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DERIVATION OF INTERMOLECULAR INTERACTION POTENTIAL FUNCTIONS BASED ON THE CAMBRIDDGE STRUCTURAL DATABASE

基于剑桥结构数据库的分子间相互作用势函数的推导

基本信息

批准号：
10304052
负责人：
OSAWA Eiji
金额：
$ 3.39万
依托单位：
TOYOHASHI UNIVERSITY OF TECHNOLOGY
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (A)
财政年份：
1998
资助国家：
日本
起止时间：
1998 至 2000
项目状态：
已结题

项目摘要

Derivation of intermolecular potential functions for the atomistic simulation has met difficulties due the lack of appropriate models for intermolecular forces. We propose here an entirely new and non-empirical approach to this problem, which uses Cambridge Structural Database as the source of information on the intermolecular interactions among organic molecules. The method uses inverse probability density distribution of the 3D geometry of pertinent structural fragments to convert structural information into energy functions. We tested the idea by using C=O...H-O ketone/alcohol hydrogen bonding as a test case and modeled its 3D energy surface.Version 5.16 of CSD was used which contains more than 190,000 crystal structures of organic compounds. Hydrogen bonding structural fragments (631) with high quality were extracted and the distributions of their structural parameters were fit the known potential functions of hydrogen bonding. We found that a combination of modified Lippincott-Sch … More roder potential for bond stretch, single Gaussian for out-of-plane deformation and a linear combination of two Gaussian functions for in-plane deformation fits best.The first 3D potential function set for the C=O...H-O type hydrogen bond satisfactorily reproduced the well-known 3D energy surface having shallow and double minima along the direction of non-bonded orbitals on a carbonyl group. Extension of this procedure for other types and forms of intermolecular interactions should provide a set of potential functions and a set of appropriate parameters useful for realistic simulations, especially for the dynamic behaviors of bio-molecules including proteins, sugars and DNA. It is well-recognized that by far the most important but the least understood among the steric terms is the intermolecular interactions, but our approach should give a realistic solution to this problem.One of the ambitious applications of the force field that we will eventually obtain will be a priori determination of crystal structure from chemical formula alone. Less

由于缺乏合适的分子间力模型，原子模拟分子间势函数的推导遇到了困难。我们在此提出了一种全新的非经验方法来解决这个问题，该方法使用剑桥结构数据库作为有机分子间相互作用的信息来源。该方法利用相关结构碎片三维几何的逆概率密度分布，将结构信息转化为能量函数。我们以C=O…H-O酮/醇氢键为例，对这一想法进行了验证，并对其三维能面进行了建模。使用CSD 5.16版本，其中包含超过190,000种有机化合物的晶体结构。提取了高质量的氢键结构片段（631），其结构参数的分布符合已知的氢键势函数。我们发现结合修正的lippincottt - sch…More roder势用于键拉伸，单高斯函数用于面外变形，两个高斯函数用于面内变形的线性组合是最合适的。C=O…H-O型氢键的第一个三维势函数集令人满意地再现了羰基上沿非键轨道方向具有浅最小值和双最小值的众所周知的三维能面。将这一过程扩展到其他类型和形式的分子间相互作用，应该提供一组对现实模拟有用的潜在函数和一组适当的参数，特别是对包括蛋白质、糖和DNA在内的生物分子的动态行为。众所周知，到目前为止，分子间相互作用是最重要但又最不为人所知的空间项，但我们的方法应该给出一个现实的解决方案。我们最终将获得的力场的一个雄心勃勃的应用将是仅从化学式先验地确定晶体结构。少