Thermodynamics of liquid Fe-Si and Fe-Ge alloys

The enthalpies of mixing of liquid binary Fe-Ge (1765±5 K) and Fe-Si (1750±5 K) alloys were determined using a high-temperature isoperibolic calorimeter. The thermodynamic properties of Fe-Ge melts were also studied by electromotive force method in the temperature range of 1250-1580 K. The comparison of our measurement results with literature data has been performed. The extreme negative values of integral enthalpy of mixing and alternating-sign deviations from Raoult's low for germanium can be explained by the influence of binary clusters formation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Radical addition reactions: factors determining the transition-state geometry

Interatomic distances in the reaction centers of the addition reactions of (i) H^· to the C=C, C=O, N≡C, and C≡C bonds, (ii) ^·CH₃ radical to the C=C, C=O, and C≡C bonds, and (iii) alkyl, aminyl, and alkoxyl radicals to olefin C=C bonds were determined using a new semiempirical method for calculating transition-state geometries of radical reactions. For all reactions of the type X^· + Y=Z → X— Y—Z^· the r ^# _X...Y distance in the transition state is a linear function of the enthalpy of reaction. Parameters of this dependence were determined for seventeen classes of radical addition reactions. The bond elongation, Δr ^# _X...Y, in the transition state decreases as the triplet repulsion, electronegativity difference between the atoms X and Y in the reaction center, and the force constant of the attacked multiple bond increase. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 894–902, April, 2005.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

A revised quantum chemistry-based potential for poly(ethylene oxide) and its oligomers in aqueous solution

We have conducted a high-level quantum chemistry study of the interactions of 1,2-dimethoxyethane (DME) with water for complexes representing both hydrophilic and hydrophobic hydration. It was found that our previous quantum chemistry-based force field for poly(ethylene oxide) (PEO) and its oligomers in aqueous solution did a poor job in describing the hydrophobic binding of water to the ether, consistent with our recent calculations of the excess free energy and entropy of hydration of DME. Our original force field was revised to more accurately reproduce the interaction of water with the carboneous portions of DME. Molecular dynamics simulations of aqueous DME solutions using the revised quantum chemistry-based potential yielded good agreement with experiment for excess free energy, enthalpy, and volume as well as excess solution viscosity and the self-diffusion of water. Comparison with our original potential revealed that the relatively hydrophobic ether-water interactions in the new potential strongly reduced the favorable excess free energy and enthalpy but have relatively little influence on the excess entropy for dilute DME solutions. Other properties of DME and PEO solutions including conformational populations and dynamics, solution viscosity, hydrogen bonding, water translational and rotational diffusion and neutron structure factor as a function of solution composition were found to be largely unchanged from those obtained using the original potential.     

分子力场进展

分子力学（简称ＭＭ）是近年来化学家常用的一种计算方法。与量子力学从头计算和半经验方法相比，用分子力学处理大分子可以大大节省计算时间，而且，在大多数情况下，用分子力学方法计算得到的分子几何构型参数与实验值之间的差值可在实验误差范围之内。所以，分子力学是研究生物化学体系的有效和可行的手段。分子力学的核心是分子力场。本文介绍了分子力场的量子力学背景、分子力场和光谱力场之间的关系。分子力场的一般形式、分力     

Analogy in adsorption behavior of homopolyelectrolyte mixtures as compared to analogous diblock polyampholytes

The adsorption behavior of aqueous mixtures of the homopolyelectrolytes poly(methacrylic acid) (PMAA) and poly[(dimethylamino)ethyl methacrylate] (PDMAEMA) was investigated in comparison with the adsorption of the ampholytic diblock copolymer PMAA‐b‐PDMAEMA on silicon substrates. Ellipsometry was used to determine the amount of adsorbed homopolyelectrolyte and diblock polyampholyte. Furthermore, the topography of the adsorbed polymers was investigated with atomic force microscopy (AFM) and compared with the structures observed in aqueous solutions by dynamic light scattering (DLS). For all types of investigated polyelectrolytic mixtures or the single polyampholyte, the adsorption was strongly influenced by the pH of the polymer solution. Although single homopolyelectrolytes showed only one maximum in adsorption according to their charge, the mixtures made from these homopolyelectrolytes showed two or three maxima. The third maximum near the isoelectric point of the mixture was assigned to a new species formed by aggregation of the two homopolyelectrolytes. Altogether, the adsorption behavior of the polyelectrolytic mixtures was in between the behavior of the pure homopolyelectrolytes and the analogous polyampholytes and therefore understandable from both of these polymer species. © 2002 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 40: 338–345, 2002; DOI 10.1002/polb.10091     

牛血清白蛋白与十二烷基硫酸钠作用的机理

利用电动势法得到了牛血清白蛋白(BSA)与十二烷基硫酸钠(SDS)相互作用的结合等温线. 通过四阶导数紫外光谱法和荧光光谱法研究了相互作用过程中芳香族氨基酸残基微环境极性的变化. 通过研究发现, 随着SDS浓度的逐渐增大, SDS在BSA上的平均结合数(v)逐渐增大, 色氨酸(Trp)残基所处微环境的极性在减弱后保持基本不变, 酪氨酸残基所处微环境的极性在明显增强后稍有减弱, 苯丙氨酸残基所处微环境的极性略有增强. 结果表明, 当v由0增大到14时, SDS主要结合在BSA的Trp-213附近并逐渐形成聚集体, 从而诱导BSA由结构域ⅡA 开始逐渐展开. 此后, SDS呈正协同作用的特点与BSA 结合, v急剧增大. 当v约为302 时, SDS在BSA上的结合基本达到饱和, BSA的构象趋于稳定.     

牛血清白蛋白与十二烷基硫酸钠作用的机理

利用电动势法得到了牛血清白蛋白(BSA)与十二烷基硫酸钠(SDS)相互作用的结合等温线. 通过四阶导数紫外光谱法和荧光光谱法研究了相互作用过程中芳香族氨基酸残基微环境极性的变化. 通过研究发现, 随着SDS浓度的逐渐增大, SDS在BSA上的平均结合数(v)逐渐增大, 色氨酸(Trp)残基所处微环境的极性在减弱后保持基本不变, 酪氨酸残基所处微环境的极性在明显增强后稍有减弱, 苯丙氨酸残基所处微环境的极性略有增强. 结果表明, 当v由0增大到14时, SDS主要结合在BSA的Trp-213附近并逐渐形成聚集体, 从而诱导BSA由结构域ⅡA 开始逐渐展开. 此后, SDS呈正协同作用的特点与BSA 结合, v急剧增大. 当v约为302 时, SDS在BSA上的结合基本达到饱和, BSA的构象趋于稳定.     

Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.