

Organic Chemistry; Principles, Reactions and Mechanisms
Lead Author(s): Dr. Guy Plourde
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The content describes in details organic chemistry principles, reactions and mechanisms, targeted to second year university students in organic chemistry.
Content Index
Table of Contents
Chapter 1: Basic Concepts and Review
Section 1.1 Atomic Orbitals and Electronic Configuration
- 1.1.1 The Atom
- 1.1.2 Atomic Orbitals and Electron Configuration
Section 1.2 Chemical Bonding
- 1.2.1 Ionic Bonds
- 1.2.2 Covalent Bonds
- 1.2.3 Lewis Structures
- 1.2.4 Formal Charges
Section 1.3 Resonance
- 1.3.1 Definition of Resonance
- 1.3.2 Rules for Drawing Resonance Structures
- 1.3.3 Major versus Minor Resonance Contributors
Section 1.4 Drawing Organic Structures
- 1.4.1 Bonding Patterns in Organic Molecules
- 1.4.2 Line-Angle Convention
- 1.4.3 Unsaturation Index
Section 1.5 Non-covalent Interactions in Organic Molecules
- 1.5.1 Dipoles
- 1.5.2 Intermolecular Forces
Section 1.6 Solubility, Melting and Boiling Points
- 1.6.1 Solubility
- 1.6.2 Melting and Boiling Points
Section 1.7 Acid and Bases: Basic Concepts
- 1.7.1 BrØnsted-Lowry Definition of Acidity
- 1.7.2 Lewis Definition of Acidity
- 1.7.3 Ka and pKa
Section 1.8 End-of-Chapter Exercises
Chapter 2: Structures and Properties of Organic Molecules
Section 2.1 Functional Groups and Organic Nomenclature
- 2.1.1 Common Functional Groups of Organic Compounds
- 2.1.2 Naming Organic Compounds
- 2.1.3 Structural Isomerism
- 2.1.4 Abbreviated Organic Structures
Section 2.2 Valence Bond Theory
- 2.2.1 Formation of Sigma (σ) Bonds
- 2.2.2 sp3 Hybridization: Tetrahedral Geometry
- 2.2.3 sp2 and sp Hybridizations: Trigonal Planar and Linear Geometries
Section 2.3 Molecular Orbital Theory
- 2.3.1 Bonding and AntiBonding Molecular Orbitals
- 2.3.2 π Bonds and the Molecular Orbital Theory
Section 2.4 End-of-Chapter Exercises
Chapter 3: Reactivity, Structure and Conformations of
Alkanes
Section 3.1 Reactivity of Alkanes
Section 3.2 Conformations of Acyclic Alkanes
- 3.2.1 Conformations of Ethane and Newman Projections
- 3.2.2 Conformations of Propane and Butane
Section 3.3 Structure and Conformations of Cyclic Alkanes
- 3.3.1 Structure and Stability of Cycloalkanes
- 3.3.2 Stereochemistry of Cycloalkanes
- 3.3.3 Conformations of Cyclohexane
- 3.3.4 Conformations of Monosubstituted Cyclohexanes
- 3.3.5 Conformations of Disubstituted Cyclohexanes
Section 3.4 End-of-Chapter Exercises
Chapter 4: Stereochemistry of Organic Molecules
Section 4.1 Chirality and Enantiomers
- 4.1.1 Chirality
- 4.1.2 Molecular Chirality
- 4.1.3 Nomenclature: Cahn-Ingold-Prelog Notation
Section 4.2 Optical Activity: A Physical Property of Chiral Molecules
- 4.2.1 Optical Activity
- 4.2.2 Enantiomeric Excess
Section 4.3 Diastereomers
- 4.3.1 Fischer Projections
- 4.3.2 Diastereomers
- 4.3.3 Meso Compounds
Section 4.4 End-of-Chapter Exercises
Chapter 5: Structure Determination
Infrared Spectroscopy and Mass Spectrometry
Section 5.1 Infrared Spectroscopy
- 5.1.1 Spectroscopy: General Concepts
- 5.1.2 Infrared Spectroscopy: Basic Principles
- 5.1.3 The Infrared Spectrum
- 5.1.4 Functional Groups and Stretching Frequencies
- 5.1.5 Ring Size and Conjugation Effects
Section 5.2 Introduction to Mass Spectrometry
- 5.2.1 Overview of Mass Spectrometry
- 5.2.2 The Mass Spectrum
Section 5.3 End-of-Chapter Exercises
Chapter 6: Structure Determination
Nuclear Magnetic Resonance (NMR) Spectroscopy
Section 6.1 General NMR Principles
- 6.1.1 The Magnetic Moment
- 6.1.2 Spin States and the Magnetic Transition
- 6.1.3 Chemical Equivalence
Section 6.2 The 1H-NMR Spectrum
- 6.2.1 The NMR Experiment
- 6.2.2 Chemical Shifts
- 6.2.3 Shielding and Deshielding
- 6.2.4 Magnetic Anisotropy
- 6.2.5 Effect of Hydrogen Bonding: Exchangeable Protons
Section 6.3 Spin-Spin Coupling
- 6.3.1 The Basic Principles of Spin-Spin Coupling
- 6.3.2 Pascal’s Triangle
- 6.3.3 The Coupling Constant
- 6.3.4 Long Range Coupling
- 6.3.5 Complex Coupling
- 6.3.6 Structure Determination
Section 6.4 Introduction to 13C-NMR Spectroscopy
- 6.4.1 The Basic Principles of 13C-NMR Spectroscopy
- 6.4.2 Interpreting 13C-NMR and DEPT-135 NMR Spectra
Section 6.5 End-of-Chapter Exercises
Chapter 7: Organic Chemical Reactions
Section 7.1 Definitions
- 7.1.1 Types of Organic Reactions
- 7.1.2 Mechanisms
- 7.1.3 Kinetics versus Thermodynamics
- 7.1.4 Nucleophiles and Electrophiles
- 7.1.5 Reactive Intermediates
Section 7.2 Organic Reactions: Introduction to Mechanisms
- 7.2.1 Homolytic versus Heterolytic Bond Cleavage
- 7.2.2 Overview of Organic Reactions: Energy Diagrams
- 7.2.3 Halogenation of Alkanes: A Radical Reaction
- 7.2.4 Polar Reactions and Mechanisms
Section 7.3 End-of-Chapter Exercises
Chapter 8: Haloalkanes
Nucleophilic Substitutions and Eliminations
Section 8.1 Introduction to Alkyl Halides
- 8.1.1 Nomenclature
- 8.1.2 Structure of Alkyl Halides
- 8.1.3 Physical Properties of Alkyl Halides
- 8.1.4 Synthesis of Alkyl Halides
Section 8.2 Bimolecular Nucleophilic Substitution: SN2
- 8.2.1 Reactions of Alkyl Halides
- 8.2.2 Bimolecular Nucleophilic Substitution (SN2)
- 8.2.3 Factors Influencing the SN2 Reaction
- 8.2.4 Stereochemistry of the SN2 Reaction
Section 8.3 Unimolecular Nucleophilic Substitution: SN1
- 8.3.1 Unimolecular Nucleophilic Substitution (SN1)
- 8.3.2 Examples of SN1 Reactions
- 8.3.3 Carbocation Rearrangement in SN1 Reactions
- 8.3.4 Comparing SN1 and SN2 Reactions
Section 8.4 Unimolecular Elimination: E1
- 8.4.1 Competition with the SN1 Reaction
- 8.4.2 Stability of Alkenes: The Zaitsev's Rule
Section 8.5 Bimolecular Elimination: E2
- 8.5.1 Competition with the SN2 Reaction
- 8.5.2 Stereochemistry of the E2 Reaction
- 8.5.3 Comparing E1 and E2 Eliminations
- 8.5.4 Competition Between Substitutions and Eliminations
Section 8.6 End-of-Chapter Exercises
Chapter 9: Structure, Syntheses and Reactions of Alkenes
Section 9.1 Introduction to Alkenes
- 9.1.1 Nomenclature of Alkenes
- 9.1.2 Structure of Alkenes
- 9.1.3 Nomenclature of Alkene Stereoisomers
- 9.1.4 Stability of Alkenes
- 9.1.5 Physical Properties of Alkenes
Section 9.2 Syntheses of Alkenes
- 9.2.1 Dehydrohalogenation
- 9.2.2 Dehydrohalogenation of Cyclohexyl Halides
- 9.2.3 Debromination
- 9.2.4 Dehydration of Alcohols
Section 9.3 Reactions of Alkenes
- 9.3.1 Hydrohalogenation: The “Markovnikov Rule”
- 9.3.2 Free-Radical Addition of HBr: “Anti-Markovnikov” Addition
- 9.3.3 Direct Hydration of Alkenes
- 9.3.4 Oxymercuration-Reduction: Indirect Hydration of Alkenes
- 9.3.5 Alkoxymercuration-Reduction: Formation of Ethers from Alkenes
- 9.3.6 Hydroboration-Oxidation of Alkenes: Indirect Hydration of Alkenes
- 9.3.7 Halogenation of Alkenes
- 9.3.8 Halohydrin Formation
- 9.3.9 Catalytic Hydrogenation
- 9.3.10 Addition of Carbenes
- 9.3.11 Epoxidation
- 9.3.12 Hydroxylation
- 9.3.13 Oxidative Cleavage
- 9.3.14 Ozonolysis
Section 9.4 End-of-Chapter Exercises
Chapter 10: Structure, Syntheses and Reactions of Alkynes
Section 10.1 Introduction to Alkynes
- 10.1.1 Nomenclature
- 10.1.2 Structure of Alkynes
- 10.1.3 Physical Properties
Section 10.2 Syntheses of Alkynes
- 10.2.1 Substitution of the Acetylide Anion
- 10.2.2 Dehydrohalogenation
Section 10.3 Reactions of Alkynes
- 10.3.1 Hydrogenation of Alkynes to Alkanes
- 10.3.2 Hydrogenation of Alkynes to cis-Alkenes
- 10.3.3 Reduction of Alkynes to trans-Alkenes
- 10.3.4 Halogenation of Alkynes
- 10.3.5 Addition of Hydrohalic Acids (HX)
- 10.3.6 Keto-Enol Tautomerism
- 10.3.7 Markovnikov Hydration of Alkynes: Synthesis of Ketones
- 10.3.8 Anti-Markovnikov Hydration of Alkynes: Synthesis of Aldehydes and Ketones
- 10.3.9 Oxidation of Alkynes
Section 10.4 End-of-Chapter Exercises
Chapter 11: Conjugated π Systems and UV-Vis Spectroscopy
Section 11.1 Structure and Stability of π Systems
- 11.1.1 Stability of Dienes
- 11.1.2 Conformations of Dienes
Section 11.2 Reactions of Conjugated π Systems
- 11.2.1 Electrocyclic Reactions
- 11.2.2 Conrotatory versus Disrotatory Cyclization
- 11.2.3 Frontier Molecular Orbitals
- 11.2.4 The Diels-Alder Reaction
Section 11.3 UV-Vis Absorption Spectroscopy
- 11.3.1 Ultraviolet Spectral Region
- 11.3.2 Electronic Transitions
- 11.3.3 The UV Spectrum
Section 11.4 End-of-Chapter Exercises
Chapter 12: Structure, Syntheses and Reactions of Aromatic
Compounds
Section 12.1 Introduction to Aromatic compounds
- 12.1.1 Benzene
- 12.1.2 Molecular Orbitals of Benzene
- 12.1.3 Aromaticity and Hückel’s Rule
- 12.1.4 Aromatic Ions
- 12.1.5 Heteroaromatic Compounds
- 12.1.6 Nomenclature of Benzene Derivatives
Section 12.2 Reactions of Benzene
- 12.2.1 Electrophilic Aromatic Substitution: General Concepts
- 12.2.2 Halogenation of Benzene
- 12.2.3 Nitration of Benzene
- 12.2.4 Reduction of the Nitro Group
- 12.2.5 Sulfonation of Benzene
- 12.2.6 Friedel-Crafts Alkylation of Benzene
- 12.2.7 Friedel-Crafts Acylation of Benzene
- 12.2.8 The Clemmensen Reduction
Section 12.3 Reactions of Substituted Benzene Derivatives
- 12.3.1 Activators versus Deactivators
- 12.3.2 Effect of Activators
- 12.3.3 Effect of Deactivators
- 12.3.4 Halogens: The Exception to the Rule
- 12.3.5 Activators and Deactivators in Friedel-Crafts Reactions
- 12.3.6 Effect of Multiple Substituents
Section 12.4 Other Reactions of Aromatic Compounds
- 12.4.1 Aromatic Substitution by Coupling Reactions
- 12.4.2 Nucleophilic Aromatic Substitution
- 12.4.3 Addition Reactions of Aromatic Compounds
- 12.4.4 Side-Chain Reactions of Aromatic Compounds
Section 12.5 End-of-Chapter Exercises
Chapter 13: Structure, Syntheses and Reactions of Alcohols
Section 13.1 Introduction to Alcohols
- 13.1.1 Structure of Alcohols
- 13.1.2 Properties of Alcohols
- 13.1.3 Acidity of Alcohols
Section 13.2 Syntheses of Alcohols
- 13.2.1 Synthesis of Alcohols: A Review
- 13.2.2 Reduction of Carbonyl Compounds with Metal Hydrides
- 13.2.3 Reduction of Carbonyl Compounds by Hydrogenation
- 13.2.4 Addition of Carbanions to Carbonyl Compounds
- 13.2.5 Addition of Carbanions to Epoxides
- 13.2.6 Limitations of the Grignard and Alkyllithium Reagents
Section 13.3 Reactions of Alcohols
- 13.3.1 Oxidation States of Carbon in Oxygenated Organic Compounds
- 13.3.2 Oxidation of Alcohols
- 13.3.3 Reduction of Alcohols
- 13.3.4 Substitution of Alcohols with Hydrohalic Acids
- 13.3.5 Substitution of Alcohols with Phosphorus Trihalides
- 13.3.6 Substitution of Alcohols with Thionyl Chloride
- 13.3.7 Dehydration of Alcohols
- 13.3.8 Dehydration of Vicinal Diols: The Pinacol Rearrangement
- 13.3.9 Esterification of Alcohols
- 13.3.10 Alcohols in the Williamson Ether Synthesis
Section 13.4 End-of-Chapter Exercises
Chapter 14: Structure, Syntheses and Reactions of Ethers
and Epoxides
Section 14.1 Introduction to Ethers
- 14.1.1 Structure of Ethers
- 14.1.2 Physical Properties of Ethers
Section 14.2 Syntheses of Ethers
- 14.2.1 Synthesis of Ethers: A Review
- 14.2.2 Synthesis of Cyclic Ethers
Section 14.3 Reactions of Ethers
- 14.3.1 Acid Cleavage of Ethers
Section 14.4 Epoxides: A Special Class of Ethers
- 14.4.1 Syntheses of Epoxides
- 14.4.2 Reaction of Epoxides
- 14.4.3 Base-Catalyzed Ring-Opening
- 14.4.4 Acid-Catalyzed Ring-Opening
Section 14.5 End-of-Chapter Exercises
Chapter 15: Structure, Syntheses and Reactions of
Carboxylic Acids
Section 15.1 Introduction to Carboxylic Acids
- 15.1.1 Structure of the Carboxyl Group
- 15.1.2 Physical Properties of Carboxylic Acids
- 15.1.3 Acidity of Carboxylic Acids
Section 15.2 Syntheses of Carboxylic Acids
- 15.2.1 Synthesis of Carboxylic Acids: A Review
- 15.2.2 Addition of Grignard Reagents to Carbon Dioxide
- 15.2.3 Hydrolysis of Nitriles
Section 15.3 Reactions of Carboxylic Acids
- 15.3.1 Reactions of Carboxylic Acids: A Review
- 15.3.2 Esterification with Diazomethane
- 15.3.3 Alkylation of Carboxylic Acids: Synthesis of Ketones
- 15.3.4 Condensation of Carboxylic Acids with Amines
- 15.3.5 Nucleophilic Acyl Substitutions
- 15.3.6 Synthesis of Acid Chlorides
Section 15.4 End-of-Chapter Exercises
Chapter 16: Structure, Syntheses and Reactions of
Carboxylic Acid Derivatives
Section 16.1 Introduction to Carboxylic Acid Derivatives
- 16.1.1 Structure of Carboxylic Acid Derivatives
- 16.1.2 Physical Properties of Carboxylic Acid Derivatives
Section 16.2 Syntheses of Carboxylic Acid Derivatives
- 16.2.1 Synthesis of Carboxylic Acid Derivatives: A Review
- 16.2.2 Interconversion of Carboxylic Acid Derivatives
- 16.2.3 Conversion of Acid Chlorides to Other Carboxylic Acid Derivatives
- 16.2.4 Conversion of Acid Anhydrides to Other Carboxylic Acid Derivatives
- 16.2.5 Transesterification
- 16.2.6 Ammonolysis
Section 16.3 Reactions of Carboxylic Acid Derivatives
- 16.3.1 Reactions of Carboxylic Acid Derivatives: A Review
- 16.3.2 Hydrolysis of Carboxylic Acid Derivatives
- 16.3.3 Reduction of Acid Chlorides: Synthesis of Aldehydes
- 16.3.4 Reduction of Amides: Synthesis of Amines
- 16.3.5 Reduction of Nitriles: Synthesis of Amines and Aldehydes
- 16.3.6 Reduction of Esters with DIBAL-H
- 16.3.7 Nucleophilic Addition of Grignard Reagents to Nitriles
Section 16.4 End-of-Chapter Exercises
Chapter 17: Structure, Syntheses and Reactions of
Aldehydes and Ketones
Section 17.1 Introduction to Aldehydes and Ketones
- 17.1.1 Structure of Aldehydes and Ketones
- 17.1.2 Physical Properties of Aldehydes and Ketones
Section 17.2 Syntheses of Aldehydes and Ketones
- 17.2.1 Synthesis of Aldehydes and Ketones: A Review
- 17.2.2 Nucleophilic Addition of Cuprate Reagents to Acid Chlorides
- 17.2.3 Synthesis of Aldehydes and Ketones from 1,3-Dithiane
Section 17.3 Reactions of Aldehydes and Ketones
- 17.3.1 Reactions of Aldehydes and Ketones: A Review
- 17.3.2 Nucleophilic Additions: General Concepts
- 17.3.3 Nucleophilic Addition of Cyanide Ion: Synthesis of Cyanohydrins
- 17.3.4 The Wittig Reaction: Synthesis of Alkenes
- 17.3.5 The Corey-Chaykovsky Reaction: Synthesis of Epoxides
- 17.3.6 Hydration of Aldehydes and Ketones
- 17.3.7 Addition of Alcohols: Synthesis of Acetals
- 17.3.8 Acetals as Protective Group in Organic Synthesis
- 17.3.9 Synthesis of Imines and Enamines
- 17.3.10 Condensation of Hydroxylamine and Hydrazine
- 17.3.11 The Wolff-Kishner Reduction
- 17.3.12 Oxidation of Ketones: The Baeyer-Villiger Oxidation
Section 17.4 End-of-Chapter Exercises
Chapter 18: Carbonyl α-Substitution and
Condensation Reactions
Section 18.1 Enolization of Carbonyls
- 18.1.1 Keto-Enol Tautomerism
- 18.1.2 Enolization of Carbonyls
- 18.1.3 Formation of Enolate Anions
- 18.1.4 Enolization of Unsymmetrical Carbonyls
Section 18.2 α-Substitution Reactions
- 18.2.1 Alkylation of the Enolate Anion
- 18.2.2 Alkylation and Acylation of Enamines
- 18.2.3 α-Halogenation of Ketones
- 18.2.4 α-Bromination of Carboxylic Acids: The Hell-Volhard-Zelinsky Reaction
- 18.2.5 Acetoacetic Ester Synthesis
- 18.2.6 Malonic Ester Synthesis
Section 18.3 Condensation Reactions
- 18.3.1 Aldol Condensation
- 18.3.2 Mixed-Aldol Condensation
- 18.3.3 Aldol Cyclization
- 18.3.4 Claisen Condensation
- 18.3.5 Dieckman Condensation
- 18.3.6 Conjugate Addition
- 18.3.7 The Michael Addition
- 18.3.8 The Robinson Annulation
Section 18.4 End-of-Chapter Exercises
Chapter 19: Structure, Syntheses and Reactions of Amines
Section 19.1 Introduction to Amines
- 19.1.1 Structure and Chirality of Amines
- 19.1.2 Physical Properties of Amines
- 19.1.3 Basicity of Amines
Section 19.2 Syntheses of Amines
- 19.2.1 Synthesis of Amines: A Review
- 19.2.2 Reduction of the Nitro Functional Group
- 19.2.3 Nucleophilic Substitution with Alkyl Halides
- 19.2.4 Nucleophilic Substitution/Reduction of the Azide Anion
- 19.2.5 Reductive Amination 19.2.6 The Gabriel Synthesis
- 19.2.7 The Hofmann Rearrangement
- 19.2.8 The Curtius Rearrangement
Section 19.3 Reactions of Amines
- 19.3.1 Reactions of Amines: A Review
- 19.3.2 Hofmann Elimination: Synthesis of Alkenes
- 19.3.3 Cope Elimination: Synthesis of Alkenes
Section 19.4 End-of-Chapter Exercises