Structural features of the adenosine conjugate in means of vibrational spectroscopy and DFT

Biophysical Chemistry

Volumn 142, Issue 1-3, 2009, Pages 17-26

  Malek, Kamilla ^a   Podstawka, Edyta ^a   Milecki, Jan ^b   Schroeder, Grzegorz ^b   Proniewicz, Leonard M ^a  

^a JAGIELLONIAN UNIVERSITY   (Poland)

^b ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

Adenosine; Charge distribution; Crown ether; DFT; IR; Raman

Indexed keywords

ADENOSINE; BENZO 15 CROWN 5 DERIVATIVE; N6 4' (BENZO 15 CROWN 5) ADENOSINE; SILVER; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; PRIORITY JOURNAL; RAMAN SPECTROMETRY; SPECTROSCOPY;

ADENOSINE; COMPUTER SIMULATION; CROWN ETHERS; MODELS, CHEMICAL; MOLECULAR STRUCTURE; QUANTUM THEORY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SPECTRUM ANALYSIS, RAMAN; VIBRATION;

EID: 64749105280     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2009.02.007     Document Type: Article

References (44)

1. Lehn J.M. Supramolecular chemistry: receptors, catalysts, and carriers. Science 227 (1985) 849-856
2. Wagner C., Rist M., Mayer-Enthart E., and Wagenknecht H.A. 1-Ethynylpyrene-modified guanine and cytosine as optical labels for DNA hybridization. Org. Biomol. Chem. 3 (2005) 2062-2063
3. Fujimoto K., and Inouye M. DNA duplex-based fluorescence probes/sensors using monomer-excimer switching. Yakugaku Zasshi - J. Pharm. Soc. Jap. 128 (2008) 1605-1613
4. Schultz P.G., Yin J., and Lerner R.A. The chemistry of the antibody molecule. Angew. Chem. Int. Ed. 41 (2002) 4427-4437
5. Wang Q., Mikkola S., and Lonnberg H. Bimetallic complexes of spiro-azacrown ligands as catalysts of phosphoester and phosphoric anhydride cleavage. Chem. Biodivers. 1 (2004) 1316-1326
6. Liu J., and Lu Y. Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew. Chem. Int. Ed. 45 (2006) 90-94
7. Morin G.T., and Smith B.D. Crown nucleoside monophosphate diesters: a new class of nucleoside prodrugs. Tetrahedron Lett. 37 (1996) 3101-3104
8. Siegel A., and Siegel H. Probing of Nucleic Acids by Metal Ion Complexes of Small Molecules vol. 33 (1996), Marcel Dekker, New York 1-678
9. Milecki J., and Schroeder G. Adenosine-N6-crown ethers as a new class of ionophores. Pol. J. Chem. 79 (2005) 1781-1785
10. Juliano R., Rowshon Alam M., Dixit V., and Kang H. Survey and summary: mechanisms and strategies for effective delivery of antisense and siRNA oligonucleotides. Nucleic Acids Res. 36 (2008) 4158-4171
11. Bailey L.E., Navarro R., and Hernanz A. Normal coordinate analysis and vibrational spectra of adenosine. Biospectroscopy 3 (1997) 47-59
12. Lee S.A., Anderson A., Smith W., Griffey R.H., and Mohan V. Temperature-dependent Raman and infrared spectra of nucleosides. Part I - adenosine. J. Raman Spectrosc. 31 (2000) 891-896
13. 2+. J. Phys. Chem. 100 (1996) 2154-2160
14. Yu J., Xu Z., and Xu G. FT-Raman and FT-IR spectral studies on rare earth complexes with octanedioyl bis(benzo-15-crown-5). Spectrochim. Acta A 52 (1996) 1499-1505
15. 2. J. Mol. Struct. 689 (2004) 61-67
16. Giese B., and McNaughton D. Surface-enhanced Raman spectroscopic and density functional theory study of adenine adsorption to silver surfaces. J. Phys. Chem. B 106 (2002) 101-112
17. Otto C., de Mul F.F.M., Huizinga A., and Greve J. Surface enhanced Raman scattering of derivatives of adenine: the importance of the external amino group in adenine for surface binding. J. Phys. Chem. 92 (1988) 1239-1244
18. Suh J.S., and Moskovits M. Surface-enhanced Raman spectroscopy of amino acids and nucleotide bases adsorbed on silver. J. Am. Chem. Soc. 108 (1986) 4711-4718
19. Chen T.T., Kuo Y.C., and Liang N.T. Surface-enhanced Raman scattering of adenosine triphosphate molecules. Langmuir 5 (1989) 887-891
20. Xiao Y.J., and Markwell J.P. Potential dependence of the conformations of nicotinamide adenine dinucleotide on gold electrode determined by FT-Near-IR-SERS. Langmuir 13 (1997) 7068-7074
21. Xiao Y.J., Chen Y.F., Wang T., and Gao X.X. Effects of glutamate dehydrogenase enzyme on the SERS spectra of nicotinamide adenine dinucleotide on a gold electrode. Langmuir 14 (1998) 7420-7426
22. + adsorbed on a silver electrode. Langmuir 18 (2002) 9888-9900
23. Mrozek M.F., and Weaver M.J. Detection and identification of aqueous saccharides by using Surface-Enhanced Raman Spectroscopy. Anal. Chem. 74 (2002) 4069-4075
24. 2+ as probed by Surface-Enhanced Raman Scattering spectroscopy. J. Phys. Chem. B 101 (1997) 4077-4084
25. Gao X., Davies J.P., and Weaver M.J. Test of surface selection rules for surface-enhanced Raman scattering: the orientation of adsorbed benzene and monosubstituted benzenes on gold. J. Phys. Chem. 94 (1990) 6858-6864
26. Podstawka E., Ozaki Y., and Proniewicz L.M. Part I: Surface enhanced Raman spectroscopy investigation of amino acids and their homodipeptides adsorbed on colloidal silver. Appl. Spectrosc. 58 (2004) 570-580
27. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery Jr. J.A., 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., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Bakken V., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., 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., and Pople J.A. Gaussian 03, Revision C.02, Gaussian, Inc., Wallingford CT (2004)
28. Lee C., Yang W., and Parr R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B37 (1988) 785-789
29. Becke A.D. Density-Functional thermochemistry. 3. The role of exact exchange. J. Chem. Phys. 98 (1993) 5648-5652
30. Wong M.W. Vibrational frequency prediction using density functional theory. Chem. Phys. Lett. 256 (1996) 391-399
31. Zborowski K., Grybos R., and Proniewicz L.M. Vibrational and computational study on maltol (3-hydroxy-2-methyl-4h-pyran-4-one) polymorphism. Vib. Spectr. 37 (2005) 233-236
32. Malek K., Skubel M., Schroeder G., Shvaika O.P., and Proniewicz L.M. Theoretical and experimental studies on selected 1,3-diazolium salts. Vib. Spectr. 42 (2006) 317-324
33. Michalska D., and Wysokinski R. The prediction of Raman spectra of platinum(II) anticancer drugs by density functional theory. Chem. Phys. Lett. 403 (2005) 211-217
34. Baker J., Jarzecki A.A., and Pulay P. Direct scaling of primitive valence force constants: An alternative approach to scaled quantum mechanical force fields. J. Phys. Chem. A 102 (1998) 1412-1424
35. Michalska D., Zierkiewicz W., Bieńko D.C., Wojciechowski W., and Zeegers- Huyskens T. "Troublesome vibrations" of aromatic molecules in second-order Möller-Plesset and Density Functional Theory calculations: infrared spectra of phenol and phenol-OD revisited. J. Phys. Chem. A 105 (2001) 8734-8739
36. Flükiger P., Lütni H.P., Portmann S., and Weber J. Molekel 4.0, Swiss Center for Scientific Computing, Manno, Switzerland (2000)
37. Martin J.M.L., and Van Alsenoy C. Gar2ped, University of Antwerp (1995)
38. Cioslowski J. A new population analysis based on atomic polar tensors. J. Amer. Chem. Soc. 111 (1989) 8333-8336
39. Malek K., Kozłowski H., and Proniewicz L.M. Interaction of Na(I), Ni(II) and Cu(II) with 2-cyano-2-(hydroxyimino)acetic acid. Spectroscopic and theoretical studies. Polyhedron 24 (2005) 1175-1184
40. Malek K., Puc A., Schroeder G., Rybachenko V.I., and Proniewicz L.M. FT-IR and FT-Raman spectroscopies and DFT modelling of benzimidazolium salts. Chem. Phys. 327 (2006) 439-451
41. Lai T.F., and Marsh R.E. The crystal structure of adenosine. Acta Crystallogr. B28 (1972) 1982-1989
42. Klooster W.T., Ruble J.R., and Craven B. Structure and thermal vibrations of adenosine from neutron diffraction data at 123 K. Acta Crystallogr. B47 (1991) 376-383
43. Toyama A., Hanada N., Abe Y., Takeuchi H., and Harada I. Assignment of adenine ring in-plane vibrations in adenosine on the basis of 15N and 13C isotopic frequency shifts and TUV resonance Raman enhancement. J. Raman Spectrosc. 25 (1994) 623-630
44. Varsanyi G. Assignments for Vibrational Spectra of 700 Benzene Derivatives (1973), Akademiai Kiado, Budapest