Thomson问题的数值解及应用计算化学

A numerical solution to Thomson problem and applied computational chemistry

提出一种能精确而有效的计算方法,用于计算分子各种表面积如容剂可及性表面积、范德华表面积和体积,对计算蛋白质溶剂化能、表征分子形状、计算药物分子在蛋白质分子表面的对接及预测有机小分子生物活性均有重要意义。本文针对n个单位点电荷在单位球面上均匀分布问题-Thomson问题,采用Metropolis Monte Carlo模拟退火方法数值求解,得到了与其它方法一致的结果,并用于小分子和大分子的容剂可及性表面积及范德华表面积和体积的快速计算,提出采用高时斯定理计算分子体积的新方法,结果很好。

An efficient and accurate algorithm for computing the molecular surface areas, such as solvent accessible surface area, van der Waals surface area, and molecular volumes, has been proposed, which is very important in calculating the solvantion energy of proteins, characterizing the shape of molecules, docking drug molecules to a protein surface and predicting the bioactivity of small organic molecules. In this study, the Metropolis Monte Carlo simulated annealing method has been applied to get the global minimum of the Thomson problem-the lowest-energy configuration of n point charges on a unit sphere. The numerical solution to the Thomson problem is used for the fast calculation of the surface areas and a new method by means of Gaussian Theorem has been proposed to calculate the volumes for small and large molecules and obtained satisfied result.