Computational Enzymology, a ReaxFF approach

This PhD project eassay is about the development of a new method to improve our understanding of enzyme catalysis with atomistic details. Currently the theory able to describe chemical systems and their reactivity is quantum mechanics (QM): electronic structure methods that use approximations of QM theory to describe molecular structure. Modeling enzyme reactions is anyway still inacessible to these methods because the size of the problem would result in many-particle equations too complicated to be solved even with rather crude approximations such as HartreeFock (HF). At the same time there are ordinary classical models - the molecular mechanics (MM) force-fields - that use newtonian mechanics to describe molecular systems. At this level it is possible to include the entire enzyme system still having light equations but renouncing to an easy modeling of chemical transformation during the simulation time. In short: on one hand we have accurate QM methods able to describe reactivity but limited in the size of the system to describe, while on the other hand we have molecular mechanics and ordinary force-fields that are virtually unlimited in size but unable to straightforwardly describe chemical reactivity. A reactive force-field (ReaxFF) is a simplified model that aims to bridge the gap between quantum chemistry methods to the ordinary force-fields of the classical molecular mechanics methods, enabling MM to model chemical reactions as a QM method with bond forming and breaking events during the simulation time. This has been accomplished by simply introducing anharmonicities in the potential energy terms of the force-field. Starting from a published ReaxFF force-field developed for modeling glycine aminoacid a novel ReaxFF force-field, ProtReaxFF, has been developed, optimized and applied to enzyme catalysis reactions.