排序方式: 共有74条查询结果,搜索用时 203 毫秒
61.
Alissa Wiengarten Julian A. Lloyd Dr. Knud Seufert Dr. Joachim Reichert Dr. Willi Auwärter Runyuan Han Dr. David A. Duncan Dr. Francesco Allegretti Dr. Sybille Fischer Dr. Seung Cheol Oh Dr. Özge Sağlam Li Jiang Dr. Saranyan Vijayaraghavan Dr. David Écija Dr. Anthoula C. Papageorgiou Prof. Dr. Johannes V. Barth 《Chemistry (Weinheim an der Bergstrasse, Germany)》2015,21(35):12285-12290
Selectivity in chemical reactions is a major objective in industrial processes to minimize spurious byproducts and to save scarce resources. In homogeneous catalysis the most important factor which determines selectivity is structural symmetry. However, a transfer of the symmetry concept to heterogeneous catalysis still requires a detailed comprehension of the underlying processes. Here, we investigate a ring‐closing reaction in surface‐confined meso‐substituted porphyrin molecules by scanning tunneling microscopy, temperature‐programmed desorption, and computational modeling. The identification of reaction intermediates enables us to analyze the reaction pathway and to conclude that the symmetry of the porphyrin core is of pivotal importance regarding product yields. 相似文献
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Alissa M. Chan Laura A. Peña Rosa E. Segura Ramya Auroprem Brent M. Harvey Caroline M. Brooke Patrick E. Hoggard 《Photochemistry and photobiology》2013,89(2):274-279
Dissolved hexachlororuthenate(IV) effectively catalyzes the photodecomposition of chloroform to hydrogen chloride and phosgene under near‐UV (λ > 345 nm) irradiation, whereby RuCl62? is not itself photocatalytically active, but is photochemically transformed into a species that is active, possibly RuCl5(CHCl3)?. Conversion to a photoactive species during irradiation is consistent with the acceleration of the decomposition rate during the early stages and with the apparent inverse dependence of the decomposition rate on the initial concentration of RuCl62?. The displacement of Cl? by CHCl3 in the coordination sphere to create the photoactive species is consistent with the retardation of photodecomposition by both Cl? and H2O. The much smaller photodecomposition rate in CDCl3 suggests that C–H bond dissociation occurs during the primary photochemical event, which is also consistent with the presence of a CHCl3 molecule in the first coordination sphere. 相似文献
64.
End-to-end contact formation rates of several peptides were recently measured by tryptophan triplet quenching (Lapidus et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220). Motivated by these experiments, we study loop-closure kinetics for two peptides of different lengths, Cys-(Ala-Gly-Gln)n-Trp (n = 1, 2), in multiple all-atom explicit-solvent molecular dynamics simulations with different initial conditions and force fields. In 150 simulations of approximately 20 ns each, we collect data covering 1.0 and 0.8 micros for the penta-peptide simulated with the AMBER and CHARMM force fields, respectively, and about 0.5 micros each with the two force fields for the octa-peptide. These extensive simulations allow us to analyze the dynamics of peptides in the unfolded state with atomic resolution, thus probing early events in protein folding, and to compare molecular dynamics simulations directly with experiment. The calculated lifetimes of the tryptophan triplet state are in the range of 50-100 ns, in agreement with experimental measurements. However, end-to-end contacts form more rapidly, with characteristic times less than 10 ns. The contact formation rates for the two force fields are similar despite differences in the respective ensembles of peptide conformations. 相似文献
65.
Hummer G 《The Journal of chemical physics》2004,120(2):516-523
Transition states are defined as points in configuration space with the highest probability that trajectories passing through them are reactive (i.e., form transition paths between reactants and products). In the high-friction (diffusive) limit of Langevin dynamics, the resulting ensemble of transition states is shown to coincide with the separatrix formed by points of equal commitment (or splitting) probabilities for reaching the product and reactant regions. Transition states according to the new criterion can be identified directly from equilibrium trajectories, or indirectly by calculating probability densities in the equilibrium and transition-path ensembles using umbrella and transition-path sampling, respectively. An algorithm is proposed to calculate rate coefficients from the transition-path and equilibrium ensembles by estimating the frequency of transitions between reactants and products. 相似文献
66.
D.G. Hummer 《Journal of Quantitative Spectroscopy & Radiative Transfer》1982,27(6):569-573
Analytical expressions are given for the coefficients, as a function of the Voigt parameter a, in the asymptotic expansions of the kernel functions K1(π), K2(π), M1(π), and M2(π) that describe the transfer of radiation scattered with complete redistribution over a Voigt profile. 相似文献
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The time, temperature, and sequence dependences of helix formation kinetics of fully atomistic peptide models in explicit solvent are described quantitatively by a diffusive search within the coil state with barrierless transitions into the helical state. Conformational diffusion leads to nonexponential kinetics and jump-width dependences in temperature jump experiments. 相似文献
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Shubert VA Baquero EE Clarkson JR James WH Turk JA Hare AA Worrel K Lipton MA Schofield DP Jordan KD Zwier TS 《The Journal of chemical physics》2007,127(23):234315
Resonant two-photon ionization (R2PI), resonant ion-dip infrared (RIDIR), and UV-UV hole-burning spectroscopies have been employed to obtain conformation-specific infrared and ultraviolet spectra under supersonic expansion conditions for O-(2-acetamidoethyl)-N-acetyltyramine (OANAT), a doubly substituted aromatic in which amide-containing alkyl and alkoxy side chains are located in para positions on a phenyl ring. For comparison, three single-chain analogs were also studied: (i) N-phenethyl-acetamide (NPEA), (ii) N-(p-methoxyphenethyl-acetamide) (NMPEA), and (iii) N-(2-phenoxyethyl)-acetamide (NPOEA). Six conformations of OANAT have been resolved, with S(0)-S(1) origins ranging from 34,536 to 35,711 cm(-1), denoted A-F, respectively. RIDIR spectra show that conformers A-C each possess an intense, broadened amide NH stretch fundamental shifted below 3400 cm(-1), indicative of the presence of an interchain H bond, while conformers D-F have both amide NH stretch fundamentals in the 3480-3495 cm(-1) region, consistent with independent-chain structures with two free NH groups. NPEA has a single conformer with S(0)-S(1) origin at 37,618 cm(-1). NMPEA has three conformers, two that dominate the R2P1 spectrum, with origin transitions between 35,580 and 35,632 cm(-1). Four conformations, one dominate and three minor, of NPOEA have been resolved with origins between 35,654 and 36,423 cm(-1). To aid the making of conformational assignments, the geometries of low-lying structures of all four molecules have been optimized and the associated harmonic vibrational frequencies calculated using density functional theory (DFT) and RIMP2 methods. The S(0)-S(1) adiabatic excitation energies have been calculated using the RICC2 method and vertical excitation energies using single-point time-dependent DFT. The sensitivity of the S(0)-S(1) energy separation in OANAT and NPOEA primarily arises from different orientations of the chain attached to the phenoxy group. Using the results of the single-chain analogs, tentative assignments have been made for the observed conformers of OANAT. The RIMP2 calculations predict that interchain H-bonded conformers of OANAT are 25-30 kJ/mol more stable than the extended-chain structures. However, the free energies of the interchain H-bonded and extended structures calculated at the preexpansion temperature (450 K) differ by less than 10 kJ/mol, and the number of extended structures far outweighs the number of H-bonded conformers. This entropy-driven effect explains the presence of the independent-chain conformers in the expansion, and cautions future studies that rely solely on relative energies of conformers in considering possible assignments. 相似文献
69.
Francis DM Różycki B Tortajada A Hummer G Peti W Page R 《Journal of the American Chemical Society》2011,133(43):17138-17141
The MAP kinase ERK2 (ERK2, extracellular signal-regulated kinase 2) is regulated by numerous phosphatases that tightly control its activity. For example, the hematopoietic tyrosine phosphatase (HePTP) negatively regulates T cell activation in lymphocytes via ERK2 dephosphorylation. However, only very limited structural information is available for these biologically important complexes. Here, we use small-angle X-ray scattering combined with EROS ensemble refinement to characterize the structures of the resting and active states of ERK2:HePTP complexes. Our data show that the resting state ERK2:HePTP complex adopts a highly extended, dynamic conformation that becomes compact and ordered in the active state complex. This work experimentally demonstrates that these complexes undergo significant dynamic structural changes in solution and provides the first structural insight into an active state MAPK complex. 相似文献
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In theory and in the analysis of experiments, protein folding is often described as diffusion along a single coordinate. We explore here the application of a one-dimensional diffusion model to interpret simulations of protein folding, where the parameters of a model that "best" describes the simulation trajectories are determined using a Bayesian analysis. We discuss the requirements for such a model to be a good approximation to the global dynamics, and several methods for testing its accuracy. For example, one test considers the effect of an added bias potential on the fitted free energies and diffusion coefficients. Such a bias may also be used to extend our approach to determining parameters for the model to systems that would not normally explore the full coordinate range on accessible time scales. Alternatively, the propagators predicted from the model at different "lag" times may be compared with observations from simulation. We then present some applications of the model to protein folding, including Kramers-like turnover in folding rates of coarse-grained models, the effect of non-native interactions on folding, and the effect of the chosen coordinate on the observed position-dependence of the diffusion coefficients. Lastly, we consider how our results are useful for the interpretation of experiments, and how this type of Bayesian analysis may eventually be applied directly to analyse experimental data. 相似文献