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Non-zero Lennard-Jones parameters for the Toukan-Rahman water model: more accurate calculations of the solvation free energy of organic substances.
Journal of Computer-Aided Molecular Design ( IF 3.0 ) Pub Date : 2019-11-25 , DOI: 10.1007/s10822-019-00256-2
Alexei Nikitin 1
Affiliation  

Application of a small radius of the hydrogen atom in molecular-mechanical models of hydrogen bonding improves the estimate of the solvation free energy of organic substances. At the same time, the density and evaporation heat of the bulk water vary slightly and are close to experimental values. Blind testing drug candidates in the SAMPL6 simulation competition showed that using the same Lennard-Jones hydrogen parameters for the hydroxyl, hydroxycarbonyl, amino, and amide groups is enough to predict log P octanol–water with MAE 0.67 and RMSD 0.75.



中文翻译:

Toukan-Rahman水模型的非零Lennard-Jones参数:更精确地计算有机物质的溶剂化自由能。

在氢键的分子力学模型中应用小半径的氢原子可以改善对有机物的溶剂化自由能的估计。同时,散装水的密度和蒸发热略有变化,接近实验值。在SAMPL6模拟竞赛中对候选药物进行盲测表明,对羟基,羟羰基,氨基和酰胺基使用相同的Lennard-Jones氢参数足以预测对数P辛醇-水,MAE为0.67,RMSD为0.75。

更新日期:2020-04-21
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