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用于线性和环状醚的加性和经典德鲁德可极化力场。

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

作者信息

Vorobyov Igor, Anisimov Victor M, Greene Shannon, Venable Richard M, Moser Adam, Pastor Richard W, MacKerell Alexander D

机构信息

Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, and Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892.

出版信息

J Chem Theory Comput. 2007 May;3(3):1120-33. doi: 10.1021/ct600350s.

Abstract

Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers. Initiation of the optimization process involved validation of the aliphatic parameters based on linear alkanes and cyclic alkanes. Results showed the transfer to cyclohexane to yield satisfactory agreement with target data; however, in the case of cyclopentane direct transfer of the Lennard-Jones parameters was not sufficient due to ring strain, requiring additional optimization of these parameters for this molecule. Parameters for the ethers were then developed starting with the available aliphatic parameters, with the nonbond parameters for the oxygens optimized to reproduce both gas- and condensed-phase properties. Nonbond parameters for the polarizable model include the use of an anisotropic electrostatic model on the oxygens. Parameter optimization emphasized the development of transferable parameters between the ethers of a given class. The ether models are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties, and the resulting parameters are transferable to test molecules. The presented force field will allow for simulation studies of ethers in condensed phase and provides a basis for ongoing developments in both additive and polarizable force fields for biological molecules.

摘要

本文给出了与CHARMM加和式及基于经典德鲁德极化力场一致的线性和环状醚的经验力场参数。优化过程的启动涉及基于线性烷烃和环状烷烃对脂肪族参数进行验证。结果表明,将参数转移至环己烷时,与目标数据吻合良好;然而,在环戊烷的情况下,由于环张力,直接转移Lennard-Jones参数并不足够,需要对该分子的这些参数进行额外优化。然后从现有的脂肪族参数出发,开发醚的参数,优化氧原子的非键参数以重现气相和凝聚相性质。极化模型的非键参数包括在氧原子上使用各向异性静电模型。参数优化着重于开发给定类别醚之间的可转移参数。醚模型与纯溶剂及水合性质均吻合良好,所得参数可转移至测试分子。所提出的力场将有助于进行凝聚相中醚的模拟研究,并为生物分子加和式及极化力场的持续发展提供基础。

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