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El. knyga: Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications

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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.
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.
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