Analysis of Fundamental Organic Reaction Mechanisms by Using Molecular Dynamics Simulations: The Dynamics Effect on the Reaction Pathway

Abstract

Recently, dynamics effect is claimed to be a very important factor in determining the reaction mechanisms. In molecular dynamics (MD) simulations of the Beckmann rearrangement/fragmentation, E2/E1cb, and carbonyl addition/substitution, the dynamic path bifurcation was observed, where two reaction products were obtained dynamically depending on the shape of the potential energy surface after passing through the corresponding transition state (TS). This is a very significant problem because the strategies of organic syntheses are generally based on the transition state theory, intending to stabilize/destabilize the TS of a desired/undesired reaction relative to the other ones. As applications of the MD simulations in solution chemistry, fundamental organic reactions (S_N2 reaction of the methyl diazonium ion, hydration and amination of formaldehyde) in water solution were examined by using the fragment molecular orbital method with MD, FMO-MD. These simulations revealed that the reactions in solution are more complicated and various than one would expect.