Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.     

A density functional study of propylene glycol conversion to propanal and propanone of various acid-catalyzed reaction models: a water-addition effect

The acid-catalyzed models on reaction mechanisms of pinacol rearrangement of propylene glycol conversion to propanal and propanone have been investigated using the density functional method at 298.15 K. Thermodynamic quantities of activation steps of four water-addition models were obtained. The number of added water interacting with the transition states of three concerted pathways has obviously affected the product ratio. The relative energetic profiles of the conversion reactions of all solvation models have been comparatively displayed. Estimation of the percent ratio of product composition computed from activation free energies of each acid-catalyzed reaction model was carried out. The percent ratios of propanal and propanone were decreased as the number of added water increased.     

Markov processes in single molecule fluorescence

This article examines the current status of Markov processes in single molecule fluorescence. For molecular dynamics to be described by a Markov process, the Markov process must include all states involved in the dynamics and the first-passage time (FPT) distributions out of those states must be describable by a simple exponential law. The observation of non-exponential FPT distributions or other evidence of non-Markovian dynamics is common in single molecule studies and offers an opportunity to expand the Markov model to include new dynamics or states that improve understanding of the system.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Effect of combining rules for cubic equations of state on the prediction of double retrograde vaporization

In this work, the phenomenon of double retrograde vaporization (DRV) is simulated using the Peng–Robinson equation of state with the classical mixing rules and several combining rules for the cross-energy and cross-co-volume parameters. The binary interaction parameters are set equal to zero in all cases, i.e., the calculations are entirely predictive. An interesting conclusion is that the predictions using the classical combining rules (geometric mean rule for a_ij and arithmetic mean rule for b_ij) provide the best agreement with the experimental data for all the systems tested: methane + n-butane, methane + n-pentane, ethane + limonene, and ethane + linalool. Another interesting observation is that several combining rules for b_ij, other than the arithmetic mean rule, predict the existence of three phases in equilibrium in a very narrow temperature range close to the critical temperature of methane in the methane + n-pentane system, even though, literature data indicates that n-hexane is the first n-alkane to present partial liquid phase immiscibility with methane.     

Molar mass distributions by gradient liquid chromatography: predicting and tailoring selectivity

Interactive liquid chromatography (iLC) for polymer analysis is usually applied to the characterisation of distributions other than molar mass. In particular, its use for the determination of chemical-composition, functionality-type and tacticity distributions has been demonstrated. The application of iLC for the determination of molar mass distributions (MMDs), however, has not yet been fully explored. An expanded version of the reversed-phase liquid chromatography model has been developed to describe and predict how the retention behaviour of polydisperse polystyrene samples changes with molar mass. The relationship between molar mass and the parameters of the model has been investigated in some detail and non-linear correlations were found. From the model and the relationships between the model parameters and molar mass, calibration curves (retention time versus molar mass) were constructed to predict changes in chromatographic selectivity across a given molar mass range. These calibration curves were compared to experimentally obtained curves and, in most cases, excellent agreement was found. The dramatic enhancement in selectivity that can be obtained with iLC in comparison to size-exclusion chromatography (SEC) was illustrated by measuring matrix-assisted laser desorption ionisation (MALDI) MS spectra of fractions collected during a gradient-LC separation. In the low-molar mass range, essentially monodisperse fractions were obtained. Calibration curves, predicted by the model and validated experimentally using narrow-dispersity standards and MALDI-MS spectra of fractions, were used to determine the molar mass distribution of some narrowly distributed polystyrene samples. Molar mass distributions for such standards were found to be somewhat lower than the values reported by the manufacturers. The results also deviated from those obtained by MALDI-MS.     

Zur Chemie der Pyrrolpigmente, 54. Mitt.: Phytochrommodellstudien: Ein 2,3-Dihydrobilatrien-abc-3-Cholesterylderivat

The diastereomeric 2,3-Dihydrobilatrienes-abc derivatives (4Z, 9Z, 15Z)-7 and (4Z, 9Z, 15E)-7 bearing a cholesterylacetate moiety in position 3 of the chromophore are prepared. The reaction sequence contains an isomerisation step providing quantitative enantioselective formation of the chiral center in position 3. Configurations and conformations of the diastereomers are elucidated using¹H- and¹³C-NMR spectra, NOE-difference spectra, 2D-NMR experiments (NOESY) and arguments from UV-VIS and CD data. It is concluded that the hydrophobic interactions between chromophore and cholesteryl-fragment yield a compact conformation where the two substructures are in close contact with each other. On the other hand these interactions seem to be too weak to induce significant changes in the chemistry, absorption spectra and conformational characterics of the bile pigment chromophore. Therefore hydrophobic interactions between chromophor and apolar amino acid residues of the protein in phytochrome should be of minor relevance for determining spectroscopic shifts.

     

胶束催化及胶束模拟酶性能的研究

本文对胶束催化的有机反应进行综述,并对其模拟酶的催化功能作了评论。     

Simple correction for perturbations of peak amplitudes in statistical models of overlap

Summary The application of statistical models of overlap (SMOs) to saturated separations is made possible by theory that addresses variable peak amplitudes. These amplitudes cause peak widths to vary, and this variation can be modeled by a random variable whose effect on the probability of overlap is expressed by a convolution integral. Modified probabilities of overlap are derived for both homogeneous and nonhomogeneous one-dimensional separations, and the new probabilities are compared to results determined from published computer simulations. The new theory can describe overlap at saturations that are 3 to 4 times larger than before. Previously reported experimental chromatograms are reinterpreted to show the capabilities of theory. The theoretical extension is an important step towards making SMOs into practical tools for screening analytical separations.     

Oxazinins from toxic mussels: isolation of a novel oxazinin and reassignment of the C-2 configuration of oxazinin-1 and -2 on the basis of synthetic models

The analysis of a batch of toxic mussels (Mytilus galloprovincialis) from the Northern Adriatic Sea led to the isolation of a novel oxazinin, oxazinin-4. Its structure including the relative stereochemistry has been elucidated through extensive NMR analysis. A synthetic route to oxazinins has been crucial in establishing the absolute stereochemistry of oxazinin-4 and for reassigning the absolute C-2 configuration of oxazinin-1 and -2 previously isolated from toxic shellfish and stereostructurally characterized.