I: AN INTRODUCTION TO THE STUDY OF ORGANIC CHEMISTRY 1. ELECTRONIC STRUCTURE AND BONDING * ACIDS AND BASES1.1 The Structure of an Atom1.2 How the Electrons in an Atom are Distributed1.3 Ionic and Covalent Bonds Ionic Bonds are Formed by the Transfer of Electrons Covalent Bonds are Formed by Sharing Electrons Polar Covalent Bonds1.4 How the Structure of a Compound is Represented Lewis Structures Kekule Structures Condensed Structures1.5 Atomic Orbitals1.6 An Introduction to Molecular Orbital Theory1.7 How Single Bonds are Formed in Organic Compounds The Bonds in Methane The Bonds in Ethane1.8 How a Double Bond is Formed: The Bonds in Ethene1.9 How a Triple Bonds is Formed: The Bonds in Ethyne1.10 The Bonds in the Methyl Cation, the Methyl Radical, and the Methyl Anion The Methyl Cation The Methyl Radical The Methyl Anion1.11 The Bonds in Water1.12 The Bonds in Ammonia and in the Ammonium Ion1.13 The Bonds in the Hydrogen Halides1.14 Summary: Hybridization, Bond Lengths, Bond Strengths, and Bond Angles1.15 The Dipole Moments of Molecules1.16 An Introduction to Acids and Bases1.17 pKa and pH1.18 Organic Acids and Bases1.19 How to Predict the Outcome of an Acid-Base Reaction1.20 How the Structure of an Acid Affects Its Acidity1.21 How Substituents Affect the Strength of an Acid1.22 An Introduction to Delocalized Electrons1.23 A Summary of the Factors that Determine Acid Strength1.24 How the pH Affects the Structure of an Organic Compound1.25 Buffer Solutions 1.26 The Second Definition of Acid and Base: Lewis Acids and Bases 2. AN INTRODUCTION TO ORGANIC COMPOUNDS NOMENCLATURE, PHYSICAL PROPERTIES, AND REPRESENTATION OF STRUCTURE 2.1 How Alkyl Substituents are Named2.2 Nomenclature of Alkanes2.3 Nomenclature of Cycloalkanes2.4 Nomenclature of Alkyl Halides2.5 Nomenclature of Ethers2.6 Nomenclature of Alcohols2.7 Nomenclature of Amines2.8 The Structures of Alkyl Halides, Alcohols, Ethers, and Amines 2.9 The Physical Properties of Alkanes, Alkyl Halides, Alcohols, Ethers, and Amines Boiling Points Melting Points Solubility2.10 Rotation Occurs About Carbon-Carbon Bonds2.11 Some Cycloalkanes Have Ring Strain 2.12 Conformations of Cyclohexane2.13 Conformers of Monosubstituted Cyclohexanes2.14 Conformers of Disubstituted Cyclohexanes II: ELECTROPHILIC ADDITION REACTIONS, STEREOCHEMISTRY, AND ELECTRON DEELOCALIZATION 3. ALKENES: STRUCTURE, NOMENCLATURE AND AN INTRODUCTION TO REACTIVITY * THERMODYNAMICS AND KINETICS3.1 Molecular Formulas and the Degree of Unsaturation 3.2 Nomenclature of Alkenes3.3 The Structures of Alkenes3.4 Alkenes Can Have Cis and Trans Isomers3.5 Naming Alkenes Using the E,Z System3.6 How Alkenes React * Curved Arrows Show the Flow of Electrons3.7 Thermodynamics and Kinetics A Reaction Coordinate Diagram Describes the Reaction Pathway Thermodynamics: How Much Product Is Formed? Kinetics: How Fast Is the Product Formed?3.8 Using a Reaction Coordinate Diagram to Describe a Reaction 4. THE REACTIONS OF ALKENES 4.1 Addition of a Hydrogen Halide to an Alkene4.2 Carbocation Stability Depends on the Number of Alkyl Groups Attached to the Positively Charged Carbon4.3 The Structure of the Transition State Lies Partway Between the Structures of the Reactants and Products4.4 Electrophilic Addition Reactions Are Regioselective 4.5 Acid-Catalyzed Addition Reactions Addition of Water to an Alkene Addition of an Alcohol to an Alkene4.6 A Carbocation will Rearrange if It Can Form a More Stable Carbocation4.7 Addition of a Halogen to an Alkene4.8 Oxymercuration-Demercuration: Are Other Ways to Add Water or Alcohol to an Alkene4.9 Addition of a Peroxyacid to an Alkene4.10 Addition of Borane to an Alkene: Hydroboration-Oxidation4.11 Addition of Hydrogen to an Alkene * The Relative Stabilities of Alkenes4.12 Reactions and Synthesis 5. STEREOCHEMISTRY: THE ARRANGEMENT OF ATOMS IN SPACE; THE STEREOCHEMISTRY OF ADDITION REACTIONS5.1 Cis-Trans Isomers Result From Restricted Rotation5.2 A Chiral Object has a Nonsuperimposable Mirror Image5.3 An Asymmetric Center Is a Cause of Chirality In a Molecule5.4 Isomers with One Asymmetric Center5.5 Asymmetric Centers and Stereocenters5.6 How to Draw Enantiomers 5.7 Naming Enantiomers by the R,S System5.8 Chiral Compounds are Optically Active5.9 How Specific Rotation is Measured5.10 Enantiomeric Excess5.11 Isomers with More than One Asymmetric Center5.12 Meso Compounds Have Asymmetric Centers but are Optically Inactive5.13 How to Name Isomers with More than One Asymmetric Center5.14 Reactions of Compounds that Contain a Asymmetric Center5.15 The Absolute Configuration of (+)-Glyceraldehyde5.16 How Enantiomers Can be Separated5.17 Nitrogen and Phosphorous Atoms Can be Asymmetric Centers5.18 The Stereochemistry of Reactions: Regioselective, Stereoselective, and Stereospecific Reactions5.19 The Stereochemistry of Electrophilic Addition Reactions of Alkenes Addition Reactions that Form a Product with One Asymmetric Center Addition Reactions that Form Products with Two Asymmetric Centers Addition Reactions that Form a Carbocation Intermediate The Stereochemistry of Hydrogen Addition The Stereochemistry of Peroxyacid Addition The Stereochemistry of Hydroboration-Oxidation Addition Reactions that Form a Cyclic Bromonium Ion Intermediate5.20 The Stereochemistry of Enzyme-Catalyzed Reactions5.21 Enantiomers can be Distinguished by Biological Molecules Enymes Receptors 6. THE REACTIONS OF ALKYNES * AN INTRODUCTION TO MULTISTEP SYNTHESIS 6.1 The Nomenclature of Alkynes6.2 How to Name a Compound That Has More than One Functional Group6.3 The Physical Properties of Unsaturated Hydrocarbons6.4 The Structure of Alkynes6.5 How Alkynes React6.6 Addition of Hydrogen Halides and Addition of Halogens to an Alkyne6.7 Addition of Water to an Alkyne6.8 Addition of Borane to an Alkyne: Hydroboration-Oxidation6.9 Addition of Hydrogen to an Alkyne6.10 A Hydrogen Bonded to an sp Carbon is "Acidic" 6.11 Synthesis Using Acetylide Ions6.12 Designing a Synthesis I: An Introduction to Multistep Synthesis 7. DELOCALIZED ELECTRONS AND THEIR EFFECT ON STABILITY, REACTIVITY, AND pKa * MORE ABOUT MOLECULAR ORBITAL THEORY7.1 Benzene Has Delocalized Electrons7.2 The Bonding in Benzene7.3 Resonance Contributors and the Resonance Hybrid7.4 How to Draw Resonance Contributors7.5 The Predicted Stabilites of Resonance Contributors7.6 Delocalization Energy Is the Additional Stability Delocalized Electrons Give to a Compound7.7 Examples That Illustrate the Effect of Delocalized Electrons on Stability Stability of Dienes Stability of Allylic and Benzylic Cations7.8 A Molecular Orbital Description of Stability 1,3-Butadiene and 1,4-Pentadiene 1,3,5-Hexatriene and Benzene7.9 How Delocalized Electrons Affect pKa7.10 Delocalized Electrons Can Affect the Product of a Reaction Reactions of Isolated Dienes Reactions of Conjugated Dienes7.11 Thermodynamic versus Kinetic Control of Reactions7.12 The Diels-Alder Reaction Is a 1,4-Addition Reaction A Molecular Orbital Description of the Diels-Alder Reaction Predicting the Product When Both Reagents Are Unsymmetrically Substituted Conformations of the Diene The Stereochemistry of the Diels-Alder Reaction III: SUBSTITUTION AND ELIMINATION REACTIONS 8. SUBSTITUTION REACTIONS OF OF ALKYL HALIDES8.1 How Alkyl Halides React8.2 The Mechanism of an SN2 Reaction8.3 Factors that Affect SN2 Reactions The Leaving Group The Nucleophile Nucleophilicity is Affected by the Solvent Nucleophilicity is Affected by Steric Effects8.4 The Reversibility of an SN2 Reaction Depends on the Basicities of the Leaving Groups in the Forward and Reverse Directions8.5 The Mechanism of an SN1 Reaction8.6 Factors that Affect an SN1 Reaction The Leaving Group The Nucleophile Carbocation Rearrangements8.7 More About the Stereochemistry of SN2 and SN1 Reactions Stereochemistry of SN2 Reactions Stereochemistry of SN1 Reactions8.8 Benzylic Halides, Allylic Halides, Vinylic Halides, and Aryl Halides8.9 Competition Between SN2 and SN1 Reactions8.10 The Role of the Solvent in SN2 and SN1 Reactions How a Solvent Affects Reaction Rates in General How a Solvent Affects the Rate of an SN1 Reaction How a Solvent Affects the Rate of an SN2 Reaction8.11 Biological Methylating Reagents Have Good Leaving Groups 9. ELIMINATION REACTIONS OF ALKYL HALIDES * COMPETITION BETWEEN SUBSTITUTION AND ELIMINATION9.1 The E2 Reaction9.2 An E2 Reaction is Regioselective9.3 The E1 Reaction9.4 Competition Between E2 and E1 Reactions9.5 E2 and E1 Reactions are Stereoselective The Stereoisomers Formed in an E2 Reaction The Stereoisomers Formed in an E1 Reaction9.6 Elimination from Substituted Cyclohexanes E2 Reactions of Substituted Cyclohexanes E1 Reactions of Substituted Cyclohexanes9.7 A Kinetic Isotope Effect Can Help Determine a Mechanism9.8 Competition Between Substitution and Elimination SN2/E2 Conditions SN1/E1 Conditions9.9 Substitution and Elimination Reactions in Synthesis Using Substitution Reactions to Synthesize Compounds Using Elimination Reactions to Synthesize Compounds9.10 Consecutive E2 Elimination Reactions9.11 Intermolecular Versus Intramolecular Reactions9.12 Designing a Synthesis II: Approaching the Problem 10. REACTIONS OF ALCOHOLS, AMINES, ETHERS, EXPOXIDES, AND SULFUR-CONTAINING COMPOUNDS * ORGANOMETALLIC COMPOUNDS10.1 Nucleophilic Substitution Reactions of Alcohols: Forming Alkyl Halides10.2 Other Methods for Converting Alcohols into Alkyl Halides10.3 Converting Alcohols into Sulfonate Esters10.4 Elimination Reactions of Alcohols: Dehydration10.5 Oxidation of Alcohols10.6 Amines do not Undergo Substitution or Elimination Reactions but Are the Most Common Organic Bases10.7 Nucleophilic Substitution Reactions of Ethers10.8 Nucleophilic Substitution Reactions of Epoxides10.9 Arene Oxides10.10 Crown Ethers10.11 Thiols, Sulfides, and Sulfonium Salts10.12 Organometallic Compounds10.13 Coupling Reactions 11. RADICALS * REACTIONS OF ALKANES11.1 Alkanes are Unreactive Compounds11.2 Chlorination and Bromination of Alkanes11.3 Radical Stability Depends on the Number of Alkyl Groups Attached to the Carbon with the Unpaired Electron11.4 The Distribution of Products Depends on Probability and Reactivity11.5 The Reactivity-Selectivity Principle11.6 Addition of Radicals to an Alkene11.7 Stereochemistry of Radical Substitution and Addition Reactions11.8 Radical Substitution of Benzylic and Allylic Hydrogens11.9 Designing a Synthesis III: More Practice with Multistep Synthesis11.10 Radical Reactions Occur in Biological Systems11.11 Radicals and Stratospheric Ozone IV: IDENTIFICATION OF ORGANIC COMPOUNDS 12. MASS SPECTROMETRY, INFRARED SPECTROSCOPY, AND ULTRAVIOLET/VISIBLE SPECTROSCOPY12.1 Mass Spectrometry12.2 The Mass Spectrum. Fragmentation 12.3 Isotopes in Mass Spectrometry12.4 High-Resolution Mass Spectrometry Can Determine Molecular Formulas12.5 Fragmentation Patterns of Functional Groups Alkyl Halides Ethers Alcohols Ketones12.6 Spectroscopy and the Electromagnetic Spectrum12.7 Infrared Spectroscopy Obtaining an Infrared Spectrum The Functional Group and Fingerprint Regions12.8 Characteristic Infrared Absorption Bands12.9 The Intensity of Absorption Bands12.10 The Position of Absorption Bands Hooke's Law The Effect of Bond Order12.11 The Position of an Absorption Band is Affected by Electron Delocalization, Electron Donation and Withdrawal, and Hydrogen Bonding O-GH Absorption Bands C-H Absortion Bands12.12 The Shape of Absorption Bands12.13 The Absence of Absorption Bands12.14 Some Vibrations are Infrared Inactive12.15 A Lesson in Interpreting Infrared Spectra12.16 Ultraviolet and Visible Spectroscopy12.17 The Beer-Lambert Law12.18 The Effect of Conjugation on lmax12.19 The Visible Spectrum and Color12.20 Uses of UV/Vis Spectroscopy 13. NMR SPECTROSCOPY13.1 An Introduction to NMR Spectroscopy13.2 Fourier Transform NMR13.3 Shielding Causes Different Hydrogens to Show Signals at Different Frequencies13.4 The Number of Signals in an 1H NMR Spectrum13.5 The Chemical Shift Tells How Far the Signal Is from the Reference Signal13.6 The Relative Positions of 1H NMR Signals13.7 Characteristic Values of Chemical Shifts13.8 Diamagnetic Anisotropy13.9 The Integration of NMR Signals Reveals the Relative Number of Protons Causing the Signal13.10 Splitting of the Signals is Desribed by the N+1 Rule13.11 More Examples of 1H NMR Spectra13.12 Coupling Constants Identify Coupled Protons13.13 Splitting Diagrams Explain the Multiplicity of a Signal13.14 The Time Dependence of NMR Spectroscopy13.15 Protons Bonded to Oxygen and Nitrogen13.16 The Use of Deuterium in 1H NMR Spectroscopy13.17 The Resolution of 1H NMR Spectra13.18 13C NMR Spectroscopy13.19 DEPT 13C NMR Spectra13.20 Two-Dimensional NMR Spectroscopy 13.21 NMR Used in Medicine is Called Magnetic Resonance Imaging V: AROMATIC COMPOUNDS 14. AROMATICITY * REACTIONS OF BENZENE14.1 Aromatic Compounds are Unusually Stable14.2 The Two Criteria for Aromaticity14.3 Applying the Criteria for Aromaticity14.4 Aromatic Heterocyclic Compounds14.5 Some Chemical Consequences of Aromaticity14.6 Antiaromaticity14.7 A Molecular Orbital Description of Aromaticity and Antiaromaticity14.8 Nomenclature of Monosubstituted Benzenes14.9 How Benzene Reacts14.10 General Mechanism for Electrophilic Aromatic Substitution Reactions14.11 Halogenation of Benzene14.12 Nitration of Benzene14.13 Sulfonation of Benzene14.14 Friedel-Crafts Acylation of Benzene14.15 Friedel-Crafts Alkylation of Benzene14.16 Alkylation of Benzene by Acylation-Reduction14.17 Using Coupling Reactions to Alkylate Benzene14.18 It is important to Have More than One Way to Carry Out a Reaction14.19 How Some Substituents on a Benzene Ring Can Be Chemically Changed 15. REACTIONS OF SUBSTITUTED BENZENES15.1 Nomenclature of Disubstituted and Polysubstituted Benzenes15.2 Some Substituents Increase the Reactivity of a Benzene Ring and Some Decrease Its Reactivity Inductive Electron Withdrawal Electron Donation by Hyperconjugation Resonance Electron Donation and Withdrawal Relative Reactivity of Substituted Benzenes15.3 The Effect of Substituents on Orientation15.4 The Effect of Substituents on pKa15.5 The Ortho/Para Ratio15.6 Additional Considerations Regarding Substituent Effects15.7 Designing a Synthesis III: Synthesis of Monosubstituted and Disubstituted Benzenes 15.8 Synthesis of Trisubstituted Benzenes15.9 Synthesis of Substituted Benzenes Using Arenediazonium Salts15.10 The Arenediazonium Ion as an Electrophile15.11 Mechanism for the Reaction of Amines with Nitrous Acid15.12 Nucleophilic Aromatic Substitution: An Addition-Elimination Mechanism15.13 Nucleophilic Aromatic Substitution: An Elimination-Addition Mechanism that Forms a Benzyne Intermediate15.14 Polycyclic Benzenoid Hydrocarbons VI: CARBONYL COMPOUNDS 16. CARBONYL COMPOUNDS I: NUCLEOPHILIC ACYL SUBSTITUTION16.1 Nomenclature of Carboxylic Acids and Caboxylic Acid Derivatives16.2 Structures of Carboxylic Acids and Carboxylic Acid Derivatives16.3 Physical Properties of Carbonyl Compounds16.4 Naturally Occurring Carboxylic Acids and Carboxylic Acid Derivatives16.5 How Class I Carbonyl Compounds React16.6 Relative Reactivities of Carboxylic Acids and Carboxylic Acid Derivatives16.7 General Mechanism for Nucleophilic Acyl Substitution Reactions16.8 Reactions of Acyl Halides16.9 Reactions of Acid Anhydrides16.10 Reactions of Esters16.11 Acid-Catalyzed Ester Hydrolysis16.12 Hydroxide-Ion Promoted Ester Hydrolysis16.13 How the Mechanism for Nucleophilic Acyl Substitution Reactions Was Confirmed16.14 Soaps, Detergents, and Micelles16.15 Reactions of Carboxylic Acids 16.16 Reactions of Amides16.17 The Hydrolysis of Amides Is Catalyzed by Acids16.18 Hydrolysis of an Imide: A Way to Synthesize Primary Amines16.19 Hydrolysis of Nitriles16.20 Designing a Synthesis V: The Synthesis of Cyclic Compounds16.21 How Chemists Activate Carboxylic Acids16.22 How Cells Activate Carboxylic Acids16.23 Dicarboxylic Acids and Their Derivatives 17. CARBONYL COMPOUNDS II: 17.1 Nomenclature of Aldehydes and Ketones17.2 Relative Reactivities of Carbonyl Compounds17.3 How Aldehydes and Ketones React17.4 Reactions of Carbonyl Compounds with Grignard Reagents17.5 Reactions of Carbonyl Compounds with Acetylide Ions17.6 Reactions of Carbonyl Compounds with Hydride Ion17.7 Reactions of Aldehydes and Ketones with Hydrogen Cyanide17.8 Reactions of Aldehydes and Ketones with Amines and Derivatives of Amines17.9 Reactions of Aldehydes and Ketones with Water17.10 Reactions of Aldehydes and Ketones with Alcohols17.11 Protecting Groups17.12 Addition of Sulfur Nucleophiles 17.13 The Wittig Reaction Forms an Alkene17.14 Stereochemistry of Nucleophilic Addition Reactions: Re and Si Faces17.15 Designing a Synthesis VI: Disconnections, Synthons, and Synthetic Equivalents17.16 Nucleophilic Addition to a,b-Unsaturated Aldehydes and Ketones17.17 Nucleophilic Addition to a,b-Unsaturated Carboxylic Acid Derivatives17.18 Enzyme-Catalyzed Additions to a,b-Unsaturated Carbonyl Compounds 18. CARBONYL COMPOUNDS III: REACTIONS AT THE a-CARBON 18.1 Acidity of an a-Hydrogens18.2 Keto-Enol Tautomers18.3 Enolization18.4 How Enols and Enolate Ions React18.5 Halogenation of the a-Carbon of Aldehydes and Ketones. Acid-Catalyzed Halogenation Base-Promoted Halogenation The Haloform Reaction18.6 Halogenation of the a-Carbon of Carboxylic Acids: The Hell-Volhard-Zelinski Reaction18.7 a-Halogenated Carbonyl Compounds Are Useful in Synthesis18.8 Using Lithium Diisopropylamide (LDA) to Form an Enolate18.9 Alkylation of the a-Carbon of Carbonyl Compounds18.10 Alkylation and Acylation of the a-Carbon Using an Enamine Intermediate18.11 Alkylation of the b-Carbon: The Michael Reaction18.12 An Aldol Addition Forms b-Hydroxyaldehydes or b -Hydroxyketones18.13 Dehydration of Aldol Addition Products Forms a,b-Unsaturated Aldehydes and Ketones18.14 The Mixed Aldol Addition18.15 A Claisen Condensation Forms a b-Keto Ester18.16 The Mixed Claisen Condensation18.17 Intramolecular Condensation and Addition Reactions Intramolecular Claisen Condensations Intramolecular Aldol Additions The Robinson Annulation18.18 3-Oxocarboxylic Acids Can Be Dehydrated18.19 The Malonic Ester Synthesis: A Way to Snthesize a Carboxylic Acid18.20 The Acetoacetic Ester Synthesis: A Way Synthesize a Methyl Ketone18.21 Designing a Synthesis VII: Making New Carbon-Carbon Bonds18.22 Reactions at the a-Carbon in Biological Systems A Biological Aldol Condensation A Biological Claisen Condensation A Biological Decarboxylation VII: OXIDATION-REDUCTION REACTIONS AND AMINES 19. MORE ABOUT OXIDATION-REDUCTION REACTIONS19.1 Reduction Reactions Reduction by Addition of Two Hydrogen Atoms Reduction by Addition of an Electron, a Proton, an Electron, and a Proton Reduction by Addition of a Hydride Ion and a Proton19.2 Oxidation of Alcohols19.3 Oxidation of Aldehydes and Ketones19.4 Designing a Synthesis VIII: Controlling Stereochemistry19.5 Hydroxylation of Alkenes19.6 Oxidative Cleavage of 1,2-Diols19.7 Oxidative Cleavage of Alkenes19.8 Oxidative Cleavage of Alkynes19.9 Designing a Synthesis IX: Functional Group Interconversion 20. MORE ABOUT AMINES. HETEROCYCLIC COMPOUNDS20.1 More About Amine Nomenclature20.2 Amines Invert Rapidly20.3 More About the Acid-Base Properties of Amines20.4 Amines React as Bases and as Nucleophiles20.5 Quaternary Ammonium Hydroxides Undergo Elimination Reactions20.6 Phase-Transfer Catalysis20.7 Oxidation of Amines: The Cope Elimination Reaction20.8 Synthesis of Amines20.9 Aromatic Five-Membered Ring Heterocycles 20.10 Aromatic Six-Membered-Ring Heterocycles 20.11 Amine Heterocycles Have Important Roles in Nature VIII: BIOORGANIC COMPOUNDS 21. CARBOHYDRATES21.1 Classification of Carbohydrtes21.2 The D and L Notation21.3 Configurations of the Aldoses21.4 Configurations of the Ketoses21.5 Reactions of Monosaccharides in Basic Solutions21.6 Redox Reactions of Monosaccharides21.7 Monosaccharides Form Crystalline Osazones21.8 Lengthening the Chain: The Kiliani-Fischer Synthesis21.9 Shortening the Chain: The Wohl Degradation21.10 Stereochemistry of Glucose: the Fischer Proof 21.11 Monosaccharides Form Cyclic Hemiacetals21.12 Glucose Is the Most Stable Aldohexose21.13 Acylation and Alkylation of Monosaccharides21.14 Formation of Glycosides21.15 The Anomeric Effect21.16 Reducing and Nonreducing Sugars21.17 Determination of Ring Size21.18 Disaccharides21.19 Polysaccharides21.20 Some Naturally Occurring Products Derived from Carbohydrates21.21 Carbohydrates on Cell Surfaces21.22 Synthetic Sweeteners 22. AMINO ACIDS, PEPTIDES, AND PROTEINS 22.1 Classification and Nomenclature of Amino Acids22.2 Configuration of the Amino Acids22.3 Acid-Base Properties of Amino Acids22.4 The Isoelectric Point22.5 Separation of Amino Acids22.6 Resolution of Racemic Mixtures of Amino Acids22.7 Peptide Bonds and Disulfide Bonds22.8 Some Interesting Peptides22.9 The Strategy of Peptide Bond Synthesis: N-Protection and C-Activation22.10 Automated Peptide Synthesis22.11 An Introduction to Protein Structure22.12 How to Determine the Primary Structure of a Peptide or a Protein22.13 Secondary Structure of Proteins22.14 Tertiary Structure of Proteins22.15 Quaternary Structure of Proteins22.16 Protein Denaturation 23. CATALYSIS 23.1 Catalysis in Organic Reactions 23.2 Acid Catalysis23.3 Base Catalysis 23.4 Nucleophilic Catalysis23.5 Metal-Ion Catalysis 23.6 Intramolecular Reactions 23.7 Intramolecular Catalysis 23.8 Catalysis in Biological Reactions 23.9 Enzyme-Catalyzed Reactions Mechanism for Carboxypeptidase A Mechanism for Serine Proteases Mechanism for Lysozyme Mechanism for Glucose-6-phosphate Isomerase Mechanism of Aldolase 24. THE ORGANIC MECHANISMS OF THE COENZYMES 24.1 An Introduction to Metabolism 24.2 The Vitamin Needed for Many Redox Reactions: Vitamin B3 24.3 Flavin Adenine Dinucleotide and Flavin Mononucleotide: Vitamin B223.4 Thiamine Pyrophosphate: Vitamin B1 23.5 Biotin: Vitamin H24.6 Pyridoxal Phosphate: Vitamin B624.7 Coenzyme B12: Vitamin B12 24.8 Tetrahydrofolate: Folic Acid24.9 Vitamin KH2: Vitamin K 25: THE CHEMISTRY OF METABOLISM 25.1 The Four Stages of Catabolism25.2 ATP Is the Carrier of Chemical Energy25.3 There Are Three Mechanisms for Phosphoryl Transfer Reactions25.4 The "High-Energy" Character of Phosphoanhydride Bonds25.5 Why ATP Is Kinetically Stable in a Cell25.6 The Catabolism of Fats25.7 The Catabolism of Carbohydrates25.8 The Fates of Pyruvate25.9 The Catabolism of Proteins25.10 The Citric Acid Cycle25.11 Oxidative Phosphorylation25.12 Anabolism 26. LIPIDS26.1 Fatty Acids Are Long-Chain Carboxylic Acids 26.2 Waxes Are High-Molecular Weight Esters26.3 Fats and Oils26.4 Phospholipids and Sphingolipids are the Components of Membranes 26.5 Prostaglandins Regulate Physiological Responses26.6 Terpenes Contain Carbon Atoms in Multiples of Five 26.7 Vitamin A Is a Terpene26.8 How Terpenes Are Biosynthesized26.9 Steroids Are Chemical Messengers26.10 How Nature Synthesizes Cholesterol26.11 Synthetic Steroids 27. NUCLEOSIDES, NUCLEOTIDES, AND NUCLEIC ACIDS27.1 Nucleosides and Nucleotides 27.2 Other Important Nucleotides27.3 Nucleic Acids Are Composed of Nucleotide Subunits 27.4 DNA Is Stable but RNA Is Easily Cleaved27.5 Biosynthesis of DNA Is Called Replication27.6 Biosynthesis of RNA Is Called Transcription27.7 There Are Three Kinds of RNA27.8 Biosynthesis of Proteins Is Called Translation 27.9 Why DNA Contains Thymine Instead of Uracil 27.10 How the Base Sequence of DNA Is Determined 27.11 Polymerase Chain Reaction (PCR) 27.12 Genetic Engineering 27.13 Laboratory Synthesis of DNA Strands IX: SPECIAL TOPICS IN ORGANIC CHEMISTRY 28. SYNTHETIC POLYMERS 28.1 There Are Two Major Classes of Synthetic Polymers 28.2 Chain-Growth Polymers Radical Polymerization Branching of the Polymer Chain Cationic Polymerization Anionic Polymerization28.3 Stereochemistry of Polymerization. Ziegler-Natta Catalysts 28.4 Polymerization of Dienes. The Manufacture of Rubber 28.5 Copolymers28.6 Step-Growth Polymers28.7 Physical Properties of Polymers 29. PERICYCLIC REACTIONS 29.1 There Are Three Kinds of Pericyclic Reations 29.2 Molecular Orbitals and Orbital Symmetry29.3 Electrocyclic Reactions 29.4 Cycloaddition Reactions 29.5 Sigmatropic Rearrangements Migration of Hydrogen Migration of Carbon29.6 Pericyclic Rections in Biological Systems Biological Cycloaddition Reactions A Biological Reaction Involving an Electrocyclic Reaction and a Sigmatropic Rearrangement 29.7 Summary of the Selection Rules for Pericyclic Reactions 30. THE ORGANIC CHEMISTRY OF DRUGS: DISCOVERY AND DESIGN30.1 Naming Drugs30.2 Lead Compounds30.3 Molecular Modification30.4 Random Screening 30.5 Serendipity in Drug Development30.6 Receptors 30.7 Drugs as Enzyme Inhibitors 30.8 Designing a Suicide Substrate30.9 Quantitative Structure-Activity Relationships (QSARs) 30.10 Molecular Modeling30.11 Combinatorial Organic Synthesis30.12 Antiviral Drugs30.13 Economics of Drugs: Governmental Regulations