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几何流隐式溶剂化模型的参数化。

Parameterization of a geometric flow implicit solvation model.

机构信息

Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.

出版信息

J Comput Chem. 2013 Mar 30;34(8):687-95. doi: 10.1002/jcc.23181. Epub 2012 Dec 5.

Abstract

Implicit solvent models are popular for their high computational efficiency and simplicity over explicit solvent models and are extensively used for computing molecular solvation properties. The accuracy of implicit solvent models depends on the geometric description of the solute-solvent interface and the solvent dielectric profile that is defined near the surface of the solute molecule. Typically, it is assumed that the dielectric profile is spatially homogeneous in the bulk solvent medium and varies sharply across the solute-solvent interface. However, the specific form of this profile is often described by ad hoc geometric models rather than physical solute-solvent interactions. Hence, it is of significant interest to improve the accuracy of these implicit solvent models by more realistically defining the solute-solvent boundary within a continuum setting. Recently, a differential geometry-based geometric flow solvation model was developed, in which the polar and nonpolar free energies are coupled through a characteristic function that describes a smooth dielectric interface profile across the solvent-solute boundary in a thermodynamically self-consistent fashion. The main parameters of the model are the solute/solvent dielectric coefficients, solvent pressure on the solute, microscopic surface tension, solvent density, and molecular force-field parameters. In this work, we investigate how changes in the pressure, surface tension, solute dielectric coefficient, and choice of different force-field charge and radii parameters affect the prediction accuracy for hydration free energies of 17 small organic molecules based on the geometric flow solvation model. The results of our study provide insights on the parameterization, accuracy, and predictive power of this new implicit solvent model.

摘要

隐溶剂模型因其在计算分子溶剂化性质方面的高计算效率和简单性而受到广泛应用。隐溶剂模型的准确性取决于溶质-溶剂界面的几何描述和溶剂介电轮廓在溶质分子表面附近的定义。通常,假定在大块溶剂介质中介电轮廓是空间均匀的,并且在溶质-溶剂界面处急剧变化。然而,这种轮廓的具体形式通常通过特定的几何模型而不是物理溶质-溶剂相互作用来描述。因此,通过更真实地在连续体设置中定义溶质-溶剂边界,提高这些隐溶剂模型的准确性具有重要意义。最近,开发了一种基于微分几何的几何流溶剂化模型,其中极性和非极性自由能通过一个特征函数耦合,该特征函数以热力学自洽的方式描述溶剂-溶质边界上的平滑介电界面轮廓。该模型的主要参数是溶质/溶剂介电系数、溶质上的溶剂压力、微观表面张力、溶剂密度和分子力场参数。在这项工作中,我们研究了压力、表面张力、溶质介电系数以及不同力场电荷和半径参数的变化如何影响基于几何流溶剂化模型对 17 种小分子水合自由能的预测精度。我们研究的结果提供了对这种新隐溶剂模型的参数化、准确性和预测能力的深入了解。

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本文引用的文献

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On the Dielectric Boundary in Poisson-Boltzmann Calculations.泊松-玻尔兹曼计算中的介电边界
J Chem Theory Comput. 2008 Mar;4(3):507-514. doi: 10.1021/ct700319x. Epub 2008 Feb 21.
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Implicit solvent models.隐式溶剂模型
Biophys Chem. 1999 Apr 5;78(1-2):1-20. doi: 10.1016/s0301-4622(98)00226-9.

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