The Principal Component Analysis of the Ring Deformation in the Nonadiabatic Surface Hopping Dynamics

The analysis of the leading active molecular motions in the on-the-fly trajectory surface hopping stimulation provides the essential information to understand the geometrical evolution in nonadiabatic dynamics. When the ring deformation is involved, the identification of the key active coordinates becomes challenging. A "hierarchical" protocol based on the dimensionality reduction method and clustering approaches is proposed for the automatic analysis of the ring deformation in the nonadiabatic molecular dynamics. The representative system keto isocytosine is taken as the prototype to illustrate this protocol. The results indicate that the current hierarchical analysis protocol is a powerful way to clearly clarify both of the major and minor active molecular motions of the ring distortion in nonadiabatic dynamics.