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Organic Chemistry
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1. Electronic Structure and Bonding - Acids and Bases
1.1 The Structure of an atom
1.2 The Distribution of Electrons in an Atom
1.3 Ionic, Covalent and polar bonds
1.4 Representation of Structure
1.5 Atomic Orbitals
1.6 AN introduction to molecular Orbital Theory
1.7 Bonding in Methane and Ethane: Single Bonds
1.8 Bonding in Ethane: A double bond
1.9 Bonding in Ethyne: A Triple Bond
1.10 Bonding in the MEthyl Cation, The methyl Radical and the methyl Anion
1.11 Bonding in water
1.12 Bonding in Ammonia and in the Ammonium ion
1.13 Bonding in the hydrogen halides
1.14 Summary: orbital Hybridization, Bond lengths, Bond Strengths and Bond Angles
1.15 Dipole Moments of Molecules
1.16 An Introduction to Acids and Bases
1.17 Organic Acids and Bases; pka and pH
1.18 The Effect of Structure on pKa
1.19 An Introduction to Declocalized Electrons and Resonance
1.20 The Effect of pH on the structure of an Organic Compound
2. An Introduction to Organic Compounds
2.1 Nomenclature of Alkyl Substituents
2.2 Nomenclature of Alkanes
2.3 Nomenclature of Cycloalkanes
2.4 Nomenclature of Alkyl Halides
2.5 Nomenclature of Ethers
2.6 Nomenclature of Alcohols
2.7 Nomenclature of Amines
2.8 Structures of Alkyl Halides, Alcohols, Ethers, and Amines
2.9 Physical Properties of Alkanes, Alkyl Halides, Alcohols, Ethers, and Amines
2.10 Conformations of Alkanes: Rotation About Carbon–Carbon Bonds
2.11 Cycloalkanes: Ring Strain
2.12 Conformations of Cyclohexane
2.13 Conformations of Monosubstituted Cyclohexanes
2.14 Conformations of Disubstituted Cyclohexanes
2.15 Conformations of Fused Rings
3. Alkenes Structure, Nomenclature and an introduction to Reactivity
Thermodynamics and Kinetics
3.1 Molecular Formula and the degree of Unsaturation
3.2 Nomenclature of Alkenes
3.3 The Structure of Alkenes
3.4 Cis Trans Isomerism
3.5 The E,Z System of Nomenclature
3.6 How Alkenes react. Curved arrows
3.7 Thermodynamics and Kinetics
4. Reactions of Alkenes
4.1 Addition of Hydrogen Halides
4.2 Carbocation Stability
4.3 The Structure of the Transition State
4.4 Regioslectivity of Electrophilic Addition Reactions
4.5 Addition of water and addition of Alcohols
4.6 Rearrangement of Carbocations
4.7 Addition of Halogens
4.8 Oxymercuration–Reduction and Alkoxymercuration–Reduction
4.9 Addition of Borane: Hydroboration–Oxidation
4.10 Addition of Radicals • The Relative Stabilities of Radicals
4.11 Addition of Hydrogen • The Relative Stabilities of Alkenes
4.12 Reactions and Synthesis
5. Stereochemistry
5.1 Cis–Trans Isomers
5.2 Chirality
5.3 Asymmetric Carbons, Chirality Centers, and Stereocenters
5.4 Isomers with One Asymmetric Carbon
5.5 Drawing Enantiomers
5.6 Naming Enantiomers: The R,S System of Nomenclature
5.7 Optical Activity
5.8 Optical Purity and Enantiomeric Excess
5.9 Isomers with More than One Asymmetric Carbon
5.10 Meso Compounds
5.11 The R,S System of Nomenclature for Isomers with More than One Asymmetric Carbon
5.12 Reactions of Compounds that Contain an Asymmetric Carbon
5.13 The Absolute Configuration of (+) Glyceraldehyde
5.14 Seperating Enantiomers
5.15 Discrimination of Enantiomers by Biological Molecules
5.16 Enantiotopic Hydrogens, Diastereotopic Hydrogens and Prochiral Carbons
5.17 Nitrogen and Phosphorus Chairality Centers
5.18 Sterochemistry of Reactions, Regioselective Stereoselective and Sterospecific Reactions
5.19 Stereochemistry of Electrophilic Addition Reactions of Alkenes
5.20 Stereochemistry of Enzyme-Catalyzed Reactions
6. Reactions of Alkynes Introduction to Multistep Synthesis
6.1 Nomenclature of Alkynes
6.2 Physical properties of unsaturated Hydrocarbons
6.3 The Structure of Alkynes
6.4 How Alkynes React
6.5 Addition of Hydrogen Halides and Addition of Halogens
6.6 Addition of Water
6.7 Addition of Borane: Hydroboration - Oxidation
6.8 Addition of Hydrogen
6.9 Acidity of a Hydrogen Bonded to an sp Hybridized Carbon
6.10 Synthesis Using Acetylide Ions
6.11 Designing a Synthesis I: An Introduction to Multistep Synthesis
6.12 Commercial Use of Ethyne
7. Electron Delocalization and Resonance • More About Molecular Orbital Theory
7.1 Delocalized Electrons: The Structure of Benzene
7.2 The Bonding in Benzene
7.3 Resonance Contributors and the Resonance Hybrid
7.4 Drawing Resonance Contributors
7.5 Predicted Stabilities of Resonance Contributors
7.6 Resonance Energy
7.7 Stability of Allylic and Benzylic Cations
7.8 Stability of Allylic and Benzylic Radicals
7.9 Some Chemical Consequences of Electron Delocalization
7.10 The Effect of Electron Delocalization on pKa
7.11 A Molecular Orbital Description of Stability
8. Reactions of Dienes Ultravoilet and Visible Spectroscopy
8.1 Nomenclature of Alkenes with More than One Functional Group
8.2 Configurational Isomers of Dienes
8.3 Relative Stabilities of Dienes
8.4 How Dienes React
8.5 Electrophilic Addition Reactions of Isolated Dienes
8.6 Electrophilic Addition Reactions of Conjugated Dienes
8.7 Thermodynamic Versus Kinetic Control of Reactions
8.8 The Diels–Alder Reaction: A 1,4-Addition Reaction
8.9 Ultraviolet and Visible Spectroscopy
8.10 The Beer–Lambert Law
8.11 Effect of Conjugation on Lmax
8.12 The Visible Spectrum and Color
8.13 Uses of UV/VIS Spectroscopy
9. Reactions of Alkanes Radicals
9.1 The Low Reactivity of Alkanes
9.2 Chlorination and Bromination of Alkanes
9.3 Factors that Determine Product Distribution
9.4 The Reactivity–Selectivity Principle
9.5 Radical Substitution of Benzylic and Allylic Hydrogens
9.6 Stereochemistry of Radical Substitution Reactions
9.7 Reactions of Cyclic Compounds
9.8 Radical Reactions in Biological Systems
9.9 Radicals and Stratospheric Ozone
10.Substitution Reactions of Alkyl Halides
10.1 How Alkyl Halides React
10.2 The Mechanism of an SN2 Reaction
10.3 Factors Affecting SN2 Reactions
10.4 The Reversibility of an SN2 Reaction
10.5 The Mechanism of an SN1 Reaction
10.6 Factors Affecting SN1 Reactions
10.7 More About the Stereochemistry of SN2 and SN1 Reactions
10.8 Benzylic Halides, Allylic Halides, Vinylic Halides, and Aryl Halides
10.9 Competition Between SN2 and SN1 Reactions
10.10 The Role of the Solvent in SN2 and SN1 Reactions
10.11 Biological Methylating Reagents
11. Elimination Reactions of Alkyl Halides • Competition Between Substitution and Elimination
11.1 The E2 Reaction
11.2 The Regioselectivity of the E2 Reaction
11.3 The E1 Reaction
11.4 Competition Between E2 and E1 Reactions
11.5 Stereochemistry of E2 and E1 Reactions
11.6 Elimination from Cyclic Compounds
11.7 A Kinetic Isotope Effect
11.8 Competition Between Substitution and Elimination
11.9 Substitution and Elimination Reactions in Synthesis
11.10 Consecutive E2 Elimination Reactions
11.11 Intermolecular Versus Intramolecular Reactions
11.12 Designing a Synthesis II: Approaching the Problem
12. Reactions of Alcohols, Ethers, Epoxides and Sulfur - Containing Compounds Organometallic Compounds
12.1 Substitution Reactions of Alcohols
12.2 Amines Do Not Undergo Substitution Reactions
12.3 Other Methods for Converting Alcohols into Alkyl Halides
12.4 Converting Alcohols into Sulfonate Esters
12.5 Elimination Reactions of Alcohols: Dehydration
12.6 Substitution Reactions of Ethers
12.7 Reactions of Epoxides
12.8 Arene Oxides
12.9 Crown Ethers
12.10 Thiols, Sulfides, and Sulfonium Salts
12.11 Organometallic Compounds
12.12 Coupling Reactions
13. Mass Spectrometry and Infrared Spectroscopy
13.1 Mass Spectrometry
13.2 The Mass Spectrum • Fragmentation
13.3 Isotopes in Mass Spectrometry
13.4 Determination of Molecular Formulas: High-Resolution Mass Spectrometry
13.5 Fragmentation at Functional Groups
13.6 Spectroscopy and the Electromagnetic Spectrum
13.7 Infrared Spectroscopy
13.8 Characteristic Infrared Absorption Bands
13.9 The Intensity of Absorption Bands
13.10 The Position of Absorption Bands
13.11 C ¬ H Absorption Bands
13.12 The Shape of Absorption Bands
13.13 Absence of Absorption Bands
13.14 Infrared Inactive Vibrations
13.15 Identifying Infrared Spectra
14. NMR Spectroscopy
14.1 Introduction to NMR Spectroscopy
14.2 Fourier Transform NMR
14.3 Shielding
14.4 The Number of Signals in the 1H NMR Spectrum
14.5 The Chemical Shift
14.6 The Relative Positions of H NMR Signals
14.7 Characteristic Values of Chemical Shifts
14.8 Integration of NMR Signals
14.9 Diamagnetic Anisotropy
14.10 Splitting of the Signals
14.11 More Examples of 1H NMR Spectra
14.12 Coupling Constants
14.13 Splitting Diagrams
14.14 Time Dependence of NMR Spectroscopy
14.15 Protons Bonded to Oxygen and Nitrogen
14.16 Use of Deuterium in 1H NMR Spectroscopy
14.17 Resolution of 1H NMR Spectra
14.18 13C NMR Spectroscopy
14.19 DEPT 13 C NMR Spectra
14.20 Two-Dimensional NMR Spectroscopy
14.21 Magnetic Resonance Imaging
15. Aromaticity Reactions of Benzene
15.1 Criteria for Aromaticity
15.2 Aromatic Hydrocarbons
15.3 Aromatic Heterocyclic Compounds
15.4 Some Chemical Consequences of Aromaticity
15.5 Antiaromaticity
15.6 A Molecular Orbital Description of Aromaticity and Antiaromaticity
15.7 Nomenclature of Monosubstituted Benzenes
15.8 How Benzene Reacts
15.9 General Mechanism for Electrophilic Aromatic Substitution Reactions
15.10 Halogenation of Benzene
15.11 Nitration of Benzene
15.12 Sulfonation of Benzene
15.13 Friedel–Crafts Acylation of Benzene
15.14 Friedel–Crafts Alkylation of Benzene
15.15 Alkylation of Benzene by Acylation–Reduction
16. Reactions of Substituted Benzenes
16.1 Nomenclature of Disubstituted and Polysubstituted Benzenes
16.2 Reactions of Substituents on Benzene
16.3 The Effect of Substituents on Reactivity
16.4 The Effect of Substituents on Orientation
16.5 The Effect of Substituents on pKa
16.6 The Ortho–Para Ratio
16.7 Additional Considerations Regarding Substituent Effects
16.8 Designing a Synthesis III: Synthesis of Monosubstituted and Disubstituted Benzenes
16.9 Synthesis of Trisubstituted Benzenes
16.10 Synthesis of Substituted Benzenes Using Arenediazonium Salts
16.11 The Arenediazonium Ion as an Electrophile
16.12 Mechanism for the Reaction of Amines with Nitrous Acid
16.13 Nucleophilic Aromatic Substitution Reactions
16.14 Benzyne
16.15 Polycyclic Benzenoid Hydrocarbons
16.16Electrophilic Substitution Reactions of Naphthalene and Substituted Naphthalenes
17. Carbonyl Compounds - Nucleophilic Acyl Substitution
17.1 Nomenclature
17.2 Structures of Carboxylic Acids and Carboxylic Acid Derivatives
17.3 Physical Properties of Carbonyl Compounds
17.4 Naturally Occurring Carboxylic Acids and Carboxylic Acid Derivatives
17.5 How Class I Carbonyl Compounds React
17.6 Relative Reactivities of Carboxylic Acids and Carboxylic Acid Derivatives
17.7 General Mechanism for Nucleophilic Acyl Substitution Reactions
17.8 Reactions of Acyl Halides
17.9 Reactions of Acid Anhydrides
17.10 Reactions of Esters
17.11 Acid-Catalyzed Ester Hydrolysis
17.12 Hydroxide-Ion-Promoted Ester Hydrolysis
17.13 Soaps, Detergents, and Micelles
17.14 Reactions of Carboxylic Acids
17.15 Reactions of amides
17.16 Acid- catalysed Hydrolysis of Amides
17.17 Hyydrolysis of an Imide
17.18 Hydrolysis of Nitriles
17.19 Designing a Synthesis IV: The Synthesis of Cyclic Compounds
17.20 Synthesis of Carboxylic Acid Derivatives
17.21 Dicarboxylic Acids and Their Derivatives
18. Carbonyl Compounds- Nucleophilic Acyl Addition, Nucleophilic Acyl Substitution, and Nucleophilic Addition–Elimination, Reactions of a, b -Unsaturated Carbonyl Compounds
18.1 Nomenclature
18.2 Relative Reactivities of Carbonyl Compounds
18.3 How Aldehydes and Ketones React
18.4 Reactions of Carbonyl Compounds with Carbon Nucleophiles
18.5 Reactions of Carbonyl Compounds with Hydride Ion
18.6 Reactions of Aldehydes and Ketones with Nitrogen Nucleophiles
18.7 Reactions of Aldehydes and Ketones with Oxygen Nucleophiles
18.8 Protecting Groups
18.9 Addition of Sulfur Nucleophiles
18.10 The Wittig Reaction
18.11 Stereochemistry of Nucleophilic Addition Reactions: Re and Si Faces
18.12 Designing a Synthesis V: Disconnections, Synthons, and Synthetic Equivalents
18.13 Nucleophilic Addition to A,B -Unsaturated Aldehydes and Ketones
18.14 Nucleophilic Addition to A,B -Unsaturated Carboxylic Acid Derivatives
18.15 Enzyme-Catalyzed Additions to A,B -Unsaturated Carbonyl Compounds
19. Carbonyl Compounds III - Reactions at the a-Carbon
19.1 Acidity of A-Hydrogens
19.2 Keto–Enol Tautomerism
19.3 How Enols and Enolate Ions React
19.4 Halogenation of the A-Carbon of Aldehydes and Ketones
19.5 Halogenation of the A-Carbon of Carboxylic Acids: The Hell–Volhard–Zelinski Reaction
19.6 A-Halogenated Carbonyl Compounds in Synthesis
19.7 Using LDA to Form an Enolate
19.8 Alkylation of the A-Carbon of Carbonyl Compounds
19.9 Alkylation and Acylation of the A-Carbon via an Enamine Intermediate
19.10 Alkylation of the B -Carbon: The Michael Reaction
19.11 The Aldol Addition
19.12 Dehydration of Aldol Addition Products: Formation of A,B -Unsaturated Aldehydes and Ketones
19.13 The Mixed Aldol Addition
19.14 The Claisen Condensation
19.15 The Mixed Claisen Condensation
19.16 Intramolecular Condensation and Addition Reactions
19.17 Decarboxylation of 3-Oxocarboxylic Acids
The Malonic Ester Synthesis: Synthesis of Carboxylic Acids
19.18 The Acetoacetic Ester Synthesis: Synthesis of Methyl Ketones
19.20 Designing a Synthesis VI: Making New Carbon–Carbon Bonds
19.21 Reactions at the A-Carbon in Biological Systems
20. More About Oxidation- Reduction Reactions
20.1 Reduction Reactions
20.2 Oxidation of Alcohols
20.3 Oxidation of Aldehydes and Ketones
20.4 Oxidation of Alkenes with Peroxyacids
20.5 Designing a Synthesis VII: Controlling Stereochemistry
20.6 Hydroxylation of Alkenes
20.7 Oxidative Cleavage of 1,2-Diols
20.8 Oxidative Cleavage of Alkenes
20.9 Oxidative Cleavage of Alkynes
20.10 Designing a Synthesis VIII: Functional Group Interconversion
20.11 Biological Oxidation–Reduction Reactions
20.12 Oxidation of Hydroquinones and Reduction of Quinones
21. More About Amines Heterocyclic Compounds
21.1 More About Nomenclature
21.2 Amine Inversion
21.3 More About the Acid–Base Properties of Amines
21.4 Reactions of Amines
21.5 Reactions of Quaternary Ammonium Hydroxides
21.6 Phase Transfer Catalysis
21.7 Oxidation of Amines; The Cope Elimination Reaction
21.8 Synthesis of Amines
21.9 Aromatic Five-Membered-Ring Heterocycles
21.10 Aromatic Six-Membered-Ring Heterocycles
21.11 Biologically Important Heterocycles
22. Carbohydrates
22.1 Classification of Carbohydrates
22.2 The D and L Notation
22.3 Configuration of Aldoses
22.4 Configurations of Ketoses
22.5 Redox Reactions of Monosaccharides
22.6 Osazone Formation
22.7 Chain Elongatin: The Kiliani - Fischer Synthesis
22.8 Chain Shortening: The Ruff Degradation
22.9 Stereochemistry of Glucose : The Fischer Proof
22.10 Cyclic Structure of Monosaccharides: Hemiacetal Formation
22.11 Stability of Glucose
22.12 Acylation and Alkylation of Monosaccharides
22.13 Formation of Glycosides
22.14 The Anomeric Effect
22.15 Reducing and Nonreducing Sugars
22.16 Determination of Ring Size
22.17 Disaccharides
22.18 Polysaccharides
22.19 Some Naturally Occurring Products Derived from Carbohydrates
22.20 Carbohydrates on Cell Surfaces
22.21 Synthetic Sweeteners
23. Amino Acids, Peptides and Proteins
23.1 Classification and Nomenclature of Amino Acids
23.2 Configuration of Amino Acids
23.3 Acid–Base Properties of Amino Acids
23.4 The Isoelectric Point
23.5 Separation of Amino Acids
23.6 Resolution of Racemic Mixtures of Amino Acids
23.7 Peptide Bonds and Disulfide Bonds
23.8 Some Interesting Peptides
23.9 Strategy of Peptide Bond Synthesis: N-Protection and C-Activation
23.10 Automated Peptide Synthesis
23.11 Protein Structure
23.12 Determining the Primary Structure of a Protein
23.13 Secondary Structure of Proteins
23.14 Tertiary Structure of Proteins
23.15 Quaternary Structure of Proteins
23.16 Protein Denaturation
24. Catalysis
24.1 Catalysis in Organic Reactions
24.2 Nucleophilic Catalysis
24.3 Acid Catalysis
24.4 Base Catalysis
24.5 Metal-Ion Catalysis
24.6 Intramolecular Reactions
24.7 Intramolecular Catalysis
24.8 Catalysis in Biological Reactions
24.9 Enzyme-Catalyzed Reactions
25. The Organic Mechanisms of the Coenzymes Metabolism
25.1 Overall View of Metabolism
25.2 Niacin: The Vitamin Needed for Many Redox Reactions
25.3 Flavin Adenine Dinucleotide and Flavin Mononucleotide: Vitamin B2
25.4 Thiamine Pyrophosphate: Vitamin B1
25.5 Biotin: Vitamin H
25.6 Pyridoxal Phosphate: Vitamin B6
25.7 Coenzyme B12 : Vitamin B12
25.8 Tetrahydrofolate: Folic Acid
25.9 Vitamin KH2 : Vitamin K
26. Lipids
26.1 Fatty Acids
26.2 Waxes
26.3 Fats and Oils
26.4 Membranes
26.5 Prostaglandins
26.6 Terpenes
26.7 Vitamin A
26.8 Biosynthesis of Terpenes
26.9 Steroids
26.10 Biosynthesis of Cholesterol
26.11 Synthetic Steroids
27.Nucleosides, Nucleotides, and Nucleic Acids
27.1 Nucleosides and Nucleotides
27.2 ATP: The Carrier of Chemical Energy
27.3 Three Mechanisms for Phosphoryl Transfer Reactions
27.4 The “High-Energy” Character of Phosphoanhydride Bonds
27.5 Kinetic Stability of ATP in the Cell
27.6 Other Important Nucleotides
27.7 The Nucleic Acids
27.8 Helical Forms of DNA
27.9 Biosynthesis of DNA: Replication
27.10 Biosynthesis of RNA: Transcription
27.11 Ribosomal RNA
27.12 Transfer RNA
27.13 Biosynthesis of proteins:translation
27.14 Why DNA Contains Thymine Instead of Uracil
27.15 Determining the Base Sequence of DNA
27.16 Laboratory Synthesis of DNA Strands
27.17 Rational Drug Design
28. Synthetic Polymers
28.1 General Classes of Synthetic Polymers
28.2 Chain-Growth Polymers
28.3 Stereochemistry of Polymerization • Ziegler–Natta Catalysts
28.4 Polymerization of Dienes • The Manufacture of Rubber
28.5 Copolymers
28.6 Step-Growth Polymers
28.7 Physical Properties of Polymers
29. Pericyclic Reactions
29.1 Three Kinds of Pericyclic Reactions
29.2 Molecular Orbitals and Orbital Symmetry
29.3 Electrocyclic Reactions
29.4 Cycloaddition Reactions
29.5 Sigmatropic Rearrangements
29.6 Pericyclic Reactions in Biological Systems
29.7 Summary of the Selection Rules for Pericyclic Reactions
30. The Organic Chemistry of Drugs
30.1 Naming Drugs
30.2 Lead Compounds
30.3 Molecular Modification
30.4 Random Screening
30.5 Serenipity in Drug Development
30.6 Receptors
30.7 Drugs as Enzyme Inhibitors
30.8 Designing a Suicide Substrate
30.9 Quantitative Structure–Activity Relationships (QSAR)
30.10 Molecular Modeling
30.11 Combinatorial Organic Synthesis
30.12 Antiviral Drugs
30.13 Economics of Drugs • Governmental Regulations
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