York / Lee Multi-scale Quantum Models for Biocatalysis

Modern Techniques and Applications
2009
ISBN: 978-1-4020-9956-4
Verlag: Springer Netherland
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 7, 420 Seiten, eBook

Reihe: Challenges and Advances in Computational Chemistry and Physics

“Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics.

This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes.

This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.

Zielgruppe

Research

Autoren/Hrsg.

Lee, Tai-Sung

York, Darrin M.

Inhaltsverzeichnis

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.