Essentials of Organic Chemistry

686 INDEX

Hydrogen bonds (continued ) Iduronic acid, in heparin 496 Intramolecular aldol reaction, see aldol
in α-helix 511 Imidazole reaction
imidazole 435
in β-pleated sheet 509–10 basicity 143, 433 Intramolecular Claisen reaction, see Claisen
in protein tertiary structure 513 Chichibabin reaction 437 reaction
pyrazole 435 hydrogen bonding 435
salicyclic acid 133 molecular structure 432 Intramolecular electrophilic addition 300
in secondary structure of proteins 509 reactivity 432 Inulin, structure 484
in water 50 structure 432 Inversion
Imidazole ring, tautomerism 517
Hydrogen cyanide Imidazoles, tautomerism 433 at nitrogen 74
acidity 128 Imines in SN2 reactions 183, 190
bonding molecular orbitals 35 from aldehydes and ketones 242–7 Invert sugar 231
in aldolase mechanism 526 Invertase 231
Hydrogen exchange as carbonyl analogues 243, 369 Ion 19
carboxylic acid derivatives 374 basicity 138 Ionic bonding, see bonding, ionic
enols and enolate anions 351 formation, comparison with acetal Ionic reactions 167–71
hydroxyl groups 158 Ionization
indole 443 formation 243 amino acids at pH 7 150
oxazolium and thiazolium salts 437 formation, intramolecular 245 calculation 150
formation, mechanism 242 morphine 163
Hydrogen halides electronic structure 34 Ionization constant, water
acidity 125 in enzyme binding 516 Kw 135
addition to alkenes 284–6 hydrolysis 243 temperature dependence 146
addition to alkynes 292–4 reduction with complex metal hydrides 246 Ionization potential 23
in reductive amination 598 Irreversible reactions, of carbonyl group 223
Hydrogen molecule, molecular orbitals 24 in Strecker synthesis of amino acids 245 Isoborneol, in synthesis of camphor 219
Hydrogenation, catalytic 332 Imine–enamine tautomerism, in Isocitrate, in Krebs cycle 586
Hydrolysis, β-ketoesters 387 Isocitrate dehydrogenase, in Krebs cycle 389,
Hydronium cation 34, 121 transamination 599
Imino acid, proline 499 587
acidity 136 Indole Isodihydrocarvone, interconversion with
formal charge 47
Hydroperoxides 334 acidity 445 dihydrocarvone 353
in autoxidation of fats 335 aldol-like reactions 445 Isoelectric point pI
Hydrophobic interactions, in protein tertiary alkylation 445
basicity 443 alanine, calculation 161
structure 512 electrophilic substitution 444 amino acids, calculation 160
Hydroxyacid–lactone equilibria, Table 255 Fischer synthesis 461 definition 160
β-Hydroxyacyl-CoA dehydrogenase, in fatty hydrogen exchange 443 glutamic acid, calculation 161
in Mannich reactions 445 lysine, calculation 161
acid β-oxidation 591 in Michael reactions 445 morphine 163
Hydroxyaldehyde–hemiacetal equilibria, reactivity 443–6 Isoleucine, structure and pKa values 500
systematic name 439 Isoliquiritigenin, synthesis by aldol reaction
Table 226 Indole-3-acetic acid, structure 447
Hydroxydiazines, tautomerism 429 Inductive effect 306
Hydroxyleucine, structure 503 influence on acidity 125–7 Isomers
β-Hydroxy-β-methylglutaryl-CoA, see influence on basicity 137
definition 37 configurational see configurational isomers
HMG-CoA in electrophilic aromatic substitution 310 conformational see conformational isomers
Hydroxyproline, structure 503 from functional groups, Table 126 constitutional 56
5-Hydroxytryptamine (5-HT, serotonin) Inhibitors geometric 83
aminoacyl-tRNA binding 558 optical see optical isomers
structure 446 enzyme, see enzyme inhibitors structural 56
receptors, 446 transcription 558 Isomerase, in unsaturated fatty acid
biosynthesis 602 translation 558
5-Hydroxytryptophan Initiation step, radical chain reaction 323 metabolism 593
decarboxylation to 5-hydroxytryptamine Inosine phosphate, in nucleotide biosynthesis Isomerism, cis –trans 30, 40
Isomerization, of glucose 467
602 563 Isopenicillin N
structure 602 myo-Inositol, conformational isomers 70
Hyoscyamine Insulin 486 in penicillin biosynthesis 376
base hydrolysis 376 as precursor of β-lactam antibiotics 537
biological activity of enantiomers 78 biosynthesis 507 Isopentenyl diphosphate, in terpenoid and
racemization 77, 375 bovine, structure 507
stereochemistry and shape 117 disulfide bridges 507 steroid biosynthesis 300
as tropane alkaloid 370 human, structure 507 Isoquinoline
Hypoxanthine, in purine metabolism 451 porcine, structure 507
Hysocine, stereochemistry and shape 117 Intermediary metabolism, definition 573 basicity 442
Intermediates Bischler–Napieralski synthesis 459
Ibuprofen definition 173 Chichibabin reaction 443
biological activity of enantiomers 79 energy diagram 174 nucleophilic substitution 443
metabolic racemization 377 International Union of Pure and Applied reactivity 442
nomenclature 13 systematic name 439
synthesis 314 Chemistry, see IUPAC Isoquinolone 443
Isothiazole
Idose basicity 438
Fischer projection 104 structure 432
structure and stereochemistry 465 Isotopic labelling
carboxylic acid derivatives 374

INDEX 687

enols and enolate anions 351 extending aldose chain 465 in SN2 reactions 183, 188–90
glucose, 14C-labelled 465 in aminosugar synthesis 492 phosphates and diphosphates 196
indole 443 Kinetic control tosylate anion 274
oxazolium and thiazolium salts 437 in addition to conjugated dienes 297 Leucine, structure and pKa values 500
using bases 157–9 in nucleophilic addition to conjugated Lewis
Isoxazole acids and bases 121
basicity 438 carbonyl derivatives 395 acid, AlH3 in LAH reductions 235
structure 432 Kinetics, reaction, see reaction kinetics acids, in electrophilic aromatic substitution
IUPAC (International Union of Pure and Knorr pyrrole synthesis 460
Krebs cycle 584–9 305
Applied Chemistry) acids, in Friedel–Crafts reactions 306
non-systematic names 15 aldol reactions 363 definition of acids and bases 121
priority rules (configuration at chiral citrate synthase mechanism 528 structures 20, 45
energy yield 589 Lidocaine, nomenclature 14
centres) 80 isocitrate dehydrogenase 389 Lignocaine, see lidocaine
priority rules (configuration at double Kw, ionization constant for water 135 Limiting structures, see resonance structures
temperature dependence 146 Limonene, biosynthesis 303
bonds) 84 Linalyl diphosphate 302
systematic nomenclature 6–14 Labelling allylic cation 107
exchange 158 Linamarin, structure 239
Jasmolone, structure 61 carboxylic acid derivatives 374 Lindane, conformational isomers 73
enols and enolate anions 351 Line drawings 1–3, 20, 32
Kekule´ forms hydroxyl groups 158 Linear combination of atomic orbitals, see
aromatic rings 2 indole 443
benzene 44, 45 oxazolium and thiazolium salts 437 atomic orbitals
isotopic, using bases 157–9 Linoleic acid
Ketals
formation 229 Lactams autoxidation 335
as protecting group 230, 268 as cyclic amides 265 metabolism 594
nomenclature 265 structure 259
Ketal and acetal groups in sucrose 231 Lipases
Ketals and acetals, cyclic, as protecting β-Lactam antibiotics 265 in hydrolysis of fats 590
hydrolysis 266 in resolution of enantiomers 100
groups 481 mode of action 539 Lipoic acid
Ketamine, nomenclature 12 shape of penicillins 115 in Krebs cycle 585, 587
Ketimine, in PLP-dependent reactions 246, structural features 537 in oxidative decarboxylation 606
Liquiritigenin, synthesis by conjugate addition
599 β-Lactamases 266
Keto–enol tautomerism, see tautomerism comparison with serine protease 523 396
β-Ketoacids mechanism of action 267, 539 Lithium aluminium hydride (LAH) 205, 235,

decarboxylation 388 Lactase 485 267
in biochemistry 389 Lactate dehydrogenase, in glycolysis 584 addition to conjugated carbonyl derivatives
in Krebs cycle 587 Lactic acid
395
β-Ketoesters in glycolysis 584 reaction with aldehydes and ketones 235
acid hydrolysis 387 from stereospecific reduction of pyruvic reaction with water 205, 236
from Claisen reaction 379 reduction of amides 269
reverse Claisen reaction 387 acid 238 reduction of carboxylic acid derivatives 267
Lactones reduction of pyridinium salts 414
α-Ketoglutarate, see 2-oxoglutarate in SN1 and SN2 reactions 205
Ketones as cyclic esters 255 Lithium diisopropylamide (LDA)
lactone–hydroxyacid equilibria, Table 255 selective action 360, 362
from carboxylic acid derivatives and macrolides 255 as strong base in aldol reaction 362
Grignard reagents 271 nomenclature 255 as strong base, enolate anions 359, 381,
reduction with sodium borohydride 466
hemiketal formation 224 Lactose, structure 483 383, 392
hemithioketal formation 235 Lactulose, structure 483 Littorine
from hydration of alkynes 293 Laevorotatory enantiomer, definition 76
ketal formation 229 LAH, see lithium aluminium hydride base hydrolysis 376
nucleophilic addition reactions 221–48 Lanosterol structure 375
reaction with acetylides 241 biosynthesis, rearrangement reactions 219 Lone pair electrons 20, 168
reaction with amines 242 in steroid biosynthesis 303 ammonia 34
reaction with cyanide 238 LDA, see lithium diisopropylamide water 34
reaction with Grignard reagents 240 Leaving groups LSD, see lysergic acid diethylamide
reduction with complex metal hydrides 235 and acidity 189, Table 189 Lycopene
thioketal formation 235 definition 171 as antioxidant 337
Ketones and aldehydes in carbonyl additions 224 structure 39
enolization 347 in carboxylic acid derivatives, 249–50 Lysergic acid diethylamide (LSD), structure
halogenation 356
hydrogen exchange 351 protonation 250 447
racemization 352 in ester–amide conversion 263 Lysine
Ketone–ester condensations, predicting the in imine formation 242
linking chemistry of amides and imines 269 ionization 502
product 384 and reactivity in carboxylic acid derivatives at pH 7 152
Ketose, definition 464
Kiliani–Fischer synthesis 249–50, Table 250 isoelectric point, calculation 161
structure and pKa values 500
Lyxose, structure and stereochemistry 465

688 INDEX

Macrolide, carbocation, electronic structure 32 Monoterpenes, interconversion through
antibiotics 494 radical, electronic structure 33 enolization 353
definition 255 Methyl cyanoacrylate, polymerization 401
polyene 256, 294 Methylcyclohexane Morphine
conformational isomers 67 biosynthesis via phenolic oxidative
Malate, in Krebs cycle 589 coupling 343
Malate dehydrogenase, in Krebs cycle 589 energy difference 67 functional groups, 4
Malathion, as acetylcholinesterase inhibitor Newman projections 67 O-glucuronides 489
Methylecgonine, stereochemistry and shape ionization 163
280 118 isoelectric point 163
Maleic acid, as enzyme inhibitor 531 Methylenedioxy group, as acetal 233 receptors 514
Malonic acid, acidity 144 N-Methylglycine (sarcosine), structure 503 selective alkylation 186
Malonyl-CoA N-Methyl-leucine, structure 503 shape 515
Methyltransferases 200 structure 62
Claisen reactions in nature 392 N-Methyltyrosine, structure 503
from carboxylation of acetyl-CoA 595, Mevalonic acid Morpholine
biosynthesis 381 conformation 72
609 as precursor of cholesterol 381 structure 404
Maltase 485 Michael acceptors, as carcinogens 399
Maltose, structure 583 Michael reaction 397–400 MRSA (methicillin-resistant Staphylococcus
Mandelonitrile, structure 477 in dicoumarol formation 419 aureus) 266
Mannich reaction 369–72 in Hantzsch pyridine synthesis 458
with indole 445 Mucopolysaccharide, definition 496
general 370 in Robinson annulation 398 Muscarine, structure 413
synthesis of tropine 370 in Skraup quinoline synthesis 459 Muscarinic acetylcholine receptors 413
with pyrrole 422 in warfarin synthesis 420 Mutarotation, glucose 226
with indole 445 Mineralocorticoids, function 291 Mycaminose, in spiramycin 494
Mannitol, structure 473 Mixed aldol reaction, see aldol reaction Mycarose, in spiramycin 494
Mannosamine, synthesis 492 Mixed anhydride, see anhydride Mycophenolic acid, structure 385
Mannose Mixed Claisen reaction, see Claisen reaction Mycosamine, in amphotericin 256
Fischer projection 104 Models, molecular 51–3
hemiacetal form, structure 471 Module NAD+ (nicotinamide adenine dinucleotide)
from isomerization of glucose 467 in non-ribosomal peptide biosynthesis 535 enantiotopic faces 98
structure and stereochemistry 465 in penicillin biosynthesis 538 as oxidizing agent 237
Mannuronic acid, in alginates 488 Molecular models 51–3 as pyridinium salt 413, 415
Markovnikov addition, electrophilic addition ball-and-stick 52 reduction 415
framework 52 structure 413
of HBr to alkenes 329 space-filling 52
Markovnikov rule, in electrophilic addition Molecular orbitals 24–35 NAD+ and NADP+
acetylene 31 in biological oxidations 576
reactions 286 ammonia 34 as nucleotides 560
Mechanism antibonding 24
benzene, antibonding 42 NADH (reduced nicotinamide adenine
overview 167–75 bonding 42 dinucleotide)
common mistakes 176–81 bonding 24
Melatonin, structure 447 1,3-butadiene, antibonding 38 as reducing agent 237
Menthol bonding 38 from reduction of NAD+ 415
conformational isomers 70 ethane 28 in reduction of pyruvic acid 97
nomenclature 12 ethylene 29 prochiral centre 98
Mercaptoethanol, in location of disulfide Frost circles 43 NADH and NADPH
hydrogen molecule, antibonding 24 in biological reductions 576
bridges 506 bonding 24 as nucleotides 560
messenger-RNA (mRNA), see RNA methane 27 NADP+ (nicotinamide adenine dinucleotide
Meso compounds 90–2 1,3-pentadiene 37
1,4-pentadiene 37 phosphate)
definition 90 σ bond 25 as pyridinium salt 413
Mesomers, see resonance structures π bond 25 reduction 415
Mesomeric effect, see resonance effect in ethylene 29 structure 413
Mesyl chloride (methanesulfonyl chloride) in acetylene 31 NADPH (reduced nicotinamide adenine
water 34
273 Molecular rearrangement, see rearrangement dinucleotide phosphate)
and SN2 reactions 190 reactions as reducing agent 237
Mesylate esters, in SN2 reactions 189 Molecular representations 1–3 Nalbuphine, structure 62
Metabolism, intermediary, definition 573 Molecularity, definition 173 Nalidixic acid, structure 442
Methane, bonding molecular orbitals 27 Mono-oxygenase, cytochrome Naltrexone, structure 62
Methanesulfonic acid, acidity 129 P-450-dependent, see cytochrome P-450 Naphthalene
Methanesulfonyl chloride, see mesyl chloride Monosaccharides 463–73 aromaticity 44
Methanimine, bonding molecular orbitals 35 definition 463 electrophilic aromatic substitution 316
Methicillin, semi-synthesis 266 Naratriptan, structure 447
Methicillin-resistant Staphylococcus aureus, NBS, see N-Bromosuccinimide
Neoisomenthol, conformational isomers 70
see MRSA Neostigmine, as acetylcholinesterase inhibitor
Methionine
279
regeneration from homocysteine 454 Neryl diphosphate 302
structure and pKa values 501
synthesis 395 allylic cation 197
Methotrexate, structure 455
Methyl
anion, electronic structure 32

formal charge 47

INDEX 689

Neutrons 19 pteridine 449, 452 Nucleophilicity
Newman projection purine 448 and basicity 185, 207, Table 186
pyranose and furanose rings 468 of N and O nucleophiles, Table 186
butane 58 systematic 6–8 common reagents, Table 186
cyclohexane, boat conformation 65 trivial 15
Non-ribosomal peptide biosynthesis 535 Nucleosides
chair conformation 63 modular 535 as antiviral agents 558
definition 57 Noradrenaline (norepinephrine) definition 549
ethane 57 biosynthesis 602 as N-glycosides 478
methylcyclohexane, conformational isomers methylation to adrenaline 200 nomenclature, Table 551
structure 447 structure 228, 550
67 Norepinephrine, see noradrenaline
Nicotinamide adenine dinucleotide, see Norfloxacin, structure 442 Nucleoside triphosphates, in DNA replication
Nucleic acids 551–8 553
NAD+ abbreviations 551
Nicotinamide adenine dinucleotide, reduced base sequence 551 Nucleotides
chemical synthesis 566–9 abbreviations, Table 551
see NADH DNA sequencing gel 565 biosynthesis 563
Nicotinamide purine bases 550 definition 549
pyrimidine bases 550 nomenclature, Table 551
in nucleotides 560 sequence determination 564 phosphoramidite coupling 568
structure 413 sequencers, automated 566 sequence determination 564
Nicotine, structure 412 structure 551
Nicotinic acetylcholine receptors 413 synthesis, solid phase 566 Numbering
Nicotinic acid, structure 413 Nucleophiles azoles 432
Nitration, of aromatic rings 305 acetylides heterocycles, fused to benzene ring 439
using acetyl nitrate, pyrrole 422 in systematic nomenclature 7
using benzoyl nitrate, indole 444 aldehydes and ketones 241
Nitriles SN1 and SN2 reactions 205 Nystatin, mode of action 294
bonding molecular orbitals 35 alcohols, SN1 and SN2 reactions 198
conjugated 396 amines, SN1 and SN2 reactions 201 Octet rule 19, 23
hydrolysis to carboxylic acid cyanide Ofloxacin, structure 442
aldehydes and ketones 238 Oils, see fats and oils
acid-catalysed 244 SN1 and SN2 reactions 204 Oleic acid
base-catalysed 244 definition 171
as stabilized anions 365 enamines 366–9 metabolism 593
useful reactions 204, 239, 366 enolate anions 357 structure 259, 593
Nitro group examples 171 Oligonucleotide synthesis 566–9
charge separation 134 Grignard reagents Oligosaccharides 482–4
aliphatic, useful reactions 366 aldehydes and ketones 240 definition 463
Nitrogen carboxylic acid derivatives 271 systematic nomenclature 483
electronic configuration 23 SN1 and SN2 reactions 204 Opium
sp hybrid orbitals, stereochemistry 56 halide, SN1 and SN2 reactions 198 alkaloids 162, 186, 343
sp2 hybrid orbitals, stereochemistry 56 hydride extraction of morphine 162
sp3 hybrid orbitals 33 reduction of aldehydes and ketones Optical
stereochemistry 56 activity 73, 76
sp3 hybridized, electronic configuration 33 235 isomers 73
Nitrogen heterocycles, basicity 143 reduction of carboxylic acid derivatives purity 76
Nitrogen inversion 74
energy barrier 74 267 – 9 calculation 77
in tropane alkaloids 118 SN1 and SN2 reactions 205 rotation, glucopyranose anomers 227
Nitromethane in SN2 reactions 183, 185 Orbitals
acidity 365 stabilized anions 365 atomic, see atomic orbitals
as stabilized anion 365 thiols, SN1 and SN2 reactions 199 molecular, see molecular orbitals
Nitronium ion, in aromatic nitration 305 water, SN1 and SN2 reactions 198 Organophosphorus derivatives
Nitrophenols, acidity 134 Nucleophilic addition as enzyme inhibitors 531
Nizatidine, structure 436 to carbonyl groups 222 as acetylcholinesterase inhibitors 280
Noble gases, electronic configuration 23 to conjugated carbonyl derivatives Ornithine, structure 503
Nodes, in atomic orbitals 22 Orotic acid, in nucleotide biosynthesis 563
Nomenclature 393 – 401 Orotidylic acid, in nucleotide biosynthesis 563
acronyms 15 to iminium ions 369 Orsellinic acid, biosynthesis 385
aromatic rings 8 to pyridinium salts 414 Oxalic acid, acidity 144
bridged ring systems 116 Nucleophilic aromatic substitution 411, Oxaloacetate
examples 8–14 in aldol reaction, Krebs cycle 363
functional groups, 5 544 from carboxylation of pyruvate 610
heterocycles 1,3-azoles 437 in Krebs cycle 585, 589
fused 448 pyridine 411 Oxalosuccinate
fused to benzene ring 438–9 isoquinoline 443 decarboxylation 389
non-aromatic 403 quinoline 441 in Krebs cycle 586
hydrocarbons, Table 7 Nucleophilic substitution reactions 198–206 Oxazole
lactams 265 derivatives of sulfuric and phosphoric acid basicity 433
lactones 255 reactivity 432
non-systematic, Table 15 272 – 82 structure 432
nucleosides and nucleotides, Table 551 in glycoside synthesis 479
oligosaccharides 483

690 INDEX

Oxazolium salts, hydrogen exchange 437 Penicillin G, see benzylpenicillin Phenyl isothiocyanate, Edman reagent 545
Oxetane, structure 404 1,3-Pentadiene Phenylacetic acid, acidity 130
Oxidation Phenylalanine, structure and pKa values
acidity 129
Baeyer–Villiger 335 molecular orbitals 37 501
reactions, and ATP synthesis 575 1,4-Pentadiene, molecular orbitals 37 Phloracetophenone, biosynthesis 385
β-Oxidation Pentoses, definition 463 Pholcodine, from selective alkylation of
of fatty acids 589–92 Peptide
antibiotics 376 morphine 186
energy yield 592 biosynthesis 533–6 Phosphates
reverse Claisen reaction 387
stereochemistry 594 epimerization of amino acids 376 as leaving groups 196
unsaturated fatty acids 593 non-ribosomal 535 in biochemical reactions 277
Oxidative ribosomal 533 in intermediary metabolism 573
coupling, phenolic see phenolic oxidative bond Phosphates and diphosphates
configuration 509 abbreviations 277
coupling definition 499 nucleophilic attack, mechanism 277
decarboxylation, in Krebs cycle 585, 587 planarity 508 Phosphodiesters, in nucleic acids 276, 551
phosphorylation 577–9 resonance stabilization 508 Phosphoenolpyruvic acid
Oxide anion 169 cyclic 536 as enol 350
N -Oxides definition 499 in glycolysis 583
of amines 410 hydrolysis 261 Phosphofructokinase, in glycolysis 580
deoxygenation 410 sequence, determination 544 Phosphoglucose isomerase, in glycolysis 580
Oxinane, structure 404 use of chymotrypsin and trypsin 546 2-Phosphoglycerate, in glycolysis 582
Oxirane, structure 404 sequencers, automated 546 3-Phosphoglycerate, in glycolysis 582
2-Oxoglutarate synthesis 540–4 Phosphoglycerate mutase, in glycolysis 582
from decarboxylation of oxalosuccinate 389 on polymeric supports 542 Phosphopantotheine group, of acyl carrier
in Krebs cycle 587 solid phase 542
reductive amination 598 synthesizers, automated 543 protein 597
2-Oxoglutarate dehydrogenase Peptide synthase Phosphoramidites, in nucleic acid synthesis
as enzyme complex 607 non-ribosomal (NRPS) 535
in Krebs cycle 587 modular mechanism 535 567
as TPP-dependent reaction 605 in penicillin biosynthesis 537 Phosphoribosyl diphosphate (PRPP), in
Oxolane, structure 404 Peptides and proteins
Oxonium cation 169 hydrolysis 505 nucleotide biosynthesis 563
Oxygen structural abbreviations 504 5-Phosphoribosylamine, in nucleotide
diradical 333 C- and N-terminus 504
electronic configuration 23 Peptidoglycan biosynthesis 563
radical addition 333 bacterial cell wall, structure 495, 538 Phosphoric acid
sp2 hybrid orbitals, stereochemistry 56 cross-linking 538
sp3 hybrid orbitals 33 action of β-lactam antibiotics 539 acidity 144, 275
Peracetic acid derivatives, nucleophilic substitution
stereochemistry 56 in epoxidation 290
sp3 hybridized, electronic configuration 33 in formation of N-oxides 410 reactions 275–82
Permethrin, structure 61 diesters in nucleic acids 276
Paal–Knorr pyrrole synthesis 461 Peroxides, in radical reactions 334 Phosphorus oxychloride
Palmitic acid, structure 259 Peroxy compounds, radical formation 319 in chlorination of diazinones 430
Pantetheine, structure 536 Peroxyacetic acid, see peracetic acid in chlorination of pyridones 417
Pantetheinyl arm, in non-ribosomal peptide pH Photolysis, radical formation 320
calculation, strong acids 146 Photosynthesis 40, 424
biosynthesis 536 strong bases 147 Physostigmine
Pantothenic acid (vitamin B5) 536 weak acids 147–8 as acetylcholinesterase inhibitor 279
weak bases 147–8 structure 448
and acyl carrier protein 597 definition 146 Pi (π) bonds, see bonds, pi
Paracetamol (acetaminophen) of neutrality, temperature dependence 146 pI, isoelectric point 160
optimum, of enzyme 517 Picolines (methylpyridines)
glutathione conjugates 400 salt solutions 148 acidity 412
synthesis 264 Phase sign in aldol reaction 412
toxic metabolites 400 atomic orbitals 22 Pictet–Spengler tetrahydroisoquinoline
Parathion, as acetylcholinesterase inhibitor wave function 25
Phenelzine, as enzyme inhibitor 531 synthesis 460
280 Phenols, acidity 133 in alkaloid biosynthesis 371
Partial structures 3 Phenol biosynthesis, aldol and Claisen α-Pinene, synthesis of camphor 218
Pauling electronegativity values, Table 36 reactions 385 β-Pinene, stereochemistry and shape 117
PCR, see polymerase chain reaction Phenolic oxidative coupling 340–5 Piperazine, structure 404
Pectins, structure 488 in biosynthesis of thyroxine 344 Piperidine
Penicillins 82 in biosynthesis of tubocurarine and basicity 143
conformation 72
as amides/lactams 265 morphine 342 dipole 406
antibiotics, tripeptide precursor 376 radical mechanism 341 structure 404
biosynthesis 537 Phenothrin, structure 61 pKa
cleavage by β-lactamase 523 definition 122
mode of action 539 and drug absorption 164
as modified tripeptides 537 values, see also acidity, basicity
stereochemistry and shape 115
amino acids in proteins, Table 503
amino acids, Table 500–1
common drugs, Table 164
Tables 123–4

INDEX 691

use of 155–65 Proinsulin 507 Pyrazine, see also diazines
water 136 Proline basicity 427
pKb, definition 135 structure 427
β-Pleated sheet, in proteins 509–10 as imino acid 499
PLP (pyridoxal 5 -phosphate) peptide chain distortion 509 Pyrazinone, tautomerism 430
enzyme binding via transimination 604 structure and pKa values 501 Pyrazole
imine derivative, acidity 600 Pronunciation 16
imine formation 246 Propagation step, radical chain reaction 323 basicity 438
PLP-dependent decarboxylation, amino Propene, acidity 129 hydrogen bonding 435
Propiolic acid, acidity 128 structure 432
acids 601–2 Prostaglandins, biosynthesis via COX 254, Pyrethric acid, structure 61
PLP-dependent racemization, amino acids Pyrethrins, general structure 61
339 Pyrethrolone, structure 61
600 Protecting group Pyridazine, see also diazines
PLP-dependent reactions 600–4 basicity 427
acetal or ketal 230 structure 427
stereochemical factors 603 benzyl ester 541 Pyridazinone, tautomerism 430
PLP-dependent reverse aldol reaction 603 BOC (tert-butoxycarbonyl) 541 Pyridine
in transamination 598 ketals 268 aromaticity 44, 405
Podophyllotoxin, derivative 233 thioacetal or thioketal 235 basicity 143, 408
Polarity, bond 35–7, 170 cyclic acetals and ketals 481 bond lengths 405
Polarization in nucleic acid synthesis 566 as catalyst in synthesis of anhydrides 251
of bonds 36 in peptide synthesis 540 as catalyst in synthesis of esters 253
carbonyl group 221 Proteins, see also peptides and proteins Chichibabin reaction 411
Polyacrylonitrile 401 binding sites 513 dipole 406
Polycyclic systems, stereochemistry 106–19 biosynthesis, ribosomal, antibiotic inhibitors electrophilic substitution 409
Polyene macrolides 256, 294 Frost circle 406
Polymerase chain reaction (PCR) 569 558 Hantzsch synthesis 458
Polymeric supports, in peptide synthesis 543 definition 499 hydroxypyridine–pyridone tautomerism 416
Polymerization globular 511 molecular structure 405
anionic 400 α-helix 511 NMR spectrum 406
cationic 300 hydrolysis 261 as nucleophilic catalyst 264
pyrrole 422 molecular shape 505–14 reactivity 407–12
radical, of alkenes 331 β-pleated sheet 509–10 resonance structures 406
Poly(methyl cyanoacrylate) (Superglue) 401 post-translational changes 558 Pyridine-N -oxide
Poly(methyl methacrylate) 401 primary, secondary and tertiary structures electrophilic substitution 410
Polypeptide, definition 499 synthesis 410
Polysaccharides 484 505 – 14 Pyridines, methyl, see picolines
definition 463 quaternary structure 513 Pyridinium salts
hydrolysis 485 secondary and tertiary interactions 514 formation 408
as polyacetals 232 secondary transformations 558 nucleophilic addition 414
Polystyrene 331 tertiary structure, molecular interactions reduction via complex metal hydrides 414
Polytetrafluoroethylene (PTFE) 331 Pyridones
Polythene (polyethylene) 331 511 – 3 acidity 416
Polyvinyl chloride (PVC) 331 β-turn 509 N-alkylation 417
Porphin Protic solvents 187 basicity 416
resonance forms 424 Protons 19, 24, 169 chlorination 417
structure 424 Protonation 24 tautomerism 416
Porphobilinogen, in porphyrin ring Protosteryl cation Pyridoxal 246
in biosynthesis of lanosterol 220 structure 600
biosynthesis 424 in steroid biosynthesis 303 Pyridoxal 5 -phosphate, see PLP
Porphyrins 423 Prunasin, structure 239, 477 Pyridoxamine 246
Pseudoephedrine, enantiomers 85 structure 600
general structure 424 Pseudotropine, stereochemistry and shape Pyridoxamine 5 -phosphate
Pravastatin, structure 382 via imine hydrolysis 246
Pregnenolone, conversion into progesterone 119 in transamination 599
Psilocin, structure 447 Pyridoxine (pyridoxol), structure 600
354 Psilocybin, structure 447 Pyrimethamine, structure 455
Preproinsulin 507 Pteridine, systematic nomenclature 449, 452 Pyrimidine, see also diazines
pro-R, pro-S convention, see configuration Pteridines, structure 452 basicity 427
Prochiral Purine structure 427
Pyrimidines
centre 94 acidity 450 bases in DNA 51
centres, citric acid 96 basicity 449 bases, in nucleic acids 431, 550
definition 94 systematic nomenclature 448 nucleotides, biosynthesis 563
pro-R, pro-S convention for prochiral Purines Pyrimidone, tautomerism 430
bases in DNA 51 Pyroglutamic acid, structure 503
centres 95 Pyrones 418
Prochirality 94–8 in nucleic acids 550 Pyrophosphatase, hydrolysis of diphosphate
metabolism, uric acid formation 451
aconitase and citric acid 96 nucleotides, biosynthesis 563 562, 590
alcohol dehydrogenase and ethanol 95 structure 449
Cahn–Ingold–Prelog system 95 tautomerism 449
in citrate 586 Purpurosamine, in gentamicin 494
Progesterone Pyranose forms 226, 468
from pregnenolone 354 Pyranose and furanose forms, aldohexoses,
stereochemistry and shape 113
equilibrium proportions, Table 470

692 INDEX

Pyrophosphates, see diphosphates in SN1 reactions 192 Reaction types 174
Pyrophosphoric acid, see diphosphoric acid in radical reactions 325 addition, see addition reactions
Pyrrole Racemization elimination, see elimination reactions
amino acids, PLP-dependent 600 ionic 167–71
acidity 421 carboxylic acid derivatives 374 radical 171
aromaticity 44, 406 definition 76 rearrangement, see rearrangement reactions
basicity 143, 407, 420 involving enols and enolate anions 352 substitution, see substitution reactions
cyclic tetramers with aldehydes and ketones
rate of reaction 353 Rearrangement reactions 175
423 hyoscyamine to atropine 375 biosynthesis of lanosterol 219
dipole 407, 427 ibuprofen, metabolic 377 carbocation (Wagner–Meerwein) 214–20
electrophilic substitution 421 2-iodobutane 184 in electrophilic addition reactions 217, 296
Frost circle 406 Radicals 33 in Friedel–Crafts alkylations 217, 307
Knorr synthesis 460 allyl 322, 325 and ring strain 217
in Mannich reaction 422 benzyl 322, 325 in steroid side-chain biosynthesis 295
molecular structure 406 tert-butoxyl 319 synthesis of camphor 218
Paal–Knorr synthesis 461 definition 319
polymerization 422 methyl, electronic structure 33 Reductive amination, in amino acid
N-substitutions 423 benzoyloxyl 319 biosynthesis 598
reactivity 420–3 2-cyano-2-propyl 319
resonance structures 407, 420 formation 319–21 Regiochemistry, in electrophilic addition
Pyrrolidine phenyl 319 reactions 286
basicity 143 resonance delocalization 322
dipole 407, 427 stability 321 Regioselectivity,
structure 404 structure 321 definition 211
Pyruvate Radical reactions 171 in electrophilic aromatic substitution 313
carboxylation to oxaloacetate 610 abstraction, of hydrogen 320
in glycolysis 584 addition reactions 328–31 Regiospecificity, definition 211
stereospecific reduction to lactic acid 238 Reserpine, structure 448
Pyruvate decarboxylase, in glycolysis 584 to alkenes 321 Resolution, of enantiomers 99
Pyruvate dehydrogenase HBr to alkenes 328
as enzyme complex 607 HBr to conjugated dienes 330 using chromatography 100
in Krebs cycle 585 chain reaction 322 using diastereoisomeric salts 99
as TPP-dependent reaction 605 coupling, in phenolic oxidative coupling using enzymes 100
Pyrylium cation, molecular structure 418 Resonance
341 arrow 46
Quantum number initiation 172 energy 49
combinations, Table 21 oxidation, in prostaglandin biosynthesis hybrid 45
magnetic 21 Resonance effects
orbital momentum 21 339 influence on acidity 129–34
principal 20 polymerization, of alkenes 331 influence on basicity 139–42
spin 21 propagation 172 in electrophilic aromatic substitution 310
termination 172 from functional groups, Table 134
Quaternary ammonium salts 201 stereochemistry 325 Resonance stabilization
curare-like 202 substitution reactions 322–8 energy 49
E2 reactions 210 Ranitidine, structure 436 enolate anions 349
Rate constant 173 peptide bond 508
Quercetin, structure 418 Rate expression 173 radicals 322
Quinic acid, conformational isomers 70 Rate of reaction 173 Resonance structures 45–9
Quinoline E1 reactions 212 acetone 49
E2 reactions 207 allylic cation 49
aminoquinolines 441 electrophilic addition reactions 283 conjugated carbonyl derivatives 393
aromaticity 45 halogenation involving enols and enolate formaldehyde 49
basicity 440 furan 426
Chichibabin reaction 441 anions 356 pyridine 406
electrophilic substitution 440 racemization involving enols and enolate pyrrole 407
nucleophilic substitution 440 rules governing use 47–9
reactivity 440 anions 353 Restriction endonucleases 564
Skraup synthesis 458 SN1 reactions 191 Resveratrol, as antioxidant 338
systematic name 439 SN2 reactions 183 Retinal, structure 40
Quinolones 441 Retinol (vitamin A1), structure 40
quinolone antibiotics 442 variables 184 Retroviruses 559
Rate-determining step 173 Reverse aldol reaction 361
R, S convention, see configuration in biochemistry 363
Racemase enzymes, PLP-dependent 600 E1 reactions 212 in glycolysis 581
Racemate, see racemic mixture E2 reactions 207 PLP-dependent 603
Racemic mixture electrophilic addition reactions 283 Reverse Claisen reaction 386, 391
SN1 reactions 191 in biochemistry 387
definition 76 SN2 reactions 183 in fatty acid β-oxidation 592, 594
in electrophilic addition reactions 285 Re, Si convention, see configuration Reverse transcriptase 559
Reaction intermediates, see intermediates Reversible reactions, of carbonyl group 223
Reaction kinetics 173 Rhamnose, hemiacetal form, structure 471
and mechanism 173 Rhodopsin, structure 40
Reaction mechanism, see mechanism Ribitol, in FAD and FMN 560
Reaction order, definition 173
Reaction rate, see rate of reaction

INDEX 693

Riboflavin (vitamin B2), structure 456 definition 57 of hexoses 473
Ribofuranose 227, 469 ethane 57 of lactones 466
Saytzeff elimination 209 of pyridinium salts 414
anomeric forms 227 Schiff base, see imine Sodium tert-butoxide, as base 157
Ribonucleic acid, see RNA Schro¨dinger wave equation 20 Sodium cyanoborohydride, reduction of
Ribopyranose 469 Scopine, stereochemistry and shape 117 imines 246
Ribose Serine, structure and pKa values 501 Sodium hydride
Serine esterase 519 as base 157
biologically important derivatives 228 Serine hydrolase 519 as strong base, enolate anions 358, 381, 392
hemiacetal form 227 Serine protease 521 Solasodine, as spiro compound 107
cleavage sites 521 Solid phase
from Fischer projection 105 Serotonin, see 5-hydroxytryptamine nucleic acid synthesis 566
structure 471 Shells 20 peptide synthesis 543
in RNA 550 filled 23 Solvents
ribofuranose forms 469 valence 19 aprotic polar, Table 188
ribopyranose forms 469 Side-chains, in steroids 294 protic 187
structure and stereochemistry 464, 465 Sigma (σ) bonds, see bonds, sigma Solvent effects
Ribosomal peptide biosynthesis 533 Sinigrin, structure 477 SN1 reactions 195
antibiotic inhibitors 558 Sitosterol, in plants 294 SN2 reactions 187
ribosomal-RNA (rRNA), see RNA Skraup quinoline synthesis 458 Sorbitol (glucitol), structure 473
Ribosome 556 SN1 reactions 191–8 Specific rotation 76
Ribulose, structure and stereochemistry 464 biological 196 Spectra
Ring currents in cyclic systems 195 absorption 25
and aromaticity 44 energy diagram 192 atomic 22
pyridine 406 mechanism 191 emission 25
Ring size, rate of reaction 191 infra-red, pyridones 416
in intramolecular aldol reaction 364 rate-determining step 191 NMR
in intramolecular Claisen reaction 382 solvent effects 195 aromatics 44
Ring strain 60 effect of substituents 193, Table 193 cyclohexane 64
cycloalkanes, Table 63 SN2 reactions 183–91 pyridine 406
cyclobutane 60 in cyclic systems 190 UV absorption 38
cyclopentane 62 energy diagram 184 Spiramycin, structure 494
cyclopropane 60 leaving groups 188–90 Spiro compounds 106
in rearrangement reactions 217 mechanism 183 chirality 93
Rivastigmine, as acetylcholinesterase inhibitor nucleophiles 185 natural 107
279 racemization 184 Spiroketal, in diosgenin 107
Rizatriptan, structure 447 rate of reaction 183 Squalene
RNA (ribonucleic acid) 50, 228, 555 rate-determining step 183 in biosynthesis of lanosterol 219
base pairing 432 selective alkylation of morphine 186 in steroid biosynthesis 303
phosphodiesters in 276 solvent effects 187 Squalene oxide, in steroid biosynthesis 303
pyrimidines 431 effect of substituents 184, Table 185 Staggered conformation, see conformation
mRNA (messenger RNA) 555 transition state 183 Standard free energy change 173
synthesis 556 variables in rate of reaction 184 Starch
rRNA (ribosomal RNA) 555 SN1 and SN2 reactions constitution 484
in ribosome 556 acetylides as nucleophile 205 as polyacetal 232
tRNA (transfer RNA) 555 amines as nucleophile 201 Statins, inhibitors of HMG-CoA reductase 382
in ribosomal peptide biosynthesis 533 cyanide as nucleophile 204 Stearic acid
in translation 556 Grignard reagents as nucleophile 204 energy yield 592
RNA polymerase, in RNA synthesis 556 halide as nucleophile 198 structure 259
Robinson annulation 398 hydride as nucleophile 205 Stereochemistry
intramolecular 206 definition 55
Salicin thiols as nucleophile 199 polycyclic systems 106–19
structure 476 water and alcohols as nucleophile 198 radical reactions 325
synthesis 479 SN1 or SN2 reactions, according to substrate Stereodrawings
manipulation 75
Salicyl alcohol, structure 476 195 Newman projection 57
Salicylic acid SN2 mechanism, in opium alkaloid sawhorse 57
wedge–dot 32, 55
acidity 133 biosynthesis 343 Stereogenic centre 73
methylation to methyl salicylate 200 SNAr mechanism 544 Stereoisomers, definition 56
Salsolinol, synthesis 371 Sodium amide Stereospecificity, enzyme 96
Salt solutions, pH calculation 148 Steroids
SAM, see S-adenosylmethionine in Chichibabin reaction 411 biosynthesis 303
Sanger reagent (2,4-dinitrofluorobenzene) as strong base, enolate anions 358, 381, 392 biosynthesis, electrophilic additions 300
N-terminal amino acid determination 544 Sodium borohydride 205, 235, 267 side-chain biosynthesis 294
Saponification, definition 259 addition to conjugated carbonyl derivatives progesterone and pregnenolone 354
Sarcosine (N-methylglycine), structure 503 stereochemistry and shape 112–15
Sarin, as acetylcholinesterase inhibitor 280 395 synthesis, via Robinson annulation 398
Saturated compounds 30 cleavage of disulfide bridges 506
Sawhorse representation reduction
butane 58
of aldehydes and ketones 235
of carboxylic acid derivatives 267

694 INDEX

Sterols, in membranes 294 Sulfuric acid Tetrahydrofolic acid (FH4)
Stigmasterol, in plants 294 acidity 144 structure 453
Strecker synthesis, of amino acids 245 derivatives, nucleophilic substitution derivatives 453
Streptamine, structure 493 reactions 272–5
Streptomycin, structure 493 esters 272 Tetrahydrofuran
Streptose, in streptomycin 493 conformation 72
Structural isomers, definition 56 Sumatriptan, structure 447 dipole 427
Strychnine, in resolution of enantiomers 99 Superglue 401 structure 404
Substituents Suxamethonium, structure 202, 211
Symmetry Tetrahydroisoquinoline
directing effects in electrophilic aromatic alkaloids, biosynthesis 371
substitution, Table 310 in achiral molecules 74, 88, 90, 91 Pictet–Spengler synthesis 460
in bornane 117
effect on SN1 reactions 193 in decalins 109 Tetrahydropyran
effect on SN2 reactions 184 in Fischer projections 102 conformation 72
Substitution reactions 175 in hydrindanes 110 structure 404
electrophilic aromatic, see electrophilic in tropine and scopine 118
syn Tetrahydrothiophene
aromatic substitution addition, definition 287 dipole 427
nucleophilic 198–206 addition, in catalytic hydrogenation structure 404
nucleophilic, of carboxylic acid derivatives
332 Tetrahydrothiopyran, structure 404
248 – 72 Tetrazole, in nucleotide coupling 568
nucleophilic aromatic, see nucleophilic Talose Thalidomide, mutagenic activity of
Fischer projection 104
aromatic substitution structure and stereochemistry 465 enantiomers 79
nucleophilic, bimolecular see SN2 reactions Thebaine
nucleophilic, unimolecular see SN1 Tamoxifen
configuration 84 in morphine biosynthesis 343
reactions synthesis 213 in opium 343
radical 322–8 Theobromine, structure 451
Substitution or elimination reaction, according Tartaric acid Theophylline
Fischer projections 102 and cyclic AMP 562
to conditions 214 in resolution of enantiomers 99 structure 451
Substrate-level phosphorylation stereoisomers 90 Thermodynamic control
meso-tartaric acid in addition to conjugated dienes 297
in glycolysis 582, 583 Fischer projections 102 in nucleophilic addition to conjugated
in Krebs cycle 588 structure 90
Succinate dehydrogenase, in Krebs cycle 588 carbonyl derivatives 395
Succinic acid Tautomer, definition 347 Thiamine (vitamin B1) 437
acidity 144 Tautomerism
from GABA 602 structure 605
in Krebs cycle 588 adenine 449 Thiamine diphosphate (TPP), see TPP
Succinyl-CoA, in Krebs cycle 587 aminodiazines 430 Thiazole
Succinyl-CoA synthetase, in Krebs cycle 588 aminopurines 449
Succinyl phosphate, as mixed anhydride 281 aminopyridines 417 basicity 433
Sucrose cytosine 431 reactivity 432
acetal and ketal groups 231 definition 347 ring, in thiamine 605
hydrolysis 231 in glycolytic pathway 350 structure 432
structure 483 guanine 449 Thiazolium salts
Sugar, invert 231 histidine 433 in TPP 438
Sugars in hydration of alkynes 294 hydrogen exchange 437
anomeric forms of common sugars 470 hydroxydiazines 429 Thiazolium ylid
cyclic hemiacetals, conformation 472 hydroxyimine–amide 244 from TPP 438
D and L 103, 464 imidazoles 433, 517 in decarboxylation of pyruvic acid 438
definition 463 imine–enamine, in transamination Thietane, structure 404
as hemiacetals or hemiketals 226 Thiinane, structure 404
hemiacetal forms from Fischer projections 599 Thiirane, structure 404
keto–enol 341, 347 Thioacetal
104, 468 formation 235
Sulfa drugs 274 equilibria, Table 348 as protecting group 235
Sulfanilamide acid-catalysed 348 Thioacids
base-catalysed 349 from carboxylic acid derivatives 261
acidity 274 in glycolysis 580, 581, 584 reactivity 250
as enzyme inhibitor 531 purines 449 Thioacids and thioesters, basicity 140
synthesis 274 pyridones 416 Thioesters
and tetrahydrofolic acid biosynthesis 455 thymine 431 acidity 372
Sulfonamides uracil 431 from carboxylic acid derivatives 261
as antibiotics 274 Termination step, radical chain reaction 323 enzyme-bound, and fatty acid synthase
as diuretics 275 C- and N-Terminus, peptides, definition 504
Sulfonation, of aromatic rings 305 Terpenoid biosynthesis, electrophilic additions 595
Sulfonic acids 273 300 in enzyme binding 516, 530
from aromatic sulfonation 306 α-Terpineol, biosynthesis 303 in glycolysis 582
derivatives, comparison with carboxylic Testosterone, structure 398 in non-ribosomal peptide biosynthesis 535
Tetracycline, structure 385 reactivity 250
acid derivatives, Table 273 Thioesterase, in non-ribosomal peptide
Sulforaphane, structure 477
Sulfur trioxide, in aromatic sulfonation biosynthesis 535
Thioethers, from nucleophilic substitution
305
reactions 199

INDEX 695

Thioketal Transesterification UDPglucose (uridine diphosphoglucose)
formation 235 acid-catalysed 254 in biosynthesis of glucosides 480
as protecting group 235 in action of acetylcholinesterase 279 oxidation to UDPglucuronic acid 489
of COX by aspirin 254 structure 480
Thiols
acidity 125 transfer-RNA (tRNA), see RNA UDPglucuronic acid (uridine
conjugate addition to acrolein 395 Transimination diphosphoglucuronic acid)
as nucleophile
hemithioacetal and hemithioketal mechanism 604 in drug conjugation 489
formation 235 and PLP binding 604 structure 487
in SN1 and SN2 reactions 199 Transition state UDPsugars
thioacetal and thioketal formation 235 definition 173 in biosynthesis oligosaccharides and
thioester formation 261 energy diagram 174
in E2 reactions 207 polysaccharides 484
Thiolane, structure 404 in SN2 reactions 183 in glycoside biosynthesis 480
Thiolase, in fatty acid β-oxidation 591 Transketolase Unsaturated compounds 30
Thionyl chloride, in synthesis of acyl mechanism 608 Uracil
reactions catalysed 608 conversion into thymine 455
chlorides 251 role of TPP 607 hydrogen bonding 51
Thiophene Translation in nucleic acids 550
definition 556 pyrimidine structure 431
dipole 427 inhibitors 558 tautomeric forms 431
molecular structure 426 of mRNA, mechanism 556 Uric acid
Thiophene and furan, reactivity 427 Translocation, definition 558 acidity 451
Threonine, structure and pKa values 501 Tricarboxylic acid cycle, see Krebs cycle structure 450
Threose, structure and stereochemistry 465 Trimethoprim, structure 455 Uridine, structure 550
Thymine Triose phosphate isomerase Uridine diphosphoglucose, see UDPglucose
formation from uracil 455 enzyme mechanism 524 Uridine diphosphoglucuronic acid, see
hydrogen bonding 51 in glycolysis 581
in nucleic acids 550 Triphenylmethyl, see trityl UDPglucuronic acid
pyrimidine structure 431 Triphosphoric acid, structure 277 Uridylic acid, in nucleotide biosynthesis 563
tautomeric forms 431 Triprolidine, configuration 85 Uronic acid
Thyroxine, biosynthesis via phenolic oxidative Trityl carbocation
resonance stabilization 194, 567 definition 485
coupling 344 Trivial names 15 derivatives, natural 488
α-Tocopherol (vitamin E) fused heterocycles 438
Tropane alkaloids 370, 375 Valence
as antioxidant 336 nitrogen inversion 118 electrons 19
regeneration 338 stereochemistry and shape 117 shell 19
p-Toluenesulfonyl chloride, see tosyl chloride Tropine
Tomatidine, as spiro compound 107 configuration 119 Valency 1, 19, 46
Torsional asymmetry 92 as meso compound 375 Valine
gossypol 94 stereochemistry and shape 117
Tosyl chloride (p-toluenesulfonyl chloride) synthesis via Mannich reaction 370 epimerization during peptide biosynthesis
Trypsin 377
273 in peptide sequence determination 546
and SN2 reactions 190 specificity 521 structure and pKa values 501
Tosyl esters, see tosylates Tryptophan Vigabatrin, nomenclature 11
Tosylate anion, as leaving group 274, 492 hydroxylation 602 Vinyl cation 292
Tosylates as indole derivative 446 Viruses, composition 558
formation 273 instability in acid 261 Vision, vitamin A 40
in elimination reactions 274 structure and pKa values 501 Vitamin A1, see retinol
in nucleophilic substitutions 273 Tubocurarine Vitamin B1, see thiamine
in SN2 reactions 189 biosynthesis via phenolic oxidative Vitamin B2, see riboflavin
TPP (thiamine diphosphate) Vitamin B5, see pantothenic acid
as carrier of acyl anion equivalents 607 coupling 342 Vitamin B6 (pyridoxal, pyridoxine,
in decarboxylation of pyruvic acid 438 structure 202
in Krebs cycle 585, 587 β-Turn, in proteins 509 pyridoxamine) 246, 600
structure 437, 605 Twist-boat conformation Vitamin B9, see folic acid
as thiazolium salt 605 cyclohexane 66 Vitamin B12, structure 425
ylid formation 438, 605 di-tert-butylcyclohexanes 72 Vitamin C (ascorbic acid)
TPP-dependent reactions 605–8 Tyrosine
trans and cis, see configuration ionization 503 acidity 490
Transaldolase, imine–enamime mechanism as antioxidant 338
at pH 7 152 biosynthesis 490
608 structure and pKa values 501 structure 490
Transaminase 598 Vitamin E see α-tocopherol
Transamination Ubiquinol, in electron transport chain 577 Vitamin H, see biotin
Ubiquinone, in electron transport chain
definition 598 Wagner–Meerwein rearrangements, see
in formation of aminosugars 492 577 rearrangement reactions, carbocation
of GABA 602
mechanism 599 Warfarin, structure and synthesis 420
Transcriptase, reverse 559 Water
Transcription
definition 556 bonding molecular orbitals 34
inhibitors 558

696 INDEX Ylid (ylide)
definition 437
Water (continued) Wedge–dot representation 32, 55 from TPP 438, 605
hydrogen bonding 50 butane 58
as nucleophile in hydrate formation 234 ethane 57
as nucleophile in SN1 and SN2 reactions
198 Xanthine, in purine metabolism 451 Zidovudine (AZT), structure 559
pKa values Xanthine oxidase, in uric acid formation 451 Zig-zag chain 2
as acid 136 Xylose Zolmitriptan, structure 447
as base 136 Zwitterion
hemiacetal form, structure 471
Wave equation 20 structure and stereochemistry 465 amino acids 160, 501
Wave function 20 Xylulose, structure and stereochemistry 464 definition 151

phase sign 22, 25
Wavy bond 226, 470