Solvation effect on conformations of 1,2:dimethoxyethane:: Charge-dependent nonlinear response in implicit solvent models
Solvation effect on conformations of 1,2:dimethoxyethane:: Charge-dependent nonlinear response in implicit solvent models
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DOI：
10.1063/1.2815764
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发表时间：
2008-01-21
影响因子：
4.4
通讯作者：
Freed, Karl F.
中科院分区：
文献类型：
--
作者：
Jha, Abhishek K.;Freed, Karl F.
的物理内容，特别是，从Langevin-Debye模型的非线性贡献说明使用两个应用程序。首先，我们提供了一个改进的Langevin-Debye模型目前使用的一些隐式溶剂模型的溶剂化自由能的小有机分子，以及生物分子的折叠和绑定的计算机模拟。该分析是基于实施的电荷依赖的Langevin-Debye（qLD）模型，该模型通过随后的校正由于Onsager和柯克伍德修改。其次，阐明了该模型的物理内容，讨论了一般处理内的LD模型的自能的电荷淹没在电介质中的三个不同的限制条件，并考虑介质的非线性响应。修改后的qLD模型是用来完善一个隐式溶剂模型（以前应用于蛋白质动力学）。修正后的隐式溶剂模型的预测进行了比较，从明确的溶剂分子动力学模拟的平衡构象种群的1，2-二甲氧基乙烷（DME），这是最短的醚分子，以重现本地的构象特性的聚环氧乙烷，具有巨大的技术重要性和广泛的各种应用的聚合物。由于DME的构象群体偏好在溶剂化后发生显着变化，DME是验证我们修改后的qLD模型的一个很好的测试案例。目前的修改qLD模型的分析提供了动机和工具，研究各种各样的其他有趣的系统与异质介电性能和空间各向异性。(c)2008年美国物理学会。
The physical content of and, in particular, the nonlinear contributions from the Langevin-Debye model are illustrated using two applications. First, we provide an improvement in the Langevin-Debye model currently used in some implicit solvent models for computer simulations of solvation free energies of small organic molecules, as well as of biomolecular folding and binding. The analysis is based on the implementation of a charge-dependent Langevin-Debye (qLD) model that is modified by subsequent corrections due to Onsager and Kirkwood. Second, the physical content of the model is elucidated by discussing the general treatment within the LD model of the self-energy of a charge submerged in a dielectric medium for three different limiting conditions and by considering the nonlinear response of the medium. The modified qLD model is used to refine an implicit solvent model (previously applied to protein dynamics). The predictions of the modified implicit solvent model are compared with those from explicit solvent molecular dynamics simulations for the equilibrium conformational populations of 1,2-dimethoxyethane (DME), which is the shortest ether molecule to reproduce the local conformational properties of polyethylene oxide, a polymer with tremendous technological importance and a wide variety of applications. Because the conformational population preferences of DME change dramatically upon solvation, DME is a good test case to validate our modified qLD model. The present analysis of the modified qLD model provides the motivation and tools for studying a wide variety of other interesting systems with heterogeneous dielectric properties and spatial anisotropy. (c) 2008 American Institute of Physics.