Chemical Applications of Molecular Modeling

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ISBN: 9780854045792 | 0854045791
Cover: Paperback
Copyright: 12/1/1998

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This book explores the molecular modeling, enabling the nonspecialist to appreciate the power as well as the limitations of the computational tools available and giving a background to the methods used and how they were developed. It also provides examples of how molecular modeling has been used to address chemical questions commonly asked by the experimental chemist, and includes practical examples and case studies. 143 illus.

1 Introduction

(14)

1.1 What is a Molecule?

(4)

1.2 Molecular Change and Energy

(4)

1.2.1 Thermodynamics

(2)

1.2.2 Kinetics

(2)

1.3 The Control of Thermodynamics and Kinetics

(3)

1.3.1 A Real Example

(1)

1.3.2 Conformation Searching

(1)

1.3.3 Molecular Orbitals and Quantum Mechanics

(1)

1.4 How Do Molecules Move?

(1)

1.5 Summary

(2)

2 Force Fields

(16)

2.1 Energy Calculation

(1)

2.1.1 What is Being Calculated?

(1)

2.2 What is in a Force Field?

(10)

2.2.1 Bond Energy: E(bonds)

(2)

2.2.2 Bond Angle Energy: E(angles)

(1)

2.2.3 van der Waals Interactions: E(vdw)

(2)

2.2.4 Torsion Angle Energy: E(torsion)

(2)

2.2.5 Charge-Charge Interactions: E(charge)

(3)

2.2.6 Miscellaneous Interactions: E(miscellaneous)

(1)

2.3 How are Molecules Described?

(3)

2.3.1 Water

(1)

2.4 Transferability

(1)

2.5 Key Points

(1)

3 Minimisation

(30)

3.1 Introduction

(4)

3.1.1 Which Way Do We Go?

(1)

3.1.2 How Far Can We Go?

(1)

3.1.3 How Do We Know When We Have Arrived?

(1)

3.2 Minimisation Algorithms

(4)

3.2.1 Non-derivative Methods

(1)

3.2.2 Derivative Methods

(2)

3.2.3 How Do We Know If We Have Arrived?

(1)

3.3 What can be Learned from Minimisation?

(1)

3.4 Key Points

(1)

Questions

(5)

Q3.1 Unbranched alkanes

(1)

Q3.2 Cyclohexane

(1)

Q3.3 Axial and equatorial substituted cyclohexanes

(1)

Q3.4 What shape is decalin?

(1)

Q3.5 Axial substituted cyclohexane

(1)

Q3.6 Chlorocyclohexane

(1)

Q3.7 Cyclohexene

(1)

Q3.8 What shape is 1,4-cyclohexadiene?

(1)

Q3.9 Biphenyl

(1)

Q3.10 Annelated benzenes

(1)

Q3.11 Aromatic stacking

(1)

Q3.12 Morphine

(1)

Q3.13 Bredt's Rule

(1)

Q3.14 An unusual rearrangement

(1)

Q3.15 DNA and RNA

(1)

Q3.16 Protein structures

(1)

Discussion

(16)

D3.1 Unbranched alkanes

(2)

D3.2 Cyclohexane: comparison of chair and boat forms

(2)

D3.3 Axial and equatorial substituted cyclohexanes

(1)

D3.4 What shape is decalin?

(1)

D3.5 Axial substituted cyclohexane

(1)

D3.6 Chlorocyclohexane

(1)

D3.7 Cyclohexene

(1)

D3.8 What shape is 1,4-cyclohexadiene?

(1)

D3.9 Biphenyl

(1)

D3.10 Annelated benzenes

(1)

D3.11 Aromatic stacking

(1)

D3.12 Morphine

(1)

D3.13 Bredt's Rule

(1)

D3.14 An unusual rearrangement

(1)

D3.15 DNA and RNA

(1)

D3.16 Protein structures

(3)

4 Conformation Searching

(32)

4.1 Introduction

(1)

4.2 Why do a Conformation Search?

(3)

4.3 Systematic Searching

(2)

4.3.1 Rings

(2)

4.4 Monte Carlo Searching (Semi-random Searching)

(3)

4.4.1 Alternative Distortions

(1)

4.5 Mutation Methods

(1)

4.6 Molecular Dynamics and Simulated Annealing

(1)

4.7 Genetic Algorithms

(1)

4.8 Distance Geometry

(1)

4.9 Expert Systems and Artificial Intelligence

(1)

4.10 Analysis of Results

(1)

4.11 Summary

(1)

4.12 Key Points

(1)

Questions

(5)

Q4.1 Alkanes--again

(1)

Q4.2 Methylcyclohexane

(1)

Q4.3 Very sterically hindered cyclohexanes

(1)

Q4.4 How large a ring is needed to fit a trans double bond?

(1)

Q4.5 Molecules with one low energy conformation

(1)

Q4.6 Various molecules

(1)

Q4.7 Erythromycin

(1)

Q4.8 Account for the selectivity of a rearrangement

(1)

Q4.9 Cram's Rule

(1)

Q4.10 Explain the selectivity of a reaction

(1)

Q4.11 Selectivity of elimination

(1)

Q4.12 Selectivity of hydrogenation

(1)

Q4.13 DNA, RNA and enzymes

(1)

Discussion

(13)

D4.1 Alkanes--again

(2)

D4.2 Methylcyclohexane

(1)

D4.3 Very sterically hindered cyclohexanes

(1)

D4.4 How large a ring is needed to fit a trans double bond?

(1)

D4.5 Molecules with one low energy conformation

(1)

D4.6 Various molecules

(1)

D4.7 Erythromycin

(1)

D4.8 Account for the selectivity of a rearrangement

(1)

D4.9 Cram's Rule

(2)

D4.10 Explain the selectivity of a reaction

(1)

D4.11 Selectivity of elimination

(1)

D4.12 Selectivity of hydrogenation

(1)

D4.13 DNA, RNA and enzymes

(1)

5 Molecular Dynamics

(29)

5.1 Analysis of Force Field Models

(5)

5.1.1 The Shape of the Landscape

(1)

5.1.2 Constraining Exploration

(1)

5.2 How Can Movement be Modelled?

(8)

5.2.1 The Molecular Dynamics Approach

(1)

5.2.2 Parameters for Molecular Dynamics

(4)

5.2.3 Constant Energy or Constant Temperature?

103

(1)

5.2.4 Simulated Annealing

104

(1)

5.2.5 Structure Modification

105

(1)

5.2.6 Free Energy Calculation

105

(1)

5.3 Analysis of Results

106

(2)

5.3.1 The Difficulty of Analysis

106

(1)

5.3.2 Energy

107

(1)

5.3.3 Structure

107

(1)

5.3.4 Movies

108

(1)

5.4 Key Points

108

(1)

Questions

109

(2)

Q5.1 Simple alkanes

109

(1)

Q5.2 Methylcyclohexane ring flipping

109

(1)

Q5.3 Hydroxyketone dynamics

110

(1)

Q5.4 Cram's Rule

110

(1)

Q5.5 Links and knots

110

(1)

Q5.6 Ristocetin

110

(1)

Discussion

111

(11)

D5.1 Simple alkanes

111

(3)

D5.2 Methylcyclohexane ring flipping

114

(3)

D5.3 Hydroxyketone dynamics

117

(1)

D5.4 Cram's Rule

117

(1)

D5.5 Links and knots

118

(2)

D5.6 Ristocetin

120

(2)

6 Molecular Orbital Theory

122

(28)

6.1 Why use Quantum Mechanics?

122

(1)

6.2 Atomic Orbitals

122

(4)

6.2.1 One-electron Atoms

123

(2)

6.2.2 Multi-electron Atoms

125

(1)

6.3 Molecular Orbitals

126

(2)

6.3.1 Orbital Interactions

126

(2)

6.4 Using Quantum Mechanics

128

(8)

6.4.1 Simple Molecular Orbital Calculations

128

(3)

6.4.2 Huckel Theory

131

(1)

6.4.3 Born-Oppenheimer Approximation

132

(1)

6.4.4 Hartree-Fock

133

(3)

6.5 Semi-empirical Methods

136

(1)

6.6 Density Functional Theory

137

(1)

6.7 Using Molecular Orbital Theory

137

(1)

6.8 Useful Information from Molecular Orbital Theory

138

(2)

6.8.1 Energy

138

(1)

6.8.2 Molecular Orbital Energy Levels

139

(1)

6.8.3 Charge Distribution

139

(1)

6.9 Key Points

140

(1)

Questions

141

(2)

Q6.1 Huckel calculations

141

(1)

Q6.2 Redox potentials

141

(1)

Q6.3 Diels-Alder reactions

141

(1)

Q6.4 Charge distribution

142

(1)

Q6.5 Reaction selectivity

142

(1)

Q6.6 A cation rearrangement

142

(1)

Discussion

143

(7)

D6.1 Huckel calculations

143

(2)

D6.2 Redox potentials

145

(1)

D6.3 Diels-Alder reactions

146

(1)

D6.4 Charge distribution

147

(1)

D6.5 Reaction selectivity

148

(1)

D6.6 A cation rearrangement

149

(1)

7 Databases

150

(11)

7.1 Introduction

150

(2)

7.1.1 Journals and Published Data

151

(1)

7.2 Text Searching

152

(2)

7.2.1 Mark-up

153

(1)

7.2.2 Substructure Searching

153

(1)

7.2.3 Three-Dimensional Searching

154

(1)

7.3 The World Wide Web

154

(4)

7.3.1 How Popular is the World Wide Web?

155

(1)

7.3.2 Simple HTML

156

(1)

7.3.3 Chemical HTML

157

(1)

7.4 Key Points

158

(1)

Questions

158

(1)

Q7.1 Searching the Cambridge Crystallographic Database

158

(1)

Q7.2 Searching the Internet

158

(1)

Q7.3 Writing HTML

159

(1)

Discussion

159

(2)

D7.1 Searching the Cambridge Crystallographic Database

159

(1)

D7.2 Searching the Internet

159

(1)

D7.3 Writing HTML

160

(1)

8 Applications

161

(21)

8.1 Introduction

161

(3)

8.1.1 What Experimental Data are Available?

161

(1)

8.1.2 Is it Possible?

162

(1)

8.1.3 Is it Realistic?

162

(1)

8.1.4 What Information can be Obtained from the Study?

163

(1)

8.2 Structures

164

(4)

8.2.1 Tilivalline

164

(1)

8.2.2 Conjugated Hydrocarbons

165

(2)

8.2.3 Conclusions

167

(1)

8.3 Reactivity

168

(8)

8.3.1 Diels-Alder Reactions

171

(2)

8.3.2 Boron-mediated Aldol Reactions

173

(2)

8.3.3 Conclusions

175

(1)

8.4 Drug Design

176

(4)

8.4.1 Does a Molecule Fit into an Active Site?

176

(1)

8.4.2 What Holds Molecules in Active Sites?

177

(1)

8.4.3 How Tightly do Ligands Bind?

178

(1)

8.4.4 How Can a Molecule be Designed to Fit in an Active Site?

178

(2)

8.4.5 Determining Protein Structures

180

(1)

8.5 Conclusions

180

(2)

Glossary

182

(3)

Appendices

185

(18)

A.1 Physical Constants and Conversion Factors

185

(1)

A.2 Electromagnetic Spectrum

186

(1)

A.3 Boltzmann Factors

186

(2)

A.4 Approximate Kinetic Graph

188

(1)

A.5 van der Waals Radii

189

(1)

A.6 Stereochemical Assignment

190

(1)

A.7 A List of Force Fields

190

(2)

A.8 Z-Matrices

192

(2)

A.9 Amino Acids

194

(2)

A.10 Nucleic Acids

196

(1)

A.11 Useful Mathematics

197

(2)

A.12 Adding Parameters to a Force Field

199

(4)

References and Further Reading

203

(9)

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Chemical Applications of Molecular Modeling

Summary

Author Biography

Table of Contents

Supplemental Materials