes have been prepared from reactions of 2-bromopyridine with the appropriate dihydroxynaphthalene and the products fully characterised by 1- and 2-D NMR spectroscopy.

Combined Function of Brønsted and Lewis Acidity in the Zeolite-Catalyzed Isomerization of Glucose to Fructose in Alcohols

DEFF Research Database (Denmark)

Shunmugavel, Saravanamurugan; Riisager, Anders; Taarning, Esben

2016-01-01

Glucose conversion via fructose to useful chemicals and fuels has attracted considerable attention. Isomerization of glucose to fructose can proceed along several different reaction pathways involving different sugar intermediates and isomeric forms. Presently, the roles of the substrate isomeric...

K isomerism and collectivity in neutron-rich rare-earth isotopes

Science.gov (United States)

Patel, Zena

Neutron-rich rare-earth isotopes were produced by in-flight fission of 238U ions at the Radioactive Isotope Beam Factory (RIBF), RIKEN, Japan. In-flight fission of a heavy, high-intensity beam of 238U ions on a light target provides the cleanest secondary beams of neutron-rich nuclei in the rare-earth region of isotopes. In-flight fission is advantageous over other methods of nuclear production, as it allows for a secondary beam to be extracted, from which the beam species can be separated and identified. The excited states of nuclei are studied by delayed isomeric or beta-delayed gamma-ray spectroscopy. New K isomers were found in Sm (Z=62), Eu (Z=63), and Gd (Z=64) isotopes. The key results are discussed here. Excited states in the N=102 isotones 166Gd and 164Sm have been observed following isomeric decay for the first time. The K-isomeric states in 166Gd and 164Sm are due to 2-quasiparticle configurations. Based on the decay patterns and potential energy surface calculations, including beta6 deformation, both isomers are assigned a (6-) spin-parity. The half-lives of the isomeric states have been measured to be 950(60)ns and 600(140)ns for 166Gd and 164Sm respectively. Collective observables are discussed in light of the systematics of the region, giving insight into nuclear shape evolution. The decrease in the ground state band energies of 166Gd and 164Sm (N=102) compared to 164Gd and 162Sm (N=100) respectively, presents evidence for the predicted deformed shell closure at N=100. A 4-quasiparticle isomeric state has been discovered in 160Sm: the lightest deformed nucleus with a 4-quasiparticle isomer to date. The isomeric state is assigned an (11+) spin-parity with a measured half-life of 1.8(4)us. The (11+) isomeric state decays into a rotational band structure, based on a (6-) v5/2-[523] ⊗ v7/2+[633] bandhead, determined from the extracted gK-gR values. Potential energy surface and blocked BCS calculations were performed in the deformed midshell region

The study of a new short-life isomeric state in 38K

International Nuclear Information System (INIS)

Iordachescu, A.

1976-01-01

The 38 K nucleus having a protone and neutron hole coupled with a 40 Ca inert core has a structure analysed easily by the shell model. A new short life, high spin and highly excited isomeric state of the 38 K nucleus has been studied in detail using this model. Theoretical aspects connected with static and dynamic electromagnetic moments of the nucleus state, with the magnetic moment of the nucleus and the selection rules according to the isotopic spin are presented in the case of gamma transitions. Experimentallz/ presented in the case of gamma transitions. Experimentally, it has been used a combination between a natural pulsation of the cyclotron beam and an external pulsation by electrostatic deflexion, thus obtaining a pulsation beam of 12-26 MeV alpha particles. As targets, a series of chemical chlorine combinations have been utilized, the isomeric state being obtained by the reaction 35 Cl(α,n) 38 K, having the isomeric level (1fsub(7/2))sub(7+)sup(2). (author)

High spin states and isomeric decays in doubly-odd {sup 208}Fr

Energy Technology Data Exchange (ETDEWEB)

Kanjilal, D.; Bhattacharya, S.; Goswami, A.; Kshetri, R.; Raut, R. [Nuclear and Atomic Physics Division, Saha Institute of Nuclear Physics, Kolkata 700064 (India); Saha, S., E-mail: satyajit.saha@saha.ac.i [Nuclear and Atomic Physics Division, Saha Institute of Nuclear Physics, Kolkata 700064 (India); Bhowmik, R.K.; Gehlot, J.; Muralithar, S.; Singh, R.P. [Inter University Accelerator Centre, New Delhi 110067 (India); Jnaneswari, G. [Department of Physics, Andhra University, Vishakhapatnam 530003 (India); Mukherjee, G. [Variable Energy Cyclotron Centre, Kolkata 700064 (India); Mukherjee, B. [Department of Physics, Visva Bharati, Santiniketan 731235 (India)

2010-10-15

Neutron deficient isotopes of francium (Z=87, N{approx}121-123) as excited nuclei were produced in the fusion-evaporation reaction: {sup 197}Au({sup 16}O, xn) {sup 213-x}Fr at 100 MeV. The {gamma} rays from the residues were observed through the high sensitivity Germanium Clover detector array INGA. The decay of the high spin states and the isomeric states of the doubly-odd {sup 208}Fr nuclei, identified from the known sequence of ground state transitions, were observed. The half-lives of the E{sub {gamma}=}194(2) keV isomeric transition, known from earlier observations, was measured to be T{sub 1/2}=233(18) ns. A second isomeric transition at E{sub {gamma}=}383(2) keV and T{sub 1/2}=33(7) ns was also found. The measured half-lives were compared with the corresponding single particle estimates, based on the level scheme obtained from the experiment.

A kinetic mechanistic study of acid-catalyzed alkylation of isobutane with C4-olefins at low temperatures

Energy Technology Data Exchange (ETDEWEB)

Doshi, B.M.

1978-01-01

A kinetic and mechanistic study of sulfuric acid-catalyzed alkylation of isobutane with C/sub 4/-Olefins at Low Temperatures(-20/sup 0/ to 0/sup 0/C) was based on a new two-step reaction sequence in which the desired first-step reactions are between acid and olefin to form sulfates and the desired second-step reactions are between sulfates and isobutane to form mostly trimethylpentanes. Linear butenes formed stable sulfates that formed alkylates of exceptionally high quality, up to 100 Research octane, whereas isobutylene and trimethylpentene mainly polymerized during the first step, and the alkylate produced had only 90 Research octane. Trimethylpentanes and dimethylhexanes, when contacted with concentrated sulfuric acid at -10/sup 0/ to +25/sup 0/C, degraded and isomerized to form C/sub 4/-C/sub 9/ and higher isoparaffins and acid-soluble hydrocarbons (conjunct polymers). For the two-step process and the degradation and isomerization reactions, kinetic models based on reaction at the interface were developed; but for isoolefins, a polymerization-cracking sequence (via C/sub 12/- and even C/sub 16/-olefins) is the preferred route. Commercial applications of the results are proposed.

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

Science.gov (United States)

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

2016-01-01

Perfluoroalkyl substances (PFASs) have been well studied in human daily intake for assessment of potential health risks. However, little is known about the isomeric compositions of PFASs in daily intake and their impacts on isomeric profiles in humans. In this study, we investigated the occurrence of PFASs with isomeric analysis in various human exposure matrices including foodstuffs, tap water and indoor dust. Perfluorooctanesulfonate (PFOS) and/or perfluorooctanoate (PFOA) were predominant in these exposure matrices collected in Tianjin, China. In fish and meat, linear (n-) PFOA was enriched with a percentage of 92.2% and 99.6%, respectively. Although n-PFOS was higher in fish (84.8%) than in technical PFOS (ca. 70%), it was much lower in meat (63.1%) and vegetables (58.5%). Dietary intake contributed >99% of the estimated daily intake (EDI) for the general population. The isomeric profiles of PFOA and PFOS in human serum were predicted based on the EDI and a one-compartment, first-order pharmacokinetic model. The isomeric percentage of n-PFOA in the EDI (98.6%) was similar to that in human serum (predicted: 98.2%, previously measured: 99.7%) of Tianjin residents. The results suggest direct PFOA intake plays an important role in its isomeric compositions in humans. For PFOS, the predicted n-PFOS (69.3%) was much higher than the previously measured values (59.2%) in human serum. This implies that other factors, such as indirect exposure to PFOS precursors and multiple excretion pathways, may contribute to the lower percentage of n-PFOS in humans than of technical PFOS. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

Energy Technology Data Exchange (ETDEWEB)

Toufen, D. L., E-mail: dennis@if.usp.br [Institute of Physics, University of São Paulo, C.P. 66318, 05315-970 São Paulo, São Paulo (Brazil); Federal Institute of Education, Science and Technology of São Paulo - IFSP, 07115-000 Guarulhos, São Paulo (Brazil); Allegro, P. R. P.; Medina, N. H.; Oliveira, J. R. B.; Cybulska, E. W.; Seale, W. A.; Ribas, R. V. [Institute of Physics, University of São Paulo, C.P. 66318, 05315-970 São Paulo, São Paulo (Brazil); Linares, R. [Fluminense Federal University, 24220-900 Niterói, Rio de Janeiro (Brazil); Silveira, M. A. G. [Universitary Center of FEI, 09850-901 São Bernardo do Campo, São Paulo (Brazil)

2014-07-15

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

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

Science.gov (United States)

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.

Conformal symmetry and non-relativistic second-order fluid dynamics

International Nuclear Information System (INIS)

Chao Jingyi; Schäfer, Thomas

2012-01-01

We study the constraints imposed by conformal symmetry on the equations of fluid dynamics at second order in the gradients of the hydrodynamic variables. At zeroth order, conformal symmetry implies a constraint on the equation of state, E 0 =2/3 P, where E 0 is the energy density and P is the pressure. At first order, conformal symmetry implies that the bulk viscosity must vanish. We show that at second order, conformal invariance requires that two-derivative terms in the stress tensor must be traceless, and that it determines the relaxation of dissipative stresses to the Navier–Stokes form. We verify these results by solving the Boltzmann equation at second order in the gradient expansion. We find that only a subset of the terms allowed by conformal symmetry appear. - Highlights: ► We derive conformal constraints for the stress tensor of a scale invariant fluid. ► We determine the relaxation time in kinetic theory. ► We compute the rate of entropy production in second-order fluid dynamics.

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

Science.gov (United States)

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

2015-09-01

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

Generative Models of Conformational Dynamics

OpenAIRE

Langmead, Christopher James

2014-01-01

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a...

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

Science.gov (United States)

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.

Kinetic, stereochemical, and molecular association factors in the hydralumination of group IV subtituted alkynes. The role of p/sub π/-d/sub π/ conjugation in the addition of diisobutylaluminum hydride to trimethyl(phenylethynyl)silane

International Nuclear Information System (INIS)

Eisch, J.J.; Rhee, S.G.

1975-01-01

The kinetic, stereochemistry, and molecular association factors for the addition of diisobutylaluminum hydride to trimethyl(phenylethynyl)silane were studied in the temperature range of -10 to 38 0 . Hydralumination was found to have a kinetic true order of essentially one in the alkyne and one-third in the hydride. Although the trans adduct is the predominating product (approximately 99 percent) after completion of the hydralumination, the variation of the proportion of cis adduct and the initial rate law are consistent with a kinetically controlled cis hydralumination by monomeric R 2 'AlH, followed by a rapid isomerization to the trans adduct. The trans adduct formed a complex with l equivalent to the hydride. This complexation had to be taken into account, in order to explain the observed rate retardation and to obtain satisfactory integrated rate expressions for hydraluminations monitored to high conversion. Since in hydralumination this silylacetylene shows a stereospecificity and regiospecificity exactly opposite that of tert-butyl(phenyl)acetylene, as well as a heightened reactivity, a critical consideration of possible p/sub π/--d/sub π/ electronic effects was undertaken. The unusually facile isomerization of the resulting silyl-substituted vinylalanes, however, does seem more persuasive evidence for a p/sub π/--d/sub π/ effect, which promotes isomerization by electrophilic attack of R 2 'AlH on the carbon α to the Me 3 Si group. (U.S.)

Study of the isomeric states of 66As

International Nuclear Information System (INIS)

Czajkowski, S.; Blank, B.; Andriamonje, S.; Attallah, F.; Boue, F.; Davi, F.; Del Moral, R.; Fleury, A.; Musquere, A.; Pravikoff, M.S.; Dufour, J-P; Grzywacz, R.; Janas, Z.; Karny, M.; Pfuetzner, M.; Donzaud, C.; Grewe, A.; Heinz, A.; Junghans, A.; Lewitowicz, M.; Sauvestre, J-E.

1997-01-01

The most neutron-deficient isotopes in the N = Z region are an important source of information on the neutron-proton interaction far off stability. The isotopes in this region are characterized by an extreme sensitivity of the deformation to the isospin variations. Here the structure of deformed shells are favoring the high spin states the lifetime of which being sufficient long to be observed after flight time of the order of the microsecond. The study of the decay of this isomeric states permits to approach the structure of the first excited levels of this isotopes. Recent experiments at GANIL with the SISSI - LISE 3 spectrometer were performed to study the neutron deficient nucleus 66 As. This nucleus was produced in the fragmentation of 70 MeV/u 78 Kr primary beam in a nickel target. Two new isomeric states have been observed. From the observed γ transitions a decay scheme is proposed

Fundamental insights into conformational stability and orbital interactions of antioxidant (+)-catechin species and complexation of (+)-catechin with zinc(II) and oxovanadium(IV)

Science.gov (United States)

Yasarawan, Nuttawisit; Thipyapong, Khajadpai; Sirichai, Somsak; Ruangpornvisuti, Vithaya

2013-09-01

Conformational stability of (+)-catechin species in water has been examined with density functional theory, associated with the polarizable continuum model (PCM) of solvation. Factors such as electron delocalization, lone-pair electron donation and intramolecular hydrogen bonding substantially contribute to the conformational stabilization. Upon deprotonation, the HOMO and LUMO energies for (+)-catechin are both elevated; the energy gaps for the deprotonated species are narrower than the energy gap for the neutral species. The preferential deprotonation occurs at the C3'-, C5-, C7- and C4'-OH groups successively. The pKa value at 9.3 predicted for the most acidic OH group agrees well with previous experimental data; however the values are overestimated for the less acidic OH groups due to limitations of the PCM for charged solutes and/or complex nature of true deprotonation pathways. Formation of hydrogen radicals should be promoted at high pH values following the bond dissociation enthalpies. Complexation of (+)-catechin with either zinc(II) or oxovanadium(IV) is favored at the 1:1 metal-to-ligand (M:L) mole ratio, with the oxovanadium(IV) complex showing higher reaction preference. At M:L = 1:2, formation of two isomeric complexes are plausible for each type of metal ion. Effects of stoichiometry and isomerism on the computational spectral features of the possibly formed metal complexes have been described.

Effect of ultrasonic waves on the stability of all-trans lutein and its degradation kinetics.

Science.gov (United States)

Song, Jiang-Feng; Li, Da-Jing; Pang, Hui-Li; Liu, Chun-Quan

2015-11-01

Ultrasound treatment has been widely applied in the extraction of biologically active compounds including carotenoids. However, there are few reports on their effects on the stability of these compounds. In the present study, the stability of all-trans lutein, one of the carotenoids, was investigated under the action of ultrasound. Results showed that ultrasound induced the isomerization of all-trans lutein to its isomers, namely to 13-cis lutein, 13'-cis lutein, 9-cis lutein and 9'-cis lutein as analyzed by HPLC coupled with DAD and LC-MS; and the percentage of the isomerization increased with increasing both ultrasonic frequency and power. The stability of all-trans lutein in dichloromethane was worst among multiple kinds of solvents. Interestingly, the retention rate of all-trans lutein improved as the temperature increased, which runs counter to the Arrhenius law. Under ultrasound irradiation, the degradation mechanism might be different with various temperatures, the degradation of all-trans lutein followed first-order kinetics at 20°C, while second-order kinetics was followed at 30-50°C. As the ultrasonic reaction time prolonged, lutein epoxidation nearly occurred. Those results presented here emphasized that UAE techniques should be carefully used in the extraction of all-trans lutein. Copyright © 2015 Elsevier B.V. All rights reserved.

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate.

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D

2008-11-25

o-Succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered bi uni uni bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first half-reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the "F" form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered bi uni uni bi iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogues with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogues tested as none were active except 4-[2-(trifluoromethyl)phenyl]-4-oxobutyric acid which exhibited a 100-fold decrease in k(cat)/K(m). On the basis of an understanding of OSB-CoA synthetase's kinetic mechanism and substrate specificity, a reaction intermediate analogue of OSB-AMP, 5'-O-{N-[2-(trifluoromethyl)phenyl]-4-oxobutyl}adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

International Nuclear Information System (INIS)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-01-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Energy Technology Data Exchange (ETDEWEB)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti, E-mail: arti@iitm.ac.in [Department of Chemistry, Indian Institute of Technology, Madras, Chennai 600036 (India)

2016-08-28

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes

Science.gov (United States)

Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti

2016-08-01

Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.

Isomerization of β-carotene by titanium tetrachloride catalyst

Indian Academy of Sciences (India)

TECS

2007-05-04

May 4, 2007 ... antioxidant because of the presence of a long chain of conjugated carbon-carbon double bonds. ... such as extraction, chromatography etc. It has been reported that the chlorinated solvents can promote isomerization of trans conjugated polyenes such as β-carotene during extraction.5. Also, the isomeriza-.

Conformational Dynamics of hSGLT1 during Na⁺/Glucose Cotransport

DEFF Research Database (Denmark)

Loo, D. D.; Hirayama, B. A.; Karakossian, M. H.

2006-01-01

at the expense of outward-facing conformations. The simulations predict, and we have observed experimentally, that presteady-state currents are blocked by saturating sugar, but not the changes in fluorescence. Thus we have isolated an electroneutral conformational change that has not been previously described......) was totally abolished, whereas Fmax was only reduced 50%. Phlorizin reduced both Qmax and Fmax (Ki 0.4 µM), with no changes in V0.5's or relaxation time constants. Simulations using an eight-state kinetic model indicate that external sugar increases the occupancy probability of inward-facing conformations...

Conformational isomerism in mixed-ligand complexes of 2,2'-bipyridine and triphenylphosphine with copper(I) halides

International Nuclear Information System (INIS)

Barron, P.F.; Engelhardt, L.M.; Healy, P.C.; Kildea, J.D.; White, A.H.

1988-01-01

Mixed-ligand complexes of triphenylphosphine and 2,2'-bipyridine and copper(I) halides have been synthesized. The 31 P NMR spectra of the complexes were measured and are reported along with data for complete structural characterization of the complexes. The results indicate a novel dichotomy of conformational isomers to be present in the chloride lattice. The Cu-P bond length was found to not vary with different halides. 8 refs., 4 figs., 6 tabs

Excitation of isomeric states 1h11/2 in (γ, n) reactions

International Nuclear Information System (INIS)

Tonchev, A.P.; Gangrskij, Yu.P.; Belov, A.G.

1995-01-01

The cross sections of (γ, n) reactions were measured for ground and isomeric states 1h 11/2 in 16 isotopes of Pd, Cd, Sn, Te, Ba, Ce, Nd and Sm. The energy of γ-rays was placed in the region of Giant Dipole Resonance. An activation method of measurements has been used. IR dependence of neutron and proton number in nucleus was detected and of excitation energy of residual nucleus as well. Different factors influencing the values of the isomeric ratios are discussed. 20 refs., 5 figs., 2 tabs

Momentum-imaging investigations of the dissociation of D2+ and the isomerization of acetylene to vinylidene by intense short laser pulses

International Nuclear Information System (INIS)

Alnaser, A S; Litvinyuk, I; Osipov, T; Ulrich, B; Landers, A; Wells, E; Maharjan, C M; Ranitovic, P; Bochareva, I; Ray, D; Cocke, C L

2006-01-01

We present momentum images of the ionic products from the ionization of D 2 and C 2 H 2 by short laser pulses. For D 2 , we use a pump-probe approach to investigate the dependence of the enhanced ionization on the internuclear distance. Evidence for two (not well separated) regions of enhancement is found near internuclear distances of 6 and 10 au. In the case of acetylene, we report clear evidence for the production of both acetylene and vinylidene dications with kinetic energy releases similar to those reported earlier by core electron removal. We also find very different angular distributions for the fragments in the two channels, consistent with a finite time for the isomerization

[Isomeric derivatives of lupinine and epilupinine--organophosphorus inhibitors of cholinesterases].

Science.gov (United States)

Basova, N E; Kormilitsyn, B N; Perchenok, A Iu; Rosengart, E V; Saakov, V S; Suvorov, A A

2012-01-01

The isomeric-structure analysis data of anticholinesterase action of organophosphorous inhibitors with similar structure help in the search of specific effectors and detection of differences in reactivity of various animals' enzymes. This study compared the data of efficacy in respect of 4 mammal and 5 arthropoda cholinesterase preparations for 26 quinolizidine inhibitors, which molecules contain both the isomeric unbranched and branched alkoxyl radicals in the phosphoryl group, and the epimeric lupinine and epilupinine derivatives in the leaving group. The changes in the alkoxyl radical structure of inhibitor molecules act on their efficacy only with respect to the mammal enzymes ("group" inhibitor specificity). The differences between lupinine and epilupinine derivatives were revealed. Highly specific inhibitors of different enzymes were detected among the tested compounds.

Determination of the production rate of low intensity isomeric transitions

International Nuclear Information System (INIS)

Lakosi, L.; Veres, A.; Tam, N.C.; Pavlicsek, I.

1992-01-01

Flat 2π and cylindrical 4π multiwire proportional counters were built for counting for low energy internal conversion electrons from the nuclear isomers 83m Kr, 103m Rh and 189m Os, induced by irradiation with high intensity 60 Co and 4 MeV bremsstrahlung sources. The β-decay of 176m Lu was recorded by a plastic scintillator. In this way higher sensitivities were attained than by detecting γ-rays or characteristic X-rays associated with the isomeric transitions, and the excitation of 189m Os by low energy 137 Cs and 300 kV X-ray sources also became detectable. Comparatively large isomeric activities produced by linac irradiation were standardizing by a Ge spectrometer for calibrating proportional and scintillation counting. (orig.)

cis-trans Isomerization of silybins A and B

Czech Academy of Sciences Publication Activity Database

Novotná, Michaela; Gažák, Radek; Biedermann, David; Di Meo, F.; Marhol, Petr; Kuzma, Marek; Bednárová, Lucie; Fuksová, Kateřina; Trouillas, P.; Křen, Vladimír

-, č. 10 (2014), s. 1047-1063 ISSN 1860-5397 R&D Projects: GA ČR GAP207/10/0288; GA MŠk LH13097; GA MŠk(CZ) LD13041 Institutional support: RVO:61388971 ; RVO:61388963 Keywords : isomerization * silibinin * silybin Subject RIV: CC - Organic Chemistry Impact factor: 2.762, year: 2014

Conformational Dynamics of Thermus aquaticus DNA Polymerase I during Catalysis

OpenAIRE

Xu, Cuiling; Maxwell, Brian A.; Suo, Zucai

2014-01-01

Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme c...

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

Energy Technology Data Exchange (ETDEWEB)

Bakhshiyan, T. M., E-mail: tiruhi44@mail.ru [Yerevan State University (Armenia)

2016-01-15

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

Bacillus anthracis o-succinylbenzoyl-CoA synthetase: reaction kinetics and a novel inhibitor mimicking its reaction intermediate †

Science.gov (United States)

Tian, Yang; Suk, Dae-Hwan; Cai, Feng; Crich, David; Mesecar, Andrew D.

2009-01-01

O-succinylbenzoyl-CoA (OSB-CoA) synthetase (EC 6.2.1.26) catalyzes the ATP-dependent condensation of o-succinylbenzoate (OSB) and CoA to form OSB-CoA, the fourth step of the menaquinone biosynthetic pathway in Bacillus anthracis. Gene knockout studies have highlighted this enzyme as a potential target for the discovery of new antibiotics. Here we report the first studies on the kinetic mechanism of B. anthracis OSB-CoA synthetase, classifying it as an ordered Bi Uni Uni Bi ping-pong mechanism. Through a series of pre-steady-state and steady-state kinetic studies in conjunction with direct-binding studies, it is demonstrated that CoA, the last substrate to bind, strongly activates the first half-reaction after the first round of turnover. The activation of the first-half reaction is most likely achieved by CoA stabilizing conformations of the enzyme in the ‘F’ form, which slowly isomerize back to the E form. Thus, the kinetic mechanism of OSB-CoA synthetase may be more accurately described as an ordered Bi Uni Uni Bi Iso ping-pong mechanism. The substrate specificity of OSB-CoA synthetase was probed using a series of OSB analogs with alterations in the carboxylate groups. OSB-CoA shows a strong preference for OSB over all of the analogs tested as none were active except 4-(2-trifluoromethylphenyl)-4-oxobutyric acid which exhibited a 100-fold decrease in kcat/Km. Based on an understanding of OSB-CoA synthetase’s kinetic mechanism and substrate specificity, a reaction intermediate analog of OSB-AMP, 5’-O-(N-(2-trifluoromethylphenyl)-4-oxobutyl) adenosine sulfonamide (TFMP-butyl-AMS), was designed and synthesized. This inhibitor was found to be an uncompetitive inhibitor to CoA and a mixed-type inhibitor to ATP and OSB with low micromolar inhibition constants. Collectively, these results should serve as an important forerunner to more detailed and extensive inhibitor design studies aimed at developing lead compounds against the OSB-CoA synthetase class of

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

Energy Technology Data Exchange (ETDEWEB)

Danagulyan, A. S.; Hovhannisyan, G. H., E-mail: hov-gohar@ysu.am; Bakhshiyan, T. M.; Martirosyan, G. V. [Yerevan State University (Armenia)

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 discrepancies may be due to the presence of high-spin yrast states and rotational bands in these nuclei. Calculations involving various level-density models included in the TALYS-1.4 code with allowance for the enhancement of collective effects do not remove the discrepancies in the majority of cases.

Catalyst compositions useful for olefin isomerization and disproportionation

International Nuclear Information System (INIS)

Drake, C.A.

1987-01-01

A process is described for the double bond isomerization of an aliphatic olefinic hydrocarbon feed which comprises contacting the feed under isomerization conditions with a catalyst prepared by: (a) impregnating an alumina support having a surface area of at least 200 m/sup 2//g and a pore volume of at least 0.45 cm/sup 3//g with: 1 up to 20 wt. % of at least one magnesium compound convertible to the oxide, based on the weight of support and calculated as the metal; 0 up to 5 wt. % of at least one alkali metal compound convertible to the oxide, based on the weight of support and calculated as the metal; and 0 up to 5 wt. % of at least one zirconium compound convertible to the oxide, based on the weight of support and calculated as the metal; and (b) heating the alumina support impregnated in accordance with step (a) in an oxygen-containing atmosphere under conditions suitable to convert at least a portion of the magnesium, alkali metal, and zirconium compounds to the oxide form

New isomeric states in {sup 152,154,156}Nd produced by spontaneous fission of {sup 252}Cf

Energy Technology Data Exchange (ETDEWEB)

Gautherin, C.; Houry, M.; Korten, W.; Le Coz, Y.; Lucas, R.; Phan, X.H.; Theisen, C. [Commissariat l`Energie Atomique de Saclay, Gif sur Yvette (France). DSM/DAPINA/SPhN; Badimon, C.; Barreau, G.; Doan, T.P.; Pedemay, G. [Centre d`Etudes Nucleaires de Bordeaux-Gradignan, Domaine du Haut Vigneau, F-33175 Gradignan (France); Belier, G.; Girod, M.; Meot, V.; Peru, S. [Commissariat a l`Energie Atomique de Bruyeres-le-Chatel, DAM/SPN, BP12, F-91680 Bruyeres-le-Chatel (France); Astier, A.; Ducroux, L.; Meyer, M.; Redon, N. [Institut de Physique Nucleaire de Lyon, F-69622 Villeurbanne Cedex (France)

1998-04-01

Isomeric states have been observed in fission-fragments produced by spontaneous fission of {sup 252}Cf. These states are found in neutron rich nuclei of different structure and deformations. About 50 isomeric nuclei have been observed using coincidences between {gamma}-rays identified in EUROGAM II and fission fragments detected in photovoltaic cells (SAPhIR). Lifetimes in the range from 20 ns to 2{mu}s have been measured. Presented calculations based on HFB+D1S force on new measured isomeric states in the {sup 152,154,156}Nd show evidence for K-isomers. (orig.) With 8 figs., 27 refs.

Kinetic study of olive oil degradation monitored by fourier transform infrared spectrometry. Application to oil characterization.

Science.gov (United States)

Román Falcó, Iván P; Grané Teruel, Nuria; Prats Moya, Soledad; Martín Carratalá, M Luisa

2012-11-28

A new approach for the determination of kinetic parameters of the cis/trans isomerization during the oxidation process of 24 virgin olive oils belonging to 8 different varieties is presented. The accelerated process of degradation at 100 °C was monitored by recording the Fourier transform infrared spectra. The parameters obtained confirm pseudo-first-order kinetics for the degradation of cis and the appearance of trans double bonds. The kinetic approach affords the induction time and the rate coefficient; these parameters are related to the fatty acid profile of the fresh olive oils. The data obtained were used to compare the oil stability of the samples with the help of multivariate statistical techniques. Fatty acid allowed a classification of the samples in five groups, one of them constituted by the cultivars with higher stability. Meanwhile, the kinetic parameters showed greater ability for the characterization of olive oils, allowing the classification in seven groups.

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

OpenAIRE

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

2010-01-01

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 containin...

Electron induced conformational changes of an imine-based molecular switch on a Au(111) surface

Energy Technology Data Exchange (ETDEWEB)

Lotze, Christian; Henningsen, Nils; Franke, Katharina; Schulze, Gunnar; Pascual, Jose Ignacio [Inst. f. Experimentalphysik, Freie Universitaet Berlin (Germany); Luo, Ying; Haag, Rainer [Inst. f. Organische Chemie, Freie Universitaet Berlin (Germany)

2009-07-01

Azobenzene-based molecules exhibit a cis-trans configurational photoisomerisation in solution. Recently, the adsorption properties of azobenzene derivatives have been investigated on different metal surfaces in order to explore the possible changes in the film properties induced by external stimuli. In azobenzene, the diazo-bridge is a key group for the isomerization process. Its interaction with a metal surface is dominated through the N lone-pair electrons, which reduces the efficiency of the conformational change. In order to reduce the molecule-surface interaction, we explore an alternative molecular architecture by substituting the diazo-bridge (-N=N-) of azobenzene by an imine-group (-N=CH-). We have investigated the imine-based compound para-carboxyl-di-benzene-imine (PCI) adsorbed on a Au(111) surface. The carboxylic terminations mediates the formation of strongly bonded molecular dimers, which align in ordered rows preferentially following the fcc regions of the Au(111) herringbone reconstruction. Low temperature scanning tunneling microscopy was used to induce conformational changes between trans and cis state of individual molecules in a molecular monolayer.

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

Science.gov (United States)

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.

Conformal Nets II: Conformal Blocks

Science.gov (United States)

Bartels, Arthur; Douglas, Christopher L.; Henriques, André

2017-08-01

Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain F?rster Resonance Energy Transfer

OpenAIRE

Maxwell, Brian A.; Xu, Cuiling; Suo, Zucai

2014-01-01

Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinetically limit the correct nucleotide incorporation rate. Additionally, structural studies have revealed a large conformational change between the apoprotein and the DNA?protein binary state for Y-fa...

Relational motivation for conformal operator ordering in quantum cosmology

International Nuclear Information System (INIS)

Anderson, Edward

2010-01-01

Operator ordering in quantum cosmology is a major as-yet unsettled ambiguity with not only formal but also physical consequences. We determine the Lagrangian origin of the conformal invariance that underlies the conformal operator-ordering choice in quantum cosmology. This arises particularly naturally and simply from relationalist product-type actions (such as the Jacobi action for mechanics or Baierlein-Sharp-Wheeler-type actions for general relativity), for which all that is required is for the kinetic and potential factors to rescale in compensation to each other. These actions themselves mathematically sharply implement philosophical principles relevant to whole-universe modelling, so that the motivation for conformal operator ordering in quantum cosmology is thereby substantially strengthened. Relationalist product-type actions also give emergent times which amount to recovering Newtonian, proper and cosmic time in various contexts. The conformal scaling of these actions directly tells us how emergent time scales; if one follows suit with the Newtonian time or the lapse in the more commonly used difference-type Euler-Lagrange or Arnowitt-Deser-Misner-type actions, one sees how these too obey a more complicated conformal invariance. Moreover, our discovery of the conformal scaling of the emergent time permits relating how this simplifies equations of motion with how affine parametrization simplifies geodesics.

Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*

Science.gov (United States)

Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.

2013-01-01

The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628

Concurrent Mass Measurement and Laser Spectroscopy for Unambiguous Isomeric State Assignment

Science.gov (United States)

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.

High-pressure liquid chromatographic determination of chlorphenesin carbamate and the beta-isomeric carbamate.

Science.gov (United States)

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.

Isomeric ratio measurements for the radiative neutron capture 176Lu(n,γ at DANCE

Directory of Open Access Journals (Sweden)

Denis-Petit D.

2017-01-01

Full Text Available 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.

Generative Models of Conformational Dynamics

Science.gov (United States)

Langmead, Christopher James

2014-01-01

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GrAphical Models of Energy LANdscapes), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc) from long timescale simulation data. PMID:24446358

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

Science.gov (United States)

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

Measurement of millisecond half-lives of isomeric levels in some nuclei

Energy Technology Data Exchange (ETDEWEB)

Garg, K C; Khurana, C S [Punjabi Univ., Patiala (India). Nuclear Science Labs.

1976-09-01

Half-lives of 2.7, 14.5, 17, 20, 20.4, 44 and 2230 msec, of isomeric levels in /sup 208/Bi, /sup 88/Y, /sup 75/As, /sup 24/Na, /sup 71/Ge, /sup 114/In and /sup 167/Er respectively have been measured, employing on-line irradiation system. These millisecond isomeric levels are produced by 14.7 MeV neutrons through (n,p), (n,..cap alpha..), (n,n') and (n,2n) reactions on natural target samples. A ..gamma..-ray scintillation detector coupled with NTA-512B, 1024 channel analyzer has been used to follow the decay of the millisecond activities. Deflected deuteron beam bursts have been used to reduce the long-time background to initial count ratios in the decay curves to achieve a better accuracy of measurements.

On induced action for conformal higher spins in curved background

Energy Technology Data Exchange (ETDEWEB)

Beccaria, Matteo, E-mail: matteo.beccaria@le.infn.it [Dipartimento di Matematica e Fisica Ennio De Giorgi, Università del Salento & INFN, Via Arnesano, 73100 Lecce (Italy); Tseytlin, Arkady A., E-mail: tseytlin@imperial.ac.uk [The Blackett Laboratory, Imperial College, London SW7 2AZ (United Kingdom)

2017-06-15

We continue the investigation of the structure of the action for a tower of conformal higher spin fields in non-trivial 4d background metric recently discussed in Grigoriev and Tseytlin (2016). The action is defined as an induced one from path integral of a conformal scalar field in curved background coupled to higher spin fields. We analyze in detail the dependence of the quadratic part of the induced action on the spin 1 and spin 3 fields, determining the presence of a curvature-dependent mixed spin 1–3 term. One consequence is that the pure spin 3 kinetic term cannot be gauge-invariant on its own beyond the leading term in small curvature expansion. We also compute the non-zero contribution of the 1–3 mixing term to the conformal anomaly c-coefficient. One is thus to determine all such mixing terms before addressing the question of possible vanishing of the total c-coefficient in the conformal higher spin theory.

On induced action for conformal higher spins in curved background

Directory of Open Access Journals (Sweden)

Matteo Beccaria

2017-06-01

Full Text Available We continue the investigation of the structure of the action for a tower of conformal higher spin fields in non-trivial 4d background metric recently discussed in Grigoriev and Tseytlin (2016 [15]. The action is defined as an induced one from path integral of a conformal scalar field in curved background coupled to higher spin fields. We analyze in detail the dependence of the quadratic part of the induced action on the spin 1 and spin 3 fields, determining the presence of a curvature-dependent mixed spin 1–3 term. One consequence is that the pure spin 3 kinetic term cannot be gauge-invariant on its own beyond the leading term in small curvature expansion. We also compute the non-zero contribution of the 1–3 mixing term to the conformal anomaly c-coefficient. One is thus to determine all such mixing terms before addressing the question of possible vanishing of the total c-coefficient in the conformal higher spin theory.

NaSO2Ph Induced Exclusive Isomerization of 1,2-Allenyl Sulfoxides to 2-Alkynylic Phenyl Sulfoxides

Institute of Scientific and Technical Information of China (English)

傅春玲; 麻生明

2005-01-01

The clean isomerization of 1,2-allenyl sulfoxides in the presence of NaSO2Ph afforded 2-alkynylic phenyl sulfoxides in good yields and selectivities. Although strong base-catalyzed isomerization of allenes to alkynes is known, the mechanism for the current reaction is interesting for the obvious reason that NaSOEPh is a weak base.

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

Science.gov (United States)

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.

Isomerization of 2-phospha-4-silabicyclo[1.10]butane

NARCIS (Netherlands)

Slootweg, J.C.; Ehlers, A.W.; Lammertsma, K.

2004-01-01

In analogy with the valence isomerism of the hydrocarbons bicyclobutane, 1,3-butadiene and cyclobutene, the rearrangements for 2-phospha-4-sila- bicyclo[1.1.0]butane were studied at the B3LYP/6-311+G** level of theory. The monocyclic 1,2-dihydro-1,2-phosphasilete is shown to be the thermodynamically

Symmetry Relations in Chemical Kinetics Arising from Microscopic Reversibility

Science.gov (United States)

Adib, Artur B.

2006-01-01

It is shown that the kinetics of time-reversible chemical reactions having the same equilibrium constant but different initial conditions are closely related to one another by a directly measurable symmetry relation analogous to chemical detailed balance. In contrast to detailed balance, however, this relation does not require knowledge of the elementary steps that underlie the reaction, and remains valid in regimes where the concept of rate constants is ill defined, such as at very short times and in the presence of low activation barriers. Numerical simulations of a model of isomerization in solution are provided to illustrate the symmetry under such conditions, and potential applications in protein folding or unfolding are pointed out.

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

Science.gov (United States)

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Determination of the isomeric fraction in a postaccelerated radioactive ion beam using the coupled decay-chain equations

CERN Document Server

Ekstrom, A; Dijulio, D D; Cederkall, J; Van de Walle, J

2010-01-01

A method based on the coupled decay-chain equations for extracting the isotopic and the isomeric composition of a postaccelerated radioactive ion beam is presented and demonstrated on a data set from a Coulomb excitation experiment. This is the first attempt of analyzing the content of a postaccelerated radioactive ion beam using this technique. The beam composition is required for an absolute normalization of the measurement. The strength of the method, as compared to present online-based methods, lies in the determination of the isomeric fraction of a partially isomeric beam using all data accumulated during the experiment. We discuss the limitations and sensitivity of the method with respect to the gamma-ray detection efficiency and the accumulated flux. (C) 2010 Elsevier B.V. All rights reserved.

Direct Measurement of the Isomerization Barrier of the Isolated Retinal Chromophore

DEFF Research Database (Denmark)

Dilger, Jonathan; Musbat, Lihi; Sheves, Mordechai

2015-01-01

Isomerizations of the retinal chromophore were investigated using the IMS-IMS technique. Four different structural features of the chromophore were observed, isolated, excited collisionally, and the resulting isomer and fragment distributions were measured. By establishing the threshold activatio...

Observation of excited states and isomeric decays in doubly-odd 208Fr

International Nuclear Information System (INIS)

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

2009-01-01

The nuclei near the doubly magic 208 Pb are predicted to exhibit various interesting structural phenomena, one of which is a wealth of isomerism. However, a detailed study of high spin states of 211, 212, 213 Fr has already been done. Structure of such trans-Lead nuclei can be interpreted in terms of the shell model states, and the high spin states of these nuclei are interpreted. One of the major interests in the spectroscopic investigation of these nuclei is the role played by the i 13/2 state in creating isomeric levels which decay through transitions of higher muiltipolarity, or are hindered by the close proximity of the levels below. A systematic study of these nuclei will possibly reveal many other interesting structural features

Src kinase conformational activation: thermodynamics, pathways, and mechanisms.

Directory of Open Access Journals (Sweden)

Sichun Yang

2008-03-01

Full Text Available Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the alphaC helix, the activation-loop, and the beta strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the alphaC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.

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

International Nuclear Information System (INIS)

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

2011-01-01

Crystallization conditions are described for the cis- and trans-imide bond-containing SH2 domain of IL-2-inducible T-cell kinase. 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

Andrographolide sodium bisulphite-induced inactivation of urease: inhibitory potency, kinetics and mechanism.

Science.gov (United States)

Mo, Zhi-Zhun; Wang, Xiu-Fen; Zhang, Xie; Su, Ji-Yan; Chen, Hai-Ming; Liu, Yu-Hong; Zhang, Zhen-Biao; Xie, Jian-Hui; Su, Zi-Ren

2015-07-16

The inhibitory effect of andrographolide sodium bisulphite (ASB) on jack bean urease (JBU) and Helicobacter pylori urease (HPU) was performed to elucidate the inhibitory potency, kinetics and mechanism of inhibition in 20 mM phosphate buffer, pH 7.0, 2 mM EDTA, 25 °C. The ammonia formations, indicator of urease activity, were examined using modified spectrophotometric Berthelot (phenol-hypochlorite) method. The inhibitory effect of ASB was characterized with IC50 values. Lineweaver-Burk and Dixon plots for JBU inhibition of ASB was constructed from the kinetic data. SH-blocking reagents and competitive active site Ni2+ binding inhibitors were employed for mechanism study. Molecular docking technique was used to provide some information on binding conformations as well as confirm the inhibition mode. The IC50 of ASB against JBU and HPU was 3.28±0.13 mM and 3.17±0.34 mM, respectively. The inhibition proved to be competitive and concentration- dependent in a slow-binding progress. The rapid formation of initial ASB-JBU complex with an inhibition constant of Ki=2.86×10(-3) mM was followed by a slow isomerization into the final complex with an overall inhibition constant of Ki*=1.33×10(-4) mM. The protective experiment proved that the urease active site is involved in the binding of ASB. Thiol reagents (L-cysteine and dithiothreithol) strongly protect the enzyme from the loss of enzymatic activity, while boric acid and fluoride show weaker protection, indicating that the active-site sulfhydryl group of JBU was potentially involved in the blocking process. Moreover, inhibition of ASB proved to be reversible since ASB-inactivated JBU could be reactivated by dithiothreitol application. Molecular docking assay suggested that ASB made contacts with the important sulfhydryl group Cys-592 residue and restricted the mobility of the active-site flap. ASB was a competitive inhibitor targeting thiol groups of urease in a slow-binding manner both reversibly and concentration

Pressure-dependent kinetics of initial reactions in iso-octane pyrolysis.

Science.gov (United States)

Ning, HongBo; Gong, ChunMing; Li, ZeRong; Li, XiangYuan

2015-05-07

This study focuses on the studies of the main pressure-dependent reaction types of iso-octane (iso-C8H18) pyrolysis, including initial C-C bond fission of iso-octane, isomerization, and β-scission reactions of the alkyl radicals produced by the C-C bond fission of iso-octane. For the C-C bond fission of iso-octane, the minimum energy potentials are calculated at the CASPT2(2e,2o)/6-31+G(d,p)//CAS(2e,2o)/6-31+G(d,p) level of theory. For the isomerization and the β-scission reactions of the alkyl radicals, the optimization of the geometries and the vibrational frequencies of the reactants, transition states, and products are performed at the B3LYP/CBSB7 level, and their single point energies are calculated by using the composite CBS-QB3 method. Variable reaction coordinate transition state theory (VRC-TST) is used for the high-pressure limit rate constant calculation and Rice-Ramsperger-Kassel-Marcus/master equation (RRKM/ME) is used to calculate the pressure-dependent rate constants of these channels with pressure varying from 0.01-100 atm. The rate constants obtained in this work are in good agreement with those available from literatures. We have updated the rate constants and thermodynamic parameters for species involved in these reactions into a current chemical kinetic mechanism and also have improved the concentration profiles of main products such as C3H6 and C4H6 in the shock tube pyrolysis of iso-octane. The results of this study provide insight into the pyrolysis of iso-octane and will be helpful in the future development of branched paraffin kinetic mechanisms.

Equilibrium and non-equilibrium conformations of peptides in lipid bilayers.

Science.gov (United States)

Boden, N; Cheng, Y; Knowles, P F

1997-04-22

A synthetic, hydrophobic, 27-amino-acid-residue peptide 'K27', modelled on the trans-membrane domain of the slow voltage-gated potassium channel, IsK, has been incorporated into a lipid bilayer and its conformational properties studied using FT-IR spectroscopy. The conformation following reconstitution is found to be dependent on the nature of the solvent employed. When the reconstitution is conducted by solvent evaporation from a methanol solution, aggregates comprised of beta-strands are stabilised and their concentration is essentially invariant with time. By contrast, when trifluoroethanol is used, the initial conformation of the peptide is alpha-helical. This then relaxes to an equilibrium state between alpha-helices and beta-strands. The alpha-helix-to beta-strand conversion rate is relatively slow, and this allows the kinetics to be studied by FT-IR spectroscopy. The reverse process is much slower but again can be demonstrated by FT-IR. Thus, it appears that a true equilibrium structure can only be achieved by starting with peptide in the alpha-helical conformation. We believe this result should be of general validity for hydrophobic peptide reconstitution. The implications for conformational changes in membrane proteins are discussed.

Isomeric cross-section ratios of some (n,2n) reactions at 14. 7 MeV

Energy Technology Data Exchange (ETDEWEB)

Garg, K C; Khurana, C S [Punjabi Univ., Patiala (India). Nuclear Science Labs.

1979-08-01

Isomeric cross-section ratios of (n,2n) reactions at 14.7 MeV leading to the millisecond isomeric levels have been calculated theoretically using the statistical theory of nuclear reactions and the spin distribution form due to Bethe and Bloch. The theoretical ratios have been compared with the experimentally measured values in order to evaluate the spin cut-off parameter sigma. This parameter has been used to calculate the effective moment of inertia of the nucleus to draw useful conclusions from the results of present calculations.

Conformational flexibility of avidin: the influence of biotin binding

International Nuclear Information System (INIS)

Soledad Celej, M.; Montich, Guillermo G.; Fidelio, Gerardo D.

2004-01-01

Ligand binding to proteins is a key process in cell biochemistry. The interaction usually induces modifications in the unfolding thermodynamic parameters of the macromolecule due to the coupling of unfolding and binding equilibria. In addition, these modifications can be attended by changes in protein structure and/or conformational flexibility induced by ligand binding. In this work, we have explored the effect of biotin binding on conformation and dynamic properties of avidin by using infrared spectroscopy including kinetics of hydrogen/deuterium exchange. Our results, along with previously thermodynamic published data, indicate a clear correlation between thermostability and protein compactness. In addition, our results also help to interpret the thermodynamic binding parameters of the exceptionally stable biotin:AVD complex

pH-Driven Ordering Transitions in Liquid Crystal Induced by Conformational Changes of Cardiolipin.

Science.gov (United States)

Sidiq, Sumyra; Verma, Indu; Pal, Santanu Kumar

2015-04-28

We report an investigation of interfacial phenomena occurring at aqueous-liquid crystal (LC) interfaces that triggers an orientational ordering transition of the LC in the presence of cardiolipin (CL) by varying pH, salt concentration and valence. In particular, the effects of three different conformational isomeric forms of the CL are observed to cause the response of the LC ordering to vary significantly from one to another at those interfaces. An ordering transition of the LC was observed when the CL is mostly in undissociated (at pH 2) and/or in bicyclic (at pH 4) conformation in which LC shows changes in the optical appearance from bright to dark. By contrast, no change in the optical appearance of the LC was observed when the pH of the system increases to 8 or higher in which the CL mostly exists in the open conformation. Fluorescence microscopy measurements further suggest that pH-dependent conformational forms of the CL have different ability to self-assemble (thus different packing efficiency) at aqueous-LC interfaces leading to dissimilar orientational behavior of the LC. Specifically, we found that change in headgroup-headgroup repulsion of the central phosphatidyl groups of the CL plays a key role in tuning the lipid packing efficiency and thus responses to interfacial phenomena. Orientational ordering transition of the LC was also observed as a function of increasing the ionic strength (buffer capacity) and strongly influenced in the presence of mono and divalent cations. Langmuir-Blodgett (LB) and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) measurements provide further insight in modulation of the lipid packing efficiency and alkyl chain conformation of the CL at different pH and ionic conditions. Overall, the results presented in this paper establish that LCs offer a promising approach to differentiate different conformations (label free detection) of the CL through ordering transition of the LC at aqueous

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

Science.gov (United States)

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.

Influences of conformations of peptides on stereoinversions and/or isomerizations of aspartic acid residues.

Science.gov (United States)

Oda, Akifumi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Takahashi, Ohgi

2018-07-01

Recently, non-enzymatic stereoinversions of aspartic acid (Asp) residues in proteins and peptides have been reported. Here, we performed replica exchange molecular dynamics (REMD) simulations of model peptides (exon 6, 26A-1, and 26A-2) extracted from elastin to investigate their structural features, thereby revealing the factor that influences stereoinversions. For REMD trajectories, we calculated distances between carboxyl carbon in Asp and amide nitrogen in the (n + 1) residue (CN distances). Because bond formation between carbon and nitrogen is indispensable to the formation of a succinimide intermediate the distance between them seems to play an important role in stereoinversion. Moreover, we calculated polar surface areas (PSAs) for the trajectories, finding that CN distances and PSA were different for each peptide, with the longest CN distance and smallest PSA observed for exon 6 peptide, where stereoinversion of Asp is the slowest. Although the average CN distance was shorter for exon 26A-1 peptide than for exon 26A-2 peptide, the number of conformations with CN distances acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca. Copyright © 2018 Elsevier B.V. All rights reserved.

Kinetic intermediates en route to the final serpin-protease complex: studies of complexes of α1-protease inhibitor with trypsin.

Science.gov (United States)

Maddur, Ashoka A; Swanson, Richard; Izaguirre, Gonzalo; Gettins, Peter G W; Olson, Steven T

2013-11-01

Serpin protein protease inhibitors inactivate their target proteases through a unique mechanism in which a major serpin conformational change, resulting in a 70-Å translocation of the protease from its initial reactive center loop docking site to the opposite pole of the serpin, kinetically traps the acyl-intermediate complex. Although the initial Michaelis and final trapped acyl-intermediate complexes have been well characterized structurally, the intermediate stages involved in this remarkable transformation are not well understood. To better characterize such intermediate steps, we undertook rapid kinetic studies of the FRET and fluorescence perturbation changes of site-specific fluorophore-labeled derivatives of the serpin, α1-protease inhibitor (α1PI), which report the serpin and protease conformational changes involved in transforming the Michaelis complex to the trapped acyl-intermediate complex in reactions with trypsin. Two kinetically resolvable conformational changes were observed in the reactions, ascribable to (i) serpin reactive center loop insertion into sheet A with full protease translocation but incomplete protease distortion followed by, (ii) full conformational distortion and movement of the protease and coupled serpin conformational changes involving the F helix-sheet A interface. Kinetic studies of calcium effects on the labeled α1PI-trypsin reactions demonstrated both inactive and low activity states of the distorted protease in the final complex that were distinct from the intermediate distorted state. These studies provide new insights into the nature of the serpin and protease conformational changes involved in trapping the acyl-intermediate complex in serpin-protease reactions and support a previously proposed role for helix F in the trapping mechanism.

Destabilization in the isomeric nitrobenzonitriles: an experimental thermochemical study

International Nuclear Information System (INIS)

Roux, Maria Victoria; Jimenez, Pilar; Davalos, Juan Z.; Temprado, Manuel; Liebman, Joel F.

2003-01-01

The enthalpies of combustion and of sublimation, respectively, of the three isomeric nitrobenzonitriles have been measured: o-, {(-3456.3±2.9), (88.1±1.4)} kJ·mol -1 ; m-, {(-3442.8±3.3), (92.8±0.3)} kJ·mol -1 ; p-, {(-3448.2±3.6), (91.1±1.3)} kJ·mol -1 . In turn, from these values, the standard molar enthalpies of formation for the condensed and gaseous state, respectively, have been derived: o-, {(130.1±3.1), (218.2±3.4)} kJ·mol -1 ; m-, {(116.5±3.5), (209.3±3.5)} kJ·mol -1 ; p-, {(122.0±3.8), (213.1±4.0)} kJ·mol -1 . Destabilization energies associated with the presence of the two electron-withdrawing groups have been determined, for o-, m-, and p-nitrobenzonitrile, {(17.6±4.1), (8.7±4.2), and (12.5±4.6)} kJ·mol -1 , respectively, and are consistent with those obtained for the corresponding sets of isomeric methyl benzenedicarboxylates, dicyanobenzenes, dinitrobenzenes, and (neutral and ionized) nitrobenzoic acids

Theoretical and NMR conformational studies of β-proline oligopeptides with alternating chirality of pyrrolidine units

Science.gov (United States)

Mantsyzov, Alexey B.; Savelyev, Oleg Y.; Ivantcova, Polina M.; Bräse, Stefan; Kudryavtsev, Konstantin V.; Polshakov, Vladimir I.

2018-03-01

Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

Theoretical and NMR Conformational Studies of β-Proline Oligopeptides With Alternating Chirality of Pyrrolidine Units

Directory of Open Access Journals (Sweden)

Alexey B. Mantsyzov

2018-03-01

Full Text Available Synthetic β-peptides are potential functional mimetics of native α-proteins. A recently developed, novel, synthetic approach provides an effective route to the broad group of β-proline oligomers with alternating patterns of stereogenic centers. Conformation of the pyrrolidine ring, Z/E isomerism of β-peptide bonds, and hindered rotation of the neighboring monomers determine the spatial structure of this group of β-proline oligopeptides. Preferences in their structural organization and corresponding thermodynamic properties are determined by NMR spectroscopy, restrained molecular dynamics and quantum mechanics. The studied β-proline oligopeptides exist in dimethyl sulfoxide solution in a limited number of conformers, with compatible energy of formation and different spatial organization. In the β-proline tetrapeptide with alternating chirality of composing pyrrolidine units, one of three peptide bonds may exist in an E configuration. For the alternating β-proline pentapeptide, the presence of an E configuration for at least of one β-peptide bond is mandatory. In this case, three peptide bonds synchronously change their configurations. Larger polypeptides may only exist in the presence of several E configurations of β-peptide bonds forming a wave-like extended structure.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

Science.gov (United States)

Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

2010-06-22

The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

Light-induced linkage isomerization of photochromic [Ru(bpy){sub 2}(R-OSO)]{sup +} compounds

Energy Technology Data Exchange (ETDEWEB)

Springfeld, Kristin; Dieckmann, Volker; Eicke, Sebastian; Imlau, Mirco [Department of Physics, University of Osnabrueck (Germany); Rack, Jeffrey J. [Department of Chemistry and Biochemistry, Ohio University, Athens, Ohio (United States)

2010-07-01

Ruthenium sulfoxides exhibit light-induced linkage isomerization of the SO-bond with remarkable photosensitivity S=(0.25{+-}0.03) Ws cm{sup -1} and extended lifetimes of the related metastable states in the order of 10{sup 4} s. The isomerization is accompanied with tremendous changes of the optical extinction up to 9350 cm{sup -1} mol{sup -1} thus enabling the study of linkage isomerization by means of time-resolved optical spectroscopy. Here, the influence of ligand substitution is studied via inspection of the photosensitivity and the generation and relaxation dynamics of the photochromic response as a function of temperature (pump at {lambda}=405 nm, probe at {lambda}=532 nm). The spectra of the modified compounds, where ligands R=Bn, BnCl, and BnMe were attached to OSO, were compared with the reference system [Ru(bpy){sub 2}(OSO)]{sup +}. It turns out, that the new ligands affect the absorption features and the photosensitivity of the system only slightly. In contrast, a strong influence of the thermal relaxation of the metastable states is uncovered. Remarkably, the influence on the frequency factors is much more pronounced than on the activation energies achieved by Arrhenius' law.

Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

Energy Technology Data Exchange (ETDEWEB)

Wang, Ruiyong, E-mail: wangry@zzu.edu.cn; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun, E-mail: chjsong@zzu.edu.cn; Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn

2014-10-15

In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking.

Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

International Nuclear Information System (INIS)

Wang, Ruiyong; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun; Chang, Junbiao

2014-01-01

In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking

Computational Studies of Bridging Structures and Isomerism in Substituted Disilynes.

Science.gov (United States)

Serafin, Lukasz M; Law, Mark M; van Mourik, Tanja

2013-06-11

The substituted disilyne molecules, Si2Li2 and Si2HX, where X = Li, F, and Cl, have been investigated using the high-level CCSD(T) and CCSD(T)-F12 ab initio methods. The calculations have found or confirmed the existence of several isomeric forms and transition states for each molecule. Optimized geometries, relative energies, and harmonic vibration frequencies are reported. Bridging structures exist in all cases. Comparisons are made with existing literature results for the related Si2H2, C2X2, and C2HX isomerizing systems. Additionally, CCSD(T) and CCSD(T)-F12 calculations were performed for Si2H2, for which experimental spectroscopic data are available. Results calculated with CCSD(T)-F12 and the cc-pVTZ-F12 basis set are of comparable quality as those computed with CCSD(T) and the much larger cc-pV(6+d)Z basis set, at much less computational cost. We recommend the CCSD(T)-F12/cc-pVTZ-F12 level of theory as a very attractive alternative to conventional CCSD(T).

Isomeric Diruthenium Complexes Bridged by Deprotonated Indigo in cis and trans Configuration

Czech Academy of Sciences Publication Activity Database

Chatterjee, M.; Ghosh, P.; Beyer, K.; Paretzki, A.; Fiedler, Jan; Kaim, W.; Lahiri, G. K.

2018-01-01

Roč. 13, č. 1 (2018), s. 118-125 ISSN 1861-4728 Institutional support: RVO:61388955 Keywords : isomerism * ruthenium * spectroelectrochemistry * structure Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.083, year: 2016

Structure of Human Pancreatic Lipase-Related Protein 2 with the Lid in an Open Conformation

Energy Technology Data Exchange (ETDEWEB)

Eydoux, Cecilia; Spinelli, Silvia; Davis, Tara L.; Walker, John R.; Seitova, Alma; Dhe-Paganon, Sirano; De Caro, Alain; Cambillau, Christian; Carriere, Frederic (CNRS-UMR); (Toronto)

2008-10-02

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.

Conformational inversion-topomerization mechanism of ethylcyclohexyl isomers and its role in combustion kinetics

KAUST Repository

Bian, Huiting; Wang, Zhandong; Sun, Jinhua; Zhang, Feng

2016-01-01

the formation of subsequent decomposition products. In this work, the conformational inversion-topomerization mechanism and H-migration reactions for six ethylcyclohexyl radical isomers were systematically studied by ab initio calculations and the transition

Perspectives on electrostatics and conformational motions in enzyme catalysis.

Science.gov (United States)

Hanoian, Philip; Liu, C Tony; Hammes-Schiffer, Sharon; Benkovic, Stephen

2015-02-17

CONSPECTUS: Enzymes are essential for all living organisms, and their effectiveness as chemical catalysts has driven more than a half century of research seeking to understand the enormous rate enhancements they provide. Nevertheless, a complete understanding of the factors that govern the rate enhancements and selectivities of enzymes remains elusive, due to the extraordinary complexity and cooperativity that are the hallmarks of these biomolecules. We have used a combination of site-directed mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear magnetic resonance (NMR), vibrational and fluorescence spectroscopies, resonance energy transfer, and computer simulations to study the implications of conformational motions and electrostatic interactions on enzyme catalysis in the enzyme dihydrofolate reductase (DHFR). We have demonstrated that modest equilibrium conformational changes are functionally related to the hydride transfer reaction. Results obtained for mutant DHFRs illustrated that reductions in hydride transfer rates are correlated with altered conformational motions, and analysis of the evolutionary history of DHFR indicated that mutations appear to have occurred to preserve both the hydride transfer rate and the associated conformational changes. More recent results suggested that differences in local electrostatic environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination of primary and solvent kinetic isotope effects, we demonstrated that the reaction mechanism is consistent across a broad pH range, and computer simulations suggested that deprotonation of the active site Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into the ecDHFR active site provided an experimental tool for interrogating these microenvironments and for investigating changes in electrostatics along the DHFR catalytic cycle

Nearly reversible conformational change of amyloid fibrils as revealed by pH-jump experiments.

Science.gov (United States)

Yamaguchi, Kei-ichi; Kamatari, Yuji O; Fukuoka, Mayuko; Miyaji, Reiji; Kuwata, Kazuo

2013-10-01

pH-jump induced conformational transitions between substates of preformed amyloid fibrils made by a fragmented peptide of helix 2 (H2 peptide) of MoPrP were detected, and their kinetics were analyzed using a novel pH-jump apparatus specially designed for observing amyloids. Previously, we reported that H2 peptide formed ordered fibrils with a minimum at 207 nm on CD spectra at pH 2.9 (named pH 2.9 fibrils), but formed aggregate-like fibrils with a minimum at 220 nm at pH 7.5 (named pH 7.5 fibrils). When pH-jump from 2.9 to 7.5 was performed, the CD spectrum changed instantly, but the finally observed ellipticities were clearly distinct from those of pH 7.5 fibrils. Thus, the finally observed state is termed 'pH 7.5-like fibrils'. However, pH 7.5-like fibrils reverted to the conformation very similar to that of the pH 2.9 fibrils when the pH of the solution was restored to 2.9. Then, we examined the kinetics of the nearly reversible conformational changes between pH 2.9 fibrils and pH 7.5-like fibrils using ANS fluorescence stopped-flow, and we observed relatively fast phases (0.7-18 s(-1)). In contrast, the conversion between pH 7.5-like fibrils and pH 7.5 fibrils never occurred (<0.2 day(-1)). Thus, H2 fibrils can be switched readily between distinct conformations separated by a low energy barrier, while a large energy barrier clearly separated the different conformations. These conformational varieties of amyloid fibrils may explain the physical basis of the diversity in prion.

Conformal field theory in conformal space

International Nuclear Information System (INIS)

Preitschopf, C.R.; Vasiliev, M.A.

1999-01-01

We present a new framework for a Lagrangian description of conformal field theories in various dimensions based on a local version of d + 2-dimensional conformal space. The results include a true gauge theory of conformal gravity in d = (1, 3) and any standard matter coupled to it. An important feature is the automatic derivation of the conformal gravity constraints, which are necessary for the analysis of the matter systems

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

Science.gov (United States)

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

2014-12-03

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

A comprehensive mechanistic picture of the isomerizing alkoxycarbonylation of plant oils

KAUST Repository

Roesle, Philipp

2014-12-03

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

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

Science.gov (United States)

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.

Kinetics of activation of the P4 promoter of pBR322 by the Escherichia coli cyclic AMP receptor protein.

Science.gov (United States)

Hoggett, J G; Brierley, I

1992-11-01

The activation of transcription initiation from the P4 promoter of pBR322 by the Escherichia coli cyclic AMP receptor protein (CRP) has been investigated using a fluorescence abortive initiation assay. The effect of the cyclic-AMP/CRP complex on the linear P4 promoter was to increase the initial binding (KB) of RNA polymerase to the promoter by about a factor of 10, but the rate of isomerization of closed to open complex (kf) was unaffected. One molecule of CRP per promoter was required for activation, and the concentration of cyclic AMP producing half-maximal stimulation was about 7-8 microM. Supercoiling caused a 2-3-fold increase in the rate of isomerization of the CRP-activated promoter, but weakened the initial binding of polymerase by about one order of magnitude. The unactivated supercoiled promoter was too weak to allow reliable assessment of kinetic parameters against the high background rate originating from the rest of the plasmid.

Excitation function and isomeric ratio of Tc-isotopes from the 93Nb(α, xn) reaction

International Nuclear Information System (INIS)

Kim, K.; Kim, G.N.; Naik, H.; Zaman, M.; Yang, S.-C.; Song, T.-Y.; Guin, R.; Das, S.K.

2015-01-01

The excitation functions of 94–96 Tc isotopes and independent isomeric ratios of 93m, g Tc, 94m, g Tc, and 95m, g Tc from the 93 Nb(α, xn) reaction within the energy range below 40 MeV have been determined by using a stacked-foil activation and an off-line γ-ray spectrometric technique at the Variable Energy Cyclotron Center, Kolkota, India. The excitation function of 94–96 Tc in the 93 Nb(α, xn) reaction was also calculated by using the computer code TALYS 1.6. The present data are found to be in general agreement with the literature data but have similar trend with some deviation from calculated data of the TALYS 1.6 code. The isomeric ratios of 93m, g Tc, 94m, g Tc, and 95m, g Tc in the 93 Nb(α, xn) reactions from the present work and literature data were compared with similar data in the 93 Nb( 3 He, xn) and 96 Mo(p, xn) reactions. In all the three reactions, the isomeric ratios increase with the increasing excitation energy. However, at all excitation energies, the isomeric ratios of 93m, g Tc, 94m, g Tc, and 95m, g Tc in the 93 Nb(α, xn) and 93 Nb( 3 He, xn) reactions are higher than those in the 96 Mo(p, xn) reactions, which indicate the role of input angular momentum besides excitation energy. Above the excitation energy of 35–55 MeV, the isomeric ratios of 95m, g Tc, 94m, g Tc, and 93m, g Tc decrease in all the 93 Nb(α, xn), 93 Nb( 3 He, xn) and 96 Mo(p, xn) reactions. This decreasing trend at higher excitation energy indicates the starting of pre-equilibrium reaction, which depends on the target, projectile, and type of reaction products

Linkage isomerism in trimeric and polymeric 2,3-cis-procyanindins

Science.gov (United States)

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...

Transport coefficients in second-order non-conformal viscous hydrodynamics

International Nuclear Information System (INIS)

Ryblewski, Radoslaw

2015-01-01

Based on the exact solution of Boltzmann kinetic equation in the relaxation-time approximation, the precision of the two most recent formulations of relativistic second-order non-conformal viscous hydrodynamics (14-moment approximation and causal Chapman-Enskog method), standard Israel-Stewart theory, and anisotropic hydrodynamics framework, in the simple case of one-dimensional Bjorken expansion, is tested. It is demonstrated that the failure of Israel-Stewart theory in reproducing exact solutions of the Boltzmann kinetic equation occurs due to neglecting and/or choosing wrong forms of some of the second-order transport coefficients. In particular, the importance of shear-bulk couplings in the evolution equations for dissipative quantities is shown. One finds that, in the case of the bulk viscous pressure correction, such coupling terms are as important as the corresponding first-order Navier-Stokes term and must be included in order to obtain, at least qualitative, overall agreement with the kinetic theory. (paper)

An isomerization-induced cage-breaking process in a molecular glass former below Tg

International Nuclear Information System (INIS)

Teboul, V.; Saiddine, M.; Accary, J.-B.; Nunzi, J.-M.

2011-01-01

A recent experimental [P. Karageorgiev, D. Neher, B. Schulz, B. Stiller, U. Pietsch, M. Giersig, L. Brehmer, Nature Mater. 4, 699 (2005)] study has found liquidlike diffusion below the glass-transition temperature in azobenzene-containing materials under irradiation. This result suggests that the isomerization-induced massive mass transport that leads to surface relief gratings formation in these materials, is induced by this huge increase of the matrix diffusion coefficient around the probe. In order to investigate the microscopic origin of the increase of the diffusion, we use molecular dynamics simulations of the photoisomerization of probe dispersed red 1 molecules dispersed inside a glassy molecular matrix. Results show that the increased diffusion is due to an isomerization-induced cage-breaking process. A process that explains the induced cooperative motions recently observed in these photoactive materials.

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.

Science.gov (United States)

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.

Glycerol acetals, kinetic study of the reaction between glycerol and formaldehyde

International Nuclear Information System (INIS)

Agirre, I.; Garcia, I.; Requies, J.; Barrio, V.L.; Gueemez, M.B.; Cambra, J.F.; Arias, P.L.

2011-01-01

The acetalization reaction between glycerol and formaldehyde using Amberlyst 47 acidic ion exchange resin was studied. These acetals can be obtained from renewable sources (bioalcohols and bioalcohol derived aldehydes) and seem to be good candidates for different applications such as oxygenated diesel additives. A preliminary kinetic study was performed in a batch stirred tank reactor studying the influence of different process parameters like temperature, feed composition and the stirring speed. A pseudo homogenous kinetic model able to explain the reaction mechanism was adjusted. Thus, the corresponding order of reaction was determined. Amberlyst 47 acidic ion exchange resin showed a fairly good behavior allowing 100% of selectivity towards acetals formation. However, the studied acetalization reaction showed high thermodynamic limitations achieving glycerol conversions around 50% using a stoichiometric feed ratio at 353 K. The product is a mixture of two isomers (1,3-Dioxan-5-ol and 1,3-dioxolane-4-methanol) and the conversion of 1,3-dioxolane-4-methanol into 1,3-Dioxan-5-ol was also observed. -- Highlights: → The reaction between glycerol and acetaldehyde shows thermodynamic limitations. → Amberlyst 47 ion exchange resins show 100% of selectivity. → A pseudo-homogeneous kinetic model is able to predict the reaction progress. → Isomerization reactions were observed from dioxalanes to dioxanes.

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

Science.gov (United States)

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.

Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

Science.gov (United States)

Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

2014-03-06

Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu - and Arg + are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

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

International Nuclear Information System (INIS)

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

2017-01-01

We have determined the isomeric ratios of isomeric pairs "9"7"m","gNb, "9"5"m","gNb and "9"1"m","gMo produced in "9"8Mo(γ, p)"9"7"m","gNb, "9"6Mo(γ, p)"9"5"m","gNb and "9"2Mo(γ, n)"9"1"m","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 "9"7"m","gNb from 14 to 19 MeV, for "1"9"5"m","gNb from 14 to 24 MeV except 20 and 23.5 MeV and for "9"1"m","gMo at 14 and 15 MeV were first measured.

Specific racemization and isomerization of the aspartyl residue of αA-crystallin due to UV-B irradiation

International Nuclear Information System (INIS)

Fujii, Noriko; Momose, Yuko; Ishibasi, Yoshihiro; Uemura, Toshimasa; Takita, Masatoshi; Takehana, Makoto

1997-01-01

We have reported that the aspartyl (Asp)-151 residue in αA-crystallin in human eye lens was inverted to the D-isomer and isomerized to β-Asp residue with age. We report here that ultraviolet (UV)-B irradiation induces the racemization and isomerization of the Asp-151 residue of αA-crystallin from lenses of 6-week-old rats to form D-isomer and β-Asp residue. Simultaneous racemization and isomerization of the specific Asp residue indicate that the reaction proceeds via formation of a succinimide intermediate. This modification was not observed in UV-A irradiated and normal lenses. UV-B irradiation induced the racemization of only the Asp-151 residue and did not affect the other Asp residues in αA-crystallin. On the other hand, the high molecular weight fraction of the lens protein increased upon UV-B irradiation. Modification of the Asp residue would affect the three-dimensional packing array of the lens protein. (author)

Modulating the Physical and Electronic Properties over Positional Isomerism: The Dispirofluorene-Dihydroindacenodithiophene (DSF-IDT) Family.

Science.gov (United States)

Peltier, Jean-David; Heinrich, Benoît; Donnio, Bertrand; Jeannin, Olivier; Rault-Berthelot, Joëlle; Poriel, Cyril

2017-12-06

We report the first studies on the intrinsic properties of a meta-substituted dihydroindacenodithienyl fragment and more generally the strong impact of positional isomerism on dihydroindacenodithiophene derivatives. The influence of the para and meta linkages has notably been highlighted not only for the electronic properties in solution (electrochemical properties, anodic polymerization, HOMO/LUMO energy levels, optical transitions, fluorescence spectra) but also on the physical properties in the solid state (molecular organization, crystallinity, and phase transitions). The positional isomerism hence appears to be a very efficient tool to drastically tune the properties of dihydroindacenodithiophene derivatives. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of the hydro-isomerization of paraffins with 7 and 8 carbon atoms on bifunctional catalysts; Etude de l'hydroisomerisation des paraffines a 7 et 8 atomes de carbone sur catalyseurs bifonctionnels

Energy Technology Data Exchange (ETDEWEB)

Patrigeon, A.

2000-10-11

Due to the suppression of lead additives and the trend to decrease the aromatic and olefinic content in gasoline, the interest for new octane enhancement processes has increased, particularly for isomerization of C{sub 7} and C{sub 8} linear paraffins into higher octane number multi-branched paraffins. Up to the present day, no industrial bifunctional catalyst exists due to the high tendency of the paraffins to be cracked limiting the amount of multi-branched products. The aim of this work is to study the possibility of isomerizing linear C{sub 7} and C{sub 8} paraffins in two steps in order to increase the amount of formed multi-branched paraffins. The first step converts linear paraffins into mono-branched paraffins (that step is supposed to be the slowest one) carried out using one bifunctional catalyst. The second step converts the formed mono-branched paraffins into multi-branched paraffins using a second bifunctional catalyst. The aim is to determine the characteristics of the two catalysts. To study the first step, Pt/zeolite or Pt/meso-porous solid catalysts, with different acidities and porosities, were tested in n-heptane and n-octane hydro-conversion. The role of solid porosity on selectivities was clearly established. Molecular modelling was utilised to explain the observed selectivities. To study the second step, the 2-methyl-hexane and 2-methyl-heptane hydro-conversion on Pt/H-beta and Pt/H-Y was carried out. This lead to maximum multi-branched yields similar to those obtained with the n-heptane and n-octane hydro-conversion. That result shows that the two steps isomerization process is not necessarily required because no more multi-branched products are formed. A kinetic study on the n-heptane hydro-conversion was performed. The decomposition of isomerization and cracking reactions into elementary steps has shown the major role of the paraffins physio-sorption step in the zeolite pores. (author)

Polymeric proanthocyanidins: Interflavanoid linkage isomerism in (epicatechin-4)-(epicatechin-4)-catechin procyanidins

Science.gov (United States)

Richard W. Hemingway; L. Yeap Foo; L. J. Porter

1981-01-01

Procyanidin trimers have been isolated from a variety of plants,1-3 but their structures remain unresolved. We have now isolated three configurational isomers of (epicatechin-4)-(epicatechin-4)-catechin from Pinus taeda L. (loblolly pine) phloem which exhibit isomerism of the interflavanoid linkages.

Pion condensation and density isomerism in nuclear matter

International Nuclear Information System (INIS)

Hecking, P.; Weise, W.

1979-01-01

The possible existence of density isomers in nuclear matter, induced by pion condensation, is discussed; the nuclear equation of state is treated within the framework of the sigma model. Repulsive short-range baryon-baryon correlations, the admixture of Δ (1232) isobars and finite-range pion-baryon vertex form factors are taken into account. The strong dependence of density isomerism on the high density extrapolation of the equation of state for normal nuclear matter is also investigated. We find that, once finite range pion-baryon vertices are introduced, the appearance of density isomers becomes unlikely

Geometrical Optimization Approach to Isomerization: Models and Limitations.

Science.gov (United States)

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.

Isomeric island in the vicinity of 66Fe

International Nuclear Information System (INIS)

Daugas, J. M.; Belier, G.; Girod, M.; Goutte, H.; Meot, V.; Perru, O.; Roig, O.; Sauvestre, J. E.; Sawicka, M.; Pfuetzner, M.; Zylicz, J.; Matea, I.; Giovinazzo, J.; Grawe, H.; Becker, F.; Mayet, P.; Grzywacz, R.; Achouri, N. L.; Angelique, J. C.; Baiborodin, D.

2006-01-01

An island of isomers have recently been observed on both sides of the N=40 shell below the Ni isotopes. Isomeric states in the 65Fe and 67Fe allow the knowledge of the single particle structure around the νg9/2 shell. Moreover, the excitation energy of the first 2+ and 4+ states in the 68Fe have been established by β-γ correlation. The evolution of the structure of the Fe isotopes going far away from the valley of stability is, for the first time, given for N>40

Surface study of mixtures containing cyclic ethers and isomeric chlorobutanes

International Nuclear Information System (INIS)

Royo, F.M.; Villares, A.; Martin, S.; Giner, B.; Lafuente, C.

2007-01-01

Experimental surface tensions and the corresponding surface tensions deviations for the mixtures containing 1,3-dioxolane or 1,4-dioxane and 1-chlorobutane, 2-chlorobutane, 1-chloro-2-methylpropane or 2-chloro-2-methylpropane, measured with a drop volume tensiometer, are reported at the temperatures of 298.15 K and 313.15 K. The excess surface concentrations of isomeric chlorobutanes are also evaluated using a monolayer model

Efficient Isomerization of Glucose to Fructose over Zeolites in Consecutive Reactions in Alcohol and Aqueous Media

DEFF Research Database (Denmark)

Shunmugavel, Saravanamurugan; Paniagua, Marta; Melero, Juan A

2013-01-01

glucose isomerization to fructose and subsequent reaction with methanol to form methyl fructoside (step 1), followed by hydrolysis to re-form fructose after water addition (step 2). NMR analysis with (13)C-labeled sugars confirmed this reaction pathway. Conversion of glucose for 1 h at 120 °C with H......-USY (Si/Al = 6) gave a remarkable 55% yield of fructose after the second reaction step. A main advantage of applying alcohol media and a catalyst that combines Brønsted and Lewis acid sites is that glucose is isomerized to fructose at low temperatures, while direct conversion to industrially important...

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

Science.gov (United States)

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

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

Science.gov (United States)

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…

Collective coordinates and an accompanying metric force in structural isomerization dynamics of molecules

International Nuclear Information System (INIS)

Yanao, Tomohiro; Takatsuka, Kazuo

2003-01-01

Structural isomerization dynamics of three- and four-atom clusters of vanishing total angular momentum is studied in terms of internal coordinates of n-body systems on the basis of a gauge theory. The so-called principal-axis hyperspherical coordinates are employed effectively as collective variables for the study of isomerization reactions. It turns out that the non-Euclidean metric on the internal space gives rise to a force, which works in response to internal motions called the democratic (kinematic) rotations in the internal space. This metric force generally tends to induce an asymmetry in mass balance of a system, and is coupled with the usual potential force to give rise to trapped motions in the vicinity of the transition states of the cluster. This observation provides a different perspective for the so-called recrossing problem in chemical reaction dynamics

Photo-isomerization induced rapid photo-degradation of optical nonlinearity in cyano substituted stilbene derivative doped poled polymer

International Nuclear Information System (INIS)

Yan Jieyun; Liu Liying; Ji Liyong; Ye Mingxin; Xu Lei; Wang Wencheng

2004-01-01

We found that, although alpha'-cyano-4'-nitro-4-N, N-dimethylaminostilbene has larger hyperpolarizability than that of conventional 4'-N, N-dimethylamino-nitrostilbene, the addition of the cyano group makes it much more easy to photo-isomerize, thus destroying the molecular ordering in poled chromophore doped polymers. Experimental evidence was obtained by monitoring the second-harmonic generation intensity, UV-Vis absorption spectrum, and FTIR spectrum. The photo-isomerization reaction process was monitored by optical pump induced absorption anisotropy measurement. Comparisons with the behaviour of a azobenzene dye are also made

Conformational lock and dissociative thermal inactivation of lentil seedling amine oxidase.

Science.gov (United States)

Moosavi-Nejad, S Zahra; Moosavi-Movahedi, Ali-Akbar; Rezaei-Tavirani, Mostafa; Floris, Giovanni; Medda, Rosaria

2003-03-31

The kinetics of thermal inactivation of copper-containing amine oxidase from lentil seedlings were studied in a 100 mM potassium phosphate buffer, pH 7, using putrescine as the substrate. The temperature range was between 47-60 degrees C. The thermal inactivation curves were not linear at 52 and 57 degrees C; three linear phases were shown. The first phase gave some information about the number of dimeric forms of the enzyme that were induced by the higher temperatures using the "conformational lock" pertaining theory to oligomeric enzyme. The "conformational lock" caused two additional dimeric forms of the enzyme when the temperature increased to 57 degrees C. The second and third phases were interpreted according to a dissociative thermal inactivation model. These phases showed that lentil amine oxidase was reversibly-dissociated before the irreversible thermal inactivation. Although lentil amine oxidase is not a thermostable enzyme, its dimeric structure can form "conformational lock," conferring a structural tolerance to the enzyme against heat stress.

On conformal-invariant behaviour of four-point theories in ultraviolet asymptotics

International Nuclear Information System (INIS)

Ushveridze, A.G.

1977-01-01

A method is presented to obtain scale- and conformal-invariant solutions of four-point field theories in the ultraviolet asymptotics by means of reduction to the three-point problem. To do this a supplementary sigma field without a kinetic term is introduced and the Lagrangian is modified correspondingly. For the three-point problems the equations in form of the generalized unitarity conditions are solved further

Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

KAUST Repository

Mohamed, Samah; Cai, Liming; Khaled, Fathi; Banyon, Colin; Wang, Zhandong; Rachidi, Mariam El; Pitsch, Heinz; Curran, Henry J.; Farooq, Aamir; Sarathy, Mani

2016-01-01

Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

Modeling Ignition of a Heptane Isomer: Improved Thermodynamics, Reaction Pathways, Kinetic, and Rate Rule Optimizations for 2-Methylhexane

KAUST Repository

Mohamed, Samah

2016-03-21

Accurate chemical kinetic combustion models of lightly branched alkanes (e.g., 2-methylalkanes) are important to investigate the combustion behavior of real fuels. Improving the fidelity of existing kinetic models is a necessity, as new experiments and advanced theories show inaccuracies in certain portions of the models. This study focuses on updating thermodynamic data and the kinetic reaction mechanism for a gasoline surrogate component, 2-methylhexane, based on recently published thermodynamic group values and rate rules derived from quantum calculations and experiments. Alternative pathways for the isomerization of peroxy-alkylhydroperoxide (OOQOOH) radicals are also investigated. The effects of these updates are compared against new high-pressure shock tube and rapid compression machine ignition delay measurements. It is shown that rate constant modifications are required to improve agreement between kinetic modeling simulations and experimental data. We further demonstrate the ability to optimize the kinetic model using both manual and automated techniques for rate parameter tunings to improve agreement with the measured ignition delay time data. Finally, additional low temperature chain branching reaction pathways are shown to improve the model’s performance. The present approach to model development provides better performance across extended operating conditions while also strengthening the fundamental basis of the model.

Quantifying polypeptide conformational space: sensitivity to conformation and ensemble definition.

Science.gov (United States)

Sullivan, David C; Lim, Carmay

2006-08-24

Quantifying the density of conformations over phase space (the conformational distribution) is needed to model important macromolecular processes such as protein folding. In this work, we quantify the conformational distribution for a simple polypeptide (N-mer polyalanine) using the cumulative distribution function (CDF), which gives the probability that two randomly selected conformations are separated by less than a "conformational" distance and whose inverse gives conformation counts as a function of conformational radius. An important finding is that the conformation counts obtained by the CDF inverse depend critically on the assignment of a conformation's distance span and the ensemble (e.g., unfolded state model): varying ensemble and conformation definition (1 --> 2 A) varies the CDF-based conformation counts for Ala(50) from 10(11) to 10(69). In particular, relatively short molecular dynamics (MD) relaxation of Ala(50)'s random-walk ensemble reduces the number of conformers from 10(55) to 10(14) (using a 1 A root-mean-square-deviation radius conformation definition) pointing to potential disconnections in comparing the results from simplified models of unfolded proteins with those from all-atom MD simulations. Explicit waters are found to roughen the landscape considerably. Under some common conformation definitions, the results herein provide (i) an upper limit to the number of accessible conformations that compose unfolded states of proteins, (ii) the optimal clustering radius/conformation radius for counting conformations for a given energy and solvent model, (iii) a means of comparing various studies, and (iv) an assessment of the applicability of random search in protein folding.

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

Directory of Open Access Journals (Sweden)

Nicolas Huguenin-Dezot

2016-07-01

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

High spin states in 63Cu. 17/2+ isomeric yrast state

International Nuclear Information System (INIS)

Tsan Ung Chan; Bruandet, J.F.; Dauchy, A.; Giorni, A.; Glasser, F.; Morand, C.; Chambon, B.; Drain, D.

1979-01-01

The 63 Cu nucleus has been studied via the reaction 61 Ni(α, pnγ), using different in beam γ spectroscopy techniques. An isomeric high-spin Yrast state 17/2 + (tau = 6.1 +- 0.6ns) is located at 4498 keV. The gsub(9/2) shell must be involved to explain positive high-spin states established in this work [fr

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

Directory of Open Access Journals (Sweden)

Neha Phadke

2015-11-01

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

Phase space conduits for reaction in multidimensional systems : HCN isomerization in three dimensions

NARCIS (Netherlands)

Waalkens, Holger; Burbanks, Andrew; Wiggins, Stephen

2004-01-01

The three-dimensional hydrogen cyanide/isocyanide isomerization problem is taken as an example to present a general theory for computing the phase space structures which govern classical reaction dynamics in systems with an arbitrary (finite) number of degrees of freedom. The theory, which is

Selecting a scale, the conformal convergence problem and R2 terms

International Nuclear Information System (INIS)

Macrae, K.I.

1981-01-01

The Einstein-Hilbert action contains negative norm terms such as the conformal factor's kinetic energy. These can be cancelled by the ghosts associated with recoordinatization invariance except when one destroys that invariance by introducing a lattice (cutoff). Regulation of gravitation by a lattice cutoff leads to a funtional integral which does not cenverge on the conformal factor. Convergence of the integral can be insured by introducing a potential depending on the flat background lattice metric, but it can also be achieved by introducing higher order (curvature squared) terms in the action. Such a term together with the usual linear term selects a scale which can be used to single out a special size for the lattice. This ties together renormalization and gravitation in an interesting way. (orig.)

Workers’ Conformism

Directory of Open Access Journals (Sweden)

Nikolay Ivantchev

2013-10-01

Full Text Available Conformism was studied among 46 workers with different kinds of occupations by means of two modified scales measuring conformity by Santor, Messervey, and Kusumakar (2000 – scale for perceived peer pressure and scale for conformism in antisocial situations. The hypothesis of the study that workers’ conformism is expressed in a medium degree was confirmed partly. More than a half of the workers conform in a medium degree for taking risk, and for the use of alcohol and drugs, and for sexual relationships. More than a half of the respondents conform in a small degree for anti-social activities (like a theft. The workers were more inclined to conform for risk taking (10.9%, then – for the use of alcohol, drugs and for sexual relationships (8.7%, and in the lowest degree – for anti-social activities (6.5%. The workers who were inclined for the use of alcohol and drugs tended also to conform for anti-social activities.

Tilting the balance between canonical and noncanonical conformations for the H1 hypervariable loop of a llama VHH through point mutations.

Science.gov (United States)

Mahajan, Sai Pooja; Velez-Vega, Camilo; Escobedo, Fernando A

2013-01-10

Nanobodies are single-domain antibodies found in camelids. These are the smallest naturally occurring binding domains and derive functionality via three hypervariable loops (H1-H3) that form the binding surface. They are excellent candidates for antibody engineering because of their favorable characteristics like small size, high solubility, and stability. To rationally engineer antibodies with affinity for a specific target, the hypervariable loops can be tailored to obtain the desired binding surface. As a first step toward such a goal, we consider the design of loops with a desired conformation. In this study, we focus on the H1 loop of the anti-hCG llama nanobody that exhibits a noncanonical conformation. We aim to "tilt" the stability of the H1 loop structure from a noncanonical conformation to a (humanized) type 1 canonical conformation by studying the effect of selected mutations to the amino acid sequence of the H1, H2, and proximal residues. We use all-atomistic, explicit-solvent, biased molecular dynamic simulations to simulate the wild-type and mutant loops in a prefolded framework. We thus find mutants with increasing propensity to form a stable type 1 canonical conformation of the H1 loop. Free energy landscapes reveal the existence of conformational isomers of the canonical conformation that may play a role in binding different antigenic surfaces. We also elucidate the approximate mechanism and kinetics of transitions between such conformational isomers by using a Markovian model. We find that a particular three-point mutant has the strongest thermodynamic propensity to form the H1 type 1 canonical structure but also to exhibit transitions between conformational isomers, while a different, more rigid three-point mutant has the strongest propensity to be kinetically trapped in such a canonical structure.

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.

Science.gov (United States)

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.

Focused conformational sampling in proteins

Science.gov (United States)

Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

2017-11-01

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

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

Science.gov (United States)

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.

Hyperbolic theory of relativistic conformal dissipative fluids

Science.gov (United States)

Lehner, Luis; Reula, Oscar A.; Rubio, Marcelo E.

2018-01-01

We develop a complete description of the class of conformal relativistic dissipative fluids of divergence form, following the formalism described in [R. Geroch and L. Lindblom, Phys. Rev. D 41, 1855 (1990), 10.1103/PhysRevD.41.1855, S. Pennisi, Some considerations on a non linear approach to extended thermodynamics and in Proceedings of Symposium of Kinetic Theory and Extended Thermodynamics, Bologna, 1987.]. This type of theory is fully described in terms of evolution variables whose dynamics are governed by total divergence-type conservation laws. Specifically, we give a characterization of the whole family of conformal fluids in terms of a single master scalar function defined up to second-order corrections in dissipative effects, which we explicitly find in general form. This allows us to identify the equilibrium states of the theory and derive constitutive relations and a Fourier-like law for the corresponding first-order theory heat flux. Finally, we show that among this class of theories—and near equilibrium configurations—there exist symmetric hyperbolic ones, implying that for them one can define well-posed initial value problems.

Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox.

Directory of Open Access Journals (Sweden)

Julien Hiblot

Full Text Available Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263 that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.

Conformation radiotherapy and conformal radiotherapy

International Nuclear Information System (INIS)

Morita, Kozo

1999-01-01

In order to coincide the high dose region to the target volume, the 'Conformation Radiotherapy Technique' using the multileaf collimator and the device for 'hollow-out technique' was developed by Prof. S. Takahashi in 1960. This technique can be classified a type of 2D-dynamic conformal RT techniques. By the clinical application of this technique, the late complications of the lens, the intestine and the urinary bladder after radiotherapy for the maxillary cancer and the cervical cancer decreased. Since 1980's the exact position and shape of the tumor and the surrounding normal tissues can be easily obtained by the tremendous development of the CT/MRI imaging technique. As a result, various kinds of new conformal techniques such as the 3D-CRT, the dose intensity modulation, the tomotherapy have been developed since the beginning of 1990'. Several 'dose escalation study with 2D-/3D conformal RT' is now under way to improve the treatment results. (author)

Silver complexation and tandem mass spectrometry for differentiation of isomeric flavonoid diglycosides.

Science.gov (United States)

Zhang, Junmei; Brodbelt, Jennifer S

2005-03-15

For detection and differentiation of isomeric flavonoids, electrospray ionization mass spectrometry is used to generate silver complexes of the type (Ag + flavonoid)+. Collisionally activated dissociation (CAD) of the resulting 1:1 silver/flavonoid complexes allows isomer differentiation of flavonoids. Eighteen flavonoid diglycosides constituting seven isomeric series are distinguishable from each other based on the CAD patterns of their silver complexes. Characteristic dissociation pathways allow identification of the site of glycosylation, the type of disaccharide (rutinose versus neohesperidose), and the type of aglycon (flavonol versus flavone versus flavanone). This silver complexation method is more universal than previous metal complexation methods, as intense silver complexes are observed even for flavonoids that lack the typical metal chelation sites. To demonstrate the feasibility of using silver complexation and tandem mass spectrometry to characterize flavonoids in complex mixtures, flavonoids extracted from grapefruit juice are separated by high-performance liquid chromatography and analyzed via a postcolumn complexation ESI-MS/MS strategy. Diagnostic fragmentation pathways of the silver complexes of the individual eluting flavonoids allow successful identification of the six flavonoids in the extract.

Cardiopulmonary Exercise Testing in Fontan Patients With and Without Isomerism (Heterotaxy) as Compared to Patients With Primary Ciliary Dyskinesia and Subjects With Structurally Normal Hearts

DEFF Research Database (Denmark)

Loomba, Rohit S; Danduran, Michael; Nielsen, Kim G

2017-01-01

with and without isomerism. We have now compared these finding with those from patients with primary ciliary dyskinesia, as many patients with isomerism have ciliary dyskinesia. We identified patients having the Fontan circulation with and without isomerism who had undergone cardiopulmonary exercise testing......, comparing the findings from healthy individuals undergoing exercise, and a comparable number of individuals with primary ciliary dyskinesia but no congenital heart disease. We were able to include a total of 68 patients in our study, with 17 in each of the four groups. Cardiopulmonary exercise testing...

Killing tensors and conformal Killing tensors from conformal Killing vectors

International Nuclear Information System (INIS)

Rani, Raffaele; Edgar, S Brian; Barnes, Alan

2003-01-01

Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition, we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate that it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors, and hence all the Killing tensors (which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors

Thermal solid-state Z/E isomerization of 2-alkylidene-4-oxothiazolidines: effects of non-covalent interactions

Directory of Open Access Journals (Sweden)

ZDRAVKO DŽAMBASKI

2011-03-01

Full Text Available Configurational isomerization of stereo-defined 5-substituted and unsubstituted 2-alkylidene-4-oxothiazolidines (1 in the solid state, giving the Z/E mixtures in various ratios, was investigated by 1H-NMR spectroscopy, X-ray powder crystallography and differential scanning calorimetry (DSC. The Z/E composition can be rationalized in terms of non-covalent interactions, involving intermolecular and intramolecular hydrogen bonding and directional non-bonded 1,5-type S×××O interactions. X-Ray powder crystallography, using selected crystalline (Z-4-oxothiazolidine substrates, revealed transformation to the amorphous state during the irreversible Z®E process. A correlation between previous results on the Z/E isomerization in solution and now in the solid state was established.

Synthesis of heterocycles through transition-metal-catalyzed isomerization reactions

DEFF Research Database (Denmark)

Ishøy, Mette; Nielsen, Thomas Eiland

2014-01-01

of structurally complex and diverse heterocycles. In this Concept article, we attempt to cover this area of research through a selection of recent versatile examples. A sea of opportunities! Transition-metal-catalyzed isomerization of N- and O-allylic compounds provides a mild, selective and synthetically...... versatile method to form iminium and oxocarbenium ions. Given the number of reactions involving these highly electrophilic intermediates, this concept provides a sea of opportunities for heterocycle synthesis, (see scheme; Nu=nucleophile). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim....

Yields and isomeric ratio of xenon and krypton isotopes from thermal neutron fission of 235U

International Nuclear Information System (INIS)

Hsu, S.S.; Lin, J.T.; Yang, C.M.; Yu, Y.W.

1981-01-01

The experimental cumulative yields of 85 Kr/sup m/, 87 Kr, 88 Kr, 133 Xe/sup g/, 135 Xe/sup m/, and 135 Xe/sup g/ and the independent isomeric yield of 133 Xe/sup m/ in the thermal neutron fission of 235 U have been measured by the gas chromatographic method. The independent yields of 133 Xe/sup g/, 135 Xe/sup m/, and 135 Xe/sup g/ were deduced with the aid of 133 I and 135 I data. The isomeric yield ratios of 133 Xe and 135 Xe have been computed and compared with theoretical values since they have the same high spin state J = 11/2 - and low spin ground state J = 3/2 + . The influence of the shell effect on the fission isomeric yield ratio is discussed. From the measured independent yield of Xe isotopes plus the reported data, the Xe-isotopic distribution curve has been constructed. The curve is compared with the isotopic distribution curves of Xe isotopes formed in 11.5 GeV proton interactions with 238 U and Cs isotopes formed in 24 GeV proton interactions with 238 U. Upon fitting the yield curves we find that only those products with N/Z> or =1.48 fit a curve typical of a binary fission process

Nonrelativistic Conformed Symmetry in 2 + 1 Dimensional Field Theory.

Science.gov (United States)

Bergman, Oren

This thesis is devoted to the study of conformal invariance and its breaking in non-relativistic field theories. It is a well known feature of relativistic field theory that theories which are conformally invariant at the classical level can acquire a conformal anomaly upon quantization and renormalization. The anomaly appears through the introduction of an arbitrary, but dimensionful, renormalization scale. One does not usually associate the concepts of renormalization and anomaly with nonrelativistic quantum mechanics, but there are a few examples where these concepts are useful. The most well known case is the two-dimensional delta -function potential. In two dimensions the delta-function scales like the kinetic term of the Hamiltonian, and therefore the problem is classically conformally invariant. Another example of classical conformal invariance is the famous Aharonov-Bohm (AB) problem. In that case each partial wave sees a 1/r^2 potential. We use the second quantized formulation of these problems, namely the nonrelativistic field theories, to compute Green's functions and derive the conformal anomaly. In the case of the AB problem we also solve an old puzzle, namely how to reproduce the result of Aharonov and Bohm in perturbation theory. The thesis is organized in the following manner. Chapter 1 is an introduction to nonrelativistic field theory, nonrelativistic conformal invariance, contact interactions and the AB problem. In Chapter 2 we discuss nonrelativistic scalar field theory, and how its quantization produces the anomaly. Chapter 3 is devoted to the AB problem, and the resolution of the perturbation puzzle. In Chapter 4 we generalize the discussion of Chapter 3 to particles carrying nonabelian charges. The structure of the nonabelian theory is much richer, and deserves a separate discussion. We also comment on the issues of forward scattering and single -valuedness of wavefunctions, which are important for Chapter 3 as well. (Copies available

At the Perphery of the Amidohydrolase Superfamily: Bh0493 from Bacillus halodurans Catalyzes the Isomerization of D-Galacturonate to D-Tagaturonate

Energy Technology Data Exchange (ETDEWEB)

Nguyen,T.; Brown, S.; Fedorov, A.; Fedorov, E.; Babbitt, P.; Almo, S.; Raushel, F.

2008-01-01

The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of d-glucuronate to d-fructuronate and d-galacturonate to d-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of d-glucuronate to d-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20% sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 Angstroms confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both d-glucuronate and d-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of d-glucuronate, whereas Bh0493 is in an operon for the metabolism of d-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for d-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for

Production cross sections and isomeric ratios for sup(110m)In/sup(110g)In formed in Cd (d,xn) reactions

International Nuclear Information System (INIS)

Herreros Usher, Oscar; Maceiras de Jefimowicz, Elena; De la Vega Vedoya, Mario; Jorge Nassiff, Sonia

1980-01-01

Excitation functions and isomeric cross sections ratios have been measured for the 110 Cd (d,2n) and 111 Cd (d,3n) reactions in which the isomeric pair sup(110m)In/sup(110g)In is produced. Activation method was employed and the irradiations were performed at the synchrocyclotron of the Comision Nacional de Energia Atomica, Argentina, with an incident energy of 27.MeV. (author) [es

Catalytic Isomerization of Dihydroxyacetone to Lactic Acid and Alkyl Lactates over Hierarchical Zeolites Containing Tin

Directory of Open Access Journals (Sweden)

Agnieszka Feliczak-Guzik

2018-01-01

Full Text Available Hierarchical zeolites containing tin were obtained, characterized and used in a reaction of catalytic isomerization of dihydroxyacetone (DHA to lactic acid and alkyl lactates. These catalysts are characterized by preserved crystallinity and primary microporosity with the simultaneous existence of secondary porosity regarding mesopores, which facilitates access of large molecules of reagents to active centers. Creation of additional porosity was confirmed by X-ray diffraction and low-temperature nitrogen adsorption/desorption studies. The reaction of dihydroxyacetone isomerization was conducted in different reaction media such as methanol, ethanol or water with the use of two heating methods: microwave radiation and conventional heating. The application of microwave radiation enabled to reduce the reaction time to 1 h and achieve dihydroxyacetone conversion of >90% and high yields of the desired reaction products.

Replacement between conformity and counter-conformity in consumption decisions.

Science.gov (United States)

Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

2013-02-01

This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

Process for paraffin isomerization of a distillate range hydrocarbon feedstock

Energy Technology Data Exchange (ETDEWEB)

Chen, N.Y.; Garwood, W.E.; McCullen, S.B.

1993-01-19

Various catalytic processes have been proposed to isomerize n-paraffins so as to lower the pour point of distillate range hydrocarbon feedstocks. However, many available feedstocks contain nitrogen impurities which tend to poison conventional paraffin isomerization catalysts. A process has been developed to obviate or alleviate this problem. According to the invention, the paraffin-containing feedstock is contacted with a crystalline aluminosilicate zeolite catalyst having pore openings defined by a ratio of sorption of n-hexane to o-xylene of over 3 vol % and the ability to crack 3-methylpentane in preference to 2,3 dimethylbutane under defined conditions. The zeolite catalyst includes a Group VIII metal and has a zeolite SiO[sub 2]/Al[sub 2]O[sub 3] ratio of at least 20:1. The contacting is carried out at 199-454 C and a pressure of 100-1,000 psig, preferably 250-600 psig. The group of medium pore zeolites which can be used in the process of the invention includes ZSM-22, ZSM-23, and ZSM-35. The Group VIII metals used in the catalyst are preferably selected from Pt, Pd, Ir, Os, Rh, and Ru and the metal is preferably incorporated into the zeolite by ion exchange up to a metal content of preferably 0.1-3 wt %. Experiments are described to illustrate the invention. 1 tab.

A new general method for simultaneous fitting of temperature and concentration dependence of reaction rates yields kinetic and thermodynamic parameters for HIV reverse transcriptase specificity.

Science.gov (United States)

Li, An; Ziehr, Jessica L; Johnson, Kenneth A

2017-04-21

Recent studies have demonstrated the dominant role of induced fit in enzyme specificity of HIV reverse transcriptase and many other enzymes. However, relevant thermodynamic parameters are lacking, and equilibrium thermodynamic methods are of no avail because the key parameters can only be determined by kinetic measurement. By modifying KinTek Explorer software, we present a new general method for globally fitting data collected over a range of substrate concentrations and temperatures and apply it to HIV reverse transcriptase. Fluorescence stopped-flow methods were used to record the kinetics of enzyme conformational changes that monitor nucleotide binding and incorporation. The nucleotide concentration dependence was measured at temperatures ranging from 5 to 37 °C, and the raw data were fit globally to derive a single set of rate constants at 37 °C and a set of activation enthalpy terms to account for the kinetics at all other temperatures. This comprehensive analysis afforded thermodynamic parameters for nucleotide binding ( K d , Δ G , Δ H , and Δ S at 37 °C) and kinetic parameters for enzyme conformational changes and chemistry (rate constants and activation enthalpy). Comparisons between wild-type enzyme and a mutant resistant to nucleoside analogs used to treat HIV infections reveal that the ground state binding is weaker and the activation enthalpy for the conformational change step is significantly larger for the mutant. Further studies to explore the structural underpinnings of the observed thermodynamics and kinetics of the conformational change step may help to design better analogs to treat HIV infections and other diseases. Our new method is generally applicable to enzyme and chemical kinetics. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Abnormal radioactive decays out of long-lived super- and hyper-deformed isomeric states

International Nuclear Information System (INIS)

Marinov, A.; Gelberg, S.; Kolb, D.

2000-01-01

Complete text of publication follows. Recently (1-3) long-lived isomeric states have been found in the super- and hyper-deformed wells of the potential. These isomers manifested themselves by abnormal particle decays. An isomeric state in the superdeformed well of the potential in the parent nucleus can decay by very enhanced α-particle groups to superdeformed states in the daughter (1) or by very retarded α-particles (3) and also by protons (2) to normal states in the daughters. Similarly an isomeric state in the hyper-deformed well may decay by very retarded α-particle groups to superdeformed states (3), or by very enhanced α-groups to hyper-deformed states in the daughter nucleus (4). All these very unusual decay modes have been observed experimentally (1-4). For instance, a very high energy α-group of 8.6 MeV with 40d ≤ t 1/2 ≤ 2y (retardation factor of ∼10 13 ) has been observed in 195 Hg and interpreted as a III min → II min α-transition (3). Likewise, relatively low-energy and very enhanced α-particle groups (enhancement factors of 10 5 to 10 7 ) have been seen in several actinide sources and interpreted as due to II min → II min and III min → III min transitions (4). These unusual decay modes introduce new considerations in the study of heavy and superheavy elements. For instance, if low-energy α-particle groups around 4.4 - 4.6 MeV have been seen in nature (5), they may be interpreted as due to very enhanced III min → III min transitions in the superheavy element region around Z = 108 (eka-Os) with t 1/2 ∼10 8 y rather than ∼10 15 y as expected for normal α-transitions of such energies in this region, or due to very retarded III min → II min or II min → I min decays in nuclei around Os itself. In both cases, if such activities have been seen in nature, they indicate that the existence of the II min and III min isomeric states may be important in the nucleosynthesis process. It should be mentioned that long-lived high

Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

Science.gov (United States)

Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

2013-07-03

An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

Science.gov (United States)

Stamogiannos, Athanasios; Maben, Zachary; Papakyriakou, Athanasios; Mpakali, Anastasia; Kokkala, Paraskevi; Georgiadis, Dimitris; Stern, Lawrence J; Stratikos, Efstratios

2017-03-14

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

Single molecule insights on conformational selection and induced fit mechanism

DEFF Research Database (Denmark)

Hatzakis, Nikos

2014-01-01

. To describe the molecular basis of this behavior, two main mechanisms have been advanced: 'induced fit' and 'conformational selection'. Our understanding of these models relies primarily on NMR, computational studies and kinetic measurements. These techniques report the average behavior of a large ensemble...... of unsynchronized molecules, often masking intrinsic dynamic behavior of proteins and biologically significant transient intermediates. Single molecule measurements are emerging as a powerful tool for characterizing protein function. They offer the direct observation and quantification of the activity, abundance...

G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch.

Science.gov (United States)

Yan, Yi-Yong; Tan, Jia-Heng; Lu, Yu-Jing; Yan, Siu-Cheong; Wong, Kwok-Yin; Li, Ding; Gu, Lian-Quan; Huang, Zhi-Shu

2013-10-01

G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates. © 2013.

Global conformational dynamics of a Y-family DNA polymerase during catalysis.

Directory of Open Access Journals (Sweden)

Cuiling Xu

2009-10-01

Full Text Available Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. The Y-family DNA polymerases, characterized by low fidelity and processivity, are able to bypass different classes of DNA lesions. A variety of kinetic and structural studies have established a minimal reaction pathway common to all DNA polymerases, although the conformational intermediates are not well defined. Furthermore, the identification of the rate-limiting step of nucleotide incorporation catalyzed by any DNA polymerase has been a matter of long debate. By monitoring time-dependent fluorescence resonance energy transfer (FRET signal changes at multiple sites in each domain and DNA during catalysis, we present here a real-time picture of the global conformational transitions of a model Y-family enzyme: DNA polymerase IV (Dpo4 from Sulfolobus solfataricus. Our results provide evidence for a hypothetical DNA translocation event followed by a rapid protein conformational change prior to catalysis and a subsequent slow, post-chemistry protein conformational change. Surprisingly, the DNA translocation step was induced by the binding of a correct nucleotide. Moreover, we have determined the directions, rates, and activation energy barriers of the protein conformational transitions, which indicated that the four domains of Dpo4 moved in a synchronized manner. These results showed conclusively that a pre-chemistry conformational change associated with domain movements was too fast to be the rate-limiting step. Rather, the rearrangement of active site residues limited the rate of correct nucleotide incorporation. Collectively, the conformational dynamics of Dpo4 offer insights into how the inter-domain movements are related to enzymatic function and their concerted interactions with other proteins at the replication fork.

Application of adjustable pulse lasers to studying rapid reaction kinetics of excited lanthanide complexing

Energy Technology Data Exchange (ETDEWEB)

Gruzdev, V.P. (Gosudarstvennyj Opticheskij Inst., Leningrad (USSR))

1983-12-01

Using some europium (3) ion complexes new possibilities to be opened by application of adjustable pulse lasers for studying rapid reactions of electron-excited metal ion complexing are demonstrated. The 6Zh rhodamine pulse laser is used as a source of nonequilibrium photoexcitation of an array of Eu/sup 3 +/ complexes in the luminescent kinetic spectroscopy method. The following results are obtained: for the first time the rate of reaction of acetate ion substitution for water molecules of an excited (/sup 5/D/sub 0/) ion of Eu/sup 3 +/ was measured to be (0.7+-0.2)x10/sup 7/ s/sup -1/; using direct experiments the lower limit for the rate of transition of one isomeric form of the excited Eu x EDTA complex into another one in an aqueous solution is determined to be 5x10/sup 5/ s/sup -1/ at 295 K; the kinetics of the excitation energy migration beteen aqueous solvates of Eu/sup 3 +/ and EuxEDTA complexes is investigated.

Conformal house

DEFF Research Database (Denmark)

Ryttov, Thomas Aaby; Sannino, Francesco

2010-01-01

fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions...... at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms...

Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites

International Nuclear Information System (INIS)

Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Jaudzems, Kristaps; Mohanty, Biswaranjan; Horst, Reto; Herrmann, Torsten; Elsliger, Marc-André; Wilson, Ian A.; Wüthrich, Kurt

2010-01-01

Tools for systematic comparisons of NMR and crystal structures developed by the JCSG were applied to two proteins with known functions: the T. maritima anti-σ factor antagonist TM1081 and the mouse γ-glutamylamine cyclotransferase A2LD1 (gi:13879369). In an attempt to exploit the complementarity of crystal and NMR data, the combined use of the two structure-determination techniques was explored for the initial steps in the challenge of searching proteins of unknown functions for putative active sites. The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the

Isomeric Detergent Comparison for Membrane Protein Stability

DEFF Research Database (Denmark)

Cho, Kyung Ho; Hariharan, Parameswaran; Mortensen, Jonas S.

2016-01-01

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...

Results of a Direct Search Using Synchrotron Radiation for the Low-Energy (229)Th Nuclear Isomeric Transition.

Science.gov (United States)

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.

First observation of high spin states and isomeric decay in 210Fr

International Nuclear Information System (INIS)

Kanjilal, D.; Saha, S.; Bhattacharya, S.; Goswami, A.; Kshetri, R.; Raut, R.; Muralithar, S.; Singh, R. P.; Mukherjee, G.; Mukherjee, B.

2011-01-01

The first observation of the prompt and the delayed γ transitions involving the high spin states in 210 Fr is reported. The decay of the high spin states and the isomeric levels of 210 Fr, identified for the first time from the known sequence of low-lying transitions found earlier in the α decay of 214 Ac, were studied. High spin states of the doubly-odd 210 Fr, which were produced by the fusion evaporation reaction 197 Au ( 16 O, xn) 213-x Fr, were populated and the subsequent emitted γ rays were detected through the high-sensitivity germanium clover detector array INGA. The level scheme up to yrast levels of 5.3 MeV excitation energy and ∼20(ℎ/2π) angular momentum could be established for the first time through γγ, γγΔT coincidence, and DCO ratio measurements. A new low-lying isomeric transition at E γ = 203(2) keV was observed. The half-life was measured to be T 1/2 = 41(2) ns. The measured half-life was compared with the corresponding single-particle estimate, based on the level scheme obtained from the experiment.

Left atrial isomerism associated with asplenia: prenatal echocardiographic detection of complex congenital cardiac malformations

NARCIS (Netherlands)

Stewart, P. A.; Becker, A. E.; Wladimiroff, J. W.; Essed, C. E.

1984-01-01

Complex congenital heart disease with suspected isomerism of the atria was diagnosed in two fetuses of 20 and 29 weeks' gestation using two-dimensional and M-mode scanning techniques. The first pregnancy was terminated at 21 weeks' gestation and stillbirth occurred at 31 weeks' gestation in the

Ruthenium Hydride/Brønsted Acid-Catalyzed Tandem Isomerization/N-Acyliminium Cyclization Sequence for the Synthesis of Tetrahydro-β-carbolines

DEFF Research Database (Denmark)

Hansen, Casper Lykke; Clausen, Janie Regitse Waël; Ohm, Ragnhild Gaard

2013-01-01

This paper describes an efficient tandem sequence for the synthesis of 1,2,3,4-tetrahydro-β-carbolines (THBCs) relying on a ruthenium hydride/Brønsted acid- catalyzed isomerization of allylic amides to N-acyliminium ion intermediates which are trapped by a tethered indolenucleophile. The methodol...... the Suzuki cross-coupling reaction to the isomerization/N-acyliminium cyclization sequence. Finally, diastereo- and enantioselective versions of the title reaction have been examined using substrate control (with dr >15: 1) and asymmetric catalysis (ee up to 57%), respectively...

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Synthesis of zeolite-zeolite (mfi-fau) composite catalysts for the isomerization of n-hexane

International Nuclear Information System (INIS)

Ghouri, A.S; Usman, M.R.

2017-01-01

In this research work, the aim is to produce a relatively novel zeolite-zeolite (MFI-FAU) composite catalyst having better potential of catalyzing isomerization of lighter hydrocarbons such as light naphtha, n-pentane, n-hexane, n-heptane and mixture thereof. A series of zeolite-zeolite (MFI-FAU) composite catalysts have been synthesized by incorporating previous practices and techniques. The catalytic performance of as-synthesized zeolite-zeolite (MFI-FAU) composite catalysts have been investigated by isomerizing 95% pure n-hexane in conventional fixed bed flow micro-reactor at temperature 200-240 ºC under atmospheric pressure. In order to explore chemical and physical features of zeolite-zeolite (MFI-FAU) composite catalysts, they are examined and characterized using powder X-ray diffraction (XRD), scanning electron microscopy (SEM) coupled with energy-dispersive X-ray spectrometry (EDX), N2 adsorption-desorption measurements (BET, BJH, t-plot measurements) and Fourier transform infrared (FTIR) spectroscopy equipped with attenuated total reflectance (ATR) arrangements. (author)

Isotopic study on mechanism for skeletal isomerization of n-butane over solid acids

International Nuclear Information System (INIS)

Suzuki, Tetsuo; Okuhara, Toshio

2000-01-01

Reaction mechanism for skeletal isomerization of n-butane over typical strong solid acids were investigated by using 1,4- 13 C 2 -n-butane. We used FI MASS for the analysis of 13 C distribution to get the parent pattern. 13 C-distribution of isobutane formed at 423 K over SO 3 2- /ZrO 2 (SZ) and Cs 2.5 H 0.5 PW 12 O 40 (Cs2.5) were close to binomial distributions, indicating that the isomerization proceeded mainly via a bimolecular mechanism on these catalysts. On the other hand, at 523 K over Cs2.5, the isotopic distribution pattern in isobutane was quite different from the binomial one; the fraction of 13 C 2 -isobutane was much greater than the binomial distribution. This result demonstrates that an intramolecular (monomolecular) rearrangement became significant at 523 K over Cs2.5. The contribution of monomolecular pathway was higher on Cs2.5 than on SZ. We presumed that the contribution of mechanism is related to the acidic property and the dehydrogenation ability of the catalyst. (S.Y.)

Retrieving molecular structural information and tracking HNC/HCN isomerization process with high harmonic generation by ultrashort laser pulses

International Nuclear Information System (INIS)

Nguyen Ngoc Ty; Le Van Hoang; Vu Ngoc Tuoc; Le Anh Thu

2010-01-01

We investigate the possibility of applying the iterative method, suggested in our previous work, for HCN molecule and its HNC isomer. We found that the high-order harmonic generation (HHG) spectra are quite insensitive to the change of H-C (or H-N) bond length so that only the inter-nuclear C-N distance can be retrieved from the high-order harmonic spectra using ultrashort intense lasers. Furthermore, by analyzing the HHG spectra emitted by HCN during the chemical reaction path of isomerization we identify the intensity peaks nearby the stable, metastable and transition states. this finding can be useful for tracking the HNC/HNC isomerization process. (author)

Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.

Directory of Open Access Journals (Sweden)

Kai Wang

Full Text Available Hierarchical organization of free energy landscape (FEL for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL, and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF. Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100 ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs.

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

Science.gov (United States)

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.

Palladium Hydride Promoted Stereoselective Isomerization of Unactivated Di(exo)methylenes to Endocyclic Dienes

OpenAIRE

Jung, Michael E.; Lee, Gloria S.; Pham, Hung V.; Houk, K. N.

2014-01-01

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 C 2 symmetry with very little formation of the analogous product with C s symmetry. A hydrogen source is essential to effect the rearrangement.

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

Science.gov (United States)

Van Hoomissen, Daniel J; Vyas, Shubham

2017-11-16

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

Magnetic dipole moments of High-K isomeric states in Hf isotopes

CERN Multimedia

Walters, W; Nishimura, K; Bingham, C R

2007-01-01

It is proposed to make precision measurements of the magnetic moments of 5 multi-quasi-particle K-isomers in Hf nuclei by the Nuclear Magnetic Resonance of Oriented Nuclei (NMR/ON) technique using the NICOLE on-line nuclear orientation facility and exploiting the unique HfF$_{3}$ beams recently available at ISOLDE. Results will be used to extract single-particle and collective g-factors of the isomeric states and their excitations and to shed new light on their structure.

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

Science.gov (United States)

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.

g-factor of the 7- isomeric state in 128Ba

International Nuclear Information System (INIS)

Kaur, J.; Bansal, N.; Bhati, A.K.; Sharma, V.R.; Kumar, H.; Kumar, R.; Bhowmik, R.K.; Kumar, V.

2014-01-01

The time differential perturbed angular distribution technique (TDPAD) has been used to measure the g-factor of the 2396 keV, 7 - isomeric state in 128 Ba. The measured value of g(7 - ) is 1.21 ± 0.01. This value is about 80% higher than the value for the expected configuration of the state and also different in sign. This clearly shows that the configuration of the state does not correspond to the pure two quasineutron configuration that was assigned to it through previous results of in-beam γ-ray spectroscopy

Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.

Directory of Open Access Journals (Sweden)

Giulio Quarta

Full Text Available Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant "downhill" pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the "new view" of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.

Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.

Science.gov (United States)

Uhlemann, Thomas; Seidel, Sebastian; Müller, Christian W

2017-06-07

We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH 2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the C i symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.

Generic Schemes for Single-Molecule Kinetics. 3: Self-Consistent Pathway Solutions for Nonrenewal Processes.

Science.gov (United States)

Piephoff, D Evan; Cao, Jianshu

2018-04-23

We recently developed a pathway analysis framework (paper 1) for describing single-molecule kinetics for renewal (i.e., memoryless) processes based on the decomposition of a kinetic scheme into generic structures. In our approach, waiting time distribution functions corresponding to such structures are expressed in terms of self-consistent pathway solutions and concatenated to form measurable probability distribution functions (PDFs), affording a simple way to decompose and recombine a network. Here, we extend this framework to nonrenewal processes, which involve correlations between events, and employ it to formulate waiting time PDFs, including the first-passage time PDF, for a general kinetic network model. Our technique does not require the assumption of Poissonian kinetics, permitting a more general kinetic description than the usual rate approach, with minimal topological restrictiveness. To demonstrate the usefulness of this technique, we provide explicit calculations for our general model, which we adapt to two generic schemes for single-enzyme turnover with conformational interconversion. For each generic scheme, wherein the intermediate state(s) need not undergo Poissonian decay, the functional dependence of the mean first-passage time on the concentration of an external substrate is analyzed. When conformational detailed balance is satisfied, the enzyme turnover rate (related to the mean first-passage time) reduces to the celebrated Michaelis-Menten functional form, consistent with our previous work involving a similar scheme with all rate processes, thereby establishing further generality to this intriguing result. Our framework affords a general and intuitive approach for evaluating measurable waiting time PDFs and their moments, making it a potentially useful kinetic tool for a wide variety of single-molecule processes.

Reaction kinetics of resveratrol with thiyl and alkoxyl radicals

International Nuclear Information System (INIS)

Dzeba, I.; Mihaljevic, B.

2011-01-01

Complete text of publication follows. Plant derived resveratrol (trans-3,5,4'-trihydroxystilbene) possesses a broad spectrum of biological activities, one of them are very well known its antioxidative properties. Our work aims to provide kinetic data with regard to the reactivity of resveratrol with uninvestigated short-lived bioradicals, identified as mediators in oxidative lipid degradation processes. Radicals of our interest are alkoxyl radicals, well known propagators of the chain free radical reactions in lipids, and thiyl radicals which protect lipids from their degradation pathway, but at the same time cause the isomerization of the double bonds. In order to investigate these reactions of resveratrol laser flash photolysis was used. On the basis of competitive kinetics the rate constants were determined under pseudo-first order conditions in acetonitrile solutions at room temperature. Thiyl radicals were generated indirectly in solution containing 1-octadecanthiol and photosensitive benzophenone in acetonitrile using the light pulses at 347 nm from ruby laser. Tert-butoxyl radicals were generated directly by peroxide bond cleavage from di-tert-butyl peroxide in acetonitrile by light pulses of Nd:YAG at 355 nm, and ruby at 347 nm. Obtained rate constants for the reactions of resveratrol and radicals generated by laser flash photolysis will be summarized and compared with rare literature data for the rate constants of investigated reactions of resveratrol and other radicals generated by pulse radiolysis.

Conformational analysis of capsaicin using 13C, 15N MAS NMR, GIAO DFT and GA calculations

Science.gov (United States)

Siudem, Paweł; Paradowska, Katarzyna; Bukowicki, Jarosław

2017-10-01

Capsaicin produced by plants from genus Capsicum exerts multiple pharmacological effects and has found applications in food and pharmaceutical industry. The alkaloid was studied by a combined approach: solid-state NMR, GA conformational search and GIAO DFT methods. The 13C CPMAS NMR spectra were recorded using variable contact time and dipolar dephasing experiments. The results of cross-polarization (CP) kinetics, such as TCP values and long T1ρH (100-200 ms), indicated that the capsaicin molecule is fairly mobile, especially at the end of the aliphatic chain. The15N MAS NMR spectrum showed one narrow signal at -255 ppm. Genetic algorithm (GA) search with multi modal optimization was used to find low-energy conformations of capsaicin. Theoretical GIAO DFT calculations were performed using different basis sets to characterize five selected conformations. 13C CPMAS NMR was used as a validation method and the experimental chemical shifts were compared with those calculated for selected stable conformers. Conformational analysis suggests that the side chain can be bent or extended. A comparison of the experimental and the calculated chemical shifts indicates that solid capsaicin does not have the same structure as those established by PWXRD.

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

Science.gov (United States)

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.

Macrocyclic effects upon isomeric Cu M and M Cu cores. Formation ...

Indian Academy of Sciences (India)

Administrator

from the iminic site to the aminic site in the synthesis of 10 is explained by ... Our previous studies suggest that isomeric MIICuII ... Calcd. for C24H27Br2ClCuN4NiO8: C 35⋅28; H 3⋅33; N 6⋅86; Cu 7⋅78; Ni .... Electronic absorption spectra in .... 3. 1497(1). 1452. ⋅3(5). 2992(1). 1860(2). 3206(1). Z. 2. 2. 4. 2. 4. D calcd. /g.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

Quantum Conformal Algebras and Closed Conformal Field Theory

CERN Document Server

Anselmi, D

1999-01-01

We investigate the quantum conformal algebras of N=2 and N=1 supersymmetric gauge theories. Phenomena occurring at strong coupling are analysed using the Nachtmann theorem and very general, model-independent, arguments. The results lead us to introduce a novel class of conformal field theories, identified by a closed quantum conformal algebra. We conjecture that they are the exact solution to the strongly coupled large-N_c limit of the open conformal field theories. We study the basic properties of closed conformal field theory and work out the operator product expansion of the conserved current multiplet T. The OPE structure is uniquely determined by two central charges, c and a. The multiplet T does not contain just the stress-tensor, but also R-currents and finite mass operators. For this reason, the ratio c/a is different from 1. On the other hand, an open algebra contains an infinite tower of non-conserved currents, organized in pairs and singlets with respect to renormalization mixing. T mixes with a se...

C-metric solution for conformal gravity with a conformally coupled scalar field

Energy Technology Data Exchange (ETDEWEB)

Meng, Kun, E-mail: mengkun@tjpu.edu.cn [School of Science, Tianjin Polytechnic University, Tianjin 300387 (China); Zhao, Liu, E-mail: lzhao@nankai.edu.cn [School of Physics, Nankai University, Tianjin 300071 (China)

2017-02-15

The C-metric solution of conformal gravity with a conformally coupled scalar field is presented. The solution belongs to the class of Petrov type D spacetimes and is conformal to the standard AdS C-metric appeared in vacuum Einstein gravity. For all parameter ranges, we identify some of the physically interesting static regions and the corresponding coordinate ranges. The solution may contain a black hole event horizon, an acceleration horizon, either of which may be cut by the conformal infinity or be hidden behind the conformal infinity. Since the model is conformally invariant, we also discussed the possible effects of the conformal gauge choices on the structure of the spacetime.

Structure–kinetic relationship study of CDK8/CycC specific compounds

Science.gov (United States)

Schneider, Elisabeth V.; Böttcher, Jark; Huber, Robert; Maskos, Klaus; Neumann, Lars

2013-01-01

In contrast with the very well explored concept of structure–activity relationship, similar studies are missing for the dependency between binding kinetics and compound structure of a protein ligand complex, the structure–kinetic relationship. Here, we present a structure–kinetic relationship study of the cyclin-dependent kinase 8 (CDK8)/cyclin C (CycC) complex. The scaffold moiety of the compounds is anchored in the kinase deep pocket and extended with diverse functional groups toward the hinge region and the front pocket. These variations can cause the compounds to change from fast to slow binding kinetics, resulting in an improved residence time. The flip of the DFG motif (“DMG” in CDK8) to the inactive DFG-out conformation appears to have relatively little influence on the velocity of binding. Hydrogen bonding with the kinase hinge region contributes to the residence time but has less impact than hydrophobic complementarities within the kinase front pocket. PMID:23630251

Isomerization of 2-butene-1,4-diol in aqueous solutions catalyzed by palladium(II) complexes

Energy Technology Data Exchange (ETDEWEB)

Kalabin, S.M.; Novikov, N.A.; Belov, A.P.

1989-02-01

The authors studied the isomerization of 2-butene-1,4-diol into 3-butene-1,2-diol at 18-25/degree/C. The concentrations of the diol and PdCl/sub 2/ were (1.0-5.0) /times/ 10/sup /minus/2/ mole/liter at 5-10-fold excess amounts of HCl and NaCl. These additives were used because of their inhibiting action on the oxidation of olefinic compounds. 3-Butene-1,2-diol was identified by /sup 1/H NMR method directly in the reaction solutions in which the reaction solutions in which the reactions in D/sub 2/O were carried out. It was found that palladium(II) complexes catalyze the isomerization of 2-butene-1,4-diol into 3-butene-1,2-diol. A mechanism is proposed for the reaction, which includes the intermediate formation of /eta//sup 3/-allyl complex of palladium with a coordinated hydroxyl group.

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

Science.gov (United States)

Skocek, Oliver; Uiberacker, Christoph; Jakubetz, Werner

2011-06-30

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

Catalytic valorization of starch-rich food waste into hydroxymethylfurfural (HMF): Controlling relative kinetics for high productivity.

Science.gov (United States)

Yu, Iris K M; Tsang, Daniel C W; Yip, Alex C K; Chen, Season S; Wang, Lei; Ok, Yong Sik; Poon, Chi Sun

2017-08-01

This study aimed to maximize the valorization of bread waste, a typical food waste stream, into hydroxymethylfurfural (HMF) by improving our kinetic understanding. The highest HMF yield (30mol%) was achieved using SnCl 4 as catalyst, which offered strong derived Brønsted acidity and moderate Lewis acidity. We evaluated the kinetic balance between these acidities to facilitate faster desirable reactions (i.e., hydrolysis, isomerization, and dehydration) relative to undesirable reactions (i.e., rehydration and polymerization). Such catalyst selectivity of SnCl 4 , AlCl 3 , and FeCl 3 was critical in maximizing HMF yield. Higher temperature made marginal advancement by accelerating the undesirable reactions to a similar extent as the desirable pathways. The polymerization-induced metal-impregnated high-porosity carbon was a possible precursor of biochar-based catalyst, further driving up the economic potential. Preliminary economic analysis indicated a net gain of USD 43-236 per kilogram bread waste considering the thermochemical-conversion cost and chemical-trading revenue. Copyright © 2017 Elsevier Ltd. All rights reserved.

Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin.

Directory of Open Access Journals (Sweden)

Ting Wang

Full Text Available In bacteriorhodopsin, the order of molecular events that control the cytoplasmic or extracellular accessibility of the Schiff bases (SB are not well understood. We use molecular dynamics simulations to study a process involved in the second accessibility switch of SB that occurs after its reprotonation in the N intermediate of the photocycle. We find that once protonated, the SB C15 = NZ bond switches from a cytoplasmic facing (13-cis, 15-anti configuration to an extracellular facing (13-cis, 15-syn configuration on the pico to nanosecond timescale. Significantly, rotation about the retinal's C13 = C14 double bond is not observed. The dynamics of the isomeric state transitions of the protonated SB are strongly influenced by the surrounding charges and dielectric effects of other buried ions, particularly D96 and D212. Our simulations indicate that the thermal isomerization of retinal from 13-cis back to all-trans likely occurs independently from and after the SB C15 = NZ rotation in the N-to-O transition.

Thermodynamic calculation of simultaneous reactions of n-butane isomerization and isobutane alkylation with ethylene

Energy Technology Data Exchange (ETDEWEB)

Batyrshin, N.N.; Beresneva, L.D.; Sidorov, V.A.

1981-08-01

Industrial production of ethylene alkylate has gained further development in connection with worldwide ecological problems and the planned changeover of automobile transport to unleaded gasolines, but the scale of production is still substantially less than that of sulfuric acid or hydrogen fluoride alkylates. This is due both to the instability of market prices for ethylene and the shortage of isobutane - a raw material for these large-tonnage production processes and for the synthetic rubber industry. The latter difficulty can be overcome by combining processes of isomerization of n-butane and alkylation of the resultant isobutane with ethylene in a single reaction unit. The possibility of combining these reactions using AlCl/sub 3/-based catalysts has been pointed out previously but in the literature there are no theoretical developments of technology or thermodynamic substantiation of a combined process. We have made a thermodynamic calculation of the consecutive (series-parallel) reactions of isomerization and alkylation with the goal of determining suitable technological conditions for carrying them out simultaneously and establishing the expected equilibrium yields of target products and the compositions of the reaction mixture.

Model-Based Analysis and Efficient Operation of a Glucose Isomerization Reactor Plant

DEFF Research Database (Denmark)

Papadakis, Emmanouil; Madsen, Ulrich; Pedersen, Sven

2015-01-01

efficiency. The objective of this study is the application of the developed framework on an industrial case study of a glucose isomerization (GI) reactor plant that is part of a corn refinery, with the objective to improve the productivity of the process. Therefore, a multi-scale reactor model...... is developedfor use as a building block for the GI reactor plant simulation. An optimal operation strategy is proposed on the basis of the simulation results...

Non-conformable, partial and conformable transposition

DEFF Research Database (Denmark)

König, Thomas; Mäder, Lars Kai

2013-01-01

and the Commission regarding a directive’s outcome, play a much more strategic role than has to date acknowledged in the transposition literature. Whereas disagreement of a member state delays conformable transposition, it speeds up non-conformable transposition. Disagreement of the Commission only prolongs...... the transposition process. We therefore conclude that a stronger focus on an effective sanctioning mechanism is warranted for safeguarding compliance with directives....

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

Energy Technology Data Exchange (ETDEWEB)

Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao [Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Huang, Xuhui, E-mail: xuhuihuang@ust.hk [Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); The HKUST Shenzhen Research Institute, Shenzhen (China)

2016-04-21

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

Science.gov (United States)

Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

2016-04-01

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states

International Nuclear Information System (INIS)

Qiao, Qin; Zhang, Hou-Dao; Huang, Xuhui

2016-01-01

Simulated tempering (ST) is a widely used enhancing sampling method for Molecular Dynamics simulations. As one expanded ensemble method, ST is a combination of canonical ensembles at different temperatures and the acceptance probability of cross-temperature transitions is determined by both the temperature difference and the weights of each temperature. One popular way to obtain the weights is to adopt the free energy of each canonical ensemble, which achieves uniform sampling among temperature space. However, this uniform distribution in temperature space may not be optimal since high temperatures do not always speed up the conformational transitions of interest, as anti-Arrhenius kinetics are prevalent in protein and RNA folding. Here, we propose a new method: Enhancing Pairwise State-transition Weights (EPSW), to obtain the optimal weights by minimizing the round-trip time for transitions among different metastable states at the temperature of interest in ST. The novelty of the EPSW algorithm lies in explicitly considering the kinetics of conformation transitions when optimizing the weights of different temperatures. We further demonstrate the power of EPSW in three different systems: a simple two-temperature model, a two-dimensional model for protein folding with anti-Arrhenius kinetics, and the alanine dipeptide. The results from these three systems showed that the new algorithm can substantially accelerate the transitions between conformational states of interest in the ST expanded ensemble and further facilitate the convergence of thermodynamics compared to the widely used free energy weights. We anticipate that this algorithm is particularly useful for studying functional conformational changes of biological systems where the initial and final states are often known from structural biology experiments.

Conformal Einstein spaces

International Nuclear Information System (INIS)

Kozameh, C.N.; Newman, E.T.; Tod, K.P.

1985-01-01

Conformal transformations in four-dimensional. In particular, a new set of two necessary and sufficient conditions for a space to be conformal to an Einstein space is presented. The first condition defines the class of spaces conformal to C spaces, whereas the last one (the vanishing of the Bach tensor) gives the particular subclass of C spaces which are conformally related to Einstein spaces. (author)

Conformal Gravity

International Nuclear Information System (INIS)

Hooft, G.

2012-01-01

The dynamical degree of freedom for the gravitational force is the metric tensor, having 10 locally independent degrees of freedom (of which 4 can be used to fix the coordinate choice). In conformal gravity, we split this field into an overall scalar factor and a nine-component remainder. All unrenormalizable infinities are in this remainder, while the scalar component can be handled like any other scalar field such as the Higgs field. In this formalism, conformal symmetry is spontaneously broken. An imperative demand on any healthy quantum gravity theory is that black holes should be described as quantum systems with micro-states as dictated by the Hawking-Bekenstein theory. This requires conformal symmetry that may be broken spontaneously but not explicitly, and this means that all conformal anomalies must cancel out. Cancellation of conformal anomalies yields constraints on the matter sector as described by some universal field theory. Thus black hole physics may eventually be of help in the construction of unified field theories. (author)

Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

Czech Academy of Sciences Publication Activity Database

Müller, Stefan; Regensburger, G.; Steuer, Ralf

2014-01-01

Roč. 347, APR 2014 (2014), s. 182-190 ISSN 0022-5193 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : metabolic optimization * enzyme kinetics * oriented matroid * elementary vector * conformal sum Subject RIV: EI - Biotechnology ; Bionics Impact factor: 2.116, year: 2014

Role of non-equilibrium conformations on driven polymer translocation.

Science.gov (United States)

Katkar, H H; Muthukumar, M

2018-01-14

One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/N K , is longer than the relaxation time τ 0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations. We have studied the role of initial conformations of a polyelectrolyte chain (which were artificially generated with a flow field) on the kinetics of its translocation across a nanopore under the action of an externally applied transmembrane voltage V (in the absence of the initial flow field). Stretched (out-of-equilibrium) polyelectrolyte chain conformations are deliberately and systematically generated and used as initial conformations in translocation simulations. Independent simulations are performed to study the relaxation behavior of these stretched chains, and a comparison is made between the relaxation time scale and the mean translocation time (⟨τ⟩). For such artificially stretched initial states, ⟨τ⟩/N K polymers including single stranded DNA (ssDNA), double stranded DNA (dsDNA), and synthetic polymers. Even when these data are rescaled assuming a constant effective velocity of translocation, it is found that for flexible (ssDNA and synthetic) polymers with N K Kuhn segments, the condition ⟨τ⟩/N K polymers such as ssDNA, a crossover from quasi-equilibrium to non-equilibrium behavior would occur at N K ∼ O(1000).

The isomerization of allylrhodium intermediates in the rhodium-catalyzed nucleophilic allylation of cyclic imines.

Science.gov (United States)

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.

Outcomes following the Kawashima procedure for single-ventricle palliation in left atrial isomerism.

Science.gov (United States)

Vollebregt, Anne; Pushparajah, Kuberan; Rizvi, Maleeha; Hoschtitzky, Andreas; Anderson, David; Austin, Conal; Tibby, Shane M; Simpson, John

2012-03-01

Patients with left atrial isomerism and interrupted inferior vena cava palliated with a superior cavopulmonary connection or Kawashima procedure (KP) have a high incidence of developing pulmonary arteriovenous malformations. The necessity for hepatic vein redirection (HVR) and its timing remains a controversy. We aimed to assess the clinical outcome of patients with left atrial isomerism following a KP. The main end points were death, requirement for HVR and the impact of HVR on oxygen saturation. Retrospective review of 21 patients with a diagnosis of left atrial isomerism, interruption of the inferior vena cava and single-ventricle physiology managed with a KP at a single centre between January 1990 and March 2010. Twenty-one patients had a KP, with 12 subsequently undergoing HVR. There was relatively a constant monthly decrement in the proportion of patients who were free from death or HVR up until 60 months following the KP, with a dramatic increase in the hazard after this time. The Cox proportional hazards regression model demonstrated a reduced early risk for HVR or death in patients who underwent pulmonary artery banding versus arterial shunt as the primary procedure (hazard ratio: 0.10; P = 0.01), and an increased risk with bilateral superior vena cavas (SVCs) (hazard ratio: 3.4; P = 0.04) and age at KP (hazard ratio: 1.02 per month increase in age at KP; P = 0.02). HVR mortality was relatively high with 3 of 12 patients dying in the early postoperative period with profound cyanosis. The timing of HVR after the KP did not influence the postoperative rate of increase in oxygen saturation. These findings confirm that the majority of patients who undergo a KP will require HVR. Patients who are older at the time of the KP or having an initial arterial shunt or bilateral SVCs are at higher risk of HVR or death. The relatively high mortality at HVR was characterized by severe postoperative cyanosis.

Kinetics and mechanism of the condensation of pyridoxal hydrochloride with L-tryptophan and D-tryptophan, and the chemical transformation of their products

Science.gov (United States)

Pishchugin, F. V.; Tuleberdiev, I. T.

2017-10-01

The kinetics and mechanism of interaction between pyridoxal and L-tryptophan, D-tryptophan, and their derivatives are studied. It is found that condensation reactions proceed via three kinetically distinguishable stages: (1) the rapid intraplanar addition of the NH2 groups of the amino acids to pyridoxal with the formation of amino alcohols; (2) the rotational isomerism of amino alcohol fragments with their subsequent dehydration and the formation of a Schiff base with a specific configuration; (3) the abstraction of α-hydrogen in the product of condensation of pyridoxal with L-tryptophan, or the abstraction of CO2 in the product of condensation of pyridoxal with D-tryptophan with the formation of quinoid structures, hydrolysis of which results in the preparation of pyridoxamine and keto acid or pyridoxal and tryptamine, respectively. Schiff bases resistant to further chemical transformations are formed in the reaction with tryptophan methyl ester.

Conformational targeting of fibrillar polyglutamine proteins in live cells escalates aggregation and cytotoxicity.

Directory of Open Access Journals (Sweden)

Erik Kvam

2009-05-01

Full Text Available Misfolding- and aggregation-prone proteins underlying Parkinson's, Huntington's and Machado-Joseph diseases, namely alpha-synuclein, huntingtin, and ataxin-3 respectively, adopt numerous intracellular conformations during pathogenesis, including globular intermediates and insoluble amyloid-like fibrils. Such conformational diversity has complicated research into amyloid-associated intracellular dysfunction and neurodegeneration. To this end, recombinant single-chain Fv antibodies (scFvs are compelling molecular tools that can be selected against specific protein conformations, and expressed inside cells as intrabodies, for investigative and therapeutic purposes.Using atomic force microscopy (AFM and live-cell fluorescence microscopy, we report that a human scFv selected against the fibrillar form of alpha-synuclein targets isomorphic conformations of misfolded polyglutamine proteins. When expressed in the cytoplasm of striatal cells, this conformation-specific intrabody co-localizes with intracellular aggregates of misfolded ataxin-3 and a pathological fragment of huntingtin, and enhances the aggregation propensity of both disease-linked polyglutamine proteins. Using this intrabody as a tool for modulating the kinetics of amyloidogenesis, we show that escalating aggregate formation of a pathologic huntingtin fragment is not cytoprotective in striatal cells, but rather heightens oxidative stress and cell death as detected by flow cytometry. Instead, cellular protection is achieved by suppressing aggregation using a previously described intrabody that binds to the amyloidogenic N-terminus of huntingtin. Analogous cytotoxic results are observed following conformational targeting of normal or polyglutamine-expanded human ataxin-3, which partially aggregate through non-polyglutamine domains.These findings validate that the rate of aggregation modulates polyglutamine-mediated intracellular dysfunction, and caution that molecules designed to

Mechanistic features of isomerizing alkoxycarbonylation of methyl oleate

KAUST Repository

Roesle, Philipp

2012-10-24

The weakly coordinated triflate complex [(P̂P)Pd(OTf)] +(OTf)- (1) (P̂P = 1,3-bis(di-tert- butylphosphino)propane) is a suitable reactive precursor for mechanistic studies of the isomerizing alkoxcarbonylation of methyl oleate. Addition of CH 3OH or CD3OD to 1 forms the hydride species [(P ̂P)PdH(CH3OH)]+(OTf)- (2-CH3OH) or the deuteride [(P̂P)PdD(CD 3OD)]+(OTf)- (2D-CD3OD), respectively. Further reaction with pyridine cleanly affords the stable and isolable hydride [(P̂P)PdH(pyridine)]+(OTf) - (2-pyr). This complex yields the hydride fragment free of methanol by abstraction of pyridine with BF3OEt2, and thus provides an entry to mechanistic observations including intermediates reactive toward methanol. Exposure of methyl oleate (100 equiv) to 2D-CD 3OD resulted in rapid isomerization to the thermodynamic isomer distribution, 94.3% of internal olefins, 5.5% of α,β-unsaturated ester and <0.2% of terminal olefin. Reaction of 2-pyr/BF3OEt 2 with a stoichiometric amount of 1-13C-labeled 1-octene at -80 °C yields a 50:50 mixture of the linear alkyls [(P ̂P)Pd13CH2(CH2) 6CH3]+ and [(P̂P)PdCH 2(CH2)6 13CH3] + (4a and 4b). Further reaction with 13CO yields the linear acyls [(P̂P)Pd13C(=O)12/13CH 2(CH2)6 12/13CH3(L)] + (5-L; L = solvent or 13CO). Reaction of 2-pyr/BF 3·OEt2 with a stoichiometric amount of methyl oleate at -80 °C also resulted in fast isomerization to form a linear alkyl species [(P̂P)PdCH2(CH2) 16C(=O)OCH3]+ (6) and a branched alkyl stabilized by coordination of the ester carbonyl group as a four membered chelate [(P̂P)PdCH{(CH2)15CH 3}C(=O)OCH3]+ (7). Addition of carbon monoxide (2.5 equiv) at -80 °C resulted in insertion to form the linear acyl carbonyl [(P̂P)PdC(=O)(CH2)17C(=O)OCH 3(CO)]+ (8-CO) and the five-membered chelate [(P ̂P)PdC(=O)CH{(CH2)15CH3}C(=O) OCH3]+ (9). Exposure of 8-CO and 9 to 13CO at -50 °C results in gradual incorporation of the 13C label. Reversibility of 7 + CO ⇄ 9 is also evidenced by ΔG = -2.9 kcal mol-1 and

Isomeric States in the Second and Third Well of the Potential and Long-Lived Superheavy Element

International Nuclear Information System (INIS)

Marinov, A.; Gelberg, S.; Kolb, D.

1999-01-01

Recently, in a study of the 16 O + 197 Au and 28 Si + 181 Ta reactions near and below the Coulomb barrier, long-lived high spin isomeric states have been found by us in the second and third well of the potential-energy surfaces. Such isomeric states have very unusual physical properties. In addition to their very long lifetimes, much longer than of their corresponding ground states, they have very unusual decay properties. They may decay by 5 to 7 orders of magnitude enhanced alpha particles, in transitions from the second or third well of the potential in the parent nuclei to the respective well in the daughters, or by very retarded alpha particles, in transitions from the second well in the parent nucleus to normal states in the daughter, or from the third well in the parent to the second well in the daughter. They also may decay by long-lived proton activities, in transitions from the second well in the parent nucleus to the normal states in the daughter. Experimental evidences for all these new phenomena will be presented in the conference. The existence of long-lived isomeric states in the second and third well of the potential is very important when the production of superheavy elements is considered. Because of the very much reduced extra-push energy needed for their production, they may be produced much easier than the normal states, in reactions between very heavy nuclei. In particular, the discovery of the long-lived superheavy element with Z = 112 can consistently be understood

Kinetic and Thermodynamic Analysis of Acetyl-CoA Activation of Staphylococcus aureus Pyruvate Carboxylase.

Science.gov (United States)

Westerhold, Lauren E; Bridges, Lance C; Shaikh, Saame Raza; Zeczycki, Tonya N

2017-07-11

Allosteric regulation of pyruvate carboxylase (PC) activity is pivotal to maintaining metabolic homeostasis. In contrast, dysregulated PC activity contributes to the pathogenesis of numerous diseases, rendering PC a possible target for allosteric therapeutic development. Recent research efforts have focused on demarcating the role of acetyl-CoA, one of the most potent activators of PC, in coordinating catalytic events within the multifunctional enzyme. Herein, we report a kinetic and thermodynamic analysis of acetyl-CoA activation of the Staphylococcus aureus PC (SaPC)-catalyzed carboxylation of pyruvate to identify novel means by which acetyl-CoA synchronizes catalytic events within the PC tetramer. Kinetic and linked-function analysis, or thermodynamic linkage analysis, indicates that the substrates of the biotin carboxylase and carboxyl transferase domain are energetically coupled in the presence of acetyl-CoA. In contrast, both kinetic and energetic coupling between the two domains is lost in the absence of acetyl-CoA, suggesting a functional role for acetyl-CoA in facilitating the long-range transmission of substrate-induced conformational changes within the PC tetramer. Interestingly, thermodynamic activation parameters for the SaPC-catalyzed carboxylation of pyruvate are largely independent of acetyl-CoA. Our results also reveal the possibility that global conformational changes give rise to observed species-specific thermodynamic activation parameters. Taken together, our kinetic and thermodynamic results provide a possible allosteric mechanism by which acetyl-CoA coordinates catalysis within the PC tetramer.

Nuclear isomerism in fission fragments produced by the spontaneous fission of {sup 252}Cf; Isomerisme nucleaire dans les fragments de fission produits dans la fission spontanee du {sup 252}Cf

Energy Technology Data Exchange (ETDEWEB)

Gautherin, C

1997-09-01

This thesis is devoted to the study of the nuclear structure of neutron-rich nuclei, via the search of isomeric nuclear states. Neutron-rich nuclei were produced in the spontaneous fission of {sup 252}Cf. The experimental study of isomeric states in these nuclei was performed with the {gamma}-array EUROGAM II, coupled to an additional and original fission fragment detector composed by photovoltaic cells, SAPhIR. The photovoltaic cells are well adapted to detect low energy heavy ions and have good energy and time resolutions to obtain a good fission fragment detection. This experiment led to the discovery of new isomeric states in {sup 135}Xe, {sup 104}Mo, {sup 146,147,148}Ce and {sup 152,154,156}Nd, with lifetimes between 60 ns and 2 {mu}s. Level schemes of these nuclei have been completed. An interpretation of the isomeric states in the nuclei {sup 154,156}Nd and {sup 156,158}Sm was performed by Hartree-Fock-Bogolyubov calculations using the DIS Gogny force with two quasi-particles excitations. The confrontation with the experimental results led to an interpretation of these isomeric states as K-isomers. (author)

Cascade olefin isomerization/intramolecular Diels-Alder reaction catalyzed by N-heterocyclic carbenes.

Science.gov (United States)

Kowalczyk, Marcin; Lupton, David W

2014-05-19

The addition of an N-heterocyclic carbene to the carbonyl group of an α,β,γ,δ-unsaturated enol ester affords a hemiacetal azolium intermediate that enables a cascade olefin isomerization/Diels-Alder reaction, for which mechanistic studies implicate Lewis base catalysis. Preliminary studies into the utility of the products have been undertaken with reductive and oxidative cleavage, giving materials for potential use in complex-target synthesis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Photoionization ion mobility spectrometry (UV-IMS) for the isomeric volatile organic compounds].

Science.gov (United States)

Li, Hu; Niu, Wen-qi; Wang, Hong-mei; Huang, Chao-qun; Jiang, Hai-he; Chu, Yan-nan

2012-01-01

The construction and performance study is reported for a newly developed ultraviolet photoionization ion mobility spectrometry (UV-IMS). In the present paper, an UV-IMS technique was firstly developed to detect eleven isomeric volatile organic compounds including the differences in the structure of carbon chain, the style of function group and the position of function group. Their reduced mobility values were determined and increased in this order: linears alcohols homemade UV-IMS was around ppb-ppm.

Conformal symmetry in two-dimensional space: recursion representation of conformal block

International Nuclear Information System (INIS)

Zamolodchikov, A.B.

1988-01-01

The four-point conformal block plays an important part in the analysis of the conformally invariant operator algebra in two-dimensional space. The behavior of the conformal block is calculated in the present paper in the limit in which the dimension Δ of the intermediate operator tends to infinity. This makes it possible to construct a recursion relation for this function that connects the conformal block at arbitrary Δ to the blocks corresponding to the dimensions of the zero vectors in the degenerate representations of the Virasoro algebra. The relation is convenient for calculating the expansion of the conformal block in powers of the uniformizing parameters q = i π tau

Resolution of isomeric new designer stimulants using gas chromatography - Vacuum ultraviolet spectroscopy and theoretical computations

Czech Academy of Sciences Publication Activity Database

Škultéty, L'udovít; Fryčák, P.; Qiu, CL.; Smuts, J.; Shear-Laude, L.; Lemr, Karel; Mao, J.X.; Kroll, P.; Schug, K. A.; Szewczak, A.; Vaught, C.; Lurie, I.; Havlíček, Vladimír

2017-01-01

Roč. 971, JUNE 8 (2017), s. 55-67 ISSN 0003-2670 R&D Projects: GA MŠk(CZ) LO1509 Institutional support: RVO:61388971 Keywords : Gas phase absorption * Time-dependent density functional theory * Isomeric drugs Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 4.950, year: 2016

Internal conversion of the (13/2+→5/2-) isomeric transition in 199Hg

International Nuclear Information System (INIS)

Radha Krishna, K.; Chandrasekhar Rao, M.V.S.; Sree Krishna Murty, G.; Venkateswara Rao, N.; Bhuloka Reddy, S.; Satyanarayana, G.; Sastry, D.L.; Iyer, M.R.; Sahasrabhude, S.G.

1990-01-01

The total conversion coefficient of the M4 transition (374 KeV) in the decay of the 13/2 + isomeric state to 5/2 - state in 199 Hg measured using the relative gamma intensity method α T is determined to be 6.34 ± 0.29 in agreement with the theory due to Rosel et al. (author). 1 tab., 3 figs., 11 refs

A detailed kinetic study of the direct ring opening of cyclohexane and methylcyclohexane over monofunctional Ir/Al{sub 2}O{sub 3} catalysts

Energy Technology Data Exchange (ETDEWEB)

Shi, Hui; Gutierrez, O.Y.; Lercher, J.A. [Technische Univ. Muenchen (Germany). Catalysis Research Center

2011-07-01

The present study analyses a series of Al{sub 2}O{sub 3}-supported iridium catalysts with different pretreatments and addresses the kinetic features and structural requirements of direct ring opening of cyclohexane and methylcyclohexane catalyzed by Ir in absence of acid-catalyzed ring contraction. Mild reaction conditions and high H{sub 2}/hydrocarbon ratios (200-1000) were used to improve accuracy of kinetic measurements and to negate deactivation. Isomerization and dehydrogenation pathways were suppressed to low extents (1-5%) over the weakly acidic catalysts under the reaction conditions applied. Three main observations are shown: 1) initial selectivity to ring opening products (ROPs) increases with iridium dispersion; 2) optimal H{sub 2} pressures differ not only between primary and secondary products, but also among ROPs and fragments; 3) the air-calcination step before catalyst reduction imposes a significant impact on both activity and product distribution. (orig.)

Multiple Conformations of Phosphodiesterase-5: Implications for Enzyme Function and Drug Developement

Energy Technology Data Exchange (ETDEWEB)

Wang,H.; Liu, Y.; Huai, Q.; Cai, J.; Zoraghi, R.; Francis, S.; Corbin, J.; Robinson, H.; Xin, Z.; et al.

2006-01-01

Phosphodiesterase-5 (PDE5) is the target for sildenafil, vardenafil, and tadalafil, which are drugs for treatment of erectile dysfunction and pulmonary hypertension. We report here the crystal structures of a fully active catalytic domain of unliganded PDE5A1 and its complexes with sildenafil or icarisid II. These structures together with the PDE5A1-isobutyl-1-methylxanthine complex show that the H-loop (residues 660-683) at the active site of PDE5A1 has four different conformations and migrates 7 to 35 Angstroms upon inhibitor binding. In addition, the conformation of sildenafil reported herein differs significantly from those in the previous structures of chimerically hybridized or almost inactive PDE5. Mutagenesis and kinetic analyses confirm that the H-loop is particularly important for substrate recognition and that invariant Gly659 which immediately precedes the H-loop is critical for optimal substrate affinity and catalytic activity.

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

Science.gov (United States)

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...

Anion-assisted trans-cis isomerization of palladium(II) phosphine complexes containing acetanilide functionalities through hydrogen bonding interactions.

Science.gov (United States)

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.

Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB

Directory of Open Access Journals (Sweden)

Beibei eWang

2015-04-01

Full Text Available The tripartite efflux pump assembly AcrAB-TolC is the major multidrug resistance transporter in E. coli. The inner membrane transporter AcrB is a homotrimer, energized by the proton movement down the transmembrane electrochemical gradient. The asymmetric crystal structures of AcrB with three monomers in distinct conformational states (access (A, binding (B and extrusion (E support a functional rotating mechanism, in which each monomer of AcrB cycles among the three states in a concerted way. However, the relationship between the conformational changes during functional rotation and drug translocation has not been totally understood. Here, we explored the conformational changes of the AcrB homotrimer during the ABE→BEA transition in different substrate-binding states using targeted MD simulations. It was found that the dissociation of substrate from the distal binding pocket of B monomer is closely related to the concerted conformational changes in the translocation pathway, especially the side chain reorientation of Phe628 and Tyr327. A second substrate binding at the proximal binding pocket of A monomer evidently accelerates the conformational transitions as well as substrate dissociation in B monomer. The acceleration effect of the multi-substrate binding mode provides a molecular explanation for the positive cooperativity observed in the kinetic studies of substrate efflux and deepens our understanding of the functional rotating mechanism of AcrB.

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.

Science.gov (United States)

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.

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2000-08-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, ``conformal infinity'' is related with almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved out of physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation and how it lends itself very naturally to solve radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

Conformal Infinity.

Science.gov (United States)

Frauendiener, Jörg

2004-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

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

International Nuclear Information System (INIS)

Han, Huixian; Li, Anyang; Guo, Hua

2014-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Wolff, Wania, E-mail: wania@if.ufrj.br; Luna, Hugo; Montenegro, Eduardo C. [Instituto de Física, Universidade Federal do Rio de Janeiro, 21941-972 Rio de Janeiro, RJ (Brazil)

2015-07-28

We present fast proton impact induced fragmentations of pyrimidine and pyridazine as an experimental resource to investigate isomeric signatures. Major isomeric imprints are identified for few fragment ions and differences of more than an order of magnitude for the cross sections of fragments of the same mass were measured. The observation of the molecular structure of these isomers gives no apparent indication for the reasons for such substantial differences. It is verified that the simple displacement of the position of one nitrogen atom strongly inhibits or favors the production of some ionic fragment species. The dependency of the fragmentation cross sections on the proton impact energy, investigated by means of time of flight mass spectroscopy and of a model calculation based in first order perturbation theory, allows us to disentangle the complex collision dynamics of the ionic fragments. The proton-induced fragmentation discriminates rather directly the association between a molecular orbital ionization and the fragment-ions creation and abundance, as well as how the redistribution of the energy imparted to the molecules takes place, triggering not only single but also double vacancy and leads to specific fragmentation pathways.

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

Science.gov (United States)

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-01

A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

Science.gov (United States)

Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

2010-03-01

Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

β-γ and isomeric decay spectroscopy of 168Dy

Directory of Open Access Journals (Sweden)

Zhang G.X.

2018-01-01

Full Text Available 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.

β-γ and isomeric decay spectroscopy of 168Dy

Science.gov (United States)

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.

Ab Initio Chemical Kinetics for the CH3 + O((3)P) Reaction and Related Isomerization-Decomposition of CH3O and CH2OH Radicals.

Science.gov (United States)

Xu, Z F; Raghunath, P; Lin, M C

2015-07-16

The kinetics and mechanism of the CH3 + O reaction and related isomerization-decomposition of CH3O and CH2OH radicals have been studied by ab initio molecular orbital theory based on the CCSD(T)/aug-cc-pVTZ//CCSD/aug-cc-pVTZ, CCSD/aug-cc-pVDZ, and G2M//B3LYP/6-311+G(3df,2p) levels of theory. The predicted potential energy surface of the CH3 + O reaction shows that the CHO + H2 products can be directly generated from CH3O by the TS3 → LM1 → TS7 → LM2 → TS4 path, in which both LM1 and LM2 are very loose and TS7 is roaming-like. The result for the CH2O + H reaction shows that there are three low-energy barrier processes including CH2O + H → CHO + H2 via H-abstraction and CH2O + H → CH2OH and CH2O + H → CH3O by addition reactions. The predicted enthalpies of formation of the CH2OH and CH3O radicals at 0 K are in good agreement with available experimental data. Furthermore, the rate constants for the forward and some key reverse reactions have been predicted at 200-3000 K under various pressures. Based on the new reaction pathway for CH3 + O, the rate constants for the CH2O + H and CHO + H2 reactions were predicted with the microcanonical variational transition-state/Rice-Ramsperger-Kassel-Marcus (VTST/RRKM) theory. The predicted total and individual product branching ratios (i.e., CO versus CH2O) are in good agreement with experimental data. The rate constant for the hydrogen abstraction reaction of CH2O + H has been calculated by the canonical variational transition-state theory with quantum tunneling and small-curvature corrections to be k(CH2O + H → CHO + H2) = 2.28 × 10(-19) T(2.65) exp(-766.5/T) cm(3) molecule(-1) s(-1) for the 200-3000 K temperature range. The rate constants for the addition giving CH3O and CH2OH and the decomposition of the two radicals have been calculated by the microcanonical RRKM theory with the time-dependent master equation solution of the multiple quantum well system in the 200-3000 K temperature range at 1 Torr to

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

Energy Technology Data Exchange (ETDEWEB)

Ligare, Marshall R.; Baker, Erin M.; Laskin, Julia; Johnson, Grant E.

2017-01-01

Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

Role of Detergents in Conformational Exchange of a G Protein-coupled Receptor*

Science.gov (United States)

Chung, Ka Young; Kim, Tae Hun; Manglik, Aashish; Alvares, Rohan; Kobilka, Brian K.; Prosser, R. Scott

2012-01-01

The G protein-coupled β2-adrenoreceptor (β2AR) signals through the heterotrimeric G proteins Gs and Gi and β-arrestin. As such, the energy landscape of β2AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β2AR with a trifluoromethyl probe, 19F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β2AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β2AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor. PMID:22893704

Role of detergents in conformational exchange of a G protein-coupled receptor.

Science.gov (United States)

Chung, Ka Young; Kim, Tae Hun; Manglik, Aashish; Alvares, Rohan; Kobilka, Brian K; Prosser, R Scott

2012-10-19

The G protein-coupled β(2)-adrenoreceptor (β(2)AR) signals through the heterotrimeric G proteins G(s) and G(i) and β-arrestin. As such, the energy landscape of β(2)AR-excited state conformers is expected to be complex. Upon tagging Cys-265 of β(2)AR with a trifluoromethyl probe, (19)F NMR was used to assess conformations and possible equilibria between states. Here, we report key differences in β(2)AR conformational dynamics associated with the detergents used to stabilize the receptor. In dodecyl maltoside (DDM) micelles, the spectra are well represented by a single Lorentzian line that shifts progressively downfield with activation by appropriate ligand. The results are consistent with interconversion between two or more states on a time scale faster than the greatest difference in ligand-dependent chemical shift (i.e. >100 Hz). Given that high detergent off-rates of DDM monomers may facilitate conformational exchange between functional states of β(2)AR, we utilized the recently developed maltose-neopentyl glycol (MNG-3) diacyl detergent. In MNG-3 micelles, spectra indicated at least three distinct states, the relative populations of which depended on ligand, whereas no ligand-dependent shifts were observed, consistent with the slow exchange limit. Thus, detergent has a profound effect on the equilibrium kinetics between functional states. MNG-3, which has a critical micelle concentration in the nanomolar regime, exhibits an off-rate that is 4 orders of magnitude lower than that of DDM. High detergent off-rates are more likely to facilitate conformational exchange between distinct functional states associated with the G protein-coupled receptor.

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

Science.gov (United States)

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.

Sensitivity of photoelectron diffraction to conformational changes of adsorbed molecules: Tetra-tert-butyl-azobenzene/Au(111

Directory of Open Access Journals (Sweden)

A. Schuler

2017-01-01

Full Text Available Electron diffraction is a standard tool to investigate the atomic structure of surfaces, interfaces, and adsorbate systems. In particular, photoelectron diffraction is a promising candidate for real-time studies of structural dynamics combining the ultimate time resolution of optical pulses and the high scattering cross-sections for electrons. In view of future time-resolved experiments from molecular layers, we studied the sensitivity of photoelectron diffraction to conformational changes of only a small fraction of molecules in a monolayer adsorbed on a metallic substrate. 3,3′,5,5′-tetra-tert-butyl-azobenzene served as test case. This molecule can be switched between two isomers, trans and cis, by absorption of ultraviolet light. X-ray photoelectron diffraction patterns were recorded from tetra-tert-butyl-azobenzene/Au(111 in thermal equilibrium at room temperature and compared to patterns taken in the photostationary state obtained by exposing the surface to radiation from a high-intensity helium discharge lamp. Difference patterns were simulated by means of multiple-scattering calculations, which allowed us to determine the fraction of molecules that underwent isomerization.

Conformal Infinity

Directory of Open Access Journals (Sweden)

Frauendiener Jörg

2004-01-01

Full Text Available The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

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

Science.gov (United States)

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

Comparison of Separation of Seed Oil Triglycerides Containing Isomeric Conjugated Octadecatrienoic Acid Moieties by Reversed-Phase HPLC

Directory of Open Access Journals (Sweden)

Anh Van Nguyen

2017-12-01

Full Text Available Relative retention analysis and increment approach were applied for the comparison of triglycerides (TGs retention of a broad set of plant seed oils with isomeric conjugated octadecatrienoic acids (CLnA by reversed-phase HPLC for “propanol-2-acetonitrile” mobile phases and Kromasil 100-5C18 stationary phase with diode array detection (DAD and mass spectrometric (MS detection. The subjects of investigation were TGs of seed oils: Calendula officinalis, Catalpa ovata, Jacaranda mimosifolia, Centranthus ruber, Momordica charantia, Trichosanthes anguina, Punica granatum, Thladiantha dubia, Valeriana officinalis, and Vernicia montana. It was found that a sequence of elution of TGs of the same types is the same without any inversions for full range of mobile phase compositions: punicic (C18:39Z11E13Z < jacaric (C18:38Z10E12Z < catalpic (C18:39E11E13Z < α-eleostearic (C18:39Z11E13E < calendic (C18:38E10E12Z < β-eleostearic (C18:39E11E13E < all-E calendic (C18:38E10E12E acids. TGs and fatty acid compositions were calculated for all oil samples. Regularities of solute retentions as a function of isomeric conjugated octadecatrienoic acid moiety structure are discussed. Thus, it was proven that it is possible to differentiate TGs of complex composition with moieties of all natural CLnA by retention control accomplished by electronic spectra comparison, even though there are only three types of electronic-vibration spectra for seven isomeric CLnA.

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

Science.gov (United States)

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.

Science.gov (United States)

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.

Ruthenium Stilbenyl and Diruthenium Distyrylethene Complexes: Aspects of Electron Delocalization and Electrocatalyzed Isomerization of the Z-Isomer

Czech Academy of Sciences Publication Activity Database

Linseis, M.; Záliš, Stanislav; Zabel, M.; Winter, R. F.

2012-01-01

Roč. 134, č. 40 (2012), s. 16671-16692 ISSN 0002-7863 R&D Projects: GA MŠk LD11086 Institutional support: RVO:61388955 Keywords : CIS-TRANS-ISOMERIZATION * MIXED-VALENCE COMPOUNDS * VIBRATIONAL TIME -SCALE Subject RIV: CG - Electrochemistry Impact factor: 10.677, year: 2012

Logarithmic conformal field theory through nilpotent conformal dimensions

International Nuclear Information System (INIS)

Moghimi-Araghi, S.; Rouhani, S.; Saadat, M.

2001-01-01

We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFTs such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor

Viscous conformal gauge theories

DEFF Research Database (Denmark)

Toniato, Arianna; Sannino, Francesco; Rischke, Dirk H.

2017-01-01

We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories.......We present the conformal behavior of the shear viscosity-to-entropy density ratio and the fermion-number diffusion coefficient within the perturbative regime of the conformal window for gauge-fermion theories....

Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose

Directory of Open Access Journals (Sweden)

J. Vincent Edwards

2018-03-01

Full Text Available Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis–Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity (Km of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased Km observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency (kcat/Km, attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding.

Structure/Function Analysis of Cotton-Based Peptide-Cellulose Conjugates: Spatiotemporal/Kinetic Assessment of Protease Aerogels Compared to Nanocrystalline and Paper Cellulose

Science.gov (United States)

Edwards, J. Vincent; Fontenot, Krystal; Liebner, Falk; Pircher, Nicole Doyle nee; French, Alfred D.; Condon, Brian D.

2018-01-01

Nanocellulose has high specific surface area, hydration properties, and ease of derivatization to prepare protease sensors. A Human Neutrophil Elastase sensor designed with a nanocellulose aerogel transducer surface derived from cotton is compared with cotton filter paper, and nanocrystalline cellulose versions of the sensor. X-ray crystallography was employed along with Michaelis–Menten enzyme kinetics, and circular dichroism to contrast the structure/function relations of the peptide-cellulose conjugate conformation to enzyme/substrate binding and turnover rates. The nanocellulosic aerogel was found to have a cellulose II structure. The spatiotemporal relation of crystallite surface to peptide-cellulose conformation is discussed in light of observed enzyme kinetics. A higher substrate binding affinity (Km) of elastase was observed with the nanocellulose aerogel and nanocrystalline peptide-cellulose conjugates than with the solution-based elastase substrate. An increased Km observed for the nanocellulosic aerogel sensor yields a higher enzyme efficiency (kcat/Km), attributable to binding of the serine protease to the negatively charged cellulose surface. The effect of crystallite size and β-turn peptide conformation are related to the peptide-cellulose kinetics. Models demonstrating the orientation of cellulose to peptide O6-hydroxymethyl rotamers of the conjugates at the surface of the cellulose crystal suggest the relative accessibility of the peptide-cellulose conjugates for enzyme active site binding. PMID:29534033

Conformal invariance in supergravity

International Nuclear Information System (INIS)

Bergshoeff, E.A.

1983-01-01

In this thesis the author explains the role of conformal invariance in supergravity. He presents the complete structure of extended conformal supergravity for N <= 4. The outline of this work is as follows. In chapter 2 he briefly summarizes the essential properties of supersymmetry and supergravity and indicates the use of conformal invariance in supergravity. The idea that the introduction of additional symmetry transformations can make clear the structure of a field theory is not reserved to supergravity only. By means of some simple examples it is shown in chapter 3 how one can always introduce additional gauge transformations in a theory of massive vector fields. Moreover it is shown how the gauge invariant formulation sometimes explains the quantum mechanical properties of the theory. In chapter 4 the author defines the conformal transformations and summarizes their main properties. He explains how these conformal transformations can be used to analyse the structure of gravity. The supersymmetric extension of these results is discussed in chapter 5. Here he describes as an example how N=1 supergravity can be reformulated in a conformally-invariant way. He also shows that beyond N=1 the gauge fields of the superconformal symmetries do not constitute an off-shell field representation of extended conformal supergravity. Therefore, in chapter 6, a systematic method to construct the off-shell formulation of all extended conformal supergravity theories with N <= 4 is developed. As an example he uses this method to construct N=1 conformal supergravity. Finally, in chapter 7 N=4 conformal supergravity is discussed. (Auth.)

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

Science.gov (United States)

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

Effects of high pressure homogenization on the activity, stability, kinetics and three-dimensional conformation of a glucose oxidase produced by Aspergillus niger.

Directory of Open Access Journals (Sweden)

Alline Artigiani Lima Tribst

Full Text Available High pressure homogenization (HPH is a non-thermal method, which has been employed to change the activity and stability of biotechnologically relevant enzymes. This work investigated how HPH affects the structural and functional characteristics of a glucose oxidase (GO from Aspergillus niger. The enzyme was homogenized at 75 and 150 MPa and the effects were evaluated with respect to the enzyme activity, stability, kinetic parameters and molecular structure. The enzyme showed a pH-dependent response to the HPH treatment, with reduction or maintenance of activity at pH 4.5-6.0 and a remarkable activity increase (30-300% at pH 6.5 in all tested temperatures (15, 50 and 75°C. The enzyme thermal tolerance was reduced due to HPH treatment and the storage for 24 h at high temperatures (50 and 75°C also caused a reduction of activity. Interestingly, at lower temperatures (15°C the activity levels were slightly higher than that observed for native enzyme or at least maintained. These effects of HPH treatment on function and stability of GO were further investigated by spectroscopic methods. Both fluorescence and circular dichroism revealed conformational changes in the molecular structure of the enzyme that might be associated with the distinct functional and stability behavior of GO.

Isomeric cross section ratios in 55Mn(α, n)58m,gCo reaction

International Nuclear Information System (INIS)

Long Xianguan; He Fuqing; Peng Xiufen; Liu Mantian

1989-01-01

The isomeric cross section ratios in 55 Mn(α, n) 58m,g Co reaction are measured for incident alpha-particle energies ranging from 10.4 to 26.5 MeV by using activation method and stacked-foil technique. The measured values are compared with theoretical calculations performed by using Huizenga and Vandenbosch method and the values of spin cutoff factor are obtained for product nucleus 58 Co

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

Science.gov (United States)

Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

2014-11-04

The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

Science.gov (United States)

2015-01-01

The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

EFFECT OF TIME AND TEMPERATURE ON ISOMERIZATION REACTION OF ?-PINENEUSING CATALYST ZR 4+ Nanik Wijayati, Supartono, Nuni Widiarti, Tri Handayani /NATURAL ZEOLITE

Directory of Open Access Journals (Sweden)

Nanik Wijayati

2016-03-01

Full Text Available Effects of time and temperature on ?-pinene isomerization reaction using catalysts Zr/natural zeolitewas studied. Characterization of the catalysts include: crystallinity, observed using X-Ray Diffraction, count Zr 4+ carried observed using X-Ray Fluorescence, area and porosity catalyst was observed using the Surface Area Analyzer, and acidity catalyst observed through gravimetric method. Isomerization reaction carried out in a batch reactor with temperature variations 90, 120 and 150 C and reaction time variations of 60, 90, 120, 150 and 180 minutes. Best results of isomerisation in this study was obtained at 150 derajat C with a reaction time of 180 minutes. Kindsof isomer obtained was observed using GCMS. Catalyst characterization results indicate that modification of the catalyst by cation Zr increases the acidity from 2.76 to 6.64 mmol/g and does not damage the crystal structure significantly. The highest product conversion in this research is 9.24%, less than the maximum results caused by pre-treatment of the catalyst produces a low area. Thus, temperature and reaction time affect the concentration of ? pinene isomerization product in addition to the effect of the catalyst used.

Acidic ionic liquids for n-alkane isomerization in a liquid-liquid or slurry-phase reaction mode

Energy Technology Data Exchange (ETDEWEB)

Meyer, C.; Hager, V.; Geburtig, D.; Kohr, C.; Wasserscheid, P. [Erlangen-Nuernberg Univ. (Germany). Lehrstuhl fuer Chemische Reaktionstechnik; Haumann, M. [Chemical Reaction Engineering, FAU Busan Campus, Korea (Korea, Republic of)

2011-07-01

Highly acidic ionic liquid (IL) catalysts offer the opportunity to convert n-alkanes at very low reaction temperatures. The results of IL catalyzed isomerization and cracking reactions of pure n-octane are presented. Influence of IL composition, [C{sub 4}C{sub 1}Im]Cl / AlCl{sub 3} / H{sub 2}SO{sub 4} and [C{sub 4}C{sub 1}Im]Cl / AlCl{sub 3} / 1-chlorooctane, on catalyst activity and selectivities to branched alkanes was investigated. Acidic chloroaluminate IL catalysts form liquid-liquid biphasic systems with unpolar organic product mixtures. Thus, recycling of the acidic IL is enabled by simple phase separation in the liquid-liquid biphasic reaction mode or the IL can be immobilized on an inorganic support with a large specific surface area. These supported ionic liquid phase (SILP) catalysts offer the advantage to get a macroscopically heterogeneous system while still preserving all benefits of the homogeneous catalyst which can be used for the slurry-phase n-alkane isomerization. The interaction of the solid support and acidic IL influences strongly the catalytic activity. (orig.)

Influence of the support on the kinetics of anaerobic purification of slaughterhouse wastewater

Energy Technology Data Exchange (ETDEWEB)

Borja, R.; Duran, M.M. (Instituto de la Grasa y sus Derivados, Seville (Spain)); Martin, A. (Cordoba Univ. (Spain). Dept. de Ingenieria Quimica)

1993-01-01

Three materials of different composition, sepiolite, saponite and bentonite, assayed as supports for the micro-organisms effecting anaerobic fermentation, were found to behave differently towards slaughterhouse wastewater from a kinetic point of view. Assuming the overall anaerobic digestion process to conform to first-order kinetics, the apparent kinetic constant for the digester including bentonite as support was 1.28 per day, while that of the digesters using the sepiolite and saponite were 0.83 and 0.56 per day, respectively. Thus, the support used to immobilize the micro-organisms that mediate the process had a marked influence on the constant. This was found to be significant at 95% confidence level. The yield coefficient, Y[sub p], was 343, 334 and 349 ml CH[sub 4] STP per g chemical oxygen demand added for the sepiolite, saponite and bentonite, respectively. (Author)

Kinetics and mechanisms of the oxide film growth on the surface of α-Fe in transitional domains

International Nuclear Information System (INIS)

Mukhambetov, D.G.; Berber, N.N.; Kargin, D.B.; Chalaya, O.V.

2003-01-01

The object of this work was to study the kinetics of the α-Fe surface oxidation with prevailing cubic texture at temperatures of 450-500 deg. C. The basic conformity to natural laws and mechanisms of the two-phase thin oxide films grows are determined. (author)

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

Energy Technology Data Exchange (ETDEWEB)

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp [Quantum Beam Science Directorate, Tokai Research and Development Center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195 (Japan); Ho, Tak-San, E-mail: tsho@Princeton.EDU [Department of Chemistry, Princeton University, Princeton, NJ 08544 (United States); Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU [Department of Chemistry, Princeton University, Princeton, NJ 08544 (United States)

2016-05-01

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

Synthesis of Heterocycles through a Ruthenium‐Catalyzed Tandem Ring‐Closing Metathesis/Isomerization/N‐Acyliminium Cyclization Sequence

DEFF Research Database (Denmark)

Ascic, Erhad; Jensen, Jakob Feldthusen; Nielsen, Thomas Eiland

2011-01-01

Tandem bicycle: In the title reaction double bonds created during ring-closing metathesis isomerize to generate reactive iminium intermediates that undergo intramolecular cyclization reactions with tethered heteroatom and carbon nucleophiles. In this way, a series of biologically interesting hete...... heterocyclic compounds can be made, including a known precursor for the total synthesis of the antiparasitic natural product harmicine....

Quantum control of isomerization by robust navigation in the energy spectrum

Energy Technology Data Exchange (ETDEWEB)

Murgida, G. E., E-mail: murgida@tandar.cnea.gov.ar [Centro Atómico Constituyentes, GIyA, CNEA, San Martín, and Consejo Nacional de Investigaciones Científicas y Técnicas, C1033AAJ Buenos Aires (Argentina); Arranz, F. J., E-mail: fj.arranz@upm.es [Grupo de Sistemas Complejos, Universidad Politécnica de Madrid, 28040 Madrid (Spain); Borondo, F., E-mail: f.borondo@uam.es [Departamento de Química, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Instituto de Ciencias Matemáticas (ICMAT), Cantoblanco, 28049 Madrid (Spain)

2015-12-07

In this paper, we present a detailed study on the application of the quantum control technique of navigation in the energy spectrum to chemical isomerization processes, namely, CN–Li⇆ Li–CN. This technique is based on the controlled time variation of a Hamiltonian parameter, an external uniform electric field in our case. The main result of our work establishes that the navigation involved in the method is robust, in the sense that quite sizable deviations from a pre-established control parameter time profile can be introduced and still get good final results. This is specially relevant thinking of a experimental implementation of the method.

Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids

DEFF Research Database (Denmark)

Berg, Rolf W.

2009-01-01

spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...

Conformal expansions and renormalons

Energy Technology Data Exchange (ETDEWEB)

Rathsman, J.

2000-02-07

The coefficients in perturbative expansions in gauge theories are factorially increasing, predominantly due to renormalons. This type of factorial increase is not expected in conformal theories. In QCD conformal relations between observables can be defined in the presence of a perturbative infrared fixed-point. Using the Banks-Zaks expansion the authors study the effect of the large-order behavior of the perturbative series on the conformal coefficients. The authors find that in general these coefficients become factorially increasing. However, when the factorial behavior genuinely originates in a renormalon integral, as implied by a postulated skeleton expansion, it does not affect the conformal coefficients. As a consequence, the conformal coefficients will indeed be free of renormalon divergence, in accordance with previous observations concerning the smallness of these coefficients for specific observables. The authors further show that the correspondence of the BLM method with the skeleton expansion implies a unique scale-setting procedure. The BLM coefficients can be interpreted as the conformal coefficients in the series relating the fixed-point value of the observable with that of the skeleton effective charge. Through the skeleton expansion the relevance of renormalon-free conformal coefficients extends to real-world QCD.

Functional Insights Revealed by the Kinetic Mechanism of CRISPR/Cas9.

Science.gov (United States)

Raper, Austin T; Stephenson, Anthony A; Suo, Zucai

2018-02-28

The discovery of prokaryotic adaptive immunity prompted widespread use of the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) endonuclease Cas9 for genetic engineering. However, its kinetic mechanism remains undefined, and details of DNA cleavage are poorly characterized. Here, we establish a kinetic mechanism of Streptococcus pyogenes Cas9 from guide-RNA binding through DNA cleavage and product release. Association of DNA to the binary complex of Cas9 and guide-RNA is rate-limiting during the first catalytic turnover, while DNA cleavage from a pre-formed ternary complex of Cas9, guide-RNA, and DNA is rapid. Moreover, an extremely slow release of DNA products essentially restricts Cas9 to be a single-turnover enzyme. By simultaneously measuring the contributions of the HNH and RuvC nuclease activities of Cas9 to DNA cleavage, we also uncovered the kinetic basis by which HNH conformationally regulates the RuvC cleavage activity. Together, our results provide crucial kinetic and functional details regarding Cas9 which will inform gene-editing experiments, guide future research to understand off-target DNA cleavage by Cas9, and aid in the continued development of Cas9 as a biotechnological tool.

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.

Science.gov (United States)

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.

Glucose isomerization in simulated moving bed reactor by Glucose isomerase

Directory of Open Access Journals (Sweden)

Eduardo Alberto Borges da Silva

2006-05-01

Full Text Available Studies were carried out on the production of high-fructose syrup by Simulated Moving Bed (SMB technology. A mathematical model and numerical methodology were used to predict the behavior and performance of the simulated moving bed reactors and to verify some important aspects for application of this technology in the isomerization process. The developed algorithm used the strategy that considered equivalences between simulated moving bed reactors and true moving bed reactors. The kinetic parameters of the enzymatic reaction were obtained experimentally using discontinuous reactors by the Lineweaver-Burk technique. Mass transfer effects in the reaction conversion using the immobilized enzyme glucose isomerase were investigated. In the SMB reactive system, the operational variable flow rate of feed stream was evaluated to determine its influence on system performance. Results showed that there were some flow rate values at which greater purities could be obtained.Neste trabalho a tecnologia de Leito Móvel Simulado (LMS reativo é aplicada no processo de isomerização da glicose visando à produção de xarope concentrado de frutose. É apresentada a modelagem matemática e uma metodologia numérica para predizer o comportamento e o desempenho de unidades reativas de leito móvel simulado para verificar alguns aspectos importantes para o emprego desta tecnologia no processo de isomerização. O algoritmo desenvolvido utiliza a abordagem que considera as equivalências entre as unidades reativas de leito móvel simulado e leito móvel verdadeiro. Parâmetros cinéticos da reação enzimática são obtidos experimentalmente usando reatores em batelada pela técnica Lineweaver-Burk. Efeitos da transferência de massa na conversão de reação usando a enzima imobilizada glicose isomerase são verificados. No sistema reativo de LMS, a variável operacional vazão da corrente de alimentação é avaliada para conhecer o efeito de sua influência no

Conformational analysis by intersection: CONAN.

Science.gov (United States)

Smellie, Andrew; Stanton, Robert; Henne, Randy; Teig, Steve

2003-01-15

As high throughput techniques in chemical synthesis and screening improve, more demands are placed on computer assisted design and virtual screening. Many of these computational methods require one or more three-dimensional conformations for molecules, creating a demand for a conformational analysis tool that can rapidly and robustly cover the low-energy conformational spaces of small molecules. A new algorithm of intersection is presented here, which quickly generates (on average heuristics are applied after intersection to generate a small representative collection of conformations that span the conformational space. In a study of approximately 97,000 randomly selected molecules from the MDDR, results are presented that explore these conformations and their ability to cover low-energy conformational space. Copyright 2002 Wiley Periodicals, Inc. J Comput Chem 24: 10-20, 2003

Isomeric and high-spin states of 94Tc and the search for yrast isomers near Napprox.50

International Nuclear Information System (INIS)

Lee, I.Y.; Johnson, N.R.; McGowan, F.K.; Young, G.R.; Guidry, M.W.; Yates, S.W.

1981-01-01

A search for isomers in the Napprox.50 region has produced no evidence of high-spin yrast isomerism. A new 4.5-ns low-multiplicity isomer has been identified and assigned to 94 Tc, while the yrast sequence of 94 Tc has been established to more than 5 MeV in excitation energy

Valence isomerization of 2-phospha-4-silabicyclo[1.1.0]butane: a high-level ab initio study

NARCIS (Netherlands)

Slootweg, J.C.; Ehlers, A.W.; Lammertsma, K.

2006-01-01

The rearrangements for 2-phospha-4-silabicyclo[1.1.0]butane, analogous to the valence isomerization of the hydrocarbons bicyclobutane, 1,3-butadiene, and cyclobutene, were studied at the (U)QCISD(T)/ 6-311+G**//(U)QCISD/6-31G* level of theory. The monocyclic 1,2-dihydro-1,2-phosphasiletes are shown

The conformal method and the conformal thin-sandwich method are the same

International Nuclear Information System (INIS)

Maxwell, David

2014-01-01

The conformal method developed in the 1970s and the more recent Lagrangian and Hamiltonian conformal thin-sandwich methods are techniques for finding solutions of the Einstein constraint equations. We show that they are manifestations of a single conformal method: there is a straightforward way to convert back and forth between the parameters for these methods so that the corresponding solutions of the Einstein constraint equations agree. The unifying idea is the need to clearly distinguish tangent and cotangent vectors to the space of conformal classes on a manifold, and we introduce a vocabulary for working with these objects without reference to a particular representative background metric. As a consequence of these conceptual advantages, we demonstrate how to strengthen previous near-CMC (constant mean curvature) existence and non-existence theorems for the original conformal method to include metrics with scalar curvatures that change sign. (paper)

Kinetics of Maleic Acid and Aluminum Chloride Catalyzed Dehydration and Degradation of Glucose

Energy Technology Data Exchange (ETDEWEB)

Zhang, Ximing; Hewetson, Barron B.; Mosier, Nathan S.

2015-04-16

We report the positive effect of maleic acid, a dicarboxylic acid, on the selectivity of hexose dehydration to 5-hydroxymethyfurfural (HMF) and subsequent hydrolysis to levulinic and formic acids. We also describe the kinetic analysis of a Lewis acid (AlCl3) alone and in combination with HCl or maleic acid to catalyze the isomerization of glucose to fructose, dehydration of fructose to HMF, hydration of HMF to levulinic and formic acids, and degradation of these compounds to humins. The results show that AlCl3 significantly enhances the rate of glucose conversion to HMF and levulinic acid in the presence of both maleic acid and HCl. In addition, the degradation of HMF to humins, rather than levulinic and formic acids, is reduced by 50% in the presence of maleic acid and AlCl3 compared to HCl combined with AlCl3. The results suggest different reaction mechanisms for the dehydration of glucose and rehydration of HMF between maleic acid and HCl.

Anisotropic power-law inflation for a conformal-violating Maxwell model

Science.gov (United States)

Do, Tuan Q.; Kao, W. F.

2018-05-01

A set of power-law solutions of a conformal-violating Maxwell model with a non-standard scalar-vector coupling will be shown in this paper. In particular, we are interested in a coupling term of the form X^{2n} F^{μ ν }F_{μ ν } with X denoting the kinetic term of the scalar field. Stability analysis indicates that the new set of anisotropic power-law solutions is unstable during the inflationary phase. The result is consistent with the cosmic no-hair conjecture. We show, however, that a set of stable slowly expanding solutions does exist for a small range of parameters λ and n. Hence a small anisotropy can survive during the slowly expanding phase.

β decay and isomeric properties of neutron-rich Ca and Sc isotopes

International Nuclear Information System (INIS)

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

2010-01-01

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

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II.

Science.gov (United States)

Nemtseva, Elena V; Lashchuk, Olesya O; Gerasimova, Marina A; Melnik, Tatiana N; Nagibina, Galina S; Melnik, Bogdan S

2017-12-21

In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Isomerization and fluorescence depolarization of merocyanine 540 ...

Indian Academy of Sciences (India)

, ... polymers resemble globular proteins and can encapsulate hydrophobic solutes. ... PAA opens up due to electrostatic repulsion, the fluorescent probe becomes exposed to ... conformational transition of such polymers have been studied by ...

Rates and equilibrium constants of the ligand-induced conformational transition of an HCN ion channel protein domain determined by DEER spectroscopy.

Science.gov (United States)

Collauto, Alberto; DeBerg, Hannah A; Kaufmann, Royi; Zagotta, William N; Stoll, Stefan; Goldfarb, Daniella

2017-06-14

Ligand binding can induce significant conformational changes in proteins. The mechanism of this process couples equilibria associated with the ligand binding event and the conformational change. Here we show that by combining the application of W-band double electron-electron resonance (DEER) spectroscopy with microfluidic rapid freeze quench (μRFQ) it is possible to resolve these processes and obtain both equilibrium constants and reaction rates. We studied the conformational transition of the nitroxide labeled, isolated carboxy-terminal cyclic-nucleotide binding domain (CNBD) of the HCN2 ion channel upon binding of the ligand 3',5'-cyclic adenosine monophosphate (cAMP). Using model-based global analysis, the time-resolved data of the μRFQ DEER experiments directly provide fractional populations of the open and closed conformations as a function of time. We modeled the ligand-induced conformational change in the protein using a four-state model: apo/open (AO), apo/closed (AC), bound/open (BO), bound/closed (BC). These species interconvert according to AC + L ⇌ AO + L ⇌ BO ⇌ BC. By analyzing the concentration dependence of the relative contributions of the closed and open conformations at equilibrium, we estimated the equilibrium constants for the two conformational equilibria and the open-state ligand dissociation constant. Analysis of the time-resolved μRFQ DEER data gave estimates for the intrinsic rates of ligand binding and unbinding as well as the rates of the conformational change. This demonstrates that DEER can quantitatively resolve both the thermodynamics and the kinetics of ligand binding and the associated conformational change.

Monte Carlo Simulation of a Solvated Ionic Polymer with Cluster Morphology

National Research Council Canada - National Science Library

Matthews, Jessica L; Lada, Emily K; Weiland, Lisa M; Smith, Ralph C; Leo, Donald J

2005-01-01

.... Traditional rotational isomeric state theory is applied in combination with a Monte Carlo methodology to develop a simulation model of the conformation of Nafion polymer chains on a nanoscopic level...

Isomerization of butene-1 on rare earth oxides. [Rare earths: La, Nd, Dy

Energy Technology Data Exchange (ETDEWEB)

Khodakov, Yu S; Nesterov, V K; Minachev, Kh M [AN SSSR, Moscow. Inst. Organicheskoj Khimii

1975-09-01

A study has been made into the isomerization of butene-1 on oxides of rare-earth elements. The dependence of the reaction rate at 20/sup 0/C on the baking temperature of La and Nd oxides have the maximum at 700/sup 0/C. A decrease in the activity of these oxides after bakinq at 800/sup 0/C is observed, as well as during experiments at -30 deq C. In the case of Dy/sub 2/O/sub 3/, the activity at 20/sup 0/C increases gradually with Tsub(bak)=500 to 800/sup 0/C Zeolite 0.57LaNaY exhibits maximum activity at Tsub(bak)=500/sup 0/C Similar data as to the effect of the baking temperature on the catalyst activity were obtained earlier for hydrogenation of ethylene. According to their maximum activity, oxides of rare-earth elements, in the isomerization as well as hydrogenation reactions, can be arranged as follows: La/sub 2/O/sub 3/>Nd/sub 2/O/sub 3/

In vitro metabolism of nitric oxide-donating aspirin: the effect of positional isomerism.

Science.gov (United States)

Gao, Jianjun; Kashfi, Khosrow; Rigas, Basil

2005-03-01

NO-donating aspirin (NO-ASA) is a potentially important chemopreventive agent against cancer. Since positional isomerism affects strongly its potency in inhibiting colon cancer cell growth, we studied the metabolic transformations of its ortho-, meta-, and para-isomers in rat liver and colon cytosolic, microsomal, and mitochondrial fractions as well as in intact HT-29 human colon cancer cells. NO-ASA and metabolites were determined by high-performance liquid chromatography and products identified by mass spectroscopy, as required. For all three isomers, the acetyl group on the ASA moiety was hydrolyzed rapidly. This was followed by hydrolysis of the ester bond linking the salicylate anion to the spacer. The ortho- and para-isomers produced salicylic acid and a putative intermediate consisting of the remainder of the molecule, which via a rapid step generated nitrate, (hydroxymethyl)phenol, and a conjugate of spacer with glutathione. The meta-isomer, in contrast, generated salicylic acid and (nitroxymethyl)phenol, the latter leading to (hydroxymethyl)phenol and the glutathione-spacer conjugate. This metabolic pathway takes place in its entirety only in the cytosolic fraction of the tissues tested and in intact human colon cancer cells, perhaps reflecting exposure to the cytosolic glutathione S-transferase, which catalyzes the formation of the spacer-glutathione conjugate. Thus, the three positional isomers of NO-ASA differ in their metabolism and these differences correlate with their differential effects on cancer cell growth, underscoring the importance of positional isomerism in modulating drug effects.

Superspace conformal field theory

Energy Technology Data Exchange (ETDEWEB)

Quella, Thomas [Koeln Univ. (Germany). Inst. fuer Theoretische Physik; Schomerus, Volker [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

2013-07-15

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

Superspace conformal field theory

International Nuclear Information System (INIS)

Quella, Thomas

2013-07-01

Conformal sigma models and WZW models on coset superspaces provide important examples of logarithmic conformal field theories. They possess many applications to problems in string and condensed matter theory. We review recent results and developments, including the general construction of WZW models on type I supergroups, the classification of conformal sigma models and their embedding into string theory.

A Kinetic Model for β-Amyloid Adsorption at the Air/Solution Interface and Its Implication to the β-Amyloid Aggregation Process

Science.gov (United States)

Jiang, Dianlu; Dinh, Kim Lien; Ruthenburg, Travis; Zhang, Yi; Su, Lei; Land, Donald; Zhou, Feimeng

2011-01-01

The kinetics of adsorption at the air/buffer solution interface of amyloid beta peptide, Aβ(1–42), whose bulk concentration (submicromolar) is more than two orders of magnitude lower than that typically used in other in vitro aggregation studies, has been studied using a Langmuir-Blodgett trough. The pressure–time curves exhibit a lag phase, wherein the surface pressure essentially remains at zero, and a rising phase, corresponding to the Aβ adsorption at the interface. The duration of the lag phase was found to be highly dependent on both the Aβ bulk concentration and the solution temperature. A large activation energy (62.2 ± 4.1 KJ/mol) was determined and the apparent adsorption rate constant was found to be linearly dependent on the Aβ bulk concentration. Attenuated total reflection-IR spectra of the adsorbed Aβ transferred to a solid substrate and circular dichroism measurements of Aβ in the solution layer near the interface reveal that the natively unstructured Aβ in the bulk undergo a conformation change (folding) to mainly the α-helical structure. The results suggest that, prior to the adsorption step, an equilibrium between Aβ conformations is established within the subsurface. The kinetic equation derived from this model confirms that the overall Aβ adsorption is kinetically controlled and the apparent rate constant is proportional to the Aβ bulk concentration. This model also indicates that interfaces such as cell membranes and lipid bilayers may facilitate Aβ aggregation/fibrillation by providing a thin hydrophobic layer adjacent to the interface for the initial Aβ conformation change (misfolding) and accumulation. Such a preconcentration effect offers a plausible explanation of the fact that Aβ fibrillation occurs in vivo at nanomolar concentrations. Another important biological implication from our work is that Aβ misfolding may occur before its adsorption onto a cell membrane. This general kinetic model should also find

A kinetic model for beta-amyloid adsorption at the air/solution interface and its implication to the beta-amyloid aggregation process.

Science.gov (United States)

Jiang, Dianlu; Dinh, Kim Lien; Ruthenburg, Travis C; Zhang, Yi; Su, Lei; Land, Donald P; Zhou, Feimeng

2009-03-12

At the air/buffer solution interface the kinetics of adsorption of amyloid beta peptide, Abeta(1-42), whose bulk concentration (submicromolar) is more than 2 orders of magnitude lower than that typically used in other in vitro aggregation studies, has been studied using a Langmuir-Blodgett trough. The pressure-time curves exhibit a lag phase, wherein the surface pressure essentially remains at zero, and a rising phase, corresponding to the Abeta adsorption at the interface. The duration of the lag phase was found to be highly dependent on both the Abeta bulk concentration and the solution temperature. A large activation energy (62.2 +/- 4.1 KJ/mol) was determined and the apparent adsorption rate constant was found to be linearly dependent on the Abeta bulk concentration. Attenuated total reflection-IR spectra of the adsorbed Abeta transferred to a solid substrate and circular dichroism measurements of Abeta in the solution layer near the interface reveal that the natively unstructured Abeta in the bulk undergo a conformation change (folding) to mainly the alpha-helical structure. The results suggest that, prior to the adsorption step, an equilibrium between Abeta conformations is established within the subsurface. The kinetic equation derived from this model confirms that the overall Abeta adsorption is kinetically controlled and the apparent rate constant is proportional to the Abeta bulk concentration. This model also indicates that interfaces such as cell membranes and lipid bilayers may facilitate Abeta aggregation/ fibrillation by providing a thin hydrophobic layer adjacent to the interface for the initial A/beta conformation change (misfolding) and accumulation. Such a preconcentration effect offers a plausible explanation of the fact that Abeta fibrillation occurs in vivo at nanomolar concentrations. Another important biological implication from our work is that Abeta misfolding may occur before its adsorption onto a cell membrane. This general kinetic model

Conformal Infinity

OpenAIRE

Frauendiener, J?rg

2000-01-01

The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, 'conformal infinity' is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory...

Recent Insight into the Kinetic Mechanisms and Conformational Dynamics of Y-Family DNA Polymerases

OpenAIRE

Maxwell, Brian A.; Suo, Zucai

2014-01-01

The kinetic mechanisms by which DNA polymerases catalyze DNA replication and repair have long been areas of active research. Recently discovered Y-family DNA polymerases catalyze the bypass of damaged DNA bases that would otherwise block replicative DNA polymerases and stall replication forks. Unlike DNA polymerases from the five other families, the Y-family DNA polymerases have flexible, solvent-accessible active sites that are able to tolerate various types of damaged template bases and all...

An Insight into Flotation Chemistry of Pyrite with Isomeric Xanthates: A Combined Experimental and Computational Study

Directory of Open Access Journals (Sweden)

Guihong Han

2018-04-01

Full Text Available The flotation chemistry between pyrite and isomeric xanthates (butyl xanthate and isobutyl xanthate was investigated by means of adsorption experiments, surface tension tests, and molecular dynamic simulations in this work. The flotation chemical results were confirmed and further interpreted by quantum chemical calculations. The experiment results demonstrated that the isobutyl xanthate exhibited superior adsorption capacity and surface activity than those of butyl xanthate in flotation chemistry. In addition, molecular dynamic simulations were simultaneously performed in constant number, constant volume and temperature (NVT, and constant number, constant volume, and pressure (NPT ensemble, indicating that the NPT ensemble was more suitable to the flotation system and the isobutyl xanthate was easier to be adsorbed on pyrite surface compared with butyl xanthate during an appropriate range of concentrations. Furthermore, the quantum chemical calculations elucidated that the isobutyl xanthate presented higher reactivity than that of the corresponding butyl xanthate based on the frontier molecular orbital theory of chemical reactivity, which was consistent with experimental and simulation results obtained. This work can provide theoretical guidance for an in-depth study of the flotation chemistry of pyrite with isomeric xanthates.

Impact of branched structures on cycloalkane ignition in a motored engine: Detailed product and conformational analyses

KAUST Repository

Kang, Dongil

2015-04-01

The ignition process of ethylcyclohexane (ECH) and its two isomers, 1,3-dimethylcyclohexane (13DMCH) and 1,2-dimethylcyclohexane (12DMCH) was investigated in a modified CFR engine. The experiment was conducted with intake air temperature of 155. °C, equivalence ratio of 0.5 and engine speed of 600. rpm. The engine compression ratio (CR) was gradually increased in a stepwise manner until autoignition occurred. It was found that ECH exhibited a significantly higher oxidation reactivity compared to its two isomers. The autoignition criterion was based on CO emissions and the apparent heat release rates. Ethylcyclohexane (ECH) indicated noticeable two stage ignition behavior, while less significant heat release occurred for the two isomers at comparable conditions. The mole fractions of unreacted fuel and stable intermediate species over a wide range of compression ratios were analyzed by GC-MS and GC-FID. Most of the species indicated constant rates of formation and the trends of relative yield to unreacted fuel are well in agreement with the oxidation reactivity in the low temperature regime. The major intermediate species are revealed as a group of conjugate olefins, which possess the same molecular structure as the original fuel compound except for the presence of a double carbon bond. Conjugate olefins were mostly formed through (1,4) H-shift isomerization during the low temperature oxidation of alkylcyclohexanes. Conformation analysis explains the reactivity differences in the three isomers as well as the fractions of intermediate species. The hydrogen availability located in alkyl substituents plays an important role in determining oxidation reactivity, requiring less activation energy for abstraction through the (1,5) H-shift isomerization. This reactivity difference contributes to building up the major intermediate species observed during oxidation of each test fuel. 12DMCH, whose ignition reactivity is the lowest, less favors β-scission of C-C backbone of

Study of the photochemical isomerization of ergosterol

International Nuclear Information System (INIS)

Mermet-Bouvier, Rene

1972-01-01

The photochemical reaction scheme of Ergosterol-Vitamin D 2 was studied. The schemes proposed in published literature are described together with earlier methods used for the analysis and determination. The method used is then discussed. In the first part, the factors concerning the changes occurring in molecular systems exposed to radiation, and the formalism used, are examined. Investigations of linear molecular systems and their applications to the reaction scheme of Ergosterol-Vitamin D 2 are discussed. The properties which enable the last three reaction schemes proposed in the literature to be distinguished are described. In the second part, the experimental analytical methods and the determinations made of the different isomers formed are presented. Chromatographic techniques (thin films, columns, gaseous phase) suitable for separating the various isomeric species are used. The existence of 8 isomers was established as well as a transformation occurring in one of them. The ultraviolet and infrared spectra were obtained. A reaction scheme is proposed (in which all the quantum yield values are given) from comparisons between the calculated and experimental values of the eigenvalue of the absolute minimum value λ m and the eigenvector corresponding to V m . (author) [fr

Pre-steady-state kinetic analysis of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis reveals partially rate-limiting product release by parallel pathways.

Science.gov (United States)

Liu, Juan; Murkin, Andrew S

2012-07-03

As part of the non-mevalonate pathway for the biosynthesis of the isoprenoid precursor isopentenyl pyrophosphate, 1-deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR) catalyzes the conversion of DXP into 2-C-methyl-D-erythritol 4-phosphate (MEP) by consecutive isomerization and NADPH-dependent reduction reactions. Because this pathway is essential to many infectious organisms but is absent in humans, DXR is a target for drug discovery. In an attempt to characterize its kinetic mechanism and identify rate-limiting steps, we present the first complete transient kinetic investigation of DXR. Stopped-flow fluorescence measurements with Mycobacterium tuberculosis DXR (MtDXR) revealed that NADPH and MEP bind to the free enzyme and that the two bind together to generate a nonproductive ternary complex. Unlike the Escherichia coli orthologue, MtDXR exhibited a burst in the oxidation of NADPH during pre-steady-state reactions, indicating a partially rate-limiting step follows chemistry. By monitoring NADPH fluorescence during these experiments, the transient generation of MtDXR·NADPH·MEP was observed. Global kinetic analysis supports a model involving random substrate binding and ordered release of NADP(+) followed by MEP. The partially rate-limiting release of MEP occurs via two pathways--directly from the binary complex and indirectly via the MtDXR·NADPH·MEP complex--the partitioning being dependent on NADPH concentration. Previous mechanistic studies, including kinetic isotope effects and product inhibition, are discussed in light of this kinetic mechanism.

Conformal superalgebras via tractor calculus

Science.gov (United States)

Lischewski, Andree

2015-01-01

We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure that has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

Measurements of 14-MeV neutron cross-sections for the production of isomeric states in hafnium isotopes

International Nuclear Information System (INIS)

Patrick, B.H.; Sowerby, M.G.; Wilkins, C.G.; Russen, L.C.

1990-01-01

The cross sections for the production of isomeric states in the reactions 179 Hf(n,2n) 178m2 Hf, 180 Hf(n,2n) 179m2 Hf, 179 Hf(n,n') 179m2 Hf with 14 MeV neutrons have been measured and compared with the theoretical ones. 4 refs, 3 figs, 4 tabs

Behavior of the excited deformed band and search for shape isomerism in 184Hg

International Nuclear Information System (INIS)

Cole, J.D.; Hamilton, J.H.; Ramayya, A.V.; Nettles, W.G.; Kawakami, H.; Spejewski, E.H.; Ijaz, M.A.; Toth, K.S.; Robinson, E.L.; Sastry, K.S.R.; Lin, J.; Avignone, F.T.; Brantley, W.H.; Rao, P.V.G.

1976-01-01

The new isotope 184 Tl has been identified with T 1 / 2 =11 +- 1 sec and the levels in 184 Hg investigated from its decay. The 0 + band head of a deformed band was found to drop to 375 keV in agreement with theoretical predictions. The mean life of the 375-keV 0 + level was measured to be 0.9 +- 0.3 nsec which is a factor of 10 faster than theoretically predicted for a shape-isomeric E2 transition

Dynamics of DNA conformations and DNA-protein interaction

DEFF Research Database (Denmark)

Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

2005-01-01

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...... denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed...... in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent...

Conformal sequestering simplified

International Nuclear Information System (INIS)

Schmaltz, Martin; Sundrum, Raman

2006-01-01

Sequestering is important for obtaining flavor-universal soft masses in models where supersymmetry breaking is mediated at high scales. We construct a simple and robust class of hidden sector models which sequester themselves from the visible sector due to strong and conformally invariant hidden dynamics. Masses for hidden matter eventually break the conformal symmetry and lead to supersymmetry breaking by the mechanism recently discovered by Intriligator, Seiberg and Shih. We give a unified treatment of subtleties due to global symmetries of the CFT. There is enough review for the paper to constitute a self-contained account of conformal sequestering

Conformity index: A review

International Nuclear Information System (INIS)

Feuvret, Loic; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

2006-01-01

We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear

Fermion-scalar conformal blocks

Energy Technology Data Exchange (ETDEWEB)

Iliesiu, Luca [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Kos, Filip [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); Poland, David [Department of Physics, Yale University,217 Prospect Street, New Haven, CT 06520 (United States); School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Pufu, Silviu S. [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States); Simmons-Duffin, David [School of Natural Sciences, Institute for Advanced Study,1 Einstein Dr, Princeton, New Jersey 08540 (United States); Yacoby, Ran [Joseph Henry Laboratories, Princeton University,Washington Road, Princeton, NJ 08544 (United States)

2016-04-13

We compute the conformal blocks associated with scalar-scalar-fermion-fermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. Conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

Effect of phospholipid, detergent and protein-protein interaction on stability and phosphoenzyme isomerization of soluble sarcoplasmic reticulum Ca-ATPase.

Science.gov (United States)

Vilsen, B; Andersen, J P

1987-12-30

The purpose of the present study was to elucidate the separate roles of lipid, detergent and protein-protein interaction for stability and catalytic properties of sarcoplasmic reticulum Ca-ATPase solubilized in the non-ionic detergent octa(ethylene glycol) monododecyl ether (C12E8). The use of large-zone high-performance liquid chromatography permitted us to define the self-association state of Ca-ATPase peptide at various detergent, phospholipid and protein concentrations, and also during enzymatic turnover with ATP. Conditions were established for monomerization of Ca-ATPase in the presence of a high concentration of phospholipid relative to detergent. The lipid-saturated monomeric preparation was relatively resistant to inactivation in the absence of Ca2+, whereas delipidated enzyme in monomeric or in oligomeric form was prone to inactivation. Kinetics of phosphoenzyme turnover were examined in the presence and absence of Mg2+. Dephosphorylation rates were sensitive to Mg2+, irrespective of whether the peptide was present in soluble monomeric form or was membrane-bound. C12E8-solubilized monomer without added phospholipid was, however, characterized by a fast initial phase of dephosphorylation in the absence of Mg2+. This was not observed with monomer saturated with phospholipid or with monomer solubilized in myristoylglycerophosphocholine or deoxycholate. The mechanism underlying this difference was shown to be a C12E8-induced acceleration of conversion of ADP-sensitive phosphoenzyme (E1P) to ADP-insensitive phosphoenzyme (E2P). The phosphoenzyme isomerization rate was also found to be enhanced by low-affinity binding of ATP. This was demonstrated both in membrane-bound and in soluble monomeric Ca-ATPase. Our results indicate that a single peptide chain constitutes the target for modulation of phosphoenzyme turnover by Mg2+ and ATP, and that detergent effects, distinct from those arising from disruption of protein-protein contacts, are the major determinants of

Fabrication challenges associated with conformal optics

Science.gov (United States)

Schaefer, John; Eichholtz, Richard A.; Sulzbach, Frank C.

2001-09-01

A conformal optic is typically an optical window that conforms smoothly to the external shape of a system platform to improve aerodynamics. Conformal optics can be on-axis, such as an ogive missile dome, or off-axis, such as in a free form airplane wing. A common example of conformal optics is the automotive head light window that conforms to the body of the car aerodynamics and aesthetics. The unusual shape of conformal optics creates tremendous challenges for design, manufacturing, and testing. This paper will discuss fabrication methods that have been successfully demonstrated to produce conformal missile domes and associated wavefront corrector elements. It will identify challenges foreseen with more complex free-form configurations. Work presented in this paper was directed by the Precision Conformal Optics Consortium (PCOT). PCOT is comprised of both industrial and academic members who teamed to develop and demonstrate conformal optical systems suitable for insertion into future military programs. The consortium was funded under DARPA agreement number MDA972-96-9-08000.

Half-lives of ground and isomeric states in {sup 97}Cd and the astrophysical origin of {sup 96}Ru

Energy Technology Data Exchange (ETDEWEB)

Lorusso, G., E-mail: lorusso@ribf.riken.j [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824 (United States); Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Becerril, A.; Amthor, A. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824 (United States); Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Baumann, T.; Bazin, D. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Berryman, J.S. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Department of Chemistry, Michigan State University, East Lansing, MI 48824 (United States); Brown, B.A. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824 (United States); Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824 (United States); Cyburt, R.H. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Joint Institute for Nuclear Astrophysics, Michigan State University, East Lansing, MI 48824 (United States); Crawford, H.L. [National Superconducting Cyclotron Laboratory, Michigan State University, East Lansing, MI 48824 (United States); Department of Chemistry, Michigan State University, East Lansing, MI 48824 (United States)

2011-05-09

First experimental evidence for a high-spin isomer (25/2{sup +}) in {sup 97}Cd, a waiting point in the astrophysical rapid proton capture process, is presented. The data were obtained in {beta}-decay studies at NSCL using the new RF Fragment Separator system and detecting {beta}-delayed protons and {beta}-delayed {gamma} rays. Decays from ground and isomeric states were disentangled, and proton emission branches were determined for the first time. We find half-lives of 1.10(8) s and 3.8(2) s, and {beta}-delayed proton emission branches of 12(2)% and 25(4)% were deduced for the ground and isomeric states, respectively. With these results, the nuclear data needed to determine an rp-process contribution to the unknown origin of solar {sup 96}Ru are in place. When the new data are included in astrophysical rp-process calculations, one finds that an rp-process origin of {sup 96}Ru is unlikely.

Along the N=126 closed shell: study of $^{205}$Au through its $\\pi h_{11/2}^{-1}$ isomeric decay

CERN Multimedia

2002-01-01

Excited states have been identified in only three of the N=126 closed shell nuclei 'below' $^{208}$Pb, $^{207}$Tl, $^{206}$Hg and very recently $^{204}$Pt. We aim to extend our knowledge of the neutron-rich N=126 nuclei by observing the internal decay of the $\\pi h^{-1}_{11/2}$ excited state in $^{205}$Au, which is expected to be isomeric. In addition, the decay of the analogous states in the N=122 and N=124 $^{201,203}$Au will be studied. The lifetimes of the expected isomeric states are crucial for the success of the experiment, and they are estimated to be in the range of 0.3-20 s. These are long enough to enable the extraction from the source, but shorter than the $\\beta$-decay half-lives. Proton single-particle energies and transition rates will be extracted, providing information about the robustness of the N=126 shell-closure. Three days of beam-time is requested.

Axiomatic conformal field theory

International Nuclear Information System (INIS)

Gaberdiel, M.R.; Goddard, P.

2000-01-01

A new rigourous approach to conformal field theory is presented. The basic objects are families of complex-valued amplitudes, which define a meromorphic conformal field theory (or chiral algebra) and which lead naturally to the definition of topological vector spaces, between which vertex operators act as continuous operators. In fact, in order to develop the theory, Moebius invariance rather than full conformal invariance is required but it is shown that every Moebius theory can be extended to a conformal theory by the construction of a Virasoro field. In this approach, a representation of a conformal field theory is naturally defined in terms of a family of amplitudes with appropriate analytic properties. It is shown that these amplitudes can also be derived from a suitable collection of states in the meromorphic theory. Zhu's algebra then appears naturally as the algebra of conditions which states defining highest weight representations must satisfy. The relationship of the representations of Zhu's algebra to the classification of highest weight representations is explained. (orig.)

Conformal description of spinning particles

International Nuclear Information System (INIS)

Todorov, I.T.

1986-01-01

This book is an introduction to the application of the conformal group to quantum field theory of particles with spin. After an introduction to the twistor representations of the conformal group of a conformally flat space-time and twistor flag manifolds with Su(2,2) orbits the classical phase space of conformal spinning particles is described. Thereafter the twistor description of classical zero mass fields is considered together with the quantization. (HSI)

Conformal boundaries of warped products

DEFF Research Database (Denmark)

Kokkendorff, Simon Lyngby

2006-01-01

In this note we prove a result on how to determine the conformal boundary of a type of warped product of two length spaces in terms of the individual conformal boundaries. In the situation, that we treat, the warping and conformal distortion functions are functions of distance to a base point....... The result is applied to produce examples of CAT(0)-spaces, where the conformal and ideal boundaries differ in interesting ways....

Conformally connected universes

International Nuclear Information System (INIS)

Cantor, M.; Piran, T.

1983-01-01

A well-known difficulty associated with the conformal method for the solution of the general relativistic Hamiltonian constraint is the appearance of an aphysical ''bag of gold'' singularity at the nodal surface of the conformal factor. This happens whenever the background Ricci scalar is too large. Using a simple model, it is demonstrated that some of these singular solutions do have a physical meaning, and that these can be considered as initial data for Universe containing black holes, which are connected, in a conformally nonsingular way with each other. The relation between the ADM mass and the horizon area in this solution supports the cosmic censorship conjecture. (author)

Yeast hexokinase. A fluorescence temperature-jump study of the kinetics of the binding of glucose to the monomer forms of hexokinases P-I and P-II.

Science.gov (United States)

Hoggett, J G; Kellett, G L

1976-09-15

The binding of glucose to the monomeric forms of hexokinases P-I and P-II in Tris and phosphate buffers at pH 8.0 in the presence of 1 mol l-1 KCl has been studied using the fluorescence temperature-jump technique. For both isozymes only one relaxation time was observed; values of tau-1 increased linearly with increasing concentration of free reacting partners. The apparent second-order rate constant for association was about 2 X 10(6) 1 mol-1 s-1 for both isozymes; the differences in the stabilities of the complexes with P-I and P-II are entirely attributable to the fact that glucose dissociates more slowly from its complex with P-I than P-II (approximately 300 s-1 and 1100 s-1 respectively). Although the kinetic data are compatible with a single-step mechanism for glucose binding the association rate constant was much lower than that expected for a diffusion-limited rate of encounter. Other mechanisms for describing an induced-fit are discussed. It is shown that the data are incompatible with a slow 'prior-isomerization' pathway of substrate binding, but are consistent with a 'substrate-guided' pathway involving isomerization of the enzyme-substrate complex.

Metallocene-catalyzed ethylene−α-olefin isomeric copolymerization: A perspective from hydrodynamic boundary layer mass transfer and design of MAO anion

KAUST Repository

Adamu, Sagir; Atiqullah, Muhammad; Malaibari, Zuhair O.; Al-Harthi, Mamdouh A.; Emwas, Abdul-Hamid M.; Ul-Hamid, Anwar

2015-01-01

-catalyzed ethylene polymerization. This approach was illustrated by conducting homo- and isomeric copolymerization of ethylene with 1-hexene and 4-methyl-1-pentene in the presence of bis(n-butylcyclopentadienyl) zirconium dichloride (nBuCp)2ZrCl2, using (i) MAO anion

Kinetic theory of nonequilibrium ensembles, irreversible thermodynamics, and generalized hydrodynamics

CERN Document Server

Eu, Byung Chan

2016-01-01

This book presents the fundamentals of irreversible thermodynamics for nonlinear transport processes in gases and liquids, as well as for generalized hydrodynamics extending the classical hydrodynamics of Navier, Stokes, Fourier, and Fick. Together with its companion volume on relativistic theories, it provides a comprehensive picture of the kinetic theory formulated from the viewpoint of nonequilibrium ensembles in both nonrelativistic and, in Vol. 2, relativistic contexts. Theories of macroscopic irreversible processes must strictly conform to the thermodynamic laws at every step and in all approximations that enter their derivation from the mechanical principles. Upholding this as the inviolable tenet, the author develops theories of irreversible transport processes in fluids (gases or liquids) on the basis of irreversible kinetic equations satisfying the H theorem. They apply regardless of whether the processes are near to or far removed from equilibrium, or whether they are linear or nonlinear with respe...

On Associative Conformal Algebras of Linear Growth

OpenAIRE

Retakh, Alexander

2000-01-01

Lie conformal algebras appear in the theory of vertex algebras. Their relation is similar to that of Lie algebras and their universal enveloping algebras. Associative conformal algebras play a role in conformal representation theory. We introduce the notions of conformal identity and unital associative conformal algebras and classify finitely generated simple unital associative conformal algebras of linear growth. These are precisely the complete algebras of conformal endomorphisms of finite ...

Prediction of binding modes between protein L-isoaspartyl (D-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening.

Science.gov (United States)

Oda, Akifumi; Noji, Ikuhiko; Fukuyoshi, Shuichi; Takahashi, Ohgi

2015-12-10

Because the aspartic acid (Asp) residues in proteins are occasionally isomerized in the human body, not only l-α-Asp but also l-β-Asp, D-α-Asp and D-β-Asp are found in human proteins. In these isomerized aspartic acids, the proportion of D-β-Asp is the largest and the proportions of l-β-Asp and D-α-Asp found in human proteins are comparatively small. To explain the proportions of aspartic acid isomers, the possibility of an enzyme able to repair l-β-Asp and D-α-Asp is frequently considered. The protein L-isoaspartyl (D-aspartyl) O-methyltransferase (PIMT) is considered one of the possible repair enzymes for l-β-Asp and D-α-Asp. Human PIMT is an enzyme that recognizes both l-β-Asp and D-α-Asp, and catalyzes the methylation of their side chains. In this study, the binding modes between PIMT and peptide substrates containing l-β-Asp or D-α-Asp residues were investigated using computational protein-ligand docking and molecular dynamics simulations. The results indicate that carboxyl groups of both l-β-Asp and D-α-Asp were recognized in similar modes by PIMT and that the C-terminal regions of substrate peptides were located in similar positions on PIMT for both the l-β-Asp and D-α-Asp peptides. In contrast, for peptides containing l-α-Asp or D-β-Asp residues, which are not substrates of PIMT, the computationally constructed binding modes between PIMT and peptides greatly differed from those between PIMT and substrates. In the nonsubstrate peptides, not inter- but intra-molecular hydrogen bonds were observed, and the conformations of peptides were more rigid than those of substrates. Thus, the in silico analytical methods were able to distinguish substrates from nonsubstrates and the computational methods are expected to complement experimental analytical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Conformal algebra of Riemann surfaces

International Nuclear Information System (INIS)

Vafa, C.

1988-01-01

It has become clear over the last few years that 2-dimensional conformal field theories are a crucial ingredient of string theory. Conformal field theories correspond to vacuum solutions of strings; or more precisely we know how to compute string spectrum and scattering amplitudes by starting from a formal theory (with a proper value of central charge of the Virasoro algebra). Certain non-linear sigma models do give rise to conformal theories. A lot of progress has been made in the understanding of conformal theories. The author discusses a different view of conformal theories which was motivated by the development of operator formalism on Riemann surfaces. The author discusses an interesting recent work from this point of view

Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics.

Directory of Open Access Journals (Sweden)

Barry J Grant

2009-03-01

Full Text Available Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25-40 and 57-75 intermediate between GTP and GDP states, or distinct loop3 (46-49, loop7 (105-110, and alpha5 C-terminus (159-166 conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of alpha2 (residues 66-74 with alpha3-loop7 (93-110, loop2 (26-37 with loop10 (145-151, and loop3 (46-49 with alpha5 (152-167. The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD simulations, is a low-frequency motion intrinsic to the structure.

Conformality lost

International Nuclear Information System (INIS)

Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A.

2009-01-01

We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, ξ∼exp(c/|T-T c | 1/2 ). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

Spectroscopic properties and conformational stability of Concholepas concholepas hemocyanin.

Science.gov (United States)

Idakieva, Krassimira; Nikolov, Peter; Chakarska, Irena; Genov, Nicolay; Shnyrov, Valery L

2008-01-01

The structure in solution and conformational stability of the hemocyanin from the Chilean gastropod mollusk Concholepas concholepas (CCH) and its structural subunits, CCH-A and CCH-B, were studied using fluorescence spectroscopy and differential scanning calorimetry (DSC). The fluorescence properties of the oxygenated and apo-form (copper-deprived) of the didecamer and its subunits were characterized. Besides tryptophan residues buried in the hydrophobic interior of the protein molecule also exposed fluorophores determine the fluorescence emission of the oxy- and apo-forms of the investigated hemocyanins. The copper-dioxygen system at the binuclear active site quenches the tryptophan emission of the oxy-forms of CCH and its subunits. The removal of this system increases the fluorescence quantum yield and causes structural rearrangement of the microenvironment of the emitting tryptophan residues in the respective apo-forms. Time-resolved fluorescence measurements show that the oxygenated and copper-deprived forms of the CCH and its subunits exist in different conformations. The thermal denaturation of the hemocyanin is an irreversible process, under kinetic control. A successive annealing procedure was applied to obtain the experimental deconvolution of the irreversible thermal transitions. Arrhenius equation parameter for the two-state irreversible model of the thermal denaturation of oxy-CCH at pH 7.2 was estimated. Both factors, oligomerization and the copper-dioxygen system at the active site, are important for stabilizing the structure of the hemocyanin molecule.

Evidence for Sequence Scrambling and Divergent H/D Exchange Reactions of Doubly-Charged Isobaric b-Type Fragment Ions

Science.gov (United States)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H.; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10 2+ that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10 2+ and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10 2+, suggesting that b10 2+ may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10 2+; over 30 % of the observed SORI-CID fragment ions from substance P b10 2+ had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10 2+, whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10 2+.

Evidence for sequence scrambling and divergent H/D exchange reactions of doubly-charged isobaric b-type fragment ions.

Science.gov (United States)

Zekavat, Behrooz; Miladi, Mahsan; Al-Fdeilat, Abdullah H; Somogyi, Arpad; Solouki, Touradj

2014-02-01

To date, only a limited number of reports are available on structural variants of multiply-charged b-fragment ions. We report on observed bimodal gas-phase hydrogen/deuterium exchange (HDX) reaction kinetics and patterns for substance P b10(2+) that point to presence of isomeric structures. We also compare HDX reactions, post-ion mobility/collision-induced dissociation (post-IM/CID), and sustained off-resonance irradiation-collision induced dissociation (SORI-CID) of substance P b10(2+) and a cyclic peptide with an identical amino acid (AA) sequence order to substance P b10. The observed HDX patterns and reaction kinetics and SORI-CID pattern for the doubly charged head-to-tail cyclized peptide were different from either of the presumed isomers of substance P b10(2+), suggesting that b10(2+) may not exist exclusively as a head-to-tail cyclized structure. Ultra-high mass measurement accuracy was used to assign identities of the observed SORI-CID fragment ions of substance P b10(2+); over 30% of the observed SORI-CID fragment ions from substance P b10(2+) had rearranged (scrambled) AA sequences. Moreover, post-IM/CID experiments revealed the presence of two conformer types for substance P b10(2+), whereas only one conformer type was observed for the head-to-tail cyclized peptide. We also show that AA sequence scrambling from CID of doubly-charged b-fragment ions is not unique to substance P b10(2+).

40 CFR 93.154 - Conformity analysis.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section 93...) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State or Federal Implementation Plans § 93.154 Conformity analysis. Any Federal...

Use of Isomerization and Hydroisomerization Reactions to Improve the Cold Flow Properties of Vegetable Oil Based Biodiesel

Directory of Open Access Journals (Sweden)

Stephen J. Reaume

2013-01-01

Full Text Available Biodiesel is a promising alternative to petroleum diesel with the potential to reduce overall net CO2 emissions. However, the high cloud point of biodiesel must be reduced when used in cold climates. We report on the use of isomerization and hydroisomerization reactions to reduce the cloud point of eight different fats and oils. Isomerization was carried out at 260 °C and 1.5 MPa H2 pressure utilizing beta zeolite catalyst, while hydroisomerization was carried out at 300 °C and 4.0 MPa H2 pressure utilizing 0.5 wt % Pt-doped beta zeolite catalyst. Reaction products were tested for cloud point and flow properties, in addition to catalyst reusability and energy requirements. Results showed that high unsaturated fatty acid biodiesels increased in cloud point, due to the hydrogenation side reaction. In contrast, low unsaturated fatty acid biodiesels yielded cloud point reductions and overall improvement in the flow properties. A maximum cloud point reduction of 12.9 °C was observed with coconut oil as the starting material. Results of the study have shown that branching can reduce the cloud point of low unsaturated fatty acid content biodiesel.

Discrete kinetic models from funneled energy landscape simulations.

Directory of Open Access Journals (Sweden)

Nicholas P Schafer

Full Text Available A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK. In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

Recursion Relations for Conformal Blocks

CERN Document Server

Penedones, João; Yamazaki, Masahito

2016-09-12

In the context of conformal field theories in general space-time dimension, we find all the possible singularities of the conformal blocks as functions of the scaling dimension $\\Delta$ of the exchanged operator. In particular, we argue, using representation theory of parabolic Verma modules, that in odd spacetime dimension the singularities are only simple poles. We discuss how to use this information to write recursion relations that determine the conformal blocks. We first recover the recursion relation introduced in 1307.6856 for conformal blocks of external scalar operators. We then generalize this recursion relation for the conformal blocks associated to the four point function of three scalar and one vector operator. Finally we specialize to the case in which the vector operator is a conserved current.

The logarithmic conformal field theories

International Nuclear Information System (INIS)

Rahimi Tabar, M.R.; Aghamohammadi, A.; Khorrami, M.

1997-01-01

We study the correlation functions of logarithmic conformal field theories. First, assuming conformal invariance, we explicitly calculate two- and three-point functions. This calculation is done for the general case of more than one logarithmic field in a block, and more than one set of logarithmic fields. Then we show that one can regard the logarithmic field as a formal derivative of the ordinary field with respect to its conformal weight. This enables one to calculate any n-point function containing the logarithmic field in terms of ordinary n-point functions. Finally, we calculate the operator product expansion (OPE) coefficients of a logarithmic conformal field theory, and show that these can be obtained from the corresponding coefficients of ordinary conformal theory by a simple derivation. (orig.)

Anesthetic implications of total anomalous systemic venous connection to left atrium with left isomerism

Directory of Open Access Journals (Sweden)

Parimala Prasanna Simha

2012-01-01

Full Text Available Total anomalous systemic venous connection (TASVC to the left atrium (LA is a rare congenital anomaly. An 11-year-old girl presented with complaints of palpitations and cyanosis. TASVC with left isomerism and noncompaction of LV was diagnosed after contrast echocardiogram and computed tomography angiogram. The knowledge of anatomy and pathophysiology is essential for the successful management of these cases. Anesthetic concerns in this case were polycythemia, paradoxical embolism and rhythm abnormalities. The patient was successfully operated by rerouting the systemic venous connection to the right atrium.

Amino acid-catalyzed conversion of citral : cis-trans isomerization and its conversion into 6-methyl-5-hepten-2-one and acetaldehyde

NARCIS (Netherlands)

Wolken, W.A.M.; Have, R. ten; Werf, M.J. van der

2000-01-01

Under alkaline conditions, amino acids or proteins catalyze the deacetylation of citral, a major aroma component, resulting in methylheptenone and acetaldehyde formation. 3-Hydroxycitronellal is an intermediate in this reaction. Amino acids also catalyze the cis-trans isomerization of the pure

Vibrational Spectroscopy and Gas-Phase Thermochemistry of the Model Dipeptide N-Acetyl Glycine Methyl Amide

Science.gov (United States)

Leavitt, Christopher; Raston, Paul; Moody, Grant; Shirley, Caitlyne; Douberly, Gary

2014-06-01

The structure-function relationship in proteins is widely recognized, motivating numerous investigations of isolated neutral and ionic polypeptides that generally employ conformation specific, multidimensional UV and IR spectroscopies. This data taken in conjunction with computed harmonic frequencies has provided a snapshot of the underlying molecular physics at play in many polypeptides, but few experiments have been able to probe the energetics of these systems. In this study, we use vibrational spectroscopy to measure the gas-phase enthalpy change for isomerization between two conformations of the dipeptide N-acetyl glycine methyl amide (NAGMA). A two-stage oven source is implemented producing a gas-phase equilibrium distribution of NAGMA molecules that is flash frozen upon pickup by He nanodroplets. Using polarization spectroscopy, the IR spectrum is assigned to a mixture of two conformers having intramolecular hydrogen bonds made up of either five- or seven-membered rings, C5 and C7, respectively. The interconversion enthalpy, obtained from the van't Hoff relation, is 4.52{±}0.12 kJ/mol for isomerization from the C7 to the C5-conformer. This experimental measurement is compared to computations employing a broad range of theoretical methods.

Phenomenology of local scale invariance: from conformal invariance to dynamical scaling

International Nuclear Information System (INIS)

Henkel, Malte

2002-01-01

Statistical systems displaying a strongly anisotropic or dynamical scaling behaviour are characterized by an anisotropy exponent θ or a dynamical exponent z. For a given value of θ (or z), we construct local scale transformations, which can be viewed as scale transformations with a space-time-dependent dilatation factor. Two distinct types of local scale transformations are found. The first type may describe strongly anisotropic scaling of static systems with a given value of θ, whereas the second type may describe dynamical scaling with a dynamical exponent z. Local scale transformations act as a dynamical symmetry group of certain non-local free-field theories. Known special cases of local scale invariance are conformal invariance for θ=1 and Schroedinger invariance for θ=2. The hypothesis of local scale invariance implies that two-point functions of quasi primary operators satisfy certain linear fractional differential equations, which are constructed from commuting fractional derivatives. The explicit solution of these yields exact expressions for two-point correlators at equilibrium and for two-point response functions out of equilibrium. A particularly simple and general form is found for the two-time auto response function. These predictions are explicitly confirmed at the uniaxial Lifshitz points in the ANNNI and ANNNS models and in the aging behaviour of simple ferromagnets such as the kinetic Glauber-Ising model and the kinetic spherical model with a non-conserved order parameter undergoing either phase-ordering kinetics or non-equilibrium critical dynamics

Recent advancements in conformal gravity

International Nuclear Information System (INIS)

O’Brien, James G.; Chaykov, Spasen S.; Moss, Robert J.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian

2017-01-01

In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing. (paper)

Stability constants of mixed ligand complexes of dioxouranium(II) and thorium(IV) with complexones and isomeric alanines

International Nuclear Information System (INIS)

Singh, R.K.; Saxena, M.C.

1992-01-01

The present work reports on the stability sequence between UO 2 II and Th IV ions for their mixed ligands complexes with the two isomeric alanines, α-alanine (α-ala) and β-alanine (β-ala) containing a complexone as primary ligand. The complexones used are iminodiacetate (IMDA), nitrilotricetate (NTA), 2-hydroxyethylenediaminetriacetate (HEDTA), ethylenediaminetetraacetate (EDTA), 1,2-diaminocyclohexanetraacetate (CDTA) and diethylenetriminepentaacetate (DTPA). (author). 9 refs., 1 tab

A conformational study of protonated noradrenaline by UV-UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method.

Science.gov (United States)

Wako, Hiromichi; Ishiuchi, Shun-Ichi; Kato, Daichi; Féraud, Géraldine; Dedonder-Lardeux, Claude; Jouvet, Christophe; Fujii, Masaaki

2017-05-03

The conformer-selected ultraviolet (UV) and infrared (IR) spectra of protonated noradrenaline were measured using an electrospray/cryogenic ion trap technique combined with photo-dissociation spectroscopy. By comparing the UV photo dissociation (UVPD) spectra with the UV-UV hole burning (HB) spectra, it was found that five conformers coexist under ultra-cold conditions. Based on the spectral features of the IR dip spectra of each conformer, two different conformations on the amine side chain were identified. Three conformers (group I) were assigned to folded and others (group II) to extended structures by comparing the observed IR spectra with the calculated ones. Observation of the significantly less-stable extended conformers strongly suggests that the extended structures are dominant in solution and are detected in the gas phase by kinetic trapping. The conformers in each group are assignable to rotamers of OH orientations in the catechol ring. By comparing the UV-UV HB spectra and the calculated Franck-Condon spectra obtained by harmonic vibrational analysis of the S 1 state, with the aid of relative stabilization energies of each conformer in the S 0 state, the absolute orientations of catechol OHs of the observed five conformers were successfully determined. It was found that the 0-0 transition of one folded conformer is red-shifted by about 1000 cm -1 from the others. The significant red-shift was explained by a large contribution of the πσ* state to S 1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

Benchmarking Commercial Conformer Ensemble Generators.

Science.gov (United States)

Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

2017-11-27

We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import, and OMEGA) and one leading free algorithm, the distance geometry algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms, the median minimum root-mean-square deviations measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit distance geometry algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the midranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parametrize them for best performance in different application scenarios.

Single-Step Access to Long-Chain α,ω-Dicarboxylic Acids by Isomerizing Hydroxycarbonylation of Unsaturated Fatty Acids

KAUST Repository

Goldbach, Verena

2016-11-09

Dicarboxylic acids are compounds of high value, but to date long-chain alpha,omega-dicarboxylic acids have been difficult to access in a direct way. Unsaturated fatty acids are ideal starting materials with their molecular structure of long methylene sequences and a carboxylate functionality, in addition to a double bond that offers itself for functionalization. Within this paper, we established a direct access to alpha,omega-dicarboxylic acids by combining isomerization and selective terminal carbonylation of the internal double bond with water as a nucleophile on unsaturated fatty acids. We identified the key elements of this reaction: a homogeneous reaction mixture ensuring sufficient contact between all reactants and a catalyst system allowing for activation of the Pd precursor under aqueous conditions. Experiments under pressure reactor conditions with [(dtbpx)Pd(OTf)(2)] as catalyst precursor revealed the importance of nucleophile and reactant concentrations and the addition of the diprotonated diphosphine ligand (dtbpxH(2))(OTf)(2) to achieve turnover numbers >120. A variety of unsaturated fatty acids, including a triglyceride, were converted to valuable long-chain dicarboxylic acids with high turnover numbers and selectivities for the linear product of >90%. We unraveled the activation pathway of the Pd-II precursor, which proceeds via a reductive elimination step forming a Pd species and oxidative addition of the diprotonated diphosphine ligand, resulting in the formation of the catalytically active Pd hydride species. Theoretical calculations identified the hydrolysis as the rate-determining step. A low nucleophile concentration in the reaction mixture in combination with this high energetic barrier limits the potential of this reaction. In conclusion, water can be utilized as a nucleophile in isomerizing functionalization reactions and gives access to long-chain dicarboxylic acids from a variety of unsaturated substrates. The activity of the catalytic

Sugar Profile, Mineral Content, and Rheological and Thermal Properties of an Isomerized Sweet Potato Starch Syrup

OpenAIRE

Dominque, Brunson; Gichuhi, Peter N.; Rangari, Vijay; Bovell-Benjamin, Adelia C.

2013-01-01

Currently, corn is used to produce more than 85% of the world's high fructose syrup (HFS). There is a search for alternative HFS substrates because of increased food demand and shrinking economies, especially in the developing world. The sweet potato is a feasible, alternative raw material. This study isomerized a high glucose sweet potato starch syrup (SPSS) and determined its sugar profile, mineral content, and rheological and thermal properties. Rheological and thermal properties were meas...

Conformal and Nearly Conformal Theories at Large N

Science.gov (United States)

Tarnoplskiy, Grigory M.

In this thesis we present new results in conformal and nearly conformal field theories in various dimensions. In chapter two, we study different properties of the conformal Quantum Electrodynamics (QED) in continuous dimension d. At first we study conformal QED using large Nf methods, where Nf is the number of massless fermions. We compute its sphere free energy as a function of d, ignoring the terms of order 1/Nf and higher. For finite Nf we use the epsilon-expansion. Next we use a large Nf diagrammatic approach to calculate the leading corrections to CT, the coefficient of the two-point function of the stress-energy tensor, and CJ, the coefficient of the two-point function of the global symmetry current. We present explicit formulae as a function of d and check them versus the expectations in 2 and 4 - epsilon dimensions. In chapter three, we discuss vacuum stability in 1 + 1 dimensional conformal field theories with external background fields. We show that the vacuum decay rate is given by a non-local two-form. This two-form is a boundary term that must be added to the effective in/out Lagrangian. The two-form is expressed in terms of a Riemann-Hilbert decomposition for background gauge fields, and is given by its novel "functional'' version in the gravitational case. In chapter four, we explore Tensor models. Such models possess the large N limit dominated by the melon diagrams. The quantum mechanics of a real anti-commuting rank-3 tensor has a large N limit similar to the Sachdev-Ye-Kitaev (SYK) model. We also discuss the quantum mechanics of a complex 3-index anti-commuting tensor and argue that it is equivalent in the large N limit to a version of SYK model with complex fermions. Finally, we discuss models of a commuting tensor in dimension d. We study the spectrum of the large N quantum field theory of bosonic rank-3 tensors using the Schwinger-Dyson equations. We compare some of these results with the 4 - epsilon expansion, finding perfect agreement. We

Kinetics of Slurry Phase Fischer-Tropsch Synthesis

Energy Technology Data Exchange (ETDEWEB)

Dragomir B. Bukur; Gilbert F. Froment; Tomasz Olewski; Lech Nowicki; Madhav Nayapati

2006-12-31

The overall objective of this project is to develop a comprehensive kinetic model for slurry-phase Fischer-Tropsch synthesis (FTS) employing iron-based catalysts. This model will be validated with experimental data obtained in a stirred-tank slurry reactor (STSR) over a wide range of process conditions. Three STSR tests of the Ruhrchemie LP 33/81 catalyst were conducted to collect data on catalyst activity and selectivity under 25 different sets of process conditions. The observed decrease in 1-olefin content and increase in 2-olefin and n-paraffin contents with the increase in conversion are consistent with a concept that 1-olefins participate in secondary reactions (e.g. 1-olefin hydrogenation, isomerization and readsorption), whereas 2-olefins and n-paraffins are formed in these reactions. Carbon number product distribution showed an increase in chain growth probability with increase in chain length. Vapor-liquid equilibrium calculations were made to check validity of the assumption that the gas and liquid phases are in equilibrium during FTS in the STSR. Calculated vapor phase compositions were in excellent agreement with experimental values from the STSR under reaction conditions. Discrepancies between the calculated and experimental values for the liquid-phase composition (for some of the experimental data) are ascribed to experimental errors in the amount of wax collected from the reactor, and the relative amounts of hydrocarbon wax and Durasyn 164 oil (start-up fluid) in the liquid samples. Kinetic parameters of four kinetic models (Lox and Froment, 1993b; Yang et al., 2003; Van der Laan and Beenackers, 1998, 1999; and an extended kinetic model of Van der Laan and Beenackers) were estimated from experimental data in the STSR tests. Two of these kinetic models (Lox and Froment, 1993b; Yang et al., 2003) can predict a complete product distribution (inorganic species and hydrocarbons), whereas the kinetic model of Van der Laan and Beenackers (1998, 1999) can

Kinetics of Slurry Phase Fischer-Tropsch Synthesis

International Nuclear Information System (INIS)

Dragomir B. Bukur; Gilbert F. Froment; Tomasz Olewski; Lech Nowicki; Madhav Nayapati

2006-01-01

The overall objective of this project is to develop a comprehensive kinetic model for slurry-phase Fischer-Tropsch synthesis (FTS) employing iron-based catalysts. This model will be validated with experimental data obtained in a stirred-tank slurry reactor (STSR) over a wide range of process conditions. Three STSR tests of the Ruhrchemie LP 33/81 catalyst were conducted to collect data on catalyst activity and selectivity under 25 different sets of process conditions. The observed decrease in 1-olefin content and increase in 2-olefin and n-paraffin contents with the increase in conversion are consistent with a concept that 1-olefins participate in secondary reactions (e.g. 1-olefin hydrogenation, isomerization and readsorption), whereas 2-olefins and n-paraffins are formed in these reactions. Carbon number product distribution showed an increase in chain growth probability with increase in chain length. Vapor-liquid equilibrium calculations were made to check validity of the assumption that the gas and liquid phases are in equilibrium during FTS in the STSR. Calculated vapor phase compositions were in excellent agreement with experimental values from the STSR under reaction conditions. Discrepancies between the calculated and experimental values for the liquid-phase composition (for some of the experimental data) are ascribed to experimental errors in the amount of wax collected from the reactor, and the relative amounts of hydrocarbon wax and Durasyn 164 oil (start-up fluid) in the liquid samples. Kinetic parameters of four kinetic models (Lox and Froment, 1993b; Yang et al., 2003; Van der Laan and Beenackers, 1998, 1999; and an extended kinetic model of Van der Laan and Beenackers) were estimated from experimental data in the STSR tests. Two of these kinetic models (Lox and Froment, 1993b; Yang et al., 2003) can predict a complete product distribution (inorganic species and hydrocarbons), whereas the kinetic model of Van der Laan and Beenackers (1998, 1999) can

Conformal radiotherapy: principles and classification

International Nuclear Information System (INIS)

Rosenwald, J.C.; Gaboriaud, G.; Pontvert, D.

1999-01-01

'Conformal radiotherapy' is the name fixed by usage and given to a new form of radiotherapy resulting from the technological improvements observed during the last ten years. While this terminology is now widely used, no precise definition can be found in the literature. Conformal radiotherapy refers to an approach in which the dose distribution is more closely 'conformed' or adapted to the actual shape of the target volume. However, the achievement of a consensus on a more specific definition is hampered by various difficulties, namely in characterizing the degree of 'conformality'. We have therefore suggested a classification scheme be established on the basis of the tools and the procedures actually used for all steps of the process, i.e., from prescription to treatment completion. Our classification consists of four levels: schematically, at level 0, there is no conformation (rectangular fields); at level 1, a simple conformation takes place, on the basis of conventional 2D imaging; at level 2, a 3D reconstruction of the structures is used for a more accurate conformation; and level 3 includes research and advanced dynamic techniques. We have used our personal experience, contacts with colleagues and data from the literature to analyze all the steps of the planning process, and to define the tools and procedures relevant to a given level. The corresponding tables have been discussed and approved at the European level within the Dynarad concerted action. It is proposed that the term 'conformal radiotherapy' be restricted to procedures where all steps are at least at level 2. (author)

The tertiary origin of the allosteric activation of E. coli glucosamine-6-phosphate deaminase studied by sol-gel nanoencapsulation of its T conformer.

Directory of Open Access Journals (Sweden)

Sergio Zonszein

Full Text Available The role of tertiary conformational changes associated to ligand binding was explored using the allosteric enzyme glucosamine-6-phosphate (GlcN6P deaminase from Escherichia coli (EcGNPDA as an experimental model. This is an enzyme of amino sugar catabolism that deaminates GlcN6P, giving fructose 6-phosphate and ammonia, and is allosterically activated by N-acetylglucosamine 6-phosphate (GlcNAc6P. We resorted to the nanoencapsulation of this enzyme in wet silica sol-gels for studying the role of intrasubunit local mobility in its allosteric activation under the suppression of quaternary transition. The gel-trapped enzyme lost its characteristic homotropic cooperativity while keeping its catalytic properties and the allosteric activation by GlcNAc6P. The nanoencapsulation keeps the enzyme in the T quaternary conformation, making possible the study of its allosteric activation under a condition that is not possible to attain in a soluble phase. The involved local transition was slowed down by nanoencapsulation, thus easing the fluorometric analysis of its relaxation kinetics, which revealed an induced-fit mechanism. The absence of cooperativity produced allosterically activated transitory states displaying velocity against substrate concentration curves with apparent negative cooperativity, due to the simultaneous presence of subunits with different substrate affinities. Reaction kinetics experiments performed at different tertiary conformational relaxation times also reveal the sequential nature of the allosteric activation. We assumed as a minimal model the existence of two tertiary states, t and r, of low and high affinity, respectively, for the substrate and the activator. By fitting the velocity-substrate curves as a linear combination of two hyperbolic functions with Kt and Kr as KM values, we obtained comparable values to those reported for the quaternary conformers in solution fitted to MWC model. These results are discussed in the

S-Adenosylmethionine conformations in solution and in protein complexes: Conformational influences of the sulfonium group

DEFF Research Database (Denmark)

Markham, George D.; Norrby, Per-Ola; Bock, Charles W.

2002-01-01

S-Adenosylmethionine (AdoMet) and other sulfonium ions play central roles in the metabolism of all organisms. The conformational preferences of AdoMet and two other biologically important sulfonium ions, S-methylmethionine and dimethylsulfonioproprionic acid, have been investigated by NMR...... and computational studies. Molecular mechanics parameters for the sulfonium center have been developed for the AMBER force field to permit analysis of NMR results and to enable comparison of the relative energies of the different conformations of AdoMet that have been found in crystal structures of complexes...... with proteins. S-Methylmethionine and S-dimethylsulfonioproprionate adopt a variety of conformations in aqueous solution; a conformation with an electrostatic interaction between the sulfonium sulfur and the carboxylate group is not noticeably favored, in contrast to the preferred conformation found by in vacuo...

Conformal Killing vectors in Robertson-Walker spacetimes

International Nuclear Information System (INIS)

Maartens, R.; Maharaj, S.d.

1986-01-01

It is well known that Robertson-Walker spacetimes admit a conformal Killingl vector normal to the spacelike homogeneous hypersurfaces. Because these spacetimes are conformally flat, there are a further eight conformal Killing vectors, which are neither normal nor tangent to the homogeneous hypersurfaces. The authors find these further conformal Killing vectors and the Lie algebra of the full G 15 of conformal motions. Conditions on the metric scale factor are determined which reduce some of the conformal Killing vectors to homothetic Killing vectors or Killing vectors, allowing one to regain in a unified way the known special geometries. The non-normal conformal Killing vectors provide a counter-example to show that conformal motions do not, in general, map a fluid flow conformally. These non-normal vectors are also used to find the general solution of the null geodesic equation and photon Liouville equation. (author)

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

Science.gov (United States)

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.

Bicyclic Guanidine Catalyzed Asymmetric Tandem Isomerization Intramolecular-Diels-Alder Reaction: The First Catalytic Enantioselective Total Synthesis of (+)-alpha-Yohimbine.

Science.gov (United States)

Feng, Wei; Jiang, Danfeng; Kee, Choon-Wee; Liu, Hongjun; Tan, Choon-Hong

2016-02-04

Hydroisoquinoline derivatives were prepared in moderate to good enantioselectivities via a bicyclic guanidine-catalyzed tandem isomerization intramolecular-Diels-Alder (IMDA) reaction of alkynes. With this synthetic method, the first enantioselective synthesis of (+)-alpha-yohimbine was completed in 9 steps from the IMDA products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformal transformations in superspace

International Nuclear Information System (INIS)

Dao Vong Duc

1977-01-01

The spinor extension of the conformal algebra is investigated. The transformation law of superfields under the conformal coordinate inversion R defined in the superspace is derived. Using R-technique, the superconformally covariant two-point and three-point correlation functions are found

Towards conformal loop quantum gravity

International Nuclear Information System (INIS)

Wang, Charles H-T

2006-01-01

A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity

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

Science.gov (United States)

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.

Decomposition mechanisms and kinetics of novel energetic molecules BNFF-1 and ANFF-1: quantum-chemical modeling.

Science.gov (United States)

Tsyshevsky, Roman V; Kuklja, Maija M

2013-07-18

Decomposition mechanisms, activation barriers, Arrhenius parameters, and reaction kinetics of the novel explosive compounds, 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (BNFF-1), and 3-(4-amino-1,2,5-oxadiazol-3-yl)-4-(4-nitro-1,2,5-oxadiazol-3-yl)-1,2,5-oxadiazole (ANFF-1) were explored by means of density functional theory with a range of functionals combined with variational transition state theory. BNFF-1 and ANFF-1 were recently suggested to be good candidates for insensitive high energy density materials. Our modeling reveals that the decomposition initiation in both BNFF-1 and ANFF-1 molecules is triggered by ring cleavage reactions while the further process is defined by a competition between two major pathways, the fast C-NO₂ homolysis and slow nitro-nitrite isomerization releasing NO. We discuss insights on design of new energetic materials with targeted properties gained from our modeling.

Decomposition Mechanisms and Kinetics of Novel Energetic Molecules BNFF-1 and ANFF-1: Quantum-Chemical Modeling

Directory of Open Access Journals (Sweden)

Maija M. Kuklja

2013-07-01

Full Text Available Decomposition mechanisms, activation barriers, Arrhenius parameters, and reaction kinetics of the novel explosive compounds, 3,4-bis(4-nitro-1,2,5-oxadiazol-3-yl-1,2,5-oxadiazole (BNFF-1, and 3-(4-amino-1,2,5-oxadiazol-3-yl-4-(4-nitro-1,2,5-oxadiazol-3-yl-1,2,5-oxadiazole (ANFF-1 were explored by means of density functional theory with a range of functionals combined with variational transition state theory. BNFF-1 and ANFF-1 were recently suggested to be good candidates for insensitive high energy density materials. Our modeling reveals that the decomposition initiation in both BNFF-1 and ANFF-1 molecules is triggered by ring cleavage reactions while the further process is defined by a competition between two major pathways, the fast C-NO2 homolysis and slow nitro-nitrite isomerization releasing NO. We discuss insights on design of new energetic materials with targeted properties gained from our modeling.

Mass generation within conformal invariant theories

International Nuclear Information System (INIS)

Flato, M.; Guenin, M.

1981-01-01

The massless Yang-Mills theory is strongly conformally invariant and renormalizable; however, when masses are introduced the theory becomes nonrenormalizable and weakly conformally invariant. Conditions which recover strong conformal invariance are discussed in the letter. (author)

Conformal group actions and Segal's cosmology

International Nuclear Information System (INIS)

Werth, J.-E.

1984-01-01

A mathematical description of Segal's cosmological model in the framework of conformal group actions is presented. The relation between conformal and causal group actions on time-orientable Lorentzian manifolds is analysed and several examples are discussed. A criterion for the conformality of a map between Lorentzian manifolds is given. The results are applied to Segal's 'conformal compactification' of Minkowski space. Furthermore, the 'unitary formulation' of Segal's cosmology is regarded. (Author) [pt

Conformal field theories and critical phenomena

International Nuclear Information System (INIS)

Xu, Bowei

1993-01-01

In this article we present a brief review of the conformal symmetry and the two dimensional conformal quantum field theories. As concrete applications of the conformal theories to the critical phenomena in statistical systems, we calculate the value of central charge and the anomalous scale dimensions of the Z 2 symmetric quantum chain with boundary condition. The results are compatible with the prediction of the conformal field theories

New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.

Science.gov (United States)

Thach, Trung Thanh; Shin, Donghyuk; Han, Seungsu; Lee, Sangho

2016-04-01

The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

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

Science.gov (United States)

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.

Ward identities for conformal models

International Nuclear Information System (INIS)

Lazzarini, S.; Stora, R.

1988-01-01

Ward identities which express the symmetry of conformal models are treated. Diffeomorphism invariance or locally holomorphic coordinate transformations are used. Diffeomorphism invariance is then understood in terms of Riemannian geometry. Two different sets of Ward identities expressing diffeomorphism invariance in a conformally invariant way are found for the free bosonic string. Using a geometrical argument, the correct invariance for a large class of conformal models is given

A pH-dependent conformational ensemble mediates proton transport through the influenza A/M2 protein†

Science.gov (United States)

Polishchuk, Alexei L.; Lear, James D.; Ma, Chunlong; Lamb, Robert A.; Pinto, Lawrence H.; DeGrado, William F.

2010-01-01

The influenza A M2 protein exhibits inwardly rectifying, pH-activated proton transport that saturates at low pH. A comparison of high-resolution structures of the transmembrane domain at high and low pH suggests that pH-dependent conformational changes may facilitate proton conduction by alternately changing the accessibility of the N-terminal and C-terminal regions of the channel as a proton transits through the transmembrane domain. Here, we show that M2 functionally reconstituted in liposomes populates at least three different conformational states over a physiologically relevant pH range, with transition midpoints that are consistent with previously reported His37 pKas. We then develop and test two similar, quantitative mechanistic models of proton transport, where protonation shifts the equilibrium between structural states having different proton affinities and solvent accessibilities. The models account well for a collection of experimental data sets over a wide range of pHs and voltages and require only a small number of adjustable parameters to accurately describe the data. While the kinetic models do not require any specific conformation for the protein, they nevertheless are consistent with a large body of structural information based on high-resolution NMR and crystallographic structures, optical spectroscopy, and MD calculations. PMID:20968306

Conformity and statistical tolerancing

Science.gov (United States)

Leblond, Laurent; Pillet, Maurice

2018-02-01

Statistical tolerancing was first proposed by Shewhart (Economic Control of Quality of Manufactured Product, (1931) reprinted 1980 by ASQC), in spite of this long history, its use remains moderate. One of the probable reasons for this low utilization is undoubtedly the difficulty for designers to anticipate the risks of this approach. The arithmetic tolerance (worst case) allows a simple interpretation: conformity is defined by the presence of the characteristic in an interval. Statistical tolerancing is more complex in its definition. An interval is not sufficient to define the conformance. To justify the statistical tolerancing formula used by designers, a tolerance interval should be interpreted as the interval where most of the parts produced should probably be located. This tolerance is justified by considering a conformity criterion of the parts guaranteeing low offsets on the latter characteristics. Unlike traditional arithmetic tolerancing, statistical tolerancing requires a sustained exchange of information between design and manufacture to be used safely. This paper proposes a formal definition of the conformity, which we apply successively to the quadratic and arithmetic tolerancing. We introduce a concept of concavity, which helps us to demonstrate the link between tolerancing approach and conformity. We use this concept to demonstrate the various acceptable propositions of statistical tolerancing (in the space decentring, dispersion).

Dissecting the large-scale galactic conformity

Science.gov (United States)

Seo, Seongu

2018-01-01

Galactic conformity is an observed phenomenon that galaxies located in the same region have similar properties such as star formation rate, color, gas fraction, and so on. The conformity was first observed among galaxies within in the same halos (“one-halo conformity”). The one-halo conformity can be readily explained by mutual interactions among galaxies within a halo. Recent observations however further witnessed a puzzling connection among galaxies with no direct interaction. In particular, galaxies located within a sphere of ~5 Mpc radius tend to show similarities, even though the galaxies do not share common halos with each other ("two-halo conformity" or “large-scale conformity”). Using a cosmological hydrodynamic simulation, Illustris, we investigate the physical origin of the two-halo conformity and put forward two scenarios. First, back-splash galaxies are likely responsible for the large-scale conformity. They have evolved into red galaxies due to ram-pressure stripping in a given galaxy cluster and happen to reside now within a ~5 Mpc sphere. Second, galaxies in strong tidal field induced by large-scale structure also seem to give rise to the large-scale conformity. The strong tides suppress star formation in the galaxies. We discuss the importance of the large-scale conformity in the context of galaxy evolution.

Entanglement evolution across a conformal interface

Science.gov (United States)

Wen, Xueda; Wang, Yuxuan; Ryu, Shinsei

2018-05-01

For two-dimensional conformal field theories (CFTs) in the ground state, it is known that a conformal interface along the entanglement cut can suppress the entanglement entropy from to , where L is the length of the subsystem A, and is the effective central charge which depends on the transmission property of the conformal interface. In this work, by making use of conformal mappings, we show that a conformal interface has the same effect on entanglement evolution in non-equilibrium cases, including global, local and certain inhomogeneous quantum quenches. I.e. a conformal interface suppresses the time evolution of entanglement entropy by effectively replacing the central charge c with , where is exactly the same as that in the ground state case. We confirm this conclusion by a numerical study on a critical fermion chain. Furthermore, based on the quasi-particle picture, we conjecture that this conclusion holds for an arbitrary quantum quench in CFTs, as long as the initial state can be described by a regularized conformal boundary state.

Tuning light-emitting properties of N-phenylcarbazole-capped anthrylvinyl derivatives by symmetric and isomeric effects

Energy Technology Data Exchange (ETDEWEB)

Hu, Qingli; Wang, Jianfeng; Yin, Ling; Chen, Mingshuai [Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao 266042 (China); Xue, Shanfeng, E-mail: sfxue@qust.edu.cn [Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao 266042 (China); State Key Laboratory of Luminescent Materials and Devices, Institute of Polymer Optoelectronic Materials and Devices, South China University of Technology, Guangzhou 510640 (China); Yang, Wenjun, E-mail: ywjph2004@qust.edu.cn [Key Laboratory of Rubber-Plastics of Ministry of Education/Shandong Province (QUST), School of Polymer Science & Engineering, Qingdao University of Science & Technology, 53-Zhengzhou Road, Qingdao 266042 (China)

2017-03-15

This paper focuses on effects of molecular symmetry and isomerisation on light-emitting properties based on N-phenylcarbazole-capped anthrylvinyl derivatives. We have designed and synthesized three isomeric 10-(arylvinyl)anthracenes with N-phenylcarbazole as the mono aryl moiety whose 2-, 3-, or carbazole-9-yl-phenyl positions are linked, and their optical and electroluminescence properties are investigated and compared with analogous 9,10-bis(arylvinyl)anthracenes. The results showed that, contrary to the dual N-phenylcarbazole-capped analogues, the three mono N-phenylcarbazole-capped isomers have neither aggregation-induced emission nor mechanofluorochromism although they are characterized by twisted π-backbone and grinding-induced amorphization. It is observed that the mono substitution can significantly blue-shift the emission spectra and greatly improve the electroluminescence performances, accompanying by the remarkably isomeric effect. This finding demonstrates that changing the molecular substitution patterns could effectively alter and tune the light-emitting properties to greatly widen the scope of molecular candidates applicable in optical and optoelectronic fields. - Highlights: • Three monoN-phenylcarbazole-capped 10-vinylanthracenes are designed to investigate the geometric symmetry and isomer effects. • The three backbone-twisted luminogens do not exhibit AIE and MFC activity. • The grinding-induced amorphization does not necessarily cause the change in fluorescence color. • 10-Arylvinylanthracenes show the better EL performances than 9,10-di(aryl- vinyl)anthracenes. • Subtly manipulating molecular geometric symmetry could tune and alter the solid-state aggregation and stimuli-responsive behaviors.

Multi-arrangement quantum dynamics in 6D: cis-trans isomerization and 1,3-hydrogen transfer in HONO