Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion

Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion.

A detailed parameterization is presented of a zinc ion with one histidine and two cysteinate ligands, together with one or two water, hydroxide, aldehyde, alcohol, or alkoxide ligands. The parameterization is tailored for the active site of alcohol dehydrogenase and is obtained entirely from quantum chemical computations. The force-field reproduces excellently the geometry of quantum chemically...

The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

The coordination number of the catalytic zinc ion in alcohol dehydrogenase has been studied by integrated ab initio quantum-chemical and molecular mechanics geometry optimisations involving the whole enzyme. A four-coordinate active-site zinc ion is 100-200 kJ/mol more stable than a five-coordinate one, depending on the ligands. The only stable binding site for a fifth ligand at the zinc ion is...

Surface Adsorption of Polyethylene Glycol and Polyvinyl Alcohol with Variable Molecular Weights on Zinc Oxide Nanoparticles

Molecular Dynamics Simulations of Atomic Collisions for Ion Irradiation Experiments

An understanding of the way damage is formed during ion implantation of solids is very important in many research and industrial applications. One of the best ways to study damage formation theoretically is provided by molecular dynamics simulations, in which the movement of atoms is followed by solving numerically the equations of motion. The purpose of work described in this thesis has been t...

Ion motions in molecular dynamics simulations on DNA.

Counterions play a significant role in DNA structure and function, and molecular dynamics (MD) simulations offer the prospect of detailed description of the dynamical structure of ions at the molecular level. However, the motions of mobile counterions are notably slow to converge in MD on DNA. Obtaining accurate and reliable MD simulations requires knowing just how much sampling is required for...