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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.用于蛋白质的OPLS(液体模拟优化势)势函数、环肽和克拉宾晶体的能量最小化。
J Am Chem Soc. 1988 Mar 1;110(6):1657-66. doi: 10.1021/ja00214a001.
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Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.用于线性和环状醚的加性和经典德鲁德可极化力场。
J Chem Theory Comput. 2007 May;3(3):1120-33. doi: 10.1021/ct600350s.
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Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields.用于使用Amber和Charmm力场进行生物模拟的水的可极化平均场模型。
J Chem Theory Comput. 2012 Sep 11;8(9):3207-3216. doi: 10.1021/ct300011h.
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Electronic Polarizability and the Effective Pair Potentials of Water.水的电子极化率与有效对势
J Chem Theory Comput. 2010 Oct 12;6(10):3153-3161. doi: 10.1021/ct1002048.
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Electronic continuum model for molecular dynamics simulations of biological molecules.用于生物分子分子动力学模拟的电子连续介质模型。
J Chem Theory Comput. 2010;6(5):1498-508. doi: 10.1021/ct9005807.
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All-atom empirical potential for molecular modeling and dynamics studies of proteins.蛋白质分子建模和动力学研究的全原子经验势。
J Phys Chem B. 1998 Apr 30;102(18):3586-616. doi: 10.1021/jp973084f.
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Force Field for Peptides and Proteins based on the Classical Drude Oscillator.基于经典德鲁德振子的肽和蛋白质力场
J Chem Theory Comput. 2013 Dec 10;9(12):5430-5449. doi: 10.1021/ct400781b.
8
The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.用于蛋白质的基于可极化原子多极矩的AMOEBA力场
J Chem Theory Comput. 2013;9(9):4046-4063. doi: 10.1021/ct4003702.
9
Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization.水合硫酸根阴离子的溶剂化和离子对特性:显式与有效电子极化。
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Accurate description of aqueous carbonate ions: an effective polarization model verified by neutron scattering.准确描述碳酸根离子的水溶液:经中子散射验证的有效极化模型。
J Phys Chem B. 2012 Jul 19;116(28):8145-53. doi: 10.1021/jp3008267. Epub 2012 Jul 10.

凝聚相中的可极化分子相互作用及其等效的非极化模型。

Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

作者信息

Leontyev Igor V, Stuchebrukhov Alexei A

机构信息

Department of Chemistry, University of California Davis, One Shields Avenue, Davis, California 95616, USA.

出版信息

J Chem Phys. 2014 Jul 7;141(1):014103. doi: 10.1063/1.4884276.

DOI:10.1063/1.4884276
PMID:25005273
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4106032/
Abstract

Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnP-type models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of 1/√(ε(el)), which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

摘要

此前,我们采用现象学方法表明,在某些情况下,凝聚相系统的可极化模型可以简化为具有缩放电荷的非可极化等效模型。此类系统的例子包括离子液体、水的TIPnP型模型、蛋白质力场等,其中固有可极化物种的相互作用和动力学可以通过非可极化模型准确描述。为了描述静电相互作用,简单离子液体的有效电荷是通过将离子的实际电荷按1/√(ε(el))的因子进行缩放得到的,这是由于电子极化屏蔽效应;中性物种的缩放因子则更为复杂。在这里,我们使用几种理论模型,研究缩放因子在理论中究竟是如何出现的,以及可极化哈密顿量如何以及在何种条件下简化为非可极化哈密顿量。这些模型使我们能够追溯缩放因子的起源,确定其值,并获得关于凝聚态物质系统中可极化相互作用本质的重要见解。