Quantum biochemistry: [electronic structure and biological activity]
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IMAGE 1
XXXV
CONTENTS
ACKNOWLEDGMENT VII CONGRATULATIONS TO PROFESSOR ADA YONATH FOR WINNING
THE 2009 NOBEL PRIZE IN CHEMISTRY IX INTRODUCTORY REFLECTIONS ON QUANTUM
BIOCHEMISTRY:
FROM CONTEXT TO CONTENTS XI CHERIFF. MATTA LIST OF CONTRIBUTORS LI
VOLL PART ONE NOVEL THEORETICAL, COMPUTATIONAL, AND EXPERIMENTAL METHODS
AND TECHNIQUES 1
1 QUANTUM KERNELS AND QUANTUM CRYSTALLOGRAPHY: APPLICATIONS IN
BIOCHEMISTRY 3 LULU HUANG, LOU MASSA, AND JEROME KARLE
1.1 INTRODUCTION 3
1.2 ORIGINS OF QUANTUM CRYSTALLOGRAPHY (QCR) 4 1.2.1 GENERAL PROBLEM OF
N-REPRESENTABILITY 4 1.2.2 SINGLE DETERMINANT AT-REPRESENTABILITY 5
1.2.3 EXAMPLE APPLICATIONS OF CLINTON'S EQUATIONS 7 1.2.3.1 BERYLLIUM 7
1.2.3.2 MALEIC ANHYDRIDE 9 1.3 BEGINNINGS OF QUANTUM KERNELS 10
1.3.1 COMPUTATIONAL DIFFICULTY OF LARGE MOLECULES 10 1.3.2 QUANTUM
KERNEL FORMALISM 11 1.3.3 KERNEL MATRICES: EXAMPLE AND RESULTS 14 1.3.4
APPLICATIONS OF THE IDEA OF KERNELS 17 1.3.4.1 HYDRATED HEXAPEPTIDE
MOLECULE 17
1.3.4.2 HYDRATED LEU^ZERVAMICIN 38 1.4 KERNEL DENSITY MATRICES LED TO
KERNEL ENERGIES 22 1.4.1 KEM APPLIED TO PEPTIDES 24
BIBLIOGRAFISCHE INFORMATIONEN HTTP://D-NB.INFO/994010621
DIGITALISIERT DURCH
IMAGE 2
XXXVI CONTENTS
1.4.2 QUANTUM MODELS WITHIN KEM 29
1.4.2.1 CALCULATIONS AND RESULTS USING DIFFERENT BASIS FUNCTIONS FOR THE
ADPGV7B MOLECULE 32 1.4.2.2 CALCULATIONS AND RESULTS USING DIFFERENT
QUANTUM METHODS FOR THE ZAIB4 MOLECULE 34
1.4.2.3 COMMENTS REGARDING KEM 36 1.4.3 KEM APPLIED TO INSULIN 36
1.4.3.1 KEM CALCULATION RESULTS 36 1.4.3.2 COMMENTS REGARDING THE
INSULIN CALCULATIONS 38 1.4.4 KEM APPLIED TO DNA 39
1.4.4.1 KEM CALCULATION RESULTS 39 1.4.4.2 COMMENTS REGARDING THE DNA
CALCULATIONS 41 1.4.5 KEM APPLIED TO TRNA 41 1.4.6 KEM APPLIED TO
RATIONAL DESIGN OF DRUGS 43
1.4.6.1 IMPORTANCE OF THE INTERACTION ENERGY FOR RATIONAL DRUG DESIGN 43
1.4.6.2 SAMPLE CALCULATION: ANTIBIOTIC DRUG IN COMPLEX (1O9M) WITH A
MODEL AMINOACYL SITE OF THE 30S RIBOSOMAL SUBUNIT 44 1.4.6.3 COMMENTS
REGARDING THE DRUG-TARGET INTERACTION CALCULATIONS 46
1.4.7 KEM APPLIED TO COLLAGEN 47 1.4.7.1 INTERACTION ENERGIES 47 1.4.7.2
COLLAGEN 1A89 47 1.4.7.3 COMMENTS REGARDING THE COLLAGEN CALCULATIONS 50
1.4.8 KEM FOURTH-ORDER CALCULATION OF ACCURACY 50 1.4.8.1 MOLECULAR
ENERGY AS A SUM OVER KERNEL ENERGIES 50 1.4.8.2 APPLICATION TO
LEU'-ZERVAMICIN OF THE FOURTH-ORDER
APPROXIMATION OF KEM 51 1.4.9 KEM APPLIED TO VESICULAR STOMATITIS VIRUS
NUDEOPROTEIN, 33 000 ATOM MOLECULE 53 1.4.9.1 VESICULAR STOMATITIS VIRUS
NUDEOPROTEIN (2QVJ) MOLECULE 53 1.4.9.2 HYDROGEN BOND CALCULATIONS 54
1.4.9.3 COMMENTS REGARDING THE 2QVJ CALCULATIONS 54 1.5 SUMMARY AND
CONDUSIONS 55
REFERENCES 57
2 GETTING THE MOST OUT OF ONIOM: GUIDELINES AND PITFALLS 61 FERNANDO R.
CLEMENTE, THORN VREVEN, AND MICHAELJ. FRISCH 2.1 INTRODUCTION 61
2.2 QM/MM 62
2.3 ONIOM 63
2.4 GUIDELINES FOR THE APPLICATION OF ONIOM 65 2.4.1 SUMMARY 72
2.5 THE CANCELLATION PROBLEM 72
2.6 USE OF POINT CHARGES 77
2.7 CONDUSIONS 81
REFERENCES 82
IMAGE 3
CONTENTS XXXVII
3 MODELING ENZYMATIC REACTIONS IN METALLOENZYMES AND PHOTOBIOLOGY
BY QUANTUM MECHANICS (QM) AND QUANTUM MECHANICS/MOLECULAR MECHANICS
(QM/MM) CALCULATIONS 85 LUNG WA CHUNG, XIN LI, AND KEIJI MOROKUMA 3.1
INTRODUCTION 85
3.2 COMPUTATIONAL STRATEGIES (METHODS AND MODELS) 86 3.2.1 QUANTUM
MECHANICAL (QM) METHODS 86 3.2.2 ACTIVE-SITE MODEL 88 3.2.3 QM/MM
METHODS 88
3.2.4 QM/MM MODEL AND SETUP 90 3.3 METALLOENZYMES 91
3.3.1 HEME-CONTAINING ENZYMES 91 3.3.1.1 BINDING AND PHOTODISSODATION OF
DIATOMIC MOLECULES 91 3.3.1.2 HEME OXYGENASE (HO) 95 3.3.1.3
INDOLEAMINES DIOXYGENASE (IDO) AND TRYPTOPHAN DIOXYGENASE
(TDO) 97
3.3.1.4 NITRIC OXIDE SYNTHASE (NOS) 101 3.3.2 COBALAMIN-DEPENDENT
ENZYMES 305 3.3.2.1 METHYLMALONYL-COA MUTASE 105 3.3.2.2 GLUTAMINE
MUTASE 108 3.4 PHOTOBIOLOGY 109
3.4.1 FLUORESCENT PROTEINS (FPS) 109 3.4.1.1 GREEN FLUORESCENT PROTEINS
(GFP) 330 3.4.1.2 REVERSIBLE PHOTOSWITCHING FLUORESCENT PROTEINS (RPFPS)
111 3.4.1.3 PHOTOCONVERSION OF FLUORESCENT PROTEINS 115 3.4.2 LUDFERASES
337
3.5 CONDUSION 120
REFERENCES 120
4 FROM MOLECULAR ELECTROSTATIC POTENTIALS TO SOLVATION MODELS AND ENDING
WITH BIOMOLECULAR PHOTOPHYSICAL PROCESSES 333 JACOPO TORNASI, CHIARA
CAPPELLI, BENEDETTA MENNUCCI, AND ROBERTO CAMMI 131 4.1 INTRODUCTION 333
4.2 THE MOLECULAR ELECTROSTATIC POTENTIAL AND NONCOVALENT INTERACTIONS
AMONG MOLECULES 132 4.2.1 MOLECULAR ELECTROSTATIC POTENTIAL 332 4.2.1.1
USEOFMEP 133
4.2.1.2 SEMIDASSICAL APPROXIMATION 133 4.2.1.3 MEP AS A COMPONENT OF THE
INTERMOLECULAR INTERACTION 134 4.2.1.4 DEFINITION OF THE COULOMB
INTERACTION TERM 335 4.2.1.5 SIMPLIFICATIONS IN THE EXPRESSION OF E ES :
POINT CHARGE
DESCRIPTIONS 135
4.2.1.6 SIMPLIFICATIONS IN THE EXPRESSION OF UEJ,: ATOMIC CHARGES 136
4.2.1.7 SIMPLIFICATIONS IN THE EXPRESSION OF E^: MULTIPOLAR EXPANSIONS
136
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XXXVIII CONTENTS
4.2.2 INTERACTION ENERGY BETWEEN TWO MOLECULES 137
4.2.3 EXAMPLES OF ENERGY DECOMPOSITION ANALYSES 139 4.2.3.1 INTERACTIONS
WITH A PROTON 139 4.2.3.2 INTERACTIONS WITH OTHER CATIONS 139 4.2.3.3
HYDROGEN BONDING 140
4.2.4 INTERACTION POTENTIALS (FORCE FIELDS) FOR COMPUTER SIMULATIONS OF
LIQUID SYSTEMS 140 4.3 SOLVATION: THE "CONTINUUM MODEL" 142 4.3.1 BASIC
FORMULATION OF PCM 142
4.3.2 BEYOND THE BASIC FORMULATION 146 4.3.2.1 DIELECTRIC FUNCTION 146
4.3.2.2 CAVITY SURFACE 147 4.3.2.3 DEFINITION OF THE APPARENT CHARGES
147
4.3.2.4 DESCRIPTION OF THE SOLUTE 147 4.3.3 OTHER CONTINUUM SOLVATION
METHODS 148 4.3.3.1 APPARENT SURFACE CHARGE (ASC) METHODS 148 4.3.3.2
MULTIPOLE EXPANSION METHODS (MPE) 349
4.3.3.3 GENERALIZED BORN MODEL 149 4.3.3.4 FINITE ELEMENT METHOD (FEM)
AND FINITE DIFFERENCE METHOD (FDM) 150 4.4 APPLICATIONS OF THE PCM
METHOD 150 4.4.1 SOLVATION ENERGIES I50
4.4.2 ABOUT THE PES 352
4.4.3 CHEMICAL EQUILIBRIA 152 4.4.3.1 TAUTOMERIE EQUILIBRIA 353 4.4.3.2
EQUILIBRIA IN MOLECULAR AGGREGATION 153 4.4.3.3 PKA OF ACIDS 153
4.4.4 REACTION MECHANISMS 154 4.4.5 SOLVENT EFFECTS ON MOLECULAR
PROPERTIES AND SPECTROSCOPY 156 4.4.5.1 N-ACETYLPROLINE AMIDE (NAP) 357
4.4.5.2 GLUCOSE 158
4.4.5.3 LOCAL FIELD EFFECTS 159 4.4.5.4 DYNAMIC EFFECTS 360 4.4.6 EFFECT
OF THE ENVIRONMENT ON FORMATION AND RELAXATION OF EXCITED STATES 161
4.4.7 ELECTRONIC TRANSITIONS AND RELATED SPECTROSCOPIES 162 4.4.8
PHOTOINDUCED ELECTRON AND ENERGY TRANSFERS 164
REFERENCES 366
5 THE FAST MARCHING METHOD FOR DETERMINING CHEMICAL REACTION MECHANISMS
IN COMPLEX SYSTEMS 373 YULI LIU, STEVEN K. BURGER, BIJOY K. DEY, UTPAL
SARKAR, MAREK R.JANICKI, AND PAUL W. AYERS 5.1 MOTIVATION 171
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CONTENTS XXXIX
5.2 BACKGROUND 172
5.2.1 MINIMUM ENERGY PATH 172 5.2.2 TWO END METHODS 372
5.2.3 SURFACE WALKING ALGORITHMS 373 5.2.4 METADYNAMICS METHODS 174
5.2.5 FAST MARCHING METHOD 174 5.3 FAST MARCHING METHOD 175
5.3.1 INTRODUCTION TO FMM 175
5.3.2 UPWIND DIFFERENCE APPROXIMATION 176 5.3.3 HEAPSORT TECHNIQUE 376
5.3.4 SHEPARD INTERPOLATION 377 5.3.5 INTERPOLATING MOVING LEAST-SQUARES
METHOD 379 5.3.6 FMM PROGRAM 180
5.3.6.1 SETUP, DEFINITIONS AND NOTATION 180 5.3.6.2 INITIALIZE THE
CALCULATION 383 5.3.6.3 UPDATING THE HEAP 181 5.3.6.4 BACKTRACING FROM
THE ENDING POINT TO THE STARTING POINT ON THE
ENERGY COST SURFACE 181 5.3.7 APPLICATION 182
5.3.7.1 FOUR-WELL ANALYTICAL PES 182 5.3.7.2 S N 2 REACTION J84
5.3.7.3 DISSODATION OF IONIZED O-METHYLHYDROXYLAMINE 185 5.4 QUANTUM
MECHANICS/MOLECULAR MECHANICS (QM/MM) METHODS APPLIED TO
ENZYME-CATALYZED REACTIONS 187 5.4.1 QM/MM METHODS 387
5.4.2 INCORPORATING THE QM/MM-MFEP METHODS WITH FMM 389 5.4.3
APPLICATION OF THE INCORPORATED FMM AND QM/MM-MFEP METHOD TO
ENZYME-CATALYZED REACTIONS 3 90 5.4.3.1 S N 2 REACTION IN SOLVENT 390
5.4.3.2 ISOMERIZATION REACTION CATALYZED BY 4-OXALOCROTONATE
TAUTOMERASE (4-OT) 190 5.4.3.3 DECHLORINATION REACTION CATALYZED BY
TRANS-3-CHLOROACRYLIC ADD DEHALOGENASE (CAAD) 393 5.5 SUMMARY 393
REFERENCES 392
PART TWO NUCLEIC ACIDS, AMINO ACIDS, PEPTIDES AND THEIR INTERACTIONS 197
6 CHEMICAL ORIGIN OF LIFE: HOW DO FIVE HCN MOLECULES COMBINE TO FORM
ADENINE UNDER PREBIOTIC AND INTERSTELLAR CONDITIONS 199 DEBJANI ROY AND
PAUL VON RAGUE SCHLEYER 6.1 INTRODUCTION 399
6.1.1 PREBIOTIC CHEMISTRY. EXPERIMENTAL ENDEAVOR TO SYNTHESIZE THE
BUILDING BLOCKS OF BIOPOLYMERS 199
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XL CONTENTS
6.1.2 KEY ROLE OF HCN AS A PRECURSOR FOR PREBIOTIC COMPOUNDS 201
6.1.3 PREBIOTIC EXPERIMENTS AND PROPOSED PATHWAYS FOR THE FORMATION OF
ADENINE 202 6.2 COMPUTATIONAL INVESTIGATION 202 6.2.1 METHOD 204
6.2.2 THERMOCHEMISTRY OF PENTAMERIZATION 204 6.2.3 DETAILED STEP BY STEP
MEDIANISM 205 6.2.3.1 DAMN VS AICN AS ADENINE PRECURSORS 205 6.2.3.2 IS
AN ANIONIC MECHANISM FEASIBLE IN ISOLATION? 205
6.2.3.3 TWO TAUTOMERIE FORMS OF AICN: WHICH ONE IS THE FAVORABLE
PRECURSOR FOR ADENINE FORMATION UNDER PREBIOTIC CONDITIONS? 207 6.2.3.4
VALIDATING THE METHODS USED FOR COMPUTING BARRIER HEIGHTS 213 6.3
CONDUSION 233
REFERENCES 216
7 HYDROGEN BONDING AND PROTON TRANSFER IN IONIZED DNA BASE PAIRS, AMINO
ACIDS AND PEPTIDES 219 LUIS RODRIGUEZ-SANTIAGO, MARC NOGUERA, JOAN
BERTRAN, AND MARIONA SODUPE 7.1 INTRODUCTION 219
7.2 METHODOLOGICAL ASPECTS 220 7.3 IONIZATIONOFDNA BASE PAIRS 221
7.3.1 EQUILIBRIUM GEOMETRIES AND DIMERIZATION ENERGIES 222 7.3.2 SINGLE
AND DOUBLE PROTON TRANSFER REACTIONS 223 7.4 IONIZATION OF AMINO ADDS
227
7.4.1 STRUCTURAL FEATURES OF NEUTRALAND RADICAL CATION AMINO ACIDS 227
7.4.2 INTRAMOLECULAR PROTON-TRANSFER PROCESSES 233 7.5 IONIZATION OF
PEPTIDES 234
7.5.1 IONIZATION OF N-GLYCYLGLYDNE 234 7.5.2 INFLUENCE OF IONIZATION ON
THE RAMACHANDRAN MAPS OF MODEL PEPTIDES 236 7.6 CONDUSIONS 239
REFERENCES 241
8 TO NANO-BIOCHEMISTRY: PICTURE OF THE INTERACTIONS OF DNA WITH GOLD 245
EUGENE S. KRYACHKO 8.1 INTRODUCTORY NANOSDENCE BACKGROUND 245 8.1.1 GOLD
IN NANODIMENSIONS 246 8.1.2 GOLD AND DNA: MEETING POINTS IN
NANODIMENSIONS 248 8.2 DNA-GOLD BONDING PATTERNS: SOME EXPERIMENTAL
FACTS 253 8.3 ADENINE-GOLD INTERACTION 254
8.3.1 ADENINE-AU AND ADENINE-AU 3 BONDING PATTERNS 254 8.3.2 PROPENSITY
OF GOLD TO ACT AS NONCONVENTIONAL PROTON ACCEPTOR 257 8.3.2.1 PAUSE: A
SHORT EXCURSION TO HYDROGEN BONDING THEORY 259
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CONTENTS XU
8.3.2.2 PROOF THAT N-H U AU = N-H- * -AU IN A-AU 3 (N I=1 ,3, 7 ) 260
8.3.2.3 NONCONVENTIONAL HYDROGEN BONDS N-H- * -AU IN A-AU 3 (N; = I 37
) 263 8.3.3 COMPLEX A-AU 3 (N 6 ) 262 8.3.4 INTERACTION BETWEEN ADENINE
AND CHAIN AU 3 CLUSTER 262 8.4 GUANINE-GOLD INTERACTION 263
8.5 THYMINE-GOLD INTERACTIONS 268
8.6 CYTOSINE-GOLD INTERACTIONS 272 8.7 BASIC TRENDS OF DNA BASE-GOLD
INTERACTION 273 8.7.1 ANCHORING BOND IN DNA BASE-GOLD COMPLEXES 276
8.7.2 ENERGETICS IN Z = 0 CHARGE STATE 278
8.7.3 Z = -1 CHARGE STATE 282
8.8 INTERACTION OF WATSON-CRICK DNA BASE PAIRS WITH GOLD CLUSTERS 286
8.8.1 GENERAL BACKGROUND 286 8.8.2 [A-TJ-AU 3 COMPLEXES 289 8.8.3 [GC]AU
3 COMPLEXES 293
8.8.4 AU 6 CLUSTER BRIDGES THE WC GC PAIR 296 8.9 SUMMARY AND
PERSPECTIVES 297
REFERENCES 298
9 QUANTUM MECHANICAL STUDIES OF NONCOVALENT DNA-PROTEIN INTERACTIONS 307
LESLEY R. RUTLEDGE AND STACEY D. WETMORE
9.1 INTRODUCTION 307
9.2 COMPUTATIONAL APPROACHES FOR STUDYING NONCOVALENT INTERACTIONS 308
9.3 HYDROGEN-BONDING INTERACTIONS 335 9.3.1 INTERACTIONS BETWEEN THE
PROTEIN BACKBONE AND DNA
NUDEOBASES 315
9.3.2 INTERACTIONS BETWEEN PROTEIN SIDE CHAINS AND DNA BACKBONE 316
9.3.3 INTERACTIONS BETWEEN PROTEIN SIDE CHAINS AND DNA NUDEOBASES 317
9.4 INTERACTIONS BETWEEN AROMATIC DNA-PROTEIN COMPONENTS 318 9.4.1
STACKING INTERACTIONS 339
9.4.2 T-SHAPED INTERACTIONS 323 9.5 CATION-IT INTERACTIONS BETWEEN
DNA-PROTEIN COMPONENTS 326 9.5.1 CATION-IT INTERACTIONS BETWEEN CHARGED
NUDEOBASES AND AROMATIC AMINO ADDS 326 9.5.2 CATION-RT INTERACTIONS
INVOLVING CHARGED AROMATIC AMINO ADDS 330
9.5.3 CATION-JT INTERACTIONS INVOLVING CHARGED NON-AROMATIC AMINO ADDS
330 9.5.4 SIMULTANEOUS CATION-JI AND HYDROGEN-BONDING INTERACTIONS
(DNA-PROTEIN STAIR MOTIFS) 332 9.6 CONDUSIONS 333
REFERENCES 333
IMAGE 8
XLILL CONTENTS
10 THE VIRIAL FIELD AND TRANSFERABILITY IN DNA BASE-PAIRING 337 RICHARD
F.W. BADERAND FERNANDO CORTES-CUZMAN 10.1 A NEW THEOREM RELATING THE
DENSITY OF AN ATOM IN A MOLECULE TO THE ENERGY 337
10.2 COMPUTATIONS 339
10.3 CHEMICAL TRANSFERABILITY AND THE ONE-ELECTRON DENSITY MATRIX 339
10.3.1 THE VIRIAL FIELD 340 10.3.2 SHORT-RANGE NATURE OF THE VIRIAL
FIELD
AND TRANSFERABILITY 342 10.4 CHANGES IN ATOMIC ENERGIES ENCOUNTERED IN
DNA BASE PAIRING 343 10.4.1 DIMERIZATION OF THE FOUR BASES A, C, G AND T
346
10.4.2 ENERGY CHANGES IN CC 349 10.4.3 ENERGY CHANGES IN AA1 349 10.4.4
ENERGY CHANGES IN GG4 350 10.4.5 ENERGY CHANGES IN TT2 350 10.5 ENERGY
CHANGES IN THE WC PAIRS GC AND AT 350
10.6 DISCUSSION 355
10.6.1 ATTRACTIVE AND REPULSIVE CONTRIBUTIONS TO THE ATOMIC VIRIAL AND
ITS SHORT-RANGE NATURE 356 10.6.2 CAN ONE GO DIRECTLY TO THE VIRIAL
FIELD? 360 REFERENCES 363
11 AN ELECTRON DENSITY-BASED APPROACH TO THE ORIGIN OF STACKING
INTERACTIONS 365 RICARDO A. MOSQUERA, MARIA J. GONZALEZ MOA, LAURA
ESTEVEZ, MARCOS MANDADO, AND ANA M. GRANA 11.1 INTRODUCTION 365
11.2 COMPUTATIONAL METHOD 366 11.3 CHARGE-TRANSFER COMPLEXES:
QUINHYDRONE 367 11.4 N-N INTERACTIONS IN HETERO-MOLECULAR COMPLEXES:
METHYL GALLATE-CAFFEINE ADDUCT 373
11.5 N-N INTERACTIONS BETWEEN DNA BASE PAIR STEPS 374 11.6 N-N
INTERACTIONS IN HOMO-MOLECULAR COMPLEXES: CATECHOL 378 11.7 C-H/N
COMPLEXES 381
11.8 PROVISIONAL CONDUSIONS AND FUTURE RESEARCH 385 REFERENCES 385
12 POLARIZABILITIES OF AMINO ACIDS: ADDITIVE MODELS AND AB INITIO
CALCULATIONS 389
NOUREDDIN EL-BAKALI KASSIMI AND AJITJ. THAKKAR 12.1 INTRODUCTION 389
12.2 MODELS OF POLARIZABILITY 389 12.3 POLARIZABILITIES OF THE AMINO
ACIDS 393
IMAGE 9
CONTENTS XLIII
12.4 CONDUDING REMARKS 398
REFERENCES 400
13 METHODS IN BIOCOMPUTATIONAL CHEMISTRY: A LESSON FROM THE AMINO ACIDS
403 HUGOJ. BOHORQUEZ, CONSTANZA CARDENAS, CHERIFF. MATTA, RUSSELLJ.
BOYD, AND MANUEL E. PATARROYO 13.1 INTRODUCTION 403
13.2 CONFORMERS, ROTAMERS AND PHYSICOCHEMICAL VARIABLES 404 13.3 QTAIM
SIDE CHAIN POLARIZATIONS AND THE THEORETICAL CLASSIFICATION OF AMINO
ADDS 408 13.4 QUANTUM MECHANICAL STUDIES OF PEPTIDE-HOST INTERACTIONS
414 13.5 CONDUSIONS 419
REFERENCES 420
14 FROM ATOMS IN AMINO ACIDS TO THE GENETIC CODE AND PROTEIN STABILITY,
AND BACKWARDS 423 CHERIFF. MATTA 14.1 CONTEXT OF THE WORK 423
14.2 THE ELECTRON DENSITY Q(R) AS AN INDIRECTLY MEASURABLE DIRAC
OBSERVABLE 426 14.3 BRIEF REVIEW OF SOME BASIC CONCEPTS OF THE QUANTUM
THEORY OF ATOMS IN MOLECULES 430
14.4 COMPUTATIONAL APPROACH AND LEVEL OF THEORY 438 14.5 EMPIRICAL
CORRELATIONS OF QTAIM ATOMIC PROPERTIES OF AMINO ADD SIDE CHAINS WITH
EXPERIMENT 439 14.5.1 PARTIAL MOLAR VOLUMES 439 14.5.2 FREE ENERGY OF
TRANSFER FROM THE GAS TO THE AQUEOUS PHASE 448 14.5.3 SIMULATION OF
GENETIC MUTATIONS WITH AMINO ACIDS PARTITION
COEFFICIENTS 448
14.5.4 EFFECT OF GENETIC MUTATION ON PROTEIN STABILITY 451 14.5.5 FROM
THE GENETIC CODE TO THE DENSITY AND BACK 454 14.6 MOLECULAR
COMPLEMENTARITY 456 14.7 CLOSING REMARKS 462
14.8 APPENDIX A X-RAY AND NEUTRON DIFFRACTION GEOMETRIES OF THE AMINO
ADDS IN THE LITERATURE 462 REFERENCES 467
15 ENERGY RICHNESS OF ATP IN TERMS OF ATOMIC ENERGIES: A FIRST STEP 473
CHERIFF. MATTA AND ALYA A ARABI 15.1 INTRODUCTION 473
15.2 HOW "(DE)LOCALIZED" IS THE ENTHALPY OF BOND DISSODATION? 474 15.3
THE CHOICE OF A THEORETICAL LEVEL 477 15.3.1 THE PROBLEM 477
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XLIV CONTENTS
15.3.2 EMPIRICAL CORRELATION OF TRENDS IN THE ATOMIC CONTRIBUTIONS TO
BDE: COMPARISON OF MP2 AND DFT(B3LYP) RESULTS 478 15.3.3 THEORY 478
15.3.3.1 QTAIM ATOMIC ENERGIES FROM THE AB INITIO METHODS 478 15.3.3.2
ATOMIC ENERGIES FROM KOHN-SHAM DENSITY FUNCTIONAL THEORY METHODS 482
15.3.3.3 ATOMIC CONTRIBUTIONS TO THE ENERGY OF REACTION 484
15.4 COMPUTATIONAL DETAILS 484 15.5 (GLOBAL) ENERGIES OF THE HYDROLYSIS
OF ATP IN THE ABSENCE AND PRESENCE OF MG 2+ 485 15.6 HOW "(DE)LOCALIZED"
IS THE ENERGY OF HYDROLYSIS OF ATP? 485
15.6.1 PHOSPHATE GROUP ENERGIES AND MODIFIED IIPMANN'S GROUP TRANSFER
POTENTIALS 485 15.6.2 ATOMIC CONTRIBUTIONS TO THE ENERGY OF HYDROLYSIS
OF ATP IN THE ABSENCE AND PRESENCE OF MG 2 " 1 " 487
15.7 OTHER CHANGES UPON HYDROLYSIS OF ATP IN THE PRESENCE AND ABSENCE OF
MG 2+ 487 15.7.1 BOND PROPERTIES AND MOLECULAR GRAPHS 487 15.7.2 GROUP
CHARGES IN ATP IN THE ABSENCE AND PRESENCE OF MG 2+ 491
15.7.3 MOLECULAR ELECTROSTATIC POTENTIAL IN THE ABSENCE AND PRESENCE OF
MG 2+ 492 15.8 CONDUSIONS 493
REFERENCES 496
VOLLI PART THREE REACTIVITY, ENZYME CATALYSIS, BIOCHEMICAL REACTION
PATHS AND MECHANISMS 499
16 QUANTUM TRANSITION STATE FOR PEPTIDE BOND FORMATION IN THE RIBOSOME
501
LOU MASSA, CHERIFF. MATTA, ADA YONATH, AND JEROME KARLE 16.1
INTRODUCTION 501
16.2 METHODOLOGY: SEARCHING FOR THE TRANSITION STATE AND CALCULATING ITS
PROPERTIES 502 16.3 RESULTS: THE QUANTUM MECHANICAL TRANSITION STATE 506
16.4 DISCUSSION 511
16.5 SUMMARY AND CONDUSIONS 533 REFERENCES 514
17 HYBRID Q M / MM SIMULATIONS OF ENZYME-CATALYZED DNA REPAIR REACTIONS
517
DENIS BUECHER, FANNY MASSON.J. SAMUEL AREY, AND URSULA ROETHLISBERGER 17.1
INTRODUCTION 517
17.2 THEORETICAL BACKGROUND 538 17.3 APPLICATIONS 521
IMAGE 11
CONTENTS XLV
17.3.1 THYMINE DIMER SPLITTING CATALYZED BY DNA PHOTOLYASE 521
17.3.2 REACTION MECHANISM OF ENDONUDEASE IV 525 17.3.3 ROLE OF WATER IN
THE CATALYSIS MECHANISM OF DNA REPAIR ENZYME, MUTY 529 17 A CONDUSIONS
533
REFERENCES 534
18 COMPUTATIONAL ELECTRONIC STRUCTURE OF SPIN-COUPLED DIIRON-OXO
PROTEINS 537 JORGE H. RODRIGUEZ 18.1 INTRODUCTION 537
18.2 (ANTI)FERROMAGNETIC SPIN COUPLING 538 18.3 SPIN DENSITY FUNCTIONAL
THEORY OF ANTIFERROMAGNETIC DIIRON COMPLEXES 539 18.4 PHENOMENOLOGICAL
SIMULATION OF MOESSBAUER SPECTRA
OF DIIRON-OXO PROTEINS 542 18.4.1 ANTIFERROMAGNETIC DIIRON CENTER OF
HEMERYTHRIN 542 18.4.2 NITRIC OXIDE DERIVATIVE OF HR 543 18.4.3
ANTIFERROMAGNETIC DIIRON CENTER OF REDUCED UTEROFERRIN 545 18.5
CONDUSION 546
REFERENCES 548
19 ACCURATE DESCRIPTION OF SPIN STATES AND ITS IMPLICATIONS FOR
CATALYSIS 551 MARCEL SWART, MIREIA GUEELL, AND MIQUEL SOLA 19.1
INTRODUCTION 551
19.2 INFLUENCE OF THE BASIS SET 553
19.3 SPIN-CONTAMINATION CORRECTIONS 556 19.4 INFLUENCE OF
SELF-CONSISTENCY 558 19.5 SPIN-STATES OF MODEL COMPLEXES 559 19.6
SPIN-STATES INVOLVED IN CATALYTIC CYDES 564
19.6.1 CYTOCHROME P450CAM 564 19.6.2 HIS-PORPHYRIN MODELS 567 19.6.2.1
REFERENCE DATA (HARVEY) 568 19.6.2.2 REFERENCE DATA (GHOSH) 570 19.6.2.3
OTHER MODEL SYSTEMS 573 19.6.3 NIFE HYDROGENASE 574 19.7 CONDUDING
REMARKS 579
19.8 COMPUTATIONAL DETAILS 579 REFERENCES 580
20 QUANTUM MECHANICAL APPROACHES TO SELENIUM BIOCHEMISTRY 585 JASON K.
PEARSON AND RUSSELL J. BOYD 20.1 INTRODUCTION 585
20.2 QUANTUM MECHANICAL METHODS FOR THE TREATMENT OF SELENIUM 586
IMAGE 12
XLVI CONTENTS
20.3 APPLICATIONS TO SELENIUM BIOCHEMISTRY 587
20.3.1 COMPUTATIONAL STUDIES OF GPX 587 20.3.2 COMPUTATIONAL STUDIES ON
GPX MIMICS 589 20.3.2.1 GPX-LIKE ACTIVITY OF EBSELEN 589 20.3.2.2
SUBSTITUENT EFFECTS ON THE GPX-LIKE ACTIVITY OF EBSELEN 596
20.3.2.3 EFFECT OF THE MOLECULAR ENVIRONMENT ON GPX-LIKE ACTIVITY 598
20.4 SUMMARY 600
REFERENCES 600
21 CATALYTIC MECHANISM OF METALLO SS-LACTAMASES: INSIGHTS FROM
CALCULATIONS AND EXPERIMENTS 605 MATTEO DAL PERORO, ALEJANDRO J. VILA,
AND PAOLO CARTONI 21.1 INTRODUCTION 605
21.2 STRUCTURAL INFORMATION 607 21.3 COMPUTATIONAL DETAILS 608 21.4
PRELIMINARY COMMENT ON THE COMPARISON BETWEEN THEORY AND EXPERIMENT 609
21.5 MICHAELIS COMPLEX IN BL MSSLS 610 21.5.1 SUBSTRATE BINDING
DETERMINANTS 610 21.5.2 NUCLEOPHILE STRUCTURAL DETERMINANTS 611 21.6
CATALYTIC MECHANISM OF BL MSSLS 612
21.6.1 CEFOTAXIME ENZYMATIC HYDROLYSIS IN CCRA 633 21.6.2 CEFOTAXIME
ENZYMATIC HYDROLYSIS IN BELL 634 21.6.3 ZINC CONTENT AND REACTIVITY OF
BL MSSLS 615 21.6.4 REACTIVITY OF SS-LACTAM ANTIBIOTICS OTHER THAN
CEFOTAXIME 615
21.7 MICHAELIS COMPLEXES OF OTHER MSSLS 636 21.7.1 B2 MONO-ZN MSSL SUBDASS
616 21.7.2 B3 MSSL SUBDASS 636 21.8 CONCLUDING REMARKS 617
REFERENCES 638
22 COMPUTATIONAL SIMULATION OF THE TERMINAL BIOGENESIS OF
SESQUITERPENES: THE CASE OF 8-EPICONFERTIN 623 JOSE ENRIQUE
BARQUERA-LOZADA AND GABRIEL CUEVAS 22.1 INTRODUCTION 623
22.2 REACTION MECHANISM 627 22.3 CONDUSIONS 639
REFERENCES 640
23 MECHANISTICS OF ENZYME CATALYSIS: FROM SMALL TO LARGE ACTIVE-SITE
MODELS 643 JORGE LLANO AND JAMES V/. GAULD 23.1 INTRODUCTION
23.1.1 FACTORS INFLUENDNG THE CATALYTIC PERFORMANCE OF ENZYMES 643
IMAGE 13
CONTENTS XLVII
23.1.2 COMPUTATIONAL MODELING IN ENZYMOLOGY 648
23.2 ACTIVE-SITE MODELS OF ENZYMATIC CATALYSIS: METHODS AND ACCURACY 650
23.3 REDOX CATALYTIC MECHANISMS 652 23.3.1 NO FORMATION IN NITRIC OXIDE
SYNTHASE 652 23.3.2 OXIDATIVE DEALKYLATION IN THE ALKB FAMILY 654 23.4
GENERAL ACID-BASE CATALYTIC MECHANISM OF DEACETYLATION
IN LPXC 658
23.5 SUMMARY 660
REFERENCES 662
PART FOUR FROM QUANTUM BIOCHEMISTRY TO QUANTUM PHARMACOLOGY,
THERAPEUTICS, AND DRUG DESIGN 667
24 DEVELOPING QUANTUM TOPOLOGICAL MOLECULAR SIMILARITY (QTMS) 669 PAUL
LA POPELIER 24.1 INTRODUCTION 669
24.2 ANCHORING IN PHYSICAL ORGANIC CHEMISTRY 671 24.3 EQUILIBRIUM BOND
LENGTHS: "THREAT" OR "OPPORTUNITY"? 678 24.4 INTRODUCING CHEMOMETRICS:
GOING BEYOND R 2 679 24.5 A HOPPING CENTER OF ACTION 681 24.6 A LEAP 684
24.7 A COUPLE OF GENERAL REFLECTIONS 687 24.8 CONDUSIONS 688
REFERENCES 689
25 QUANTUM-CHEMICAL DESCRIPTORS IN QSAR/QSPR MODELING: ACHIEVEMENTS,
PERSPECTIVES AND TRENDS 693 ANNA V. GUBSKAYA 25.1 INTRODUCTION 693
25.2 QUANTUM-CHEMICAL METHODS AND DESCRIPTORS 694 25.2.1
QUANTUM-CHEMICAL METHODS 694 25.2.2 QUANTUM-CHEMICAL DESCRIPTORS:
CLASSIFICATION, UPDATES 697 25.3 COMPUTATIONAL APPROACHES FOR
ESTABLISHING QUANTITATIVE
STRUCTURE-ACTIVITY RELATIONSHIPS 703 25.3.1 SELECTION OF DESCRIPTORS 703
25.3.2 LINEAR REGRESSION TECHNIQUES 705 25.3.3 MACHINE-LEARNING
ALGORITHMS 706 25.4 QUANTUM-CHEMICAL DESCRIPTORS IN QSAR/QSPR MODELS 710
25.4.1 BIOCHEMISTRY AND MOLECULAR BIOLOGY 710 25.4.2 MEDIDNAL CHEMISTRY
AND DRUG DESIGN 712 25.4.3 MATERIAL AND BIOMATERIAL SDENCE 714
25.5 SUMMARY AND CONDUSIONS 715 REFERENCES 717
IMAGE 14
XLVIII CONTENTS
26 PLATINUM COMPLEXES AS ANTI-CANCER DRUGS: MODELING OF
STRUCTURE, ACTIVATION AND FUNCTION 723 KONSTANTINOS GKIONIS, MARK HICKS,
ARTURO ROBERTAZZI, J. GRANT HILL,
AND JAMES A. PLATTS
26.1 INTRODUCTION TO CISPLATIN CHEMISTRY AND BIOCHEMISTRY 723 26.2
CALCULATION OF CISPLATIN STRUCTURE, ACTIVATION AND DNA INTERACTIONS 726
26.3 PLATINUM-BASED ALTERNATIVES 732
26.4 NON-PLATINUM ALTERNATIVES 735 26.5 ABSORPTION, DISTRIBUTION,
METABOLISM, EXCRETION (ADME) ASPECTS 739 REFERENCES 740
27 PROTEIN MISFOLDING: THE QUANTUM BIOCHEMICAL SEARCH FOR A SOLUTION TO
ALZHEIMER'S DISEASE 743 DONALD F. WEAVER 27.1 INTRODUCTION 743
27.2 PROTEIN FOLDING AND MISFOLDING 744 27.2.1 PROTEIN FOLDING 744
27.2.2 PROTEIN MISFOLDING 745 27.3 QUANTUM BIOCHEMISTRY IN THE STUDY OF
PROTEIN MISFOLDING 745
27.3.1 MOLECULAR MECHANICS 746 27 A ALZHEIMER'S DISEASE: A DISORDER OF
PROTEIN MISFOLDING 747 27A.I ALZHEIMER'S - A PROTEIN MISFOLDING DISORDER
748 27.4.2 PROTEIN MISFOLDING OF BETA-AMYLOID 748
27.5 QUANTUM BIOCHEMISTRY AND DESIGNING DRUGS FOR ALZHEIMER'S DISEASE
750 27.5.1 APPROACH 1 - HOMOTAURINE 751 27.5.2 APPROACH 2 - MELATONIN
752
27.6 CONDUSIONS 753
REFERENCES 754
28 TARGETING BUTYRYLCHOLINESTERASE FOR ALZHEIMER'S DISEASE THERAPY 757
KATHERINE V. DARVESH, IAN R. POTTIE, ROBERT S. MCDONALD, EARL MARTIN,
AND SULTAN DARVESH
28.1 BUTYRYLCHOLINESTERASE AND THE REGULATION OF CHOLINERGIC
NEUROTRANSMISSION 757 28.2 BUTYRYLCHOLINESTERASE: THE SIGNIFICANT OTHER
CHOLINESTERASE, IN SICKNESS AND IN HEALTH 760 28.3 OPTIMIZING SPERINE
INHIBITORS OF BUTYRYLCHOLINESTERASE
BASED ON THE PHENOTHIAZINE SCAFFOLD 763 28.4 BIOLOGICAL EVALUATION OF
PHENOTHIAZINE DERIVATIVES AS CHOLINESTERASE INHIBITORS 761 28.5
COMPUTATION OF PHYSICAL PARAMETERS TO INTERPRET STRUCTURE-ACTIVITY
RELATIONSHIPS 769
IMAGE 15
CONTENTS XLIX
28.6 ENZYME-INHIBITOR STRUCTURE-ACTIVITY RELATIONSHIPS 772
28.7 CONDUSIONS 777
REFERENCES 778
29 REDUCTION POTENTIALS OF PEPTIDE-BOUND COPPER (II) - RELEVANCE FOR
ALZHEIMER'S DISEASE AND PRION DISEASES 781 ARVI RAUK
29.1 INTRODUCTION 781
29.2 COPPER BINDING IN ALBUMIN - TYPE 2 783 29.3 COPPER BINDING TO
CERULOPLASMIN - TYPE 1 785 29.4 THE PRION PROTEIN OCTAREPEAT REGION 787
29.5 COPPER AND THE AMYLOID BETA PEPTIDE (ASS)
OF ALZHEIMER'S DISEASE 789 29.6 CU(II)/CU(I) REDUCTION POTENTIALS IN
CU/ASS 793 29.7 CONCLUDING REMARKS 794
29.A APPENDIX 795
29.A.1 CALCULATION OF REDUCTION POTENTIALS, E, OF COPPER/PEPTIDE
COMPLEXES 795 29.A.2 COMPUTATIONAL METHODOLOGY 796 REFERENCES 798
30 THEORETICAL INVESTIGATION OF NSAID PHOTODEGRADATION MECHANISMS 805
KIEF AH A.K. MUSA AND LEIFA. ERIKSSON 30.1 DRUG SAFETY 805
30.2 DRUG PHOTOSENSITIVITY 806 30.2.1 PHOTOALLERGIES 807 30.2.2
PHOTOPHOBIA 807
30.2.3 PHOTOTOXICITY 807 30.3 NON-STEROID ANTI-INFLAMMATORY DRUGS
(NSAIDS) 808 30.3.1 NSAID: DEFINITION AND CLASSIFICATION 808 30.3.2
PHARMACOLOGICAL ACTION 808 30.3.3 NSAID USES 809
30.3.4 SIDE EFFECTS 830
30.4 NSAID PHOTOTOXIRITY 833 30.5 THEORETICAL STUDIES 812
30.5.1 OVERVIEW 812
30.5.2 METHODOLOGY 814 30.6 REDOX CHEMISTRY 835
30.7 NSAID ORBITAL STRUCTURES 817 30.8 NSAID ABSORPTION SPECTRA 820 30.9
EXDTED STATE REACTIONS 823 30.9.1 PHOTODEGRADATION FROM THE TI STATE 825
30.9.2 POSSIBLE PHOTODEGRADATION FROM SINGLET EXDTED STATES 826 30.10
REACTIVE OXYGEN SPEDES (ROS) AND RADICAL FORMATION 827
IMAGE 16
LI CONTENTS
30.11 EFFECTS OF THE FORMED ROS AND RADICALS DURING THE
PHOTODEGRADATION MECHANISMS 828 30.12 CONDUSIONS 830
REFERENCES 831
PART FIVE BIOCHEMICAL SIGNATURE OF QUANTUM INDETERMINISM 835
31 QUANTUM INDETERMINISM, MUTATION, NATURAL SELECTION, AND THE MEANING
OF LIFE 837 DAVID N. STAMOS 31.1 INTRODUCTION 837
31.2 A SHORT HISTORY OF THE DEBATE IN PHILOSOPHY OF BIOLOGY 839 31.3
REPLIES TO MY PAPER 842
31.4 THE QUANTUM INDETERMINISTIC BASIS OF MUTATIONS 845 31.4.1
TAUTOMERIC SHIFTS 845 31.4.2 PROTON TUNNELING 849 31.4.3 AQUEOUS THERMAL
MOTION 852
31.5 MUTATION AND THE DIRECTION OF EVOLUTION 853 31.6 MUTATIONAL ORDER
855
31.7 THE NATURE OF NATURAL SELECTION 857 31.8 THE MEANING OF LIFE 863
REFERENCES 867
32 MOLECULAR ORBITALS: DISPOSITIONS OR PREDICTIVE STRUCTURES? 873
JEAN-PIERRE LLORED AND MICHEL BITBOL 32.1 ORIGINS OF QUANTUM MODELS IN
CHEMISTRY: THE COMPOSITE AND THE AGGREGATE 874 32.2 EVOLUTION OF THE
QUANTUM APPROACHES AND BIOLOGY 876 32.3 PHILOSOPHICAL IMPLICATIONS OF
MOLECULAR QUANTUM HOLISM:
DISPOSITIONS AND PREDICTIVE STRUCTURES 882 32.3.1 MOLECULAR LANDSCAPES
AND PROCESS 882 32.3.2 REALISM OF DISPOSITION AND PREDICTIVE STRUCTURES
886 32.4 CLOSING REMARKS 893
REFERENCES 893
INDEX 897 |
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| spelling | Quantum biochemistry [electronic structure and biological activity] ed. by Chérif F. Matta Weinheim Wiley-VCH txt rdacontent n rdamedia nc rdacarrier Quantenbiochemie (DE-588)4176595-3 gnd rswk-swf Quantenbiochemie (DE-588)4176595-3 s DE-604 Matta, Chérif F. Sonstige (DE-588)132780372 oth http://deposit.dnb.de/cgi-bin/dokserv?id=3294468&prov=M&dok_var=1&dok_ext=htm Inhaltstext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=019100186&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Quantum biochemistry [electronic structure and biological activity] Quantenbiochemie (DE-588)4176595-3 gnd |
| subject_GND | (DE-588)4176595-3 |
| title | Quantum biochemistry [electronic structure and biological activity] |
| title_auth | Quantum biochemistry [electronic structure and biological activity] |
| title_exact_search | Quantum biochemistry [electronic structure and biological activity] |
| title_full | Quantum biochemistry [electronic structure and biological activity] ed. by Chérif F. Matta |
| title_fullStr | Quantum biochemistry [electronic structure and biological activity] ed. by Chérif F. Matta |
| title_full_unstemmed | Quantum biochemistry [electronic structure and biological activity] ed. by Chérif F. Matta |
| title_short | Quantum biochemistry |
| title_sort | quantum biochemistry electronic structure and biological activity |
| title_sub | [electronic structure and biological activity] |
| topic | Quantenbiochemie (DE-588)4176595-3 gnd |
| topic_facet | Quantenbiochemie |
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