Analyses of trajectory on-the-fly based on the global reaction route map

Abstract

A methodology to analyze a trajectory on-the-fly (TOF) based on a global reaction route map consisting of intrinsic reaction coordinate (IRC) pathways is proposed. By using the distance functions in the configurational space, the location of each point on the trajectories is detected, providing a dynamical picture that the molecular system goes over several minima and transition states in the reaction path network. In its application to structural transformations of an Au cluster, a variety of reaction routes are obtained, and the hopping from one IRC to another IRC (IRC-jump) is analyzed. The branching of trajectories over many minima on the potential energy surface via valley-ridge transition points is also discussed.

Benchmark ab initio and dynamical characterization of the stationary points of reactive atom + alkane and SN2 potential energy surfaces

“…We perform this transformation for all the stationary points, and the assignment is made by minimizing the root-mean-square distances of the Cartesian coordinates of the actual trajectory geometry and the stationary points with respect to the different stationary-point structures. Note that similar automated reaction mechanism assignment technique was also reported by Taketsugu and co-workers, 130 where the trajectory geometries are assigned to structures along intrinsic reaction coordinates using a minimum-distance method via the Kabsch algorithm. 131 Fig.…”

A Trajectory-Based Method to Explore Reaction Mechanisms

“…By contrast, GRRM predicted three consecutive steps for the shortest path of the WGSR [35]. The discovery of the new TS is a consequence of the highly non-IRC [96] nature of the trajectories employed in tsscds [45]; in other words, IRC jumps are not uncommon events [97]. This exemplifies one of the advantages of using trajectory-based methods to discover new reactions: we are not restricted to unimolecular reactions and the only constrain to discover new processes is the molecular formula of the system.…”

A Trajectory-Based Method to Explore Reactions Mechanisms

“…By contrast, GRRM predicted a shortest path for the WGSR with three TSs [35]. The discovery of the new TS is a consequence of the highly non-IRC [83] nature of the trajectories employed in tsscds [45]; in other words, IRC jumps are not an uncommon event [84]. The huge amounts of vibrational energy put in the normal modes enhances configurational space sampling in tsscds.…”