Organic Chemistry; Principles, Reactions and Mechanisms
Organic Chemistry; Principles, Reactions and Mechanisms

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.

                        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: SN

  • 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