Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations
Treating electrostatics with Wolf summation in combined quantum mechanical and molecular mechanical simulations
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DOI：
10.1063/1.4934880
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发表时间：
2015-11-07
影响因子：
4.4
通讯作者：
Pu, Jingzhi
中科院分区：
文献类型：
--
作者：
Ojeda-May, Pedro;Pu, Jingzhi
[D]。Wolf et al.， J. Chem。[j] .地球物理学报，1999,8(1):1 - 4。J. Fennell和J. D. Gezelter， J. Chem。物理学报，124,234104(2006)]，扩展了在量子力学和分子力学（QM/MM）分子动力学模拟中处理静电的方法。在此开发中，我们将QM/MM静电势能函数拆分为常规库仑r（-1）项和包含DSF贡献的项。前者由基于截止的QM/MM模拟的标准机制处理，而后者作为Fock矩阵校正被纳入QM/MM相互作用哈密顿量。我们用QM/MM-DSF方法测试了两个溶液相反应，即铵离子和氯离子的缔合反应和两个氯离子之间交换甲基的对称SN2反应。通过与QM/MM-Ewald和QM/ mm各向同性周期和（IPS）方法的平均力势（PMF）剖面进行比较，评价了QM/MM-DSF方法的性能，QM/MM-DSF方法均明确包含了远程静电。对于离子结合，QM/MM-DSF方法成功地消除了QM/MM-Cutoff模拟中观察到的人为自由能漂移，与两种远程包含方法非常一致。对于SN2反应，QM/MM-DSF方法得到的活化自由能与QM/MM-Ewald和QM/MM-IPS的结果吻合较好。然而，后者需要比QM/MM-DSF更大的截止距离才能使PMF适当收敛。与QM/MM-Ewald方法相比，QM/MM-DSF方法避免了耗时的点阵求和，计算成本降低了55%。这些结果表明，除了QM/MM-IPS方法外，QM/MM-DSF方法可以作为QM/MM-Ewald方法的另一种有效和准确的方法来处理化学反应凝聚相模拟中的静电。(C) 2015 AIP出版有限责任公司
The Wolf summation approach [D. Wolf et al., J. Chem. Phys. 110, 8254 (1999)], in the damped shifted force (DSF) formalism [C. J. Fennell and J. D. Gezelter, J. Chem. Phys. 124, 234104 (2006)], is extended for treating electrostatics in combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulations. In this development, we split the QM/MM electrostatic potential energy function into the conventional Coulomb r(-1) term and a term that contains the DSF contribution. The former is handled by the standard machinery of cutoff-based QM/MM simulations whereas the latter is incorporated into the QM/MM interaction Hamiltonian as a Fock matrix correction. We tested the resulting QM/MM-DSF method for two solution-phase reactions, i. e., the association of ammonium and chloride ions and a symmetric SN2 reaction in which a methyl group is exchanged between two chloride ions. The performance of the QM/MM-DSF method was assessed by comparing the potential of mean force (PMF) profiles with those from the QM/MM-Ewald and QM/MM-isotropic periodic sum (IPS) methods, both of which include long-range electrostatics explicitly. For ion association, the QM/MM-DSF method successfully eliminates the artificial free energy drift observed in the QM/MM-Cutoff simulations, in a remarkable agreement with the two long-range-containing methods. For the SN2 reaction, the free energy of activation obtained by the QM/MM-DSF method agrees well with both the QM/MM-Ewald and QM/MM-IPS results. The latter, however, requires a greater cutoff distance than QM/MM-DSF for a proper convergence of the PMF. Avoiding time-consuming lattice summation, the QM/MM-DSF method yields a 55% reduction in computational cost compared with the QM/MM-Ewald method. These results suggest that, in addition to QM/MM-IPS, the QM/MM-DSF method may serve as another efficient and accurate alternative to QM/MM-Ewald for treating electrostatics in condensed-phase simulations of chemical reactions. (C) 2015 AIP Publishing LLC.