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运用 FiSH 和 LIE 模型从 SAMPL-3 数据集预测多氯芳烃的水合自由能。

Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models.

机构信息

Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada.

出版信息

J Comput Aided Mol Des. 2012 May;26(5):661-7. doi: 10.1007/s10822-011-9522-1. Epub 2011 Dec 22.

Abstract

Next-generation solvation models are devised to mimic the accuracy and generality of explicit solvation models at the speed of current popular implicit solvation models. One such method is the first-shell of hydration (FiSH) continuum model that was trained on hydration energetics from LIE calculations and molecular dynamics simulations in explicit solvent. Here we tested prospectively the FiSH model on the SAMPL-3 hydration data set that zooms in the effect of chlorination on solvation. We compare these FiSH predictions with those from retrospective LIE calculations. We find that neither FiSH nor LIE can reproduce well the absolute values and the trend of hydration free energies in the biphenyl and dioxin aromatic chlorination series. Some of the hypotheses behind this performance are discussed and tested. The LIE explicit-solvent model shows some improvement relative to the FiSH continuum model, and we correct a systematic deviation in the continuum van der Waals term of FiSH associated with aromatic Cl atom type.

摘要

下一代溶剂化模型旨在以当前流行的隐式溶剂化模型的速度模拟显式溶剂化模型的准确性和通用性。其中一种方法是第一壳层水化(FiSH)连续体模型,该模型是基于 LIE 计算和显溶剂化分子动力学模拟中的水化能训练的。在这里,我们前瞻性地在 SAMPL-3 水化数据集上测试了 FiSH 模型,该数据集重点研究了氯化对溶剂化的影响。我们将这些 FiSH 预测与回顾性 LIE 计算进行了比较。我们发现,FiSH 和 LIE 都不能很好地重现联苯和二恶英芳香族氯化系列中溶剂化自由能的绝对值和趋势。讨论并测试了这种性能背后的一些假设。与连续体模型相比,LIE 显式溶剂模型显示出一些改进,并且我们纠正了与芳香族 Cl 原子类型相关的 FiSH 连续体范德华项中的系统偏差。

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