Multi-scale Quantum Models for Biocatalysis

Overview of methodologies: 1. Mixed Quantum-Classical Calculations in Biological Systems. 2. The ONIOM Method and its Applications to Enzymatic Reactions. 3. Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis. 4. Quantum Mechanical Methods for Electronic Structure and Internuclear Quantum - Statistical Calculations in Enzyme Catalysis. Fast quantum models with empirical treatments: 5. Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions. 6. Design of next generation force fields from ab initio computations: beyond point charges electrostatics. 7. Multi-scale QM/MM methods with Self-Consistent-Charge Density-Functional- Tight - Binding (SCC-DFTB). 8. Coarse-Grained Intermolecular Potentials Derived from the Effective Fragment Potential: Application to Water, Benzene, and Carbon Tetrachloride. 9. Formalisms for the explicit inclusion of electronic polarizability in molecular modeling and dynamics studies. Biocatalysis applications: 10. Modeling Protonation Equilibria in Biological Macromolecules. 11. Quantum Mechanical Studies of the Photophysics of DNA and RNA bases. 12. Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes. 13. Interpreting the Observed Substrate Selectivity and the Product Regioselectivity in Orf2-Catalyzed Prenylation from X-ray structures. 14. Unraveling the mechanisms of ribozyme catalysis with multi-scale simulations.