Adopting a novel approach, this textbook explains the structure and reactivity of organic molecules along with simple chemical reaction mechanisms pertinent to cell metabolism, with assignments and corresponding answers for self-study in every chapter. In addition, biologically relevant substances and enzymatic reactions are described, building a bridge to biology. As opposed to textbooks in biochemistry, this book considers both primary metabolites, including their prebiotic formation, as well as important nutrients.
Alongside the detailed nomenclature and etymology of the scientific terms, examples of natural and artificial products provide an insight into the wide range of materials found in everyday life, whetting the readers` appetite for a deeper study of the chemistry of biological processes. Finally, the biographies of over one hundred famous scientists illustrate the major achievements of chemistry and biology in the 20th century.
Table of Contents
1.Introduction 1
1.1. The Field of Organic Chemistry 1
1.2. Origin of Natural Compounds 2
1.3. Classes of Natural Compounds 7
1.4. The Covalent Bond 8
1.5. Bond Dissociation Energy 9
1.6. Bond Polarization and Electronegativity 12
1.7. Dipole Moment 15
1.8. Intermolecular Interactions 17
1.9. Van der Waals Forces 17
1.10. Mechanisms of Chemical Reactions 19
1.11. Kinetics of Chemical Reactions 21
1.12. 'Stable' and Reactive Molecules 31
1.13. Molecular Shape 34
1.14. Isomerism 38
1.15. Functional Groups 39
1.16. Nomenclature of Organic Compounds 40
2. Alkanes 43
2.1. Hydrocarbons 43
2.2. Origin of Petroleum 44
2.3. Isomerism of Alkanes 46
2.4. Nomenclature of Hydrocarbons 46
2.5. Methane 48
2.6. Structure of the Methane Molecule 49
2.7. Chirality 50
2.8. Chirality and Symmetry 51
2.9. Optical Activity 56
2.10. Specification of Molecular Chirality 61
2.11. Diastereoisomers 64
2.12. Experimental Determination of Bond Energies 69
2.13. Determination of the Molecular Formulas of Organic Compounds 73
2.14. Mechanism of Combustion: Radical Substitution 74
2.15. Transition States in Chemical Reactions 77
2.16. Respiration 79
2.17. Enzymatic Oxidation of Alkanes 83
2.18. Ethane 87
2.19. Conformational Isomers 88
2.20. Butane 90
2.21. Cycloalkanes 91
2.22. Cyclohexane 94
2.23. Alkylcyclohexanes 96
2.24. Polycyclic Alkanes 99
2.25. Nomenclature of Polycycloalkanes 100
3. Unsaturated Hydrocarbons 103
3.1. Alkenes 103
3.2. Ethylene 104
3.3. p-Conformers: (Z/E)-Isomerism 106
3.4. Reactivity of Alkenes 107
3.5. Catalytic Hydrogenation 107
3.6. Stereoselectivity of Catalytic Hydrogenation 109
3.7. Stereospecificity 110
3.8. Electrophilic Addition 112
3.9. Regioselectivity of Electrophilic Addition: Markovnikov’s Rule 114
3.10. Prochirality 115
3.11. Polymerization 117
3.12. Conjugated Alkenes 121
3.13. Theory of Resonance 121
3.14. Resonance Energy 123
3.15. 1,4-Addition 124
3.16. The Diels ̶ Alder Reaction 125
3.17. The Allylic Bond 126
3.18. Sigmatropic Rearrangements 126
3.19. Terpenes 129
3.20. Semiochemicals 140
3.21. Pigments 142
3.22. Carotenoids 145
3.23. Reactivity of Photoexcited Molecules 149
3.24. Electrocyclic Reactions 151
3.25. Autoxidation 151
3.26. Cycloalkenes 156
3.27. Allenes and Alkynes 160
4. Aromatic Hydrocarbons 165
4.1. Aromaticity 165
4.2. Polycyclic Aromatic Hydrocarbons 170
4.3. Valence Isomers 174
4.4. Electrophilic Aromatic Substitution 175
4.5. The Inductive Effect 177
4.6. Pericyclic Reactions 179
4.7. Biogenesis of Benzene Derivatives 180
5. Alcohols, Phenols, and Their Derivatives 183
5.1. Nomenclature of Alcohols 183
5.2. Biosynthesis of Alcohols 184
5.3. Polyalcohols 186
5.4. Reactivity of Alcohols 188
5.5. Hydrogen Bonding 188
5.6. Acidity of Alcohols 189
5.7. Polar and Nonpolar Solvents 191
5.8. Phenols 191
5.9. Reactivity of Phenols: the Mesomeric Effect 193
5.10. Oxidation Numbers of Carbon Atoms 198
5.11. Oxidation of Alcohols 199
5.12. Oxidation of Phenols 199
5.13. The SN2 Reaction 202
5.14. Intermolecular Dehydration of Alcohols: Ether Formation 205
5.15. Unimolecular Nucleophilic Substitution (SN1 Reaction) 206
5.16. The Walden Inversion 209
5.17. The SN1’ Reaction 210
5.18. Reactivity of Carbenium Ions 211
5.19. Dehydration of Alcohols 212
5.20. Regioselectivity of the E1 Reaction 213
5.21. Wagner – Meerwein Rearrangement 214
5.22. Pinacol Rearrangement 217
5.23. Ethers 218
5.24. Reactivity of Ethers 220
5.25. Air Oxidation of Ethers 221
5.26. Oxonium Salts 222
5.27. Epoxides 223
5.28. Steroids 229
6. Thiols and Their Derivatives 233
6.1. Thiols and Thioethers 233
6.2. Disulfides 235
6.3. Redox Reactions 236
6.4. Sulfoxides and Sulfones 242
6.5. Organic Sulfur Acids 243
7. Amines 245
7.1. Nomenclature of Amines 245
7.2. Structures of Amines 246
7.3. Biogenic Amines 247
7.4. Hormones 251
7.5. Alkaloids 254
7.6. Reactivity of Amines 256
7.7. Basicity of Amines 256
7.8. Nucleophilicity of Amines 258
7.9. The Hofmann Elimination 260
7.10. Aromatic Amines 261
7.11. Formation of Diazonium Ions 263
7.12. Dyes 264
7.13. Chemotherapy 266
8. Carbonyl Compounds 271
8.1. The Carbonyl Group 271
8.2. Steroid Hormones 272
8.3. Quinones 276
8.4. Quinones in Cell Metabolism 277
8.5. Natural Pigments 279
8.6. Reactivity of the Carbonyl Group 282
8.7. The Prins Reaction 285
8.8. Polymerization of Aldehydes 286
8.9. The α-Ketol Rearrangement 287
8.10. Reactivity of Aldehydes and Ketones 288
8.11. Reduction of the Carbonyl Group 288
8.12. Oxidation of the Carbonyl Group 290
8.13. Nucleophilic Addition of Alcohols: Formation of Acetals 294
8.14. Nucleophilic Addition of Amines: Imine Formation 296
8.15. Reduction of Imines 301
8.16. C - H-Acidic Compounds: Enolates 302
8.17. Oxidation of Enolates 307
8.18. Enol Ethers: Claisen Rearrangement 309
8.19. Imine – Enamine Tautomerism 310
8.20. Aldol Addition 311
8.21. The Principle of Vinylogy: Michael Addition 315
8.22. Cyanohydrins: the Benzoin Condensation 316
8.23. Carbohydrates 318
8.24. Fischer’s Specification of Chirality 319
8.25. Structures of Monosaccharides 323
8.26. Conformations of Sugar Molecules 327
8.27. Analytical Tests for Saccharides 328
8.28. Prebiotic Synthesis of Monosaccharides 330
8.29. Metabolism of Monosaccharides 333
8.30. Sugar Acids 335
8.31. Disaccharides 338
8.32. Glycosides 341
8.33. Polysaccharides 342
9. Carboxylic Acids and Their Derivatives 351
9.1. Nomenclature of Carboxylic Acids 351
9.2. Acidity of Carboxylic Acids 352
9.3. Saturated Carboxylic Acids 357
9.4. Unsaturated Carboxylic Acids 358
9.5. Hydroxy and Oxo Carboxylic Acids 361
9.6. Amino Acids 370
9.7. Nonproteinogenic Amino Acids 373
9.8. Biosynthesis of Amino Acids 373
9.9. Metabolism of Amino Acids 378
9.10. Aromatic Carboxylic Acids 382
9.11. Reactivity of Carboxylic Acids 385
9.12. Carboxylic Acid Anhydrides 385
9.13. Decarboxylation 386
9.14. Exchange of O-Atoms 393
9.15. Esterification 394
9.16. Lipids 398
9.17. Reactivity of Carboxylic Acid Esters 405
9.18. Hydrolysis of Esters 406
9.19. Transesterification 407
9.20. Ammonolysis of Esters 408
9.21. Ester Enolates: Claisen Condensation 409
9.22. Thiocarboxylic Acids 413
9.23. Metabolism of Fatty Acids 414
9.24. Acetogenins 418
9.25. Amides 423
9.26. Amide-Like Functional Groups 425
9.27. Reactivity of Amides 429
9.28. Peptides 431
9.29. Structures of Peptides 433
9.30. Oligopeptides 437
9.31. Proteins 442
9.32. Enzymes 451
9.33. Metabolism of Proteins 458
9.34. Nitriles 461
9.35. Prebiotic Synthesis of Amino Acids 463
10. Heterocyclic Compounds 465
10.1. Nomenclature of Heterocycles 465
10.2. Heteroaromatic Compounds 467
10.3. Azoles 468
10.4. Pyrrole Pigments 472
10.5. 1H-Indole 476
10.6. Indole Alkaloids 481
10.7. Oxazoles 484
10.8. Imidazoles 484
10.9. Thiazoles 486
10.10. Azines 488
10.11. Benzopyridines 495
10.12. Tautomerism of Heteroaromatic Compounds 502
10.13. Diazines 504
10.14. Pteridines 506
10.15. Purines 513
10.16. Nucleosides and Nucleotides 517
10.17. Nucleic Acids 524
10.18. The Role of Nucleic Acids 529
10.19. Biosynthesis of Nucleic Acids 541
10.20. Prebiotic Synthesis of Nucleotides 544
10.21. Catabolism of Nucleotides 547
Exercises 555
Chapter 1 555
Chapter 2 556
Chapter 3 557
Chapter 4 560
Chapter 5 561
Chapter 6 565
Chapter 7 566
Chapter 8 568
Chapter 9 574
Chapter 10 582
Answers 585
Chapter 1 585
Chapter 2 586
Chapter 3 588
Chapter 4 590
Chapter 5 592
Chapter 6 596
Chapter 7 597
Chapter 8 601
Chapter 9 606
Chapter 10 614
Glossary 617
Index 629
