Efficient solvent boundary potential for hybrid potential simulations
Efficient solvent boundary potential for hybrid potential simulations
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DOI：
10.1039/c0cp02828b
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发表时间：
2011-01-01
影响因子：
3.3
通讯作者：
Field, Martin
中科院分区：
文献类型：
--
作者：
Aleksandrov, Alexey;Field, Martin
计算生物物理学中的一个常见挑战是从有限大小的系统的模拟中获得类似于无限大系统的统计性质。在这项工作中，我们描述了一种计算效率高的算法，用于执行具有溶剂边界势的量子化学/分子力学(QC/MM)混合计算。系统被划分为发生催化反应的QC区域、包裹量子区域并用MM模型处理的具有显式溶剂的球形区域、以及被边界势隐式处理的周围主体溶剂。后者被构造为再现嵌入在变半径低介电球内的有限个原子的溶剂化自由能，并考虑了隐含溶剂与中心区域的QC和MM原子之间的静电和van der Waals相互作用。该方法在模拟程序pDynamo中实现，并通过检测柠檬酸合成酶和乳酸脱氢酶两种酶的反应机理的基本步骤进行测试。用该方法计算的反应谱线上物种的能量和几何构型与以前的实验和计算结果符合得很好。讨论了进一步提高该方法的实用性的方向。
A common challenge in computational biophysics is to obtain statistical properties similar to those of an infinite bulk system from simulations of a system of finite size. In this work we describe a computationally efficient algorithm for performing hybrid quantum chemical/molecular mechanical (QC/MM) calculations with a solvent boundary potential. The system is partitioned into a QC region within which catalytic reactions occur, a spherical region with explicit solvent that envelops the quantum region and is treated with a MM model, and the surrounding bulk solvent that is treated implicitly by the boundary potential. The latter is constructed to reproduce the solvation free energy of a finite number of atoms embedded inside a low-dielectric sphere with variable radius, and takes into account electrostatic and van der Waals interactions between the implicit solvent and the QC and MM atoms in the central region. The method was implemented in the simulation program pDynamo and tested by examining elementary steps in the reaction mechanisms of two enzymes, citrate synthase and lactate dehydrogenase. Good agreement is found for the energies and geometries of the species along the reaction profiles calculated with the method and those obtained by previous experimental and computational studies. Directions in which the utility of the method can be further improved are discussed.