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

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

David R. Dalton

ISBN: 978-1-118-00538-5 August 2011 1532 Pages

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This book differs from other organic chemistry textbooks in that it is not focused purely on the needs of students studying premed, but rather for all students studying organic chemistry. It directs the reader to question present assumptions rather than to accept what is told, so the second chapter is largely devoted to spectroscopy (rather than finding it much later on as with most current organic chemistry textbooks). Additionally, after an introduction to spectroscopy, thermodynamics and kinetics, the presentation of structural information of compounds and organic families advances from hydrocarbons to alcohols to aldehydes and ketones and, finally, to carboxylic acids.

Preface xvii

Acknowledgments xix

Part I Background 1

1. An Introduction to Structure and Bonding 5

A. The Sources of Carbon Compounds 5

I. How Do We Know a Material Is Pure? 6

B. More about Hydrocarbons 11

I. Combustion—Heats of Reaction 12

C. On the Nature of the Chemical Bond 17

I. Ionic and Nonpolar Covalent Bonds 17

II. Polar Covalent Bonds 22

III. Orbital Hybridization 26

IV. Allotropes of Carbon 39

V. Combination of Ionic and Covalent Bonding 40

Notice to the Student 43

Additional Problems 43

Reference 45

2. An Introduction to Spectroscopy and Selected Spectroscopic Methods in Organic Chemistry 46

A. General Introduction 46

B. X-ray Crystallography 49

C. Photon Spectroscopy 50

I. General Introduction 50

II. UV and VIS Spectroscopy 52

III. IR Spectroscopy 55

IV. Raman Spectroscopy 60

V. Microwave Spectroscopy 60

VI. Magnetic Resonance Spectroscopy 61

a. NMR 61

b. ESR 79

D. MS 80

I. Creation of Ions in the Mass Spectrometer: The Ionization Chamber 81

II. The Separation of Ions by Mass: The Mass Analyzer 82

III. Detecting the Ions 83

Additional Problems 83

Reference 84

3. Structure: The Nomenclature of Hydrocarbons and the Shape of Things to Come 85

A. Introduction 85

B. Nomenclature and Spectroscopy 86

I. Alkanes 86

a. Acyclic Alkanes 86

b. Cyclic Alkanes 93

II. Alkenes, Arenes, and Alkynes 97

a. Alkenes 98

b. Arenes 103

c. Alkynes 108

C. Physical and Chemical Properties; Oxidation and Reduction of Hydrocarbons 111

I. The Concept of Homology 111

II. Oxidation and Reduction 113

a. Oxidation 113

b. Reduction 116

Additional Problems 120

References 123

4. An Introduction to Dynamics 124

A. Introduction 124

B. Review of Some Energy Considerations 126

C. The Barrier between Reactants and Products 128

D. More about the Transition State 130

E. Rotation about Sigma (σ) Bonds in Acyclic Alkanes, Alkenes, Alkynes, and Alkyl-Substituted Arenes 133

I. Alkanes 133

II. Alkenes, Alkynes, and Arenes 137

F. Conformational Analysis of Medium-Ring Cyclic Alkanes 138

G. The Conservation of Symmetry during Reactions 156

H. The Measurement of Chirality 169

I. The Wave Nature of Light 169

II. Plane-Polarized Light and Handedness 172

III. Optical Rotatory Dispersion (ORD) and Circular Dichroism (CD) 175

Additional Problems 177

5. Classes of Organic Compounds—A Survey: An Introduction to Solvents and to Acids and Bases and to Computational Chemistry 180

A. Introduction 180

B. General Characteristics of Functional Group Placement 182

C. The Functional Groups and Their Names 183

I. Hydrocarbons 183

a. Alkanes 184

b. Alkenes 184

c. Alkynes 186

d. Arenes 187

II. Alkyl and Aryl Halides 188

III. Alcohols and Phenols 194

IV. Ethers 200

V. Thiols, Thioethers, Disulfi des, and Their Oxides 204

VI. Amines, Hydrazines, and Other Nitrogenous Materials 207

VII. Phosphines, Phosphonium Salts, and Other Phosphorus Derivatives 212

VIII. An Introduction to Organometallic Compounds 214

IX. Compounds Containing Unsaturated Functional Groups 217

a. Aldehydes 217

b. Ketones 223

c. Nitrogen, Sulfur, and Phosphorus Analogues of Aldehydes and Ketones 227

d. Carboxylic Acids 227

e. Carboxylic Acid Derivatives 232

D. An Introduction to Solvents 254

I. Protic and Aprotic Solvents 255

II. Polar and Nonpolar Solvents 256

III. Polarizability 257

IV. Choosing a Solvent 257

a. Solvents for Spectroscopy 257

b. Immiscible Liquids 259

c. Organic Compounds that Dissolve in Water 259

d. Phase Transfer Catalysts 261

E. Acids and Bases 261

I. Brønsted Acids and Bases 262

II. Lewis Acids and Bases 264

III. Hard and Soft Acids and Bases (HSABs) 270

F. Computational Methods 271

I. MM 272

a. Stretching Energy Contribution (Estretch) 272

b. Bending Energy Contribution (Ebend) 272

c. Stretch-Bend Energy Contribution (Estretch-bend) 272

d. van der Waals Energy Contribution (Evan der Waals) 272

e. Torsional Energy Contribution (Etorsional) 273

f. Dipole Interaction Energy and Dipole Moment Contribution (Edipole) 273

Additional Problems 274

Part II Middleground 277

6. The Reactions of Hydrocarbons: Oxidation, Reduction, Substitution, Addition, Elimination, and Rearrangement 291

A. Introduction 291

B. Alkanes 292

I. Oxidation 292

II. Reduction 295

III. Substitution 296

IV. Rearrangement 301

C. Alkenes 301

I. Oxidation 301

II. Reduction 312

III. Addition 316

a. Electrophilic Addition 317

b. Nucleophilic Addition to Alkenes, Dienes, and Polyenes 351

c. Radical Addition to Alkenes, Dienes, and Polyenes 354

d. Intermolecular Cheletropic and Other Cycloaddition Reactions 359

IV. Substitution 369

V. Rearrangement 371

D. Alkynes 382

I. Oxidation 382

II. Reduction 385

III. Addition 386

a. Electrophilic Addition 387

b. Nucleophilic Addition to Alkynes and Conjugated Enynes 394

c. Radical Addition to Alkynes 398

d. Intermolecular Cheletropic and Other Cycloaddition Reactions 398

E. Arenes and Aromaticity: Special Introduction 403

I. Oxidation 413

a. Oxidation of the Aromatic Ring 413

b. Oxidation of Alkyl Substituents on the Aromatic Ring 419

II. Reduction 420

III. Addition 422

IV. Substitution 424

a. Electrophilic Aromatic Substitution 425

b. Nucleophilic Aromatic Substitution 447

c. Free Radical Substitution 448

Additional Problems 450

7. The Reactions of Alkyl, Alkenyl, and Aryl Halides: Oxidation, Reduction, Substitution, Addition, Elimination, and Rearrangement 452

A. Introduction 452

B. Fluorocarbons 456

I. Freons and Halons 457

II. Polymers of Highly Fluorinated Monomers 459

III. Use of Fluorocarbons to Carry Oxygen 459

C. Oxidation 459

D. Reduction of Alkyl, Alkenyl, and Aryl Halides 462

I. Dehalogenation and Reductions at Carbon 462

a. Hydrogenolysis 463

b. Substitution of Hydride for Halide 463

c. Radical Replacement of Halogen by Hydrogen 464

d. Reaction of Alkyl, Alkenyl, and Aryl Halides with Metals 466

II. Reductions at Halogen 473

E. Nucleophilic Substitution 476

I. Nucleophiles and Nucleophilicity 480

II. SN1 481

a. The Kinetics 482

b. Electronegativity Differences 485

c. The Structure of the Alkyl Group 486

d. The Role of the Solvent 487

e. The Substrate Stereochemistry Attending the SN1 Reaction 488

III. SN2 492

a. The Kinetics 495

b. The Stereochemistry of the SN2 Reaction 498

c. The Nature of the Leaving Group 500

d. The Nature of the Nucleophile 501

e. The Nature of the Solvent 502

IV. The SN2′ Reaction 502

V. Nucleophilic Aromatic Substitution 504

a. The Elimination-Addition Pathway (Benzyne) 504

b. The Addition-Elimination Pathway (SNAr Substitution) 506

VI. Electrophilic Aromatic Substitution 506

VII. Substitution by Carbon 507

VIII. Photochemically Induced Substitution of Vinyl and Aryl Halides 510

F. Addition Reactions 512

I. Addition Reactions to Vinyl Halides 513

G. Elimination Reactions of Alkyl and Alkenyl Halides 517

I. α-Elimination (1,1-Elimination) 519

a. α-Elimination of HX (X = Cl, Br) from Alkyl and Alkenyl Halides 519

b. α-Elimination of X2 (X = Cl) from Alkyl Dihalides 521

II. β-Elimination (1,2-Elimination) 521

a. β-Elimination of HX (X = F, Cl, Br, I) from Alkyl and Alkenyl Halides 521

b. 1,2- or α,β-Elimination of X2 (X = Cl, Br) from Alkyl and Alkenyl Dihalides 551

III. γ-Elimination (1,3-Elimination) and δ-Elimination (1,4-Elimination) 551

a. γ-Elimination of HX (X = Cl, Br, I) from Alkyl and Alkenyl Halides 551

b. γ-Elimination of X2 (X = Cl, Br, I) from Alkyl Halides 553

c. δ-Elimination of X2 (X = Cl, Br, I) from Alkenyl Halides 553

H. Rearrangement Reactions of Alkyl and Alkenyl Halides 553

Additional Problems 560

References 561

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 562

Special Introduction to Chapter 8 562

Part I. Alcohols, Enols, and Phenols 566

A. Acidity and Basicity 566

B. Oxidation of Alcohols, Enols, and Phenols 573

I. Introduction 573

II. Oxidation at the Hydroxyl-Bearing Carbon 574

a. Chemical Oxidation of Alcohols 574

b. Biological Oxidation of Alcohols 594

III. Oxidation at Sites That Do Not Bear Hydroxyl 596

a. Oxidation of Enols 596

b. Oxidation of Phenols 600

c. Oxidation at the Double Bond of Allylic Alcohols 604

C. Reduction of Alcohols, Enols, and Phenols 608

I. Reduction of Alcohols 608

II. Reduction of Enols and Phenols 613

D. Substitution Reactions of Alcohol, Enols, and Phenols 615

I. Introduction 615

II. Substitution Reactions of Alcohols, Enols, and Phenols at Oxygen 617

III. Substitution Reactions of Alcohols at Carbon 618

a. Formation of Alkyl Halides 618

b. Replacement of the Hydroxyl (–OH) Functional Group by Other Substituents 623

c. Replacement of the Hydroxyl (–OH) Functional Group by Carbon: An Example from Nature 627

IV. Substitution Reactions of Enols and Phenols at Carbon 630

a. Substitution at the Carbon-Bearing Oxygen 630

b. Electrophilic Aromatic Substitution of Phenols 632

E. Addition Reactions of Alcohols, Enols, and Phenols 642

I. Introduction 642

II. Addition of the Oxygen of Alcohols to Carbon (with Loss of Hydrogen) 643

F. Elimination Reactions of Alcohols, Enols, and Phenols 663

I. Introduction 663

II. Acid-Catalyzed Elimination of Water 665

III. Elimination from Derivatives of Alcohols 669

G. Rearrangement Reactions of Alcohols, Enols, and Phenols 678

I. Introduction 678

Part II. Ethers 690

A. Introduction 690

B. The Reactions of Ethers 692

Part III. Thiols, Thioethers, and Some Products of Their Oxidation 708

Additional Problems 717

References 718

9. Part I. The Reactions of Aldehydes and Ketones: Oxidation, Reduction, Addition, Substitution, and Rearrangement Part II. The Reactions of Carboxylic Acids and Their Derivatives: Oxidation, Reduction, Addition, Substitution, Elimination, and Rearrangement 719

A. Introduction 719

Part I. Aldehydes and Ketones 725

A. Oxidation of Aldehydes and Ketones 725

B. Reduction of Aldehydes and Ketones 743

I. Introduction 743

II. Reduction of Aldehydes and Ketones to Hydrocarbons 744

III. Reduction of Aldehydes and Ketones to Alcohols 745

C. Addition to Aldehydes and Ketones 758

I. Introduction 758

II. Photochemical Reactions of Aldehydes and Ketones 762

a. Nonconjugated Carbonyl Compounds 762

b. Conjugated Carbonyl Compounds 764

III. Thermal Electrocyclic and Related Reactions of Aldehydes and Ketones 769

a. Nonconjugated Carbonyl Compounds 769

b. Conjugated Carbonyl Compounds 770

c. The Carbonyl “ene” Reaction 771

IV. Nucleophilic Addition Reactions Retaining the Carbonyl Oxygen 772

a. General Comments 772

b. Addition of H–X 774

c. Addition of Carbon Nucleophiles 775

V. Nucleophilic Addition Reactions with Loss of the Carbonyl Oxygen 800

a. General Comments 800

b. Formation of Acetals, Ketals, and Thioketals 800

c. Reaction of Aldehydes and Ketones with Nitrogen Nucleophiles 803

d. Replacement of the Carbonyl Oxygen by Halogen and Sulfur 813

e. Replacement of the Oxygen of the Carbonyl by Carbon 816

f. Addition to the Carbon Alpha (α) to the Carbonyl (C=O) 831

D. Substitution Reactions Producing Aldehydes and Ketones 841

I. Introduction 841

II. Reimer–Tiemann Synthesis 842

III. Gatterman–Koch (Friedel–Crafts) Formylation 844

IV. The Pauson–Khand Reaction 846

E. Rearrangement Reaction of Aldehydes and Ketones 847

I. Introduction 847

II. The Benzilic Acid Rearrangement 847

III. The Dienone–Phenol Rearrangement 847

IV. Anionic Rearrangements 849

Part II. Carboxylic Acids and Their Derivatives 852

A. General Introduction 852

B. Oxidation 854

C. Reduction 861

D. Substitution: Addition and Elimination 870

E. Additional Reactions and Rearrangements of Esters and β-Dicarbonyl Compounds 926

Additional Problems 936

10. Part I. The Reactions of Amines: Oxidation, Reduction, Addition, Substitution, and Rearrangement Part II. Some Organophosphorus Chemistry Part III. Some Organosilicon Chemistry 937

Part I. The Reactions of Amines 937

A. Introduction 937

B. Some Comments on the Preparation of Amines 945

C. Oxidation of Amines 951

I. Oxygen and Peroxide Oxidations 951

II. Other Oxidizing Agents 959

a. General 959

b. Oxidation by Halogen 960

c. Oxidation with Nitrous Acid 963

D. Reduction of Amines 966

E. Addition and Substitution Reactions of Amines 967

I. General Introduction 967

F. Addition and Rearrangement Reactions of Amines 977

Part II. Some Organophosphorus Chemistry 995

Part III. Some Organosilicon Chemistry 1005

Additional Problems 1019

References 1019

Part III Foreground 1021

11. An Introduction to Carbohydrates, Acetogenins, and Steroids 1027

A. Introduction 1027

B. The Calvin Cycle 1028

C. Carbohydrates 1037

I. Biosynthesis 1037

II. Chemistry 1039

III. Oligosaccharides 1052

IV. Polysaccharides 1057

D. Acetogenins 1058

I. Acetyl-CoA (CH3COSCoA) 1058

II. Acetyl-CoA (CH3COSCoA) to Fatty Acids and Related Compounds 1062

III. Isoprenoides: To Dimethylallyl Diphosphate and Beyond 1071

a. Dimethylallyl Diphosphate from Acetyl-CoA via Mevalonate 1071

b. Dimethylallyl Diphosphate from Pyruvate and Glyceraldehyde 1072

c. Terpenes 1076

d. Loose Ends 1108

Additional Problems 1120

References 1120

12. An Introduction to Amino Acids, Peptides and Proteins, Enzymes, Coenzymes, and Metabolic Processes 1121

A. Introduction 1121

B. Amino Acids 1129

I. Biosynthesis 1129

II. Synthesis 1157

C. Peptides and Proteins—Introduction 1184

I. Amino Acids from Peptides 1185

II. Peptides from Amino Acids—In Vivo 1194

III. Peptides from Amino Acids—In Vitro 1206

D. The Coenzymes 1210

I. Pyridoxal Phosphate 1212

II. Lipoic Acid 1215

III. Thiamine Diphosphate 1217

a. 4-Amino-5-hydroxymethyl-2-methylpyrimidine 1218

b. 4-Methyl-5-(2-Phosphonooxyethyl) thiazole 1219

c. Thiamine Diphosphate 1220

IV. Biotin 1223

V. Adenosine 1227

VI. NAD+ 1232

VII. Coenzyme A (CoA-SH) 1236

VIII. FAD 1239

IX. SAM 1246

X. Tetrahydrofolate 1247

Reference 1251

13. An Introduction to Alkaloids and Some Other Heterocyclic Compounds 1252

A. Introduction 1252

B. Tropane Alkaloids 1254

I. Chemistry of Hyoscyamine 1254

II. Chemistry of Nicotine 1262

III. Biosynthesis of Hyoscyamine and Nicotine 1267

a. The Common Feature 1267

b. The Biosynthesis of Nicotine 1269

c. The Biosynthesis of Hyoscyamine 1271

d. The Biosynthesis of Tropic Acid 1272

C. Morphine (and Codeine and Thebaine) 1275

I. Chemistry of Morphine (and Codeine and Thebaine) 1275

II. The Biosynthesis of Morphine (and Codeine and Thebaine) 1290

III. The Synthesis of Morphine 1296

D. Vinblastine 1301

I. Chemistry of Vinblastine 1301

II. Biosynthesis of Vinblastine 1311

E. Caffeine 1315

I. Some History and the Synthesis of Caffeine 1315

II. Biosynthesis of Caffeine 1318

14. Part I. On the Genetic Code: Unity and Diversity Part II. The Tetrapyrrolic Cofactors: Unity and Diversity 1322

Part I. On the Genetic Code: Unity and Diversity 1322

A. Introduction (the Genetic Code) 1322

B. Part A 1323

I. The Bases of DNA and RNA 1323

a. Adenine (A) 1324

b. Guanine (G) 1324

c. Uracil (U) and Thymine (T) 1326

d. Cytosine (C) 1329

II. Deoxynucleotides 1331

III. The Role of Phosphate 1336

C. Part B 1340

I. The Sequencing of DNA 1340

II. Chemical Synthesis of DNA 1340

III. Modification to DNA 1345

Part II. The Tetrapyrrolic Cofactors: Unity and Diversity 1347

A. The Tetrapyrrolic Cofactors 1347

I. Introduction 1347

II. Some Early Chemistry 1349

III. Current Biosynthetic Understanding 1354

Epilogue 1365

Appendix I The Schrödinger Equation 1366

Appendix II The Literature 1371

Index 1373

““It provides the reader with the necessary support to learn and properly understand organic chemistry, and with a good overview of this interdisciplinary field and its relationship to other branches of chemistry and natural sciences.” (Angewandte Chemie, 2012)

  • Includes broad coverage of all topics relevant to organic chemistry     
  • Suitable for chemistry majors rather than just pre-med students, setting it apart from other competing textbooks
  • Directs the reader to question present assumptions rather than to accept what is told, unlike other books that stress uncritical thinking and applications
  • Provides an easy-to-use one volume textbook for all students of chemistry
  • Discusses thermodynamics and kinetics, the structural information advances from hydrocarbons to alcohols to aldehydes and ketones and, finally, to carboxylic acids
  • Devotes almost an entire chapter to spectroscopy early on in the text, as opposed to similar texts that include it much later