Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol

IF 1 Q4 ENGINEERING, CHEMICAL

Chemical Product and Process Modeling Pub Date : 2021-06-21 DOI:10.1515/cppm-2021-0014

M. Emamian, H. Azizpour, H. Moradi, K. Keynejad, H. Bahmanyar, Z. Nasrollahi

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引用次数: 4

Abstract

Abstract In this study, molecular dynamics simulation was applied for calculating solvation free energy of 16 solute molecules in methanol solvent. The thermodynamic integration method was used because it was possible to calculate the difference in free energy in any thermodynamic path. After comparing results for solvation free energy in different force fields, COMPASS force field was selected since it had the lowest error compared to experimental result. Group-based summation method was used to compute electrostatic and van der Waals forces at 298.15 K and 1 atm. The results of solvation free energy were obtained from molecular dynamics simulation and were compared to the results from Solvation Model Density (SMD) and Universal Continuum Solvation Model (denoted as SM8), which were obtained from other research works. Average square-root-error for molecular dynamics simulation, SMD and SM8 models were 0.096091, 0.595798, and 0.70649. Furthermore, the coefficient of determination (R2) for molecular dynamics simulation was 0.9618, which shows higher accuracy of MD simulation for calculating solvation free energy comparing to two other models.

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分子动力学模拟预测甲醇中性溶质溶剂化自由能的性能

摘要本研究采用分子动力学模拟方法计算了16个溶质分子在甲醇溶剂中的溶剂化自由能。采用热力学积分法是因为它可以计算任意热力学路径下的自由能差。在比较不同力场下溶剂化自由能的结果后，选择COMPASS力场，因为它与实验结果的误差最小。采用分组求和法计算298.15 K和1 atm下的静电力和范德华力。通过分子动力学模拟得到了溶剂化自由能的结果，并与其他研究工作中得到的溶剂化模型密度(SMD)和通用连续体溶剂化模型(SM8)的结果进行了比较。分子动力学模拟、SMD和SM8模型的平均平方根误差分别为0.096091、0.595798和0.70649。分子动力学模拟的决定系数(R2)为0.9618，表明MD模拟计算溶剂化自由能的精度高于其他两种模型。

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来源期刊

Chemical Product and Process Modeling ENGINEERING, CHEMICAL-

CiteScore

2.10

自引率

11.10%

发文量

期刊介绍： Chemical Product and Process Modeling (CPPM) is a quarterly journal that publishes theoretical and applied research on product and process design modeling, simulation and optimization. Thanks to its international editorial board, the journal assembles the best papers from around the world on to cover the gap between product and process. The journal brings together chemical and process engineering researchers, practitioners, and software developers in a new forum for the international modeling and simulation community. Topics: equation oriented and modular simulation optimization technology for process and materials design, new modeling techniques shortcut modeling and design approaches performance of commercial and in-house simulation and optimization tools challenges faced in industrial product and process simulation and optimization computational fluid dynamics environmental process, food and pharmaceutical modeling topics drawn from the substantial areas of overlap between modeling and mathematics applied to chemical products and processes.