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从隐式到显式:分子溶剂化能的相互作用-重组方法

From Implicit to Explicit: An Interaction-Reorganization Approach to Molecular Solvation Energy.

作者信息

Huang Kaifang, Duan Lili, Zhang John Z H

机构信息

Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.

School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.

出版信息

J Chem Theory Comput. 2024 Dec 24;20(24):10961-10971. doi: 10.1021/acs.jctc.4c01283. Epub 2024 Dec 13.

Abstract

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.

摘要

长期以来,精确计算溶剂化能一直吸引着研究人员,但大量水分子之间复杂的相互作用带来了重大挑战。目前,分子溶剂化能计算大多基于隐式溶剂近似,即将溶剂分子视为连续介质。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应,如第一溶剂化层的效应等。在此,我们提出一种用于分子溶剂化能计算的显式溶剂方法——相互作用重组溶剂化(IRS)方法。IRS方法实现的预测精度与基于密度的广泛认可的溶剂化模型(SMD)方法相当,且比泊松-玻尔兹曼/广义玻恩表面积(PB/GBSA)方法精确得多。这在与实验数据相关的相关系数和平均绝对误差(MAE)中均得到了证明。IRS方法基于显式溶剂中的分子动力学模拟,无需求解泊松-玻尔兹曼方程或薛定谔方程。另一方面,IRS方法的精度确实取决于分子动力学模拟中使用的分子力场的精度。我们预计IRS方法对分子的溶剂化能计算将非常有用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/1776/11674157/904d14d1d7ae/ct4c01283_0001.jpg

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