Chem 226: General Topics & Textbook Chapters

Textbook (Klein )
ChemWiki Virtual Textbook
with a Biological Emphasis
    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
    Conformational Analysis: cyclic and acyclic
    Cyclohexane,Substituted rings, cis- trans- ring isomerism
    Ring size, Strain, Stability
    Bicyclic and Polycyclic ring systems
    Synthesis and Reactions

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

    Other (Acid / Base)

    Free Radical
    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
    Steric effects
    Transition States and Free Energy Reaction Diagrams/ Pathways
    Elimination vs. Substitution
    Synthetic Applications: Novel Antibiotic for Staph Resistance
    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
    Markovnikov's Rule
    Oxidations, Reduction, Polymerization
    Nomenclature, Physical Properties
    Acidity,Synthesis, Reactions, Acetylides
    Alcohols ,  Phenols, Structure
    Nomenclature, Physical Properties, Acidity
    Alcohol Synthesis:
    Grignard Reaction and Other Organometallic Reactions
    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


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

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

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

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

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

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

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

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

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

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

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

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

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

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
Analysis of Molecular Formulas
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
Reaction Energetics
Bond Energy
Electronic Effects
Steric Effects
Solvent Effects
Reaction Mechanisms
Curved Arrow Notation
Reactive Intermediates
Reaction Illustrations
Nucleophilicity & Basicity
Acid-Base Catalysi
Practice Problems

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

Practice Problems
Alkenes & Alkynes
Substituted Benzenes
Other Functional Groups

Practice Problems

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

Practice Problems

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

Practice Problems

Summary of Isomerism

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

Introduction to Synthesis
Principles of Modern Synthesis
Stereoselective Synthesis

Functional Group Reactions
Halogenation of Alkanes
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
Oxidative Cleavage of Double Bonds
Free Radical Reactions of Alkanes
Addition of Radicals to Alkenes
Allylic Substitution

Addition Reactions
Diels-Alder Cycloaddition
Addition Reactions
Addition Reactions by Elecrophilic Reagents

Catalytic Hydrogenation
Hydration & Tautomerism
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

Alcohol Nomenclature
Electrophilic Substitution at Oxygen
Elimination Reactions
Hydroxyl Groups

Acidity of Phenols
Ring Substitution of Phenols
Oxidation to Quinones

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
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
Phosphorus Analogs of Amines
Aldehydes & Ketones
Nomenclature of Aldehydes & Ketones
Occurrence of Aldehydes & Ketones
Properties of Aldehydes & Ketones
alpha-carbon Reactions
Carbonyl Group Reactions
Irreversible Addition Reactions
Reversible Addition Reactions
Carboxylic Acids
Nomenclature of Carboxylic Acids
Natural Products
Related Derivatives
Physical Properties
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
Reactions of Carboxylic Acid Derivatives
Acyl Group Substitution
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


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
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
Ion-ion, dipole-dipole and ion-dipole interactions
van der Waals forces
Hydrogen bonds
Section 4: The relationship between noncovalent interactions physical properties
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