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Abstract
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 manyparticle 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) forcefields  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 forcefields that are virtually unlimited in size but unable to straightforwardly describe chemical reactivity. A reactive forcefield (ReaxFF) is a simplified model that aims to bridge the gap between quantum chemistry methods to the ordinary forcefields 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 forcefield. Starting from a published ReaxFF forcefield developed for modeling glycine aminoacid a novel ReaxFF forcefield, ProtReaxFF, has been developed, optimized and applied to enzyme catalysis reactions.
Original language  English 

Place of Publication  Kgs. Lyngby 

Publisher  Technical University of Denmark 
Number of pages  251 
Publication status  Published  2013 
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 1 Finished

Atomistic Modelling of Chemical Reactions  A New Approach in Drug Design
Corozzi, A. (PhD Student), Fristrup, P. (Main Supervisor), Henriksen, N. E. (Examiner), Ahlquist, M. S. G. (Examiner) & Jensen, J. H. (Examiner)
01/10/2009 → 30/09/2013
Project: PhD