Although molecular dynamics (MD) simulations of biomolecular systems often run for days
to months, many events of great scientific interest and pharmaceutical relevance occur on …

Results of a series of hybrid quantum mechanical/molecular mechanical (QM/MM) activated
dynamics simulations of thio effects in the transphosphorylation (methanolysis) of a 2‘-ribose…

Na + /H + antiporters are central to cellular salt and pH homeostasis. The structure of Escherichia
coli NhaA was recently determined, but its mechanisms of transport and pH regulation …

Transphosphorylation thio effects in solution are studied using hybrid QM/MM calculations
with a d-orbital semiempirical Hamiltonian. Activated dynamics simulations were performed …

In constrained molecular dynamics simulations using some of the most popular molecular
dynamics codes, calculation of the velocities of constrained particles is based solely on the …

Advances in computational chemistry create an ongoing need for larger and higher-quality
datasets that characterize noncovalent molecular interactions. We present three benchmark …

New methods for the calculation of electrostatic interactions between the active dynamical
region and surrounding external solvated macromolecular environment in hybrid quantum …

A series of high-order surface element discretization schemes for variational boundary
element methods are introduced. The surface elements are chosen in accord with angular …

Primary and secondary kinetic and equilibrium isotope effects are calculated with density-functional
methods for the in-line dianionic methanolysis of the native (unsubstituted) and thio-…

Two new charge‐scaling methods for efficient modeling of the solvated macromolecular
environment in hybrid QM/MM calculations of biological reactions are presented. The methods …