Foundations of Organic Chemistry : Unity and Diversity of Structures, Pathways, and Reactions

Chapter 1. An Introduction to Structure and Bonding.

A. The Sources of Carbon Compounds.

B. More About Hydrocarbons.

C. On the Nature of the Chemical Bond.

Chapter 2. An Introduction to Spectroscopy and Selected Spectroscopic Methods in Organic Chemistry.

A. General Introduction.

B. X-Ray Crystallography.

C. Photon Spectroscopy.

D. Mass Spectrometry.

Chapter 3. Structure: The Nomenclature of Hydrocarbons and the Shape of Things to Come.

A. Introduction.

B. Nomenclature and Spectroscopy.

C. Physical and Chemical Properties; Oxidation and Reduction of Hydrocarbons.

Chapter 4. An Introduction to Dynamics.

A. Introduction.

B. Review of Some Energy Considerations.

C. The Barrier Between Reactants and Products.

D. More About the Transition State.

E. Rotation About Sigma (s) Bonds in Acyclic Alkanes, Alkenes, Alkynes and Alkyl Substituted Arenes.

F. Conformational Analysis of Medium-Ring Cyclic Alkanes .

G. The Conservation of Symmetry During Reactions.

H. The Measurement of Chirality.

Chapter 5. Classes of Organic Compounds - A Survey. An Introduction to Solvents, Acids and Bases; Computational Chemistry.

A. Introduction.

B. General Characteristics of Functional Group Placement.

C. The Functional Groups and Their Names.

D. An Introduction to Solvents.

E. Acids and Bases.

F. Computational Methods.

Introduction to Part II Middleground.

Chapter 6. Reactions of Hydrocarbons: Oxidation, Reduciton, Substitution, Addition, Elimination and Rearrangement.

A. Introduction.

B. Alkanes.

C. Alkenes.

D. Alkynes.

E. Arenes and Aromaticity: Special Introduction.

Chapter 7. The Reactions of Alkl, Alkenyl and Aryl Halides: Oxidation Reduction, Substitution, Addition Elimination, and Rearrangement.

A. Introduction.

B. Fluorocarbons.

C. Oxidation.

D. Reduction of Alkyl, Aldenyl and Aryl Halides.

E. Nucleophilic Substitution.

F. Addition Reactions.

G. Elimination Reactions of Alkyl and Alkenyl Halides.

H. Rearrangement Reactions of Alkyl and Alkenyl Halides.

Chapter 8. Part I The Reactions of Alcohols, Enols and Phenols: Oxidation Reduction, Substitution, Addition Elimination, and Rearrangement. Part II Ethers. Part III Selected Reactions Of Alkyl and Aryl Thiols and Thioethers.

Special Introduction.

Part I. Alcohols, Enols and Phenols.

A. Acidity and Basicity.

B. Oxidation of Alcohols, Enols and Phenols.

C. Reduction of Alcohols, Enols and Phenols.

D. Substitution Reactions of Alcohols, Enols and Phenols.

E. Addition Reactions of Alcohols, Enols and Phenols.

G. Rearrangement Reactions of Alcohols, Enols and Phenols.

Part II. Ethers.

I. Introduction

II. The Reactions of Ethers.

Part III. Thiols, Thioethers, and Some Products of Their Oxidation.

Chapter 9. Part I The Reactions of Aldehydes and Ketones: Oxidation, Reduction, Substitution, Addition Elimination, and Rearrangement.

Part II The Reactions of Carboxylic Acids and Their Derivatives:

Oxidation, Reduction, Substitution, Addition Elimination, and

Rearrangement.

Introduction.

Part I. Aldehydes and Ketones.

A. Oxidation of Aldehydes and Ketones.

B. Reduction of Aldehydes and Ketetones.

C. Addition to Aldehydes and Ketones.

D. Substitution Reactions Producing Aldehydes and Ketones.

E. Rearrangement Reactions of Aldehydes and Ketones.

Part II. Carboxylic Acids and Their Derivatives.

A. General Introduction.

B. Oxidation.

C. Reduction.

D. Substitution: Addition and Elimination.

E. Additional Reactions and Rearrangements of Esters and ß-Dicarbonyl Compounds.

Chapter 10. Part I The Reactions of Amines: Oxidation.Reduction,

Addition, Substitution and Rearrangement. Part II Some Organo-

phosphorus Chemistry. Part III Some Organosilicon Chemistry.

Part I. The Reactions of Amines: Introduction.

A. Oxidation of Amines.

B. Reduction of Amines.

C. Addition and Substitution Reactions of Amines with a General Introduction.

D. Addition and Rearrangement Reactions of Amines.

Part II: Some Organophosphorus Chemistry.

Part III. Some Organosilicon Chemistry.

Introduction to Part III Foreground.

Chapter 11 An Introduction to Carbohydrates, Acetogenins and Steroids.

I. Introduction.

II. The Calvin Cycle.

III.Carbohydrates.

A. Biosynthesis.

B. Chemistry.

C. Oligosaccharides.

D. Polysaccharides.

IV. Actetogenins.

A. Acetyl Coenzyme A.

B. Acetyl CoA to Fatty-Acids and Related Compounds.

C. Isoprenoides: To Dimethylallyl Diphosphate and Beyond.

Chapter 12 An Introduction to Amino Acids, Peptides and Proteins, Enzymes, Coenzymes and Metabolic Processes.

I Introduction.

II Amino Acids.

A. Biosynthesis.

B. Synthesis.

III Peptides and Proteins.

A. Amino Acids from Peptides.

B. Peptides from Amino Acids – in vivo.

C. Peptides from Amino Acids – in vitro.

IV. The Coenzymes.

A. Pyridoxal Phosphate.

B. Lipoic Acid.

C. Thiamin Diphosphate.

D. Biotin.

E. Adenosine.

F. Nicotinamide Adenine Dinucleotide (NAD⁺).

G. Coenzyme A (CoA-SH).

H. Flavin Adenine Dinucleotide (FAD).

I. S-Adenosylmethionine.

J. Tetrahydrofolate.

Chapter 13 An Introduction to Alkaloids and Some Other Heterocyclic Compounds.

I. Introduction.

II. Tropane Alkaloids.

A. Chemistry of Hyoscyamine.

B. Chemistry of Nicotine.

C. Biosynthesis of Hyoscyamine and Nicotine.

III. Morphine (and Codeine and Thebaine).

A. Chemistry of Morphine (and Codeine and Thebaine).

B. The Biosynthesis of Morphine (and Codeine and Thebaine).

C. The Synthesis of Morphine.

IV. Vinblastine.

A. Chemistry of Vinblastine.

B. Biosynthesis of Vinblastine.

V. Caffeine.

A. Some History and the Synthesis of Caffeine.

B. Biosynthesis of Caffeine.

Chapter 14 Part I. On the Genetic Code: Unity and Diversity. Part II The Tetrapyrrolic Cofactors: Unity and Diversity.

Part I. Introduction (The Genetic Code).

Part A The Bases of Deoxyribonucleic Acid (DNA and Ribonucleic

Acid (RNA).

A. Deoxynucleotides.

B. The Role of Phosphate

Part B.

A. The Sequencing of DNA.

B. Chemical Synthesis of DNA.

C. Modification to DNA.

Part II The Tetrapyrrolic Cofactors.

A. Introduction.

B. Some Early Chemistry.

C. Current Biosynthetic Understanding.

Epilogue.

Appendix I The Schrodinger Equation.

Appendix II The Literature.

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