Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States.
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan and Elements Strategy Initiative for Catalysts and Batteries, Kyoto University , Katsura, Kyoto 615-8520, Japan.
J Phys Chem B. 2017 Apr 20;121(15):3825-3841. doi: 10.1021/acs.jpcb.6b12889. Epub 2017 Feb 28.
Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.
不均匀溶剂化理论(IST)和经典密度泛函理论(DFT)各自提供了一种将溶液的分布函数与其热力学性质联系起来的框架。正如本文所综述的,IST 和 DFT 都可以采用两种“端点”模拟的方式来构建,一种是纯溶剂的模拟,另一种是溶液的模拟,从而确定溶质的化学势和溶液以及溶质周围包含水合水的亚体积的其他热力学性质。与 IST 不同,在 IST 中,溶液的超额能量和熵的表达式是分析的对象,而在 DFT 问题的端点公式中,溶剂化位势平均力(PMF)起着核心作用。PMF 的间接部分对应于 IST 表达式的最低阶(1 体)截断。由于 PMF 是一种自由能函数,因此可以使用强大的数值方法来估计它。我们表明,溶质超额化学势的 DFT 表达式可以写成一种形式,这种形式是局部的,只涉及到靠近溶质的区域的积分。通过 DFT 端点方法估计溶剂化自由能,为分析溶剂化对溶液中分子识别和构象变化的影响提供了另一种途径,这可能会带来新的见解。为了说明溶质-溶剂 PMF 中包含的信息类型,我们对β-环糊精在水中的情况进行了模拟。这种溶质是一种研究得很好的“主体”分子,“客体”分子与之结合;主体-客体系统是分子识别的模型。我们说明了当一个水分子从本体被带到β-环糊精的界面时,溶质-溶剂 PMF 的直接和间接部分可能具有的范围;我们讨论了这两个术语之间的“竞争”,以及它在分子识别中所起的作用。