Abinitio calculations and the chemical reaction molecular dynamics simulation

Abstract

To clarify the mechanism of chemical reactions in solution, each solvent molecule was classified as either a reactive-solvent molecule or a medium-solvent molecule in accordance with its role in the reaction. The proton transfer reaction of formamidine in water was treated as a model reaction. Abinitio molecular orbital calculations were performed for the complex made up of a formamidine, a reactive-water molecule, and a medium-water molecule. The optimized geometries and the solvation energies were obtained and the orbital interaction analysis carried out along the intrinsic reaction coordinate (IRC). It was found that the medium-water molecule influences the reaction dynamically rather than energetically. There was no energy change in the potential barrier under the influence of the medium-water molecule, in contrast to the remarkable barrier-reducing effect of the reactive-water molecule. The situation is different from that in chemical reactions involving ionic states. Chemical reaction molecular dynamics (CRMD) simulation for this system was performed in order to investigate the energy relaxation mechanism. It was found that just after the reaction finishes, a relative translational motion is first induced between the super molecule, which consists of a formamidine and a reactive-water molecule, and the medium-water molecule, and is then followed by a rotational motion of the medium-water molecule. Keywords: formamidine, chemical reaction molecular dynamics method, reactive-solvent molecule, medium-solvent molecule, energy relaxation mechanism.