当前位置: X-MOL 学术J. Chem. Theory Comput. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network.
Journal of Chemical Theory and Computation ( IF 5.5 ) Pub Date : 2020-06-11 , DOI: 10.1021/acs.jctc.0c00018
Takuro Tsutsumi 1 , Yuriko Ono 2 , Zin Arai 3 , Tetsuya Taketsugu 1, 2, 4
Affiliation  

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 SN2 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 Au5 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.

中文翻译:

动态效果的可视化:将飞行轨迹投影到静态反应路径网络所跨越的子空间。

继我们最近的工作,以减少一组参考结构的沿内禀反应坐标(IRC)的经典多维尺度(CMDS)方法(的尺寸J.化学理论COMPUT。201814,4263-4270),我们建议该方法使用CMDS的样本外扩展将飞行轨迹投影到IRC网络确定的降维子空间中。该方法应用于S Ñ 2反应,OH - + CH 3女,其中轨迹示出了IRC路径的高度弯曲的区域周围分叉性质,以及Au中的结构转变5集群中,全球反应路径网络由五个平衡结构和14个IRC组成。已经证明,本分析可以通过基于静态反应路径显示动态反应路径来可视化动力学效果。
更新日期:2020-07-14
down
wechat
bug