Calix[4]arene-based ditopic receptor for dicarboxylates

Shape-selective recognition for the dicarboxylates in DMSO can be attained by a new calix[4]arene-based receptor 1 having two urea groups. Biologically active chorismate selectively bound in 1 over its dehydrated derivative. Molecular mechanics calculations gave a plausible explanation for the selective binding.     

Internal dynamics of flexible molecules: Cyclohexane

Summary The international motions of a single cyclohexane molecule are studied by molecular dynamics calculations. Classical trajectories are calculated by integrating Newton's equation of motion. The potential functions used are essentially the same as in Allinger's MM2 program which is widely applied for calculations on conformational energies of organic molecules.Geometries and relative energies are reported for all stable low energy conformers and some transition states of cyclohexane. Vibrational frequencies of classical oscillations of individual bonds — computed for ethane as reference system — are close to the experimental values.Two trajectories of the molecular dynamics of cyclohexane were simulated. In the first we were able to follow the process of ring inversion: chair twisted forms inverted chair. The reaction path is analysed in detail and compared with static approaches. The second trajectory shows the correlated reorientation of the possible twisted forms alone. This process is known as pseudorotation.Dedicated to Prof. Dr. Karl Schlögl     

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K.     

Effective atom volumes for implicit solvent models: comparison between Voronoi volumes and minimum fluctuation volumes

An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001     

Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations

Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH₃X, CF₃X, CCl₃X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7.     

缩聚合成聚芳酯和聚酯－聚醚弹性体的微相复合物

通过原位直接缩聚反应，制备了刚性棒状聚对羟基苯甲酸酯（ＰＨＢ）和聚对苯二甲酸丁二醇酯－聚四亚甲基醚多嵌段共聚物（ＰＢＴ－ＰＴＭＧ）的微相复合物．复合物可溶于氯仿等溶剂，可以浇铸成膜．本文研究了ＰＨＢ含量和聚合过程中，基体聚合物溶液浓度对微相复合物形态以及力学性能影响．同共混法相比，原位缩聚法可得到分散更均匀，力学性能更优良的微相复合物．     

Atomistic Simulation Study of Calcium,Phosphate and Fluoride Ion Association to the Teleopeptide‐Tails of Collagen – Initial Steps to Biomineral Formation

The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.     

聚N-异丙基丙烯酰胺溶液的粘度的温度依赖关系

用自由基聚合法合成了聚Ｎ 异丙基丙烯酰胺（ＰＮＩＰＡＡＭ）样品，用乌氏粘度计考查了该聚合物的四氢呋喃（ＴＨＦ）溶液和水溶液的粘度与温度的依赖关系．发现ＰＮＩＰＡＡＭ ＴＨＦ体系的特性粘数随温度升高而增大，ＰＮＩＰＡＡＭ Ｈ２Ｏ体系的特性粘数 温度曲线表现出较为复杂的变化规律．并用实验确定的特性粘数对合成样品的分子量进行了表征Ｍｎ＝８４４×１０５ｇ·ｍｏｌ－１．     

含铅聚合物微凝胶与硫化氢反应前后在良溶剂中的分子扩散行为

用溶液聚合法制备出轻度交联的含铅微凝胶,用光子相关光谱技术测定其在良溶剂中与H2S反应前、后的扩散行为,由外推法得到在浓度无限稀时的分子扩散系数,给出微凝胶的流体力学半径。结果表明:相同量的含铅微凝胶在不同的初始浓度下与H2S反应,生成含PbS纳米微粒的凝胶；但其体积增大不同,这说明H2S与含铅微凝胶的反应既可以在分子内也可以在分子间进行,分子间的反应使含硫化铅微凝胶扩散系数随浓度的变化曲线的线性范围变小。     

用计算模拟方法研究Al_3P_4O_(16)~(3-)计量比的二维层状磷酸铝中的有机胺模板能力

将快速 Monte Carlo方法与分子动力学方法相结合 ,研究了不同种类有机分子在 Al3P4 O3- 1 6 计量比的二维层状磷酸铝形成中的模板能力 .依据主 -客体之间非键相互作用能 (包括范德华能、氢键能和库仑能 ) ,可合理地解释已知实验现象 ,并能有效地预测出适于形成某一特定无机层结构的有机胺模板剂 .通过选择理论预测的有机胺分子作为模板剂 ,成功地合成了二维层状磷酸铝化合物 Al3P4 O1 6 · 1 .5 H3NC6 H1 0 NH3.