Interaction of gold nanoclusters of different size with adenine: A density functional theory study of neutral, anionic and cationic forms of [adenine+(Au) n=3,6,9,12] complexes

Computational and Theoretical Chemistry

Volumn 984, Issue , 2012, Pages 93-101

  Vyas, Nidhi ^a   Ojha, Animesh K ^a  

^a MOTILAL NEHRU NATIONAL INSTITUTE OF TECHNOLOGY   (India)

Author keywords

Adenine; DFT; Gold nanoclusters

Indexed keywords

EID: 84857781529     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2012.01.016     Document Type: Article

References (51)

1. Ratner M., Ratner D. Nanotechnology, a Gentle Introduction to the Next Big Idea 2002, Prentice Hall, Upper Saddle River, NJ.
2. Tao N.J., de Rose J.A., Lindsay S.M. Self-assembly of molecular superstructures studied by in situ scanning tunneling microscopy: DNA bases on Au (111). J. Phys. Chem. 1993, 97:910-919.
3. Mirkin C.A., Letsinger R.L., Mucic R.C., Storhoff J.J. A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 1996, 382:607-609.
4. Alivisatos A.P., Johnsson K.P., Peng X., Wislon T.E., Loweth C.J., Bruchez M.P., Schultz G.C. Organization of 'nanocrystal molecules' using DNA. Nature 1996, 382:609-611.
5. Storhoff J.J., Mirkin C.A. Programmed materials assembly with DNA. Chem. Rev. 1999, 99:1849-1862.
6. Storhoff J.J., Lazarides A.A., Mucic R.C., Mirkin C.A., Letsinger R.L., Schatz G.C. What controls the optical properties of DNA-linked gold nanoparticle assemblies?. J. Am. Chem. Soc. 2000, 122:4640-4650.
7. Park J., Lazarides A.A., Mirkin C.A., Letsinger R.L. Directed assembly of periodic materials from protein and oligonucleotide-modified nanoparticle building blocks. Angew. Chem. Int. Ed. 2001, 40:2909-2912.
8. Niemeyer C.M. Nanoparticles, proteins, and nucleic acids: biotechnology meets materials science. Angew. Chem. Int. Ed. 2001, 40:4128-4158.
9. Pirrung M.C. How to make a DNA chip. Angew. Chem. Int. Ed. 2002, 41:1277-1289.
10. Harnack O., Ford W.E., Yasuda A., Wessels J.M. Tris (hydroxymethyl) phosphine-capped gold particles templated by DNA as nanowire precursors. Nano Lett. 2002, 2:919-923.
11. Parak W.J., Pellegrino T., Micheel C.M., Gerion D., Williams S.C., Alivisatos A.P. Conformation of oligonucleotides attached to gold nanocrystals probed by gel electrophoresis. Nano Lett. 2003, 3:33-36.
12. Alivisatos A.P. The use of nanocrystals in biological detection. Nat. Biotechnol. 2004, 22:47-52.
13. Daniel M.C., Astruc D. Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem. Rev. 2004, 104:246-293.
14. Seeman N.C. DNA in a material world. Nature 2003, 421:427-431.
15. Demers L.M., östblom M., Zhang H., Jang N.-H., Liedberg B., Mirkin C.A. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 2002, 124:11248-11249.
16. Storhoff J.J., Elghanian R., Mirkin C.A., Letsinger R.L. Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir 2002, 18:6666-6670.
17. Chen Q., Frankel D.J., Richardson N.V. Self-assembly of adenine on Cu (110) surfaces. Langmuir 2002, 18:3219-3225.
18. Giese B., McNaughton D.J. J. Phys. Chem. B 2002, 106:101-112.
19. Li W.H., Haiss W., Floate S., Nichols R. In-situ infrared spectroscopic and scanning tunneling microscopy investigations of the chemisorption phases of uracil, thymine, and 3-methyl uracil on Au (111) electrodes. Langmuir 1999, 15:4875-4883.
20. Gourishankar A., Shukla S., Ganesh K.N., Sastry M. Isothermal titration calorimetry studies on the binding of DNA bases and PNA B base monomers to gold nanoparticles. J. Am. Chem. Soc. 2004, 126:13186-13187.
21. Liu Y., Meyer-Zaika W., Franzka S., Schmid G., Tsoli M., Kuhn H. Gold-cluster degradation by the transition of B-DNA into A-DNA and the formation of nanowires. Angew. Chem. Int. Ed. 2003, 42:2853-2857.
22. Roelfs B., Baumgärtel H., Bunsenges B. Adsorption and film formation of thymine on a gold (100), single crystal. Electrode Phys. Chem. 1995, 99:677-681.
23. Xiao Y.J., Chen Y.F., Gao X.X. Comparative study of the surface enhanced near infrared Raman spectra of adenine and NAD+ on a gold electrode. Spectrochim. Acta A 1999, 55:1209-1218.
24. Srinivasan R., Gopalan P. Order and stability of an electrochemically condensed adenine layer on graphite. J. Phys. Chem. 1993, 97:8770-8775.
25. Camargo A.P.M., Baumgärtel H., Donner C. Coadsorption of the DNA bases thymine and adenine at the Au (111) electrode. Phys. Chem. Chem. Phys. 2003, 5:1657-1664.
26. Braun E., Eichen Y., Sivan U., Ben-Yoseph G. DNA templated self-assembly of a conductive wire connecting two electrodes. Nature 1998, 391:775-778.
27. Richter J., Mertig M., Pompe W., Monch I., Schackert H.K. Construction of highly conductive nanowires on a DNA template. Appl. Phys. Lett. 2001, 78:536-538.
28. Cai Z., Sevilla M.D. Electron and hole transfer from DNA base radicals to oxidized products of guanine in DNA. Dalton Res. 2003, 159:411-419.
29. Giese B. Long-distance charge transport in DNA: the Hopping mechanism. Acc. Chem. Res. 2000, 33:631-636.
30. Yang X., Wang X.B., Vorpagel E.R., Wang L.S. Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy. Proc. Natl. Acad. Sci. 2004, 101:17588-17592.
31. n (n=4, 8) complexes. J. Phys. Chem. A 2006, 110:7719-7727.
32. Shukla M.K., Dubey M., Zakar E., Leszczynski J. DFT investigation of the interaction of gold nanoclusters with nucleic acid base guanine and the Watson-Crick guanine-cytosine base pair. J. Phys. Chem. C 2009, 113:3960-3966.
33. Giese B., Amaudrut J., Köhler A.-K., Spormann M., Wessely S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunneling. Nature 2001, 412:318-320.
34. Schiedt J., Weinkauf R., Neumark D.M., Schlag E.W. Anion spectroscopy of uracil, thymine and the amino-oxo and amino-hydroxy tautomers of cytosine and their water clusters. Chem. Phys. 1998, 239:511-524.
35. Seeman N.C. At the crossroads of chemistry, biology, and materials: structural DNA nanotechnology. Chem. Biol. 2003, 10:1151-1159.
36. Endres R.G., Cox D.L., Singh R.R.P. Colloquium: the quest for high-conductance DNA. Rev. Mod. Phys. 2004, 76:195-214.
37. Demers L.M., Ostblom M., Zhang H., Jang N.H., Liedberg B., Mirkin C.A. Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold. J. Am. Chem. Soc. 2002, 124:11248-11249.
38. Kimura-Suda H., Petrovykh D.Y., Tarlov M.J., Whitman L.J. Base-dependent competitive adsorption of single-stranded DNA on gold. J. Am. Chem. Soc. 2003, 125:9014-9015.
39. Storhoff J.J., Elghanian R., Mirkin C.A., Letsinger R.L. Sequence-dependent stability of DNA-modified gold nanoparticles. Langmuir 2002, 18:6666-6670.
40. Kryachko E.S., Remacle F. Complexes of DNA bases and gold clusters Au3 and Au4 involving nonconventional N-H...Au hydrogen bonding. Nano Lett. 2005, 5:735-739.
41. Kryachko E.S., Remacle F.J. Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters. J. Phys. Chem. B 2005, 109:22746-22757.
42. Krüger D., Fuchs H., Rousseau R., Marx D., Parrinello M. Pulling monatomic gold wires with single molecules: an ab initio simulation. Phys. Rev. Lett. 2002, 89:186402-186405.
43. Becke A.D. A new mixing of Hartree-Fock and local density-functional theories. J. Chem. Phys. 1993, 98:1372-1377.
44. Stephen P.J., Devlin F.J., Frisch M.J., Chabalowski C.F. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 1994, 98:11623-11627.
45. Lee C., Yang W., Parr R.G. Development of the colle-salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37:785-789.
46. Hay P.J., Wadt W.R. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg. J. Chem. Phys. 1985, 82:270-283.
47. Wadt W.R., Hay P.J. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J. Chem. Phys. 1985, 82:284-298.
48. Hay P.J., Wadt W.R. Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J. Chem. Phys. 1985, 82:299-310.
49. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R Cheeseman, J. A. Montgomery, Jr. T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V.Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K.Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E.Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A.Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C.Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K.Raghavachari, J. B. Foresman, J. V.Ortiz, Q.Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y.Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W.Wong, C.Gonzalez, J.A.Pople, Computational Models, Gaussian 03W program, Gaussian, Inc., Pittsburgh, PA, USA, 2003.
50. Computational Models, GaussView03W, Gaussian, Inc., Pittsburgh, PA, USA, 2003.
51. Kolandaivel P., Jayakumar N. Studies of isomer stability using the maximum hardness principle (MHP). Int. J. Quantum Chem. 2000, 76:648-655.