Guanine: A combined study using vibrational spectroscopy and theoretical methods

Spectroscopy (New York)

Volumn 27, Issue 5-6, 2012, Pages 273-292

  Lopes, R Pedro ^a   Marques, M Paula M ^a,b   Valero, Rosendo ^a   Tomkinson, John ^c   De Carvalho, Luís A E Batista ^a  

^a UNIVERSITY OF COIMBRA   (Portugal)

^b UNIVERSITY OF COIMBRA   (Portugal)

^c RUTHERFORD APPLETON LABORATORY   (United Kingdom)

Author keywords

conformational analysis; DFT; Guanine; infrared spectroscopy; INS spectroscopy; Plane Wave calculations; Raman spectroscopy

Indexed keywords

CONDENSED STATE; CONFORMATIONAL ANALYSIS; CONFORMATIONAL STUDY; DFT; DFT LEVELS; GUANINE; INELASTIC NEUTRONS; ISOLATED MOLECULES; PLANE WAVE; POLYCRYSTALLINE; QUANTUM MECHANICAL METHOD; SPECTROSCOPIC CHARACTERIZATION;

CONFORMATIONS; INFRARED SPECTROSCOPY; QUANTUM THEORY; RAMAN SPECTROSCOPY; VIBRATIONAL SPECTROSCOPY;

POSITIVE IONS;

GUANINE;

ARTICLE; CHEMICAL STRUCTURE; MATHEMATICAL ANALYSIS; QUANTUM MECHANICS; SPECTROSCOPY; THEORETICAL STUDY;

EID: 84866257920     PISSN: 07124813     EISSN: 1875922X     Source Type: Journal    
DOI: 10.1155/2012/168286     Document Type: Article

References (50)

1. Piacenza M., Grimme S., Systematic quantum chemical study of DNA-base tautomers. Journal of Computational Chemistry 2004 25 1 83 99 2-s2.0-0345763760 10.1002/jcc.10365
2. Liang W., Li H., Hu X., Han S., Systematic theoretical investigations on all of the tautomers of guanine: from both dynamics and thermodynamics viewpoint. Chemical Physics 2006 328 1 3 93 102 2-s2.0-33748758710 10.1016/j.chemphys.2006.06.025
3. Choi M. Y., Miller R. E., Four tautomers of isolated guanine from infrared laser spectroscopy in helium nanodroplets. Journal of the American Chemical Society 2006 128 22 7320 7328 2-s2.0-33744946042 10.1021/ja060741l (Pubitemid 43849134)
4. Florián J., Baumruk V., Scaled quantum mechanical force fields and vibrational spectra of solid-state nucleic acid constituents. 4. N7-protonated guanine. Journal of Physical Chemistry 1992 96 23 9283 9287 2-s2.0-33751390777
5. Chandra A. K., Nguyen M. T., Uchimaru T., Zeegers-Huyskens T., DFT study of the interaction between guanine and water. Journal of Molecular Structure 2000 555 61 66 2-s2.0-0034727559 10.1016/S0022-2860(00)00587-1 (Pubitemid 32064908)
6. Shukla M. K., Leszczynski J., Guanine in water solution: comprehensive study of hydration cage versus continuum solvation model. International Journal of Quantum Chemistry 2010 110 15 3027 3039 2-s2.0-77958109591 10.1002/qua.22873
7. Thewalt U., Bugg C. E., Marsh R. E., The crystal structure of guanosine dihydrate and inosine dihydrate. Acta Crystallographica B 1970 26 8 1089 1101 2-s2.0-0014948829 10.1107/S0567740870003667
8. Maixner J., Zachova J., Redetermination of the structure of guanine hydrochloride monohydrate. Acta Crystallographica Section C 1991 47 11 2474 2476
9. Guille K., Clegg W., Anhydrous guanine: a synchrotron study. Acta Crystallographica Section C 2006 62 8 o515 o517 2-s2.0-33747153934 10.1107/S0108270106026011 (Pubitemid 44226249)
10. Maia F. F., Freire V. N., Caetano E. W. S., Azevedo D. L., Sales F. A. M., Albuquerque E. L., Anhydrous crystals of DNA bases are wide gap semiconductors. Journal of Chemical Physics 2011 134 17 2-s2.0-79957508851 10.1063/1.3584680 175101
11. Delabar J. M., Majoube M., Infrared and Raman spectroscopic study of 15N and D-substituted guanines. Spectrochimica Acta A 1978 34 2 129 140 2-s2.0-0000445098
12. Coulombeau C., Dhaouadi Z., Ghomi M., Jobic H., Tomkinson J., Vibrational mode analysis of guanine by neutron inelastic scattering. European Biophysics Journal 1991 19 6 323 326 2-s2.0-0025728576
13. Majoube M., Guanine residue: a normal-coordinate analysis of the vibrational spectra. Biopolymers 1984 24 6 1075 1087 2-s2.0-33748919093
14. Letellier R., Ghomi M., Taillandier E., Out-of-plane vibration modes of nucleic acid bases. I. Pyrimidine bases. European Biophysics Journal 1987 14 4 227 241 2-s2.0-0023095952 (Pubitemid 17013105)
15. Majoube M., Vibrational spectra of guanine. A normal coordinate analysis. Journal of Molecular Structure 1984 114 403 406 2-s2.0-33748919093
16. Gaigeot M. P., Leulliot N., Ghomi M., Jobic H., Coulombeau C., Bouloussa O., Analysis of the structural and vibrational properties of RNA building blocks by means of neutron inelastic scattering and density functional theory calculations. Chemical Physics 2000 261 1-2 217 237 2-s2.0-0034333094 10.1016/S0301-0104(00)00224-X
17. Dhaouadi Z., Ghomi M., Coulombeau C., Coulombeau C., Jobie H., Mojzes P., Chinsky L., Turpin P. Y., The molecular force field of guanine and its deuterated species as determined from neutron inelastic scattering and resonance Raman measurements. European Biophysics Journal 1993 22 3 225 236 2-s2.0-0027182659 (Pubitemid 23279502)
18. Florián J., Scaled quantum mechanical force fields and vibrational spectra of solid-state nucleic acid constituents. 6. Guanine and guanine residue. Journal of Physical Chemistry 1993 97 41 10649 10658 2-s2.0-0001375236
19. Giese B., McNaughton D., Density functional theoretical (DFT) and surface-enhanced Raman spectroscopic study of guanine and its alkylated derivatives: part 2: surface-enhanced Raman scattering on silver surfaces. Physical Chemistry Chemical Physics 2002 4 20 5171 5182 2-s2.0-0036399324 10.1039/b203830g
20. Duguid J., Bloomfield V. A., Benevides J., Thomas G. J., Raman spectroscopy of DNA-metal complexes. I. Interactions and conformational effects of the divalent cations: Mg, Ca, Sr, Ba, Mn, Co, Ni, Cu, Pd, and Cd. Biophysical Journal 1993 65 5 1916 1928 2-s2.0-0027365639 (Pubitemid 23334859)
21. Marian C. M., The guanine tautomer puzzle: quantum chemical investigation of ground and excited states. Journal of Physical Chemistry A 2007 111 8 1545 1553 2-s2.0-33947510007 10.1021/jp068620v (Pubitemid 46463844)
22. Gaussian 03 Revision D.01,. Gaussian, Inc., Wallingford, CT, USA, 2004
23. Lee C., Yang W., Parr R. G., Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Physical Review B 1988 37 2 785 789 2-s2.0-34250817103
24. Becke A. D., Density-functional exchange-energy approximation with correct asymptotic behavior. Physical Review A 1988 38 6 3098 3100 2-s2.0-4243553426 10.1103/PhysRevA.38.3098
25. Becke A. D., Density-functional thermochemistry. III. The role of exact exchange. Journal of Chemical Physics 1993 98 7 5648 5652 2-s2.0-0000189651
26. Petersson G. A., Bennett A., Tensfeldt T. G., Al-Laham M. A., Shirley W. A., Mantzaris J., A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. Journal of Chemical Physics 1988 89 4 2193 2218 2-s2.0-36549091806
27. Peng C., Ayala P. Y., Schlegel H. B., Frisch M. J., Using redundant internal coordinates to optimize equilibrium geometries and transition states. Journal of Computational Chemistry 1996 17 1 49 56 2-s2.0-2442481958 (Pubitemid 126581859)
28. Merrick J. P., Moran D., Radom L., An evaluation of harmonic vibrational frequency scale factors. Journal of Physical Chemistry A 2007 111 45 11683 11700 2-s2.0-36649020243 10.1021/jp073974n (Pubitemid 350197612)
29. Gorelsky S. I.,. University of Ottawa, Ottawa, Canada, 2010 http://www.sg-chem.net/
30. Gorelsky S. I., Lever A. B. P., Electronic structure and spectra of ruthenium diimine complexes by density functional theory and INDO/S. Comparison of the two methods. Journal of Organometallic Chemistry 2001 635 1-2 187 196 10.1016/S0022-328X(01)01079-8 (Pubitemid 33618338)
31. Ramirez-Cuesta A. J., aCLIMAX 4.0.1, the new version of the software for analyzing and interpreting INS spectra. Computer Physics Communications 2004 157 3 226 238 2-s2.0-1042277310 10.1016/S0010-4655(03)00520-4
32. Perdew J. P., Zunger A., Self-interaction correction to density-functional approximations for many-electron systems. Physical Review B 1981 23 10 5048 5079 2-s2.0-26144450583 10.1103/PhysRevB.23.5048
33. Giannozzi P., Baroni S., Bonini N., Calandra M., Car R., Cavazzoni C., Ceresoli D., Chiarotti G. L., Cococcioni M., Dabo I., Dal Corso A., De Gironcoli S., Fabris S., Fratesi G., Gebauer R., Gerstmann U., Gougoussis C., Kokalj A., Lazzeri M., Martin-Samos L., Marzari N., Mauri F., Mazzarello R., Paolini S., Pasquarello A., Paulatto L., Sbraccia C., Scandolo S., Sclauzero G., Seitsonen A. P., Smogunov A., Umari P., Wentzcovitch R. M., Quantum espresso: a modular and open-source software project for quantum simulations of materials. Journal of Physics Condensed Matter 2009 21 39 2-s2.0-70349568754 10.1088/0953-8984/21/ 39/395502 395502
34. Dal Corso A., Baroni S., Resta R., De Gironcoli S., Ab initio calculation of phonon dispersions in II-VI semiconductors. Physical Review B 1993 47 7 3588 3592 2-s2.0-0005054939 10.1103/PhysRevB.47.3588
35. Troullier N., Martins J. L., Efficient pseudopotentials for plane-wave calculations. Physical Review B 1991 43 3 1993 2006 2-s2.0-33645426115 10.1103/PhysRevB.43.1993
36. Monkhorst H. J., Pack J. D., Special points for Brillouin-zone integrations. Physical Review B 1976 13 12 5188 5192 2-s2.0-1842816907 10.1103/PhysRevB.13.5188
37. Gianozzi P., Baroni S., Yip S., Kaxiras E., Marzari N., Trout B., Methods and Models 2005 1 Springer 195 214 Handbook of MaterialsModeling
38. Giese B., McNaughton D., Density functional theoretical (DFT) and surface-enhanced Raman spectroscopic study of guanine and its alkylated derivatives: part 1. DFT calculations on neutral, protonated and deprotonated guanine. Physical Chemistry Chemical Physics 2002 4 20 5161 5170 2-s2.0-0036399323 10.1039/b203829c
39. * studies. International Journal of Quantum Chemistry 1992 44 supplement S19 43 55
40. Leszczynski J., The potential energy surface of guanine is not flat: an ab initio study with large basis sets and higher order electron correlation contributions. Journal of Physical Chemistry A 1998 102 13 2357 2362 2-s2.0-4244184231 (Pubitemid 128620473)
41. Šponer J., Hobza P., Nonplanar geometries of DNA bases. Ab initio second-order Moller-Plesset study. Journal of Physical Chemistry 1994 98 12 3161 3164 2-s2.0-33751158761
42. Jones D. B., Wang F., Winkler D. A., Brunger M. J., Orbital based electronic structural signatures of the guanine keto G-7H/G-9H tautomer pair as studied using dual space analysis. Biophysical Chemistry 2007 125 2-3 560 2-s2.0-33847002031 10.1016/j.bpc.2006.10.003 (Pubitemid 46242126)
43. Kushwaha P. S., Kumar A., Mishra P. C., Electronic transitions of guanine tautomers, their stacked dimers, trimers and sodium complexes. Spectrochimica ActaA 2004 60 3 719 728 2-s2.0-1642518624 10.1016/S1386-1425(03)00283-X
44. Shanmugasundaram M., Puranik M., Computational prediction of vibrational spectra of normal and modified DNA nucleobases. Journal of Raman Spectroscopy 2009 40 12 1726 1748 2-s2.0-72249121691 10.1002/jrs.2533
45. Rao L., Ke H., Fu G., Xu X., Yan Y., Performance of several density functional theory methods on describing hydrogen-bond interactions. Journal of Chemical Theory and Computation 2009 5 1 86 96 2-s2.0-61449126033 10.1021/ct800237n
46. Fellers R. S., Barsky D., Gygi F., Colvin M., An ab initio study of DNA base pair hydrogen bonding: a comparison of plane-wave versus Gaussian-type function methods. Chemical Physics Letters 1999 312 5-6 548 555 2-s2.0-0000908545 (Pubitemid 129592714)
47. Plazanet M., Fukushima N., Johnson M. R., Modelling molecular vibrations in extended hydrogen-bonded networkscrystalline bases of RNA and DNA and the nucleosides. Chemical Physics 2002 280 1-2 53 70 2-s2.0-0037097511 10.1016/S0301-0104(02)00441-X
48. Seuvre A. M., Mathlouthi M., F.T.-I.R. spectra of oligo- and poly-nucleotides. Carbohydrate Research 1987 169 83 103 2-s2.0-0023656636
49. Mathlouthi M., Seuvre A. M., Koenig J. L., F.T.-I.R. and laser-raman spectra of guanine and guanosine. Carbohydrate Research 1986 146 1 15 27 2-s2.0-0023048855
50. Santamaria R., Charro E., Zacarías A., Castro M., Vibrational spectra of nucleic acid bases and their Watson-Crick pair complexes. Journal of Computational Chemistry 1999 20 5 511 530 2-s2.0-0000823662 (Pubitemid 129652347)