Gas-phase interaction of calcium (Ca) with seleno derivatives of uracil

Journal of Chemical Theory and Computation

Volumn 4, Issue 6, 2008, Pages 1002-1011

  Lamsabhi, Mokhtar ^a   Mó, Otilia ^a   Yáñez, Manuel ^a   Boyd, Russell J ^b  

^a UNIVERSIDAD AUTÓNOMA DE MADRID   (Spain)

^b DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 53549102637     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct800017j     Document Type: Article

References (58)

1. Blount, K. F.; Zhao, F.; Hermann, T.; Tor, Y. Conformational constraint as a means for understanding RNA-aminoglycoside specificity. J. Am. Chem. Soc. 2005, 127, 9818.
2. Eddy, S. R. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2001, 2, 919.
3. Latham, M. R.; Brown, D. J.; McCallum, S. A.; Pardi, A. NMR methods for studying the structure and dynamics of RNA. ChemBioChem 2005, 6, 1492.
4. Storz, G. An expanding universe of noncoding RNAs. Science 2002, 296, 1260.
5. Sprinzl, M.; Scheit, K. H.; Cramer, F. Preparation in-vitro of a 2-thiocytidine-containing yeast transfer-RNA PHE-A73-C74-S2C75-A76 and its interaction with para-hydroxymercuribenzoate Eur. J. Biochem. 1973, 34, 306.
6. Lezius, A. G.; Scheit, K. H. enzymatic synthesis of DNA with 4-thio-thymidine triphosphate as substitute for dttp Eur. J. Biochem. 1967, 3, 85.
7. Kutyavin, I. V.; Rhinehart, R. L.; Lukhtanov, E. A.; GornVv; Meyer, R. B.; Gamper, H. B. Oligonucleotides containing 2-aminoadenine and 2-thiothymine act as selectively binding complementary agents. Biochemistry 1996, 35, 11170.
8. Coleman, R. S.; Kesicki, E. A. Synthesis and postsynthetic modification of oligodeoxynucleotides containing 4-Thio-2 - Deoxyuridine (D(S4)U). J. Am. Chem. Soc. 1994, 116, 11636.
9. Sismour, A. M.; Benner, S. A. The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system. Nucl. Acids. Res. 2005, 33, 5640.
10. Sintim, H. O.; Kool, E. T. Remarkable sensitivity to DNA base shape in the DNA polymerase active site. J. Am. Chem. Soc. 2006, 128, 396.
11. Salon, J.; Sheng, J.; Jiang, J. S.; Chen, G. X.; Caton-Williams, J.; Huang, Z. Oxygen replacement with selenium at the thymidine 4-position for the Se base pairing and crystal structure studies. J. Am. Chem. Soc.: 2007, 129, 4862.
12. Sheng, J.; Jiang, J. S.; Salon, J.; Huang, Z. Synthesis of a 2 -Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study. Org. Lett. 2007, 9, 749.
13. Stadtman, T. C. Selenium biochemistry. Science 1974, 183, 915.
14. Stadtman, T. C. Selenium-dependent enzymes. Annu. Rev. Biochem. 1980, 49, 93.
15. Ching, W. M.; Stadtman, T. C. Selenium-containing transfer RNA-GLU from clostridium-sticklandii - correlation of aminoacylation with selenium content. Proc. Natl. Acad. Sci. U.S. Am. Biol. Sci. 1982, 79, 374.
16. 2+ Reactions in Gas Phase. Similarities and dissimilarities with urea and thiourea. J. Phys. Chem. B. 2008, in press.
17. Fraudo da Silva, J. J. R.; Williams, R. J. P. The Biological Chemistry of Elements; Oxford University Press: Oxford, 1991; p 180.
18. Forsen, S.; Kordel, J. Bioinorganic Chemistry; University Science Books: Mill Valley, CA, 1994; p 107.
19. 2+): Nonempirical ab initio calculations on structures, energies, and nonadditivity of the interaction. J. Phys. Chem. B 1997, 101, 9670.
20. 2+) metal cations. J. Phys. Chem. A 1998, 102, 5951.
21. 2+) metal cations: Absence of the base pair stabilization by metal-induced polarization effects. J. Phys. Chem. B 1999, 103, 2528.
22. 2+ for n=1 to 7 from gas phase equilibrium determinations and theoretical calculations. J. Am. Chem. Soc. 2000, 122, 10440.
23. 2+ binding to pectate lyase C. J. Biol. Chem. 2003, 278, 12271.
24. 2+ affinity for nucleic acid bases. A theoretical determination. J. Phys. Chem. A 2003, 107, 11533.
25. 2+). Mol. Phys. 2005, 103, 163.
26. +] interactions with the aromatic motifs of naturally occurring amino acids: A theoretical study. J. Phys. Chem. A 2005, 109, 8893.
27. 2+ metal cations. J. Phys. Chem. A 2006, 110, 6139.
28. 2+ ions and their relation with the bacteriostatic activity. J. Phys. Chem. A 2006, 110, 4564.
29. 2+) and water coordination on the structure of glycine and zwitterionic glycine. J. Phys. Chem. A 2006, 110, 1960.
30. 2+ interaction modes of the nifedipine calcium channel antagonist. ChemPhysChem 2007, 8, 304.
31. 2+-ATPase studied by a combination of infrared Spectroscopy and electrostatic calculations. Biophys. J. 2008, 94, 600.
32. Becke, A. D. Density-Functional Thermochemistry 0.3. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648.
33. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle and Salvetti correlation-energy formula into a functional of the electron-density. Phys. Rev. B 1988, 37, 785.
34. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A.,. Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y., Kitao, O.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, J.; Cammi, R.; Pomelli, C; Ochterski, J.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian03; Gaussian03, Revision C.02 ed.; Gaussian, Inc.: Wallingford, CT, 2003.
35. Scott, A. P.; Radom, L. Harmonic vibrational frequencies: An evaluation of Hartree-Fock, Møller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors. J. Phys. Chem. 1996, 100, 16502.
36. 4)M(+) (M=Cu, Ag, and Au). J. Phys. Chem. 1996, 100, 12253.
37. Bader, R. F. W. Atoms In Molecules: A Quantum Theory; Clarendon Press: Oxford University, Oxford, 1990; p 1.
38. Matta, C. F.; Boyd, R. J. The Quantum Theory of Atoms in Molecules; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, 2007; p 1.
39. Biegler-König, F.; Schönbohm, J. AIM2000, 2nd ed.; 2002.
40. Alikhani, M. E.; Fuster, F.; Silvi, B.; Silvi, B. What can tell die topological analysis of ELF on hydrogen bonding? Struct. Chem. 2005, 16, 203.
41. Savin, A.; Nesper, R.; Wengert, S.; Fassler, T. F. ELF: The electron localization function. Angew. Chem., Int. Ed. Engl. 1997, 36, 1809.
42. Silvi, B.; Savin, A. Classification of chemical-bonds based on topological analysis of electron localization functions. Nature (London) 1994, 371, 683.
43. Noury, S.; Krokidis, X.; Fuster, F.; Silvi, B. TopMod Package; Université Pierre et Marie Curie: 1997.
44. Leszczynski, J.; Sponer, J. 2,4-Diselenouracil tautomers: Structures, energies, and a comparison with uracil and 2,4-dithiouracil. J. Mol. Struct. (Theochem) 1996, 388, 237.
45. Trujillo, C.; Mó, O.; Yáñez, M. A theoretical study of hydration effects on the prototropic tautomerism of selenouracils. Org. Biomol. Chem. 2007, 5, 3092.
46. Lamsabhi, A. M.; Alcami, M.; Mo, O.; Bouab, W.; Esseffar, M.; Abboud, J. L.-M.; Yáñez, M. Are the thiouracils sulfur bases in the gas-phase. J. Phys. Chem. A 2000, 104, 5122.
47. + cation: A DFT study. ChemPhysChem 2003, 4, 1011.
48. 2+ complexes in the gas phase. ChemPhysChem 2007, 8, 181.
49. 2+ with uracil and its thio derivatives: A theoretical study. ChemPhysChem 2004, 5, 1871.
50. Guillaumont, S.; Tortajada, J.; Salpin, J.-Y.; Lamsabhi, A. M. Experimental and computational study of the gas-phase interactions between lead(II) ions and two pyrimidic nucleobases: Uracil and thymine. Int. J. Mass Spectrom. 2005, 243, 279.
51. + cation: A DFT study. J. Phys. Chem A 2007, 111, 2213.
52. 2+ complexes. J. Phys. Chem. A 2006, 110, 1943.
53. Zhu, W. L.; Luo, X. M.; Puah, C. M.; Tan, X. J.; Shen, J. H.; Gu, J. D.; Chen, K. X.; Jiang, H. L. 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 2004, 108, 4008.
54. Trujillo, C.; Lamsabhi, A. M.; Mo, O.; Salpin, J.-Y.; Tortajada, J.; Yáñez, M. Manuscript in preparation, 2008.
55. Cremer, D.; Kraka, E. Chemical-bonds without bonding electron-density - does the difference electron-density analysis suffice for a description of the chemical-bond. Angew. Chem. 1984, 96, 612.
56. 2+: The importance of Coulomb explosions. J. Phys. Chem. A 2004, 108, 10080.
57. Alcamí, M.; Mó, O.; Yáñez, M. In Molecular Electrostatic Potentials: Concepts and Applications; Elsevier: Amsterdam, 1996; Vol. 3, p 407.
58. Alcamí, M.; Mó, O.; Yáñez, M.; Abboud, J. L. M.; Elguero, J. Bond activation by protonation in the gas-phase. Chem. Phys. Lett. 1990, 172, 471.