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E-grāmata: Chemical Modelling: Applications and Theory Volume 3

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Contributions by (The Open University, UK), Contributions by (Shiraz University, Iran), Contributions by (The Rudjer Boskovic Institu), Contributions by (University of Saarland, Germany), Contributions by (University of Peloponnese, Greece), Contributions by (University of Strathclyde, UK), Contributions by , Contributions by , Edited by , Contributions by (The University of Queensland, Australia)
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Chemical Modelling: Applications and Theory Volume 3Palielināt
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Chemical Modelling: Applications and Theory comprises critical literature reviews of molecular modelling, both theoretical and applied. Molecular modelling in this context refers to modelling the structure, properties and reactions of atoms, molecules & materials. Each chapter is compiled by experts in their fields and provides a selective review of recent literature, incorporating sufficient historical perspective for the non-specialist to gain an understanding. With chemical modelling covering such a wide range of subjects, this Specialist Periodical Report serves as the first port of call to any chemist, biochemist, materials scientist or molecular physicist needing to acquaint themselves with major developments in the area.


Reflecting the growing volume of published work in this field, researchers will find this book an invaluable source of information on current methods and applications.

Recenzijas

"... a first class account ..." * Aslib Book Guide, Vol 66, No 5, May 2001 * "... a timely and detailed overview of the recent literature ..." * Journal of the American Chemical Society, Vol 123, No 39, 2001, p 9725-9726 * "... the 12 reporters have done a good job of providing an informative and useful guide to recent literature, as well as an overview of the relevant theory." * Chemistry and Industry, No 24, 17 December 2001, p 806 *

Chapter 1 Calculations of the Vibration-Rotation Spectra of Small Molecules
1(44)
B.T. Sutcliffe
1 Introduction
1(1)
2 History
2(7)
3 Symmetry
9(3)
4 The Eckart-Watson Hamiltonian and its Context
12(5)
4.1 The Permutational Symmetry of the Eckart-Watson Hamiltonian
14(3)
5 The General Form of a Tailor-made Hamiltonian
17(8)
5.1 The Permutational Symmetry in the General Form of the Hamiltonian
23(2)
6 Computational Considerations
25(20)
6.1 Perturbational Computations
29(7)
6.2 Variational Computations
36(5)
References
41(4)
Chapter 2 Computer-aided Drug Design 2001-2003
45(24)
Richard A. Lewis
1 Introduction
45(1)
2 ADME/Tox and Druggability
45(4)
2.1 Metabolism by Cytochrome P450
46(1)
2.2 Human Ether-a-go-go-related Gene K+ Channel
47(1)
2.3 What makes a Compound Drug-like?
47(2)
2.4 General Models
49(1)
3 Docking and Scoring
49(5)
3.1 Validation Protocols
50(1)
3.2 Entropy
51(1)
3.3 Pharmacophore and Local Docking Schemes
51(1)
3.4 Protein Flexibility
52(1)
3.5 Docking and Virtual Screening
53(1)
4 De Novo
54(1)
5 3D-QSAR
55(1)
6 Pharmacophores
56(1)
6.1 Conformational Analysis
56(1)
7 Library Design
57(2)
8 Cheminformatics and Data Mining
59(2)
8.1 Data Mining
59(1)
8.2 Similarity and Descriptors
60(1)
9 Inverse QSAR and Automated Iterative Design
61(1)
10 Structure-based Drug Design
61(2)
10.1 G-Protein Coupled Receptors (GPCRs)
62(1)
10.2 A Case Study
63(1)
11 Conclusions
63(6)
References
63(6)
Chapter 3 Density Functional Theory
69(57)
Michael Springborg
1 Introduction
69(1)
2 Theoretical Foundations
70(4)
3 Structure and Energies
74(26)
3.1 Ionization Potentials of Nickel-benzene Clusters
74(2)
3.2 Bronsted Acidity of Some Zeolites
76(2)
3.3 Van der Waals Interactions
78(1)
3.4 Structure and Energetics for N-Acetyl-L-Glutamate-N-Methylamide
79(1)
3.5 Photodissociation of Triplet Acetaldehyde
80(2)
3.6 Vibrations of Benzimidazole
82(2)
3.7 Chemical Reactions Involving Hydrogen Bonds
84(1)
3.8 Metal-Sulphur bonds for Sulphur on the Au(111) Surface
85(3)
3.9 NOx on MgO
88(1)
3.10 Rotational Stability of Substituted Acetanilides
89(1)
3.11 The Reaction of Methylformate with Ammonia
89(3)
3.12 The Rearrangement of Azulene to Naphthalene
92(1)
3.13 Dissociation of Azomethane
93(1)
3.14 Reactions Between Transition Metals and Ammonia
94(1)
3.15 Dynamics of Chemical Reactions
95(1)
3.16 Hydrogen Bonds
95(2)
3.17 DNA Base-stacking Interactions
97(1)
3.18 Vibrations of Fe2CO
97(1)
3.19 Anharmonic Vibrational Modes in Adenine
98(1)
3.20 Cumulenes and Polyynes
99(1)
4 Orbitals and Densities
100(4)
4.1 Conductivity in DNA
100(2)
4.2 Momentum-space Densities in Ethane
102(1)
4.3 Electron Density in [ FeCo(CO)8]-
103(1)
5 Excitations
104(9)
5.1 Bandgap in Molecular Crystals
104(2)
5.2 Binding Energies of Electrons
106(2)
5.3 Band Gap in Conjugated Oligomers
108(1)
5.4 (Hyper)polarizability of Si4
109(1)
5.5 Electronic Absorption in Polycyclic Aromatic Hydrocarbons
110(1)
5.6 Nonadiabatic Processes
111(1)
5.7 NMR Chemical Shifts of Benzoxazine Oligomers
111(1)
5.8 NMR Shielding Constants
112(1)
6 Getting Further Information with Density-functional Calculations
113(3)
6.1 Classification of Reactions
113(2)
6.2 Hydrogen Bond Descriptors
115(1)
7 Limitations and Perspectives
116(6)
7.1 Polyenes and Current-density-functional Theory
116(3)
7.2 Anions and Exact-exchange Methods
119(1)
7.3 The Long-ranged Behaviour of Exchange Interactions
120(2)
7.4 Other Improvements
122(1)
8 Conclusions
122(4)
References
124(2)
Chapter 4 Combinatorial Enumeration in Chemistry
126(45)
D. Babic
D.J. Klein
J. von Knop
N. Trinajstic
1 Introduction
126(1)
2 Current Results
126(31)
2.1 Isomer Enumeration
126(9)
2.2 Kekule Structure Count
135(3)
2.3 Counting Walks
138(6)
2.4 Combinatorial Measures of Molecular Complexity
144(10)
2.5 Other Enumerations
154(3)
3 Concluding Remarks
157(14)
References
159(12)
Chapter 5 Photo-reduction and -oxidation
171(46)
Andrew Gilbert
1 Introduction
171(1)
2 Electric Field Related Properties
172(33)
2.1 High Level Ab Initio and DFT Calculations
172(18)
2.2 Semi-empirical Calculations
190(5)
2.3 Solvent and Other Environmental Effects
195(2)
2.4 Polymers
197(2)
2.5 Dendritic Structures
199(1)
2.6 Octupolar Molecules
200(1)
2.7 Crystals
201(1)
2.8 Clusters
202(1)
2.9 Theoretical Developments
203(2)
3 Magnetic Field Response Functions in Diamagnetic Molecules
205(12)
3.1 Magnetizability and Nuclear Shielding
205(3)
3.2 Higher Order Response Functions - The Cotton-Mouton Effect
208(2)
References
210(7)
Chapter 6 Simulation of the Liquid State
217(54)
Karl P. Travis
1 Introduction
217(1)
2 Transport Properties
218(11)
2.1 Theories of Diffusion
218(4)
2.2 Computational Methodology
222(2)
2.3 Bulk Liquid Transport Properties
224(3)
2.4 NEMD
227(2)
3 Phase Equilibria
229(2)
4 Supercooled Liquids and Glasses
231(9)
4.1 Phenomenology
232(3)
4.2 Structural Models for Supercooled Liquids
235(5)
5 Confined Liquids
240(13)
5.1 Structure
240(1)
5.2 Phase Equilibria
241(2)
5.3 Glass Transition
243(1)
5.4 Diffusion
244(5)
5.5 Rheology
249(2)
5.6 Chemical Reactions
251(1)
5.7 Water Adsorption
252(1)
5.8 Applications of Density Functional Theory
252(1)
6 Water and its Solutions
253(2)
7 Mesoscale Simulations
255(3)
7.1 Dissipative Particle Dynamics
256(1)
7.2 Lattice Boltzmann
257(1)
8 Simulation Methodology
258(13)
8.1 Reverse Monte Carlo
258(1)
8.2 New Monte Carlo Algorithms
259(1)
8.3 Intermolecular Potentials
260(2)
8.4 Multiscale Methods
262(1)
8.5 Miscellaneous Developments
263(1)
References
263(8)
Chapter 7 Numerical Methods in Chemistry
271(108)
T.E. Simos
1 Introduction
271(2)
2 Multi Derivative Methods
273(10)
2.1 Stability and Phase-lag Analysis of Multi-derivative Methods
273(1)
2.2 A New Family of Multi-derivative Methods
274(1)
2.3 A New Family of Multi-derivative Methods with Minimal Phase-lag
275(1)
2.4 Computational Implementation
276(4)
2.5 Numerical Illustrations
280(2)
2.6 Remarks and Conclusions
282(1)
3 Symplectic Methods for the Numerical Solution of the Radical Schrodinger Equation
283(9)
3.1 Introduction
283(1)
3.2 Symplectic Integrators - Basic Theory
283(1)
3.3 Construction of Symplectic Integrators
284(1)
3.4 Development of the New Methods
285(3)
3.5 Numerical Examples
288(3)
3.6 Remarks and Conclusions
291(1)
4 Numerical Solution of the Two-dimensional Schrodinger Equation
292(13)
4.1 Introduction
292(1)
4.2 Partial Discretisation of the Two-dimensional Equation
292(1)
4.3 Application of Symplectic Methods
293(6)
4.4 Application of Numerov-type Methods
299(5)
4.5 Remarks and Conclusions
304(1)
5 General Comments on the Bibliography of the Numerical Methods in Chemistry
305(74)
Appendix A
313(4)
Appendix B
317(23)
Appendix C
340(5)
Appendix D
345(1)
Appendix E
346(3)
Appendix F
349(17)
Appendix G
366(11)
References
377(2)
Chapter 8 Many-body Perturbation Theory and Its Application to the Molecular Structure Problem
379
S. Wilson
1 Introduction
379(1)
2 Diagrammatic Many-body Perturbation Theory of Molecular Structure Including Nuclear and Electronic Motion
380(19)
2.1 The Total Molecular Hamiltonian Operator
381(2)
2.2 The Hartree-Fock Theory of Nuclei and Electrons
383(1)
2.3 The Many-perturbation Theory of Nuclei and Electrons
384(5)
2.4 The Diagrammatic Perturbation Theory of Nuclei and Electrons
389(9)
2.5 Prospects
398(1)
3 Diagrammatic Many-body Perturbation Theory of Molecular Electronic Structure: Low Order Approximants
399(10)
3.1 Summation Approximants
399(2)
3.2 Feenberg Scaling
401(3)
3.3 Digression: Scaled Many-body Perturbation Theory and Systematically Extended Basis Sets
404(1)
3.4 Pade Approximants
405(1)
3.5 Quadratic Pade Approximants
406(2)
3.6 Prospects
408(1)
4 Diagrammatic Many-body Perturbation Theory of Molecular Electronic Structure for Larger Systems
409(7)
4.1 Local Correlation Methods
409(1)
4.2 Linear Scaling Correlation Methods
410(1)
4.3 Local "MP2" Methods
410(1)
4.4 Splitting of the Coulomb Operator
411(1)
4.5 Multipole Expansion of Long Range Integrals
412(2)
4.6 Density Fitting Approximations
414(2)
4.7 Prospects
416(1)
5 Diagrammatic Many-body Perturbation Theory of Molecular Electronic Structure: A Review of Applications
416(4)
5.1 Incidence of the String "MP2" in Titles and/or Keywords
416(1)
5.2 Comparison with Other Methods
417(1)
5.3 Synopsis of Applications of Second Order Many-body Perturbation Theory
418(2)
5.4 Prospects
420(1)
6 Summary and Prospects
420
References
421
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