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在凝聚相原子模拟中计算多极静电。

Scoring multipole electrostatics in condensed-phase atomistic simulations.

机构信息

Department of Chemistry, University of Basel, 4056 Basel, Switzerland.

出版信息

J Phys Chem B. 2013 May 9;117(18):5460-71. doi: 10.1021/jp400593c. Epub 2013 Apr 25.

DOI:10.1021/jp400593c
PMID:23560873
Abstract

Permanent multipoles (MTPs) embody a natural extension to common point-charge (PC) representations in atomistic simulations. In this work, we propose an alternative to the computationally expensive MTP molecular dynamics simulations by running a simple PC simulation and later reevaluate-"score''-all energies using the more detailed MTP force field. The method, which relies on the assumption that the PC and MTP force fields generate closely related phase spaces, is accomplished by enforcing identical sets of monopoles between the two force fields-effectively highlighting the higher MTP terms as a correction to the PC approximation. We first detail our consistent parametrization of the electrostatics and van der Waals interactions for the two force fields. We then validate the method by comparing the accuracy of protein-ligand binding free energies from both PC and MTP-scored representations with experimentally determined binding constants obtained by us. Specifically, we study the binding of several arylsulfonamide ligands to human carbonic anhydrase II. We find that both representations yield an accuracy of 1 kcal/mol with respect to experiment. Finally, we apply the method to rank the energetic contributions of individual atomic MTP coefficients for molecules solvated in water. All in all, MTP scoring is a computationally appealing method that can provide insight into the multipolar electrostatic interactions of condensed-phase systems.

摘要

永久多极矩(MTP)在原子模拟中是对常见点电荷(PC)表示的自然扩展。在这项工作中,我们提出了一种替代计算昂贵的 MTP 分子动力学模拟的方法,即运行简单的 PC 模拟,然后使用更详细的 MTP 力场重新评估-“评分”-所有能量。该方法依赖于 PC 和 MTP 力场生成密切相关的相空间的假设,通过在两个力场之间强制施加相同的单极子集来实现-有效地突出更高的 MTP 项作为对 PC 近似的修正。我们首先详细描述了我们对两种力场的静电和范德华相互作用进行一致参数化。然后,我们通过将两种力场得分表示的蛋白质-配体结合自由能与我们通过实验获得的实验确定的结合常数进行比较来验证该方法的准确性。具体来说,我们研究了几种芳基磺酰胺配体与人类碳酸酐酶 II 的结合。我们发现两种表示方法相对于实验的准确性均为 1 kcal/mol。最后,我们将该方法应用于对水中溶解分子的单个原子 MTP 系数的能量贡献进行排序。总的来说,MTP 评分是一种计算上有吸引力的方法,可以深入了解凝聚相系统的多极静电相互作用。

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