Multi-scale quantum models for biocatalysis: modern techniques and applications

Gustavo M. Seabra, Jason Swails, Adrian E. Roitberg (auth.), Prof. Darrin M. York, Dr. Tai-Sung Lee (eds.)140209955X, 978-1-4020-9955-7, 978-1-4020-9956-4

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.

Table of contents :
Front Matter….Pages I-XIV
Front Matter….Pages 1-1
Mixed Quantum-Classical Calculations in Biological Systems….Pages 3-20
The Oniom Method and its Applications to Enzymatic Reactions….Pages 21-55
Comparison Of Reaction Barriers In Energy And Free Energy For Enzyme Catalysis….Pages 57-78
Quantum Mechanical Methods for Biomolecular Simulations….Pages 79-101
Front Matter….Pages 103-103
Towards an Accurate Semi-Empirical Molecular Orbital Treatment of Covalent and Non-Covalent Biological Interactions….Pages 105-136
Design Of Next Generation Force Fields From AB Initio Computations: Beyond Point Charges Electrostatics….Pages 137-172
“Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB)….Pages 173-196
Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride….Pages 197-218
Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies….Pages 219-257
Front Matter….Pages 259-259
Modeling Protonation Equilibria In Biological Macromolecules….Pages 261-284
Quantum Mechanical Studies of the Photophysics of DNA and RNA Bases….Pages 285-339
Ab Initio Quantum Mechanical/Molecular Mechanical Studies of Histone Modifying Enzymes….Pages 341-350
Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures….Pages 351-375
Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations….Pages 377-408
Back Matter….Pages 409-420