General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions.
General methodology to optimize damping functions to account for charge penetration effects in electrostatic calculations using multicentered multipolar expansions.
复制标题
使用多中心多极展开优化阻尼函数以考虑静电计算中的电荷穿透效应的一般方法。
DOI：
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发表时间：
2008
影响因子：
2.9
通讯作者：
L. Dardenne
中科院分区：
文献类型：
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作者：
A. S. Werneck;T. R. Filho;L. Dardenne
我们开发了一种优化指数阻尼函数的方法，以在使用多中心多极展开法 (MME) 计算分子静电特性时考虑电荷穿透效应。该方法基于使用两步快速局部拟合程序和以一组同心网格点作为参考计算的从头开始（Hartree-Fock/6-31G**和6-31G**+）静电势来优化阻尼参数集。该方法的主要方面是第一个局部拟合步骤，该步骤生成集中的初始猜测，以提高单纯形方法的性能，避免使用多次运行和初始猜测的选择。在以下研究中测试了三种不同的确定优化阻尼参数的策略：（1）研究了标准和非标准氢键几何形状以及非平衡几何形状下五种氢键二聚体的静电相互作用能的计算误差； (2) 计算八种小分子体系（甲醇、氨、水、甲酰胺、二氯甲烷、丙酮、二甲基亚砜和乙腈）和20种氨基酸的静电分子性质（电位和电场）。我们的结果表明，该方法不仅适用于小分子，而且适用于相对较大的分子系统。对与不同优化策略相关的不同参数集的分析表明，（i）特定参数集更适合且更通用地用于静电相互作用能量计算，氢键几何结构的平均绝对误差为0.46 kcal/mol； (ii) 第二个参数集更适合范德华 (vdW) 包络线内外的静电势和电场计算，在 vdW 表面平均误差降低 >72%。更通用的氨基酸阻尼参数集是根据小片段和氨基酸衍生的原始阻尼参数构建的。该阻尼组对蛋白质主链和残基侧链构象变化更加不敏感，对于未来使用基于极化经典方法的从头开始的对接和分子动力学蛋白质模拟非常有用。
We developed a methodology to optimize exponential damping functions to account for charge penetration effects when computing molecular electrostatic properties using the multicentered multipolar expansion method (MME). This methodology is based in the optimization of a damping parameter set using a two-step fast local fitting procedure and the ab initio (Hartree-Fock/6-31G** and 6-31G**+) electrostatic potential calculated in a set of concentric grid of points as reference. The principal aspect of the methodology is a first local fitting step which generates a focused initial guess to improve the performance of a simplex method avoiding the use of multiple runs and the choice of initial guesses. Three different strategies for the determination of optimized damping parameters were tested in the following studies: (1) investigation of the error in the calculation of the electrostatic interaction energy for five hydrogen-bonded dimers at standard and nonstandard hydrogen-bonded geometries and at nonequilibrium geometries; (2) calculation of the electrostatic molecular properties (potential and electric field) for eight small molecular systems (methanol, ammonia, water, formamide, dichloromethane, acetone, dimethyl sulfoxide, and acetonitrile) and for the 20 amino acids. Our results show that the methodology performs well not only for small molecules but also for relatively larger molecular systems. The analysis of the distinct parameter sets associated with different optimization strategies show that (i) a specific parameter set is more suitable and more general for electrostatic interaction energy calculations, with an average absolute error of 0.46 kcal/mol at hydrogen-bond geometries; (ii) a second parameter set is more suitable for electrostatic potential and electric field calculations at and outside the van der Waals (vdW) envelope, with an average error decrease >72% at the vdW surface. A more general amino acid damping parameter set was constructed from the original damping parameters derived for the small fragments and for the amino acids. This damping set is more insensitive to protein backbone and residue side-chain conformational changes and can be very useful for future docking and molecular dynamics protein simulations using ab initio based polarizable classical methods.