Li Libo, Fennell Christopher J, Dill Ken A
Laufer Center for Physical and Quantitative Biology, and Departments of Physics and Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
J Phys Chem B. 2014 Jun 19;118(24):6431-7. doi: 10.1021/jp4115139. Epub 2013 Dec 13.
Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute's free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom's solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes.
先前的工作描述了一种名为半显式组装（SEA）的计算溶剂化模型。SEA水模型能够高效且准确地计算非极性和极性溶质在水中的溶剂化自由能。然而，SEA在离子和带电溶质的溶剂化自由能计算中存在系统误差。在此，我们描述了场SEA，这是一种改进的处理方法，它能给出带电溶质（包括单原子和多原子离子以及模型二肽）以及非极性和极性分子的准确溶剂化自由能。对于给定的溶质，场SEA的计算成本较低，这是因为显式溶剂模型模拟被归入预计算步骤，并且它根据溶质的自由能场来表示溶剂化水。本质上，场SEA在计算效率高的框架内近似显式模型模拟的物理过程。一个关键发现是，原子的溶剂化壳层继承了相邻原子的特性，尤其是强带电的相邻原子。在需要进行溶剂化自由能计算的情况下，场SEA可能会很有用，这种计算比显式溶剂模拟更快，并且对于广泛的溶质比传统隐式溶剂模拟更准确。
