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Chemistry - Theoretical and Computational Chemistry | Multi-scale Quantum Models for Biocatalysis - Modern Techniques and Applications

Multi-scale Quantum Models for Biocatalysis

Modern Techniques and Applications

York, Darrin M., Lee, Tai-Sung (Eds.)

2009, XIV, 420 p.

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  • Furnishes an understanding of how catalysis is achieved by biological macromolecules
  • Written for those engaged in biotechnology and biomedical research
  • A single-source guide to the most promising computational methods used to study biocatalysis
  • Provides an invaluable resource to researchers interested in the further development of these theoretical methods

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications 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 has three sections that group together different aspects of multi-scale quantum simulations. The first section consists of four chapters that describe strategies for multi-scale quantum models and present an overview of the current state-of-the-art molecular modelling methodologies most relevant to handling these complex systems with quantum mechanics and molecular simulation. With five chapters, the second section mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. The last section consists of five chapters focused on the applications of important biological systems using multi-scale quantum models. 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.

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology. It is also likely to be of interest to graduate and undergraduate students exposed to these research areas.

Content Level » Research

Keywords » Biocatalysis - Free Energy Methods - Linear Scaling Techniques - Path Integrals - Polarizable Force Fields - Potential - QM/MM methods - Solvent Boundries - abinitio MD - catalysis - nanotechnology

Related subjects » Catalysis - Materials - Nanotechnology - Theoretical and Computational Chemistry

Table of contents 

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.

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