Laboratory of Theoretical and Computational Chemistry, Theoretical Chemistry Institute, Jilin University, Changchun 130023, China.
Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA.
Molecules. 2018 Oct 15;23(10):2644. doi: 10.3390/molecules23102644.
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 O 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.
描述了一种用于计算平衡同位素效应的双量子力学和经典力学方法。在第一个分区中，势能面由量子力学和经典力学（QM/MM）方法表示，其中溶质分子被量子力学处理，剩余的溶剂分子通过经典力学近似处理。在第二个 QM/MM 分区中，负责同位素效应的差分核量子效应通过统计力学双平均形式确定，其中核质心分布通过牛顿分子动力学经典地采样，并且关于质心位置的量化粒子的量子力学扩展使用路径积分（PI）方法处理。这些分区允许正确表示势能面，使得在核量子力学模拟中，溶质部分没有核量子效应，并且双平均方法具有溶剂构型和路径积分收敛的采样效率优势。重要的是，通过自由能微扰（FEP）理论实现计算精度，将一种同位素化学转化为另一种同位素。将 PI-FEP 方法应用于树木纤维素中发现的 O 富集的模型系统，以确定水中羰基化合物的同位素富集因子。本方法可作为研究生物和地球化学系统中同位素分馏的一般工具。
