Ishii Yoshiki, Yamamoto Naoki, Matubayasi Nobuyuki, Zhang Bin W, Cui Di, Levy Ronald M
Division of Chemical Engineering, Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan.
Elements Strategy Initiative for Catalysts and Batteries , Kyoto University , Katsura , Kyoto 615-8520 , Japan.
J Chem Theory Comput. 2019 May 14;15(5):2896-2912. doi: 10.1021/acs.jctc.8b01309. Epub 2019 Apr 16.
A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decomposed energetics of solvation were analyzed for small molecules with a methyl, amine, or hydroxyl group and alanine dipeptide in solvent water. It was observed that the density of the solvation free energy is weakly dependent on the solute site in the excluded-volume region and is distinctively favorable in the first shells of the solute atoms that can readily form hydrogen bonds with water. The solvent-reorganization term reduces faster with the separation from the solute than the direct interaction between the solute and solvent, and the latter governs the energetics in the second shell and outer regions. The sum of the contributions to the free energy from the excluded volume and first shell was found to deviate significantly from the total sum over all the regions, implying that the solvation free energy is not spatially localized near the solute in a quantitative sense. Still, a local description was shown to be valid as confirmed by the correlation of the total value of free energy with the corresponding value obtained by integrating the free-energy density to the second shell. The theoretical framework developed in the present work to spatially decompose the solvation free energy can thus be useful to identify stabilizing or destabilizing regions of solvent proximate to a solute and to analyze the role that the displacement of interfacial water plays in the thermodynamics of molecular association.
通过扩展先前在一维能量表示中建立的自由能泛函，并在混合四维表示（三维位置和一维能量）中制定新的表达式，提出了一种用于溶剂化热力学的密度泛函方法的空间分辨版本。根据溶剂分子相对于溶质的相对位置，将空间进一步划分为一组离散区域，并分析了溶剂化过程中空间分解的能量学，研究对象包括在溶剂水中带有甲基、胺基或羟基的小分子以及丙氨酸二肽。研究发现，溶剂化自由能的密度在排除体积区域中对溶质位点的依赖性较弱，而在能够与水轻松形成氢键的溶质原子的第一壳层中则明显有利。溶剂重组项随着与溶质距离的增加而比溶质与溶剂之间的直接相互作用更快地减小，并且后者决定了第二壳层和外部区域的能量学。发现排除体积和第一壳层对自由能的贡献之和与所有区域的总和有显著偏差，这意味着从定量意义上讲，溶剂化自由能并非在溶质附近空间局部化。尽管如此，正如自由能总值与通过将自由能密度积分到第二壳层获得的相应值之间的相关性所证实的那样，局部描述仍然是有效的。因此，本工作中开发的用于在空间上分解溶剂化自由能的理论框架，对于识别溶质附近溶剂的稳定或不稳定区域以及分析界面水的位移在分子缔合热力学中所起的作用可能是有用的。
