See also my personal webpage: http://www.acmm.nl/ensing
Protons and electrons are very light particles that can move with a high velocity, but in practice their transfer is strongly affected by the medium. The conductivity is governed by the solvent fluctuations. Confinement of the solvent in one or more dimensions affects the transfer mechanism. The solvent reorganization free energy is an important part of both the redox potential and the acidity constants of acceptor solutes.
Photoactive proteins are light sensors that allow plants to turn their leafs toward the sun and allow animals (and people) to see. They form the perfect study ground to understand how (sensor) proteins work, because they can simply be activated with a flash of (laser) light, after which their functioning is probed.
We have developed a hybrid molecular dynamics method that is multiscale in both space and in time. This is particularly useful for large systems for which overall only a coarsegrained description is feasible. The hybrid MD method allows molecules to adapt their representation, between a fully atomistic and a coarsegrained resolution, on the fly in a smooth manner.
Chemical reactions are rare events on the picosecond time scale available to ab initio dynamics simulations. Using the metadynamics method we can nevertheless probe the multi-dimensional free energy landscape underlying (concerted) reactions. The lowest free energy path in this landscape provides important insight into the mechanism and rate of reactions.
thesis work with prof. E.J. Baerends
Solvent effects can have a very large influence on the thermodynamics and the kinetics of chemical reactions in water. We used Car-Parrinello molecular dynamics simulations to study these effects on prototypical organic reactions and on certain transition metal catalyzed oxidation reactions (Fenton chemistry).