Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules.
Coupling the Level-Set Method with Molecular Mechanics for Variational Implicit Solvation of Nonpolar Molecules.
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DOI：
10.1021/ct800297d
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发表时间：
2009-02-10
影响因子：
5.5
通讯作者：
Li, Bo
中科院分区：
文献类型：
--
作者：
Cheng, Li-Tien;Xie, Yang;Dzubiella, Joachim;McCammon, J. Andrew;Che, Jianwei;Li, Bo
我们建立了一个变分显溶质隐溶剂模型的分子溶剂化。该模型的核心是一个有效的溶剂化自由能泛函，它仅依赖于溶质-溶剂界面和溶质原子的位置。总自由能耦合溶质的体积能和界面能、溶质-溶剂货车德瓦尔斯相互作用和溶质-溶质机械相互作用。曲率依赖的表面张力是通过所谓的托尔曼长度，作为唯一的拟合参数在模型中。我们的方法扩展了Dzubiella、Swanson和McCammon [Phys. Rev. Lett. 2006，96，087802和J. Chem. Phys. 2006，124，084905]以包括溶质分子力学。我们还开发了一种新的计算方法，结合水平集技术与优化算法，以确定数值的非极性分子的平衡构象。数值结果表明，我们的新模型和方法可以捕捉到非极性分子的基本性质及其与溶剂的相互作用。特别是，与一个合适的选择的Tolman长度的曲率校正的表面张力，我们得到的溶剂化自由能的苯分子在一个很好的协议与实验结果。
We construct a variational explicit-solute implicit-solvent model for the solvation of molecules. Central in this model is an effective solvation free-energy functional that depends solely on the position of solute-solvent interface and solute atoms. The total free energy couples altogether the volume and interface energies of solutes, the solute-solvent van der Waals interactions, and the solute-solute mechanical interactions. A curvature dependent surface tension is incorporated through the so-called Tolman length which serves as the only fitting parameter in the model. Our approach extends the original variational implicit-solvent model of Dzubiella, Swanson, and McCammon [Phys. Rev. Lett. 2006, 96, 087802 and J. Chem. Phys. 2006, 124, 084905] to include the solute molecular mechanics. We also develop a novel computational method that combines the level-set technique with optimization algorithms to determine numerically the equilibrium conformation of nonpolar molecules. Numerical results demonstrate that our new model and methods can capture essential properties of nonpolar molecules and their interactions with the solvent. In particular, with a suitable choice of the Tolman length for the curvature correction to the surface tension, we obtain the solvation free energy for a benzene molecule in a good agreement with experimental results.
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影响因子：
6.1
作者：
CONNOLLY, ML
通讯作者：
CONNOLLY, ML
影响因子：
5.6
作者：
LEE, B;RICHARDS, FM
通讯作者：
RICHARDS, FM
影响因子：
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作者：
Chen, Jianhan;Brooks, Charles L., III
通讯作者：
Brooks, Charles L., III
影响因子：
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作者：
RICHMOND, TJ
通讯作者：
RICHMOND, TJ
影响因子：
4.4
作者：
BUFF, FP
通讯作者：
BUFF, FP