从隐式到显式:分子溶剂化能的相互作用-重组方法

IF 5.5 1区 化学 Q2 CHEMISTRY, PHYSICAL
Kaifang Huang, Lili Duan* and John Z.H. Zhang*, 
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引用次数: 0

摘要

长期以来,精确计算溶剂化能一直吸引着研究人员,但大体积水分子内复杂的相互作用构成了重大挑战。目前,分子溶剂化能的计算大多基于隐式溶剂近似,其中溶剂分子被视为连续介质。然而,隐式溶剂方法并不理想,因为它缺乏某些实际的溶剂化效果,如第一溶剂化壳的效果等。在这里,我们提出了一种明确的溶剂方法,相互作用-重组溶剂化(IRS)方法,用于分子溶剂化能的计算。IRS方法的预测精度可与广泛认可的基于密度(SMD)方法的溶剂化模型相比较,并明显高于泊松-玻尔兹曼/广义玻恩表面积(PB/GBSA)方法的预测精度。这在相关系数和相对于实验数据的平均绝对误差(MAE)中都得到了证明。IRS方法基于显式溶剂中的分子动力学模拟,不需要求解泊松-玻尔兹曼方程或Schrödinger方程。另一方面,IRS方法的精度确实依赖于分子动力学模拟中所用分子力场的精度。我们期望IRS方法对分子的溶剂化能计算是非常有用的。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
From Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy

Accurate calculation of solvation energies has long fascinated researchers, but complex interactions within bulk water molecules pose significant challenges. Currently, molecular solvation energy calculations are mostly based on implicit solvent approximations in which the solvent molecules are treated as continuum dielectric media. However, the implicit solvent approach is not ideal because it lacks certain real solvation effects, such as that of the first solvation shell, etc. Here, we propose an explicit solvent approach, interaction-reorganization solvation (IRS) method, for molecular solvation energy calculations. The IRS approach achieves predictive accuracy comparable to that of the widely recognized solvation model based on the density (SMD) method and is significantly more accurate than that of the Poisson–Boltzmann/generalized Born surface area (PB/GBSA) methods. This is demonstrated in both the correlation coefficient and the mean absolute error (MAE) with respect to the experimental data. The IRS method is based on molecular dynamics simulation in explicit solvent and does not need to solve Poisson–Boltzmann or Schrödinger equations. On the other hand, the accuracy of the IRS method does depend on the accuracy of the molecular force field used in MD simulations. We expect that the IRS method will be very useful for the solvation energy calculations of molecules.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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