Modern Physical Organic Chemistry

Citation

Anslyn, E. V., & Dougherty, D. A. (2006). Modern Physical Organic Chemistry. University Science Books.

Chapter Summary

The book runs to about 1,100 pages in seventeen chapters, arranged in three parts: molecular structure and thermodynamics, reactivity, kinetics and mechanisms, and electronic structure with its applications. Six appendixes follow the main text: conversion factors and other useful data; electrostatic potential surfaces for representative organic molecules; group orbitals of common functional groups; the organic structures of biology; electron pushing; and reaction-to-mechanism nomenclature. Chapters close with a "Summary and Outlook" section, further reading and exercises, and the contents list short titled topics within chapters that tie the theory to specific examples.

Part 1: Molecular Structure and Thermodynamics (Chapters 1–6)

• Chapter 1: Introduction to Structure and Models of Bonding. The starting point for the book's picture of bonding, from which later chapters draw their language.
• Chapter 2: Strain and Stability. How strain and relative stability are understood and compared.
• Chapter 3: Solutions and Non-Covalent Binding Forces. The effect of solvent on equilibria and the forces that hold molecules together without covalent bonds.
• Chapter 4: Molecular Recognition and Supramolecular Chemistry. Applies non-covalent forces to host–guest binding and related systems; the contents list drug–receptor cooperativity, salt bridges and calixarenes among its topics.
• Chapter 5: Acid-Base Chemistry. Acidity and basicity as a framework for reactivity.
• Chapter 6: Stereochemistry. The three-dimensional structure of molecules and its consequences.

Part 2: Reactivity, Kinetics, and Mechanisms (Chapters 7–13)

• Chapter 7: Energy Surfaces and Kinetic Analyses. The language of reaction coordinates and the kinetic treatment of reactions, which the rest of this part uses.
• Chapter 8: Experiments Related to Thermodynamics and Kinetics. The experimental toolkit for establishing mechanisms; the contents list topics on kinetic isotope effects and on experiments that trap or probe a proposed intermediate.
• Chapter 9: Catalysis. General acid-base catalysis, organocatalysis and enzyme-related examples such as the catalytic triad.
• Chapters 10–11: Organic Reaction Mechanisms, Part 1 (Reactions Involving Additions and/or Eliminations); Part 2 (Substitutions at Aliphatic Centers and Thermal Isomerizations/Rearrangements). The core catalogue of organic mechanisms, organised by reaction type, with eliminations, aliphatic substitutions, carbocation rearrangements and isomerizations among the listed topics.
• Chapter 12: Organotransition Metal Reaction Mechanisms and Catalysis. Mechanisms in organometallic chemistry, including C–H activation as a listed topic.
• Chapter 13: Organic Polymer and Materials Chemistry. Organic polymers and materials, with dendrimers, self-assembled monolayers and living polymerisation among the listed topics.

Part 3: Electronic Structure: Theory and Applications (Chapters 14–17)

• Chapter 14: Advanced Concepts in Electronic Structure Theory. A fuller treatment of electronic structure than the bonding models of Chapter 1.
• Chapter 15: Thermal Pericyclic Reactions. Concerted reactions analysed through orbital theory; cycloadditions and electrocyclisations appear in the contents.
• Chapter 16: Photochemistry. Excited-state behaviour and photochemical reactions.
• Chapter 17: Electronic Organic Materials. Organic materials whose function depends on electronic structure.

Key Concepts

Part 1

• Models of bonding and strain: the frameworks used to describe structure and judge stability.
• Non-covalent binding forces and solvation: the interactions that control equilibria in solution.
• Molecular recognition: selective binding between molecules, as in host–guest and drug–receptor systems.
• Stereochemistry: the consequences of three-dimensional structure.

Part 2

• Energy surfaces and kinetic analysis: describing reactions in terms of potential energy and rate.
• Isotope effects and mechanistic experiments: ways of testing proposed mechanisms.
• Catalysis: how acids, bases, organocatalysts and enzymes change reaction pathways.
• Reaction mechanism types: additions, eliminations, substitutions, rearrangements and organometallic steps.

Part 3

• Electronic structure theory: orbital-based and computational descriptions of molecules.
• Pericyclic reactions: thermal concerted reactions.
• Photochemistry and electronic materials: excited states and electronically functional organic compounds.

Critical Analysis

Strengths

• A mechanism-centred sequence. Thermodynamic ideas (bonding, strain, solvation, binding) come first, kinetic and experimental tools second, and the catalogue of mechanisms third, so the later chapters rest on earlier ones.
• Reach beyond classical physical organic chemistry. Molecular recognition, polymers and materials, organometallic mechanisms and electronic organic materials each have their own chapter, and the contents list biological examples such as the catalytic triad and protein disulfide linkages.
• Study support. Each chapter ends with a "Summary and Outlook" and further reading, and exercises are placed throughout. The appendixes include a refresher on electron pushing and a guide to the organic structures of biology.

Limitations

• Demanding prerequisites. The book builds on a full undergraduate organic sequence and on thermodynamics and kinetics from physical chemistry; students without both will find Part 2 and Part 3 hard going.
• Size. At about 1,100 pages and seventeen chapters it is more than a single course can cover, so instructors and readers must choose, for example by omitting the materials-oriented chapters.
• Breadth over a single thread. Chapters range from solution thermodynamics to polymer science and electronic materials, so readers who want only reaction mechanisms will use a subset of the book.

Where It Fits in the Course

Within the organic chemistry course this is the graduate text on the physical principles behind mechanisms. It comes after a full introductory sequence such as McMurry's Organic Chemistry (a freely accessible text for the usual two-course sequence) or Clayden, Greeves and Warren's Organic Chemistry (organised around reaction mechanisms), which supply the reactions it assumes. Klein's Organic Chemistry as a Second Language and Patrick's Organic Chemistry: A Very Short Introduction are companion and overview books for earlier stages.

The closest comparison is Carey et al.'s Advanced Organic Chemistry: Part A, Structure and Mechanisms, a comprehensive graduate treatment of structure, bonding and mechanisms. The two cover overlapping ground; Anslyn and Dougherty's contents list dedicated chapters on molecular recognition, polymers, electronic structure and organic materials, and a reader may use one as the main text and the other as a second perspective.

How to Use This Book

The book is meant for graduate students, and for advanced undergraduates with strong organic and physical chemistry, who need to reason about why reactions behave as they do. A full year of undergraduate organic chemistry and some thermodynamics and kinetics should be in place before starting.

A practical plan:

• Core for a mechanism-oriented course: Chapters 1–3 and 5–6 for structure and energetics, Chapters 7–8 for kinetics and experiments, and Chapters 10–11 for the mechanism catalogue.
• Add as needed: Chapter 4 for supramolecular chemistry, Chapter 9 for catalysis, Chapter 12 for organometallic mechanisms, Chapter 13 for polymers and materials.
• Electronic-structure sequence: Chapters 14–16 read well together for orbital theory, pericyclic reactions and photochemistry, with Chapter 17 as a materials application.
• Work the exercises and read the further reading at the end of each chapter; use the appendix on electron pushing for review where needed.