690
INDEX
Oxazolium salts, hydrogen exchange 437
Oxetane, structure 404
Oxidation
Baeyer–Villiger 335
reactions, and ATP synthesis 575
β-Oxidation
of fatty acids 589–92
energy yield 592
reverse Claisen reaction 387
stereochemistry 594
unsaturated fatty acids 593
Oxidative
coupling, phenolic see phenolic oxidative
coupling
decarboxylation, in Krebs cycle 585, 587
phosphorylation 577–9
Oxide anion 169
N-Oxides
of amines 410
deoxygenation 410
Oxinane, structure 404
Oxirane, structure 404
2-Oxoglutarate
from decarboxylation of oxalosuccinate 389
in Krebs cycle 587
reductive amination 598
2-Oxoglutarate dehydrogenase
as enzyme complex 607
in Krebs cycle 587
as TPP-dependent reaction 605
Oxolane, structure 404
Oxonium cation 169
Oxygen
diradical 333
electronic configuration 23
radical addition 333
sp
2 hybrid orbitals, stereochemistry 56
sp
3 hybrid orbitals 33
stereochemistry 56
sp
3 hybridized, electronic configuration 33
Paal–Knorr pyrrole synthesis 461
Palmitic acid, structure 259
Pantetheine, structure 536
Pantetheinyl arm, in non-ribosomal peptide
biosynthesis 536
Pantothenic acid (vitamin B5) 536
and acyl carrier protein 597
Paracetamol (acetaminophen)
glutathione conjugates 400
synthesis 264
toxic metabolites 400
Parathion, as acetylcholinesterase inhibitor
280
Partial structures 3
Pauling electronegativity values, Table 36
PCR, see polymerase chain reaction
Pectins, structure 488
Penicillins 82
as amides/lactams 265
antibiotics, tripeptide precursor 376
biosynthesis 537
cleavage by β-lactamase 523
mode of action 539
as modified tripeptides 537
stereochemistry and shape 115
Penicillin G, see benzylpenicillin
1,3-Pentadiene
acidity 129
molecular orbitals 37
1,4-Pentadiene, molecular orbitals 37
Pentoses, definition 463
Peptide
antibiotics 376
biosynthesis 533–6
epimerization of amino acids 376
non-ribosomal 535
ribosomal 533
bond
configuration 509
definition 499
planarity 508
resonance stabilization 508
cyclic 536
definition 499
hydrolysis 261
sequence, determination 544
use of chymotrypsin and trypsin 546
sequencers, automated 546
synthesis 540–4
on polymeric supports 542
solid phase 542
synthesizers, automated 543
Peptide synthase
non-ribosomal (NRPS) 535
modular mechanism 535
in penicillin biosynthesis 537
Peptides and proteins
hydrolysis 505
structural abbreviations 504
C- and N-terminus 504
Peptidoglycan
bacterial cell wall, structure 495, 538
cross-linking 538
action of β-lactam antibiotics 539
Peracetic acid
in epoxidation 290
in formation of N-oxides 410
Permethrin, structure 61
Peroxides, in radical reactions 334
Peroxy compounds, radical formation 319
Peroxyacetic acid, see peracetic acid
pH
calculation, strong acids 146
strong bases 147
weak acids 147–8
weak bases 147–8
definition 146
of neutrality, temperature dependence 146
optimum, of enzyme 517
salt solutions 148
Phase sign
atomic orbitals 22
wave function 25
Phenelzine, as enzyme inhibitor 531
Phenols, acidity 133
Phenol biosynthesis, aldol and Claisen
reactions 385
Phenolic oxidative coupling 340–5
in biosynthesis of thyroxine 344
in biosynthesis of tubocurarine and
morphine 342
radical mechanism 341
Phenothrin, structure 61
Phenyl isothiocyanate, Edman reagent 545
Phenylacetic acid, acidity 130
Phenylalanine, structure and pK a values
501
Phloracetophenone, biosynthesis 385
Pholcodine, from selective alkylation of
morphine 186
Phosphates
as leaving groups 196
in biochemical reactions 277
in intermediary metabolism 573
Phosphates and diphosphates
abbreviations 277
nucleophilic attack, mechanism 277
Phosphodiesters, in nucleic acids 276, 551
Phosphoenolpyruvic acid
as enol 350
in glycolysis 583
Phosphofructokinase, in glycolysis 580
Phosphoglucose isomerase, in glycolysis 580
2-Phosphoglycerate, in glycolysis 582
3-Phosphoglycerate, in glycolysis 582
Phosphoglycerate mutase, in glycolysis 582
Phosphopantotheine group, of acyl carrier
protein 597
Phosphoramidites, in nucleic acid synthesis
567
Phosphoribosyl diphosphate (PRPP), in
nucleotide biosynthesis 563
5-Phosphoribosylamine, in nucleotide
biosynthesis 563
Phosphoric acid
acidity 144, 275
derivatives, nucleophilic substitution
reactions 275–82
diesters in nucleic acids 276
Phosphorus oxychloride
in chlorination of diazinones 430
in chlorination of pyridones 417
Photolysis, radical formation 320
Photosynthesis 40, 424
Physostigmine
as acetylcholinesterase inhibitor 279
structure 448
Pi (π) bonds, see bonds, pi
pI, isoelectric point 160
Picolines (methylpyridines)
acidity 412
in aldol reaction 412
Pictet–Spengler tetrahydroisoquinoline
synthesis 460
in alkaloid biosynthesis 371
α-Pinene, synthesis of camphor 218
β-Pinene, stereochemistry and shape 117
Piperazine, structure 404
Piperidine
basicity 143
conformation 72
dipole 406
structure 404
pK a
definition 122
and drug absorption 164
values, see also acidity, basicity
amino acids in proteins, Table 503
amino acids, Table 500–1
common drugs, Table 164
Tables 123–4
INDEX
Oxazolium salts, hydrogen exchange 437
Oxetane, structure 404
Oxidation
Baeyer–Villiger 335
reactions, and ATP synthesis 575
β-Oxidation
of fatty acids 589–92
energy yield 592
reverse Claisen reaction 387
stereochemistry 594
unsaturated fatty acids 593
Oxidative
coupling, phenolic see phenolic oxidative
coupling
decarboxylation, in Krebs cycle 585, 587
phosphorylation 577–9
Oxide anion 169
N-Oxides
of amines 410
deoxygenation 410
Oxinane, structure 404
Oxirane, structure 404
2-Oxoglutarate
from decarboxylation of oxalosuccinate 389
in Krebs cycle 587
reductive amination 598
2-Oxoglutarate dehydrogenase
as enzyme complex 607
in Krebs cycle 587
as TPP-dependent reaction 605
Oxolane, structure 404
Oxonium cation 169
Oxygen
diradical 333
electronic configuration 23
radical addition 333
sp
2 hybrid orbitals, stereochemistry 56
sp
3 hybrid orbitals 33
stereochemistry 56
sp
3 hybridized, electronic configuration 33
Paal–Knorr pyrrole synthesis 461
Palmitic acid, structure 259
Pantetheine, structure 536
Pantetheinyl arm, in non-ribosomal peptide
biosynthesis 536
Pantothenic acid (vitamin B5) 536
and acyl carrier protein 597
Paracetamol (acetaminophen)
glutathione conjugates 400
synthesis 264
toxic metabolites 400
Parathion, as acetylcholinesterase inhibitor
280
Partial structures 3
Pauling electronegativity values, Table 36
PCR, see polymerase chain reaction
Pectins, structure 488
Penicillins 82
as amides/lactams 265
antibiotics, tripeptide precursor 376
biosynthesis 537
cleavage by β-lactamase 523
mode of action 539
as modified tripeptides 537
stereochemistry and shape 115
Penicillin G, see benzylpenicillin
1,3-Pentadiene
acidity 129
molecular orbitals 37
1,4-Pentadiene, molecular orbitals 37
Pentoses, definition 463
Peptide
antibiotics 376
biosynthesis 533–6
epimerization of amino acids 376
non-ribosomal 535
ribosomal 533
bond
configuration 509
definition 499
planarity 508
resonance stabilization 508
cyclic 536
definition 499
hydrolysis 261
sequence, determination 544
use of chymotrypsin and trypsin 546
sequencers, automated 546
synthesis 540–4
on polymeric supports 542
solid phase 542
synthesizers, automated 543
Peptide synthase
non-ribosomal (NRPS) 535
modular mechanism 535
in penicillin biosynthesis 537
Peptides and proteins
hydrolysis 505
structural abbreviations 504
C- and N-terminus 504
Peptidoglycan
bacterial cell wall, structure 495, 538
cross-linking 538
action of β-lactam antibiotics 539
Peracetic acid
in epoxidation 290
in formation of N-oxides 410
Permethrin, structure 61
Peroxides, in radical reactions 334
Peroxy compounds, radical formation 319
Peroxyacetic acid, see peracetic acid
pH
calculation, strong acids 146
strong bases 147
weak acids 147–8
weak bases 147–8
definition 146
of neutrality, temperature dependence 146
optimum, of enzyme 517
salt solutions 148
Phase sign
atomic orbitals 22
wave function 25
Phenelzine, as enzyme inhibitor 531
Phenols, acidity 133
Phenol biosynthesis, aldol and Claisen
reactions 385
Phenolic oxidative coupling 340–5
in biosynthesis of thyroxine 344
in biosynthesis of tubocurarine and
morphine 342
radical mechanism 341
Phenothrin, structure 61
Phenyl isothiocyanate, Edman reagent 545
Phenylacetic acid, acidity 130
Phenylalanine, structure and pK a values
501
Phloracetophenone, biosynthesis 385
Pholcodine, from selective alkylation of
morphine 186
Phosphates
as leaving groups 196
in biochemical reactions 277
in intermediary metabolism 573
Phosphates and diphosphates
abbreviations 277
nucleophilic attack, mechanism 277
Phosphodiesters, in nucleic acids 276, 551
Phosphoenolpyruvic acid
as enol 350
in glycolysis 583
Phosphofructokinase, in glycolysis 580
Phosphoglucose isomerase, in glycolysis 580
2-Phosphoglycerate, in glycolysis 582
3-Phosphoglycerate, in glycolysis 582
Phosphoglycerate mutase, in glycolysis 582
Phosphopantotheine group, of acyl carrier
protein 597
Phosphoramidites, in nucleic acid synthesis
567
Phosphoribosyl diphosphate (PRPP), in
nucleotide biosynthesis 563
5-Phosphoribosylamine, in nucleotide
biosynthesis 563
Phosphoric acid
acidity 144, 275
derivatives, nucleophilic substitution
reactions 275–82
diesters in nucleic acids 276
Phosphorus oxychloride
in chlorination of diazinones 430
in chlorination of pyridones 417
Photolysis, radical formation 320
Photosynthesis 40, 424
Physostigmine
as acetylcholinesterase inhibitor 279
structure 448
Pi (π) bonds, see bonds, pi
pI, isoelectric point 160
Picolines (methylpyridines)
acidity 412
in aldol reaction 412
Pictet–Spengler tetrahydroisoquinoline
synthesis 460
in alkaloid biosynthesis 371
α-Pinene, synthesis of camphor 218
β-Pinene, stereochemistry and shape 117
Piperazine, structure 404
Piperidine
basicity 143
conformation 72
dipole 406
structure 404
pK a
definition 122
and drug absorption 164
values, see also acidity, basicity
amino acids in proteins, Table 503
amino acids, Table 500–1
common drugs, Table 164
Tables 123–4