从原子模拟计算空间分辨旋转水合熵
Computing spatially resolved rotational hydration entropies from atomistic simulations
摘要：
对于大分子过程的第一原理理解，对潜在的自由能景观的定量理解，特别是其熵贡献是至关重要的。生物分子（如蛋白质）的稳定性受疏水效应的控制，该疏水效应是由溶剂壳层的自由能的竞争性熵和熵贡献引起的。虽然液体的统计力学以及分子动力学模拟提供了很多见解，但溶剂化壳层熵仍然非常难以计算，特别是当需要空间分辨率时。在这里，我们提出了一种方法，允许通过非参数k-近邻密度估计空间分辨旋转溶剂熵的计算。我们验证了我们的方法，使用分析测试分布，并将其应用到原子模拟的水箱。与优于9.6%的准确度，所获得的空间分辨率应该新的光的疏水效应和溶剂化的热力学一般。
英文摘要：
For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins, is governed by the hydrophobic effect, which arises from competing enthalpic and entropic contributions to the free energy of the solvent shell. While the statistical mechanics of liquids, as well as molecular dynamics simulations have provided much insight, solvation shell entropies remain notoriously difficult to calculate, especially when spatial resolution is required. Here, we present a method that allows for the computation of spatially resolved rotational solvent entropies via a non-parametric k-nearest-neighbor density estimator. We validated our method using analytic test distributions and applied it to atomistic simulations of a water box. With an accuracy of better than 9.6%, the obtained spatial resolution should shed new light on the hydrophobic effect and the thermodynamics of solvation in general.
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