Quantum biochemistry

Edited by Chérif F Matta Quantum Biochemistry Edited by Che´rif F Matta Quantum Biochemistry Related Titles Feig, M (Ed.) Morokuma, K., Musaev, D (eds.) Modeling Solvent Environments Computational Modeling for Homogeneous and Enzymatic Catalysis Applications to Simulations of Biomolecules 2010 Hardcover ISBN: 978-3-527-32421-7 A Knowledge-Base for Designing Efficient Catalysts 2008 Hardcover ISBN: 978-3-527-31843-8 Reiher, M., Wolf, A Relativistic Quantum Chemistry The Fundamental Theory of Molecular Science 2009 Hardcover ISBN: 978-3-527-31292-4 Matta, C F., Boyd, R J (eds.) The Quantum Theory of Atoms in Molecules From Solid State to DNA and Drug Design 2007 Hardcover ISBN: 978-3-527-30748-7 Meyer, H.-D., Gatti, F., Worth, G A (eds.) Multidimensional Quantum Dynamics Rode, B.M., Hofer, T., Kugler, M MCTDH Theory and Applications The Basics of Theoretical and Computational Chemistry 2009 2007 Hardcover ISBN: 978-3-527-32018-9 Hardcover ISBN: 978-3-527-31773-8 Comba, P., Hambley, T W., Martin, B Molecular Modeling of Inorganic Compounds 2009 Hardcover ISBN: 978-3-527-31799-8 Edited by Chérif F Matta Quantum Biochemistry The Editor Prof Chérif F Matta Dept of Chemistry & Physics Mount Saint Vincent Univ Halifax, Nova Scotia Canada B3M 2J6 and Dept of Chemistry Dalhousie University Halifax, Nova Scotia, Canada B3H 4J3 Cover: About the cover graphic (from Chapter 14): A superimposition of (1) the electron density r contour map of a Guanine-Cytosine WatsonCrick base pair in the molecular plane (the outermost contour is the 0.001 e-/bohr3 isocontour followed by 2×10n, 4×10n, and 8×10n e-/bohr3 with n starting at –3 and increasing in steps of unity); and (2) representative lines of the gradient of the density rr The density is partitioned into non-spherical color-coded “atomsin-molecules (AIM)”, each containing a single nucleus (Adapted from: C F Matta, PhD Thesis, McMaster University, Hamilton, Canada, 2002) (Courtesy of Chérif F Matta) Credit: The phrase “Quantum Biochemistry” used in the title of this book has been coined by Bernard Pullman and Alberte Pullman (B Pullman and A Pullman, Quantum Biochemistry; Interscience Publishers: New York, 1963) All books published by Wiley-VCH are carefully produced Nevertheless, authors, editors, and publisher not warrant the information contained in these books, including this book, to be free of errors Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate Library of Congress Card No.: applied for British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http://dnb.d-nb.de # 2010 WILEY-VCH Verlag GmbH & Co KGaA, Weinheim All rights reserved (including those of translation into other languages) No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers Registered names, trademarks, etc used in this book, even when not specifically marked as such, are not to be considered unprotected by law Printed in the Federal Republic of Germany Printed on acid-free paper ISBN: 978-3-527-32322-7 To every experimentalist and theoretician who has contributed to Quantum Biochemistry, and to every scientist, practitioner, and philosopher in whom its advancement, use, and interpretation finds fruition VII Acknowledgment This book is the result of the contributions of Ms Alya A Arabi, Dr J Samuel Arey, Prof Paul W Ayers, Prof Richard F.W Bader, Dr José Enrique Barquera-Lozada, Dr Joan Bertran, Dr Michel Bitbol, Mr Hugo J Bohrquez, Prof Russell J Boyd, Dr Denis Bucher, Dr Steven K Burger, Prof Roberto Cammi, Prof Chiara Cappelli, Dr Constanza Cárdenas, Prof Paolo Carloni, Dr Lung Wa Chung, Dr Fernando Clemente, Prof Fernando Cortés-Guzmán, Prof Gabriel Cuevas, Prof Matteo Dal Peraro, Prof Katherine V Darvesh, Prof Sultan Darvesh, Prof Bijoy K Dey, Prof Leif A Eriksson, Dr Laura Estévez, Dr Michael J Frisch, Prof James W Gauld, Dr Konstantinos Gkionis, Dr María J González Moa, Dr Ana M Graña, Dr Anna V Gubskaya, Ms Mireia Güell, Dr Mark Hicks, Dr J Grant Hill, Dr Lulu Huang, Dr Marek R Janicki, Dr Jerome Karle, Dr Noureddin El-Bakali Kassimi, Prof Eugene S Kryachko, Dr Xin Li, Ms Yuli Liu, Dr Jorge Llano, Mr Jean-Pierre Llored, Dr Marcos Mandado, Prof Earl Martin, Prof Lou Massa, Dr Fanny Masson, Prof Robert S McDonald, Prof Benedetta Mennucci, Prof Keiji Morokuma, Prof Ricardo A Mosquera, Dr Klefah A.K Musa, Dr Marc Noguera, Prof Manuel E Patarroyo, Prof Jason K Pearson, Dr James A Platts, Prof Paul L.A Popelier, Prof Ian R Pottie, Prof Arvi Rauk, Dr Arturo Robertazzi, Prof Jorge H Rodriguez, Dr Luis RodríguezSantiago, Prof Ursula Rưthlisberger, Ms Debjani Roy, Ms Lesley R Rutledge, Dr Utpal Sarkar, Prof Paul von Ragué Schleyer, Prof Mariona Sodupe, Prof Miquel Solà, Dr David N Stamos, Dr Marcel Swart, Prof Ajit J Thakkar, Prof Jacopo Tomasi, Prof Alejandro J Vila, Dr Thom Vreven, Prof Donald F Weaver, Prof Stacey D Wetmore, and Prof Ada Yonath I cannot thank each contributor enough for accepting my invitation I feel honored to have had the chance of working with such an exceptional group of scientists The staff of Wiley-VCH has been instrumental in all phases of the development of this project from its conception by copy-editing, proof reading, preparing galley proofs, contacting authors, and for the timely production of this book I have been very lucky to work with them and extend my deepest thanks to Dr Heike Noethe, Dr Eva-Stina Riihimäki, Dr Ursula Schling-Brodersen, Dr Martin Ottmar, Ms Claudia Nussbeck, and Ms Hiba-tul-Habib Nayyer for their considerable effort, professionalism, experience, and expertise on which I have constantly relied in the past two years Quantum Biochemistry Edited by Chérif F Matta Copyright Ó 2010 WILEY-VCH Verlag GmbH & Co KGaA, Weinheim ISBN: 978-3-527-32322-7 Index guanine-cytosine Watson–Crick DNA dimer 430, 432 – chemical structure 430 – electron density, relief map 432 – gradient field 432 guanine-gold interaction 263–268 – anchoring 265 – B3LYP/RECP 265 – bond lengths 267, 282 – PES 263 h H4B cofactor 104 Hamiltonian kinetic energy densities 702 Hamiltonian operator 877 Hammond’s postulate 638, 885 Handy and Cohen’s optimized exchange functional 552 hard-soft acid-base (HSAB) principle 740 harmonic frequency data, analysis 796 harmonic functions 136 HF approximation 32 Hartree–Fock (HF) methods XIV, 220, 676, 695, 726, 728 – calculation 21, 24, 48, 877 – density 18 – energy – exchange 558, 562 – orbitals 17 – polarizabilities 392 – – ZD00 model 397 – theory 482 Heisenberg–Dirac–Van Vleck Hamiltonian 539 Heisenberg equivalent matrix approach 891 Heisenberg exchange constant 544 Heisenberg exchange Hamiltonian 541 – eigenstates 541 helanolides, stereogenic center, stereochemistry 626 Hellmann–Feynman theorem 479, 480, 483, 520 heme – degradation, reaction mechanisms 96 – a-meso carbon 96 – propionate groups, role 566 heme-containing enzyme, see nitric oxide synthase (NOS) hemerythrin 542, 543 – diiron-oxo proteins 542 hemibond 2-center-3-electron interactions 239 Hermitian operator 437, 887 Hessian matrix, eigenvalues 174 hetero-molecular complexes 371 – p-p interactions 371–374 HHQK-BBXB 750, 751 – motif, histidine/lysine residues 751 – receptor 750 high-energy phosphate bond 473, 489 Hilbertian quantum approach 887 Hilbert space 890, 892 histidine – basic amino acid 201 – complexes 792 – radical cations 231 – – carbonyl group 788 – – dimmers, interaction energies, structures 329 – – ligands 785 – – lowest conformer, single occupied molecular orbital 231 – – residues 793, 794 Hodgkin–Richards indices 698 Hohenberg–Kohn theorem 86, 337, 338, 426 holistic approach, biology 877 HOMO–LUMO 248, 371, 702, 710, 732 – energy 710 – energy gap 248, 702, 732 – overlap 371 homo-molecular complexes, see catechol – p-p interactions 378–381 homotaurine, see 3-aminopropane-1-sulfonic acid (3-APS) Hooke’s law, harmonic potentials 747 Huntington’s disease 745 hybrid DNA sensors 252 hybrid Hartree–Fock DFT functional B3LYP level of theory 814 hybridization, ad hoc concept 875 hybrid meta-GGA exchange-correlation functionals 520 hydrated hexapeptide, kernel calculations 15, 17, 18 hydrated Leu1–Zervamicin 18–22 – fragment calculations 18–21 hydrogen – atom transfer reactions 232 – bonded systems 219 – bridge 260 – capped amino acid side chains 450 – electrode 796 – elimination models 392, 395, 397 hydrogen bond 140, 219, 259, 278, 315–318, 344, 354, 359, 374, 376, 432, 433, 507, 510, 729, 882 – anchoring 278 – A-site and P-site 510 j907 j Index 908 – – calculations 54 – classes 315 – conventional 259 – definition 260 – distances 222 – formation 507 – interaction 140, 219, 259, 315–318, 432 – – DNA backbone 315, 316 – – DNA nucleobases 315, 317, 318 – – protein side chains 316–318 – Linus Pauling’s model 852 – networks, rearrangements 661 – NMR shift 261 – nonconventional 259, 260, 261, 278 – properties 376 – QTAIM characterization 344 – surface 433 – system, uracil-glycine dimer 317 hydrogen peroxide, reduction reaction 591 – atomic electronic energy changes 595 – by selenolate 598 – catalytic cycles, summary 590 – Gibbs energy barriers, summary 592, 593 – proton transfer 600 – schematic reaction mechanisms 593, 594 – thiol exchange reactions 596, 600 1,3 hydrogen shift, see tautomerization hydrolase enzymes 757 hydroquinone, atomic properties 370, 371 i imidazole framework 598 independent atom model (IAM) 429 indoleamines dioxygenase (IDO) 98–100 – alternative mechanistic pathway 98–100 – – potential energy surface 100 – tryptophan dioxygenase (TDO) 99 – – dioxygen activation process 99 insulin 36–39 – KEM 36–39 – calculations, comments 38, 39 – chain, KEM Hartree–Fock energies 36 integral equation formalism polarizable continuum model (IEFPCM) 650, 651, 797, 815, 816 integrated molecular orbital + molecular orbital (IMOMO) method 599 – calculation 599 interactions – types 140 – potential 141, 143 intermolecular bond critical points 373, 379, 380 – molecular graphs 379 – properties 373, 380 interpret structure-activity relationships 769 – physical parameters, computation of 769–772 intramolecular chemically initiated electronexchange luminescence 118 intrinsic reaction coordinate (IRC) axis analysis 204, 505, 634, 637 in vivo anti-tumor activity 738 ionized system – Ramachandran surface 237 – N-glycylglycine conformations 235 – – representative structures, optimized geometries 235 – O-methylhydroxylamine 187 – – dissociation reaction, energy profile 187 iron complexes, benchmark 563 iron-porphyrazin 572 – axial chloride ligand 572 – Collins’ Fe(IV)-complex 572 iron-porphyrazine-chloride, spin groundstate 571 iron-porphyrin 560, 571, 572 – axial chloride ligand 572 – Collins’ Fe(IV)-complex 572 iron-porphyrin-chloride 571 iron-porphyrin-imidazole (FePorIm) system 568, 569, 572–574 – Fe-ligand distances 573 – spin-state splittings 569, 573 isodensity polarizable continuum model (IPCM) 596 isoelectronic side chains, rotamers 407 isomerization reaction 190, 191, 233 – catalyzed by 4-oxalocrotonate tautomerase 190 k kernel energy method (KEM) 22, 25, 29, 36, 46, 47, 49–53 – approximation 50 – – fourth-order 51–53 – – X-ray crystal structure 52 – calculation 49 – – comparison 30, 31 – – fourth-order 50–53 – – interaction energy 49 – – results 36–41 – – time comparison 29–31 – quantum models 29–36 – use 46 Index kernel 14–17, 21, 27 – idea, applications 17–22 – calculations 11, 14 – comments 21, 22 – definition 23 – density matrices 14–17, 22–55 – – biological activity 24 – – KEM 24–29 – – peptide 24 – double 23, 24 – – interaction energies 43 – total energy 27 kinetic isotope effect (KIE) 530 Klopman–Salem equation 884 k-nearest neighbor method 708 Kohn–Sham orbitals 478, 505, 520, 558 Kohn–Sham approximation 362 Kohn–Sham highest occupied molecular orbital 370 Kohonen nets 687 Kolmogorovian theory of probability 892 Koopman’ s theorem 713 l Laboratory of Molecular Structure and Spectroscopy (LMSS) 877, 891 – projects 877 Lagrangian approach 520 – kinetic energy densities 702 – multipliers latent variables (LVs) 679 Lee–Yang–Parrcorrelationfunctional 502,650 Lewis acid-base model 362, 458 linear combination of atomic orbitals (LCAO) 876, 877 – approximation 876 linear-free energy relations (LFERs) 669 – isolated molecule, intrinsic features 669 linear regression equation 448 linear regression models 450, 454 linear response approach 165 Lineweaver–Burk double reciprocal plot 766 link atoms (LAs), approach 63, 188 lipopolysaccharides (LPSs) 658 – components 658 – membrane 658 – metabolic pathway 658 liquid systems, computer simulations 140 – interaction potentials 140–142 – properties 140 liver alcohol dehydrogenase (LADH) 647 localized orbitals (LOs) 133, 134 – degree of transferability 134 locally dense basis set approach (LDBS) 495 local virial theorem 435 low-barrier hydrogen bond (LBHB) 647 – proton transfer 648 Lowdin’s theory 851 LpxC deacetylase, amide bond hydrolysis 659 LpxC metalloenzyme deacetylation 658 – acid-base catalytic mechanism 658–660 – N-methylacetamide deacylation, potential energy surface 660 m machine learning method 688 – algorithms 710 – – genetic 688 – partial least-squares 688 macrocycle, properties 560 major histocompatibility complex-peptide (MHC-P) 416–418 – class II-peptide complex 415, 417 – – peptide binding region (PBR) 415 – interaction 414 – quantum study, diagram 416–418 maleic anhydride 10 – electrons per atom 10 – energies 10 Marcus ET theory 164, 647 Max Born’s probabilistic interpretation 875 Mayr’s two-step process 861 metallo b-lactamases (MbLs) 607, 609, 616 – chemical feature 617 – computational details 608 – DCH/DHH site 616 – – role 616 – di-Zn B1 MbLs 617 – di-Zn/mono-Zn based MbL hydrolysis 617 – – DCH/DHH-bound Zn2, role 617 – enzymatic reaction mechanism 607 – GOB MbL 616 – metal occupancy 609 – Michaelis complexes 616, 617 – – B2 mono-Zn MbL subclass 616 – – B3 MbL subclass 616 – metal site conformations 607 – rate-determining steps 609 – structural information 607 – – atomistic structures 607 – – DCH site 607 – – DHH site 607 – – 3H site 607 – – X-ray crystallography 607 – subclasses 605, 616 – theory vs experiment, preliminary comment 609 j909 j Index 910 mean absolute deviation (MAD) 562 mean absolute percent deviation (MAPD) 391, 394, 398 methyl elimination (ME) models 397 molecular electrostatic potential (MEP) maps, calculations 133 METAGGA scheme 558 meta-heuristic method 705 metal drugs, metabolism 739 metalloenzymes 85, 91–108, 564, 650, 658 – active site 564 – cobalamin-dependent enzymes 105–108 – – methylmalonyl-CoA mutase 105–108 – computational strategies 86–90 – – active-site model 88 – – QM/MM methods 88–90 – LpxC 658 – reaction mechanisms 85 – heme-containing enzymes 91–105 – – heme oxygenase 95–97 – – indoleamines dioxygenase 97–100 – – nitric oxide synthase 101–105 – – tryptophan dioxygenase 97–100 metalloporphyrins 560 metalloprotein 781 metal organic chemical vapor deposition (MOCVD) 585 methane-benzene complexes 381, 382 – atomic properties, relative values 382 methane monooxygenase (MMO) 537 methyl elimination (ME) model 392, 395 methyl gallate (MG) molecule 372 – caffeine adduct 371–375 Michaelis complex 610, 611 – architecture 611 Michaelis–Menten kinetics 766 Miertuš–Scrocco–Tomasi code (MST) 148 Miller–Urey synthesis 201 minimum energy conical intersection (MECI) 119 – derivative coupling vector (DCV) 119 – gradient difference vector (GDV) 119 minimum energy pathways (MEPs) 171, 172, 204 – algorithms for 172 minimum energy reaction pathway (MERP) 186, 505 model systems 64, 74 – calculation, MM bonded terms 74 modified neglect of differential overlap (MNDO) 694 modified partial equalization of orbital electronegativity (MPEOE) method 391 (m-OH)bis(m-acetato)-bridged complexes 539, 540 – broken symmetry calculations, results 540 Mfller–Plesset perturbation theory 310, 694, 726 Mfller–Plesset polarizabilities 391 Mössbauer simulation 543 Mössbauer spectroscopy 560 molecular calculations 27, 134 – ab initio approach 134 molecular complementarity 456–461 – Lewis 457 – van der Waals 457 molecular complex 887 – physicochemical properties 887 molecular correlation kinetic energy 483 molecular dynamics technique 649 – simulations 157, 532 molecular electron density lego assembler (MEDLA) 696 molecular electrostatic potential (MEP) 132–137, 492, 493 – as component of intermolecular interaction 134 – Coulomb interaction term, definition 135 – Ees expression, simplifications 135, 136 – – atomic charges 136 – – multipolar expansions 136 – – point charge descriptions 135 – isovalue envelopes 493 – semiclassical approximation 133 – use 133 molecular maps 686 molecular mechanical description 142, 649 molecular mechanics methods XVIII, 72, 403 – bonded terms 73 – energy components 75 – energy function 72 molecular orbital 132, 873, 875, 882, 893 – approach 878 – approximation, role 882 – contributions 132 – dispositions 873 – holistic model 875 – predictive structures 873 molecular orbital self-consistent field (MO-SCF) approach 873 molecular quantum holism 882 – philosophical implications 882–893 – – molecular landscapes and process 882–885 – – predictive structures 886–893 Index – – realism of disposition 886–893 molecular quantum self-similarity measures (MQS-SMs) 702 molecular quantum similarity (MQS) 698 molecular quantum similarity measures (MQSMs) 687, 688, 695 molecular similarity index, see Carbó index molecular spin states, Kohn–Sham energies 541 molecular structure theory, factors 133 molecular virial theorem 481, 482 molecular visualization tool, EVolVis 461 molecular wavefunctions 131, 891 – ab initio calculation 131 Monte Carlo multiple minimum (MCMM) conformational search 227, 234 Monte Carlo pseudo-experiments 705 Monte Carlo simulations XVI Morokuma’s integrated method 148 mRNA 424, 457 – genetic code 457 Mulliken analysis 288 Mulliken charges 277, 287, 288, 293, 711, 714, 817 – distributions 817 – DNA base-gold complexes, PAs and DPEs 287 Mulliken-derived electrostatic multipoles 416 Mulliken population analysis 15, 729 multi-center expansion, adoption 137 multicenter proton relay mechanism 485 multiple linear regression (MLR) 705, 713 – based model 713 – equation 705 multipolar coefficients 136 multi-reference methods 86 – multi-reference perturbation theory (MRPT) 86 – multi-reference self-consistent field (MRSCF) 86 mutations 838, 845, 848, 852, 855 – causes 848 – Lowdin model 852 – order 855–857 – – importance 856 – quantum indeterministic basis 845–853 – – aqueous thermal motion 852, 853 – – proton tunneling 849–852 – – tautomeric shifts 845–849 – role 855 – Watson–Crick model 848 MutY catalysis mechanism 530 – crystal structure, data 531 Mycobacterium tuberculosis 525 myoglobin 94 – photodissociation, schematic presentation 94 n N-acetylproline amide (NAP), ball stick model 157 n-alkanes, bond dissociation enthalpies 476 N-allyliminium ions 75 – C–N bond activation reaction, oxidative addition step 75 nanobiotechnology, applications 250 nanodimensions 246 – DNA 248–253 – gold 246–253 nano-sized gold clusters 247, 248 – catalytic activity 247 – chemical reactivity 248 nanotechnology, types 248 naphthalen-1-yl(10H-phenothiazin-10-yl) methanone 767 – Lineweaver–Burk plot 767 natural bond orbital (NBO) method 134, 261, 596, 730 natural nucleobases, structure 327 natural population atomic (NPA) charge 261 natural selection 838, 854, 857, 860 – nature 857–863 natural sesquiterpenic lactones 626 – biogenetic hypotheses 626 – double bonds, configurations 626 near-attack conformation (NAC) hypothesis 646 – substrate, Gibbs energies 646 Nernst equation 796 neurodegenerative disorders 760 – Alzheimer’s disease, treatment 760 neurotoxic inflammatory 750 neurotransmitter dopamine 787 neutral selenol, interconversion 593 Newton’s laws 245 Newton trajectory (NT) 174 N-glycolyside hydrolysis 530 N-glycylglycine 236 No-hydroxy-L-arginine (NHA) 101, 104 No-hydroxy-L-arginine, substrate model 652, 653 nickel complexes 574, 575 – high-spin 574 nickel-ligand distances 575 NiFe hydrogenase 555, 574–576 – catalytic cycle 575, 576 – model 574 j911 j Index 912 nitric oxide, formation 101 nitric oxide synthase (NOS) 103, 104, 652, 653 – catalytic mechanism 653 – half-reaction, mechanism 103, 104 nitrogen oxide (NO) 652 – effects 652 – oxidation, potential energy surface 654 – produced by nitric oxide synthases 652 N-methylacetamide (AcNMe) 658 – mechanistic pathways 658 – oxidation 101 non-cisplatin drugs, properties 732 noncovalent interactions 132, 307, 308 – computational approaches 308–314 non-DNA drug targets 734 nonnuclear attractors (NNA) 434 non-steroidal anti-inflammatory agents/ analgesics (NSAIAs) 808 non-steroid anti-inflammatory drugs (NSAIDs) 807–823, 826, 827, 829 – absorption spectra 820–823 – acetylsalicylic acid 810 – classification 808 – definition 808 – highest occupied molecular orbitals (HOMOs) 817 – indomethacin 810 – lowest unoccupied molecular orbitals (LUMOs) 817 – orbital structures 817–820 – pharmacological action 808, 809 – redox chemistry 815–817 – side effects 810, 811 – uses 809, 810 – pain relievers 807 – photodegradation mechanisms 812, 813, 823, 827 – – steps 823 – phototoxicity 811, 812 – theoretical studies 812–815 – chemical structures 813 – computed dipole moment 820 – decarboxylation/dechlorination 816 – – C–C bond lengths 816 – – C–Cl bond lengths 816 – deprotonated species, absorption spectra 821 – excited state reactions 823–827 – – singlet excited states, photodegradation 826, 827 – – T1 state, photodegradation 825, 826 – neutral species, absorption spectra 821 – photodegradation mechanisms 826 – reactive oxygen species (ROS) 827, 828 – suprofen (SUP) 829 non-zwitterionic amino acid models 405 N-10-phenothiazine amides 762–764 – inhibition constants 762 – molecular volumes 762 N-10-phenothiazine carbamates 765, 766 – deactivation constants 765 – inhibition constants 765 – molecular volumes 765 N-representability problem 4, N-representable matrix 18 nuclear DNA oxidation adducts 791 nuclear magnetic resonance (NMR) shifts 269 nuclear-nuclear repulsion potential energy 479 nucleic acid bases 423, 446, 447 – calculated vs experimental partial molar volumes 446, 447 nucleic-acid system 248 nucleobases 316 – amino acid T-shaped interactions 325 – hydrogen bonding 316 – methylation 327 nucleophilic agent, HOMO 610 nucleophilic hydroxide 525 – mechanism 526 – oxygen atom 525 nucleophilic reaction, simulations 533 nucleophilic water addition 530 nucleosides, partial volume 445 nucleotide excision repair (NER) 517 nudged elastic band (NEB) method 172 o octanol-water partitioning coefficient 681 oligonucleotide-directed mutagenesis 451 olvatochromism 162 one-electron density matrix 339–343, 361 Onsager–Lorentz theory 159 ontological potentiality concept 889 OPBE, reliability 562 optimized H-bond distances 223 organo-selenium therapeutic agents 586, 596, 597 own N-layer integrated molecular orbital molecular mechanics (ONIOM) 61, 63–65, 76, 89, 649, 731 – application, guidelines 65–72 – cancellation problem 72–76 – energy expression 63 – potential energy surface 76 Index – scheme 64, 649 – – components 64 – three-layer methods, schematic diagrams 89 oxaliplatin 723, 725 oxidase iron enzymes, catalytic mechanisms 652 oxidative stress, 588, 791 – human body, defense mechanism 588 – metabolic signs of 791 oxygen-coupled electron-transfer (OCET) 104 p parallel dissociation process 154 para-substituted phenols 681 – biodegradability/toxicity 681 – molecular skeleton 682 – substituents/properties 682 Pariser–Parr–Pople (PPP) method XVII Parkinson’s disease 743 partial least-squares (PLS) procedure 679, 688, 706 – regression method 706 – use 679, 686 partial molar volumes 439, 445, 446 – experimental vs calculated group contributions 445 – principal contributions 440 partitioning coefficient 683 pattern recognition techniques 671 Pauli exclusion principle 138 Pauling configurations 93 P450 enzymes 565, 566, 567 – catalytic activity 567 – hydrogen-abstraction chemistry 566 peptide(s) 26, 28, 30, 234 – bond formation pathway 508 – bond transition 506 – calculation time 30 – energy calculation 26, 28 – ionization 234–239 – – N-glycylglycine, ionization 234–236 – – Ramachandran maps, ionization, influence 236–239 – structures 25 peptide-bound copper (II) 781 – electrostatic effects 783 – enthalpic component 782 – ligand 782 – polarity 783 – reduction potentials 781 peptide-host interactions 414 – quantum mechanical studies 414–419 peptidyl transferase center (PTC) 501 perturbation theory (PT) approaches 134, 505, 884 – symmetry-adapted 134 – twofold symmetry 505 – use 134 phenothiazine 761, 770, 772, 776, 778 – AChE inhibition 778 – amides 771, 778 – 4-biphenylcarbamate 776 – B3LYP/6-31G(d) level 770 – butterfly angles 770 – carbamate derivatives 775, 777 – – action 776 – – inhibitory properties 777 – – 3-N,N-dimethylaminophenyl derivative 775 – – structure-activity comparison 777 – N-10-carbonyl derivatives 761 – scaffold moiety 760, 770, 772 – structure-activity relationships 761, 778 – substituent size 771 – synthesis 761 – tricycle 773 – – ring system 769 phenyl alkylamine hallucinogens 698 – drug-receptor correlations 698 phosphate backbone 317 – hydrogen-bonding interactions 317 photoactivatable fluorescent proteins (PAFPs), category 109 photoactivation mechanisms 110 photobiology 85, 109–119 – fluorescent proteins (FPs) 109–117 – – photoconversion 115–117 – – green fluorescent proteins (GFP) 110, 111 – – reversible photoswitching fluorescent proteins (RPFPs) 111–115 – luciferases 117–119 photodegradation mechanism 814, 828 – ROS effects 828–830 photosensitivity reactions 806 – definition 806 – pathways 806 – photoallergic 806 – phototoxic 806 phototoxic response pathways 812 physicochemical variables 404–408 p-cation interaction 758 – aromatic ring system 758 ping-pong mechanism 105 platinum – anti-cancer drug, diaminocyclohexane (DACH) 723 j913 j Index 914 – bonding interactions 734 – chloroaqua complexes 729 – DNA adducts, formation of 725 – drugs 723 – – development 723 – – structures 724 – moiety 733 Poincaré-Hopf relationship 509 – topological relationship 506 point charges 77–81 – use 77 point mutation 846, 853 – tautomeric shift 846 – theory 853 Poisson–Boltzmann equations (PBEs) 113, 145, 150 – self-consistent reaction field model (SCRF) 650 polarizability effects 162, 389, 885 – decomposition methods 392 – definition 389 – models 389–392 polarizable continuum model (PCM) method 142, 143, 145–147, 150, 151, 204, 210 – ab initio versions 151 – applications 150–165 – – chemical equilibria 152–154 – – electronic transitions 162 – – energy transfers 164 – – environment on formation 161 – – PES 152 – – photoinduced electron 164 – – reaction mechanisms 154–156 – – relaxation of excited states effect 161 – – solvation energies 150–152 – – solvent effects on molecular properties/ spectroscopy 156–161 – – spectroscopies 162 – approach 164 – codes 151 – C-PCM/D-PCM 147 – formulation 144 – framework 160, 165 – Hamiltonian 142 – IEF-PCM scheme 147 – integral equation methods 145 – PCM-ZINDO version 147 – solvation model 323 – use 147 – versatility 146 – versions 146 polarization 63, 89, 90, 133, 134, 138, 140, 141, 145, 148, 149, 151, 159–161, 163, 220, 276, 374, 380, 382, 383, 385, 406, 408, 410, 412, 554–556, 558, 650, 651, 656, 727, 729 polychlorinated dibenzo-p-dioxins (PCDDs) 685 polycyclic aromatic hydrocarbons (PAHs) 696, 712 – electronic structure of XVII polymer chains 714 – conformational properties 714 polyunsaturated fatty acids (PUFAs) 790 pople basis set 565, 592, 593 – GTO basis sets 555 population genetics 843 potential energy surface (PES) reaction XXIII, 87, 100, 152, 172, 186, 204, 221, 312, 320, 635, 650, 651, 727 – concept XIV – energy-cost surface 185 – four-well analytical, parameters 182 – – energy cost surface, MEP on 183 – potential value, isosurface 186 – spin-singlet 653 potential of mean force (PMF) 189, 521 pragmatic transcendental approach 873 prebiotic chemistry 199–201 prebiotic compounds 201 – precursor, HCN 201 prediction of acidity constant (pKa) 706 primordial conditions 200 principal components analysis (PCA) 679–681, 704 – ANN approaches 712 – SIMCA-P package 681, 682 principle of least action, expression 361 prion diseases 781 – peptide-bound copper (II) 781 – – reduction potentials of 781 prion protein 787, 789 – copper binding 789 – octarepeat region 787–789 – reduction potential 787 protein backbone 316 – hydrogen bonding 316 protein chains triplet 47 – interaction energies 47 protein data bank (PDB) 42, 315, 321, 414, 518, 751 – accession code 531 protein folding 744, 745 protein misfolding 743, 745 – Alzheimer’s disease 747–750 – – beta-amyloid 748–750 – – neurodegenerative disease 747 – – neuropathological hallmarks 748 Index – disorders 743, 745 – quantum biochemistry 745 – – drug design 745, 750–753 – – molecular mechanics 746, 747 protein stability 451 – genetic mutation, effect 451 protein synthesis 502 – production line 502 proton acceptor 282, 286 – gold atom 281 proton affinities (PA) 286 proton-coupled electron-transfer (PCET) 104 proton interactions 139 proton shift mechanism 594 proton shuttle mechanism 512, 513 proton transfer reactions 222 proton tunneling 851 – Lowdin’s mechanism 851 pseudoguaianolides 625 – biogenetic origin 624, 639 – generation 625 – terminal biogenesis 628 – transformation mechanism 639 pseudo-reversible cholinesterase inhibitors 769 P-site sugar 513 – ribose sugar 509 p-systems 878, 884 – molecular orbital 878 – reactivity 884 pyrazine-pyridine biheteroaryls 708 pyrimidines, KP-photoinduced dimerization 829 q quadratic string method (QSM) 172, 173 – PES, local quadratic approximation 173 quantitative structure-activity relationship (QSAR) models 404, 407, 425, 659, 674, 676–678, 693, 694, 698, 703, 710, 713–715, 733 – approaches 712 – biochemistry and molecular biology 710–712 – 2D/3D QSAR 669 – descriptors 678, 688, 710 – – quantum-chemical 710 – – selection 703–705 – drug design 712–714 – linear regression techniques 705, 706 – machine-learning algorithms 706–710 – material and biomaterial science 714, 715 – mathematical technique 706 – medicinal chemistry 712–714 – polymeric materials, comparison 715 – power/weakness 670 – surging prominence 685 – use of 714 – validation 680 – VIP plots 683 quantitative structure-property relationships (QSPR) models 407, 693, 694, 698, 703, 710, 713–715, 733 – approaches 712 – biochemistry and molecular biology 710–712 – drug design 712–714 – material and biomaterial science 714, 715 – mathematical technique 706 – medicinal chemistry 712–714 – polymeric materials, comparison 715 – quantum-chemical descriptors 710 – use of 714 quantum approaches, evolution 876–882 quantum biochemistry (QB) methods XVII, 3, 133, 746, 841, 887 – approximations 890 – introducton XI–XXVI – spectrum 746 quantum biology 131 quantum chemical methods 554, 570, 694–697, 725, 879, 885 – calculations 202, 331, 599 – descriptors 695, 697–699, 703, 705, 713, 714 – – ab initio methods 695 – – classification of 697–703 – parameters 693 – use 879 quantum chemical topology (QCT) 670, 688, 689 – descriptors 688 quantum computations quantum-confined electronic transitions 247 quantum crystallography (QCr) 4, 13, 21, 501 – comments 21, 22 – KEM method XVIII – mathematical objective 13 – origins 4–10 quantum electrodynamics (QED) theory 165 quantum fingerprint 671 quantum framework 890 quantum indeterminism 840, 853, 863 quantum jump 845, 850 quantum kernels 10 – beginnings 10–22 – formalism 11–14 j915 j Index 916 quantum mechanics/molecular mechanics (QM/MM) schemes 61–63, 112, 132, 136, 142, 163, 171, 187–189, 192, 339, 403, 518, 585, 586, 599, 600, 608, 648–650, 841, 876, 879, 888, 889, 892 – approach 213 – Bohr’s interpretation 888 – boundary 90 – calculations 88, 90, 93, 102, 132, 135, 140, 502, 559, 560, 565 – chemistry models 32 – development 171, 188 – expectation value 438 – free-energy perturbation (FEP) method 189 – Hamiltonian 519 – Hilbertian structure 889 – implementation 519 – interaction energy 89 – minimum free-energy path (MFEP) method 189 – modeling – nondeterministic nature 888 – partitioning scheme 730 – potential, energy surface 72 – procedure 142 – region 567 – semiempirical approach 151 – simulations 523, 529, 532, 611 – – Endo IV 529 – – MD, 528, 734 – structure 879 – subsystem 188, 190 – – free-energy gradients 190 – transition state 506 – types 188 – use 876 quantum methods 34, 879, 882 quantum models 874 – aggregate 874 – composite 874 – origins 874–876 quantum molecular similarity (QMS) method 676 – measurement 688 quantum probabilities 840 quantum system 670 quantum theory 850, 888, 892 – of probability 892 – probabilistic algorithm 892 – statistical algorithm 888 quantum theory of atoms in molecules (QTAIM) methods XXII, 339, 344, 346, 360, 365, 366, 374, 404, 410, 415, 430–438, 462, 474, 477, 505, 594, 696, 735 – analysis 370, 372, 484, 737 – atomic moments, electrostatic potential 437 – basic concepts 430 – electron density analysis 367 – framework 477 – group energy 494 – multipoles 438 – properties 377, 383, 462 – utility 462 quantum topological molecular similarity (QTMS) 670, 676, 681, 685, 687, 697 – ability 689 – applications 679 – chemometrics 679–681 – computational modules 680 – descriptors 686, 687 – development 669, 672 – equilibrium bond lengths 678 – feature 675 – general reflections 687 – hopping center of action 681 – hypothesis 683 – leap 684–687 – para-substituted benzoic acids generation 676 – physical organic chemistry, anchoring in 671–678 – steroid set 685 – study 677, 686 – work 686 quantum transition, see quantum jump quartet-doublet splitting 557 quartet-sextet splitting 555 QUILD program 557, 579 quinhydrone 367–369 – intermolecular BCPs, properties 369 – molecular graph 369 – stacking energies 368 quinone 370 – atomic properties 370 – hydroquinone complex, electron density transfer 371 r radial basis function (RBF) kernel 708 – neural network (NN) 708 radical-rebound-type mechanism 656 Ramachandran maps 237 Raman bands 732 Raman scattering 160 Raman spectrum 733 rational drug design 43, 44 – interaction energy, importance 43, 44 Index reaction coordinate (RC) 608, 613 – constraint 613 reactive oxygen species (ROS) 587 real system, low-level calculation 64 rebound pathway 564 – vs cationic pathway 566 redox-active blue copper proteins 794 redox catalytic mechanisms 652–657 – AlkB family, oxidative dealkylation 654–657 – nitric oxide synthase, NO formation 652–654 – – first half-reaction 652 – – second half-reaction 652, 654 redox enzymes, catalytic mechanisms 661 reduced gradient following (RGF) method 173 – curves 174 reduction scale spectrum 787 relaxed spin-state splittings 554, 559 RESP charges, sets 79 RESP program 78 restricted RCCSD(T) method 220 ribonucleic acid (RNA) nucleobases 309 – atomic numbering 309 – structure 309 ribosome 501, 505, 645 – crystallography 501 – peptide bond formation, transition state 645 – ribonucleic acid (RNA) 245 – 30S ribosomal subunit, aminoacyl site 44–46 – thermodynamic parameters 505 – tRNA 503 ribozyme catalysis 501 ring critical points (RCP) 434 rotamers 404–408 ruthenium complexes 736, 737 – bond dissociation energies 737 – treatment of cancers 738 s scaled hypersphere search (SHS) methods 173 scaled particle theory (SPT) 144 Schizosaccharomyces pombe 529 Schlegel’s synchronous transit-guided quasiNewton (STQN) method 592 Schrödinger equation XIII, 144, 688 Schrödinger’s wave-mechanical formalism 891 Schwinger’s principle 338, 435 secondary a-deuterium kinetic isotope effect (sec-KIE) 97 secondary interaction hypothesis (SIH) 343 secondary metabolites 623 – functions 623 – structures 623 – as taxonomic markers 623 selenium 585, 587, 597, 598 – biochemical applications 585 – – glutathione peroxidase (GPx) mimics, computational studies 589–600 – chemical properties 586 – discovery 585 – electronic energy barriers 597 – quantum mechanical approaches 585 – role 585, 586 – steric effect 598 – vs sulfur 586 – treatment, quantum mechanical methods 586 selenoenzyme 590 selenol anion reaction 592 selenoxide oxygen 595 self-consistent reaction field (SCRF) method XIX, 149, 650, 651, 729, 733, 736 – solvation models 737 self organized maps, see Kohonen nets semi-dynamic approach 152 sesquiterpenes 623 – reaction mechanism 627–639 – synthetases enzyme 625 – – cyclic compounds, generation 625 – terminal biogenesis, computational simulation 623 – – 8-epiconfertin, case 623 Shannon’s sense, definition 423 – information 424 sigmoidal dielectric function 147 simple linear equation 454 single-determinant approach 13 – N-representability 5–7 single point mutations 450 – DDH, correlation 455 single proton transfer reactions 731 singlet-quintet splittings 562, 570 singlet-triplet splitting 556 singlet-triplet states 576 site-directed mutagenesis 98 Slater-type orbital (STO) basis sets 553 – ADF program 558 – 3G basis functions 34 SMx framework 149 SN2 reaction mechanism 184, 185, 190 – energy profile 185 – PES 184 – in solvent 190 j917 j Index 918 solute accessible to the solvent (SAS) 150 solute-solute interaction 439 solute-solvent system 160, 161 solvated system 131, 142–144, 146, 150–152, 157 – continuum model 142–150 – continuum solvation methods 148–150 – development 157 – free energy 149 – from molecular electrostatic potentials 131 – Hamiltonians 143 – insulin, energy calculation 38 – interaction, components 144 – PCM, basic formulation 142–148 – – apparent charges, definition 147 – – cavity surface 147 – – dielectric function 146 – – solute description 147 – with biomolecular photophysical processes 131 solvatochromic shifts 162 solvent effects 157, 160, 162 – dynamic effects 160 – kinetic isotope effect 97 – polarization, assumption 160 – reorganization energy 164 – role 157 somersault pathway 565 space-filling density 436 spin contamination 220 – corrections 556–558 spin-crossover phenomena 563 spin density functional theory (SDFT) 537, 538 – calculations 544 spin states 551, 561 – accurate description 551 – basis set, influence 553–556 – contamination 557 – model complexes 559–564 – self-consistency, influence 558 – splittings 552, 553, 555, 575, 577–579 – – ECPBs, use 553 – validation studies, iron complexes uses 561 – vertical vs relaxed 553 stacking interactions 322, 365 – computational method 366, 367 – orientations 322 standard hydrogen electrode (SHE) 781, 795 staphylococcal nuclease stability 453 – experimental vs calculated change 453 statistical mechanics 143 – molecular partition function 143 stepwise multiple regression (SMLR) 705 Stevens, Basch and Krauss (SBK) pseudopotential schemes 726 Stuttgart–Dresden pseudopotentials 732 substituent ring system 773 substrate ester hydrolysis 768 support vector machines (SVMs) 707 – algorithm 708 – schematic presentation 707 surface and volume polarization for electrostatic (SVPE) 148 surface walking algorithms 173 t tautomeric shifts 850 – roles 849 – Watson–Crick model 850 tautomerization 212 – keto-enol 208 taxonomic markers, 623 see also secondary metabolites T-cell receptor (TCR) molecules 414 terpenes, origin 624 – biogenetic hypothesis 624 tesserae 145, 146 thermodynamic integration 518, 526, 533 thiocholine hydrolysis 761 – kinetic analysis, using Ellman method 761 thymine dimer 522 – radical 522 – splitting, catalyzed by DNA photolyase 521 thymine-gold (T-Au) interactions 268–271 – basic features 269 – bond lengths 270, 271 – hybridization 271 – three conformers 268 time-dependent B3LYP method 113 – calculations 94 time-dependent density functional theory (TD-DFT) 156, 158, 164, 394, 820 – calculations 824 – method 87 transferability 337, 342 – short-range nature 342, 343 transferable atom equivalent (TAE) method 697 transition-metal complexes 559, 563, 579 transition state (TS) model 501, 509, 510, 527, 613, 615, 628, 634, 637, 883 – asynchrony 633 – B3LYP/6-31+G(d,p) level 635 – molecular graph 510 – MP2/6-31+G(d,p) level 635 – nature 627 Index – structure, SMM energies 76 – sugar moiety 505 – {1-2} transference of hydrogen 638 transmissible spongiform encephalopathies (TSEs) 787 transmission coefficient 648 triarylmethane (TRAM) derivatives 711 tricyclic ring system 770 tRNA 41, 42, 503–505, 507, 511, 512 – acceptor stem mimic (ASM) 504 – analog 504 – A-site 503, 511 – crystal structure 42 – ester carbonyl group 512 – KEM 41–43 – non-hydrolysable nitrogen 504 – P-site 503, 505, 511 – quantum mechanical molecular energy 41 – stems 503 – 1YFG picture 42 – – crystal structure 42 – – energy calculation 42 tryptophan dioxygenase (TDO) pathway 98–100 – alternative mechanistic pathway, 99, 100 – – potential energy surface 100 T-shaped interactions 312, 313, 318, 329 – potential energy surface scans 313 twisted intramolecular charge transfer (TICT) state 114 two-body interaction operator 142 tyrosine 782 – amino acid structure 504 – residue 551, 566 u ultraviolet (UV) radiation 806 – UV-A/B 806 united atom Hartree–Fock (UAHF) radii 797 united atom topological model 651 universal Darwinism 862 universal force field (UFF) 651, 731 unrestricted Hartree–Fock (UHF) method 556 a,b -unsaturated ketone (E)-1-(4hydroxyphenyl)but-1-en-3-one, antitumor agent 684 unweighted pair group method with arithmetic mean (UPGMA) method 406 uracil-glycine dimmers, hydrogen bonding 317 uteroferrin – oxidized diferric form 545 – purple acid phosphatase 545 v valence bond (VB) theory XIV, 881 – advantages 881 – approach 878 – use 878 valence shell charge concentrations (VSCCs) 460 valproic acid (VPA) 713 van der Waals envelope 491 van der Waals interactions 524 van der Waals molecular sizes 436 van der Waals potential functions 746 van der Waals radii 269 van der Waals volume 441, 442, 444, 446, 451 variable importance in projection (VIP) values 682 vascular endothelial growth factor receptor-2, inhibitors 708 vesicular stomatitis virus nucleoprotein 53 – KEM 53–55 – 2QVJ molecule 53, 54 – Ser290Trp mutant (2QVJ), crystal–structure of XIX vibrational circular dichroism (VCD) spectroscopies 157 vibrational Raman optical activity (VROA) 158 viral theorem 341 virial field 340–342, 435 – short-range nature 342, 343 VSEPR model 459 w Warshel’s electrostatic hypothesis 646 water molecule 77, 529, 614–616 – ASP85 system 78 – binding energy, calculation model 77 – cisplatin complex 728 – ligand, displacement of 793 – proton transfer 213, 532 – role 529, 616 Watson–Crick (WC) model 315, 318, 352, 847, 848 – atomic numbering 352 – A-T pairing 292, 350 – – energy changes 350–355 – CG/TA pairs 288, 728 – DNA base pairs, interaction of 286 – – [AÁT]ÁAu3 complexes 289–293 – – Au6 cluster bridges the WC GÁC pair 296, 297 – – [GÁC]ÁAu3 complexes 293–296 – – general background 286–289 – GÁC duplex 294 – intermolecular H-bonds 294 j919 j Index 920 – – stretching vibrational modes 292 – molecular graphs 352 wavefunction theory (WFT) 649, 650 weak molecular interactions theory 137 weighted holistic invariant molecular descriptors (WHIM) 693 Wilson’s disease 782 Woodward–Hoffmann rules 884 x X-ray crystallography 22 – data 737 – results 22 – structure 732, 733 X-ray diffraction 726 – experiment 428 – – observed vs calculated diffraction pattern 428 X-ray scattering data – experiment 21 – N-representable density descriptions X-ray structure 525, 608, 731 z Zaib4 molecule 34–36 – KEM calculation 35 – quantum methods 34–36 – – calculations 34–36 – X-ray crystal structure 35 zero-field splitting (ZFS) 542 zero-flux surface 432, 433 zero-memory Markov chain 424 zero-point energy (ZPE) 729 – electronic energies 819 – vibrational energy 503, 815 – –corrections 651 zero-temperature string method 172 zervamicin molecules 51 – crystal structures 52 zinc – enzymes 606, 609 – – catalytic mechanism 606 – – MbLs 609 – flexibility 527 – ligands 615 zwitterionic structures 395 – 3-APS 752 – chromophores 115 – glycine form 231 – species 442 ...Edited by Chérif F Matta Quantum Biochemistry Edited by Che´rif F Matta Quantum Biochemistry Related Titles Feig, M (Ed.) Morokuma, K., Musaev, D (eds.)... Matta) Credit: The phrase Quantum Biochemistry used in the title of this book has been coined by Bernard Pullman and Alberte Pullman (B Pullman and A Pullman, Quantum Biochemistry; Interscience... Jerome Karle Quantum Biochemistry Edited by Chérif F Matta Copyright Ó 2010 WILEY-VCH Verlag GmbH & Co KGaA, Weinheim ISBN: 978-3-527-32322-7 XI Introductory Reflections on Quantum Biochemistry: