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用分子模拟预测疏水性溶剂化:1. 测试统一原子烷烃模型。

Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

机构信息

Department of Chemical and Process Engineering, University of Strathclyde, 75 Montrose Street, Glasgow, G1 1XJ, United Kingdom.

LSRE - Laboratory of Separation and Reaction Engineering - Associate Laboratory LSRE/LCM, Faculdade de Engenharia, Universidade do Porto, Rua Dr. Roberto Frias, Porto, 4200-465, Portugal.

出版信息

J Comput Chem. 2017 Mar 5;38(6):346-358. doi: 10.1002/jcc.24690.

DOI:10.1002/jcc.24690
PMID:28032384
Abstract

We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

摘要

我们对三种流行的 united-atom 力场(OPLS-UA、GROMOS 和 TraPPE)在预测疏水溶剂化方面的性能进行了系统测试,更具体地说,是在描述烷烃在烷烃中的溶剂化方面。利用 IBERCIVIS 志愿者计算平台,通过分子动力学模拟和热力学积分,计算了 52 种溶质/溶剂对的溶剂化吉布斯自由能。我们的结果表明,当溶质和溶剂都是小的线性或支链烷烃(最多戊烷)时,所有力场都能得到很好的预测。然而,随着烷烃大小的增加,所有模型都倾向于以系统的方式越来越偏离实验数据。此外,我们的结果证实,在 united-atom 表示中需要针对环状烷烃的特定相互作用参数来考虑环内的额外排除体积。总体而言,TraPPE 模型对所有烷烃的表现最好,但系统地低估了溶剂化自由能的幅度约 6%(均方根偏差为 1.2 kJ/mol)。相反,GROMOS 和 OPLS-UA 都系统地高估了溶剂化自由能(分别为约 13%和 15%)。系统趋势表明,所有模型都可以通过略微调整它们的 Lennard-Jones 参数来改进。© 2016 年 Wiley 期刊公司

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