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Kinetics and dynamics : from nano- to bio-scale

Author: Piotr Paneth; Agnieszka Dybala-Defratyka
Publisher: Dordrecht ; New York : Springer, ©2010.
Series: Challenges and advances in computational chemistry and physics, 12.
Edition/Format:   eBook : Document : EnglishView all editions and formats
Database:WorldCat
Summary:
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  Read more...
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Genre/Form: Electronic books
Additional Physical Format: Print version:
Kinetics and dynamics.
Dordrecht ; New York : Springer, ©2010
(OCoLC)495781729
Material Type: Document, Internet resource
Document Type: Internet Resource, Computer File
All Authors / Contributors: Piotr Paneth; Agnieszka Dybala-Defratyka
ISBN: 9789048130344 9048130344 9789048130337 9048130336
OCLC Number: 668095796
Description: 1 online resource (xvii, 530 pages) : illustrations (some color).
Contents: Note continued: 3.6. Effect of Environment on Photodissociation of Formamide --
3.7. Conclusions and Final Remarks --
References --
4. Design of Catalysts for Asymmetric Organic Reactions Through Density Functional Calculations / Raghavan B. Sunoj --
4.1. Introduction --
4.1.1. Organocatalytic Reactions and Theoretical Models --
4.1.2. Sulfur Ylide Promoted Reactions --
4.2. Computational Methods --
4.2.1. Terminology --
4.3. Results and Discussion --
4.3.1. Intermolecular Aldol Reaction --
4.3.2. Sulfur Ylide Promoted Reactions --
4.4. Summary --
References --
5. Reactive Processes with Molecular Simulations / Markus Meuwly --
5.1. Introduction --
5.2. Conceptual Approaches --
5.2.1. Molecular Mechanics with Proton Transfer --
5.2.2. Reactive Molecular Dynamics --
5.2.3. Empirical Valence Bond --
5.2.4. ReaxFF --
5.2.5. Other Approaches --
5.3. Applications --
5.3.1. Proton Transfer Reactions --
5.3.2. Ligand Binding in Heme Proteins --
5.4. Outlook --
References --
6. Theoretical Studies of Polymerisation Reactions / Grzegorz Krasinski --
6.1. Introduction --
6.1.1. Methods for Modelling of Polymers --
6.1.2. Large-Scale Molecular Modelling Calculations on Biological Systems --
6.1.3. Molecular Modelling Software for Describing Transition Structures and Minimum Energy Paths --
6.2. Computational Quantum Chemistry Studies of Polymerisation Mechanisms --
6.2.1. Solvent Effects --
6.2.2. Free-Radical Polymerisation --
6.2.3. Ionic Polymerisation --
6.2.4. Coordination Polymerisation --
6.2.5. Polycondensation --
6.3. Enzymatic Reactions --
6.4. Structural Studies --
6.5. Summary --
References --
7. Evaluation of Proton Transfer in DNA Constituents: Development and Application of Ab Initio Based Reaction Kinetics / Jerzy Leszczynski --
7.1. Introduction --
7.2. Methodology. Note continued: 7.2.1. Ab Initio Based Computation of Reaction Rates --
7.2.2. Numerical Solution of a System of Rate Equations --
7.3. Applications of the Reaction Kinetics Models to the Studies of Proton Transfer in DNA Constituents --
7.3.1. Tautomerization of Nucleobases in the Gas Phase --
7.3.2. Tautomerization of Isolated and Monohydrated Cytosine and Guanine at Room Temperature --
7.3.3. Role of Hydrated Metal Ions for Nucleic Acids Stabilization --
7.3.4. Gas Phase Tautomerization in AT and GC Pairs of DNA Bases --
7.4. Conclusions --
References --
8. Simulation of Charge Transfer in DNA / Marcus Elstner --
8.1. Introduction --
8.1.1. Basics of Hole Transfer in DNA --
8.1.2. Experimental Studies --
8.1.3. Theory and Computation --
8.1.4. Subject of This Contribution --
8.2. Charge-Transfer Parameters --
8.2.1. Ionization Potentials --
8.2.2. Electronic Couplings --
8.2.3. CT Parameters Within the Fragment-Orbital Approach --
8.2.4. Summary --
8.3. Effect of Dynamics and Environment on CT Parameters --
8.3.1. Electronic Couplings --
8.3.2. Ionization Potentials --
8.3.3. Computation of CT Parameters Along MD Trajectories --
8.3.4. Summary --
8.4. Quantum Dynamics of a Hole in DNA --
8.4.1. Integration of the Time-Dependent Schrodinger Equation --
8.4.2. Simulation of Hole Transfer Over Adenine Bridges --
8.4.3. Summary --
8.5. Solvent Reorganization Energy and De-Localization of the Hole --
8.5.1. Polarization of the Environment by the Hole Charge --
8.5.2. Solvent Reorganization Energy --
8.5.3. Spatial Extent of the Hole --
8.5.4. How to Include the Response of Solvent in the Simulation? --
8.6. Summary, Conclusions and Outlook --
8.6.1. Fundamental Mechanism of Charge Transfer --
8.6.2. De/localization of the Hole --
8.6.3. Requirements on a Computational Model --
References. Note continued: 9. Quantum-Mechanical Molecular Dynamics of Charge Transfer / Claudio N. Cavasotto --
9.1. Introduction --
9.2. Theoretical Part --
9.3. Notion of Charge Transfer --
9.3.1. QM MD of Ubiquitin in Explicit Water --
9.3.2. Charge Transfer Inside Protein --
9.3.3. Charge Transfer Channel --
9.3.4. Inequality Among Same-Type Amino Acids --
9.3.5. Protein-Solvent Charge Transfer --
9.4. Implications of Charge Transfer --
References --
10. Beyond Standard Quantum Chemical Semi-Classic Approaches: Towards a Quantum Theory of Enzyme Catalysis / Orlando Tapia --
10.1. Introduction --
10.2. Enzyme Catalyzed Reactions --
10.2.1. Transition Structures and Chemical Mechanisms --
10.3. Exact Quantum Schemes --
10.4. Semi-Classic Schemes and Beyond --
10.4.1. Semi-classic Hamiltonian Models --
10.4.2. Invariant Electronic Configuration Space Models --
10.4.3. "Mobile" Electronic-Configuration-Space: Nodal Envelope States --
10.5. Quantum Aspects of Catalysis --
10.5.1. Model Quantum Catalyst: H + H and H2 --
10.5.2. Quantum Transition States --
10.5.3. Abstract BO Transition Structures --
10.6. Angular Momentum (Spin) and Chemical reactivity --
10.6.1. Spin-Space Separation and Chemical Reactivity --
10.7. Photorespiration: Dioxygen --
10.8. More Light --
References --
11. Molecular Dynamics Simulations: Difficulties, Solutions and Strategies for Treating Metalloenzymes / Maria Joao Ramos --
11.1. Introduction --
11.2. Biomolecular Force Fields --
11.2.1. AMBER --
11.2.2. CHARMM --
11.2.3. OPLS --
11.3. Difficulties in Treating a Metalloenzyme --
11.4. Parameterization Strategies for Metalloproteins --
11.4.1. Non-Bonded Model Approach --
11.4.2. Bonded Model Approach --
11.4.3. Cationic Dummy Atom Approach --
11.4.4. Alternative Formulations --
11.5. Farnesyltransferase as a Test Case --
11.5.1. Target Protein. Note continued: 11.5.2. Initial Strategies --
11.5.3. Setting a Bonded Model Simulation --
11.5.4. Validation and Application --
11.6. Summary --
References --
12. QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis / Haiyan Liu --
12.1. Enzyme Catalysis and QM/MM Modeling --
12.1.1. Non-Covalent Contributions to Enzyme Catalysis --
12.1.2. Modeling Non-Covalent Interactions in Enzyme Reactions by QM/MM --
12.2. QM/MM as Potential Energy Models --
12.2.1. Mechanical Embedding QM/MM --
12.2.2. Electrostatic QM/MM --
12.2.3. QM/MM Partitioning and the Treatment of Boundaries --
12.2.4. Long Range Electrostatic Effects --
12.3. Optimization and Sampling in QM/MM Configuration Spaces --
12.3.1. Effects of System Sizes and Computational Characteristics of QM/MM --
12.3.2. Optimization on QM/MM Potential Energy Surfaces --
12.3.3. Free Energies and Sampling in QM/MM Configuration Spaces --
12.4. Applying QM/MM to Enzymatic Systems --
12.4.1. Practical Issues --
12.4.2. Learning How Enzymes Work Through QM/MM Modeling --
References --
13. Computational Modeling of Biological Systems: The LDH Story / Inaki Tunon --
13.1. Introduction --
13.2. Gas Phase Calculations --
13.3. Inclusion of Environment Effects --
13.3.1. Cluster Models --
13.3.2. QM/MM Methods --
13.4. Statistical Simulations --
13.4.1. Free Energy Perturbation (FEP) --
13.4.2. Potential of Mean Force (PMF) --
13.5. Large Scale Conformational Changes and Averaged Kinetic Properties --
13.6. Conclusions --
References --
14. Enzyme Dynamics and Catalysis: Insights from Simulations / Adrian J. Mulholland --
14.1. Introduction --
14.2. Challenges in Biomolecular Simulation --
14.3. Protein Dynamics and Enzyme Conformational Changes --
14.3.1. Scavenger Decapping Enzyme (DcpS) --
14.3.2. Phosphomannomutase/Phosphoglucomutase. Note continued: 14.4. Enzyme Catalysis --
14.4.1. Chorismate Mutase --
14.5. Enzyme Reaction Mechanisms --
14.5.1. Citrate Synthase --
14.5.2. Hen Egg White Lysozyme --
14.5.3. Aromatic Amine Dehydrogenase --
14.6. Conclusions --
References --
15. Transport Mechanism in the Escherichia coli Ammonia Channel AmtB: A Computational Study / Yuchun Lin --
15.1. Overview --
15.2. Experimental Evidences on Escherichia coli AmtB Channel --
15.3. Computational Methods --
15.4. Computational Studies --
15.4.1. Molecular Dynamics at the Molecular Mechanical Level --
15.4.2. Combined QM(DFT)/MM Studies --
15.4.3. Combined QM(PM3)/MM Molecular Dynamics Simulations --
15.5. Summary --
References --
16. Challenges for Computer Simulations in Drug Design / Klaus R. Liedl --
16.1. Introduction --
16.2. MD Simulations --
16.3. Role of Simulations in the Drug Discovery Process --
16.4. Virtual Screening and MD Simulations --
16.4.1. Pharmacophore Modelling --
16.4.2. Docking --
16.5. Prediction of Gibbs Free Energy of Binding --
16.5.1. MM/PB (GB)SA --
16.5.2. LIE Approach --
16.5.3. FEP/TI --
16.6. Elucidation of Structural Function Using Simulations --
16.6.1. GPCRs --
16.6.2. Water --
16.7. Perspective --
References --
17. Interpretation of Kinetic Isotope Effects in Enzymatic Cleavage of Carbon-Hydrogen Bonds / Zorka Smedarchina --
17.1. Introduction --
17.2. Model --
17.3. Physical Parameters --
17.4. Application to Lipoxygenase-1 --
17.5. Application to Free Radical Transfer --
17.6. Application to Methylamine Dehydrogenase --
17.7. Discussion --
References --
18. Tunneling Transmission Coefficients: Toward More Accurate and Practical Implementations / Antonio Fernandez-Ramos --
18.1. Introduction --
18.2. Tunneling Transmission Coefficients --
18.3. Practical Implementation of the LCG4 and LAG4 Methods. Note continued: 18.4. Transmission Coefficients and KIEs --
References --
19. Integrating Computational Methods with Experiment Uncovers the Role of Dynamics in Enzyme-Catalysed H-Tunnelling Reactions / Nigel S. Scrutton --
19.1. Introduction --
19.2. H-Tunneling Reactions as Probes of Dynamics --
19.2.1. Hydrogen Atom Transfer in Soybean Lipoxygenase-1 --
19.2.2. Hydride Transfer in Morphinone Reductase --
19.3. Computational Techniques for Atomistic Analysis of Promoting Vibrations --
19.3.1. Spectral Density Analysis Reveals a Promoting Vibration in Horse Liver Alcohol Dehydrogenase --
19.3.2. Spectral Densities Coupled with Digital Filtering of Atomic Motions Reveal a Complicated Picture in Aromatic Amine Dehydrogenase --
19.3.3. Potential Energy Scans Reveal the Effect of the Promoting Vibration on Barrier Scaling in AADH --
19.4. Role of Long-Range Coupled Motions --
19.4.1. Coupled Motions of Different Timescales in DHFR --
19.4.2. Proposed Conserved Network of Vibrations in HLADH --
19.4.3. Small-Scale, Local Promoting Vibration in AADH --
19.5. Discussion and Future Perspectives --
References.
Series Title: Challenges and advances in computational chemistry and physics, 12.
Responsibility: edited by Piotr Paneth, Agnieszka Dybala-Defratyka.

Abstract:

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  Read more...

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