Modern Physical Organic Chemistry

Eric V. Anslyn
The University of Texas, Austin

Dennis A. Dougherty
California Institute of Technology


Chapter 1: Introduction to Structure and Models of Bonding

Intent and Purpose.

1.1 A Review of Basic Bonding Concepts.

1.2 A More Modern Theory of Organic Bonding          

1.3 Orbital Mixing – Building Larger Molecules           

1.4 Bonding and Structure of Reactive Intermediates           

1.5 A Very Quick Look at Organometallic and Inorganic Bonding 

Chapter 2: Strain and Stability

Intent and Purpose

2.1 Thermochemistry of Stable Molecules           

2.2 Thermochemistry of Reactive Intermediates        

2.3 Relationships between Structure and Energetics; Basic Conformational Analysis           

2.4 Electronic Effects            

2.5 Highly Strained Molecules           

2.6 Molecular Mechanics              

Chapter 3: Solutions and Noncovalent Binding Forces

Intent and Purpose

3.1 Solvent and Solution Properties         

3.2 Binding Forces          

3.3 Computational Modeling of Solvation       

Chapter 4: Molecular Recognition and Supramolecular Chemistry

Intent and Purpose

4.1 Thermodynamic Analyses of Binding Phenomena           

4.2 Molecular Recognition          

4.3 Supramolecular Chemistry          

 Chapter 5: Acid-Base Chemistry

Intent and Purpose

5.1 Brønsted Acid and Base Chemistry

5.2 Aqueous Solutions           

5.3 Nonaqueous Systems           

5.4 Predicting Acid Strength           

5.5 Acids-Bases of Bioorganic Interest

5.6 Lewis Acids/Bases and Electrophiles/Nucleophiles

Chapter 6: Stereochemistry

Intent and Purpose

6.1 Stereogenicity and Stereoisomerism           

6.2 Symmetry and Stereochemistry          

6.3  Topicity Relationships          

6.4  Reaction Stereochemistry:  Stereoselectivity and Stereospecificity           

6.5  Symmetry and Timescale

6.6  Topological and Supramolecular Stereochemistry           

6.7 Stereochemical Issues in Polymer Chemistry

6.8 Stereochemical Issues in Chemical Biology           

Summary and Outlook

Chapter 7: Energy Surfaces and Kinetic Analyses

Intent and Purpose:

7.1 Energy Surfaces and Related Concepts          

7.2 Transition State Theory (TST), and Related Topics           

7.3 Postulates and Principles Related to Kinetic Analysis           

7.4 Kinetic Experiments          

7.5 Complex Reactions - Deciphering Mechanisms          

7.6 Methods for Following Kinetics           

7.7 Calculating Rate Constants          

7.8 Considering Multiple Reaction Coordinates           

Summary and Outlook 

Chapter 8: Experiments Related to Thermodynamics and Kinetics

Intent and Purpose

8.1 Isotope Effects           

8.2 Substituent Effects

8.3 Hammett Plots, The Most Common LFER. A General Method for Examining Changes in Charges During a Reaction

8.4 Other Linear Free Energy Relationships           

8.5 Acid/Base Related Effects / Brønsted Relationships           

8.6 Why do Linear Free Energy Relationships Work?          

8.7 Summary of Linear Free Energy Relationships

8.8 Miscellaneous Experiments for Studying Mechanisms          

Chapter 9: Catalysis

Intent and Purpose

9.1 General Principles of Catalysis           

9.2 Forms of Catalysis                     

9.3 Brønsted Acid/Base Catalysis          

9.4 Enzymatic Catalysis           

Chapter 10: Organic Reaction Mechanisms Part 1: Reactions Involving Additions and/or Eliminations

Intent and Purpose

10.1 Predicting Organic Reactivity           

10.2 Hydration of Carbonyl Structures

10.3 Electrophilic Addition of Water to Alkenes and Alkynes: Hydration

10.4 Electrophilic Addition of Hydrogen Halides to Alkenes and Alkynes           

10.5 Electrophilic Addition of Halogens to Alkenes           

10.6 Hydroboration

10.7 Epoxidation           

10.8 Nucleophilic Additions to Carbonyl Compounds

10.9 Nucleophilic Additions to Olefins

10.10 Radical Additions to Unsaturated Systems          

10.11 Carbene Additions and Insertions          

10.12 Eliminations to Form Carbonyls or “Carbonyl-Like” Intermediates

10.13 Elimination Reactions for Aliphatic Systems, Formation of Alkenes           

10.14 Eliminations from Radical Intermediates

10.15 Addition of Nitrogen Nucleophiles To Carbonyl Structures, Followed by Elimination

10.16 Addition of Carbon Nucleophiles, Followed by Elimination – The Wittig Reaction          

10.17 Acyl Transfers            

10.18 Electrophilic Aromatic Substitution               

10.19 Nucleophilic Aromatic Substitution

10.20 Reactions Involving Benzyne

10.21 The SRN1 Reaction on Aromatic Rings

10.22 Radical Aromatic Substitutions 

Chapter 11: Organic Reaction Mechanisms Part II: Substitutions at Aliphatic Centers and Thermal Isomerizations/Rearrangements

Intent and Purpose

11.1 Tautomerization           

11.2 a-Halogenation

11.3 a-Alkylations           

11.4 The Aldol Reaction           

11.5 Nucleophilic Aliphatic Substitution Reactions         

11.6 Substitution – Radical - Nucleophilic   
11.7 Radical Aliphatic Substitutions

11.8 Migrations to Electrophilic Carbon

11.9 Migrations to Electrophilic Heteroatoms

11.10 The Favorskii Rearrangement and Other Carbanion Rearrangements            

11.11 Rearrangements Involving Radicals            

11.12 Rearrangements and Isomerizations Involving Biradicals            

Chapter 12: Organotransition Metal Reaction Mechanisms and Catalysis

Intent and Purpose:

12.1 The Basics of Organometallic Complexes

12.2 Common Organometallic Reactions

12.3 Combining the Individual Reactions into Overall Transformations and Cycles           

Chapter 13. Organic Polymer and Materials Chemistry

Intent and Purpose

13.1 Structural Issues in Materials Chemistry          

13.2 Common Polymerization Mechanisms           

Chapter 14.  Advanced Concepts in Electronic Structure Theory

Intent and Purpose

14.1 Introductory Quantum Mechanics          

14.2 Calculational Methods - Solving the Schrödinger Equation for Complex Systems           

14.3  A Brief Overview of the Implementation and Results of HMOT          

14.4  Perturbation Theory - Orbital Mixing Rules          

14.5 Some Topics in Organic Chemistry for Which Molecular Orbital Theory Lends Important Insights          

14.6 Organometallic Complexes             

Chapter 15: Thermal Pericyclic Reactions

Intent and Purpose

15.1 Background

15.2 A Detailed Analysis of Two Simple Cycloadditions           

15.3. Cycloadditions

15.4 Electrocyclic Reactions           

15.5  Sigmatropic Rearrangements           

15.6 Chelotropic Reactions

15.7 In Summary, Applying the Rules

Summary and Outlook 

Chapter 16: Photochemistry

Intent and Purpose

16.1 Photophysical Processes – the Jablonski Diagram           

16.2 Bimolecular Photophysical Processes          

16.3 Photochemical Reactions           

16.4 Chemiluminescence           

16.5 Singlet Oxygen 

Chapter 17:  Electronic Organic Materials

Intent and Purpose

17.1  Theory

17.2 Conducting Polymers

17.3 Organic Magnetic Materials

17.4 Superconductivity

17.5 Nonlinear Optics (NLO)

17.6 Photoresists           

17.7 Summary