Help with molecular dynamics and computational modelling to check validity of hypothesis regarding SN2 reaction mechanisms
Your hypothesis concerning a "bouncing" contribution to the reaction kinetics would be incredibly difficult to observe or quantify even with the best supercomputers.  

The likelihood of a molecule to react in a manner like the SN2 reaction is actually an incredibly rare event at the molecular time scale (femtoseconds 10^-15 s). This may sound contradictory since these reactions are commonplace and occur readily under appropriate conditions (e.g. a few hours heating). However, the two timescales are separated by over 15 orders of magnitude. Many reactions which do approach the transition state can also revert back to the reactant, or in other words abort. So you'd have to run the incredibly long simulations thousands of times in order to see only a small number of reactions. This is the meaning of the pre-factor in the Arrhenius rate  equation

$k = Aexp(\frac{-\Delta G^\ddagger}{k_B T})$ 

Nevertheless, some of your intuition is correct. A molecule would indeed require momentum along the transition vector in order to overcome the highest energy point (the transition state) and pass over to the product. Otherwise it would return to reactant. Some of this velocity may naturally come from bouncing off a nearby solvent molecule.



Extra Information: 

The topic concerning the relationship of transition states and molecular dynamics is actually very complex and a major challenge in the field of chemistry.  The challenge essentially boils down 1) the size of the system and 2) the time length of the simulation. 

Fortunately for most practical cases we can simply ignore dynamical effects and study isolated because it is known that solvent interactions are generally weak and reactions closely follow the minimum energy paths.Therefore, the free energy at the transition state ($G^{\ddagger}$) can be approximated in solution using the Harmonic approximation and implicit solvent models like PCM. If you'd like to see how some of these calculations are done, please check out my GitHub on the growing string method (ref 1). These are much simpler to model and actually give a lot of information. Usually the transmission coefficient is assumed to be 1. or 0.5. 

If you're interested in some more advanced considerations of the relationship between dynamics and reaction barriers I'd recommend the following references: ref 2,3

References


"Single-ended transition state finding with the growing string method" Journal of Computational Chemistry 2015, 36, 601–611
"QM/MM Protocol for Direct Molecular Dynamics of Chemical Reactions in Solution: The Water-Accelerated Diels–Alder Reaction" J. Chem. Theory Comput. 2015, 11, 12, 5606-5612
https://cims.nyu.edu/~eve2/string.htm