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Microscopic simulations of chemical reactions in solution were pioneered in Warshel's work [1]. This included the use of molecular dynamics to evaluate the activation free energies of chemical reactions in solution, developing the microscopic equivalent of Marcus' parabolas for electron transfer reactions [2] [3], and introducing the practical microscopic simulations of Dispersed Polaron approach for simulating nuclear tunneling effects in electron transfer reactions. This Dispersed Polaron approach is sometime known as the Spin-Boson model. We were also the first that implemented path integral centroid methods in simulating chemical reactions in solutions and enzymes [4] [5]. Our "work horse" in the studies of chemical reactions in solution has been the EVB method. This method, which is now used widely by other research groups [6], provided for the first time a correct coupling between the solute Hamiltonian and the solvent field and allows us to evaluate nonequilibrium solvation effets in a consistent way. The EVB also provides what is at present the most consistent way of transferring ab initio gas phase potential surfaces to solution. We also made significant advances in pioneering QM/MM studies of chemical reactions in solution [7]. Our progress in this direction is now focused on approaches that couple the Langevin Dipole (LD) model with ab initio methods [8] and in using the EVB model as a reference potential for ab initio QM/MM simulations [9] and on EVB driven ab initio simulations of all-atom solvent models.
More recently, with the emergence of more computer power we started to use ab initio QM/MM (QM(ai)/MM) methods with the EVB as a reference potential, which we named paradynamics (PD) [10] in studies of chemical reactions in solutions. We also advanced in evaluating the QM(ai)/MM free energy surfaces in solution reactions that serve as reference reactions for key biological processes [11]. Overall a major part of our current studies of reactions in solution is focused on constructing the reference reactions for biological reactions:
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