在连续介质溶剂计算中显式表示溶剂化壳层。
Explicitly representing the solvation shell in continuum solvent calculations.
作者信息
da Silva Eirik F, Svendsen Hallvard F, Merz Kenneth M
机构信息
Department of Chemical Engineering, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.
出版信息
J Phys Chem A. 2009 Jun 4;113(22):6404-9. doi: 10.1021/jp809712y.
Abstract
A method is presented to explicitly represent the first solvation shell in continuum solvation calculations. Initial solvation shell geometries were generated with classical molecular dynamics simulations. Clusters consisting of solute and 5 solvent molecules were fully relaxed in quantum mechanical calculations. The free energy of solvation of the solute was calculated from the free energy of formation of the cluster, and the solvation free energy of the cluster was calculated with continuum solvation models. The method has been implemented with two continuum solvation models, a Poisson-Boltzmann model and the IEF-PCM model. Calculations were carried out for a set of 60 ionic species. Implemented with the Poisson-Boltzmann model the method gave an unsigned average error of 2.1 kcal/mol and a rmsd of 2.6 kcal/mol for anions; for cations the unsigned average error was 2.8 kcal/mol and the rmsd 3.9 kcal/mol. Similar results were obtained with the IEF-PCM model.
摘要
提出了一种在连续介质溶剂化计算中明确表示第一溶剂化层的方法。初始溶剂化层几何结构通过经典分子动力学模拟生成。由溶质和5个溶剂分子组成的簇在量子力学计算中完全弛豫。溶质的溶剂化自由能由簇的形成自由能计算得出，而簇的溶剂化自由能则用连续介质溶剂化模型计算。该方法已用两种连续介质溶剂化模型实现，即泊松-玻尔兹曼模型和IEF-PCM模型。对一组60种离子物种进行了计算。用泊松-玻尔兹曼模型实现该方法时，阴离子的平均绝对误差为2.1 kcal/mol，均方根偏差为2.6 kcal/mol；对于阳离子，平均绝对误差为2.8 kcal/mol，均方根偏差为3.9 kcal/mol。使用IEF-PCM模型也得到了类似的结果。
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