A model SN2 reaction of 2-chlorobutane with OH− is examined from the dynamical point of view by means of the molecular dynamics (MD) methods. The reactions are simulated in both the gas phase and the water solvent by the QM- and the ONIOM-MD methods, respectively. The MD simulations show that a migration of the kinetic energy between the atoms generated by the fluctuation of the kinetic energy of the atoms triggers the reaction. When some requirements of the velocity vector with a certain direction of the specific atoms participating in the reaction are satisfied by the migration of the kinetic energy, the substrate is led to the transition state and then to the product in turn. The time required to pass the transition state becomes shorter in the water solvent compared to the case of the gas phase, which shows that the reaction proceeds more quickly in the water solvent. Another pattern of the requirement of the velocity vector with a certain direction of the specific atoms for the reaction, which makes the reaction rate faster, is also found at a higher temperature in the water solvent.
We had previously developed o2p, a parameter conversion semi-automation program for polymers with repeating structures, and PolyParGen, a parameter acquisition program primarily meant for chainlike macromolecules. These programs use the parameters obtained via the automatic parameter generation tool. However, with these programs, it is difficult to acquire parameters of molecules with crosslinked structures or large condensed ring structures. To acquire these parameters, herein we improved the algorithm to develop PolyParGen v2. Further, this program adds Antechamber as the automatic parameter generation tool and can obtain the Amber force field parameter for polymers. This program was evaluated via simulations using graphene, carbon nanotubes, and fullerene. Our results agree with those of previous studies and verify the effectiveness of the proposed program.