Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.
Dual QM and MM Approach for Computing Equilibrium Isotope Fractionation Factor of Organic Species in Solution.
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用于计算溶液中有机物质的平衡同位素分馏因子的双QM和MM方法。
DOI：
10.3390/molecules23102644
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发表时间：
2018-10-15
期刊：
影响因子：
--
通讯作者：
Gao J
中科院分区：
文献类型：
--
作者：
Liu M;Youmans KN;Gao J
本文描述了计算平衡同位素效应的QM和MM双重方法。在第一部分中，势能面由结合量子力学和分子力学（QM/MM）方法表示，其中溶质分子被量子力学处理，其余溶剂分子由分子力学经典近似。在第二个QM/MM分区，微分核量子效应的同位素效应是由统计力学双平均形式主义，其中的核质心分布是经典的牛顿分子动力学采样和量子力学传播的量子粒子的质心位置的处理使用路径积分（PI）的方法确定。这些分区允许正确地表示势能面，使得溶质部分在核量子力学模拟中不受核量子效应的影响，并且双平均方法具有溶剂配置和路径积分收敛的采样效率的优点。重要的是，计算精度是通过自由能微扰（FEP）理论来实现的，以炼金术将一种同位素突变为另一种。PI-FEP方法适用于模型系统中发现的18 O富集在纤维素的树木，以确定同位素富集因子的羰基化合物在水中。本方法可作为研究生物和地球化学体系同位素分馏的通用工具。
A dual QM and MM approach for computing equilibrium isotope effects has been described. In the first partition, the potential energy surface is represented by a combined quantum mechanical and molecular mechanical (QM/MM) method, in which a solute molecule is treated quantum mechanically, and the remaining solvent molecules are approximated classically by molecular mechanics. In the second QM/MM partition, differential nuclear quantum effects responsible for the isotope effect are determined by a statistical mechanical double-averaging formalism, in which the nuclear centroid distribution is sampled classically by Newtonian molecular dynamics and the quantum mechanical spread of quantized particles about the centroid positions is treated using the path integral (PI) method. These partitions allow the potential energy surface to be properly represented such that the solute part is free of nuclear quantum effects for nuclear quantum mechanical simulations, and the double-averaging approach has the advantage of sampling efficiency for solvent configuration and for path integral convergence. Importantly, computational precision is achieved through free energy perturbation (FEP) theory to alchemically mutate one isotope into another. The PI-FEP approach is applied to model systems for the 18O enrichment found in cellulose of trees to determine the isotope enrichment factor of carbonyl compounds in water. The present method may be useful as a general tool for studying isotope fractionation in biological and geochemical systems.
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影响因子：
--
作者：
Gao J
通讯作者：
Gao J
影响因子：
15
作者：
Byun, Y;Mo, YR;Gao, JL
通讯作者：
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影响因子：
4.4
作者：
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通讯作者：
Voth, GA
影响因子：
2.9
作者：
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通讯作者：
Gao J
影响因子：
4.4
作者：
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通讯作者：
VOTH, GA