网格非均匀溶剂化理论研究分子水化的结构和热力学
Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory
摘要：
水合作用的变化是生物分子识别现象的核心，但很难正确地构建和回答有关其精确热力学作用的问题。我们通过引入网格非均匀溶剂化理论（GIST）来解决这个问题，该理论在感兴趣的体积中的3D网格上离散非均匀溶剂化理论的方程。在这里，溶剂体积被划分成小的网格框和局部热力学熵，能量和自由能被定义为每个网格框。热力学溶剂化量以这样的方式定义，即对所有网格框上的量求和产生系统的所需总量。这种方法顺利占热力学不仅高度占用水的网站，但也部分占用和水耗尽的地区的溶剂，而不需要从其他理论的特设条款。GIST方法具有允许严格的终态分析的进一步优点，例如在分子识别的问题中，不仅可以解释从表面置换水的热力学，而且可以解释结合复合物周围的溶剂重组的热力学。作为一个初步的应用，我们提出了GIST计算在1-体水平的主机葫芦[7]脲，低分子量受体分子，这代表了一个易于处理的生物分子识别模型。最引人注目的结果之一是观察到一个环形区域的水密度，在中心的主机的非极性腔，这是显着不利的熵，因此可能有助于这个小受体的能力，结合客体分子具有异常高的亲和力。
英文摘要：
Changes in hydration are central to the phenomenon of biomolecular recognition, but it has been difficult to properly frame and answer questions about their precise thermodynamic role. We address this problem by introducing Grid Inhomogeneous Solvation Theory (GIST), which discretizes the equations of Inhomogeneous Solvation Theory on a 3D grid in a volume of interest. Here, the solvent volume is divided into small grid boxes and localized thermodynamic entropies, energies and free energies are defined for each grid box. Thermodynamic solvation quantities are defined in such a manner that summing the quantities over all the grid boxes yields the desired total quantity for the system. This approach smoothly accounts for the thermodynamics of not only highly occupied water sites but also partly occupied and water depleted regions of the solvent, without the need for ad hoc terms drawn from other theories. The GIST method has the further advantage of allowing a rigorous end-states analysis that, for example in the problem of molecular recognition, can account for not only the thermodynamics of displacing water from the surface but also for the thermodynamics of solvent reorganization around the bound complex. As a preliminary application, we present GIST calculations at the 1-body level for the host cucurbit[7]uril, a low molecular weight receptor molecule which represents a tractable model for biomolecular recognition. One of the most striking results is the observation of a toroidal region of water density, at the center of the host's nonpolar cavity, which is significantly disfavored entropically, and hence may contribute to the ability of this small receptor to bind guest molecules with unusually high affinities.
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