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巴恩斯更新在高斯-牛顿法中的应用:一种改进的键断裂点定位算法。

Barnes Update Applied in the Gauss-Newton Method: An Improved Algorithm to Locate Bond Breaking Points.

机构信息

Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.

Institut de Química Teòrica i Computacional, (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain.

出版信息

J Chem Theory Comput. 2021 Feb 9;17(2):996-1007. doi: 10.1021/acs.jctc.0c00910. Epub 2021 Jan 19.

Abstract

A mechanochemical reaction is a reaction induced by mechanical energy. A general accepted model for this type of reaction consists of a first-order perturbation on the associated potential energy surface (PES) of the unperturbed molecular system due to mechanical stress or pulling force. Within this theoretical framework, the so-called optimal barrier breakdown points or optimal bond breaking points (BBPs) are critical points of the unperturbed PES where the Hessian matrix has a zero eigenvector that coincides with the gradient vector. Optimal BBPs are "catastrophe points" that are particularly important because their associated gradient indicates how to optimally harness tensile forces to induce reactions by transforming a chemical reaction into a barrierless process. Building on a previous method based on a nonlinear least-squares minimization to locate BBPs (Bofill et al., , 147, 152710-10), we propose a new algorithm to locate BBPs of any molecular system based on the Gauss-Newton method combined with the Barnes update for a nonsymmetric Jacobian matrix, which is shown to be more appropriate than the Broyden update. The efficiency of the new method is demonstrated for a multidimensional model PES and two medium size molecular systems of interest in enzymatic catalysis and mechanochemistry.

摘要

机械化学反应是由机械能引起的反应。这种类型反应的一个普遍接受的模型包括由于机械应力或拉力对未受扰分子系统的相关势能面(PES)的一级微扰。在这个理论框架内,所谓的最优势垒断裂点或最优键断裂点(BBPs)是未受扰 PES 的关键点,其中 Hessian 矩阵具有与梯度向量重合的零特征向量。最优 BBPs 是“灾变点”,它们特别重要,因为它们相关的梯度指示如何通过将化学反应转化为无势垒过程来最佳地利用拉伸力来诱导反应。在先前基于非线性最小二乘法定位 BBPs 的方法(Bofill 等人,[147],152710-10)的基础上,我们提出了一种新的算法,该算法基于 Gauss-Newton 方法并结合 Barnes 更新用于非对称 Jacobian 矩阵,事实证明,该方法比 Broyden 更新更合适。该新方法的效率在多维模型 PES 和两个中等大小的分子系统中得到了证明,这两个系统在酶催化和机械化学中具有重要意义。

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