[1]
Levine I. Quantum Chemistry. 4th ed. Prentice Hall, Englewood Cliffs: New York 1991.
[2]
Cramer CJ. Essentials of Computational Chemistry. Wiley: Chichester 2002.
[3]
Stewart JJP. Semiempirical Molecular Orbital Methods. In: Lipkowitz KB, Boyd DB, Eds Reviews in Computational Chemistry. Volume 1. New York: VCH 1990; pp. 45-81.
[4]
Zerner MC. Semiemperical Molecular Orbital Methods. In: Lipkowitz KB, Boyd DB, Eds Reviews in Computational Chemistry. Volume 2 New York: VCH 1991; pp. 313-65.
[5]
Nanda DN, Jug K. SINDO1. A semiempirical scf mo method for molecular binding energy and geometry. i. approximations and parametrization. Theor Chim Acta 1980; 57: 95-106.
[6]
Leach AR. Molecular modelling: Principles and applications. 2nd ed. Pearson Education Limited: London 2001.
[7]
Park KC, Dodd LR, Levon K, Kwei TK. Conformational Study of Poly(p-phenylene) by Molecular Mechanics Minimization. Macromolecules 1996; 29: 7149-54.
[8]
Rappe AK, Casewit CJ. Molecular Mechanics across Chemistry. University Science Books: California 1997.
[9]
Ziebarth J, Wang Y. Molecular dynamics simulation of complexation between DNA-polycations. Biophys J 2009; 97: 1971-83.
[10]
Helfrich J, Hentschke R. Molecular Dynamics Simulation of Macromolecular Interactions in Solution: Poly(.gamma.-benzyl glutamate) in Dimethylformamide and Tetrahydrofuran. Macromolecules 1995; 28: 3831-41.
[11]
Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4: 187-217.
[12]
MacKerell Jr AD, Brooks B, Brooks CL, et al. CHARMM: The Energy Function and Its Parameterization with an Overview of the Program. In: Schleyer PvR et al Eds The Encyclopedia of Computational Chemistry. 1. Chichester; John Wiley & Sons 1998; p. 271-277.
[13]
MacKerell Jr AD, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102: 3586-616.
[14]
Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 2006; 418: 245-9.
[15]
Tzlil S, Ben-Shaul A. Flexible charged macromolecules on mixed fluid lipid membranes: Theory and monte carlo simulations. Biophys J 2005; 89: 2972-87.
[16]
Jiang W, Wang Y. Thermodynamics and partitioning of homopolymers into a slit-a grand canonical Monte Carlo simulation study. J Chem Phys 2004; 121: 3905-13.
[17]
Potemkin VA, Grishina MA. A new paradigm for pattern recognition of drugs. J Comput Aided Mol Des 2008; 22: 489-505.
[18]
Grishina M, Bolshakov O, Potemkin A, Potemkin V. Theoretical investigation of electron structure and surface morphology of titanium dioxide anatase nano-particles. Comput Theor Chem 2016; 1091: 122-36.
[19]
Tsirelson VG, Ozerov RP. Electron Density and Bonding in Crystals: Theory and Diffraction Experiments in Solid State Physics and Chemistry. Inst Physics Publ: Bristol 1996.
[20]
Tsirelson V, Stash A, Zhurova E, et al. Electron-density Properties of the Functionally-substituted Hydropyrimidines. Acta Cryst 2005; A61: 427.
[21]
Tsirelson VG, Stash AI, Potemkin VA, et al. Molecular and crystal properties of ethyl 4,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate from experimental and theoretical electron densities. Acta Crystallogr 2006; B62: 676-88.
[22]
Zhurova EA, Stash AI, Tsirelson VG, et al. Atoms-in-molecules study of intra- and intermolecular bonding in the pentaerythritol tetranitrate crystal. J Am Chem Soc 2006; 128: 14728-34.
[23]
Tsirelson VG, Bartashevich EV, Stash AI, Potemkin VA. Determination of covalent bond orders and atomic valence indices using topological features of the experimental electron density. Acta Crystallogr 2007; B63: 142-50.
[24]
Lowdin P-O, Sabin JR, Zerner MC, Eds. Advances in Quantum Chemistry. Vol. 25. Academic Press: San Diego 1995.
[25]
Todd A, Keith TK. AIMAll (Version 171114). Gristmill Software, Overland Park KS, USA 2017.
[26]
Lu T, Chen F. Multiwfn: A multifunctional wavefunction analyzer. J Comput Chem 2012; 33(5): 580-92.
[27]
Slater JC. Atomic Shielding Constants. Phys Rev 1930; 36: 57-64.
[28]
Slater JC. Frank NH Introduction to Theoretical Physics. McGraw-Hill: New York 1933.
[29]
Slater JC. Quantum Theory of Atomic Structure. McGraw-Hill: New York 1960.
[30]
Slater JC. Quantum Theory of Molecules and Solids, Vol. 1: Electronic
Structure of Molecules. McGraw-Hill: New York 1963-74.
[31]
Potemkin V, Grishina M. Electron-based descriptors in the study of physicochemical properties of compounds. Comput Theor Chem 2018; 1123: 1-10.
[32]
Salmina E, Grishina MA, Potemkin VA. An approximation of the Cioslowski–Mixon bond order indexes using the AlteQ approach. J Comput Aided Mol Des 2013; 27: 793-805.
[33]
Moore CE. Ionization potentials and ionization limits derived from the analysis of optical spectra Office of Standard Reference Data. (National Bureau of Standards): Washington, DC 1970.
[34]
Harris FE, Michels HH. Multicenter integrals in quantum mechanics. 2. Evaluation of electron-repulsion integrals for Slater-type orbitals. J Chem Phys 1966; 45: 116.
[35]
Mulliken RS. A new electroaffinity scale; together with data on valence states and on valence ionization potentials and electron affinities. J Chem Phys 1934; 2: 782-93.
[36]
Mulliken RS. Electronic structures of molecules XI. Electroaffinity, molecular orbitals and dipole moments. J Chem Phys 1935; 3: 573-85.
[37]
Allred AL, Rochow EG. A scale of electronegativity based on electrostatic force. J Inorg and Nuclear Chem 1958; 5: 264-8.
[38]
Allred AL. Electronegativity values from thermochemical data. J Inorg and Nuclear Chem 1961; 17: 215-21.
[39]
Pauling L. The nature of the chemical bond. IV. The energy of single bonds and the relative electronegativity of atoms. J Am Chem Soc 1932; 54: 3570-82.
[40]
Potemkin V, Grishina M. Princiles for 3D/4D QSAR classification of drugs. Drug Discov Today 2008; 13: 952-9.
[41]
Afonkina E, Palko N, Toreeva N, Potemkin V, Grishina M. Restricted docking of the DHFR inhibitors to the DHFR receptor. Drugs Future 2010; 35: 182.
[42]
Potemkin VA, Grishina MA, Bartashevich EV. Modeling of drug molecule orientation within a receptor cavity in the BiS algorithm framework. J Struct Chem 2007; 48: 155-60.
[43]
Potemkin V, Pogrebnoy A, Grishina M. A Technique for Energy Decomposition in the Study of “Receptor-Ligand” Complexes. J Chem Inf Model 2009; 49: 1389-406.
[44]
Potemkin V, Grishina M. Grid-based technologies for in silico screening and drug design. Curr Med Chem 2018; 25(29): 3526-37.
[45]
Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000; 28: 235-42.
[46]
Voorman RL, Maio SM, Hauer MJ, et al. Metabolism of Delavirdine, a Human Immunodeficiency Virus Type-1 Reverse Transcriptase Inhibitor, by Microsomal Cytochrome P450 in Humans, Rats, and Other Species: Probable Involvement of CYP2D6 and CYP3A. Drug Metab Dispos 1998; 26: 631-9.
[47]
Kudo S, Okumura H, Miyamoto G, Ishizaki T. Cytochrome P-450 isoforms involved in carboxylic acid ester cleavage of hantzsch pyridine ester of pranidipine. Drug Metab Dispos 1999; 27: 303-8.
[48]
Patten CJ, Thomas PE, Guy RL, et al. Cytochrome P450 enzymes involved in acetaminophen activation by rat and human liver microsomes and their kinetics. Chem Res Toxicol 1993; 6: 511-8.
[49]
Wienkers LC, Steenwyk RC, Sanders PE, Pearson PG. Biotransformation of tirilazad in human: 1. Cytochrome P450 3A-mediated hydroxylation of tirilazad mesylate in human liver microsomes. J Pharmacol Exp Ther 1996; 277: 982-90.
[50]
Ghosal A, Satoh H, Thomas PE, Bush E, Moore D. Inhibition and kinetics of cytochrome P4503A activity in microsomes from rat, human, and cdna-expressed human cytochrome P450. Drug Metab Dispos 1996; 24: 940-7.
[51]
Nielsen TL, Rasmussen BB, Flinois JP, Beaune P, Brosen K. In vitro metabolism of quinidine: The (3S)-3-hydroxylation of quinidine is a specific marker reaction for cytochrome P-4503A4 activity in human liver microsomes. J Pharmacol Exp Ther 1999; 289: 31-7.
[52]
Rochat B, Amey M, Gillet M, Meyer UA, Baumann P. Identification of three cytochrome P450 isozymes involved in N-demethylation of citalopram enantiomers in human liver microsomes. Pharmacogenetics 1997; 7: 1-10.
[53]
Ishiguro N, Senda C, Kishimoto W, et al. Identification of CYP3A4 as the predominant isoform responsible for the metabolism of ambroxol in human liver microsomes. Xenobiotica 2000; 30: 71-80.
[54]
Olesen OV, Linnet K. Metabolism of the tricyclic antidepressant amitriptyline by cDNA-expressed human cytochrome P450 enzymes. Pharmacology 1997; 55: 235-43.
[55]
Haaz MC, Rivory L, Richã C, Vernillet L, Robert J. Metabolism of CPT-11 by human hepatic microsomes: Participation of cytochrome P-450 3A and drug interactions. Cancer Res 1998; 58: 468-72.
[56]
Koudriakova T, Iatsimirskaia E, Utkin I, et al. Metabolism of the human immunodeficiency virus protease inhibitors indinavir and ritonavir by human intestinal microsomes and expressed cytochrome P4503A4/3A5: Mechanism-based inactivation of cytochrome P4503A by ritonavir. Drug Metab Dispos 1998; 26: 552-61.
[57]
Shou M, Martinet M, Korzekwa KR, et al. Role of human cytochrome P450 3A4 and 3A5 in the metabolism of taxotere and its derivatives: enzyme specificity, interindividual distribution and metabolic contribution in human liver. Pharmacogenetics 1998; 8: 391-401.
[58]
Yaïch M, Popon M, Mãdard Y, Aigrain EJ. In-vitro cytochrome P450 dependent metabolism of oxybutynin to N-deethyloxybutynin in humans. Pharmacogenetics 1998; 8: 449-51.
[59]
Dupont I, Berthou F, Bodenez P, et al. Involvement of cytochromes P450 2E1 and 3A4 in the 5-hydroxylation of salicylate in humans. Drug Metab Dispos 1999; 27: 322-6.
[60]
Tracy TS, Korzekwa KR, Gonzalez FJ, Wainer IW. Cytochrome P450 isoforms involved in metabolism of the enantiomers of verapamil and norverapamil. Br J Clin Pharmacol 1999; 47: 545-52.
[61]
Zhang QY, Dunbar D, Kaminsky L. Human cytochrome P-450 metabolism of retinals to retinoic acids. Drug Metab Dispos 2000; 28: 292-7.
[62]
Gantenbein M, Attolini L, Bruguerolle B, et al. Oxidative metabolism of bupivacaine into pipecolylxylidine in humans is mainly catalyzed by CYP3A. Drug Metab Dispos 2000; 28: 383-5.
[63]
Prakash C, Kamel A, Cui D, et al. Identification of the major human liver cytochrome P450 isoform(s) responsible for the formation of the primary metabolites of ziprasidone and prediction of possible drug interactions. Br J Clin Pharmacol 2000; 49: 35S-42S.
[64]
Tang C, Shou M, Mei Q, Rushmore TH, Rodrigues AD. Major role of human liver microsomal cytochrome P450 2C9 (CYP2C9) in the oxidative metabolism of celecoxib, a novel cyclooxygenase-II inhibitor. J Pharmacol Exp Ther 2000; 293: 453-9.
[65]
Bournique B, Lambert N, Boukaiba R, Martinet M. In vitro metabolism and drug interaction potential of a new highly potent anti-cytomegalovirus molecule, CMV423 (2-chloro 3-pyridine 3-yl 5,6,7,8-tetrahydroindolizine I-carboxamide). Br J Clin Pharmacol 2001; 52: 53-63.
[66]
Molden E, Asberg A, Christensen H. Desacetyl-Diltiazem Displays Severalfold Higher Affinity to CYP2D6 Compared with CYP3A4. Drug Metab Dispos 2002; 30: 1-3.
[67]
Zhou Q, Yao TW, Yu YN, Zeng S. Stereoselective metabolism of propafenone by human liver CYP3A4 expressed in transgenic Chinese hamster CHL cells lines. Acta Pharmaco Sin 2001; 22: 944-8.
[68]
Zhao G, Allis JW. Kinetics of bromodichloromethane metabolism by cytochrome P450 isoenzymes in human liver microsomes. Chem Biol Interact 2002; 140: 155-68.
[69]
Kalgutkar AS, Taylor TJ, Venkatakrishnan K, Isin EM. Assessment of the contributions of CYP3A4 and CYP3A5 in the metabolism of the antipsychotic agent haloperidol to its potentially neurotoxic pyridinium metabolite and effect of antidepressants on the bioactivation pathway. Drug Metab Dispos 2003; 31: 243-9.
[70]
Zhang W, Ramamoorthy Y, Tyndale RF, Sellers EM. Interaction of buprenorphine and its metabolite norbuprenorphine with cytochromes p450 in vitro. Drug Metab Dispos 2003; 31: 768-72.
[71]
Rodrigues AD, Mulford DJ, Lee RD, et al. In vitro metabolism of terfenadine by a purified recombinant fusion protein containing cytochrome P4503A4 and NADPH-P450 reductase. Comparison to human liver microsomes and precision-cut liver tissue slices. Drug Metab Dispos 1995; 23: 765-75.
[72]
Wang RW, Newton DJ, Scheri TD, Lu AYH. Human cytochrome P450 3A4-catalyzed testosterone 6β-hydroxylation and erythromycin N-demethylation: competition during catalysis. Drug Metab Dispos 1997; 25: 502-7.
[73]
Ekroos M, Sjogren T. Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci USA 2006; 103: 13682-7.
[74]
Bader RFW. Atoms in Molecules: A Quantum Theory. Clarendon Press: Oxford 1990.
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