Atomic  Structure-orbitals, Bonding, Octet Rule, Lewis Structures, Formal Charge, Electronegativity, Electron/Charge Density, Bond Polarity
Resonance, Formulas, Molecular Structure, 2-d & 3-d Structural Formulas:
Lewis or Dash, Condensed, Bond-Line or Line-Angle, 3-d
 
Organic Acids and Bases, their Chemistry & Reactivity, Equilibrium

Molecular Orbitals, Hydridization, Molecular Shape, Dipole moment

Bond rotation, Isomerism: constitutional (structural), vicinal, geminal, stereochemical

Structure Drawing (jme/Marvin/ISIS Draw)

Molecular Modeling,Viewing (Jmol/Chime/RasMol)

Hydrocarbons, Unsaturation, Hetero atoms, Organic Functionality (Carbon Skeleton & Molecular Differentiation)

Alkanes, Alkenes, Alkynes, Aromatics (Arenes)

Halocarbons (Haloalkanes), Alcohols, Ethers, Amines

Aldehydes, Ketones, Carboxylic Acids, Esters, Amides

Physical Properties / Molecular Structure / Intermolecular Forces

Hydrogen Bonding

Melting point, Boliing Point, Solubility

 

Alkanes and Cycloalkanes

Nomenclature

Conformational Analysis: cyclic and acyclic

Cyclohexane,Substituted rings, cis- trans- ring isomerism

Ring size, Strain, Stability

Bicyclic and Polycyclic ring systems

Synthesis and Reactions

 

Kinetics:
Free Energy, Enthalpy, Entropy, Activation energy, Transition state
Reaction Mechanisms:
Ionic :

Carbocations
Carbanions
Other (Acid / Base)

Free Radical
Carbenes
Concerted
llustrating Reactions & Reaction Mechanisms

Generic Types of Reactions:

Substitution, Addition, Elimination, Rearrangement, Oxidation, Reduction

Stereochemistry, Chirality, Symmetry

Optical Activity, Relative & Absolute Configuration

Enantiomers, R- and S-, carvone, analgesics, Multiple Stereocenters I, Multiple Stereocenters II,Diastereomers

Enzymes & specificity, Stereoisomerism in Cyclic Systems

Synthesis & Resolution, Resolving Racemates,Stereospecific Synthesis

Fischer Projection Formulas I, Fischer Projection Formulas II  

 

Nucleophilic Substitution

Nucleophiles and Leaving Groups

Thermodynamics and Kinetics of Organic Reactions

Sn1 and Sn2 Mechanisms and kinetic factors

Stereochemistry
Regiochemistry
Steric effects
Nucleophile
Electrophile

Transition States and Free Energy Reaction Diagrams/ Pathways

Carbocations

Elimination vs. Substitution

Synthetic Applications: Novel Antibiotic for Staph Resistance

Alkenes

Nomenclature

Physical Properties, Synthesis

Unsaturation, Hydrogenation / Hydrogen Deficiency

Stabilities, Preparation

 

Alkenes: Reactions

Reaction Outline

Carbocations / Rearrangement / Free Radicals
Addition Reactions: HX, -X -OH, Bromine, Chlorine

Oxymercuration, Hydroboration

Stereochemistry


Markovnikov's Rule

Oxidations, Reduction, Polymerization

Alkynes

Nomenclature, Physical Properties

Acidity,Synthesis, Reactions, Acetylides

Alcohols ,  Phenols, Structure

Nomenclature, Physical Properties, Acidity

Alcohol Synthesis:

Grignard Reaction and Other Organometallic Reactions

Reductions

Reactions of Alcohols / Acidity

Alcohols ,Oxidation

Various  Other Reactions

Ethers, Sulfides & Epoxides

Synthesis: Williamson Ether Synthesis

Reactions of Ethers & Epoxides

Special Topics: Resolution of Racemates
Chromatography

 

 

CHAPTER 1
1.1: Introduction to Organic Chemistry
1.2: The Structural Theory of Matter
1.3: Electrons, Bonds, and Lewis Structures
1.4: Identifying Formal Charges
1.5: Induction and Polar Covalent Bonds
1.6: Atomic Orbitals
1.7: Valence Bond Theory
1.8: Molecular Orbital Theory
1.9: Hybridized Atomic Orbitals
1.10: VSEPR Theory: Predicting Geometry
1.11: Dipole Moments and Molecular Polarity
1.12: Intermolecular Forces and Physical Properties
1.13: Solubility

CHAPTER 2
2.1: Molecular Representations
2.2: Bond-Line Structures
2.3: Identifying Functional Groups
2.4: Carbon Atoms with Formal Charges
2.5: Identifying Lone Pairs
2.6: Three-Dimensional Bond-Line Structures
2.7: Introduction to Resonance
2.8: Curved Arrows
2.9: Formal Charges in Resonance Structures
2.10: Drawing Resonance Structures via Pattern Recognition
2.11: Assessing Relative Importance of Resonance Structures
2.12: Delocalized and Localized Lone Pairs

CHAPTER 3
3.1: An Introduction to BrØnsted-Lowry Acids and Bases
3.2: Flow of Electron Density: Curved Arrow Notation
3.3: BrØnsted-Lowry Acidity: A Quantitative Perspective
3.4: BrØnsted-Lowry Acidity: Qualitative Perspective
3.5: Position of Equilibrium and Choice of Reagents
3.6: Choice of Solvent
3.7: Solvating Effects
3.8: Counterions
3.9: Lewis Acids and Bases

CHAPTER 4
4.1: Introduction to Alkanes
4.2: Nomenclature of Alkanes
4.3: Constitutional Isomers of Alkanes
4.4: Relative Stability of Isomeric Alkanes
4.5: Sources and Uses of Alkanes
4.6: Drawing Newman Projections
4.7: Conformational Analysis of Ethane and Propane
4.8: Conformational Analysis of Butane
4.9: Cycloalkanes
4.10: Conformations of Cyclohexane
4.11: Drawing Chair Conformations
4.12: Monosbstituted Cyclohexane
4.13: Disubstituted Cyclohexane
4.14: cis-trans Stereoisomerism
4.15: Polycyclic Systems

CHAPTER 5
5.1: Overview of Isomerism
5.2: Introduction to Stereoisomerism
5.3: Designating Configuration Using the Cahn-Ingold-Prelog System
5.4: Optical Activity
5.5: Stereoisomeric Relationships: Enantiomers and Diastereomers
5.6: Symmetry and Chirality
5.7: Fischer Projections
5.8: Conformationally Mobile Systems
5.9: Resolution of Enantiomers

CHAPTER 6
6.1: Enthalpy
6.2: Entropy
6.3: Gibbs Free Energy
6.4: Equilibria
6.5: Kinetics
6.6: Reading Energy Diagrams
6.7: Nucleophiles and Electrophiles
6.8: Mechanisms and Arrow Pushing
6.9: Combining the Patterns of Arrow Pushing
6.10: Drawing Curved Arrows
6.11: Carbocation Rearrangements

CHAPTER 7
7.1: Introduction to Substitution Reactions
7.2: Alkyl Halides
7.3: Possible Mechanisms for Substitution Reactions
7.4: The SN2 Mechanism
7.5: The SN1 Mechanism
7.6: Drawing the Complete Mechanism of an SN1 Reaction
7.7: Drawing the Complete Mechanism of an SN2 Reaction
7.8: Determining Which Mechanism Predominates
7.9: Selecting Reagents to Accomplish Functional Group Transformation

CHAPTER 8
8.1: Introduction to Elimination Reactions
8.2: Alkenes in Nature and in Industry
8.3: Nomenclature of Alkenes
8.4: Stereoisomerism in Alkenes
8.5: Alkene Stability
8.6: Possible Mechanisms for Elimination
8.7: The E2 Mechanism
8.8: Drawing the Products of an E2 Reaction
8.9: The E1 Mechanism
8.10: Drawing the Complete Mechanism of an E1 Process
8.11: Drawing the Complete Mechanism of an E2 Process 372
8.12: Substitution vs. Elimination: Identifying the Reagent
8.13: Substitution vs. Elimination: Identifying the Mechanism(s)
8.14: Substitution vs. Elimination: Predicting the Products

CHAPTER 9
9.1: Introduction to Addition Reactions
9.2: Addition vs. Elimination: A Thermodynamic Perspective
9.3: Hydrohalogenation
9.4: Acid-Catalyzed Hydration
9.5: Oxymercuration-Demercuration
9.6: Hydroboration-Oxidation
9.7: Catalytic Hydrogenation
9.8: Halogenation and Halohydrin Formation
9.9: Anti Dihydroxylation
9.10: Syn Dihydroxylation
9.11: Oxidative Cleavage
9.12: Predicting Products of an Addition Reaction
9.13: Synthesis Strategies

CHAPTER 10
10.1: Introduction to Alkynes
10.2: Nomenclature of Alkynes
10.3: Acidity of Acetylene and Terminal Alkynes
10.4: Preparing Alkynes
10.5: Reduction of Alkynes
10.6: Hydrohalogenation of Alkynes
10.7: Hydration of Alkynes
10.8: Halogenation of Alkynes
10.9: Ozonolysis of Alkynes
10.10: Alkylation of Terminal Alkynes
10.11: Synthesis Strategies

CHAPTER 11
11.1: Radicals
11.2: Common Patterns in Radical Mechanisms
11.3: Chlorination of Methane
11.4: Thermodynamic Considerations for Halogenation Reactions
11.5: Regioselectivity of Halogenation
11.6: Stereochemistry of Halogenation
11.7: Allylic Bromination
11.8: Atmospheric Chemistry and the Ozone Layer
11.9: Autooxidation and Antioxidants
11.10: Addition of HBr: Anti-Markovnikov Addition
11.11: Radical Polymerization
11.12: Radical Processes in the Petrochemical Industry
11.13: Halogenation as a Synthetic Technique

CHAPTER 12
12.1: One-Step Syntheses
12.2: Functional Group Transformations
12.3: Reactions that Change the Carbon Skeleton
12.4: How to Approach a Synthesis Problem
12.5: Retrosynthetic Analysis
12.6: Practical Tips for Increasing Proficiency
12.5: Retrosynthetic Analysis
12.6: Practical Tips for Increasing Proficiency

CHAPTER 13
13.1: Structure and Properties of Alcohols
13.2: Acidity of Alcohols and Phenols
13.3: Preparation of Alcohols via Substitution or Addition
13.4: Preparation of Alcohols via Reduction
13.5: Preparation of Diols
13.6: Preparation of Alcohols via Grignard Reagents
13.7: Protection of Alcohols
13.8: Preparation of Phenols
13.9: Reactions of Alcohols: Substitution and Elimination
13.10: Reactions of Alcohols: Oxidation
13.11: Biological Redox Reactions
13.12: Oxidation of Phenol
13.13: Synthesis Strategies

CHAPTER 14
14.1: Introduction to Ethers
14.2: Nomenclature of Ethers
14.3: Structure and Properties of Ethers
14.4: Crown Ethers
14.5: Preparation of Ethers
14.6: Reactions of Ethers
14.7: Nomenclature of Epoxides
14.8: Preparation of Epoxides
14.9: Enantioselective Epoxidation
14.10: Ring-Opening Reactions of Epoxides
14.11: Thiols and Sulfides
14.12: Synthesis Strategies Involving Epoxides

General Principles
Structure & Bonding
Electron Configurations of Atoms
Chemical Bonding & Valence
Charge Distribution in Molecules
Practice Problems

The Shape of Molecules
Isomers
Analysis of Molecular Formulas
Resonance
Atomic and Molecular Orbitals
Practice Problems

Intermolecular Forces
Boiling & Melting Points
Hydrogen Bonding
Crystalline Solids
Water Solubility
Practice Problems

Chemical Reactivity
Reaction Classification
By Structural Change
By Reaction Type
Acid-Base Reactions
Oxidations & Reductions
By Functional Group
Reaction Variables
Reactants & Reagents
Product Selectivity
Other Variables
Reaction Rate
Intermediates
Reaction Energetics
Bond Energy
Electronic Effects
Steric Effects
Solvent Effects
Reaction Mechanisms
Curved Arrow Notation
Reactive Intermediates
Reaction Illustrations
Nucleophilicity & Basicity
Acid-Base Catalysis
Practice Problems

Aromaticity
Aromatic Systems and Factors Required for Aromaticity
Aromatic ions and Anti-aromaticity
Benzene and Other Aromatic Compounds
Fused Benzene Ring Compounds

Nomenclature
Alkanes
Cycloalkanes
Practice Problems
Alkenes & Alkynes
Substituted Benzenes
Other Functional Groups
Practice Problems

Stereoisomers Part I
Alkene Configurational Isomers
Cycloalkane Configurational Isomers
Practice Problems
Conformational Isomers
Ethane
Butane
Cycloalkanes
Substituted Cyclohexanes
Practice Problems

Stereoisomers Part II
Chirality & Symmetry
Symmetry Elements
Enantiomorphism
Optical Activity
Configurational Nomenclature
Compounds with Several Stereogenic Centers
Stereogenic Nitrogen
Fischer Projection Formulas
Achiral Diastereomers
Other Configurational Notations
Resolution
Conformational Enantiomorphism
Practice Problems

Summary of Isomerism

Other Topics
Spectroscopy
Mass Spectrometry
Ultraviolet-Visible Spectroscopy
Infrared Spectroscopy
Nuclear Magnetic Resonance Spectroscopy
Biochemicals
Carbohydrates
Lipids
Proteins and Amino Acids
Nucleic Acids
Free Radicals
Heterocycles
Macromolecules
Organometallic Chemistry
Pericyclic Reactions
Photochemistry
Anionic Rearrangements
Cationic Rearrangements

Introduction to Synthesis
Principles of Modern Synthesis
Stereoselective Synthesis

Functional Group Reactions
Alkanes
Combustion
Halogenation of Alkanes
Alkenes
Addition Reactions
Addition of Strong Bronsted Acids
Addition of Lewis Acids (Electrophilic Reagents)
Rearrangement of Carbocations
Stereoselectivity in Addition Reactions to Double Bonds
Addition Reactions Initiated by Electrophilic Halogen
Addition Reactions involving other Cyclic Onium Intermediates
Brønsted Acid Additions
Hydrogenation of Alkenes
Oxidations
Epoxidation
Hydroxylation
Oxidative Cleavage of Double Bonds
Free Radical Reactions of Alkanes
Addition of Radicals to Alkenes
Allylic Substitution
Dienes
Addition Reactions
Diels-Alder Cycloaddition
Alkynes
Addition Reactions
Addition Reactions by Elecrophilic Reagents
Catalytic Hydrogenation
Hydration & Tautomerism
Hydroboration
Nucleophilic Addition & Reduction
Acidity of Terminal Alkynes
Alkyl Halides
Alkyl Halide Occurrence

General Reactivity
Reactions with Reducing Metals
Reactions of Dihalides
Substitution and Elimination Reactions
E1 Elimination
E2 Elimination
Planar Configuration & Bredt's Rule
Stereochemistry of E2 reactions
SN1 Substitution

Molecularity & Kinetics
Nucleophilicity & Solvent Effects
Steric Hindrance to Rear-side Approach
SN2 Substitutions & Alkyl Moiety

Alcohols
Alcohol Nomenclature
Electrophilic Substitution at Oxygen
Elimination Reactions
Hydroxyl Groups
Phenols
Acidity of Phenols
Ring Substitution of Phenols
Oxidation to Quinones

Ethers
Nomenclature
Ether Synthesis
Reactions of Ethers
Epoxide Reactions
Thiols & Sulfides
Sulfur Analogs of Alcohols & Ethers

Benzene & Derivatives
Electrophilic Aromatic Substitution
Characteristics of Specific Substitution Reactions of Benzenes
Substitution Reactions of Benzene Derivatives
Nucleophilic Reactions of Benzene Derivatives
Reactions of Substituent Groups
Reactions of Fused Benzene Rings
Electrophilic Substitution of Di-substituted Benze Rings
Amines
Nomenclature & Structure
Natural Nitrogen Compounds
Properties of Amines
Preparation of Amines
Amine Reactivity
Oxidation States of Nitrogen
Substitution and Elimination Reactions of Amines
Reactions with Nitrous Acid
Reactions of Aryl Diazonium Intermediates
Phosphines
Phosphorus Analogs of Amines
Aldehydes & Ketones
Nomenclature of Aldehydes & Ketones
Occurrence of Aldehydes & Ketones
Properties of Aldehydes & Ketones
Reactions
alpha-carbon Reactions
Carbonyl Group Reactions
Irreversible Addition Reactions
Reversible Addition Reactions
Carboxylic Acids
Nomenclature of Carboxylic Acids
Natural Products
Related Derivatives
Physical Properties
Acidity
Preparation of Carboxylic Acids
Reactions of Carboxylic Acids
Salt Formation
Substitution of Hydroxyl Hydrogen
Substitution of the Hydroxyl Group
Reduction & Oxidation
Practice Problems
Carboxylic Derivatives
Physical Properties
Nomenclature
Reactions of Carboxylic Acid Derivatives
Acyl Group Substitution
Mechanism
Reduction
Catalytic Reduction
Metal Hydride Reduction
Diborane Reduction
Reaction with Organometallic Reagents
Practice Problems

Reactions at the alpha Carbon
Acidity of alpha C–H
The Claisen Condensation
Synthesis Applications
Practice Problems

Introduction
Chapter 1: Introduction to organic structure and bonding I
Section 1: Atomic orbitals and electron configuration
The atom
Atomic orbitals
Section 2: Chemical Bonds
Ionic bonds
Covalent bonds and Lewis structures
Formal charges
Section 3: Drawing organic structures
Common bonding patterns in organic structures
Using the 'line structure' convention
Constitutional isomers
The Index of Hydrogen Deficiency
Section 4: Functional groups and organic nomenclature
Common functional groups in organic compounds
Naming organic compounds
Abbreviated organic structures
Section 5: Valence bond theory
Formation of sigma bonds: the H2 molecule
Hybrid orbitals: sp3 hybridization and tetrahedral bonding
Formation of pi bonds: sp2 and sp hybridization
The valence bonding picture in carbocations, carbanions, and carbon free radicals

Chapter 2: Introduction to organic structure and bonding II
Section 1: Molecular orbital theory
Another look at the H2 molecule: bonding and antibonding sigma molecular orbitals
MO theory and pi bonds: conjugation
Aromaticity
Section 2: Resonance
The meaning of resonance contributors: benzene and its derivatives
Resonance contributors of the carboxylate group
Rules for drawing resonance structures
Major vs minor resonance contributors - four more rules to follow
More examples of resonance: peptide bonds, enolates, and carbocations
Section 3: Non-covalent interactions
Dipoles
Ion-ion, dipole-dipole and ion-dipole interactions
van der Waals forces
Hydrogen bonds
Section 4: The relationship between noncovalent interactions physical properties
Solubility
Illustrations of solubility concepts - metabolic intermediates, lipid bilayer membranes, soaps and detergent
Boiling points and melting points
The melting behavior of lipid structures

Chapter 3: Conformations and Stereochemistry
Section 1: Conformations of straight-chain organic molecules
Conformations of ethane
Conformations of butane
Section 2: Conformations of cyclic organic molecules
Introduction to sugars and other cyclic molecules
Ring size
Conformations of glucose and other six-membered ring structures
Conformations of pentose and other five-membered ring structures
The importance of conformation in organic reactivity
Section 3: Stereoisomerism – chirality, stereocenters, enantiomers
Section 4: Defining stereochemical configuration - the Cahn-Ingold-Prelog system
Section 5: Interactions between chiral molecules and proteins
Section 6: Optical activity
Section 7: Diastereomers
Compounds with multiple stereocenters
Meso compounds
Stereoisomerism of alkenes
Section 8: Fischer and Haworth projections
Section 9: Stereochemistry and organic reactivity
Section 10: Prochirality
Prochiral substituents on tetrahedral carbons
Carbonyl and imine carbons as prochiral centers

Chapter 6: Introduction to organic reactivity and catalysis
Section 1: A first look at reaction mechanisms
acid-base (proton transfer) reaction
one-step nucleophilic substitution reaction (SN2)
Two-step nucleophilic substitution reaction (SN1)
Section 2: Describing the thermodynamics and kinetics of chemical reactions - energy diagrams
Section 3: Enzymatic catalysis - the basic ideas
Section 4: Protein structure
Amino acids and peptide bonds
Visualizing protein structure: X-ray crystallography
The four levels of protein structure
The molecular forces that hold proteins together
Section 5: How enzymes work
The active site
Transition state stabilization
Site-directed mutagenesis
Enzyme inhibition
Catalysts in the laboratory

Chapter 7: Organic compounds as acids and bases
Section 1: The ‘basic’ idea of an acid-base reaction
The Brønsted-Lowry definition of acidity
The Lewis definition of acidity
Section 2: Comparing the acidity and basicity of organic functional groups– the acidity constant
Defining Ka and pKa
Using pKa values to predict reaction equilibria
pKa and pH: the Henderson-Hasselbalch equation
Section 3: Structural effects on acidity and basicity
Periodic trends
The resonance effect
The inductive effect
Section 4: More on resonance effects on acidity and basicity
The acidity of phenols
The basicity of nitrogen-containing groups: aniline, imines, pyridine, and pyrrole
Section 5: Carbon acids and enolate ions
Section 6: Polyprotic acids
Section 7: The effects of solvent and enzyme microenvironment on acidity

Chapter 8: Nucleophilic substitution reactions, part I
Section 1: Introduction to the nucleophilic substitution reaction
Section 2: Two mechanistic models for a nucleophilic substitution reaction
Associative nucleophilic substitution: the SN2 reaction
Dissociative nucleophilic substitution: the SN1 reaction
Nucleophilic substitutions occur at sp3-hybridized carbons
Section 3: More about nucleophiles
What makes a nucleophile?
Protonation states and nucleophilicity
Periodic trends in nucleophilicity
Resonance effects on nucleophilicity
Steric effects on nucleophilicity
Section 4: Electrophiles and carbocation stability
Steric effects on electrophilicity
Stability of carbocation intermediates
Section 5: Leaving groups
What makes a good leaving group?
Leaving groups in biochemical reactions
Synthetic parallel - conversion of alcohols to alkyl halides, tosylates and mesylates
SN1 or SN2? Predicting the mechanism.
Section 6: Epoxides as electrophiles in nucleophilic substitution reactions
Epoxide structure
Epoxide ring-opening reactions - SN1 vs SN2, regioselectivity, and stereoselectivity

Chapter 17: Radical reactions
Section 1: Structure and reactivity of radical species
The geometry and relative stability of carbon radicals.
The diradical character of triplet oxygen
Section 2: Radical chain reactions
The three phases of radical chain reactions
Radical halogenation in the lab
Useful polymers formed by radical chain reactions
Destruction of the ozone layer by CFC radicals
Harmful radical species in cells and natural antioxidants
Section 3: Enzymatic reactions with free radical intermediates
Hydroxylation of alkanes
Reductive dehydroxylation of alcohols
Radical mechanisms for flavin-dependent reactions
Appendix: Review of laboratory synthesis reactions