Realization of three-dimensional solvation-structures from the site-site radial distribution functions in liquids
Realization of three-dimensional solvation-structures from the site-site radial distribution functions in liquids
复制标题
从液体中位点径向分布函数实现三维溶剂化结构
DOI：
10.1246/bcsj.74.1831
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发表时间：
2001
影响因子：
4
通讯作者：
F. Hirata
中科院分区：
文献类型：
--
作者：
Hirofumi Sato;F. Hirata
我们提出了一个新的程序来实现一个三维（3D）溶剂化结构的溶质分子从一组径向分布函数（RDF），或距离信息。该方法包括最小化的罚函数定义为均方差的溶质-溶剂的原子间距离从试验3D配置和目标RDFs。几个不同的溶质分子周围的水化结构可视化演示的方法。用本方法实现的溶剂化结构对应于最合理的溶剂化结构（MPSS），它看起来像一个“快照”的分子动力学轨迹。然而，MPSS本质上不同于“快照”，因为它代表平均配置，因此是可观察的量。本程序最初是为分析从参考相互作用位点模型（RISM）获得的RDF结果而开发的，但也可以直接应用于RDF。
We propose a new procedure to realize a three-dimensional (3D) solvation structure around a solute molecule from a set of radial distribution functions (RDF), or distance information. The method consists of the minimization of a penalty function defined as the mean-square difference of the solute–solvent interatomic distances obtained from trial 3D configurations and from target RDFs. The hydration structures around several different solute molecules are visualized to demonstrate the method. The solvation structures realized with the present method correspond to the most plausible solvation structure (MPSS), which looks like a “snap shot” of the molecular dynamics trajectory. However, the MPSS is essentially different from the “snap shot,” since it represents an average configuration, and is therefore an observable quantity. The present procedure was originally developed for analyses of the RDF results obtained from the reference interaction site model (RISM), but can be applied straightforwardly to RDFs ...