(6hm) Molecular Simulations of Chemical Reactions

A 
chemical 
reaction 
requires 
the 
activation 
of 
reactants 
and 
successful 
passage 
through
 transition
 states
 to
 products.
 Reactants
 and
 products
 are
 long‐lived
 stable
 (or
 metastable)
 states, 
whereas 
transition 
states 
are 
activated 
complexes 
that 
are 
rarely 
and 
briefly 
visited.
 This
 separation
 of
 timescales
 inherent in chemical reactions is characteristic of rare events generally, including
 nucleation
 of
 1st‐order
 phase
 transitions,
 molecular
 isomerizations
 such
 as
 protein
 folding,
 and
 transport
 phenomena 
in 
solids 
and 
glasses.

Molecular simulation of rare events are complicated by the long waiting times for a transition to spontaneously occur. In my PhD work with Baron Peters and Joan-Emma Shea at the University of California, Santa Barbara, we developed new, simple methods for simulating rare events at the molecular level. We applied these methods to study aqueous ion-pair dissociation, vacancy diffusion in crystals, and the association of biomolecules in water.

One of my key frustrations as a PhD student was only being able to model systems at the classical level. In my postdoctoral work with Ed Maginn at the University of Notre Dame, we are integrating quantum calculations into classical simulations of condensed phases. To model CO2 reactivity in a task specific ionic liquid, we compute the change in free energy as CO2 binds to an anion via DFT and the solubility of CO2 in the ionic liquid via reaction ensemble Monte Carlo.