There are many ways of looking at the rare events.
I am concentrating on ways to find the minimum free
energy path, that is the path that minimze the free energy while going from
the reactant to the product during a chemical reaction.
Mechanism of Organic reactions
In collaborations with experimentalist chemists, we use computational chemistry to study the mechanism of different organic and organometallic reactions.
One of our last study consisted in comparing the Ugi and the Ugi-Smiles reactions.
Mechanism of Heck reaction as a Ugi(-Smiles) post-condensation
We used computational chemistry to study the mechanism of the indole formation via a Heck reaction.
Reaction path construction and determination
Computational chemistry has now become a standard tool to evaluate
energy (and free energy) differences along a reaction path.
However, when dealing with
chemical reactions, one often
relies on ab initio programs. This
leads in turn to simulation costs much higher than for classical
force fields. As a consequence, one must look for ways to i)
generate initial path as close as possible to the unknown actual
path, and ii) efficient ways to optimize this path.
Many methods already exist for the
optimization of reaction path such as the Nudged Elastic Band (NEB)
method and the String method. In both approaches, the reaction
path is discretized as an ensemble of intermediate structures
(called images) describing the transformation of the reactants into
the products. The originality of our approach is to use different sets of
coordinates to describe the system. This is implemented in a home