模拟水,疏水效应,和离子溶剂化。

Ken A Dill, Thomas M Truskett, Vojko Vlachy, Barbara Hribar-Lee
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引用次数: 336

摘要

水在生物分子(蛋白质、核酸和膜)的结构和性质以及它们与配体和药物的相互作用中起着核心作用。在过去的半个世纪里,由于理论和计算模型的发展,我们对水的理解有了很大的进步。然而,就像盲人和大象一样,不同的模型描述了水行为的不同方面。水模型的趋势是向更精细的尺度性质和越来越多的结构细节发展,这增加了计算成本。最近,我们的实验室和其他实验室朝着相反的方向发展,转向更简单的物理模型,专注于更全局的性质——例如水的热力学、相图和溶剂化性质——以及更少的计算费用。简化的模型可以指导我们更好地理解水,以补充我们从更复杂的模型中学到的东西。一个最终目标是为计算机模拟生物分子建立更易于处理的模型。本文从简单模型的角度阐述了水作为纯液体和溶剂的物理性质是如何从水的几何性质和氢键性质中推导出来的。
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Modeling water, the hydrophobic effect, and ion solvation.

Water plays a central role in the structures and properties of biomolecules--proteins, nucleic acids, and membranes--and in their interactions with ligands and drugs. Over the past half century, our understanding of water has been advanced significantly owing to theoretical and computational modeling. However, like the blind men and the elephant, different models describe different aspects of water's behavior. The trend in water modeling has been toward finer-scale properties and increasing structural detail, at increasing computational expense. Recently, our labs and others have moved in the opposite direction, toward simpler physical models, focusing on more global properties-water's thermodynamics, phase diagram, and solvation properties, for example-and toward less computational expense. Simplified models can guide a better understanding of water in ways that complement what we learn from more complex models. One ultimate goal is more tractable models for computer simulations of biomolecules. This review gives a perspective from simple models on how the physical properties of water-as a pure liquid and as a solvent-derive from the geometric and hydrogen bonding properties of water.

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