Solvated ensemble averaging in the calculation of partial atomic charges
Solvated ensemble averaging in the calculation of partial atomic charges
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DOI：
10.1002/jcc.1072
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发表时间：
2001-08-01
影响因子：
3
通讯作者：
Woods, RJ
中科院分区：
文献类型：
--
作者：
Basma, M;Sundara, S;Woods, RJ
在计算部分原子电荷时，为了用于分子力学或动力学模拟，通常的做法是只为感兴趣的分子选择单一构象。对于包含可旋转键的分子，最好从几个相关构象计算电荷。我们在这里展示电荷推导协议的结果，该协议通过对从在周期性边界条件下执行的显式溶剂化 MD 模拟中选择的构象计算的平均电荷来确定部分电荷。这种方法产生的部分电荷是由现实的构象群体加权的，并且适合凝聚相模拟。原则上，该协议可以应用于任何类别的分子和非水溶剂化。碳水化合物含有大量羟基，它们在溶液中以集合方向存在，在本报告中，我们将集合平均应用于一系列甲基糖苷。我们报告了整体平均导致各种单糖之间以及给定单糖内的组成原子之间的电荷收敛的程度。由于我们的集合中有大量构象 (200)，我们能够计算部分电荷的统计相关标准差。对标准偏差的分析使我们能够评估等效原子类型可能需要独特的部分电荷的程度。羟基的构型对内能有相当大的影响，并且根据这些性质讨论了系综平均电荷的极限。 (C) 2001 约翰威利父子公司
In the calculation of partial atomic charges, for use in molecular mechanics or dynamics simulations, it is common practice to select only a single conformation for the molecule of interest. For molecules that contain rotatable bonds, it is preferable to compute the charges from several relevant conformations. We present here results from a charge derivation protocol that determines the partial charges by averaging charges computed for conformations selected from explicitly solvated MD simulations, performed under periodic boundary conditions. This approach leads to partial charges that are weighted by a realistic population of conformations and that are suitable for condensed phase simulations. This protocol can, in principle, be applied to any class of molecule and to nonaqueous solvation. Carbohydrates contain numerous hydroxyl groups that exist in an ensemble of orientations in solution, and in this report we apply ensemble averaging to a series of methyl glycosides. We report the extent to which ensemble averaging leads to charge convergence among the various monosaccharides and among the constituent atoms within a given monosaccharide. Due to the large number of conformations (200) in our ensembles, we are able to compute statistically relevant standard deviations for the partial charges. An analysis of the standard deviations allows us to assess the extent to which equivalent atom types may, nevertheless, require unique partial charges. The configurations of the hydroxyl groups exert considerable influence on internal energies, and the limits of ensemble averaged charges are discussed in terms of these properties. (C) 2001 John Wiley & Sons, Inc.