DFT investigation of the intermolecular interactions of a thieno-separated tricyclic guanine analog with gold nanoclusters

Computational and Theoretical Chemistry

Volumn 1019, Issue 1, 2013, Pages 1-10

  Zhang, Laibin ^a   Ren, Tingqi ^a,b   Zhou, Liuzhu ^a   Tian, Jianxiang ^a   Li, Xiaoming ^a  

^a QUFU NORMAL UNIVERSITY   (China)

^b SHANDONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

DFT; Gold clusters; Intermolecular interaction; NBO; Nucleobase analog

Indexed keywords

EID: 84880658816     PISSN: 2210271X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.comptc.2013.06.003     Document Type: Article

References (63)

1. Boyen H.G., Kastle G., Weigl F., Koslowski B., Dietrich C., Ziemann P., Spatz J.P., Riethmuller S., Hartmann C., Moller M., Schmid G., Garnier M.G., Oelhafen P. Oxidation-resistant gold-55 clusters. Science 2002, 297:1533-1536.
2. Burda C., Chen X.B., Narayanan R., El-Sayed M.A. Chemistry and properties of nanocrystals of different shapes. Chem. Rev. 2005, 105:1025-1102.
3. Fernandez C.A., Wai C.W. A simple and rapid method of making 2D and 3D arrays of gold nanoparticles. J. Nanosci. Nanotechnol. 2006, 6:669-674.
4. Yu J.S., Kim M., Kim S., Ha D.H., Chung B.H., Chung S.J., Yu J.S. Characteristics of localized surface plasmon resonance of nanostructured Au patterns for biosensing. J. Nanosci. Nanotechnol. 2008, 8:4548-4552.
5. Wang J. From DNA biosensors to gene chips. Nucleic Acids Res. 2000, 28:3011-3016.
6. Kim H.J., Choi S.H., Oh S.H., Woo J.C., Kim K. Horseradish peroxidase immobilized on poly(thiophene-2-aminophenol-3-thiopheneacetic acid) film electrode with Au nanoparticle-fabrication and evaluation as hydrogen peroxide sensor. J. Nanosci. Nanotechnol. 2008, 8:4962-4967.
7. Pissuwan D., Niidome T., Cortie M.B. The forthcoming applications of gold nanoparticles in drug and gene delivery systems. J. Controlled Release 2011, 149:65-71.
8. Murphy C.J., Gole A.M., Stone J.W., Sisco P.N., Alkilany A.M., Goldsmith E.C., Baxter S.C. Gold nanoparticles in biology: beyond toxicity to cellular imaging. Acc. Chem. Res. 2008, 41:1721-1730.
9. El-Sayed I.H., Huang X.H., El-Sayed M.A. Surface plasmon resonance scattering and absorption of anti-EGFR antibody conjugated gold nanoparticles in cancer diagnostics: applications in oral cancer. Nano Lett. 2005, 5:829-834.
10. Jain P.K., Huang X.H., El-Sayed I.H., El-Sayed M.A. Noble metals on the nanoscale: optical and photothermal properties and some applications in imaging, sensing, biology, and medicine. Acc. Chem. Res. 2008, 41:1578-1586.
11. Pyykko P. Theoretical chemistry of gold. Angew. Chem. Int. Ed. 2004, 43:4412-4456.
12. Pyykko P. Theoretical chemistry of gold. Inorgan. Chim. Acta 2005, 358:4113-4130.
13. Pyykko P. Theoretical chemistry of gold. Chem. Soc. Rev. 2008, 37:1967-1997.
14. 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.
15. Adessi C., Walch S., Anantram M.P. Environment and structure influence on DNA conduction. Phys. Rev. B 2003, 67:081405.
16. Long Y.T., Li C.Z., Kraatz H.B., Lee J.S. AC impedance spectroscopy of native DNA and M-DNA. Biophys. J. 2003, 84:3218-3225.
17. Moreno-Herrero F., Herrero P., Moreno F., Colchero J., Gomez-Navarro C., Gomez-Herrero J., Baro A.M. Topographic characterization and electrostatic response of M-DNA studied by atomic force microscopy. Nanotechnology 2003, 14:128-133.
18. 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.
19. Avvakumova V., Verderio P., Speranza G., Porta F. Gold nanoparticles modified with guanine and its derivatives: study of conformational changes. J. Phys. Chem. C 2013, 117:3002-3010.
20. 4 involving nonconventional NH⋯Au hydrogen bonding. Nano Lett. 2005, 5:735-739.
21. Kryachko E.S., Remacle F. Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters. J. Phys. Chem. B 2005, 109:22746-22757.
22. Cao G.-J., Xu H.-G., Li R.-Z., Zheng W. Hydrogen bonds in the nucleobase-gold complexes: photoelectron spectroscopy and density functional calculations. J. Chem. Phys. 2012, 136:8.
23. Rapino S., Zerbetto F. Modeling the stability and the motion of DNA nucleobases on the gold surface. Langmuir 2005, 21:2512-2518.
24. n (n=4, 8) complexes. J. Phys. Chem. A 2006, 110:7719-7727.
25. 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.
26. n (n=2-4) and adenine. J. Nanosci. Nanotechnol. 2010, 10:809-818.
27. n (n=2-4) and thymine. J. Mol. Struct. (Theochem) 2009, 915:98-104.
28. Sun W., Felice R.D. Nature of the interaction between natural and size-expanded guanine with gold clusters: a density functional theory study. J. Phys. Chem. C 2012, 116:24954-24961.
29. n=3,6,9,12] complexes. Comput. Theor. Chem. 2012, 984:93-101.
30. Zhang L., Ren T., Yang X., Zhou L., Li X. Intermolecular interactions of a size-expanded guanine analogue with gold nanoclusters. Int. J. Quantum Chem. 2013, 10.1002/qua.24436.
31. Hirao I. Unnatural base pair systems for DNA/RNA-based biotechnology. Curr. Opin. Chem. Biol. 2006, 10:622-627.
32. Wilson J.N., Kool E.T. Fluorescent DNA base replacements: reporters and sensors for biological systems. Org. Biomol. Chem. 2006, 4:4265-4274.
33. Seley K.L., Januszczyk P., Hagos A., Zhang L., Dransfield D.T. Synthesis and antitumor activity of thieno-separated tricyclic purines. J. Med. Chem. 2000, 43:4877-4883.
34. Wauchope O.R., Tomney M.J., Pepper J.L., Korba B.E., Seley-Radtke K.L. Tricyclic 2'-C-modified nucleosides as potential anti-HCV therapeutics. Org. Lett. 2010, 12:4466-4469.
35. Liu H.B., Gao J.M., Lynch S.R., Saito Y.D., Maynard L., Kool E.T. A four-base paired genetic helix with expanded size. Science 2003, 302:868-871.
36. Lu H.G., He K.Z., Kool E.T. YDNA: a new geometry for size-expanded base pairs. Angew. Chem. Int. Ed. 2004, 43:5834-5836.
37. Lee A.H.F., Kool E.T. Exploring the limits of DNA size: naphtho-homologated DNA bases and pairs. J. Am. Chem. Soc. 2006, 128:9219-9230.
38. Zhang L., Chen X.H., Liu H.Y., Han L., Cukier R.I., Bu Y.X. Exploration of the biological micro-surrounding effect on the excited states of the size-expanded fluorescent base x-cytosine in DNA. J. Phys. Chem. B 2010, 114:3726-3734.
39. Zhang L., Li H.F., Chen X.H., Cukier R.I., Bu Y.X. Absorption and fluorescence emission spectroscopic characters of size-expanded yDNA bases and effect of deoxyribose and base pairing. J. Phys. Chem. B 2009, 113:1173-1181.
40. Zhang L., Li H.F., Li J.L., Chen X.H., Bu Y.X. Absorption and fluorescence emission spectroscopic characters of naphtho-homologated yy-DNA bases and effect of methanol solution and base pairing. J. Comput. Chem. 2010, 31:825-836.
41. Fuentes-Cabrera M., Sumpter B.G., Lipkowski P., Wells J.C. Size-expanded yDNA bases: an ab initio study. J. Phys. Chem. B 2006, 110:6379-6384.
42. Fuentes-Cabrera M., Sumpter B.G., Wells J.C. Size-expanded DNA bases: an ab initio study of their structural and electronic properties. J. Phys. Chem. B 2005, 109:21135-21139.
43. Fuentes-Cabrera M., Zhao X., Kent P.R.C., Sumpter B.G. Electronic structure of xDNA. J. Phys. Chem. B 2007, 111:9057-9061.
44. n (n=4, 6, 8) with xDNA base pairs. J. Biomol. Struct. Dyn. 2009, 27:65-81.
45. Sharma P., Singh H., Sharma S., Singh H. Binding of gold nanoclusters with size-expanded DNA bases: a computational study of structural and electronic properties. J. Chem. Theory Comput. 2007, 3:2301-2311.
46. n (n=2-20) clusters: lowest-energy structures and electronic properties. Phys. Rev. B 2002, 66:035418.
47. n, 2≤N≤10) and their anions. Phys. Rev. B 2000, 62:R2287-R2290.
48. Xiao L., Tollberg B., Hu X., Wang L. Structural study of gold clusters. J. Chem. Phys. 2006, 124:114309.
49. Becke A.D. A new mixing of Hartree-Fock and local density functional theories. J. Chem. Phys. 1993, 98:1372-1377.
50. 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: Condens. Matter. 1988, 37:785-789.
51. Reed A.E., Weinhold F. Natural localized molecular orbitals. J. Chem. Phys. 1983, 78:735-746.
52. Reed A.E., Curtiss L.A., Weinhold F. Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint. Chem. Rev. 1988, 88:899-926.
53. Boys S.F., Bernadi F. The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol. Phys. 1970, 19:533-566.
54. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery J.A., Vreven T., Kudin K., Mennucci B., et al. Gaussian 03, Revision B.03 2003, Gaussian, Inc., Pittsburgh, PA.
55. 60-gold nanocontacts. ACS Nano 2008, 2:227-234.
56. 70. J. Chem. Phys. 2006, 125:214706.
57. Seminario J.M., De La Cruz C.E., Derosa P.A. A theoretical analysis of metal-molecule contacts. J. Am. Chem. Soc. 2001, 123:5616-5617.
58. Close D.M. Calculation of the ionization potentials of the DNA bases in aqueous medium. J. Phys. Chem. A 2004, 108:10376-10379.
59. Caruso T., Carotenuto M., Vasca E., Peluso A. Direct experimental observation of the effect of the base pairing on the oxidation potential of guanine. J. Am. Chem. Soc. 2005, 127:15040-15041.
60. Crespo-Hernandez C.E., Close D.M., Gorb L., Leszczynski J. Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues. J. Phys. Chem. B 2007, 111:5386-5395.
61. 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.
62. Giese B. Long-distance charge transport in DNA: the hopping mechanism. Acc. Chem. Res. 2000, 33:631-636.
63. 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.