Part Ⅰ MOLECULAR ORBITALS FOR BIOCHEMISTS 1
Ⅰ．Why molecular orbitals? 3
Ⅱ．Fundamental concepts 9
Ⅰ．The wave-mechanical description of an electron 9
1．The wave function 10
2．The wave equation 11
3．The spin 14
4．One electron in the field of a single nucleus:the hydrogen atom and the notion of atomic orbitals 15
A．General considerations 15
B．The ground state:the descriptions of an atomic orbital 17
C．Excited states:s,p,d,．．．orbitals 19
D．The generalized notion of atomic orbitals 21
5．One electron in the field of two nuclei:the notion of molecular orbitals 22
A．General considerations 22
B．σ orbitals 24
C．π orbitals 25
Ⅱ．The representation of polyelectronic systems 26
1．The principles of the quantum mechanics of systems of particles 26
2．The＂individual orbital approach＂to the polyelectronic problem;the＂autbau＂principle 27
3．The variation method 31
A．The principle 31
B．An example 31
Ⅲ．Atomic orbitals 34
1．The structure of polyelectronic atoms 34
2．The valence shell:valence electrons and lone pairs 37
3．Valence states and hybridization 38
4．Electronegativity 41
Ⅳ．The LCAO approximation for molecular orbitals 43
1．The basic principle 43
2．The variation method in the case of a linear trial function 45
3．LCAO molecular orbitals for diatomics 48
A．LCAO approximations for the monoelectronic case 48
B．The representation of diatomic molecules 53
4．Polyatomic molecules 56
A．Localized and non-localized (delocalized) bonds 56
B．The structure of fundamental carbon compounds 60
Ⅲ．Conjugated molecules 62
Ⅰ．Delocalized π electrons and polycentric molecular orbitals 62
Ⅱ．The principle of the LCAO approximation for conjugated systems 64
Ⅲ．The Hückel approximation for hydrocarbons 67
1．The assumptions 67
2．Writing and solving the secular equations 68
A．Examples and notations 68
B．The use of the molecular symmetry 70
3．The energy values and the energy indices 79
4．The structural indices 80
Ⅳ．Refinements of the Hückel approximation 85
Ⅴ．Substituted and heterocyclic molecules 91
1．The general scheme 91
2．The different types of substituents and heteroatoms 92
3．The choice of parameters 98
A．General considerations 98
B．Numerical values 104
4．Examples of calculations 110
5．Energy indices and structural indices 115
Ⅳ．The principal applications of the indices of the electronic structure 118
Ⅰ．Resonance energy 118
1．Keto-enol tautomerism 121
2．Oxidation-reduction potentials of reversible systems 123
3．Formation and stability of free radicals 123
4．Acidic and basic strength 124
5．Product stabilities in chemical transformations 125
Ⅱ．Energies of the highest filled and lowest empty molecular orbitals 128
1．Electron-donor properties 128
2．Electron-acceptor properties 132
3．Charge-transfer complexes 135
Ⅲ．Transition (excitation) energies 138
Ⅳ．Diamagnetic anisotropy 145
Ⅴ．Electronic charges 147
Ⅵ．Bond orders 148
Ⅶ．Chemical reactivity 155
1．The isolated-molecule approximation 155
2．The reacting-molecule approximation 160
3．The relation between the two approximations 169
Ⅷ．Supplementary applications of the index of free valence 171
Ⅸ．The scope of the molecular-orbital approach to biochemistry 178
Ⅹ．General references for Part Ⅰ 181
Part Ⅱ ELECTRONIC STRUCTURE OF FUNDAMENTAL BIOCHEMICAL SUBSTANCES 183
Ⅴ．Purines,pyrimidines and the submolecular structure of nucleic acis 185
Ⅰ．The molecular structure of the nucleic acids 185
Ⅱ．The biochemical role of the nucleic acids 195
Ⅲ．Related biologically important purines and pyrimidines 198
1．Metabolically important purines and pyrimidines 198
A．Purines 198
B．Pyrimidines 202
2．Isomers 204
Ⅳ．Tautomerism in purines and pyrimidines 205
Ⅴ．The significance of the resonance energy 209
Ⅵ．Electron-donor and electron-acceptor properties 215
Ⅶ．Local structural properties 224
Ⅷ．The properties of the carbon atoms 226
Ⅸ．The properties of the ring nitrogen atoms 230
1．The pyridine-type nitrogens 230
2．The N9 nitrogen of purines and the N1 nitrogen of pyrimidines 238
Ⅹ．The antitumor activity of purine antimetabolites 240
Ⅺ．The reactions concerning the amino groups of the purines and pyrimidines 248
Ⅻ．Formation of metal complexes 253
ⅩⅢ．Mechanism of the metabolic degradation of purines by xanthine oxidase 258
ⅩⅣ．Structural aspects of radiation effects 267
1．General aspects 267
2．The experimental data 270
3．The interpretation 277
ⅩⅤ．Miscellaneous reactions 283
ⅩⅥ．A general view 287
Ⅵ．Proteins as conjugated systems 292
Ⅰ．The molecular structure of proteins 292
Ⅱ．The biochemical role of proteins 300
Ⅲ．The existence of energy bands and the semiconductivity of proteins 301
1．The hypothesis 301
2．Conductors and insulators 303
3．Semiconductivity of proteins 306
4．Quantum-mechanical calculations on the electronic states of proteins 308
5．The peptide free radical 318
Ⅳ．Some electronic properties of the aromatic amino acid residues of proteins 320
1．Generalities 320
2．Electron-donor properties of tryptophan 322
3．Metabolism of tryptophan 326
4．Remarks on the remaining aromatic amino acids 331
Ⅶ．Energy-rich compounds 335
Ⅰ．Elementary concepts of bioenergetics 335
1．Free energy change 335
2．Free energy of activation 337
3．Some properties of ？F 339
4．The coupling of reactions 340
Ⅱ．The main types of energy-rich substances 348
1．Energy-rich phosphates 348
A．Major types 348
B．The theory of energy wealth 354
(1) The qualitative theory 354
(2) The calculations 356
(3) Factors contributing to the energy wealth of phosphates 357
C．Phosphates as electrophilic reactants 370
D．The structure of ATP 374
2．Other types of energy-rich compounds 376
A．Acyl thioesters 376
B．Acetyl-imidazole 381
C．Onium compounds 383
Ⅷ．Pteridines 385
Ⅰ．General role 385
Ⅱ．The metabolism of riboflavin and of folic acid 386
1．The synthesis and degradation of riboflavin 386
2．The synthesis and degradation of folic acid 389
Ⅲ．Electronic properties 391
1．Isomerism and tautomerism 391
2．The significance of resonance energy 393
3．Electron-donor and -acceptor properties 396
4．The reactivity of the carbon atoms 397
5．Properties of the nitrogen atoms 400
A．Pyrimidine-type nitrogens 400
B．Pyrrole-type nitrogens 400
6．Enzymic oxidation by xanthine oxidase 403
Ⅸ．Porphyrins and bile pigments 406
Ⅰ．Porphyrins 406
1．General view 406
2．Electronic structure of metal-free porphyrins 408
3．General characteristics of the iron-porphyrin complexes 416
4．Molecular-orbital calculations on the iron-porphyrin complexes 419
A．Building of the molecular orbitals of the complex 420
B．Distribution of energy levels 422
C．Distribution of the electronic charges 424
Ⅱ．Bile pigments 427
Ⅹ．Conjugated biochemical polyenes 435
Ⅰ．Carotenoids and vitamins A 435
1．General aspects 435
2．The in vivo transformation of carotenoids into vitamin A 440
A．Vitamin A 441
B．The mechanism of the transformation of carotenoids into vitamin A 441
C．Structure and provitamin A activity 453
Ⅱ．Retinenes and the visual pigments 457
1．The composition of the visual pigments 457
2．The occurrence of the 11-cis isomer of retinene in the rhodopsin system 460
3．The electronic structure of the different isomers of retinene 466
Ⅺ．Quinones 471
Ⅰ．General features 471
1．Oxido-reductive properties of quinones 472
A．Experimental data 472
B．Correlation with theoretical indices 475
2．Quinones in charge-transfer complexes 479
3．Aspects of the chemical reactivity of quinones 480
A．The electronic indices 480
B．Characteristic reactivities 483
Ⅱ．Particular quinones of outstanding biological importance 486
1．Vitamin K 486
A．Definition 486
B．Blood-clotting activity 487
C．Other possible roles of vitamin K 490
2．Ubiquinone (Coenzyme Q) and related compounds 491
3．Vitamin E 492
A．General features 492
B．The antioxidant activity of vitamin E and of other phenolic compounds 494
Ⅲ．The band structure of melanins 497
Part Ⅲ ELECTRONIC ASPECTS OF ENZYMIC REACTIONS 501
Ⅻ．General aspects of enzymic reactions 503
ⅩⅢ．Oxidation-reduction enzymes 508
Ⅰ．The electron-transport chain 508
Ⅱ．The electron-donor and electron-acceptor properties of the respiratory coenzymes 517
Ⅲ．The mechanism of functioning of the pyridinoproteins 519
1．The principal reactions 519
2．The chemical aspects 520
3．The electronic interpretation 525
Ⅳ．The mechanism of functioning of the flavoprotains 533
1．The principal reactions 533
2．The chemical aspects 534
3．The electronic aspects 541
Ⅴ．Molecular orbitals and oxidation-reduction potentials 545
Ⅵ．The oxido-reductive properties of organic dyes of biochemical importance 549
Ⅶ．The cytochromes 552
Ⅷ．Oxidative phosphorylation 555
ⅩⅣ．Folic acid coenzymes 564
Ⅰ．General characteristics 564
Ⅱ．The principal metabolic reactions catalyzed by folic acid coenzymes 565
Ⅲ．The principal functions of folic acid coenzymes:A general view 569
Ⅳ．Folic acid coenzymes as carriers of one-carbon units:The experimental data 571
1．FH4 as one-carbon unit acceptor 572
A．Reactions necessitating FH4 as the only cofactor 572
B．Reactions necessitating,besides FH4,a complementary activator,K+ or ATP 575
C．Chemical reactions of FH4 with C1 units in strong acid medium 576
D．Conclusion 577
2．FH4 as one-carbon unit donor 577
Ⅴ．Folic acid coenzymes as carriers of one-carbon units:The electronic aspects 579
1．General remarks on the molecular-orbital calculations on folic acid and its derivatives 579
2．FH4 as one-carbon unit acceptor 580
3．FH4 as one-carbon unit donor 586
Ⅵ．Folic acid coenzymes as subtrates for the oxido-reduction of a one-carbon unit 589
Ⅶ．The oxido-reductive transformations of folic acid and its coenzymes 591
1．FH4 as a coenzyme for the reduction of one-carbon units 591
2．The transformation F ？ FH4 593
3．The mechanism of the oxido-reductive transformations 594
Ⅷ．Folic acid antimetabolites 596
1．Types of antifolic agents 598
2．Electronic structure and mode of action of antifolic agents 601
ⅩⅤ．Pyridoxal phosphate enzymes 609
Ⅰ．General aspects 609
Ⅱ．An outline of the theory of Braunstein and Snell 611
Ⅲ．The electronic interpretation 615
1．General remarks on the quantum-mechanical calculations on pyridoxal phosphates 615
2．The structure of the primary Schiff＇s base 616
3．Reactions resulting from the labilization of the α-proton 617
A．Transamination 617
B．Racemization 623
C．α-β eliminations 624
D．γ-eliminations 628
4．Reactions resulting from the labilization of the α-carboxy group 631
5．Reactions resulting from the labilization of the R group of the amino acid 633
6．Conclusion 634
ⅩⅥ．Thiamine-pyrophosphate catalyzed reactions 636
Ⅰ．The principal functions of thiamine-pyrophosphate enzymes 636
Ⅱ．Theories of mode of action 640
Ⅲ．The electronic aspects 645
1．The calculations 645
2．The results 646
ⅩⅦ．Enzymic hydrolysis 657
Ⅰ．General features of substrates for enzymic hydrolysis 657
Ⅱ．Common features of the active sites of hydrolytic enzymes 669
Ⅲ．Electronic structure and activity of organophosphorus inhibitors of esterases 671
ⅩⅧ．Conclusion:electronic delocalization and the processes of life 673
Appendix 677
Index of Authors 845
Index of Principal Compounds and Subjects 861