Multi-scale Quantum Models for Biocatalysis

Overview of Methodologies.- Mixed Quantum-Classical Calculations in Biological Systems.- The Oniom Method and its Applications to Enzymatic Reactions.- Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis.- Quantum Mechanical Methods for Biomolecular Simulations.- Fast Quantum Models with Empirical Treatments.- Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions.- Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics.- “Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB).- Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride.- Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies.- Biocatalysis Applications.- Modeling Protonation Equilibria In Biological Macromolecules.- Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases.- Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes.- Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures.- Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations.