Influence of metal complexation on acidity of cytosine nucleosides: Part I, Li+, Na+ and K+ cation

Scientia Iranica - Tập 19 - Trang 535-545 - 2012
Z. Aliakbar Tehrani1, A. Fattahi1, A. Pourjavadi1
1Department of Chemistry, Sharif University of Technology, Tehran, P.O. Box: 11155-9516, Iran

Tài liệu tham khảo

Kong, 2004, Mammalian nucleoside transporters, J. Curr. Drug Metab., 5, 63, 10.2174/1389200043489162 Dunwiddie, 1985, The physiological role of adenosine in the central nervous system, Int. Rev. Neurobiol., 27, 63, 10.1016/S0074-7742(08)60556-5 Mathew, 1993, Nucleosides and glutamine are primary energy substrates for embryonic and adult chicken red cells, Biochem. Cell Biol., 71, 288, 10.1139/o93-043 Osti, 1997, Human leukemia K562 cells: induction to erythroid differentiation by guanine, guanosine and guanine nucleotides, Haematologica, 82, 395 Shryock, 1997, Adenosine and adenosine receptors in the cardiovascular system: biochemistry, physiology, and pharmacology, Am. J. Cardiol., 79, 2, 10.1016/S0002-9149(97)00256-7 Kolb, 1997, Novel and unusual nucleosides as drugs, Prog. Drug Res., 48, 195 Watson, 1953, A structure for deoxyribose nucleic acid, Nature, 171, 737, 10.1038/171737a0 Ponnuswamy, 1994, On the conformational stability of oligonucleotide duplexes and tRNA molecules, J. Theoret. Biol., 169, 419, 10.1006/jtbi.1994.1163 Jordan, 1999, Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases, Biochemistry, 38, 6369, 10.1021/bi990373g Simonson, 1996, Charge screening and the dielectric constant of proteins: insights from molecular dynamics, J. Am. Chem. Soc., 118, 8452, 10.1021/ja960884f Gilson, 1986, The dielectric constant of a folded protein, Biopolymers, 25, 2097, 10.1002/bip.360251106 Dewar, 1985, Alternative view of enzyme reactions, Proc. Natl. Acad. Sci. USA, 82, 2225, 10.1073/pnas.82.8.2225 Petrushka, 1986, Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity, Proc. Natl. Acad. Sci. USA, 83, 1559, 10.1073/pnas.83.6.1559 Kool, 2001, Hydrogen bonding, base stacking, and steric effects in DNA replication, Annu. Rev. Biophys. Biomol. Struct., 30, 1, 10.1146/annurev.biophys.30.1.1 Lowry, 1987 McEwen, 1936, A further study of extremely weak acids, J. Am. Chem. Soc., 58, 1124, 10.1021/ja01298a017 Kurinovich, 2000, The acidity of uracil from the gas phase to solution: the coalescence of the N1 and N3 sites and implications for biological glycosylation, J. Am. Chem. Soc., 122, 6258, 10.1021/ja000549y Crowder, 1993, Gas-phase acidities of diols, J. Am. Soc. Mass Spectrom., 4, 723, 10.1016/1044-0305(93)80051-Y Zamora, 1997, Metal-stabilized rare tautomers of nucleobases. 6. Imino tautomer of adenine in a mixed-nucleobase complex of mercury (II), Inorg. Chem., 36, 1583, 10.1021/ic961167p Moussatova, 2003, Theoretical study of the structure and bonding of a metal-DNA base complex: al-guanine, Phys. Chem. A, 107, 9415, 10.1021/jp030651s Arpalahti, 1999, Platination of the exocyclic amino group of the adenine nucleobase by PtII migration, Eur. J. Inorg. Chem., 11, 99 Day, 1994, Structural evidence for a new metal-binding mode for guanine bases: implications for the binding of dinuclear antitumor agents to DNA, J. Am. Chem. Soc., 116, 2201, 10.1021/ja00084a093 Noguera, 2004, A quantum chemical study of Cu2+ interacting with guanine-cytosine base pair. Electrostatic and oxidative effects on intermolecular proton-transfer processes, J. Phys. Chem. A, 108, 333, 10.1021/jp036573q Sponer, 1999, Metal-stabilized rare tautomers and mispairs of DNA bases: N6-metalated adenine and N4-metalated cytosine, theoretical and experimental views, J. Phys. Chem. A, 103, 11406, 10.1021/jp992337x Griesser, 2003, Intrinsic acid–base properties of purine derivatives in aqueous solution and comparison of the acidifying effects of platinum (II) coordinated to N1 or N7: acidifying effects are reciprocal and the proton outruns divalent metal ions, Inorg. Chem., 42, 32, 10.1021/ic020535o Lamsabhi, 2006, Gas-phase deprotonation of uracil- Cu2+ and thiouracil- Cu2+ complexes, J. Phys. Chem. A, 110, 1943, 10.1021/jp055163u Burda, 2003, The influence of N7 guanine modifications on the strength of Watson–Crick base pairing and guanine N1 acidity: comparison of gas-phase and condensed-phase trends, J. Phys. Chem. B, 107, 5349, 10.1021/jp027850g Schroder, 1995, Unusual hydrogen bonding patterns of N7 metallated, N1 deprotonated guanine nucleobases: acidity constants of cis-[Pt(NH3)2(Hegua)2]2+ and crystal structures of cis-[Pt(NH3)2(egua)2]⋅4H2O and cis-[Pt(NH3)2(egua)2]⋅Hegua⋅7H2O(Hegua=9−ethylguanine), J. Chem. Soc. Dalton Trans., 3767, 10.1039/DT9950003767 Meiser, 1998, Dimerization of metallated nucleobase pairs via hydrogen-bond formation: open metallated base quartets of mixed adenine- N3, guanine- N7 complexes of trans- (H3N)2PtII with two different guanine–guanine pairing schemes, J. Chem. Soc., Dalton Trans., 2059, 10.1039/a801507d Faggiani, 1982, Model complexes of possible crosslinking products of cis-Pt(NH3)22+ with cytosine and guanine bases of DNA: X-ray structures of three mixed-ligand complexes of cis-diammineplatinum(II) with 1-methylcytosine and neutral and anionic 9-ethylguanine, Inorg. Chem., 21, 3216, 10.1021/ic00138a057 Faggiani, 1980, An unexpected G–G base pairing caused by the coordination of platinum (II) at the N(7) position of 9-ethylguanine, J. Am. Chem. Soc., 102, 5418, 10.1021/ja00536a062 Pyle, 1993, Ribozymes: a distinct class of metalloenzymes, Science, 261, 709, 10.1126/science.7688142 Pan, 1993 Tainer, 1982, Determination and analysis of the 2 Å structure of copper, zinc superoxide dismutase, J. Mol. Biol., 160, 181, 10.1016/0022-2836(82)90174-7 Pena, 2004, Identification of surface species on titania-supported manganese, chromium, and copper oxide low-temperature SCR catalysts, J. Phys. Chem. B, 108, 9927, 10.1021/jp0313122 Kennedy, 2002, Dramatic rate enhancement with preservation of stereospecificity in the first metal-catalyzed additions of allylboronates, J. Am. Chem. Soc., 124, 11586, 10.1021/ja027453j Fattahi, 2008, Conversion of weak organic acid to super acid in the gas phase, J. Phys. Org. Chem., 21, 112, 10.1002/poc.1292 Leitner, 1998, Direct Monitoring of cytosine protonation in an intramolecular DNA triple helix, J. Am. Chem. Soc., 120, 7123, 10.1021/ja972694q Gehring, 1993, A tetrameric DNA structure with protonated cytosine–cytosine base pairs, Nature, 363, 561, 10.1038/363561a0 Wang, 1991, Nitrogen-15-labeled oligodeoxynucleotides. 3. Protonation of the adenine N1 in the A.cntdot.C and A.cntdot.G mispairs of the duplexes {d[CG(15N1)AGAATTCCCG]}2 and {d[CGGGAATTC(15N1)ACG]}2, J. Am. Chem. Soc., 113, 5486, 10.1021/ja00014a068 Cai, 1996, Solution structure of loop a from the hairpin ribozyme from tobacco ringspot virus satellite, Biochemistry, 35, 6026, 10.1021/bi952985g Maskos, 1993, NMR study of G.cntdot.A and A.cntdot.A pairing in (dGCGAATAAGCG)2, Biochemistry, 32, 3583, 10.1021/bi00065a009 Legault, 1997, Unusual dynamics and pKa shift at the active site of a lead-dependent ribozyme, J. Am. Chem. Soc., 119, 6621, 10.1021/ja9640051 Oyelere, 2002, pKa perturbation in genomic hepatitis delta virus ribozyme catalysis evidenced by nucleotide analogue interference mapping, Biochemistry, 41, 3667, 10.1021/bi011816v Sun, 2005, Marked variations of dissociation energy and H-bond character of the guanine-cytosine base pair induced by one-electron oxidation and Li+ cation coupling, J. Phys. Chem. B, 109, 593, 10.1021/jp0459817 Sponer, 2000, The effect of metal binding to the N7 site of purine nucleotides on their structure, energy and involvement in base pairing, J. Phys. Chem. B, 104, 7535, 10.1021/jp001711m Munõz, 2001, Interactions of hydrated Mg2+ cation with bases, base pairs, and nucleotides. Electron topology, natural bond orbital, electrostatic and vibrational study, J. Phys. Chem. B, 105, 6051, 10.1021/jp010486l Wu, 2009, Theoretical studies on the bonding of Cd2+ to adenine and thymine: tautomeric equilibrium and metalation in base pairing, Chem. Phys. Lett., 467, 387, 10.1016/j.cplett.2008.11.073 Noguera, 2008, Cu2+/+ cation coordination to adenine–thymine base pair. Effects on intermolecular proton-transfer processes, J. Phys. Chem. B, 112, 4817, 10.1021/jp711982g Xing, 2008, Theoretical study on the gas-phase acidity of multiple sites of Cu+-adenine and Cu2+-adenine complexes, J. Phys. Chem. A, 112, 7418, 10.1021/jp800256v Spartan ‘06V102’; Wavefunction, Inc., Irvine, CA. Becke, 1993, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98, 5648, 10.1063/1.464913 Lee, 1988, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B, 37, 785, 10.1103/PhysRevB.37.785 Meng, 2002, Gas phase model of an ionic liquid: semi-empirical and ab initio bonding and molecular structure, J. Mol. Struct. (THEOCHEM), 585, 119, 10.1016/S0166-1280(02)00056-8 Rappe, 2000, Ab initio calculation of nonbonded interactions: are we there yet?, J. Phys. Chem. A, 104, 6117, 10.1021/jp0008997 Weiliang, 2004, The multiplicity, strength, and nature of the interaction of nucleobases with alkaline and alkaline earth metal cations: a density functional theory investigation, J. Phys. Chem. A, 108, 4008, 10.1021/jp036911n Reed, 1985, Natural localized molecular orbitals, J. Chem. Phys., 83, 1736, 10.1063/1.449360 Reed, 1985, Natural population analysis, J. Chem. Phys., 83, 735, 10.1063/1.449486 Reed, 1983, Natural bond orbital analysis of near-Hartree-Fock water dimer, J. Chem. Phys., 78, 4066, 10.1063/1.445134 Foster, 1980, Natural hybrid orbitals, J. Am. Chem. Soc., 102, 7211, 10.1021/ja00544a007 Altona, 1972, Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation, J. Am. Chem. Soc., 94, 8205, 10.1021/ja00778a043 Saenger, 1984 Furberg, 1965, A refinement of the crystal structure of cytidine, Acta Crystallogr., 18, 313, 10.1107/S0365110X65000749 Chocholousova, 2004, First local minimum of the formic acid dimer exhibits simultaneously red-shifted O–H–O and improper blue-shifted C–H–O hydrogen bonds, Phys. Chem. Chem. Phys., 6, 37, 10.1039/B314148A Wahl, 1997, C-H…O hydrogen bonding in biology, Trends Biochem. Sci., 22, 97, 10.1016/S0968-0004(97)01004-9 Auffinger, 1997, Rules governing the orientation of the 2′-hydroxyl group in RNA, J. Mol. Biol., 274, 54, 10.1006/jmbi.1997.1370 Nakamura, 1985, Z-RNA: the solution NMR structure of r(CGCGCG), Nucleic Acids Res. Symp. Ser., 16, 29 Davis, 1990, Z-RNA: the solution NMR structure of r(CGCGCG), Biopolymers, 29, 109, 10.1002/bip.360290116 Wang, 1979, Molecular structure of a left-handed double helical DNA fragment at atomic resolution, Nature, 282, 680, 10.1038/282680a0 Varani, 1991, Structure of an unusually stable RNA hairpin, Biochemistry, 30, 3280, 10.1021/bi00227a016 Ramond, 2000, Vibronic structure of alkoxy radicals via photoelectron spectroscopy, J. Chem. Phys., 112, 1158, 10.1063/1.480767 Muftakhov, 1999, Thermochemistry of negatively charged ions. II. Energetics of formation of negative ions from acridanone and some of its derivatives, Rapid Commun. Mass Spectrom., 13, 1104, 10.1002/(SICI)1097-0231(19990630)13:12<1104::AID-RCM619>3.0.CO;2-C Viggiano, 1992, Gas-phase reactions of weak Broensted bases I−,PO3−,HSO4−,FSO3−, and CF3SO3−s with strong Broensted acids H2SO4,FSO3H, and CF3SO3H. A quantitative intrinsic superacidity scale for the sulfonic acids XSO3H (X=HO, F, and CF3), J. Am. Chem. Soc., 114, 4299, 10.1021/ja00037a039