Modern physical organic chemistry:
Gespeichert in:
| Hauptverfasser: | , |
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| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Sausalito, Calif.
Univ. Science Books
2006
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| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XXVIII, 1099 S. Ill., graph. Darst. |
| ISBN: | 1891389319 9781891389313 |
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| 100 | 1 | |a Anslyn, Eric V. |d 1960- |e Verfasser |0 (DE-588)136650759 |4 aut | |
| 245 | 1 | 0 | |a Modern physical organic chemistry |c Eric V. Anslyn ; Dennis A. Dougherty |
| 264 | 1 | |a Sausalito, Calif. |b Univ. Science Books |c 2006 | |
| 300 | |a XXVIII, 1099 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
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| 689 | 1 | 1 | |a Organische Chemie |0 (DE-588)4043793-0 |D s |
| 689 | 1 | |5 DE-604 | |
| 700 | 1 | |a Dougherty, Dennis A. |d 1952- |e Verfasser |0 (DE-588)133002667 |4 aut | |
| 856 | 4 | 2 | |m HBZ Datenaustausch |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014567444&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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Datensatz im Suchindex
| _version_ | 1804135012776280064 |
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| adam_text | Abbreviated Contents
part I: Molecular Structure and Thermodynamics
chapter 1. Introduction to Structure and Models of Bonding 3
2. Strain and Stability 65
3. Solutions and Non-Covalent Binding Forces 145
4. Molecular Recognition and Supramolecular Chemistry 207
5. Acid-Base Chemistry 259
6. Stereochemistry 297
part II: Reactivity, Kinetics, and Mechanisms
chapter 7. Energy Surfaces and Kinetic Analyses 355
8. Experiments Related to Thermodynamics and Kinetics 421
9. Catalysis 489
10. Organic Reaction Mechanisms, Part 1:
Reactions Involving Additions and / or Eliminations 537
11. Organic Reaction Mechanisms, Part 2:
Substitutions at Aliphatic Centers and Thermal
Isomerizations / Rearrangements 627
12. Organotransition Metal Reaction Mechanisms and Catalysis 705
13. Organic Polymer and Materials Chemistry 753
part III: Electronic Structure: Theory and Applications
chapter 14. Advanced Concepts in Electronic Structure Theory 807
15. Thermal Pericyclic Reactions 877
16. Photochemistry 935
17. Electronic Organic Materials 1001
appendix 1. Conversion Factors and Other Useful Data 1047
2. Electrostatic Potential Surfaces for Representative Organic Molecules 1049
3. Group Orbitals of Common Functional Groups:
Representative Examples Using Simple Molecules 1051
4. The Organic Structures of Biology 1057
5. Pushing Electrons 1061
6. Reaction Mechanism Nomenclature 1075
index 1079
Contents
List of Highlights xix
Preface xxiii
Acknowledgments xxv
A Note to the Instructor xxvii
PART I
MOLECULAR STRUCTURE AND
THERMODYNAMICS
chapter 1: Introduction to Structure and
Models of Bonding 3
Intent and Purpose 3
1.1 A Review of Basic Bonding Concepts 4
1.1.1 Quantum Numbers and Atomic Orbitals 4
1.1.2 Electron Configurations and Electronic Diagrams
1.1.3 Lewis Structures 6
1.1.4 Formal Charge 6
1.1.5 VSEPR 7
1.1.6 Hybridization 8
1.1.7 A Hybrid Valence Bond / Molecular Orbital
Model of Bonding 10
Creating Localized a and n Bonds 11
1.1.8 Polar Covalent Bonding 12
Electronegativity 12
Electrostatic Potential Surfaces 14
Inductive Effects 15
Group Electronegativities 16
Hybridization Effects 17
1.1.9 Bond Dipoles, Molecular Dipoles,
and Quadrupoles 17
Bond Dipoles 17
Molecular Dipole Moments 18
Molecular Quadrupole Moments 19
1.1.10 Resonance 20
1.1.11 Bond Lengths 22
1.1.12 Polarizability 24
1.1.13 Summary of Concepts Used for the Simplest
Model of Bonding in Organic Structures 26
1.2 A More Modern Theory of Organic Bonding 26
1.2.1 Molecular Orbital Theory 27
1.2.2 A Method for QMOT 28
1.2.3 Methyl in Detail 29
Planar Methyl 29
The Walsh Diagram: Pyramidal Methyl 31
Group Orbitals for Pyramidal Methyl 32
Putting the Electrons In—The MH3 System 33
1.2.4 The CH2 Group in Detail 33
The Walsh Diagram and Group Orbitals 33
Putting the Electrons In — The MH2 System 33
1.3 Orbital Mixing—Building Larger Molecules 35
1.3.1 Using Group Orbitals to Make Ethane 36
1.3.2 Using Group Orbitals to Make Ethylene 38
1.3.3 The Effects of Heteroatoms—Formaldehyde 40
1.3.4 Making More Complex Alkanes 43
1.3.5 Three More Examples of Building Larger
Molecules from Group Orbitals 43
Propene 43
Methyl Chloride 45
Butadiene 46
1.3.6 Group Orbitals of Representative it Systems:
Benzene, Benzyl, and Allyl 46
1.3.7 Understanding Common Functional
Groups as Perturbations of Allyl 49
1.3.8 The Three Center-Two Electron Bond 50
1.3.9 Summary of the Concepts Involved in
Our Second Model of Bonding 51
1.4 Bonding and Structures of Reactive Intermediates 52
1.4.1 Carbocations 52
Carbenium Ions 53
Interplay with Carbonium Ions 54
Carbonium Ions 55
1.4.2 Carbanions 56
1.4.3 Radicals 57
1.4.4 Carbenes 58
1.5 A Very Quick Look at Organometallic
and Inorganic Bonding 59
Summary and Outlook 61
EXERCISES 62
FURTHER READING 64
CHAPTER 2: Strain and Stability 65
Intent and Purpose 65
2.1 Thermochemistry of Stable Molecules
2.1.1 The Concepts of Internal Strain
and Relative Stability 66
2.1.2 Types of Energy 68
Gibbs Free Energy 68
Enthalpy 69
Entropy 70
2.1.3 Bond Dissociation Energies 70
Using BDEs to Predict Exothermicity
and Endothermkity 72
2.1.4 An Introduction to Potential Functions
and Surfaces—Bond Stretches 73
Infrared Spectroscopy 77
2.1.5 Heats of Formation and Combustion
2.1.6 The Group Increment Method 79
2.1.7 Strain Energy 82
66
77
CONTENTS
2.2 Thermochemistry of Reactive Intermediates 82
2.2.1 Stability vs. Persistence 82
2.2.2 Radicals 83
BDEs as a Measure ofStability 83
Radical Persistence 84
Group Incremen tsfor Radicals 86
2.2.3 Carbocations 87
Hydride Ion Affinities as a Measure of Stability 87
Lifetimes of Carbocations 90
2.2.4 Carbanions 91
2.2.5 Summary 91
2.3 Relationships Between Structure and Energetics—
Basic Conformational Analysis 92
2.3.1 Acyclic Systems—Torsional Potential Surfaces 92
Ethane 92
Butane—The Gauche Interaction 95
Barrier Height 97
Barrier Foldedness 97
Tetraalkylethanes 98
The g+g-Pentane Interaction 99
Allylic (A™) Strain 100
2.3.2 Basic Cyclic Systems 100
Cyclopropane 100
Cyclobutane 100
Cyclopentane 101
Cyclohexane 102
Larger Rings—Transannular Effects 107
Group Increment Corrections for Ring Systems 109
Ring Torsional Modes 109
Bicyclic Ring Systems 110
Cycloalkenes and Bredt s Rule 110
Summary of Conformational Analysis and
Its Connection to Strain 112
2.4 Electronic Effects 112
2.4.1 Interactions Involving it Systems 112
Substitution on Alkenes 112
Conformations of Substituted Alkenes 113
Conjugation 115
Aromaticity 116
Antiaromaticity, An Unusual Destabilizing Effect 117
NMR Chemical Shifts 118
Polycyclic Aromatic Hydrocarbons 119
Large Annulenes 119
2.4.2 Effects of Multiple Heteroatoms 120
Bond Length Effects 120
Orbital Effects 120
2.5 Highly-Strained Molecules 124
2.5.1 Long Bonds and Large Angles 124
2.5.2 Small Rings 125
2.5.3 Very Large Rotation Barriers 127
2.6 Molecular Mechanics 128
2.6.1 The Molecular Mechanics Model 129
Bond Stretching 129
Angle Bending 130
Torsion 130
Nonbonded Interactions 130
Cross Terms 131
Electrostatic Interactions 131
Hydrogen Bonding 131
The Parameterization 132
Heat of Formation and Strain Energy 132
2.6.2 General Comments on the Molecular
Mechanics Method 133
2.6.3 Molecular Mechanics on Biomolecules and
Unnatural Polymers— Modeling 135
2.6.4 Molecular Mechanics Studies of Reactions 136
Summary and Outlook 137
EXERCISES 138
FURTHER READING 143
CHAPTER 3: Solutions and Non-Covalent
Binding Forces 145
Intent and Purpose 145
3.1 Solvent and Solution Properties 145
3.1.1 Nature Abhors a Vacuum 146
3.1.2 Solvent Scales 146
Dielectric Constant 147
Other Solvent Scales 148
Heat of Vaporization 150
Surface Tension and Wetting 150
Water 151
3.1.3 Solubility 153
General Overview 153
Shape 154
Using the Like-Dissolves-Like Paradigm 154
3.1.4 Solute Mobility 155
Diffusion 155
Fick s Law of Diffusion 156
Correlation Times 156
3.1.5 The Thermodynamics of Solutions 157
Chemical Potential 158
The Thermodynamics of Reactions 160
Calculating AH0 and AS° 162
3.2 Binding Forces 162
3.2.1 Ion Pairing Interactions 163
Salt Bridges 164
3.2.2 Electrostatic Interactions Involving Dipoles 165
Ion-Dipole Interactions 165
A Simple Model of Ionic Solvation —
The Born Equation 166
Dipole-Dipole Interactions 168
3.2.3 Hydrogen Bonding 168
Geometries 169
Strengths of Normal Hydrogen Bonds 171
i. Solvation Effects 171
ii. Electronegativity Effects 172
Hi. Resonance Assisted Hydrogen Bonds 173
iv. Polarization Enhanced Hydrogen Bonds 174
v. Secondary Interactions in Hydrogen
Bonding Systems 175
CONTENTS
vi. Cooperativity in Hydrogen Bonds 175
Vibrational Properties of Hydrogen Bonds 176
Short-Strong Hydrogen Bonds 177
3.2.4 tt Effects 180
Cation-K Interactions 181
Polar-K Interactions 183
Aromatic-Aromatic Interactions (n Stacking) 184
The Arene-Perfluoroarene Interaction 184
k Donor-Acceptor Interactions 186
3.2.5 Induced-Dipole Interactions 186
Ion-Induced-Dipole Interactions 187
Dipole-Induced-Dipole Interactions 187
Induced-Dipole-Induced-Dipole Interactions 188
Summarizing Monopole, Dipole, and
Induced-Dipole Binding Forces 188
3.2.6 The Hydrophobie Effect 189
Aggregation ofOrganics 189
The Origin of the Hydrophobie Effect 192
3.3 Computational Modeling of Solvation
3.3.1 Continuum Solvation Models 196
3.3.2 Explicit Solvation Models 197
3.3.3 Monte Carlo (MC) Methods 198
3.3.4 Molecular Dynamics (MD) 199
3.3.5 Statistical Perturbation Theory/
Free Energy Perturbation 200
Summary and Outlook 201
EXERCISES 202
FURTHER READING 204
194
CHAPTER 4: Molecular Recognition and
Supramolecular Chemistry 207
Intent and Purpose 207
4.1 Thermodynamic Analyses of Binding
Phenomena 207
4.1.1 General Thermodynamics of Binding 208
The Relevance of the Standard State 210
The Influence of a Change in Heat Capacity 212
Cooperativity 213
Enthalpy-Entropy Compensation 216
4.1.2 The Binding Isotherm 216
4.1.3 Experimental Methods 219
UV/Vis or Fluorescence Methods 220
NMR Methods 220
Isothermal Calorimetry 12
4.2 Molecular Recognition 222
4.2.1 Complementarity and Preorganization 224
Crowns, Cryptands, and Spherands—Molecular
Recognition with a Large Ion-Dipole Component 224
Tweezers and Clefts 228
4.2.2 Molecular Recognition with a Large
Ion Pairing Component 228
4.2.3 Molecular Recognition with a Large Hydrogen
Bonding Component 230
Representative Structures 230
Molecular Recognition via Hydrogen
Bonding in Water 232
4.2.4 Molecular Recognition with a Large
Hydrophobie Component 234
Cyclodextrins 234
Cyclophanes 234
A Summary of the Hydrophobie Component
of Molecular Recognition in Water 238
4.2.5 Molecular Recognition with a Large tt
Component 239
Cation-K In teractions 239
Polar-n and Related Effects 241
4.2.6 Summary 241
4.3 Supramolecular Chemistry 243
4.3.1 Supramolecular Assembly of Complex
Architectures 244
Self-Assembly via Coordination Compounds 244
Self-Assembly via Hydrogen Bonding 245
4.3.2 Novel Supramolecular Architectures—Catenanes,
Rotaxanes, and Knots 246
Nanotechnology 248
4.3.3 Container Compounds—Molecules within
Molecules 249
Summary and Outlook 252
exercises 253
further reading 256
CHAPTER 5: Acid-Base Chemistry 259
Intent and Purpose 259
5.1 Brensted Acid-Base Chemistry 259
5.2 Aqueous Solutions 261
5.2.1 pKa 261
5.2.2 pH 262
5.2.3 The Leveling Effect 264
5.2.4 Activity vs. Concentration 266
5.2.5 Acidity Functions: Acidity Scales for Highly
Concentrated Acidic Solutions 266
5.2.6 Super Acids 270
5.3 Nonaqueous Systems 271
5.3.1 pKa Shifts at Enzyme Active Sites 273
5.3.2 Solution Phase vs. Gas Phase 273
5.4 Predicting Acid Strength in Solution 276
5.4.1 Methods Used to Measure Weak Acid Strength 276
5.4.2 Two Guiding Principles for Predicting
Relative Acidities 277
5.4.3 Electronegativity and Induction 278
5.4.4 Resonance 278
5.4.5 Bond Strengths 283
5.4.6 Electrostatic Effects 283
5.4.7 Hybridization 283
CONTENTS
5.4.8 Aromaticity 284
5.4.9 Solvation 284
5.4.10 Cationic Organic Structures
285
5.5 Acids and Bases of Biological Interest 285
5.6 Lewis Acids/Bases and Electrophiles/
Nucleophiles 288
5.6.1 The Concept of Hard and Soft Acids and Bases, General
Lessons for Lewis Acid-Base Interactions, and Relative
Nucleophilicity and Electrophilicity 289
Summary and Outlook 292
EXERCISES 292
FURTHER READING 294
CHAPTER 6: Stereochemistry 297
Intent and Purpose 297
6.1 Stereogenicity and Stereoisomerism 297
6.1.1 Basic Concepts and Terminology 298
Classic Terminology 299
More Modern Terminology 301
6.1.2 Stereochemical Descriptors 303
R,S System 304
E,Z System 304
DandL 304
Erythro and Threo 305
Helical Descriptors— Mand P 305
EntandEpi 306
Using Descriptors to Compare Structures 306
6.1.3 Distinguishing Enantiomers 306
Optical Activity and Chirality 309
Why is Plane Polarized Light Rotated
byaChiralMedium? 309
Circular Dichroism 310
X-Ray Crystallography 310
6.2 Symmetry and Stereochemistry 311
6.2.1 Basic Symmetry Operations 311
6.2.2 Chirality and Symmetry 311
6.2.3 Symmetry Arguments 313
6.2.4 Focusing on Carbon 314
6.3 Topicity Relationships 315
6.3.1 Homotopic, Enantiotopic, and Diastereotopic
6.3.2 Topicity Descriptors—Pro-K/Pro-S and Re I Si
6.3.3 Chirotopicity 317
315
316
6.4 Reaction Stereochemistry: Stereoselectivity
and Stereospecificity 317
6.4.1 Simple Guidelines for Reaction Stereochemistry 317
6.4.2 Stereospecific and Stereoselective Reactions 319
6.5 Symmetry and Time Scale 322
6.6 Topological and Supramolecular Stereochemistry
6.6.1 Loops and Knots 325
6.6.2 Topological Chirality 326
324
6.6.3 Nonplanar Graphs 326
6.6.4 Achievements in Topological and Supramolecular
Stereochemistry 327
6.7 Stereochemical Issues in Polymer Chemistry 331
6.8 Stereochemical Issues in Chemical Biology
6.8.1 The Linkages of Proteins, Nucleic Acids,
and Polysaccharides 333
Proteins 333
Nucleic Acids 334
Polysaccharides 334
6.8.2 Helicity 336
Synthetic Helical Polymers 337
6.8.3 The Origin of Chirality in Nature 339
6.9 Stereochemical Terminology 340
Summary and Outlook 344
EXERCISES 344
FURTHER READING 350
333
PART II
REACTIVITY, KINETICS, AND
MECHANISMS
356
CHAPTER 7: Energy Surfaces and
Kinetic Analyses 355
Intent and Purpose 355
7.1 Energy Surfaces and Related Concepts
7.1.1 Energy Surfaces 357
7.1.2 Reaction Coordinate Diagrams 359
7.1.3 What is the Nature of the Activated
Complex / Transition State? 362
7.1.4 Rates and Rate Constants 363
7.1.5 Reaction Order and Rate Laws 364
7.2 Transition State Theory (TST) and Related Topics 365
7.2.1 The Mathematics of Transition State Theory 365
7.2.2 Relationship to the Arrhenius Rate Law 367
7.2.3 Boltzmann Distributions and Temperature
Dependence 368
7.2.4 Revisiting What is the Nature of the Activated
Complex? and Why Does TST Work? 369
7.2.5 Experimental Determinations of Activation Parameters
and Arrhenius Parameters 370
7.2.6 Examples of Activation Parameters and
Their Interpretations 372
7.2.7 Is TST Completely Correct? The Dynamic Behavior
of Organic Reactive Intermediates 372
7.3 Postulates and Principles Related
to Kinetic Analysis 374
7.3.1 The Hammond Postulate 374
7.3.2 The Reactivity vs. Selectivity Principle 377
CONTENTS
7.3.3 The Curtin-Hammett Principle 378
7.3.4 Microscopic Reversibility 379
7.3.5 Kinetic vs. Thermodynamic Control 380
7.4 Kinetic Experiments 382
7.4.1 How Kinetic Experiments are Performed 382
7.4.2 Kinetic Analyses for Simple Mechanisms 384
First Order Kinetics 385
Second Order Kinetics 386
Pseudo-First Order Kinetics 387
Equilibrium Kinetics 388
Initial-Rate Kinetics 389
Tabulating a Series of Common Kinetic Scenarios 389
7.5 Complex Reactions—Deciphering Mechanisms 390
7.5.1 Steady State Kinetics 390
7.5.2 Using the SSA to Predict Changes
in Kinetic Order 395
7.5.3 Saturation Kinetics 396
7.5.4 Prior Rapid Equilibria 397
7.6 Methods for Following Kinetics 397
7.6.1 Reactions with Half-Lives Greater
than a Few Seconds 398
7.6.2 Fast Kinetics Techniques 398
Flow Techniques 399
Flash Photolysis 399
Pulse Radiolysis 401
7.6.3 Relaxation Methods 401
7.6.4 Summary of Kinetic Analyses 402
7.7 Calculating Rate Constants 403
7.7.1 Marcus Theory 403
7.7.2 Marcus Theory Applied to Electron Transfer 405
7.8 Considering Multiple Reaction Coordinates 407
7.8.1 Variation in Transition State Structures Across
a Series of Related Reactions—An Example
Using Substitution Reactions 407
7.8.2 More O Ferrall-Jencks Plots 409
7.8.3 Changes in Vibrational State Along the Reaction
Coordinate—Relating the Third Coordinate
to Entropy 412
Summary and Outlook 413
EXERCISES 413
FURTHER READING 417
CHAPTER 8: Experiments Related to
Thermodynamics and Kinetics
Intent and Purpose 421
8.1 Isotope Effects 421
8.1.1 The Experiment 422
8.1.2 The Origin of Primary Kinetic Isotope Effects
Reaction Coordinate Diagrams and Isotope
Effects 424
421
422
Primary Kinetic Isotope Effects for Linear
Transition States as a Function ofExothermicity
and Endothermicity 425
Isotope Effects for Linear vs. Non-Linear
Transition States 428
8.1.3 The Origin of Secondary Kinetic Isotope Effects 428
Hybridization Changes 429
Steric Isotope Effects 430
8.1.4 Equilibrium Isotope Effects 432
Isotopic Perturbation of Equilibrium —
Applications to Carbocations 432
8.1.5 Tunneling 435
8.1.6 Solvent Isotope Effects 437
Fractionation Factors 437
Proton Inventories 438
8.1.7 Heavy Atom Isotope Effects 441
8.1.8 Summary 441
8.2 Substituent Effects 441
8.2.1 The Origin of Substituent Effects 443
Field Effects 443
Inductive Effects 443
Resonance Effects 444
Polarizability Effects 444
Steric Effects 445
Solvation Effects 445
8.3 Hammett Plots—The Most Common LFER.
A General Method for Examining Changes
in Charges During a Reaction 445
8.3.1 Sigma (ff) 445
8.3.2 Rho(p) 447
8.3.3 The Power of Hammett Plots for
Deciphering Mechanisms 448
8.3.4 Deviations from Linearity 449
8.3.5 Separating Resonance from Induction 451
8.4 Other Linear Free Energy Relationships 454
8.4.1 Steric and Polar Effects—Taft Parameters 454
8.4.2 Solvent Effects—Grunwald-Winstein Plots 455
8.4.3 Schleyer Adaptation 457
8.4.4 Nucleophilicity and Nucleofugality 458
Basicity/Acidity 459
Solvation 460
Polarizability, Basicity, and Solvation Interplay 460
Shape 461
8.4.5 Swain-Scott Parameters—Nucleophilicity
Parameters 461
8.4.6 Edwards and Ritchie Correlations 463
8.5 Acid-Base Related Effects—
Bronsted Relationships 464
8.5.1 /3Nuc 464
8.5.2 ßLG 464
8.5.3 Acid-Base Catalysis 466
8.6 Why do Linear Free Energy Relationships Work? 466
8.6.1 General Mathematics of LFERs 467
8.6.2 Conditions to Create an LFER 468
8.6.3 The Isokinetic or Isoequilibrium Temperature 469
CONTENTS
8.6.4 Why does Enthalpy-Entropy
Compensation Occur? 469
Steric Effects 470
Solvation 470
8.7 Summary of Linear Free Energy Relationships 470
8.8 Miscellaneous Experiments for
Studying Mechanisms 471
8.8.1 Product Identification 472
8.8.2 Changing the Reactant Structure to Divert
or Trap a Proposed Intermediate 473
8.8.3 Trapping and Competition Experiments 474
8.8.4 Checking for a Common Intermediate 475
8.8.5 Cross-Over Experiments 476
8.8.6 Stereochemical Analysis 476
8.8.7 Isotope Scrambling 477
8.8.8 Techniques to Study Radicals: Clocks and Traps 478
8.8.9 Direct Isolation and Characterization
of an Intermediate 480
8.8.10 Transient Spectroscopy 480
8.8.11 Stable Media 481
Summary and Outlook 482
exercises 482
further reading 487
CHAPTER 9: Catalysis 489
Intent and Purpose 489
9.1 General Principles of Catalysis 490
9.1.1 Binding the Transition State Better
than the Ground State 491
9.1.2 A Thermodynamic Cycle Analysis 493
9.1.3 A Spatial Temporal Approach 494
9.2 Forms of Catalysis 495
9.2.1 Binding is Akin to Solvation 495
9.2.2 Proximity as a Binding Phenomenon 495
9.2.3 Electrophilic Catalysis 499
Electrostatic Interactions 499
Metal Ion Catalysis 500
9.2.4 Acid-Base Catalysis 502
9.2.5 Nucleophilic Catalysis 502
9.2.6 Covalent Catalysis 504
9.2.7 Strain and Distortion 505
9.2.8 Phase Transfer Catalysis 507
9.3 Bronsted Acid-Base Catalysis 507
9.3.1 Specific Catalysis 507
The Mathematics of Specific Catalysis 507
Kinetic Plots 510
9.3.2 General Catalysis 510
The Mathematics of General Catalysis 511
Kinetic Plots 512
9.3.3 A Kinetic Equivalency 514
9.3.4 Concerted or Sequential General-Acid-
General-Base Catalysis 515
9.3.5 The Bronsted Catalysis Law
and Its Ramifications 516
A Linear Free Energy Relationship 516
The Meaning of a and ß 517
a+ß=l 518
Deviations from Linearity 519
9.3.6 Predicting General-Acid or
General-Base Catalysis 520
The Libido Rule 520
Potential Energy Surfaces Dictate
General or Specific Catalysis 521
9.3.7 The Dynamics of Proton Transfers 522
Marcus Analysis 522
524
9.4 Enzymatic Catalysis 523
9.4.1 Michaelis-Menten Kinetics 523
9.4.2 The Meaning of KM, kat, and kcajKM
9 A3 Enzyme Active Sites 525
9.4.4 [S] vs. KM—Reaction Coordinate Diagrams
9.4.5 Supramolecular Interactions 529
Summary and Outlook 530
EXERCISES 531
FURTHER READING 535
527
CHAPTER 10: Organic Reaction Mechanisms,
Part 1: Reactions Involving Additions
and/or Eliminations 537
Intent and Purpose 537
10.1 Predicting Organic Reactivity 538
10.1.1 A Useful Paradigm for Polar Reactions 539
Nucleophiles and Electrophiles 539
Lewis Acids and Lewis Bases 540
Donor-Acceptor Orbital Interactions 540
10.1.2 Predicting Radical Reactivity 541
10.1.3 In Preparation for the Following Sections 541
—ADDITION REACTIONS— 542
10.2 Hydration of Carbonyl Structures 542
10.2.1 Acid-Base Catalysis 543
10.2.2 The Thermodynamics of the Formation
of Geminal Diols and Hemiacetals 544
10.3 Electrophilic Addition of Water to Alkenes
and Alkynes: Hydration 545
10.3.1 Electron Pushing 546
10.3.2 Acid-Catalyzed Aqueous Hydration 546
10.3.3 Regiochemistry 546
10.3.4 Alkyne Hydration 547
10.4 Electrophilic Addition of Hydrogen Halides
to Alkenes and Alkynes 548
10.4.1 Electron Pushing 548
CONTENTS
10.4.2 Experimental Observations Related to
Regiochemistry and Stereochemistry 548
10.4.3 Addition to Alkynes 551
10.5 Electrophilic Addition of Halogens
toAlkenes 551
10.5.1 Electron Pushing 551
10.5.2 Stereochemistry 552
10.5.3 Other Evidence Supporting a cr Complex 552
10.5.4 Mechanistic Variants 553
10.5.5 Addition to Alkynes 554
10.6 Hydroboration 554
10.6.1 Electron Pushing 555
10.6.2 Experimental Observations 555
10.7 Epoxidation 555
10.7.1 Electron Pushing 556
10.7.2 Experimental Observations 556
10.8 Nucleophilic Additions to
Carbonyl Compounds 556
10.8.1 Electron Pushing for a Few Nucleophilic
Additions 557
10.8.2 Experimental Observations for
Cyanohydrin Formation 559
10.8.3 Experimental Observations for
Grignard Reactions 560
10.8.4 Experimental Observations in
LAH Reductions 561
10.8.5 Orbital Considerations 561
The Bürgi-Dunitz Angle 561
Orbital Mixing 562
10.8.6 Conformational Effects in Additions
to Carbonyl Compounds 562
10.8.7 Stereochemistry of Nucleophilic Additions 563
10.9 Nucleophilic Additions to Olefins 567
10.9.1 Electron Pushing 567
10.9.2 Experimental Observations 567
10.9.3 Regiochemistry of Addition 567
10.9.4 Baldwin s Rules 568
10.10 Radical Additions to Unsaturated
Systems 569
10.10.1 Electron Pushing for Radical Additions 569
10.10.2 Radical Initiators 570
10.10.3 Chain Transfer vs. Polymerization 571
10.10.4 Termination 571
10.10.5 Regiochemistry of Radical Additions 572
10.11 Carbene Additions and Insertions 572
10.11.1 Electron Pushing for Carbene Reactions 574
10.11.2 Carbene Generation 574
10.11.3 Experimental Observations for
Carbene Reactions 575
—ELIMINATIONS— 576
10.12 Eliminations to Form Carbonyls or Carbonyl-Like
Intermediates 577
10.12.1 Electron Pushing 577
10.12.2 Stereochemical and Isotope
Labeling Evidence 577
10.12.3 Catalysis of the Hydrolysis of Acetals 578
10.12.4 Stereoelectronic Effects 579
10.12.5 CrO3 Oxidation—The Jones Reagent 580
Electron Pushing 580
A Few Experimental Observations 581
10.13 Elimination Reactions for Aliphatic Systems—
Formation of Alkenes 581
10.13.1 Electron Pushing and Definitions 581
10.13.2 Some Experimental Observations
for E2 and El Reactions 582
10.13.3 Contrasting Elimination
and Substitution 583
10.13.4 Another Possibility—ElcB 584
10.13.5 Kinetics and Experimental Observations
for ElcB 584
10.13.6 Contrasting E2, El, and ElcB 586
10.13.7 Regiochemistry of Eliminations 588
10.13.8 Stereochemistry of Eliminations—
Orbital Considerations 590
10.13.9 Dehydration 592
Electron Pushing 592
Other Mechanistic Possibilities 594
10.13.10 Thermal Eliminations 594
10.14 Eliminations from Radical Intermediates 596
—COMBINING ADDITION AND ELIMINATION
REACTIONS (SUBSTITUTIONS AT sp2 CENTERS)—
10.15 The Addition of Nitrogen Nucleophiles
to Carbonyl Structures, Followed
by Elimination 597
10.15.1 Electron Pushing 598
10.15.2 Acid-Base Catalysis 598
10.16 The Addition of Carbon Nucleophiles,
Followed by Elimination—
The Wittig Reaction 599
10.16.1 Electron Pushing 600
10.17 Acyl Transfers 600
10.17.1 General Electron-Pushing Schemes 600
10.17.2 Isotope Scrambling 601
10.17.3 Predicting the Site of Cleavage for
Acyl Transfers from Esters 602
10.17.4 Catalysis 602
10.18 Electrophilic Aromatic Substitution 607
10.18.1 Electron Pushing for Electrophilic
Aromatic Substitutions 607
10.18.2 Kinetics and Isotope Effects 608
10.18.3 Intermediate Complexes 608
10.18.4 Regiochemistry and Relative Rates of
Aromatic Substitution 609
10.19 Nucleophilic Aromatic Substitution 611
10.19.1 Electron Pushing for Nucleophilic
Aromatic Substitution 611
10.19.2 Experimental Observations 611
596
CONTENTS
10.20 Reactions Involving Benzyne 612
10.20.1 Electron Pushing for Benzyne Reactions 612
10.20.2 Experimental Observations 613
10.20.3 Substituent Effects 613
10.21 The SrnI Reaction on Aromatic Rings 615
10.21.1 Electron Pushing 615
10.21.2 A Few Experimental Observations 615
10.22 Radical Aromatic Substitutions
10.22.1 Electron Pushing 615
10.22.2 Isotope Effects 616
10.22.3 Regiochemistry 616
Summary and Outlook 617
exercises 617
further reading 624
615
CHAPTER 11: Organic Reaction Mechanisms,
Part 2: Substitutions at Aliphatic
Centers and Thermal Isomerizations/
Rearrangements 627
Intent and Purpose 627
—SUBSTITUTION a TO A CARBONYL CENTER:
ENOL AND ENOLATE CHEMISTRY— 627
11.1 Tautomerization 628
11.1.1 Electron Pushing for Keto-Enol
Tautomerizations 628
11.1.2 The Thermodynamics of Enol Formation 628
11.1.3 Catalysis of Enolizations 629
11.1.4 Kinetic vs. Thermodynamic Control
in Enolate and Enol Formation 629
11.2 a-Halogenation 631
11.2.1 Electron Pushing 631
11.2.2 A Few Experimental Observations
631
11.3 a-Alkylations 632
11.3.1 Electron Pushing 632
11.3.2 Stereochemistry: Conformational Effects 633
11.4 The Aldol Reaction 634
11.4.1 Electron Pushing 634
11.4.2 Conformational Effects on the Aldol Reaction 634
—SUBSTITUTIONS ON ALIPHATIC CENTERS— 637
11.5 Nucleophilic Aliphatic Substitution Reactions 637
11.5.1 Sn2 and SN1 Electron-Pushing Examples 637
11.5.2 Kinetics 638
11.5.3 Competition Experiments and Product Analyses 639
11.5.4 Stereochemistry 640
11.5.5 Orbital Considerations 643
11.5.6 Solvent Effects 643
11.5.7 Isotope Effect Data 646
11.5.8 An Overall Picture of SN2 and SN1 Reactions 646
11.5.9 Structure-Function Correlations
with the Nucleophile 648
11.5.10 Structure-Function Correlations
with the Leaving Group 651
11.5.11 Structure-Function Correlations
with the R Group 651
Effect of the R Group Structure on SN2 Reactions 651
Effect of the R Group Structure on SN1 Reactions 653
11.5.12 Carbocation Rearrangements 656
11.5.13 Anchimeric Assistance in SN1 Reactions 659
11.5.14 SnI Reactions Involving Non-Classical
Carbocations 661
Norbornyl Cation 662
Cyclopropyl Carbinyl Carbocation 664
11.5.15 Summary of Carbocation Stabilization
in Various Reactions 667
11.5.16 The Interplay Between Substitution
and Elimination 667
11.6 Substitution, Radical, Nucleophilic 668
11.6.1 The SET Reaction—Electron Pushing 668
11.6.2 The Nature of the Intermediate
in an SET Mechanism 669
11.6.3 Radical Rearrangements as Evidence 669
11.6.4 Structure-Function Correlations
with the Leaving Group 670
11.6.5 The SrnI Reaction—Electron Pushing 670
11.7 Radical Aliphatic Substitutions 671
11.7.1 Electron Pushing 671
11.7.2 Heats of Reaction 671
11.7.3 Regiochemistry of Free Radical
Halogenation 671
11.7.4 Autoxidation: Addition of O2
into C-H Bonds 673
Electron Pushing for Autoxidation 673
—ISOMERIZATIONS AND REARRANGEMENTS— 674
11.8 Migrations to Electrophilic Carbons 674
11.8.1 Electron Pushing for the
Pinacol Rearrangement 675
11.8.2 Electron Pushing in the Benzilic Acid
Rearrangement 675
11.8.3 Migratory Aptitudes in the Pinacol
Rearrangement 675
11.8.4 Stereoelectronic and Stereochemical Considerations
in the Pinacol Rearrangement 676
11.8.5 A Few Experimental Observations for the Benzilic
Acid Rearrangement 678
11.9 Migrations to Electrophilic Heteroatoms 678
11.9.1 Electron Pushing in the Beckmann
Rearrangement 678
11.9.2 Electron Pushing for the Hofmann
Rearrangement 679
11.9.3 Electron Pushing for the Schmidt
Rearrangement 680
11.9.4 Electron Pushing for the Baeyer-Villiger
Oxidation 680
11.9.5 A Few Experimental Observations for the
Beckmann Rearrangement 680
CONTENTS
11.9.6 A Few Experimental Observations for the
Schmidt Rearrangement 681
11.9.7 A Few Experimental Observations for the
Baeyer-Villiger Oxidation 681
11.10 The Favorskii Rearrangement and Other
Carbanion Rearrangements 682
11.10.1 Electron Pushing 682
11.10.2 Other Carbanion Rearrangements 683
11.11 Rearrangements Involving Radicals 683
11.11.1 Hydrogen Shifts 683
11.11.2 Aryl and Vinyl Shifts 684
11.11.3 Ring-Opening Reactions 685
11.12 Rearrangements and Isomerizations
Involving Biradicals 685
11.12.1 Electron Pushing Involving Biradicals
11.12.2 Tetramethylene 687
11.12.3 Trimethylene 689
11.12.4 Trimethylenemethane 693
Summary and Outlook 695
EXERCISES 695
FURTHER READING 703
686
CHAPTER 12: Organotransition Metal Reaction
Mechanisms and Catalysis 705
Intent and Purpose 705
12.1 The Basics of Organometallic Complexes 705
12.1.1 Electron Counting and Oxidation State 706
Electron Counting 706
Oxidation State 708
d Electron Count 708
Ambiguities 708
12.1.2 The 18-Electron Rule 710
12.1.3 Standard Geometries 710
12.1.4 Terminology 711
12.1.5 Electron Pushing with Organometallic
Structures 711
12.1.6 d Orbital Splitting Patterns 712
12.1.7 Stabilizing Reactive Ligands 713
12.2 Common Organometallic Reactions 714
12.2.1 Ligand Exchange Reactions 714
Reaction Types 714
Kinetics 716
Structure-Function Relationships with the Metal 716
Structure-Function Relationships
with the Ligand 716
Substitutions of Other Ligands 717
12.2.2 Oxidative Addition 717
Stereochemistry of the Metal Complex 718
Kinetics 718
Stereochemistry of the R Group 719
Structure-Function Relationship for the R Group 720
Structure-Function Relationships
for the Ligands 720
Oxidative Addition at sp2 Centers 721
Summary of the Mechanisms for Oxidative
Addition 721
12.2.3 Reductive Elimination 724
Structure-Function Relationship for the
R Group and the Ligands 724
Stereochemistry at the Metal Center 725
Other Mechanisms 725
Summary of the Mechanisms for
Reductive Elimination 726
12.2.4 a-and ß-Eliminations 727
General Trends for a- and ß-Eliminations 727
Kinetics 728
Stereochemistry ofß-Hydride Elimination 729
12.2.5 Migratory Insertions 729
Kinetics 730
Studies to Decipher the Mechanism of Migratory
Insertion Involving CO 730
Other Stereochemical Considerations 732
12.2.6 Electrophilic Addition to Ligands 733
Reaction Types 733
Common Mechanisms Deduced from
Stereochemical Analyses 734
12.2.7 Nucleophilic Addition to Ligands 734
Reaction Types 735
Stereochemical and Regiochemical Analyses 735
12.3 Combining the Individual Reactions into Overall
Transformations and Cycles 737
12.3.1 The Nature of Organometallic Catalysis—
Change in Mechanism 738
12.3.2 The Monsanto Acetic Acid Synthesis 738
12.3.3 Hydroformylation 739
12.3.4 The Water-Gas Shift Reaction 740
12.3.5 Olefin Oxidation—The Wacker Process 741
12.3.6 Palladium Coupling Reactions 742
12.3.7 AllylicAlkylation 743
12.3.8 Olefin Metathesis 744
Summary and Outlook 747
EXERCISES 748
FURTHER READING 750
CHAPTER 13: Organic Polymer and
Materials Chemistry 753
Intent and Purpose 753
13.1 Structural Issues in Materials Chemistry 754
13.1.1 Molecular Weight Analysis of Polymers 754
Number Average and Weight Average Molecular
Weights —M„ and Mw 754
13.1.2 Thermal Transitions—Thermoplastics
and Elastomers 757
13.1.3 Basic Polymer Topologies 759
CONTENTS
13.1.4 Polymer-Polymer Phase Behavior 760
13.1.5 Polymer Processing 762
13.1.6 Novel Topologies—Dendrimers and
Hyperbranched Polymers 763
Dendrimers 763
Hyperbranched Polymers 768
13.1.7 Liquid Crystals 769
13.1.8 Fullerenes and Carbon Nanotubes 775
13.2 Common Polymerization Mechanisms 779
13.2.1 General Issues 779
13.2.2 Polymerization Kinetics 782
Step-Growth Kinetics 782
Free-Radical Chain Polymerization 783
Living Polymerizations 785
Thermodynamics of Polymerizations 787
13.2.3 Condensation Polymerization 788
13.2.4 Radical Polymerization 791
13.2.5 Anionic Polymerization 793
13.2.6 Cationic Polymerization 794
13.2.7 Ziegler-Natta and Related Polymerizations 794
Single-Site Catalysts 796
13.2.8 Ring-Opening Polymerization 797
13.2.9 Group Transfer Polymerization (GTP) 799
Summary and Outlook 800
EXERCISES 801
FURTHER READING 803
PART III
ELECTRONIC STRUCTURE:
THEORY AND APPLICATIONS
CHAPTER 14: Advanced Concepts in Electronic
Structure Theory 807
Intent and Purpose 807
14.1 Introductory Quantum Mechanics 808
14.1.1 The Nature of Wavefunctions 808
14.1.2 The Schrödinger Equation 809
14.1.3 The Hamiltonian 809
14.1.4 The Nature of the V2 Operator 811
14.1.5 Why do Bonds Form? 812
14.2 Calculational Methods—Solving the Schrödinger
Equation for Complex Systems 815
14.2.1 Ablnitio Molecular Orbital Theory 815
Born-Oppenheimer Approximation 815
The Orbital Approximation 815
Spin 816
The Pauli Principle and Determinantal
Wavefunctions 816
The Hartree-Fock Equation and
the Variational Theorem 818
SCF Theory 821
Linear Combination of Atomic Orbitals —
Molecular Orbitals (LCAO-MO) 821
Common Basis Sets —Modeling Atomic Orbitals 822
Extension Beyond HF—Correlation Energy 824
Solvation 825
General Considerations 825
Summary 826
14.2.2 Secular Determinants—A Bridge Between Ab lnitio,
Semi-Empirical/ Approximate, and Perturbational
Molecular Orbital Theory Methods 828
The Two-Orbital Mixing Problem 829
Writing the Secular Equations and Determinant
for Any Molecule 832
14.2.3 Semi-Empirical and Approximate Methods 833
Neglect of Differential Overlap
(NDO) Methods 833
i. CNDO, 1NDO, PNDO (C = Complete,
1 = Intermediate, P = Partial) 834
ii. The Semi-Empirical Methods:
MNDO,AMl,andPM3 834
Extended Hückel Theory (EHT) 834
Hückel Molecular Orbital Theory (HMOT) 835
14.2.4 Some General Comments on Computational
Quantum Mechanics 835
14.2.5 An Alternative: Density Functional
Theory (DFT) 836
14.3 A Brief Overview of the Implementation
and Results of HMOT 837
14.3.1 Implementing Hückel Theory 838
14.3.2 HMOT of Cyclic 17 Systems 840
14.3.3 HMOT of Linear it Systems 841
14.3.4 Alternate Hydrocarbons 842
14.4 Perturbation Theory—Orbital Mixing Rules 844
14.4.1 Mixing of Degenerate Orbitals—
First-Order Perturbations 845
14.4.2 Mixing of Non-Degenerate Orbitals—
Second-Order Perturbations 845
14.5 Some Topics in Organic Chemistry for
Which Molecular Orbital Theory Lends
Important Insights 846
14.5.1 Arenes: Aromaticity and Antiaromaticity 846
14.5.2 Cyclopropane and Cyclopropylcarbinyl—
Walsh Orbitals 848
The Cyclic Three-Orbital Mixing Problem 849
The MOs of Cyclopropane 850
14.5.3 Planar Methane 853
14.5.4 Through-Bond Coupling 854
14.5.5 Unique Bonding Capabilities of Carbocations—
Non-Classical Ions and Hypervalent Carbon 855
Transition State Structure Calculations 856
Application of These Methods to Carbocations 857
NMR Effects in Carbocations 857
The Norbomyl Cation 858
14.5.6 Spin Preferences 859
Two Weakly Interacting Electrons:
H2 vs. Atomic C 859
CONTENTS
14.6 Organometallic Complexes 862
14.6.1 Group Orbitals for Metals 863
14.6.2 The Isolobal Analogy 866
14.6.3 Using the Group Orbitals to Construct
Organometallic Complexes 867
Summary and Outlook 868
EXERCISES 868
FURTHER READING 875
CHAPTER 15: Thermal Pericyclic Reactions 877
Intent and Purpose 877
15.1 Background 878
15.2 A Detailed Analysis of Two Simple
Cycloadditions 878
15.2.1 Orbital Symmetry Diagrams 879
[2+2] 879
[4+2] 881
15.2.2 State Correlation Diagrams 883
[2+2] 883
[4+2] 886
15.2.3 Frontier Molecular Orbital
(FMO) Theory 888
Contrasting the [2+2] and [4+2] 888
15.2.4 Aromatic Transition State
Theory /Topology 889
15.2.5 The Generalized Orbital
Symmetry Rule 890
15.2.6 Some Comments on Forbidden and
Allowed Reactions 892
15.2.7 Photochemical Pericyclic Reactions 892
15.2.8 Summary of the Various Methods 893
15.3 Cycloadditions 893
15.3.1 An Allowed Geometry for [2+2]
Cycloadditions 894
15.3.2 Summarizing Cycloadditions 895
15.3.3 General Experimental Observations 895
15.3.4 Stereochemistry and Regiochemistry
of the Diels-Alder Reaction 896
An Orbital Approach to Predicting
Regiochemistry 896
The Endo Effect 899
15.3.5 Experimental Observations for
[2+2] Cycloadditions 901
15.3.6 Experimental Observations for
1,3-Dipolar Cycloadditions 901
15.3.7 Retrocycloadditions 902
15.4 Electrocyclic Reactions 903
15.4.1 Terminology 903
15.4.2 Theoretical Analyses 904
15.4.3 Experimental Observations:
Stereochemistry 906
15.4.4 Torquoselectivity 908
15.5 Sigmatropic Rearrangements 910
15.5.1 Theory 911
15.5.2 Experimental Observations: A Focus on
Stereochemistry 913
15.5.3 The Mechanism of the
Cope Rearrangement 916
15.5.4 The Claisen Rearrangement 921
Uses in Synthesis 921
Mechanistic Studies 923
15.5.5 The Ene Reaction 924
15.6 Cheletropic Reactions 924
15.6.1 Theoretical Analyses 926
15.6.2 Carbene Additions 927
15.7 In Summary—Applying the Rules 928
Summary and Outlook 928
EXERCISES 929
FURTHER READING 933
CHAPTER 16: Photochemistry 935
Intent and Purpose 935
16.1 Photophysical Processes—
The Jablonski Diagram 936
16.1.1 Electromagnetic Radiation 936
Multiple Energy Surfaces Exist 937
16.1.2 Absorption 939
16.1.3 Radiationless Vibrational Relaxation 944
16.1.4 Fluorescence 945
16.1.5 Internal Conversion (IC) 949
16.1.6 Intersystem Crossing (ISC) 950
16.1.7 Phosphorescence 951
16.1.8 Quantum Yield 952
16.1.9 Summary of Photophysical Processes 952
16.2 Bimolecular Photophysical Processes 953
16.2.1 General Considerations 953
16.2.2 Quenching, Excimers, and Exciplexes 953
Quenching 954
Excimers and Exciplexes 954
Photoinduced Electron Transfer 955
16.2.3 Energy Transfer I. The Dexter Mechanism—
Sensitization 956
16.2.4 Energy Transfer II. The Förster Mechanism
16.2.5 FRET 960
16.2.6 Energy Pooling 962
16.2.7 An Overview of Bimolecular Photophysical
Processes 962
958
16.3 Photochemical Reactions 962
16.3.1 Theoretical Considerations—Funnels
Diabatic Photoreactions 963
Other Mechanisms 964
16.3.2 Acid-Base Chemistry 965
962
CONTENTS
16.3.3 Olefin Isomerization 965
16.3.4 Reversal of Pericyclic Selection Rules 968
16.3.5 Photocycloaddition Reactions 970
Making Highly Strained Ring Systems 973
Breaking Aromaticity 974
16.3.6 The Di-Tr-Methane Rearrangement 974
16.3.7 Carbonyls Part I: The Norrish I Reaction 976
16.3.8 Carbonyls Part II: Photoreduction and
the Norrish II Reaction 978
16.3.9 Nitrobenzyl Photochemistry: Caged
Compounds 980
16.3.10 Elimination of N2: Azo Compounds, Diazo
Compounds, Diazirines, and Azides 981
Azoalkanes (1,2-Diazenes) 981
Diazo Compounds and Diazirines 982
Azides 983
16.4 Chemiluminescence 985
16.4.1 Potential Energy Surface for a
Chemiluminescent Reaction 985
16.4.2 Typical Chemiluminescent Reactions 986
16.4.3 Dioxetane Thermolysis 987
16.5 Singlet Oxygen 989
Summary and Outlook 993
EXERCISES 993
FURTHER READING 999
CHAPTER 17: Electronic Organic Materials 1001
Intent and Purpose 1001
17.1 Theory 1001
17.1.1 Infinite tt Systems—An Introduction
to Band Structures 1002
17.1.2 The Peierls Distortion 1009
17.1.3 Doping 1011
1016
17.2 Conducting Polymers
17.2.1 Conductivity 1016
17.2.2 Polyacetylene 1017
17.2.3 Polyarenes and Polyarenevinylenes
17.2.4 Polyaniline 1021
1022
1018
17.3 Organic Magnetic Materials
17.3.1 Magnetism 1023
17.3.2 The Molecular Approach to Organic Magnetic
Materials 1024
17.3.3 The Polymer Approach to Organic Magnetic
Materials—Very High-Spin Organic Molecules 1027
17.4 Superconductivity 1030
17.4.1 Organic Metals/Synthetic Metals 1032
17.5 Non-Linear Optics (NLO) 1033
17.6 Photoresists 1036
17.6.1 Photolithography 1036
17.6.2 Negative Photoresists 1037
17.6.3 Positive Photoresists 1038
Summary and Outlook 1041
EXERCISES 1042
FURTHER READING 1044
appendix 1: Conversion Factors and Other
Useful Data 1047
appendix 2: Electrostatic Potential Surfaces for
Representative Organic Molecules 1049
appendix 3: Group Orbitals of Common Functional
Groups: Representative Examples Using
Simple Molecules 1051
appendix4: The Organic Structures of Biology 1057
appendix 5: Pushing Electrons 1061
A5.1 The Rudiments of Pushing Electrons 1061
A5.2 Electron Sources and Sinks for
Two-Electron Flow 1062
A5.3 How to Denote Resonance 1064
A5.4 Common Electron-Pushing Errors 1065
Backwards Arrow Pushing 1065
Not Enough Arrows 1065
Losing Track of the Octet Rule 1066
Losing Track of Hydrogens and Lone Pairs 1066
Not Using the Proper Source 1067
Mixed Media Mistakes 1067
Too Many Arrows—Shortcuts 1067
A5.5 Complex Reactions—Drawing a Chemically
Reasonable Mechanism 1068
A5.6 Two Case Studies of Predicting
Reaction Mechanisms 1069
A5.7 Pushing Electrons for Radical Reactions 1071
Practice Problems for Pushing Electrons 1073
appendix 6: Reaction Mechanism Nomenclature 1075
Index 1079
Highlights
CHAPTER 1
How Realistic are Formal Charges? 7
NMR Coupling Constants 10
Scaling Electrostatic Surface Potentials 15
1-Fluorobutane 16
Particle in a Box 21
Resonance in the Peptide Amide Bond? 23
A Brief Look at Symmetry and Symmetry Operations 29
CH5+—Not Really a Well-Defined Structure 55
Pyramidal Inversion: NH3 vs. PH3 57
Stable Carbenes 59
CHAPTER2
Entropy Changes During Cyclization Reactions 71
A Consequence of High Bond Strength:
The Hydroxyl Radical in Biology 73
The Half-Life for Homolysis of Ethane
at Room Temperature 73
The Probability of Finding Atoms at Particular
Separations 75
How do We Know That n = 0 is Most Relevant
for Bond Stretches at T = 298 K? 76
Potential Surfaces for Bond Bending Motions 78
How Big is 3 kcal / mol? 93
Shouldn t Torsional Motions be Quantized? 94
The Geometry of Radicals 96
Differing Magnitudes of Energy Values in
Thermodynamics and Kinetics 100
Sugar Pucker in Nucleic Acids 102
Alternative Measurements of Steric Size 104
The Use of A Values in a Conformational Analysis
Study for the Determination of Intramolecular
Hydrogen Bond Strength 105
The NMR Time Scale 106
Ring Fusion—Steroids 108
A Conformational Effect on the Material Properties
ofPoly(3-Alkylthiophenes) 116
Cyclopropenyl Cation 117
Cyclopropenyl Anion 118
Porphyrins 119
Protein Disulfide Linkages 123
From Strained Molecules to Molecular Rods 126
Cubane Explosives? 126
Molecular Gears 128
CHAPTER 3
The Use of Solvent Scales to Direct Diels-Alder
Reactions 149
The Use of Wetting and the Capillary Action
Force to Drive the Self-Assembly of
Macroscopic Objects 151
The Solvent Packing Coefficient and
the 55% Solution 152
Solvation Can Affect Equilibria 155
A van t Hoff Analysis of the Formation of a
Stable Carbene 163
The Strength of a Buried Salt Bridge 165
The Angular Dependence of Dipole-Dipole Interactions—
The Magic Angle 168
An Unusual Hydrogen Bond Acceptor 169
Evidence for Weak Directionality Considerations 170
Intramolecular Hydrogen Bonds are Best
for Nine-Membered Rings 170
Solvent Scales and Hydrogen Bonds 172
The Extent of Resonance can be Correlated with
Hydrogen Bond Length 174
Cooperative Hydrogen Bonding in Saccharides 175
How Much is a Hydrogen Bond in an a-Helix Worth? 176
Proton Sponges 179
The Relevance of Low-Barrier Hydrogen Bonds
to Enzymatic Catalysis 179
ß-PeptideFoldamers 180
A Cation-TT Interaction at the Nicotine Receptor 183
The Polar Nature of Benzene Affects Acidities
in a Predictable Manner 184
Use of the Arene-Perfluorarene Interaction in the
Design of Solid State Structures 185
Donor-Acceptor Driven Folding 187
The Hydrophobie Effect and Protein Folding 194
More Foldamers: Folding Driven by
Solvophobic Effects 195
Calculating Drug Binding Energies by SPT 201
CHAPTER4
The Units of Binding Constants 209
Cooperativity in Drug Receptor Interactions 215
The Hill Equation and Cooperativity in
Protein-Ligand Interactions 219
The Benesi-Hildebrand Plot 221
How are Heat Changes Related to Enthalpy? 223
Using the Helical Structure of Peptides and the
Complexation Power of Crowns to Create
an Artificial Transmembrane Channel 226
Preorganization and the Salt Bridge 229
A Clear Case of Entropy Driven Electrostatic
Complexation 229
Salt Bridges Evaluated by Non-Biological Systems 230
Does Hydrogen Bonding Really Play a Role in
DNA Strand Recognition? 233
Calixarenes—Important Building Blocks for Molecular
Recognition and Supramolecular Chemistry 238
Aromatics at Biological Binding Sites 239
Combining the Cation-TT Effect and Crown Ethers 240
A Thermodynamic Cycle to Determine the Strength
of a Polar-ir Interaction 242
Molecular Mechanics/Modeling and Molecular
Recognition 243
Biotin/Avidin: A Molecular Recognition/
Self-Assembly Tool from Nature 249
Taming Cyclobutadiene—A Remarkable Use of
Supramolecular Chemistry 251
HIGHLIGHTS
CHAPTERS
Using a pH Indicator to Sense Species Other
Than the Hydronium Ion 264
Realistic Titrations in Water 265
An Extremely Acidic Medium is Formed During
Photo-Initiated Cationic Polymerization in
Photolithography 269
Super Acids Used to Activate Hydrocarbons 270
The Intrinsic Acidity Increase of a Carbon Acid
by Coordination of BF3 276
Direct Observation of Cytosine Protonation During
Triple Helix Formation 287
A Shift of the Acidity of an N-H Bond in Water Due to
the Proximity of an Ammonium or Metal Cation 288
The Notion of Superelectrophiles Produced by
Super Acids 289
CHAPTER 6
Stereoisomerism and Connectivity 300
Total Synthesis of an Antibiotic with a Staggering
Number of Stereocenters 303
The Descriptors for the Amino Acids Can Lead
to Confusion 307
Chiral Shift Reagents 308
C2 Ligands in Asymmetric Synthesis 313
Enzymatic Reactions, Molecular Imprints, and
Enantiotopic Discrimination 320
Biological Knots—DNA and Proteins 325
Polypropylene Structure and the Mass of the Universe 331
Controlling Polymer Tacticity—The Metallocenes 332
CD Used to Distinguish a-Helices from ß-Sheets 335
Creating Chiral Phosphates for Use as Mechanistic
Probes 335
A Molecular Helix Created from Highly Twisted
Building Blocks 338
CHAPTER 7
Single-Molecule Kinetics 360
Using the Arrhenius Equation to Determine Differences
in Activation Parameters for Two Competing
Pathways 370
Curvature in an Eyring Plot is Used as Evidence for an
Enzyme Conformational Change in the Catalysis
of the Cleavage of the Co-C Bond of Vitamin B12 371
Where TST May be Insufficient 374
The Transition States for SN1 Reactions 377
Comparing Reactivity to Selectivity in Free Radical
Halogenation 378
Using the Curtin-Hammett Principle to Predict the
Stereochemistry of an Addition Reaction 379
Applying the Principle of Microscopic Reversibility
to Phosphate Ester Chemistry 380
Kinetic vs. Thermodynamic Enolates 382
Molecularity vs. Mechanism. Cyclization Reactions and
Effective Molarity 384
First Order Kinetics: Delineating Between a Unimolecular
and a Bimolecular Reaction of Cyclopentyne and
Dienes 386
The Observation of Second Order Kinetics to Support
a Multistep Displacement Mechanism for a
Vitamin Analog 387
Pseudo-First Order Kinetics: Revisiting the
Cyclopentyne Example 388
Zero Order Kinetics 393
An Organometallic Example of Using the SS A
to Delineate Mechanisms 395
Saturation Kinetics That We Take for Granted—
SN1 Reactions 397
Prior Equilibrium in an SN1 Reaction 398
Femtochemistry: Direct Characterization of
Transition States, Part I 400
Seeing Transition States, Part II: The Role of
Computation 401
The Use of Pulse Radiolysis to Measure the pKas
of Protonated Ketyl Anions 402
Discovery of the Marcus Inverted Region 406
Using a More O Ferrall-Jencks Plot in Catalysis 410
CHAPTER 8
The Use of Primary Kinetic Isotope Effects to Probe
the Mechanism of Aliphatic Hydroxylation by
Iron(III) Porphyrins 425
An Example of Changes in the Isotope Effect with Varying
Reaction Free Energies 428
The Use of an Inverse Isotope Effect to Delineate an
Enzyme Mechanism 431
An Ingenious Method for Measuring Very Small
Isotope Effects 432
An Example of Tunneling in a Common Synthetic
Organic Reaction 436
Using Fractionation Factors to Characterize Very Strong
Hydrogen Bonds 439
The Use of a Proton Inventory to Explore the Mechanism
of Ribonuclease Catalysis 440
A Substituent Effect Study to Decipher the Reason
for the High Stability of Collagen 444
Using a Hammett Plot to Explore the Behavior of a
Catalytic Antibody 450
An Example of a Change in Mechanism in a Solvolysis
Reaction Studied Using a+ 452
A Swain-Lupton Correlation for Tungsten-Bipyridine-
Catalyzed Ally lie Alkylation 453
Using Taft Parameters to Understand the Structures
of Cobaloximes; Vitamin B12 Mimics 455
The Use of the Schleyer Method to Determine the Extent of
Nucleophilic Assistance in the Solvolysis of Arylvinyl
Tosylates 459
The Use of Swain-Scott Parameters to Determine
the Mechanism of Some Acetal Substitution
Reactions 462
ATP Hydrolysis—How ßtG and /?muc Values Have Given
Insight into Transition State Structures 465
How Can Some Groups be Both Good Nucleophiles and
Good Leaving Groups? 466
An Example of an Unexpected Product 472
Designing a Method to Divert the Intermediate 473
Trapping a Phosphorane Legitimizes Its Existence 474
Checking for a Common Intermediate in Rhodium-
Catalyzed Allylic Alkylations 475
Pyranoside Hydrolysis by Lysozyme 476
Using Isotopic Scrambling to Distinguish Exocyclic vs.
Endocyclic Cleavage Pathways for a Pyranoside 478
HIGHLIGHTS
Determination of 1,4-Biradical Lifetimes Using
a Radical Clock 480
The Identification of Intermediates from a Catalytic Cycle
Needs to be Interpreted with Care 481
CHAPTER 9
The Application of Figure 9.4 to Enzymes 494
High Proximity Leads to the Isolation of a Tetrahedral
Intermediate 498
The Notion of Near Attack Conformations 499
Toward an Artificial Acetylcholinesterase 501
Metal and Hydrogen Bonding Promoted Hydrolysis
of2 ,3 -cAMP 502
Nucleophilic Catalysis of Electrophilic Reactions 503
Organocatalysis 505
Lysozyme 506
A Model for General-Acid-General-Base Catalysis 514
Anomalous Bransted Values 519
Artificial Enzymes: Cyclodextrins Lead the Way 530
CHAPTER 10
Cyclic Forms of Saccharides and Concerted Proton
Transfers 545
Squalene to Lanosterol 550
Mechanisms of Asymmetric Epoxidation Reactions 558
Nature s Hydride Reducing Agent 566
The Captodative Effect 573
Stereoelectronics in an Acyl Transfer Model 579
The Swern Oxidation 580
Gas Phase Eliminations 588
Using the Curtin-Hammett Principle 593
Aconitase—An Enzyme that Catalyzes Dehydration
and Rehydration 595
Enzymatic Acyl Transfers I: The Catalytic Triad 604
Enzymatic Acyl Transfers II: Zn(II) Catalysis 605
Enzyme Mimics for Acyl Transfers 606
Peptide Synthesis—Optimizing Acyl Transfer 606
CHAPTER 11
Enolate Aggregation 631
Control of Stereochemistry in Enolate Reactions 636
Gas Phase SN2 Reactions—A Stark Difference in Mechanism
from Solution 641
A Potential Kinetic Quandary 642
Contact Ion Pairs vs. Solvent-Separated Ion Pairs 647
An Enzymatic SN2 Reaction: Haloalkane
Dehydrogenase 649
The Meaning of ß^c Values 651
Carbocation Rearrangements in Rings 658
Anchimeric Assistance in War 660
Further Examples of Hypervalent Carbon 666
Brominations Using N-Bromosuccinimide 673
An Enzymatic Analog to the Benzilic Acid Rearrangement:
Acetohydroxy-Acid Isomeroreductase 677
Femtochemistry and Singlet Biradicals 693
CHAPTER 12
Bonding Models 709
Electrophilic Aliphatic Substitutions (SE2 and SE1) 715
C-H Activation, Part I 722
C-H Activation, Part II 723
The Sandmeyer Reaction 726
Olefin Slippage During Nucleophilic Addition to
Alkenes 737
Pd(0) Coupling Reactions in Organic Synthesis 742
Stereocontrol at Every Step in Asymmetric Allylic
Alkylations 745
Cyclic Rings Possessing Over 100,000 Carbons! 747
CHAPTER 13
Monodisperse Materials Prepared Biosynthetically 756
An Analysis of Dispersity and Molecular Weight 757
A Melting Analysis 759
Protein Folding Modeled by a Two-State Polymer
Phase Transition 762
Dendrimers, Fractals, Neurons, and Trees 769
Lyotropic Liquid Crystals: From Soap Scum to
Biological Membranes 774
Organic Surfaces: Self-Assembling Monolayers and
Langmuir-Blodgett Films 778
Free-Radical Living Polymerizations 787
Lycra /Spandex 790
Radical Copolymerization—Not as Random
as You Might Think 792
PMMA—One Polymer with a Remarkable Range
of Uses 793
Living Polymers for Better Running Shoes 795
Using 13C NMR Spectroscopy to Evaluate Polymer
Stereochemistry 797
CHAPTER 14
The Hydrogen Atom 811
Methane—Molecular Orbitals or Discrete Single
Bonds with sf Hybrids? 827
Koopmans Theorem—A Connection Between Ab Initio
Calculations and Experiment 828
A Matrix Approach to Setting Up the LCAO Method 832
Through-Bond Coupling and Spin Preferences 861
Cyclobutadiene at the Two-Electron Level of Theory 862
CHAPTER 15
Symmetry Does Matter 887
Allowed Organometallic [2+2] Cycloadditions 895
Semi-Empirical vs. Ab Initio Treatments of Pericyclic
Transition States 900
Electrocyclization in Cancer Therapeutics 910
Fluxional Molecules 913
A Remarkable Substituent Effect: The Oxy-Cope
Rearrangement 921
A Biological Claisen Rearrangement—The Chorismate
Mutase Reaction 922
Hydrophobie Effects in Pericyclic Reactions 923
Pericyclic Reactions of Radical Cations 925
CHAPTER 16
Excited State Wavefunctions 937
Physical Properties of Excited States 944
The Sensitivity of Fluorescence—Good News and
Bad News 946
GFP, Part I: Nature s Fluorophore 947
HIGHLIGHTS
Isosbestic Points—Hallmarks of One-to-One Stoichiometric
Conversions 949
The Free Rotor or Loose Bolt Effect on
Quantum Yields 953
Single-Molecule FRET 961
Trans-Cyclohexene? 967
Retinal and Rhodopsin—The Photochemistry
of Vision 968
Photochromism 969
UV Damage of DNA—A [2+2] Photoreaction 971
Using Photochemistry to Generate Reactive Intermediates:
Strategies Fast and Slow 983
Photoaffinity Labeling—A Powerful Tool for
Chemical Biology 984
Light Sticks 987
GFP,PartII:Aequorin 989
Photodynamic Therapy 991
CHAPTER 17
Solitons in Polyacetylene 1015
Scanning Probe Microscopy 1040
Soft Lithography 1041
|
| adam_txt |
Abbreviated Contents
part I: Molecular Structure and Thermodynamics
chapter 1. Introduction to Structure and Models of Bonding 3
2. Strain and Stability 65
3. Solutions and Non-Covalent Binding Forces 145
4. Molecular Recognition and Supramolecular Chemistry 207
5. Acid-Base Chemistry 259
6. Stereochemistry 297
part II: Reactivity, Kinetics, and Mechanisms
chapter 7. Energy Surfaces and Kinetic Analyses 355
8. Experiments Related to Thermodynamics and Kinetics 421
9. Catalysis 489
10. Organic Reaction Mechanisms, Part 1:
Reactions Involving Additions and / or Eliminations 537
11. Organic Reaction Mechanisms, Part 2:
Substitutions at Aliphatic Centers and Thermal
Isomerizations / Rearrangements 627
12. Organotransition Metal Reaction Mechanisms and Catalysis 705
13. Organic Polymer and Materials Chemistry 753
part III: Electronic Structure: Theory and Applications
chapter 14. Advanced Concepts in Electronic Structure Theory 807
15. Thermal Pericyclic Reactions 877
16. Photochemistry 935
17. Electronic Organic Materials 1001
appendix 1. Conversion Factors and Other Useful Data 1047
2. Electrostatic Potential Surfaces for Representative Organic Molecules 1049
3. Group Orbitals of Common Functional Groups:
Representative Examples Using Simple Molecules 1051
4. The Organic Structures of Biology 1057
5. Pushing Electrons 1061
6. Reaction Mechanism Nomenclature 1075
index 1079
Contents
List of Highlights xix
Preface xxiii
Acknowledgments xxv
A Note to the Instructor xxvii
PART I
MOLECULAR STRUCTURE AND
THERMODYNAMICS
chapter 1: Introduction to Structure and
Models of Bonding 3
Intent and Purpose 3
1.1 A Review of Basic Bonding Concepts 4
1.1.1 Quantum Numbers and Atomic Orbitals 4
1.1.2 Electron Configurations and Electronic Diagrams
1.1.3 Lewis Structures 6
1.1.4 Formal Charge 6
1.1.5 VSEPR 7
1.1.6 Hybridization 8
1.1.7 A Hybrid Valence Bond / Molecular Orbital
Model of Bonding 10
Creating Localized a and n Bonds 11
1.1.8 Polar Covalent Bonding 12
Electronegativity 12
Electrostatic Potential Surfaces 14
Inductive Effects 15
Group Electronegativities 16
Hybridization Effects 17
1.1.9 Bond Dipoles, Molecular Dipoles,
and Quadrupoles 17
Bond Dipoles 17
Molecular Dipole Moments 18
Molecular Quadrupole Moments 19
1.1.10 Resonance 20
1.1.11 Bond Lengths 22
1.1.12 Polarizability 24
1.1.13 Summary of Concepts Used for the Simplest
Model of Bonding in Organic Structures 26
1.2 A More Modern Theory of Organic Bonding 26
1.2.1 Molecular Orbital Theory 27
1.2.2 A Method for QMOT 28
1.2.3 Methyl in Detail 29
Planar Methyl 29
The Walsh Diagram: Pyramidal Methyl 31
"Group Orbitals"for Pyramidal Methyl 32
Putting the Electrons In—The MH3 System 33
1.2.4 The CH2 Group in Detail 33
The Walsh Diagram and Group Orbitals 33
Putting the Electrons In — The MH2 System 33
1.3 Orbital Mixing—Building Larger Molecules 35
1.3.1 Using Group Orbitals to Make Ethane 36
1.3.2 Using Group Orbitals to Make Ethylene 38
1.3.3 The Effects of Heteroatoms—Formaldehyde 40
1.3.4 Making More Complex Alkanes 43
1.3.5 Three More Examples of Building Larger
Molecules from Group Orbitals 43
Propene 43
Methyl Chloride 45
Butadiene 46
1.3.6 Group Orbitals of Representative it Systems:
Benzene, Benzyl, and Allyl 46
1.3.7 Understanding Common Functional
Groups as Perturbations of Allyl 49
1.3.8 The Three Center-Two Electron Bond 50
1.3.9 Summary of the Concepts Involved in
Our Second Model of Bonding 51
1.4 Bonding and Structures of Reactive Intermediates 52
1.4.1 Carbocations 52
Carbenium Ions 53
Interplay with Carbonium Ions 54
Carbonium Ions 55
1.4.2 Carbanions 56
1.4.3 Radicals 57
1.4.4 Carbenes 58
1.5 A Very Quick Look at Organometallic
and Inorganic Bonding 59
Summary and Outlook 61
EXERCISES 62
FURTHER READING 64
CHAPTER 2: Strain and Stability 65
Intent and Purpose 65
2.1 Thermochemistry of Stable Molecules
2.1.1 The Concepts of Internal Strain
and Relative Stability 66
2.1.2 Types of Energy 68
Gibbs Free Energy 68
Enthalpy 69
Entropy 70
2.1.3 Bond Dissociation Energies 70
Using BDEs to Predict Exothermicity
and Endothermkity 72
2.1.4 An Introduction to Potential Functions
and Surfaces—Bond Stretches 73
Infrared Spectroscopy 77
2.1.5 Heats of Formation and Combustion
2.1.6 The Group Increment Method 79
2.1.7 Strain Energy 82
66
77
CONTENTS
2.2 Thermochemistry of Reactive Intermediates 82
2.2.1 Stability vs. Persistence 82
2.2.2 Radicals 83
BDEs as a Measure ofStability 83
Radical Persistence 84
Group Incremen tsfor Radicals 86
2.2.3 Carbocations 87
Hydride Ion Affinities as a Measure of Stability 87
Lifetimes of Carbocations 90
2.2.4 Carbanions 91
2.2.5 Summary 91
2.3 Relationships Between Structure and Energetics—
Basic Conformational Analysis 92
2.3.1 Acyclic Systems—Torsional Potential Surfaces 92
Ethane 92
Butane—The Gauche Interaction 95
Barrier Height 97
Barrier Foldedness 97
Tetraalkylethanes 98
The g+g-Pentane Interaction 99
Allylic (A™) Strain 100
2.3.2 Basic Cyclic Systems 100
Cyclopropane 100
Cyclobutane 100
Cyclopentane 101
Cyclohexane 102
Larger Rings—Transannular Effects 107
Group Increment Corrections for Ring Systems 109
Ring Torsional Modes 109
Bicyclic Ring Systems 110
Cycloalkenes and Bredt's Rule 110
Summary of Conformational Analysis and
Its Connection to Strain 112
2.4 Electronic Effects 112
2.4.1 Interactions Involving it Systems 112
Substitution on Alkenes 112
Conformations of Substituted Alkenes 113
Conjugation 115
Aromaticity 116
Antiaromaticity, An Unusual Destabilizing Effect 117
NMR Chemical Shifts 118
Polycyclic Aromatic Hydrocarbons 119
Large Annulenes 119
2.4.2 Effects of Multiple Heteroatoms 120
Bond Length Effects 120
Orbital Effects 120
2.5 Highly-Strained Molecules 124
2.5.1 Long Bonds and Large Angles 124
2.5.2 Small Rings 125
2.5.3 Very Large Rotation Barriers 127
2.6 Molecular Mechanics 128
2.6.1 The Molecular Mechanics Model 129
Bond Stretching 129
Angle Bending 130
Torsion 130
Nonbonded Interactions 130
Cross Terms 131
Electrostatic Interactions 131
Hydrogen Bonding 131
The Parameterization 132
Heat of Formation and Strain Energy 132
2.6.2 General Comments on the Molecular
Mechanics Method 133
2.6.3 Molecular Mechanics on Biomolecules and
Unnatural Polymers—"Modeling" 135
2.6.4 Molecular Mechanics Studies of Reactions 136
Summary and Outlook 137
EXERCISES 138
FURTHER READING 143
CHAPTER 3: Solutions and Non-Covalent
Binding Forces 145
Intent and Purpose 145
3.1 Solvent and Solution Properties 145
3.1.1 Nature Abhors a Vacuum 146
3.1.2 Solvent Scales 146
Dielectric Constant 147
Other Solvent Scales 148
Heat of Vaporization 150
Surface Tension and Wetting 150
Water 151
3.1.3 Solubility 153
General Overview 153
Shape 154
Using the "Like-Dissolves-Like" Paradigm 154
3.1.4 Solute Mobility 155
Diffusion 155
Fick's Law of Diffusion 156
Correlation Times 156
3.1.5 The Thermodynamics of Solutions 157
Chemical Potential 158
The Thermodynamics of Reactions 160
Calculating AH0 and AS° 162
3.2 Binding Forces 162
3.2.1 Ion Pairing Interactions 163
Salt Bridges 164
3.2.2 Electrostatic Interactions Involving Dipoles 165
Ion-Dipole Interactions 165
A Simple Model of Ionic Solvation —
The Born Equation 166
Dipole-Dipole Interactions 168
3.2.3 Hydrogen Bonding 168
Geometries 169
Strengths of Normal Hydrogen Bonds 171
i. Solvation Effects 171
ii. Electronegativity Effects 172
Hi. Resonance Assisted Hydrogen Bonds 173
iv. Polarization Enhanced Hydrogen Bonds 174
v. Secondary Interactions in Hydrogen
Bonding Systems 175
CONTENTS
vi. Cooperativity in Hydrogen Bonds 175
Vibrational Properties of Hydrogen Bonds 176
Short-Strong Hydrogen Bonds 177
3.2.4 tt Effects 180
Cation-K Interactions 181
Polar-K Interactions 183
Aromatic-Aromatic Interactions (n Stacking) 184
The Arene-Perfluoroarene Interaction 184
k Donor-Acceptor Interactions 186
3.2.5 Induced-Dipole Interactions 186
Ion-Induced-Dipole Interactions 187
Dipole-Induced-Dipole Interactions 187
Induced-Dipole-Induced-Dipole Interactions 188
Summarizing Monopole, Dipole, and
Induced-Dipole Binding Forces 188
3.2.6 The Hydrophobie Effect 189
Aggregation ofOrganics 189
The Origin of the Hydrophobie Effect 192
3.3 Computational Modeling of Solvation
3.3.1 Continuum Solvation Models 196
3.3.2 Explicit Solvation Models 197
3.3.3 Monte Carlo (MC) Methods 198
3.3.4 Molecular Dynamics (MD) 199
3.3.5 Statistical Perturbation Theory/
Free Energy Perturbation 200
Summary and Outlook 201
EXERCISES 202
FURTHER READING 204
194
CHAPTER 4: Molecular Recognition and
Supramolecular Chemistry 207
Intent and Purpose 207
4.1 Thermodynamic Analyses of Binding
Phenomena 207
4.1.1 General Thermodynamics of Binding 208
The Relevance of the Standard State 210
The Influence of a Change in Heat Capacity 212
Cooperativity 213
Enthalpy-Entropy Compensation 216
4.1.2 The Binding Isotherm 216
4.1.3 Experimental Methods 219
UV/Vis or Fluorescence Methods 220
NMR Methods 220
Isothermal Calorimetry 12\
4.2 Molecular Recognition 222
4.2.1 Complementarity and Preorganization 224
Crowns, Cryptands, and Spherands—Molecular
Recognition with a Large Ion-Dipole Component 224
Tweezers and Clefts 228
4.2.2 Molecular Recognition with a Large
Ion Pairing Component 228
4.2.3 Molecular Recognition with a Large Hydrogen
Bonding Component 230
Representative Structures 230
Molecular Recognition via Hydrogen
Bonding in Water 232
4.2.4 Molecular Recognition with a Large
Hydrophobie Component 234
Cyclodextrins 234
Cyclophanes 234
A Summary of the Hydrophobie Component
of Molecular Recognition in Water 238
4.2.5 Molecular Recognition with a Large tt
Component 239
Cation-K In teractions 239
Polar-n and Related Effects 241
4.2.6 Summary 241
4.3 Supramolecular Chemistry 243
4.3.1 Supramolecular Assembly of Complex
Architectures 244
Self-Assembly via Coordination Compounds 244
Self-Assembly via Hydrogen Bonding 245
4.3.2 Novel Supramolecular Architectures—Catenanes,
Rotaxanes, and Knots 246
Nanotechnology 248
4.3.3 Container Compounds—Molecules within
Molecules 249
Summary and Outlook 252
exercises 253
further reading 256
CHAPTER 5: Acid-Base Chemistry 259
Intent and Purpose 259
5.1 Brensted Acid-Base Chemistry 259
5.2 Aqueous Solutions 261
5.2.1 pKa 261
5.2.2 pH 262
5.2.3 The Leveling Effect 264
5.2.4 Activity vs. Concentration 266
5.2.5 Acidity Functions: Acidity Scales for Highly
Concentrated Acidic Solutions 266
5.2.6 Super Acids 270
5.3 Nonaqueous Systems 271
5.3.1 pKa Shifts at Enzyme Active Sites 273
5.3.2 Solution Phase vs. Gas Phase 273
5.4 Predicting Acid Strength in Solution 276
5.4.1 Methods Used to Measure Weak Acid Strength 276
5.4.2 Two Guiding Principles for Predicting
Relative Acidities 277
5.4.3 Electronegativity and Induction 278
5.4.4 Resonance 278
5.4.5 Bond Strengths 283
5.4.6 Electrostatic Effects 283
5.4.7 Hybridization 283
CONTENTS
5.4.8 Aromaticity 284
5.4.9 Solvation 284
5.4.10 Cationic Organic Structures
285
5.5 Acids and Bases of Biological Interest 285
5.6 Lewis Acids/Bases and Electrophiles/
Nucleophiles 288
5.6.1 The Concept of Hard and Soft Acids and Bases, General
Lessons for Lewis Acid-Base Interactions, and Relative
Nucleophilicity and Electrophilicity 289
Summary and Outlook 292
EXERCISES 292
FURTHER READING 294
CHAPTER 6: Stereochemistry 297
Intent and Purpose 297
6.1 Stereogenicity and Stereoisomerism 297
6.1.1 Basic Concepts and Terminology 298
Classic Terminology 299
More Modern Terminology 301
6.1.2 Stereochemical Descriptors 303
R,S System 304
E,Z System 304
DandL 304
Erythro and Threo 305
Helical Descriptors— Mand P 305
EntandEpi 306
Using Descriptors to Compare Structures 306
6.1.3 Distinguishing Enantiomers 306
Optical Activity and Chirality 309
Why is Plane Polarized Light Rotated
byaChiralMedium? 309
Circular Dichroism 310
X-Ray Crystallography 310
6.2 Symmetry and Stereochemistry 311
6.2.1 Basic Symmetry Operations 311
6.2.2 Chirality and Symmetry 311
6.2.3 Symmetry Arguments 313
6.2.4 Focusing on Carbon 314
6.3 Topicity Relationships 315
6.3.1 Homotopic, Enantiotopic, and Diastereotopic
6.3.2 Topicity Descriptors—Pro-K/Pro-S and Re I Si
6.3.3 Chirotopicity 317
315
316
6.4 Reaction Stereochemistry: Stereoselectivity
and Stereospecificity 317
6.4.1 Simple Guidelines for Reaction Stereochemistry 317
6.4.2 Stereospecific and Stereoselective Reactions 319
6.5 Symmetry and Time Scale 322
6.6 Topological and Supramolecular Stereochemistry
6.6.1 Loops and Knots 325
6.6.2 Topological Chirality 326
324
6.6.3 Nonplanar Graphs 326
6.6.4 Achievements in Topological and Supramolecular
Stereochemistry 327
6.7 Stereochemical Issues in Polymer Chemistry 331
6.8 Stereochemical Issues in Chemical Biology
6.8.1 The Linkages of Proteins, Nucleic Acids,
and Polysaccharides 333
Proteins 333
Nucleic Acids 334
Polysaccharides 334
6.8.2 Helicity 336
Synthetic Helical Polymers 337
6.8.3 The Origin of Chirality in Nature 339
6.9 Stereochemical Terminology 340
Summary and Outlook 344
EXERCISES 344
FURTHER READING 350
333
PART II
REACTIVITY, KINETICS, AND
MECHANISMS
356
CHAPTER 7: Energy Surfaces and
Kinetic Analyses 355
Intent and Purpose 355
7.1 Energy Surfaces and Related Concepts
7.1.1 Energy Surfaces 357
7.1.2 Reaction Coordinate Diagrams 359
7.1.3 What is the Nature of the Activated
Complex / Transition State? 362
7.1.4 Rates and Rate Constants 363
7.1.5 Reaction Order and Rate Laws 364
7.2 Transition State Theory (TST) and Related Topics 365
7.2.1 The Mathematics of Transition State Theory 365
7.2.2 Relationship to the Arrhenius Rate Law 367
7.2.3 Boltzmann Distributions and Temperature
Dependence 368
7.2.4 Revisiting "What is the Nature of the Activated
Complex?" and Why Does TST Work? 369
7.2.5 Experimental Determinations of Activation Parameters
and Arrhenius Parameters 370
7.2.6 Examples of Activation Parameters and
Their Interpretations 372
7.2.7 Is TST Completely Correct? The Dynamic Behavior
of Organic Reactive Intermediates 372
7.3 Postulates and Principles Related
to Kinetic Analysis 374
7.3.1 The Hammond Postulate 374
7.3.2 The Reactivity vs. Selectivity Principle 377
CONTENTS
7.3.3 The Curtin-Hammett Principle 378
7.3.4 Microscopic Reversibility 379
7.3.5 Kinetic vs. Thermodynamic Control 380
7.4 Kinetic Experiments 382
7.4.1 How Kinetic Experiments are Performed 382
7.4.2 Kinetic Analyses for Simple Mechanisms 384
First Order Kinetics 385
Second Order Kinetics 386
Pseudo-First Order Kinetics 387
Equilibrium Kinetics 388
Initial-Rate Kinetics 389
Tabulating a Series of Common Kinetic Scenarios 389
7.5 Complex Reactions—Deciphering Mechanisms 390
7.5.1 Steady State Kinetics 390
7.5.2 Using the SSA to Predict Changes
in Kinetic Order 395
7.5.3 Saturation Kinetics 396
7.5.4 Prior Rapid Equilibria 397
7.6 Methods for Following Kinetics 397
7.6.1 Reactions with Half-Lives Greater
than a Few Seconds 398
7.6.2 Fast Kinetics Techniques 398
Flow Techniques 399
Flash Photolysis 399
Pulse Radiolysis 401
7.6.3 Relaxation Methods 401
7.6.4 Summary of Kinetic Analyses 402
7.7 Calculating Rate Constants 403
7.7.1 Marcus Theory 403
7.7.2 Marcus Theory Applied to Electron Transfer 405
7.8 Considering Multiple Reaction Coordinates 407
7.8.1 Variation in Transition State Structures Across
a Series of Related Reactions—An Example
Using Substitution Reactions 407
7.8.2 More O'Ferrall-Jencks Plots 409
7.8.3 Changes in Vibrational State Along the Reaction
Coordinate—Relating the Third Coordinate
to Entropy 412
Summary and Outlook 413
EXERCISES 413
FURTHER READING 417
CHAPTER 8: Experiments Related to
Thermodynamics and Kinetics
Intent and Purpose 421
8.1 Isotope Effects 421
8.1.1 The Experiment 422
8.1.2 The Origin of Primary Kinetic Isotope Effects
Reaction Coordinate Diagrams and Isotope
Effects 424
421
422
Primary Kinetic Isotope Effects for Linear
Transition States as a Function ofExothermicity
and Endothermicity 425
Isotope Effects for Linear vs. Non-Linear
Transition States 428
8.1.3 The Origin of Secondary Kinetic Isotope Effects 428
Hybridization Changes 429
Steric Isotope Effects 430
8.1.4 Equilibrium Isotope Effects 432
Isotopic Perturbation of Equilibrium —
Applications to Carbocations 432
8.1.5 Tunneling 435
8.1.6 Solvent Isotope Effects 437
Fractionation Factors 437
Proton Inventories 438
8.1.7 Heavy Atom Isotope Effects 441
8.1.8 Summary 441
8.2 Substituent Effects 441
8.2.1 The Origin of Substituent Effects 443
Field Effects 443
Inductive Effects 443
Resonance Effects 444
Polarizability Effects 444
Steric Effects 445
Solvation Effects 445
8.3 Hammett Plots—The Most Common LFER.
A General Method for Examining Changes
in Charges During a Reaction 445
8.3.1 Sigma (ff) 445
8.3.2 Rho(p) 447
8.3.3 The Power of Hammett Plots for
Deciphering Mechanisms 448
8.3.4 Deviations from Linearity 449
8.3.5 Separating Resonance from Induction 451
8.4 Other Linear Free Energy Relationships 454
8.4.1 Steric and Polar Effects—Taft Parameters 454
8.4.2 Solvent Effects—Grunwald-Winstein Plots 455
8.4.3 Schleyer Adaptation 457
8.4.4 Nucleophilicity and Nucleofugality 458
Basicity/Acidity 459
Solvation 460
Polarizability, Basicity, and Solvation Interplay 460
Shape 461
8.4.5 Swain-Scott Parameters—Nucleophilicity
Parameters 461
8.4.6 Edwards and Ritchie Correlations 463
8.5 Acid-Base Related Effects—
Bronsted Relationships 464
8.5.1 /3Nuc 464
8.5.2 ßLG 464
8.5.3 Acid-Base Catalysis 466
8.6 Why do Linear Free Energy Relationships Work? 466
8.6.1 General Mathematics of LFERs 467
8.6.2 Conditions to Create an LFER 468
8.6.3 The Isokinetic or Isoequilibrium Temperature 469
CONTENTS
8.6.4 Why does Enthalpy-Entropy
Compensation Occur? 469
Steric Effects 470
Solvation 470
8.7 Summary of Linear Free Energy Relationships 470
8.8 Miscellaneous Experiments for
Studying Mechanisms 471
8.8.1 Product Identification 472
8.8.2 Changing the Reactant Structure to Divert
or Trap a Proposed Intermediate 473
8.8.3 Trapping and Competition Experiments 474
8.8.4 Checking for a Common Intermediate 475
8.8.5 Cross-Over Experiments 476
8.8.6 Stereochemical Analysis 476
8.8.7 Isotope Scrambling 477
8.8.8 Techniques to Study Radicals: Clocks and Traps 478
8.8.9 Direct Isolation and Characterization
of an Intermediate 480
8.8.10 Transient Spectroscopy 480
8.8.11 Stable Media 481
Summary and Outlook 482
exercises 482
further reading 487
CHAPTER 9: Catalysis 489
Intent and Purpose 489
9.1 General Principles of Catalysis 490
9.1.1 Binding the Transition State Better
than the Ground State 491
9.1.2 A Thermodynamic Cycle Analysis 493
9.1.3 A Spatial Temporal Approach 494
9.2 Forms of Catalysis 495
9.2.1 "Binding" is Akin to Solvation 495
9.2.2 Proximity as a Binding Phenomenon 495
9.2.3 Electrophilic Catalysis 499
Electrostatic Interactions 499
Metal Ion Catalysis 500
9.2.4 Acid-Base Catalysis 502
9.2.5 Nucleophilic Catalysis 502
9.2.6 Covalent Catalysis 504
9.2.7 Strain and Distortion 505
9.2.8 Phase Transfer Catalysis 507
9.3 Bronsted Acid-Base Catalysis 507
9.3.1 Specific Catalysis 507
The Mathematics of Specific Catalysis 507
Kinetic Plots 510
9.3.2 General Catalysis 510
The Mathematics of General Catalysis 511
Kinetic Plots 512
9.3.3 A Kinetic Equivalency 514
9.3.4 Concerted or Sequential General-Acid-
General-Base Catalysis 515
9.3.5 The Bronsted Catalysis Law
and Its Ramifications 516
A Linear Free Energy Relationship 516
The Meaning of a and ß 517
a+ß=l 518
Deviations from Linearity 519
9.3.6 Predicting General-Acid or
General-Base Catalysis 520
The Libido Rule 520
Potential Energy Surfaces Dictate
General or Specific Catalysis 521
9.3.7 The Dynamics of Proton Transfers 522
Marcus Analysis 522
524
9.4 Enzymatic Catalysis 523
9.4.1 Michaelis-Menten Kinetics 523
9.4.2 The Meaning of KM, kat, and kcajKM
9 A3 Enzyme Active Sites 525
9.4.4 [S] vs. KM—Reaction Coordinate Diagrams
9.4.5 Supramolecular Interactions 529
Summary and Outlook 530
EXERCISES 531
FURTHER READING 535
527
CHAPTER 10: Organic Reaction Mechanisms,
Part 1: Reactions Involving Additions
and/or Eliminations 537
Intent and Purpose 537
10.1 Predicting Organic Reactivity 538
10.1.1 A Useful Paradigm for Polar Reactions 539
Nucleophiles and Electrophiles 539
Lewis Acids and Lewis Bases 540
Donor-Acceptor Orbital Interactions 540
10.1.2 Predicting Radical Reactivity 541
10.1.3 In Preparation for the Following Sections 541
—ADDITION REACTIONS— 542
10.2 Hydration of Carbonyl Structures 542
10.2.1 Acid-Base Catalysis 543
10.2.2 The Thermodynamics of the Formation
of Geminal Diols and Hemiacetals 544
10.3 Electrophilic Addition of Water to Alkenes
and Alkynes: Hydration 545
10.3.1 Electron Pushing 546
10.3.2 Acid-Catalyzed Aqueous Hydration 546
10.3.3 Regiochemistry 546
10.3.4 Alkyne Hydration 547
10.4 Electrophilic Addition of Hydrogen Halides
to Alkenes and Alkynes 548
10.4.1 Electron Pushing 548
CONTENTS
10.4.2 Experimental Observations Related to
Regiochemistry and Stereochemistry 548
10.4.3 Addition to Alkynes 551
10.5 Electrophilic Addition of Halogens
toAlkenes 551
10.5.1 Electron Pushing 551
10.5.2 Stereochemistry 552
10.5.3 Other Evidence Supporting a cr Complex 552
10.5.4 Mechanistic Variants 553
10.5.5 Addition to Alkynes 554
10.6 Hydroboration 554
10.6.1 Electron Pushing 555
10.6.2 Experimental Observations 555
10.7 Epoxidation 555
10.7.1 Electron Pushing 556
10.7.2 Experimental Observations 556
10.8 Nucleophilic Additions to
Carbonyl Compounds 556
10.8.1 Electron Pushing for a Few Nucleophilic
Additions 557
10.8.2 Experimental Observations for
Cyanohydrin Formation 559
10.8.3 Experimental Observations for
Grignard Reactions 560
10.8.4 Experimental Observations in
LAH Reductions 561
10.8.5 Orbital Considerations 561
The Bürgi-Dunitz Angle 561
Orbital Mixing 562
10.8.6 Conformational Effects in Additions
to Carbonyl Compounds 562
10.8.7 Stereochemistry of Nucleophilic Additions 563
10.9 Nucleophilic Additions to Olefins 567
10.9.1 Electron Pushing 567
10.9.2 Experimental Observations 567
10.9.3 Regiochemistry of Addition 567
10.9.4 Baldwin's Rules 568
10.10 Radical Additions to Unsaturated
Systems 569
10.10.1 Electron Pushing for Radical Additions 569
10.10.2 Radical Initiators 570
10.10.3 Chain Transfer vs. Polymerization 571
10.10.4 Termination 571
10.10.5 Regiochemistry of Radical Additions 572
10.11 Carbene Additions and Insertions 572
10.11.1 Electron Pushing for Carbene Reactions 574
10.11.2 Carbene Generation 574
10.11.3 Experimental Observations for
Carbene Reactions 575
—ELIMINATIONS— 576
10.12 Eliminations to Form Carbonyls or "Carbonyl-Like"
Intermediates 577
10.12.1 Electron Pushing 577
10.12.2 Stereochemical and Isotope
Labeling Evidence 577
10.12.3 Catalysis of the Hydrolysis of Acetals 578
10.12.4 Stereoelectronic Effects 579
10.12.5 CrO3 Oxidation—The Jones Reagent 580
Electron Pushing 580
A Few Experimental Observations 581
10.13 Elimination Reactions for Aliphatic Systems—
Formation of Alkenes 581
10.13.1 Electron Pushing and Definitions 581
10.13.2 Some Experimental Observations
for E2 and El Reactions 582
10.13.3 Contrasting Elimination
and Substitution 583
10.13.4 Another Possibility—ElcB 584
10.13.5 Kinetics and Experimental Observations
for ElcB 584
10.13.6 Contrasting E2, El, and ElcB 586
10.13.7 Regiochemistry of Eliminations 588
10.13.8 Stereochemistry of Eliminations—
Orbital Considerations 590
10.13.9 Dehydration 592
Electron Pushing 592
Other Mechanistic Possibilities 594
10.13.10 Thermal Eliminations 594
10.14 Eliminations from Radical Intermediates 596
—COMBINING ADDITION AND ELIMINATION
REACTIONS (SUBSTITUTIONS AT sp2 CENTERS)—
10.15 The Addition of Nitrogen Nucleophiles
to Carbonyl Structures, Followed
by Elimination 597
10.15.1 Electron Pushing 598
10.15.2 Acid-Base Catalysis 598
10.16 The Addition of Carbon Nucleophiles,
Followed by Elimination—
The Wittig Reaction 599
10.16.1 Electron Pushing 600
10.17 Acyl Transfers 600
10.17.1 General Electron-Pushing Schemes 600
10.17.2 Isotope Scrambling 601
10.17.3 Predicting the Site of Cleavage for
Acyl Transfers from Esters 602
10.17.4 Catalysis 602
10.18 Electrophilic Aromatic Substitution 607
10.18.1 Electron Pushing for Electrophilic
Aromatic Substitutions 607
10.18.2 Kinetics and Isotope Effects 608
10.18.3 Intermediate Complexes 608
10.18.4 Regiochemistry and Relative Rates of
Aromatic Substitution 609
10.19 Nucleophilic Aromatic Substitution 611
10.19.1 Electron Pushing for Nucleophilic
Aromatic Substitution 611
10.19.2 Experimental Observations 611
596
CONTENTS
10.20 Reactions Involving Benzyne 612
10.20.1 Electron Pushing for Benzyne Reactions 612
10.20.2 Experimental Observations 613
10.20.3 Substituent Effects 613
10.21 The SrnI Reaction on Aromatic Rings 615
10.21.1 Electron Pushing 615
10.21.2 A Few Experimental Observations 615
10.22 Radical Aromatic Substitutions
10.22.1 Electron Pushing 615
10.22.2 Isotope Effects 616
10.22.3 Regiochemistry 616
Summary and Outlook 617
exercises 617
further reading 624
615
CHAPTER 11: Organic Reaction Mechanisms,
Part 2: Substitutions at Aliphatic
Centers and Thermal Isomerizations/
Rearrangements 627
Intent and Purpose 627
—SUBSTITUTION a TO A CARBONYL CENTER:
ENOL AND ENOLATE CHEMISTRY— 627
11.1 Tautomerization 628
11.1.1 Electron Pushing for Keto-Enol
Tautomerizations 628
11.1.2 The Thermodynamics of Enol Formation 628
11.1.3 Catalysis of Enolizations 629
11.1.4 Kinetic vs. Thermodynamic Control
in Enolate and Enol Formation 629
11.2 a-Halogenation 631
11.2.1 Electron Pushing 631
11.2.2 A Few Experimental Observations
631
11.3 a-Alkylations 632
11.3.1 Electron Pushing 632
11.3.2 Stereochemistry: Conformational Effects 633
11.4 The Aldol Reaction 634
11.4.1 Electron Pushing 634
11.4.2 Conformational Effects on the Aldol Reaction 634
—SUBSTITUTIONS ON ALIPHATIC CENTERS— 637
11.5 Nucleophilic Aliphatic Substitution Reactions 637
11.5.1 Sn2 and SN1 Electron-Pushing Examples 637
11.5.2 Kinetics 638
11.5.3 Competition Experiments and Product Analyses 639
11.5.4 Stereochemistry 640
11.5.5 Orbital Considerations 643
11.5.6 Solvent Effects 643
11.5.7 Isotope Effect Data 646
11.5.8 An Overall Picture of SN2 and SN1 Reactions 646
11.5.9 Structure-Function Correlations
with the Nucleophile 648
11.5.10 Structure-Function Correlations
with the Leaving Group 651
11.5.11 Structure-Function Correlations
with the R Group 651
Effect of the R Group Structure on SN2 Reactions 651
Effect of the R Group Structure on SN1 Reactions 653
11.5.12 Carbocation Rearrangements 656
11.5.13 Anchimeric Assistance in SN1 Reactions 659
11.5.14 SnI Reactions Involving Non-Classical
Carbocations 661
Norbornyl Cation 662
Cyclopropyl Carbinyl Carbocation 664
11.5.15 Summary of Carbocation Stabilization
in Various Reactions 667
11.5.16 The Interplay Between Substitution
and Elimination 667
11.6 Substitution, Radical, Nucleophilic 668
11.6.1 The SET Reaction—Electron Pushing 668
11.6.2 The Nature of the Intermediate
in an SET Mechanism 669
11.6.3 Radical Rearrangements as Evidence 669
11.6.4 Structure-Function Correlations
with the Leaving Group 670
11.6.5 The SrnI Reaction—Electron Pushing 670
11.7 Radical Aliphatic Substitutions 671
11.7.1 Electron Pushing 671
11.7.2 Heats of Reaction 671
11.7.3 Regiochemistry of Free Radical
Halogenation 671
11.7.4 Autoxidation: Addition of O2
into C-H Bonds 673
Electron Pushing for Autoxidation 673
—ISOMERIZATIONS AND REARRANGEMENTS— 674
11.8 Migrations to Electrophilic Carbons 674
11.8.1 Electron Pushing for the
Pinacol Rearrangement 675
11.8.2 Electron Pushing in the Benzilic Acid
Rearrangement 675
11.8.3 Migratory Aptitudes in the Pinacol
Rearrangement 675
11.8.4 Stereoelectronic and Stereochemical Considerations
in the Pinacol Rearrangement 676
11.8.5 A Few Experimental Observations for the Benzilic
Acid Rearrangement 678
11.9 Migrations to Electrophilic Heteroatoms 678
11.9.1 Electron Pushing in the Beckmann
Rearrangement 678
11.9.2 Electron Pushing for the Hofmann
Rearrangement 679
11.9.3 Electron Pushing for the Schmidt
Rearrangement 680
11.9.4 Electron Pushing for the Baeyer-Villiger
Oxidation 680
11.9.5 A Few Experimental Observations for the
Beckmann Rearrangement 680
CONTENTS
11.9.6 A Few Experimental Observations for the
Schmidt Rearrangement 681
11.9.7 A Few Experimental Observations for the
Baeyer-Villiger Oxidation 681
11.10 The Favorskii Rearrangement and Other
Carbanion Rearrangements 682
11.10.1 Electron Pushing 682
11.10.2 Other Carbanion Rearrangements 683
11.11 Rearrangements Involving Radicals 683
11.11.1 Hydrogen Shifts 683
11.11.2 Aryl and Vinyl Shifts 684
11.11.3 Ring-Opening Reactions 685
11.12 Rearrangements and Isomerizations
Involving Biradicals 685
11.12.1 Electron Pushing Involving Biradicals
11.12.2 Tetramethylene 687
11.12.3 Trimethylene 689
11.12.4 Trimethylenemethane 693
Summary and Outlook 695
EXERCISES 695
FURTHER READING 703
686
CHAPTER 12: Organotransition Metal Reaction
Mechanisms and Catalysis 705
Intent and Purpose 705
12.1 The Basics of Organometallic Complexes 705
12.1.1 Electron Counting and Oxidation State 706
Electron Counting 706
Oxidation State 708
d Electron Count 708
Ambiguities 708
12.1.2 The 18-Electron Rule 710
12.1.3 Standard Geometries 710
12.1.4 Terminology 711
12.1.5 Electron Pushing with Organometallic
Structures 711
12.1.6 d Orbital Splitting Patterns 712
12.1.7 Stabilizing Reactive Ligands 713
12.2 Common Organometallic Reactions 714
12.2.1 Ligand Exchange Reactions 714
Reaction Types 714
Kinetics 716
Structure-Function Relationships with the Metal 716
Structure-Function Relationships
with the Ligand 716
Substitutions of Other Ligands 717
12.2.2 Oxidative Addition 717
Stereochemistry of the Metal Complex 718
Kinetics 718
Stereochemistry of the R Group 719
Structure-Function Relationship for the R Group 720
Structure-Function Relationships
for the Ligands 720
Oxidative Addition at sp2 Centers 721
Summary of the Mechanisms for Oxidative
Addition 721
12.2.3 Reductive Elimination 724
Structure-Function Relationship for the
R Group and the Ligands 724
Stereochemistry at the Metal Center 725
Other Mechanisms 725
Summary of the Mechanisms for
Reductive Elimination 726
12.2.4 a-and ß-Eliminations 727
General Trends for a- and ß-Eliminations 727
Kinetics 728
Stereochemistry ofß-Hydride Elimination 729
12.2.5 Migratory Insertions 729
Kinetics 730
Studies to Decipher the Mechanism of Migratory
Insertion Involving CO 730
Other Stereochemical Considerations 732
12.2.6 Electrophilic Addition to Ligands 733
Reaction Types 733
Common Mechanisms Deduced from
Stereochemical Analyses 734
12.2.7 Nucleophilic Addition to Ligands 734
Reaction Types 735
Stereochemical and Regiochemical Analyses 735
12.3 Combining the Individual Reactions into Overall
Transformations and Cycles 737
12.3.1 The Nature of Organometallic Catalysis—
Change in Mechanism 738
12.3.2 The Monsanto Acetic Acid Synthesis 738
12.3.3 Hydroformylation 739
12.3.4 The Water-Gas Shift Reaction 740
12.3.5 Olefin Oxidation—The Wacker Process 741
12.3.6 Palladium Coupling Reactions 742
12.3.7 AllylicAlkylation 743
12.3.8 Olefin Metathesis 744
Summary and Outlook 747
EXERCISES 748
FURTHER READING 750
CHAPTER 13: Organic Polymer and
Materials Chemistry 753
Intent and Purpose 753
13.1 Structural Issues in Materials Chemistry 754
13.1.1 Molecular Weight Analysis of Polymers 754
Number Average and Weight Average Molecular
Weights —M„ and Mw 754
13.1.2 Thermal Transitions—Thermoplastics
and Elastomers 757
13.1.3 Basic Polymer Topologies 759
CONTENTS
13.1.4 Polymer-Polymer Phase Behavior 760
13.1.5 Polymer Processing 762
13.1.6 Novel Topologies—Dendrimers and
Hyperbranched Polymers 763
Dendrimers 763
Hyperbranched Polymers 768
13.1.7 Liquid Crystals 769
13.1.8 Fullerenes and Carbon Nanotubes 775
13.2 Common Polymerization Mechanisms 779
13.2.1 General Issues 779
13.2.2 Polymerization Kinetics 782
Step-Growth Kinetics 782
Free-Radical Chain Polymerization 783
Living Polymerizations 785
Thermodynamics of Polymerizations 787
13.2.3 Condensation Polymerization 788
13.2.4 Radical Polymerization 791
13.2.5 Anionic Polymerization 793
13.2.6 Cationic Polymerization 794
13.2.7 Ziegler-Natta and Related Polymerizations 794
Single-Site Catalysts 796
13.2.8 Ring-Opening Polymerization 797
13.2.9 Group Transfer Polymerization (GTP) 799
Summary and Outlook 800
EXERCISES 801
FURTHER READING 803
PART III
ELECTRONIC STRUCTURE:
THEORY AND APPLICATIONS
CHAPTER 14: Advanced Concepts in Electronic
Structure Theory 807
Intent and Purpose 807
14.1 Introductory Quantum Mechanics 808
14.1.1 The Nature of Wavefunctions 808
14.1.2 The Schrödinger Equation 809
14.1.3 The Hamiltonian 809
14.1.4 The Nature of the V2 Operator 811
14.1.5 Why do Bonds Form? 812
14.2 Calculational Methods—Solving the Schrödinger
Equation for Complex Systems 815
14.2.1 Ablnitio Molecular Orbital Theory 815
Born-Oppenheimer Approximation 815
The Orbital Approximation 815
Spin 816
The Pauli Principle and Determinantal
Wavefunctions 816
The Hartree-Fock Equation and
the Variational Theorem 818
SCF Theory 821
Linear Combination of Atomic Orbitals —
Molecular Orbitals (LCAO-MO) 821
Common Basis Sets —Modeling Atomic Orbitals 822
Extension Beyond HF—Correlation Energy 824
Solvation 825
General Considerations 825
Summary 826
14.2.2 Secular Determinants—A Bridge Between Ab lnitio,
Semi-Empirical/ Approximate, and Perturbational
Molecular Orbital Theory Methods 828
The "Two-Orbital Mixing Problem" 829
Writing the Secular Equations and Determinant
for Any Molecule 832
14.2.3 Semi-Empirical and Approximate Methods 833
Neglect of Differential Overlap
(NDO) Methods 833
i. CNDO, 1NDO, PNDO (C = Complete,
1 = Intermediate, P = Partial) 834
ii. The Semi-Empirical Methods:
MNDO,AMl,andPM3 834
Extended Hückel Theory (EHT) 834
Hückel Molecular Orbital Theory (HMOT) 835
14.2.4 Some General Comments on Computational
Quantum Mechanics 835
14.2.5 An Alternative: Density Functional
Theory (DFT) 836
14.3 A Brief Overview of the Implementation
and Results of HMOT 837
14.3.1 Implementing Hückel Theory 838
14.3.2 HMOT of Cyclic 17 Systems 840
14.3.3 HMOT of Linear it Systems 841
14.3.4 Alternate Hydrocarbons 842
14.4 Perturbation Theory—Orbital Mixing Rules 844
14.4.1 Mixing of Degenerate Orbitals—
First-Order Perturbations 845
14.4.2 Mixing of Non-Degenerate Orbitals—
Second-Order Perturbations 845
14.5 Some Topics in Organic Chemistry for
Which Molecular Orbital Theory Lends
Important Insights 846
14.5.1 Arenes: Aromaticity and Antiaromaticity 846
14.5.2 Cyclopropane and Cyclopropylcarbinyl—
Walsh Orbitals 848
The Cyclic Three-Orbital Mixing Problem 849
The MOs of Cyclopropane 850
14.5.3 Planar Methane 853
14.5.4 Through-Bond Coupling 854
14.5.5 Unique Bonding Capabilities of Carbocations—
Non-Classical Ions and Hypervalent Carbon 855
Transition State Structure Calculations 856
Application of These Methods to Carbocations 857
NMR Effects in Carbocations 857
The Norbomyl Cation 858
14.5.6 Spin Preferences 859
Two Weakly Interacting Electrons:
H2 vs. Atomic C 859
CONTENTS
14.6 Organometallic Complexes 862
14.6.1 Group Orbitals for Metals 863
14.6.2 The Isolobal Analogy 866
14.6.3 Using the Group Orbitals to Construct
Organometallic Complexes 867
Summary and Outlook 868
EXERCISES 868
FURTHER READING 875
CHAPTER 15: Thermal Pericyclic Reactions 877
Intent and Purpose 877
15.1 Background 878
15.2 A Detailed Analysis of Two Simple
Cycloadditions 878
15.2.1 Orbital Symmetry Diagrams 879
[2+2] 879
[4+2] 881
15.2.2 State Correlation Diagrams 883
[2+2] 883
[4+2] 886
15.2.3 Frontier Molecular Orbital
(FMO) Theory 888
Contrasting the [2+2] and [4+2] 888
15.2.4 Aromatic Transition State
Theory /Topology 889
15.2.5 The Generalized Orbital
Symmetry Rule 890
15.2.6 Some Comments on "Forbidden" and
"Allowed" Reactions 892
15.2.7 Photochemical Pericyclic Reactions 892
15.2.8 Summary of the Various Methods 893
15.3 Cycloadditions 893
15.3.1 An Allowed Geometry for [2+2]
Cycloadditions 894
15.3.2 Summarizing Cycloadditions 895
15.3.3 General Experimental Observations 895
15.3.4 Stereochemistry and Regiochemistry
of the Diels-Alder Reaction 896
An Orbital Approach to Predicting
Regiochemistry 896
The Endo Effect 899
15.3.5 Experimental Observations for
[2+2] Cycloadditions 901
15.3.6 Experimental Observations for
1,3-Dipolar Cycloadditions 901
15.3.7 Retrocycloadditions 902
15.4 Electrocyclic Reactions 903
15.4.1 Terminology 903
15.4.2 Theoretical Analyses 904
15.4.3 Experimental Observations:
Stereochemistry 906
15.4.4 Torquoselectivity 908
15.5 Sigmatropic Rearrangements 910
15.5.1 Theory 911
15.5.2 Experimental Observations: A Focus on
Stereochemistry 913
15.5.3 The Mechanism of the
Cope Rearrangement 916
15.5.4 The Claisen Rearrangement 921
Uses in Synthesis 921
Mechanistic Studies 923
15.5.5 The Ene Reaction 924
15.6 Cheletropic Reactions 924
15.6.1 Theoretical Analyses 926
15.6.2 Carbene Additions 927
15.7 In Summary—Applying the Rules 928
Summary and Outlook 928
EXERCISES 929
FURTHER READING 933
CHAPTER 16: Photochemistry 935
Intent and Purpose 935
16.1 Photophysical Processes—
The Jablonski Diagram 936
16.1.1 Electromagnetic Radiation 936
Multiple Energy Surfaces Exist 937
16.1.2 Absorption 939
16.1.3 Radiationless Vibrational Relaxation 944
16.1.4 Fluorescence 945
16.1.5 Internal Conversion (IC) 949
16.1.6 Intersystem Crossing (ISC) 950
16.1.7 Phosphorescence 951
16.1.8 Quantum Yield 952
16.1.9 Summary of Photophysical Processes 952
16.2 Bimolecular Photophysical Processes 953
16.2.1 General Considerations 953
16.2.2 Quenching, Excimers, and Exciplexes 953
Quenching 954
Excimers and Exciplexes 954
Photoinduced Electron Transfer 955
16.2.3 Energy Transfer I. The Dexter Mechanism—
Sensitization 956
16.2.4 Energy Transfer II. The Förster Mechanism
16.2.5 FRET 960
16.2.6 Energy Pooling 962
16.2.7 An Overview of Bimolecular Photophysical
Processes 962
958
16.3 Photochemical Reactions 962
16.3.1 Theoretical Considerations—Funnels
Diabatic Photoreactions 963
Other Mechanisms 964
16.3.2 Acid-Base Chemistry 965
962
CONTENTS
16.3.3 Olefin Isomerization 965
16.3.4 Reversal of Pericyclic Selection Rules 968
16.3.5 Photocycloaddition Reactions 970
Making Highly Strained Ring Systems 973
Breaking Aromaticity 974
16.3.6 The Di-Tr-Methane Rearrangement 974
16.3.7 Carbonyls Part I: The Norrish I Reaction 976
16.3.8 Carbonyls Part II: Photoreduction and
the Norrish II Reaction 978
16.3.9 Nitrobenzyl Photochemistry: "Caged"
Compounds 980
16.3.10 Elimination of N2: Azo Compounds, Diazo
Compounds, Diazirines, and Azides 981
Azoalkanes (1,2-Diazenes) 981
Diazo Compounds and Diazirines 982
Azides 983
16.4 Chemiluminescence 985
16.4.1 Potential Energy Surface for a
Chemiluminescent Reaction 985
16.4.2 Typical Chemiluminescent Reactions 986
16.4.3 Dioxetane Thermolysis 987
16.5 Singlet Oxygen 989
Summary and Outlook 993
EXERCISES 993
FURTHER READING 999
CHAPTER 17: Electronic Organic Materials 1001
Intent and Purpose 1001
17.1 Theory 1001
17.1.1 Infinite tt Systems—An Introduction
to Band Structures 1002
17.1.2 The Peierls Distortion 1009
17.1.3 Doping 1011
1016
17.2 Conducting Polymers
17.2.1 Conductivity 1016
17.2.2 Polyacetylene 1017
17.2.3 Polyarenes and Polyarenevinylenes
17.2.4 Polyaniline 1021
1022
1018
17.3 Organic Magnetic Materials
17.3.1 Magnetism 1023
17.3.2 The Molecular Approach to Organic Magnetic
Materials 1024
17.3.3 The Polymer Approach to Organic Magnetic
Materials—Very High-Spin Organic Molecules 1027
17.4 Superconductivity 1030
17.4.1 Organic Metals/Synthetic Metals 1032
17.5 Non-Linear Optics (NLO) 1033
17.6 Photoresists 1036
17.6.1 Photolithography 1036
17.6.2 Negative Photoresists 1037
17.6.3 Positive Photoresists 1038
Summary and Outlook 1041
EXERCISES 1042
FURTHER READING 1044
appendix 1: Conversion Factors and Other
Useful Data 1047
appendix 2: Electrostatic Potential Surfaces for
Representative Organic Molecules 1049
appendix 3: Group Orbitals of Common Functional
Groups: Representative Examples Using
Simple Molecules 1051
appendix4: The Organic Structures of Biology 1057
appendix 5: Pushing Electrons 1061
A5.1 The Rudiments of Pushing Electrons 1061
A5.2 Electron Sources and Sinks for
Two-Electron Flow 1062
A5.3 How to Denote Resonance 1064
A5.4 Common Electron-Pushing Errors 1065
Backwards Arrow Pushing 1065
Not Enough Arrows 1065
Losing Track of the Octet Rule 1066
Losing Track of Hydrogens and Lone Pairs 1066
Not Using the Proper Source 1067
Mixed Media Mistakes 1067
Too Many Arrows—Shortcuts 1067
A5.5 Complex Reactions—Drawing a Chemically
Reasonable Mechanism 1068
A5.6 Two Case Studies of Predicting
Reaction Mechanisms 1069
A5.7 Pushing Electrons for Radical Reactions 1071
Practice Problems for Pushing Electrons 1073
appendix 6: Reaction Mechanism Nomenclature 1075
Index 1079
Highlights
CHAPTER 1
How Realistic are Formal Charges? 7
NMR Coupling Constants 10
Scaling Electrostatic Surface Potentials 15
1-Fluorobutane 16
Particle in a Box 21
Resonance in the Peptide Amide Bond? 23
A Brief Look at Symmetry and Symmetry Operations 29
CH5+—Not Really a Well-Defined Structure 55
Pyramidal Inversion: NH3 vs. PH3 57
Stable Carbenes 59
CHAPTER2
Entropy Changes During Cyclization Reactions 71
A Consequence of High Bond Strength:
The Hydroxyl Radical in Biology 73
The Half-Life for Homolysis of Ethane
at Room Temperature 73
The Probability of Finding Atoms at Particular
Separations 75
How do We Know That n = 0 is Most Relevant
for Bond Stretches at T = 298 K? 76
Potential Surfaces for Bond Bending Motions 78
How Big is 3 kcal / mol? 93
Shouldn't Torsional Motions be Quantized? 94
The Geometry of Radicals 96
Differing Magnitudes of Energy Values in
Thermodynamics and Kinetics 100
"Sugar Pucker" in Nucleic Acids 102
Alternative Measurements of Steric Size 104
The Use of A Values in a Conformational Analysis
Study for the Determination of Intramolecular
Hydrogen Bond Strength 105
The NMR Time Scale 106
Ring Fusion—Steroids 108
A Conformational Effect on the Material Properties
ofPoly(3-Alkylthiophenes) 116
Cyclopropenyl Cation 117
Cyclopropenyl Anion 118
Porphyrins 119
Protein Disulfide Linkages 123
From Strained Molecules to Molecular Rods 126
Cubane Explosives? 126
Molecular Gears 128
CHAPTER 3
The Use of Solvent Scales to Direct Diels-Alder
Reactions 149
The Use of Wetting and the Capillary Action
Force to Drive the Self-Assembly of
Macroscopic Objects 151
The Solvent Packing Coefficient and
the 55% Solution 152
Solvation Can Affect Equilibria 155
A van't Hoff Analysis of the Formation of a
Stable Carbene 163
The Strength of a Buried Salt Bridge 165
The Angular Dependence of Dipole-Dipole Interactions—
The "Magic Angle" 168
An Unusual Hydrogen Bond Acceptor 169
Evidence for Weak Directionality Considerations 170
Intramolecular Hydrogen Bonds are Best
for Nine-Membered Rings 170
Solvent Scales and Hydrogen Bonds 172
The Extent of Resonance can be Correlated with
Hydrogen Bond Length 174
Cooperative Hydrogen Bonding in Saccharides 175
How Much is a Hydrogen Bond in an a-Helix Worth? 176
Proton Sponges 179
The Relevance of Low-Barrier Hydrogen Bonds
to Enzymatic Catalysis 179
ß-PeptideFoldamers 180
A Cation-TT Interaction at the Nicotine Receptor 183
The Polar Nature of Benzene Affects Acidities
in a Predictable Manner 184
Use of the Arene-Perfluorarene Interaction in the
Design of Solid State Structures 185
Donor-Acceptor Driven Folding 187
The Hydrophobie Effect and Protein Folding 194
More Foldamers: Folding Driven by
Solvophobic Effects 195
Calculating Drug Binding Energies by SPT 201
CHAPTER4
The Units of Binding Constants 209
Cooperativity in Drug Receptor Interactions 215
The Hill Equation and Cooperativity in
Protein-Ligand Interactions 219
The Benesi-Hildebrand Plot 221
How are Heat Changes Related to Enthalpy? 223
Using the Helical Structure of Peptides and the
Complexation Power of Crowns to Create
an Artificial Transmembrane Channel 226
Preorganization and the Salt Bridge 229
A Clear Case of Entropy Driven Electrostatic
Complexation 229
Salt Bridges Evaluated by Non-Biological Systems 230
Does Hydrogen Bonding Really Play a Role in
DNA Strand Recognition? 233
Calixarenes—Important Building Blocks for Molecular
Recognition and Supramolecular Chemistry 238
Aromatics at Biological Binding Sites 239
Combining the Cation-TT Effect and Crown Ethers 240
A Thermodynamic Cycle to Determine the Strength
of a Polar-ir Interaction 242
Molecular Mechanics/Modeling and Molecular
Recognition 243
Biotin/Avidin: A Molecular Recognition/
Self-Assembly Tool from Nature 249
Taming Cyclobutadiene—A Remarkable Use of
Supramolecular Chemistry 251
HIGHLIGHTS
CHAPTERS
Using a pH Indicator to Sense Species Other
Than the Hydronium Ion 264
Realistic Titrations in Water 265
An Extremely Acidic Medium is Formed During
Photo-Initiated Cationic Polymerization in
Photolithography 269
Super Acids Used to Activate Hydrocarbons 270
The Intrinsic Acidity Increase of a Carbon Acid
by Coordination of BF3 276
Direct Observation of Cytosine Protonation During
Triple Helix Formation 287
A Shift of the Acidity of an N-H Bond in Water Due to
the Proximity of an Ammonium or Metal Cation 288
The Notion of Superelectrophiles Produced by
Super Acids 289
CHAPTER 6
Stereoisomerism and Connectivity 300
Total Synthesis of an Antibiotic with a Staggering
Number of Stereocenters 303
The Descriptors for the Amino Acids Can Lead
to Confusion 307
Chiral Shift Reagents 308
C2 Ligands in Asymmetric Synthesis 313
Enzymatic Reactions, Molecular Imprints, and
Enantiotopic Discrimination 320
Biological Knots—DNA and Proteins 325
Polypropylene Structure and the Mass of the Universe 331
Controlling Polymer Tacticity—The Metallocenes 332
CD Used to Distinguish a-Helices from ß-Sheets 335
Creating Chiral Phosphates for Use as Mechanistic
Probes 335
A Molecular Helix Created from Highly Twisted
Building Blocks 338
CHAPTER 7
Single-Molecule Kinetics 360
Using the Arrhenius Equation to Determine Differences
in Activation Parameters for Two Competing
Pathways 370
Curvature in an Eyring Plot is Used as Evidence for an
Enzyme Conformational Change in the Catalysis
of the Cleavage of the Co-C Bond of Vitamin B12 371
Where TST May be Insufficient 374
The Transition States for SN1 Reactions 377
Comparing Reactivity to Selectivity in Free Radical
Halogenation 378
Using the Curtin-Hammett Principle to Predict the
Stereochemistry of an Addition Reaction 379
Applying the Principle of Microscopic Reversibility
to Phosphate Ester Chemistry 380
Kinetic vs. Thermodynamic Enolates 382
Molecularity vs. Mechanism. Cyclization Reactions and
Effective Molarity 384
First Order Kinetics: Delineating Between a Unimolecular
and a Bimolecular Reaction of Cyclopentyne and
Dienes 386
The Observation of Second Order Kinetics to Support
a Multistep Displacement Mechanism for a
Vitamin Analog 387
Pseudo-First Order Kinetics: Revisiting the
Cyclopentyne Example 388
Zero Order Kinetics 393
An Organometallic Example of Using the SS A
to Delineate Mechanisms 395
Saturation Kinetics That We Take for Granted—
SN1 Reactions 397
Prior Equilibrium in an SN1 Reaction 398
Femtochemistry: Direct Characterization of
Transition States, Part I 400
"Seeing" Transition States, Part II: The Role of
Computation 401
The Use of Pulse Radiolysis to Measure the pKas
of Protonated Ketyl Anions 402
Discovery of the Marcus Inverted Region 406
Using a More O'Ferrall-Jencks Plot in Catalysis 410
CHAPTER 8
The Use of Primary Kinetic Isotope Effects to Probe
the Mechanism of Aliphatic Hydroxylation by
Iron(III) Porphyrins 425
An Example of Changes in the Isotope Effect with Varying
Reaction Free Energies 428
The Use of an Inverse Isotope Effect to Delineate an
Enzyme Mechanism 431
An Ingenious Method for Measuring Very Small
Isotope Effects 432
An Example of Tunneling in a Common Synthetic
Organic Reaction 436
Using Fractionation Factors to Characterize Very Strong
Hydrogen Bonds 439
The Use of a Proton Inventory to Explore the Mechanism
of Ribonuclease Catalysis 440
A Substituent Effect Study to Decipher the Reason
for the High Stability of Collagen 444
Using a Hammett Plot to Explore the Behavior of a
Catalytic Antibody 450
An Example of a Change in Mechanism in a Solvolysis
Reaction Studied Using a+ 452
A Swain-Lupton Correlation for Tungsten-Bipyridine-
Catalyzed Ally lie Alkylation 453
Using Taft Parameters to Understand the Structures
of Cobaloximes; Vitamin B12 Mimics 455
The Use of the Schleyer Method to Determine the Extent of
Nucleophilic Assistance in the Solvolysis of Arylvinyl
Tosylates 459
The Use of Swain-Scott Parameters to Determine
the Mechanism of Some Acetal Substitution
Reactions 462
ATP Hydrolysis—How ßtG and /?muc Values Have Given
Insight into Transition State Structures 465
How Can Some Groups be Both Good Nucleophiles and
Good Leaving Groups? 466
An Example of an Unexpected Product 472
Designing a Method to Divert the Intermediate 473
Trapping a Phosphorane Legitimizes Its Existence 474
Checking for a Common Intermediate in Rhodium-
Catalyzed Allylic Alkylations 475
Pyranoside Hydrolysis by Lysozyme 476
Using Isotopic Scrambling to Distinguish Exocyclic vs.
Endocyclic Cleavage Pathways for a Pyranoside 478
HIGHLIGHTS
Determination of 1,4-Biradical Lifetimes Using
a Radical Clock 480
The Identification of Intermediates from a Catalytic Cycle
Needs to be Interpreted with Care 481
CHAPTER 9
The Application of Figure 9.4 to Enzymes 494
High Proximity Leads to the Isolation of a Tetrahedral
Intermediate 498
The Notion of "Near Attack Conformations" 499
Toward an Artificial Acetylcholinesterase 501
Metal and Hydrogen Bonding Promoted Hydrolysis
of2',3'-cAMP 502
Nucleophilic Catalysis of Electrophilic Reactions 503
Organocatalysis 505
Lysozyme 506
A Model for General-Acid-General-Base Catalysis 514
Anomalous Bransted Values 519
Artificial Enzymes: Cyclodextrins Lead the Way 530
CHAPTER 10
Cyclic Forms of Saccharides and Concerted Proton
Transfers 545
Squalene to Lanosterol 550
Mechanisms of Asymmetric Epoxidation Reactions 558
Nature's Hydride Reducing Agent 566
The Captodative Effect 573
Stereoelectronics in an Acyl Transfer Model 579
The Swern Oxidation 580
Gas Phase Eliminations 588
Using the Curtin-Hammett Principle 593
Aconitase—An Enzyme that Catalyzes Dehydration
and Rehydration 595
Enzymatic Acyl Transfers I: The Catalytic Triad 604
Enzymatic Acyl Transfers II: Zn(II) Catalysis 605
Enzyme Mimics for Acyl Transfers 606
Peptide Synthesis—Optimizing Acyl Transfer 606
CHAPTER 11
Enolate Aggregation 631
Control of Stereochemistry in Enolate Reactions 636
Gas Phase SN2 Reactions—A Stark Difference in Mechanism
from Solution 641
A Potential Kinetic Quandary 642
Contact Ion Pairs vs. Solvent-Separated Ion Pairs 647
An Enzymatic SN2 Reaction: Haloalkane
Dehydrogenase 649
The Meaning of ß^c Values 651
Carbocation Rearrangements in Rings 658
Anchimeric Assistance in War 660
Further Examples of Hypervalent Carbon 666
Brominations Using N-Bromosuccinimide 673
An Enzymatic Analog to the Benzilic Acid Rearrangement:
Acetohydroxy-Acid Isomeroreductase 677
Femtochemistry and Singlet Biradicals 693
CHAPTER 12
Bonding Models 709
Electrophilic Aliphatic Substitutions (SE2 and SE1) 715
C-H Activation, Part I 722
C-H Activation, Part II 723
The Sandmeyer Reaction 726
Olefin Slippage During Nucleophilic Addition to
Alkenes 737
Pd(0) Coupling Reactions in Organic Synthesis 742
Stereocontrol at Every Step in Asymmetric Allylic
Alkylations 745
Cyclic Rings Possessing Over 100,000 Carbons! 747
CHAPTER 13
Monodisperse Materials Prepared Biosynthetically 756
An Analysis of Dispersity and Molecular Weight 757
A Melting Analysis 759
Protein Folding Modeled by a Two-State Polymer
Phase Transition 762
Dendrimers, Fractals, Neurons, and Trees 769
Lyotropic Liquid Crystals: From Soap Scum to
Biological Membranes 774
Organic Surfaces: Self-Assembling Monolayers and
Langmuir-Blodgett Films 778
Free-Radical Living Polymerizations 787
Lycra /Spandex 790
Radical Copolymerization—Not as Random
as You Might Think 792
PMMA—One Polymer with a Remarkable Range
of Uses 793
Living Polymers for Better Running Shoes 795
Using 13C NMR Spectroscopy to Evaluate Polymer
Stereochemistry 797
CHAPTER 14
The Hydrogen Atom 811
Methane—Molecular Orbitals or Discrete Single
Bonds with sf Hybrids? 827
Koopmans' Theorem—A Connection Between Ab Initio
Calculations and Experiment 828
A Matrix Approach to Setting Up the LCAO Method 832
Through-Bond Coupling and Spin Preferences 861
Cyclobutadiene at the Two-Electron Level of Theory 862
CHAPTER 15
Symmetry Does Matter 887
Allowed Organometallic [2+2] Cycloadditions 895
Semi-Empirical vs. Ab Initio Treatments of Pericyclic
Transition States 900
Electrocyclization in Cancer Therapeutics 910
Fluxional Molecules 913
A Remarkable Substituent Effect: The Oxy-Cope
Rearrangement 921
A Biological Claisen Rearrangement—The Chorismate
Mutase Reaction 922
Hydrophobie Effects in Pericyclic Reactions 923
Pericyclic Reactions of Radical Cations 925
CHAPTER 16
Excited State Wavefunctions 937
Physical Properties of Excited States 944
The Sensitivity of Fluorescence—Good News and
Bad News 946
GFP, Part I: Nature's Fluorophore 947
HIGHLIGHTS
Isosbestic Points—Hallmarks of One-to-One Stoichiometric
Conversions 949
The "Free Rotor" or "Loose Bolt" Effect on
Quantum Yields 953
Single-Molecule FRET 961
Trans-Cyclohexene? 967
Retinal and Rhodopsin—The Photochemistry
of Vision 968
Photochromism 969
UV Damage of DNA—A [2+2] Photoreaction 971
Using Photochemistry to Generate Reactive Intermediates:
Strategies Fast and Slow 983
Photoaffinity Labeling—A Powerful Tool for
Chemical Biology 984
Light Sticks 987
GFP,PartII:Aequorin 989
Photodynamic Therapy 991
CHAPTER 17
Solitons in Polyacetylene 1015
Scanning Probe Microscopy 1040
Soft Lithography 1041 |
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| illustrated | Illustrated |
| index_date | 2024-07-02T13:38:09Z |
| indexdate | 2024-07-09T20:33:44Z |
| institution | BVB |
| isbn | 1891389319 9781891389313 |
| language | English |
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| physical | XXVIII, 1099 S. Ill., graph. Darst. |
| publishDate | 2006 |
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| publisher | Univ. Science Books |
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| spelling | Anslyn, Eric V. 1960- Verfasser (DE-588)136650759 aut Modern physical organic chemistry Eric V. Anslyn ; Dennis A. Dougherty Sausalito, Calif. Univ. Science Books 2006 XXVIII, 1099 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Physikalische Chemie (DE-588)4045959-7 gnd rswk-swf Organische Chemie (DE-588)4043793-0 gnd rswk-swf Theoretische organische Chemie (DE-588)4185101-8 gnd rswk-swf Theoretische organische Chemie (DE-588)4185101-8 s DE-604 Physikalische Chemie (DE-588)4045959-7 s Organische Chemie (DE-588)4043793-0 s Dougherty, Dennis A. 1952- Verfasser (DE-588)133002667 aut HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014567444&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Anslyn, Eric V. 1960- Dougherty, Dennis A. 1952- Modern physical organic chemistry Physikalische Chemie (DE-588)4045959-7 gnd Organische Chemie (DE-588)4043793-0 gnd Theoretische organische Chemie (DE-588)4185101-8 gnd |
| subject_GND | (DE-588)4045959-7 (DE-588)4043793-0 (DE-588)4185101-8 |
| title | Modern physical organic chemistry |
| title_auth | Modern physical organic chemistry |
| title_exact_search | Modern physical organic chemistry |
| title_exact_search_txtP | Modern physical organic chemistry |
| title_full | Modern physical organic chemistry Eric V. Anslyn ; Dennis A. Dougherty |
| title_fullStr | Modern physical organic chemistry Eric V. Anslyn ; Dennis A. Dougherty |
| title_full_unstemmed | Modern physical organic chemistry Eric V. Anslyn ; Dennis A. Dougherty |
| title_short | Modern physical organic chemistry |
| title_sort | modern physical organic chemistry |
| topic | Physikalische Chemie (DE-588)4045959-7 gnd Organische Chemie (DE-588)4043793-0 gnd Theoretische organische Chemie (DE-588)4185101-8 gnd |
| topic_facet | Physikalische Chemie Organische Chemie Theoretische organische Chemie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014567444&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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