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Organic Chemistry

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Organic Chemistry Chemistry

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01: Introduction and Review
1.01: The Origins of Organic Chemistry
1.02: Principles of Atomic Structure (Review)
1.03: Electronic Structure (Review)
1.04: Electron Configurations and Electronic Orbital Diagrams (Review)
1.05: Octet Rule - Ionic and Covalent Bonding (Review)
1.06: Lewis Structures and Formal Charges (Review)
1.07: Common Bonding Patterns for Organic Chemistry
1.08: Structural Formulas - Lewis Kekule Bond-line Condensed and Perspective
1.09: Electronegativity and Bond Polarity (Review)
1.10: Resonance
1.11: Arrhenius Acids and Bases (Review)
1.12: Lewis Acids and Bases
1.13: Distinguishing between pH and pKa
1.14: Predicting Relative Acidity
1.15: Molecular Formulas and Empirical Formulas (Review)
1.16: Additional Exercises
1.17: Solutions to Additional Exercises
1.18: Brnsted-Lowry Acids and Bases (Review)
02: Structure and Properties of Organic Molecules
2.01: Pearls of Wisdom
2.02: Molecular Orbital (MO) Theory (Review)
2.03: Hybridization and Molecular Shapes (Review)
2.04: 2.4 Conjugated Pi Bond Systems
2.05: Lone Pair Electrons and Bonding Theories
2.06: Bond Rotation
2.07: Isomerism Introduction
2.08: Hydrocarbons and the Homologous Series
2.09: Organic Functional Groups
2.10: Intermolecular Forces (IMFs) - Review
2.11: Intermolecular Forces and Relative Boiling Points (bp)
2.12: Intermolecular Forces and Solubilities
2.13: Additional Practice Problems
2.14: Organic Functional Groups- H-bond donors and H-bond acceptors
2.15: Solutions to Additional Exercises
2.16: Additional Exercises
03: Functional Groups and Nomenclature
3.01: Generic (Abbreviated) Structures (aka R Groups)
3.02: Overview of the IUPAC Naming Strategy
3.03: Alkanes
3.04: Cycloalkanes
3.05: Haloalkane - Classification and Nomenclature
3.06: Alkenes
3.07: Alkynes
3.08: 3.8 Alcohols - Classification and Nomenclature
3.09: Ethers Epoxides and Sulfides
3.10: Benzene and its Derivatives
3.11: Aldehydes and Ketones
3.12: Amines - Classification and Nomenclature
3.13: Carboxylic Acids
3.14: The Carboxylic Acid Derivatives
3.15: Additional Exercises
3.16: Solutions to Additional Exercises
3.17: Appendix - IUPAC Nomenclature Rules
04: Structure and Stereochemistry of Alkanes
4.01: Hydrocarbon Functional Groups
4.02: Physical Properties of Alkanes
4.03: Structure and Conformations of Alkanes
4.04: Conformations of Butane
4.05: Conformations of Higher Alkanes
4.06: Cycloalkanes and Ring Strain
4.07: Cyclohexane Conformations
4.08: Conformations of Monosubstituted Cyclohexanes
4.09: Cis-trans Isomerism in Cycloalkanes
4.10: Conformations of Disubstituted Cyclohexanes
4.11: Joined Rings
4.12: Uses and Sources of Alkanes
4.13: Reactions of Alkanes - a Brief Overview
4.14: Additional Exercises
4.15: Solutions to Additional Exercises
05: An Introduction to Organic Reactions using Free Radical Halogenation of Alkanes
5.01: Types of Organic Reactions
5.02: Reaction Mechanism Notation and Symbols
5.03: Polar Reactions- the Dance of the Nucleophile and Electrophile
5.04: Describing a Reaction - Equilibrium and Free Energy Changes
5.05: Homolytic Cleavage and Bond Dissociation Energies
5.06: Reaction Energy Diagrams and Transition States
5.07: Reactive Intermediates - Carbocations
5.08: Reactive Intermediates - Radicals
5.09: Reactive Intermediates- Carbanions and Carbon Acids
5.10: The Free-Radical Halogenation of Alkanes
5.11: Reactivity and Selectivity
5.12: A Comparison between Biological Reactions and Laboratory Reactions
5.13: Additional Exercises
5.14: Solutions to Additional Exercises
06: Stereochemistry at Tetrahedral Centers
6.01: Chirality
6.02: Fischer Projections to communicate Chirality
6.03: Absolute Configuration and the (R) and (S) System
6.04: Diastereomers - more than one chiral center
6.05: Meso Compounds
6.06: Isomerism Summary Diagram
6.07: Optical Activity and Racemic Mixtures
6.08: Resolution (Separation) of Enantiomers
6.09: Stereochemistry of Molecules with Three or More Asymmetric Carbons
6.10: Absolute and Relative Configuration - the distinction
6.11: Chirality at Nitrogen Phosphorus and Sulfur
6.12: Biochemistry of Enantiomers
6.13: The Discovery of Enantiomers
6.14: Additional Exercises
6.15: Solutions to Additional Exercises
07: Alkyl Halides- Nucleophilic Substitution and Elimination
7.01: Alkyl Halides - Structure and Physical Properties
7.02: Common Uses of Alkyl Halides
7.03: Preparation of Alkyl Halides
7.04: Reactions of Alkyl Halides- Substitution and Elimination
7.05: The S2 Reaction
7.06: Characteristics of the S2 Reaction
7.07: Stereochemistry of the SN2 Reaction
7.08: The S1 Reaction
7.09: Characteristics of the S1 Reaction
7.10: Rearrangements of the Carbocation and S1 Reactions
7.11: The Hammond Postulate and Transition States
7.12: Comparison of SN1 and SN2 Reactions
7.13: Characteristics of the E2 Reaction
7.14: Zaitsev's Rule
7.15: Characteristics of the E1 Reaction
7.16: E2 Regiochemistry and Cyclohexane Conformations
7.17: The E2 Reaction and the Deuterium Isotope Effect
7.18: Comparison of E1 and E2 Reactions
7.19: Comparing Substitution and Elimination Reactions
7.20: Biological Substitution Reactions
7.21: Biological Elimination Reactions
7.22: Additional Exercises
7.23: Solutions to Additional Exercises
08: Structure and Synthesis of Alkenes
8.01: Alkene Structure
8.02: Physical Properties and Important Common Names
8.03: The Alkene Double Bond and Stereoisomerism
8.04: Degrees of Unsaturation
8.05: The E Z System (when cis trans does not work)
8.06: Stability of Alkenes
8.07: Alkene Synthesis by Elimination of Alkyl Halides
8.08: Alkene Synthesis by Dehydration of Alcohols
8.09: Uses and Sources of Alkenes
8.10: Additional Exercises
8.11: Solutions to Additional Exercises
09: Reactions of Alkenes
9.01: Electrophilic Addition Reactions (EARs)
9.02: Addition of Hydrogen Halides to Symmetrical Alkenes
9.03: Alkene Asymmetry and Markovnikov's Rule
9.04: Hydration- Acid Catalyzed Addition of Water
9.05: Hydration- Oxymercuration-Demercuration
9.06: Hydration - Hydroboration-Oxidation
9.07: Stereochemistry of Reactions - Hydration of Achiral Alkenes
9.08: Stereochemistry of Reactions - Hydration of Chiral Alkenes
9.09: Addition of Halogens
9.10: Formation of Halohydrins
9.11: Reduction of Alkenes - Catalytic Hydrogenation
9.12: Oxidation of Alkenes - Epoxidation
9.13: Dihydroxylation of Alkenes
9.14: Opening of Epoxides - Acidic versus Basic Conditions
9.15: Oxidative Cleavage of Alkenes
9.16: Addition of Carbenes to Alkenes - Cyclopropane Synthesis
9.17: Radical Chain-Growth Polymerization
9.18: Biological Additions of Radicals to Alkenes
9.19: Additional Exercises
9.20: Solutions to Additional Exercises
10: Alkynes
10.01: Structure and Physical Properties
10.02: 10.2 Synthesis of Alkynes - Elimination Reactions of Dihalides
10.03: Reactions of Alkynes - Addition of HX and X
10.04: Hydration of Alkynes for Markovnikov Products
10.05: Hydration of Alkynes for Anti-Markovnikov Products
10.06: 10.6 Reduction of Alkynes
10.07: Oxidation of Alkynes
10.08: Acidity of Terminal Alkynes and Acetylide Ions
10.09: Synthesis of Larger Alkynes from Acetylides
10.10: An Introduction to Multiple Step Synthesis
10.11: Additional Exercises
10.12: Solutions to Additional Exercises
11: Infrared Spectroscopy and Mass Spectrometry
11.01: The Electromagnetic Spectrum and Spectroscopy
11.02: Infrared (IR) Spectroscopy
11.03: IR-Active and IR-Inactive Vibrations
11.04: Interpretting IR Spectra
11.05: Infrared Spectra of Some Common Functional Groups
11.06: Summary and Tips to Distinguish between Carbonyl Functional Groups
11.07: Mass Spectrometry - an introduction
11.08: Fragmentation Patterns in Mass Spectrometry
11.09: Useful Patterns for Structure Elucidation
11.10: Determination of the Molecular Formula by High Resolution Mass Spectrometry
12: Nuclear Magnetic Resonance Spectroscopy
12.01: Theory of Nuclear Magnetic Resonance (NMR)
12.02: NMR Spectra - an introduction and overview
12.03: Chemical Shifts and Shielding
12.04: H NMR Spectroscopy and Proton Equivalence
12.05: Functional Groups and Chemical Shifts in H NMR Spectroscopy
12.06: Integration of H NMR Absorptions- Proton Counting
12.07: Spin-Spin Splitting in H NMR Spectra
12.08: More Complex Spin-Spin Splitting Patterns
12.09: Uses of H NMR Spectroscopy
12.10: C NMR Spectroscopy
12.11: Chemical Shifts and Interpreting C NMR Spectra
12.12: C NMR Spectroscopy and DEPT
12.13: Uses of C NMR Spectroscopy
12.14: More NMR Examples
12.15: Sample NMR Spectra
13: Structure and Synthesis of Alcohols
13.01: Introduction to Structure and Synthesis of Alcohols
13.02: Classification of Alcohols
13.03: Physical Properties of Alcohols
13.04: Spectroscopy of Alcohols
13.05: Acidity of Alcohols and Phenols
13.06: Synthesis of Alcohols - Review
13.07: Reduction of the Carbonyl Group - Synthesis of 1 and 2 Alcohols
13.08: Organometallic Reagents
13.09: Organometallic Reagents in Alcohol Synthesis
13.10: Thiols (Mercaptans)
13.11: Commercially Important Alcohols
13.12: 13.12 Additional Exercises
13.13: Solutions to Additional Exercises
14: Reactions of Alcohols
14.01: Reactions of Alcohols with Hydrohalic Acids
14.02: Reactions with Phosphorus Halides and Thionyl Chloride
14.03: Alcohol conversion to Esters - Tosylate and Carboxylate
14.04: Dehydration Reactions of Alcohols
14.05: Oxidation States of Alcohols and Related Functional Groups
14.06: Oxidation Reactions of Alcohols
14.07: Determining Alcohol Classifications in the Lab - alternate reactions
14.08: Protection of Alcohols
14.09: Cleavage of Diols
14.10: Reactions of Alkoxides
14.11: Biological Oxidation - An Introduction
14.12: Additional Exercises
14.13: Solutions to Additional Exercises
15: Ethers Epoxides and Thioethers
15.01: Physical Properties of Ethers
15.02: Spectroscopy of Ethers
15.03: The Williamson Ether Synthesis
15.04: Alkoxymercuration-Demercuration Synthesis of Ethers
15.05: Acidic Cleavage of Ethers
15.06: Autoxidation of Ethers
15.07: Synthesis of Epoxides
15.08: Opening of Epoxides
15.09: Reactions of Epoxides with Grignard and Organolithium Reagents
15.10: Crown Ethers
15.11: Epoxy Resins - The Advent of Modern Glues
15.12: Thioethers (Sulfides) and Silyl Ethers
15.13: Additional Exercises
15.14: Solutions to Additional Exercises
16: Conjugated Systems Orbital Symmetry and Ultraviolet Spectroscopy
16.01: Stability of Conjugated Dienes - Molecular Orbital Theory
16.02: Allylic Cations
16.03: Electrophilic Additions to Conjugated Dienes
16.04: Kinetic versus Thermodynamic Control
16.05: SN2 Reactions of Allylic Halides and Tosylates
16.06: The Diels-Alder (4 2) Cycloaddition Reaction
16.07: Diels-Alder Stereochemistry
16.08: Diene Polymers - Natural and Synthetic Rubbers
16.09: Structure Determination in Conjugated Systems - Ultraviolet Spectroscopy
16.10: Interpreting Ultraviolet Spectra - The Effect of Conjugation
16.11: Conjugation Color and the Chemistry of Vision
16.12: Additional Exercises
16.13: Solutions to Additional Exercises
17: Aromatic Compounds
17.01: Introduction- The Discovery of Benzene
17.02: The Structure and Properties of Benzene and its Derivatives
17.03: Resonance and the Molecular Orbitals of Benzene
17.04: The Molecular Orbital Picture of Cyclobutadiene
17.05: Aromaticity and Huckel's Rule
17.06: Aromatic Ions - a closer look
17.07: Heterocyclic Aromatic Compounds - a closer look
17.08: Polycyclic Aromatic Hydrocarbons
17.09: Spectroscopy of Aromatic Compounds
17.10: Additional Exercises
17.11: Solutions to Additional Exercises
18: Reactions of Aromatic Compounds
18.01: Electrophilic Aromatic Substitution (EAS)
18.02: Halogenation of Benzene (an EAS Reaction)
18.03: Nitration of Benzene (an EAS Reaction)
18.04: Sulfonation of Benzene (an EAS Reaction)
18.05: Alkylation and Acylation of Benzene - The Friedel-Crafts EAS Reactions
18.06: Substituent Effects on the EAS Reaction
18.07: Side-Chain Reactions of Benzene Derivatives
18.08: Synthetic Strategies for Di-substituted Benzenes
18.09: Trisubstituted Benzenes - Effects of Multiple Substituents
18.10: Nucleophilic Aromatic Substitution - The Addition-Elimantion Mechanism
18.11: NAS Reactions - the Elimination-Addition (Benzyne) Mechanism
18.12: Reduction of Aromatic Compounds
18.13: Additional Exercises
18.14: Solutions to Additional Exercises
19: Ketones and Aldehydes
19.01: Carbonyl Compound Structure and Properties
19.02: Spectroscopy of Ketones and Aldehydes
19.03: Review of Ketone and Aldehyde Synthesis
19.04: 19.4 New Synthesis of Aldehydes and Ketones
19.05: Nucleophilic Addition Reactions of Ketones and Aldehydes
19.06: Nucleophilic Addition of Water (Hydration)
19.07: Nucleophilic Addition of Cyanide and Acetylide
19.08: Nucleophilic Addition of Grignards
19.09: Nucelophilic Addition of Amines (Imine and Enamine Formation)
19.10: Nucleophilic Addition of Hydrazine (Wolff-Kishner Reaction)
19.11: Nucelophilic Addition of Alcohols (Acetal Formation)
19.12: Acetals as Protecting Groups
19.13: Nucelophilic Addition of Phosphorus Ylides (The Wittig Reaction)
19.14: Oxidation of Aldehydes
19.15: Reductions of Ketones and Aldehydes
19.16: Additional Exercises
19.17: Solutions to Additional Exercises
20: Amines
20.01: Structure and Physical Properties of Amines
20.02: Basicity of Amines and Ammonium Salt Formation
20.03: Spectroscopy of Amines
20.04: Synthesis of Amines
20.05: Synthesis of Primary Amines
20.06: Reactions of Amines
20.07: Reactions of Arylamines
20.08: The Hofmann Elimination- Amines as Leaving Groups
20.09: Oxidation of Amines - The Cope Elimination
20.10: Sulfa Drugs - a closer look
20.11: Additional Exercises
20.12: Solutions to Additional Exercises
21: Carboxylic Acids
21.01: Structure and Properties of Carboxylic Acids and their Salts
21.02: Acidity of Carboxylic Acids
21.03: Spectroscopy of Carboxylic Acids
21.04: Synthesis of Carboxylic Acids
21.05: Reactions of Carboxylic Acids Overview
21.06: Condensation of Acids with Alcohols- The Fischer Esterification
21.07: Methyl Ester Synthesis Using Diazomethane
21.08: Condensation of Acids with Amines
21.09: Reduction of Carboxylic Acids
21.10: Biochemically Interesting Carboxylic Acids
21.11: Additional Exercises
21.12: Solutions to Additional Exercises
22: Carboxylic Acid Derivatives and Nitriles
22.01: Structure and Physical Properties of Acid Derivatives
22.02: Spectroscopy of Carboxylic Acid Derivatives
22.03: Interconversion of Acid Derivatives by Nucleophilic Acyl Substitution
22.04: Acid Halide Chemistry
22.05: Acid Anhydride Chemistry
22.06: Ester Chemistry
22.07: Amide Chemistry
22.08: Nitrile Chemistry
22.09: Thioesters- Biological Carboxylic Acid Derivatives
22.10: Polyamides and Polyesters- Step-Growth Polymers
22.11: Beta-Lactams- An Application
22.12: Biological Acylation Reactions
22.13: Additional Exercises
22.14: Solutions to Additional Exercises
23: Alpha Substitutions and Condensations of Carbonyl Compounds
23.01: Relative Acidity of alpha-Hydrogens
23.02: Enols Enolate Ions and Tautomerization
23.03: Reaction Overview
23.04: Alpha Halogenation of Carbonyls
23.05: Bromination of Acids- The HVZ Reaction
23.06: Alkylation of the alpha-Carbon via the LDA pathway
23.07: Alkylation of the Alpha-Carbon via the Enamine Pathway
23.08: The Aldol Reaction and Condensation of Ketones and Aldehydes
23.09: The Claisen Condensation Reactions of Esters
23.10: Conjugate Additions- The Michael Reaction
23.11: Decarboxylation Reactions
23.12: Additional Exercises
23.13: Solutions to Additional Exercises
24: Carbohydrates
24.01: Introduction
24.02: Classification of Carbohydrates
24.03: Fischer Projections
24.04: D and L Sugars
24.05: Configuration of Aldoses
24.06: Cyclic Structures of Monosaccharides
24.07: Reactions of Monosaccharides
24.08: Disaccharides and Glycosidic Bonds
24.09: Polysaccharides
24.10: Other Important Carbohydrates
24.11: Cell Surface Carbohydrates and Influenza Viruses
25: Amino Acids Peptides and Proteins
25.01: Introduction
25.02: Structure and Stereochemistry of the Amino Acids
25.03: Isoelectric Points and Electrophoresis
25.04: Synthesis of Amino Acids
25.05: Peptides and Proteins
25.06: Amino Acid Analysis of Peptides
25.07: Peptide Sequencing- The Edman Degradation
25.08: Peptide Synthesis
25.09: Automated Peptide Synthesis- The Merrifield Solid-Phase Technique
25.10: Levels of Protein Structure
25.11: Enzymes and Coenzymes
25.12: How do enzymes work
26: Lipids
26.01: Introduction
26.02: Waxes Fats and Oils
26.03: Saponification of Fats and Oils Soaps and Detergents
26.04: Phospholipids
26.05: Prostaglandins and other Eicosanoids
26.06: Terpenes and Terpenoids
26.07: Steroids
26.08: Biosynthesis of Steroids
27: Nucleic Acids
27.01: Nucleotides and Nucleic Acids
27.02: DNA Base Pairs
27.03: DNA Replication
27.04: Transcription of DNA
27.05: Translation of RNA- Protein Biosynthesis
27.06: DNA Sequencing
27.07: Polymerase Chain Reactions