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本文引用的文献

1
Reactive molecular dynamics models from molecular dynamics data using relative entropy minimization.基于相对熵最小化,从分子动力学数据构建反应性分子动力学模型。
Chem Phys Lett. 2017 Sep 1;683:573-578. doi: 10.1016/j.cplett.2017.04.064. Epub 2017 Apr 22.
2
Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data.通讯:通过最小化实验数据偏差改进从头算分子动力学
J Chem Phys. 2017 Jan 28;146(4):041102. doi: 10.1063/1.4974837.
3
Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.水中分子相互作用的建模:从成对到多体势能函数
Chem Rev. 2016 Jul 13;116(13):7501-28. doi: 10.1021/acs.chemrev.5b00644. Epub 2016 May 17.
4
Perspective: How good is DFT for water?观点:密度泛函理论对水的适用性如何?
J Chem Phys. 2016 Apr 7;144(13):130901. doi: 10.1063/1.4944633.
5
A Direct Method for Incorporating Experimental Data into Multiscale Coarse-Grained Models.一种将实验数据纳入多尺度粗粒度模型的直接方法。
J Chem Theory Comput. 2016 May 10;12(5):2144-53. doi: 10.1021/acs.jctc.6b00043. Epub 2016 Apr 15.
6
Defining Condensed Phase Reactive Force Fields from ab Initio Molecular Dynamics Simulations: The Case of the Hydrated Excess Proton.从从头算分子动力学模拟定义凝聚相反应力场:水合过量质子的案例。
J Chem Theory Comput. 2010 Oct 12;6(10):3223-32. doi: 10.1021/ct1004438. Epub 2010 Sep 23.
7
Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient.具有柔性单体的“第一性原理”水势的发展:二聚体势能面、VRT光谱和第二维里系数。
J Chem Theory Comput. 2013 Dec 10;9(12):5395-403. doi: 10.1021/ct400863t. Epub 2013 Nov 25.
8
Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data.利用实验数据使分子模拟产生偏差的高效极简方法。
J Chem Theory Comput. 2014 Aug 12;10(8):3023-30. doi: 10.1021/ct500320c. Epub 2014 Jul 2.
9
Development of a "First-Principles" Water Potential with Flexible Monomers. III. Liquid Phase Properties.具有柔性单体的“第一性原理”水势的发展。III. 液相性质。
J Chem Theory Comput. 2014 Aug 12;10(8):2906-10. doi: 10.1021/ct5004115. Epub 2014 Jul 8.
10
Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport.预溶剂化与非谐性在水相水合质子溶剂化和传输中的作用
J Phys Chem B. 2016 Mar 3;120(8):1793-804. doi: 10.1021/acs.jpcb.5b09466. Epub 2015 Dec 1.

使用从头算分子动力学模拟最小化偏向实验数据的方法开发反应力场。

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.

机构信息

Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.

出版信息

J Chem Phys. 2017 Oct 28;147(16):161719. doi: 10.1063/1.4985903.

DOI:10.1063/1.4985903
PMID:29096465
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5584654/
Abstract

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

摘要

将量子力学电子结构数据纳入其中对于正确捕捉许多化学过程的物理性质是必要的。质子在水中的跳跃,涉及化学和氢键的重排,就是这样一个内在的量子力学过程的例子。然而,标准的从头算分子动力学 (AIMD) 方法还不能准确预测水的结构,因此对于开发力场来说不太理想。我们转而利用了一种新开发的方法,该方法最小化地偏向 AIMD 模拟,以匹配有限的实验数据,通过使用相对熵最小化来开发新的多尺度反应分子动力学 (MS-RMD) 力场。在本文中,我们提出了两种使用这种参数化的新的 MS-RMD 模型:一种使用具有谐波内振动的水,另一种使用非谐波水。我们表明,新开发的 MS-RMD 模型非常紧密地再现了目标 AIMD 数据中水合过量质子的溶剂化结构。我们还发现使用非谐波水会增加质子跳跃,从而增加质子扩散常数。