Kinetics and Dynamics: From Nano- to Bio-Scale

ISBN-13: 9789048130337 / Angielski / Twarda / 2010 / 530 str.

Piotr Paneth;Agnieszka Dybala-Defratyka

Opis

This book on molecular modeling of dynamic processes opens with an introductory overview before discussing approaches to reactivity of small systems in the gas phase. Then it examines studies of systems of increasing complexity up to the dynamics of DNA.

Spis treści

Preface.- 1. Ca2+ Reactivity in the Gas Phase. Bonding, Catalytic Effects and Coulomb Explosions.- 2. From the Gas Phase to a Lipid Membrane Environment: DFT and MD Simulations of Structure and Dynamics of Hydrogen-bonded Solvates of Bifunctional Heteroazaaromatic Compounds.- 3. Formamide as the Model Compound for Photodissociation Studies of the Peptide Bond.- 4. Design of Catalysts for Asymmetric Organic Reactions through Density Functional Calculations.- 5. Reactive Processes with Molecular Simulations.- 6. Theoretical Studies of Polymerisation Reactions.- 7. Evaluation of Proton Transfer in DNA Constituents: Development and Application of Ab Initio Based Reaction Kinetics.- 8. Simulation of Charge Transfer in DNA.- 9. Quantum Mechanical Molecular Dynamics Approach to Study Charge Transfer.- 10. Beyond Standard Quantum Chemical Semi-Classic Approaches: Towards a Quantum Theory of Enzyme Catalysis.- 11. Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes.- 12. QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis.- 13. Computational Modelling of Biological Systems: The LDH Story.- 14. Enzyme Dynamics and Catalysis: Insights from Simulations.- 15. Transport Mechanism in the Escherichia coli Ammonia Channel AmtB: A Computational Study.- 16. Challenges for Computer Simulations in Drug Design.- 17. Interpretation of Kinetic Isotope Effects in Enzymatic Cleavage of Carbon-hydrogen Bonds.- 18. Tunneling Transmission Coefficients: Toward More Accurate and Practical Implementations.- 19. Integrating Computational Methods with Experiment Uncovers the Role of Dynamics in Enzyme-catalysed H-tunnelling Reactions.

O autorze

P. Paneth is Professor of Physical and Theoretical Chemistry at the Technical University of Lodz.

A. Dybala-Defratyka is Assistant Professor at the Technical University of Lodz.

Blurb

Computational chemistry is a rapidly developing discipline. This is due to the development of faster algorithms and the increasing power of computers. This book explores the novel applications of these computational tools by focusing on studies which feature chemical and biochemical reactions at various scales and environments. Kinetics and Dynamics: from Nano- to Bio-Scale presents numerous examples which range from simple reactions in the gas phase to polymerization to complex biochemical systems. The reader is shown how the complexity of these systems necessitates the use of different theoretical approaches and methodologies hence broadening our understanding of these fundamental phenomena.

Kinetics and Dynamics: from Nano- to Bio- Scale consists of a collection of chapters written by experts in the field. Their contributions have been selected to illustrate a variety of systems and techniques. Whilst it is impossible to be exhaustive on this subject within a single volume, an attempt has been made to describe different systems of interest in the life sciences.

This book provides contemporary and comprehensive reference material. It is useful for graduate students as well as independent scientists either entering the field of computational chemistry for the first time or those who are aiming to augment their expertise.