Metal ions play significant roles in numerous fields including chemistry, geochemistry,
biochemistry, and materials science. With computational tools increasingly becoming …

In this work, we review recent extensions of the density functional tight binding (DFTB)
methodology and its application to organic and biological molecules. DFTB denotes a class …

MCPB. py, a python based metal center parameter builder, has been developed to build
force fields for the simulation of metal complexes employing the bonded model approach. It …

Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD)
simulations on these systems require a validated set of parameters. Although there are more …

Highly charged metal ions act as catalytic centers and structural elements in a broad range
of chemical complexes. The nonbonded model for metal ions is extensively used in …

We report the parametrization of the approximate density functional theory, DFTB3, for
magnesium and zinc for chemical and biological applications. The parametrization strategy …

Allostery is a ubiquitous biological regulatory process in which distant binding sites within a
protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions …

Commonly seen in rare-earth chemistry and materials science, highly charged metal ions
play key roles in many chemical processes. Computer simulations have become an …

Due to the higher computational cost relative to pure molecular mechanical (MM)
simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy …

Allosteric communication between two ligand-binding sites in a protein is a central aspect of
biological regulation that remains mechanistically unclear. Here we show that perturbations …