Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network
Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network
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DOI：
10.1021/acs.jctc.0c00018
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发表时间：
2020-07-14
影响因子：
5.5
通讯作者：
Taketsugu, Tetsuya
中科院分区：
文献类型：
--
作者：
Tsutsumi, Takuro;Ono, Yuriko;Taketsugu, Tetsuya
在我们最近通过经典多维标度（CMDS）方法（J. Chem. Theory Comput. 2018，14，4263-4270），我们提出了使用CMDS的样本外扩展将飞行轨迹投影到由IRC网络确定的降维子空间中的方法。该方法被应用于S（N）2反应OH- + CH 3F，其中轨迹在IRC路径的高度弯曲区域附近表现出分叉的性质，以及Au-5团簇的结构转变，其中全局反应路径网络由5个平衡结构和14个IRC组成。结果表明，本分析可以可视化的动力学效果，显示动态反应路径的基础上的静态反应路径。
Following our recent work to reduce a dimension of a set of reference structures along the intrinsic reaction coordinate (IRC) by a classical multidimensional scaling (CMDS) approach (J. Chem. Theory Comput. 2018, 14, 4263-4270), we propose the method to project on-the-fly trajectories into a reduced-dimension subspace determined by the IRC network, using the out-of-sample extension of CMDS. The method was applied to the S(N)2 reaction, OH- + CH3F, in which trajectories show a bifurcating nature around the highly curved region of the IRC path, and to the structural transformation of Au-5 cluster in which the global reaction path network consists of five equilibrium structures and 14 IRCs. It was demonstrated that the present analysis can visualize the dynamics effect by showing a dynamic reaction route on the basis of the static reaction paths.