Implicit solvation models are popular alternatives to explicit solvent methods due to their ability to "pre-average" solvent behavior and thus reduce the need for computationally-expensive sampling. Previously, we have demonstrated that Poisson-Boltzmann models for polar solvation and integral-based models for nonpolar solvation can reproduce explicit solvation forces in a low-charge density pr...

Continuum electrostatics methods have become increasingly popular due to their ability to provide approximate descriptions of solvation energies and forces without expensive sampling required by explicit solvent models. In particular, the Poisson-Boltzmann equation (PBE) provides electrostatic potentials, solvation energies, and forces by modeling the solvent as a featureless, dielectric materi...

A theoretical study at the B3LYP/6-31++G(d,p) level was performed on the tatumerization of 7H-purine-2, 6-diamine into 9H-purine-2, 6-diamine. Such a tautomerism can take place via three different pathways namely A, B, and C. The energetic results associated with the gas phase reveal that pathways A, B, and C display a very high activation Gibbs free energy of 45.1, 68.6 and 48.9 kcal/mol, resp...

Is an all-atom representation for protein and solvent necessary for simulating protein folding kinetics or can simpler models reproduce the results of more complex models? This question is relevant not just for simulation methodology, but also for the general understanding of the chemical details relevant for protein dynamics. With recent advances in computational methodology, it is now possibl...

Density-functional and semiempirical quantum methods and continuum dielectric and explicit solvation models are applied to study the role of solvation on the stabilization of native and thio-substituted transphosphorylation reactions. Extensive comparison is made between results obtained from the different methods. For the semiempirical methods, explicit solvation was treated using a hybrid qua...