Time-Resolved Chemical Bonding Structure Evolution by Direct-Dynamics Chemical Simulations.

Direct-dynamics simulations monitor atomic nuclei trajectories during chemical reactions, where chemical bonds are broken and new ones are formed. While they provide valuable information about the ongoing nuclear dynamics, the evolution of the chemical bonds is customarily overlooked, thus, hindering key information about the reaction mechanism. Here we examine the evolution of the chemical bonds for the three main mechanisms of the F + CHCHCl reaction using quasi-classical trajectories for the nuclei, and global natural orbitals for the electrons. Key findings include (i) bimolecular nucleophilic substitution (S2) resembles a one-step bond breaking and formation process; (ii) the elimination mechanisms (- and -E2) feature a sequential two-step process of proton abstraction and Cl elimination; and (iii) the -E2 mechanism is slower, exhibits rebound effects, and gets activated by specific vibrational modes. This study highlights the importance of correctly describing and thoroughly analyzing the dynamical evolution of chemical bonds for chemical reaction mechanistic studies.