Molecular dynamics of a model S N2 reaction in water

Abstract

Molecular dynamics are computed for a model SN2 reaction Cl−+CH3Cl→ClCH3+Cl− in water and are found to be strongly dependent on the instantaneous local configuration of the solvent at the transition state barrier. There are significant deviations from the simple picture of passage over a free energy barrier in the reaction coordinate, and thus, a marked departure from transition state theory occurs in the form of barrier recrossings. Factors controlling the dynamics are discussed, and, in particular, the rate of change of atomic charge distribution along the reaction coordinate is found to have a major effect on the dynamics. A simple frozen solvent theory involving nonadiabatic solvation is presented which can predict the outcome of a particular reaction trajectory by considering only the interaction with the solvent of the reaction system at the gas-phase transition barrier. The frozen solvent theory also gives the transmission coefficient κ needed to make the transition state theory rate agree with the outcome of the molecular dynamics trajectories. This theoretical κ value, which is the implementation for the SN2 reaction of the van der Zwan–Hynes nonadiabatic solvation transmission coefficient, is in good agreement with the trajectory results. In contrast, a Kramers theory description fails dramatically.

Molecules in Motion: Chemical Reaction and Allied Dynamics in Solution and Elsewhere

“…But there are no such physical oscillators responsible for the binary collisional friction! Rather than belabor such points here, I simply refer the interested reader to recent developments on the general basic issue (67,68) and instead discuss what we ourselves focused on: testing the theory and applying it to learn important things about assorted reaction types.GHT testing via MD computer simulations began in earnest collaboration with Wilson and his students for reasonably realistic models of several activated reaction types: the A + BC reaction in rare-gas solvents mentioned above and the Cl − + CH 3 Cl S N 2 nucleophilic substitution reaction in liquid water (42,69,70). The first notable result was that the theory agreed with the MD results, to within the latter's error bars.…”

Statistical Analyses and Theoretical Models of Single-Molecule Enzymatic Dynamics

“…Wilson, Hynes, and coworkers have pioneered MD simulations of solution phase chemical reactions. 32 Neria and Karplus have done MD simulation of triosephosphate isomerase and shown that small structural changes have large effects on the rate enhancement. 33 The MD trajectories allowed them to obtain the transmission coefficient correction to transition state theory.…”

Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions

“…Because of the existence of recrossings the transition state theory (TST) rate constant must be corrected by a transmission coefficient, , which will be less than unity. To compute  we used the "positive flux" formulation, 31 by assuming that the trajectory was initiated …”

“…3). 31 As seen in Figure 3, 65 fs after the passage over the top of the barrier, the transmission coefficient arrives to a plateau value of 0.51, which means that the fate of the reaction is completely The information obtained from the time-evolution of the transmission coefficient can be combined with the atomistic description obtained from the reactive trajectories presented in Figure 4 to have a more detailed view of the reaction process. The average evolution of the C6-C7 distance and the total charge on carbon dioxide are plotted versus the reaction time.…”