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机器智能引导的药物设计。

Diabatization by Machine Intelligence.

机构信息

Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States.

出版信息

J Chem Theory Comput. 2020 Oct 13;16(10):6456-6464. doi: 10.1021/acs.jctc.0c00623. Epub 2020 Sep 21.

DOI:10.1021/acs.jctc.0c00623
PMID:32886513
Abstract

Understanding nonadiabatic dynamics is important for chemical and physical processes involving multiple electronic states. Direct nonadiabatic dynamics simulations are often employed to observe such processes on a femtosecond time scale. One often needs to do the simulation on a longer time scale, but direct simulation based on electronic structure calculations of the surfaces and couplings is expensive due to the large number of electronic structure calculations needed for ensemble averaging or simulation of longer-time processes. An alternative approach is to construct an analytical representation of potential energy surfaces (PESs) and couplings, which allows for faster dynamics calculations. Diabatic representations are preferred for such purposes because of the smoothness of the surfaces and couplings and the scalar nature of the couplings. However, many diabatization procedures are complicated by the need to consider orbitals or vector coupling elements, and these can make the process very labor-intensive. To circumvent these difficulties, we here propose diabatization by a deep neural network (DDNN) based on a new architecture for a deep neural network that requires neither orbital input nor vector input. The DDNN method allows convenient and semiautomatic diabatization, and it is demonstrated here for a model problem and for producing diabatic potential energy matrices for thiophenol.

摘要

理解涉及多个电子态的化学和物理过程中的非绝热动力学很重要。直接非绝热动力学模拟常用于在飞秒时间尺度上观察这些过程。人们通常需要在更长的时间尺度上进行模拟,但由于需要进行大量的表面和耦合电子结构计算来进行集合平均或模拟更长时间的过程,基于电子结构计算的直接模拟代价很高。一种替代方法是构建势能面(PES)和耦合的解析表示,这允许进行更快的动力学计算。由于表面和耦合的光滑性以及耦合的标量性质,因此首选绝热表示。然而,许多绝热化程序由于需要考虑轨道或矢量耦合元素而变得复杂,这使得过程非常耗费人力。为了规避这些困难,我们在这里提出了一种基于深度神经网络(DDNN)的绝热化方法,该方法基于一种新的深度神经网络架构,既不需要轨道输入也不需要矢量输入。DDNN 方法允许方便和半自动的绝热化,并且在这里针对模型问题和生成噻酚的非绝热势能矩阵进行了演示。

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