Multi-scale Quantum Models for Biocatalysis

Part I. Overview of Methodologies

1. Mixed Quantum-Classical Calculations in Biological Systems
Gustavo M. Seabra, Jason Swails, Adrian E. Roitberg

2. The Oniom Method and its Applications to Enzymatic Reactions
Marcus Lundberg, and Keiji Morokuma

3. Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis
G. Andrés Cisneros, Weitao Yang

4. Quantum Mechanical Methods for Biomolecular Simulations
Kin-Yiu Wong, Lingchun Song, Wangshen Xie, Dan T. Major, Yen-Lin Lin, Alessandro Cembran, Jiali Gao

Part II. Fast Quantum Models with Empirical Treatments

5. Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions
Jonathan P. Mcnamara, Ian H. Hillier

6. Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics
G.A. Cisneros, T.A. Darden, N. Gresh, J. Pilmé, P. Reinhardt, O. Parisel, J.-P. Piquemal

7. “Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB)
Qiang Cui, Marcus Elstner

8. Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride
Gaurav Pranami, Lyudmila Slipchenko, Monica H. Lamm, Mark S. Gordon

9. Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies
Pedro E.M. Lopes, Edward Harder, Benoît Roux, Alexander D. Mackerell

Part III. Biocatalysis Applications

10. Modeling Protonation Equilibria In Biological Macromolecules
Jana Khandogin

11. Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases
Kurt A. Kistler, Spiridoula Matsika

12. Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes
Yingkai Zhang

13. Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures
Guanglei Cui, Xue Li, Ning Yu, Kenneth M. Merz

14. Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations
Tai-Sung Lee, George M. Giambaşu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Timothy J. Giese, Jiali Gao, Darrin M. York

Avainsanat: Chemistry, Theoretical and Computational Chemistry, Catalysis, Materials Science, general, Nanotechnology