Journal of Molecular Modeling

, Volume 17, Issue 12, pp 3265–3274 | Cite as

Localization and anharmonicity of the vibrational modes for GC Watson–Crick and Hoogsteen base pairs

  • Attila Bende
  • Diana Bogdan
  • Cristina M. Muntean
  • Cristian Morari
Original Paper

Abstract

We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson–Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H+ vibration in the case of the Hoogsteen base pair configuration is discussed.

Keywords

DFT DNA Watson–Crick Hoogsteen Vibrational density of states Anharmonic frequencies 

Notes

Acknowledgements

We acknowledge financial support from CNCSIS-UEFISCDI, project PNII-IDEI ID 875/2008, contract no. 519/2009, as well as Core Program, project PN 09-440101, contract no. 44 N/2009. Thanks are due to NIRDIMT, Cluj-Napoca Data Center for providing computer facilities.

Supplementary material

894_2011_1002_MOESM1_ESM.pdf (2.7 mb)
ESM 1(PDF 2781 kb)

References

  1. 1.
    Jeffrey GA, Saenger W (1991) Hydrogen bonding in biological structure. Springer, BerlinGoogle Scholar
  2. 2.
    Marcus MA, Corelli JC (1974) Infrared spectroscopy of the photo- and radiobiology of DNA bases and their derivatives. Radiat Res 57(1):20–37CrossRefGoogle Scholar
  3. 3.
    Fischer BM, Walther M, Jepsen PU (2002) Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy. Phys Med Biol 47(21):3807–3814. doi:10.1088/0031-9155/47/21/320 Google Scholar
  4. 4.
    Nir E, Kleinermans K, de Vries MS (2000) Pairing of isolated nucleic-acid bases in the absence of the DNA backbone. Nature 408(6815):949–951. doi:10.1038/35050053 CrossRefGoogle Scholar
  5. 5.
    Segers-Nolten GMJ, Sijtsema NM, Otto C (1997) Evidence for Hoogsteen GC base pairs in the proton-induced transition from right-handed to left-handed poly(dG-dC)·poly(dG-dC). Biochemistry 36(43):13241–13247. doi:10.1021/bi971326w CrossRefGoogle Scholar
  6. 6.
    Puppels GJ, Otto C, Greve J, Robert-Nicoud M, Arndt-Jovin DJ, Jovin TM (1994) Raman microspectroscopic study of low-pH-induced changes in DNA structure of polytene chromosomes. Biochemistry 33(11):3386–3395. doi:10.1021/bi00177a032 CrossRefGoogle Scholar
  7. 7.
    Taillandier E, Liquier J (2002) Vibrational spectroscopy of nucleic acids. In: Chalmers JM, Griffiths PR (ed) Handbook of vibrational spectroscopy, vol. 5. Wiley, New York, pp 3465–3480Google Scholar
  8. 8.
    Ten GN, Burova TG, Baranov VI (2009) Calculation and analysis of vibrational spectra of adenine–thymine, guanine–cytosine, and adenine–uracil complementary pairs in the condensed state. J Appl Spectrosc 76(1):73–81. doi:10.1007/s10812-009-9149-3 Google Scholar
  9. 9.
    Santamaria R, Charro E, Zacarías A, Castro M (1998) Vibrational spectra of nucleic acid bases and their Watson–Crick pair complexes. J Comput Chem 20(5):511–530. doi:10.1002/(SICI)1096-987X(19990415)20:5<511::AID-JCC4>3.0.CO;2-8 Google Scholar
  10. 10.
    Morari CI, Muntean CM (2003) Numerical simulations of Raman spectra of guanine–cytosine Watson–Crick and protonated Hoogsteen base pair. Biopolymers 72(5):339–344. doi:10.1002/bip.10418 Google Scholar
  11. 11.
    Jurečka P, Hobza P (2003) True stabilization energies for the optimal planar hydrogen-bonded and stacked structures of guanine···cytosine, adenine···thymine, and their 9- and 1-methyl derivatives: complete basis set calculations at the MP2 and CCSD(T) levels and comparison with experiment. J Chem Am Soc 125:15608–15613. doi:10.1021/ja036611j
  12. 12.
    Jeziorski B, Moszynski R, Szalewicz K (1994) Perturbation theory approach to intermolecular potential energy surfaces of van der Waals complexes. Chem Rev 94:1887. doi:10.1021/cr00031a008
  13. 13.
    Misquitta AJ, Podeszwa R, Jeziorski B, Szalewicz K (2005) Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations. J Chem Phys 123:214103. doi:10.1063/1.2135288, and references therein
  14. 14.
    Hesselmann A, Jansen G, Schütz M (2006) Interaction energy contributions of H-bonded and stacked structures of the AT and GC DNA base pairs from the combined density functional theory and intermolecular perturbation theory approach. J Chem Am Soc 128:11730–11731. doi:10.1021/ja0633363 Google Scholar
  15. 15.
    Han SY, Lee SH, Chung J, Oh HB (2007) Base-pair interactions in the gas-phase proton-bonded complexes of C+G andC+ GC. J Chem Phys 127:245102. doi:10.1063/1.2817604 CrossRefGoogle Scholar
  16. 16.
    Bikwood R, Gruebele M, Leitner DM, Wolynes PG (1998) The vibrational energy flow transition in organic molecules: theory meets experiment. Proc Natl Acad Sci USA 95(11):5960–5964Google Scholar
  17. 17.
    Rekik N, Oujia B, Wócik MJ (2008) Theoretical infrared spectral density of H-bonds in liquid and gas phases: anharmonicities and dampings effects. Chem Phys 352:65–76. doi:10.1016/j.chemphys.2008.05.009 Google Scholar
  18. 18.
    Pelel L, Gerber RB (2008) On the number of significant mode-mode anharmonic couplings in vibrational calculations: correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides. J Chem Phys 128:165105. doi:10.1063/1.2909558 Google Scholar
  19. 19.
    Watanabe Y, Maeda S, Ohno K (2008) Intramolecular vibrational frequencies of water clusters (H2O)n (n = 2–5): Anharmonic analyses using potential functions based on the scaled hypersphere search method. J Chem Phys 129:074315. doi:10.1063/1.2973605 Google Scholar
  20. 20.
    Lundell J, Latajka Z (2008) Vibrational calculations for the H2O···CO complex. J Mol Struct 887:172–179. doi:10.1016/j.molstruc.2007.12.013 Google Scholar
  21. 21.
    Ordejón P, Artacho E, Soler JM (1996) Self-consistent order-N density-functional calculations for very large systems. Phys Rev B53(16):R10441. doi:10.1103/PhysRevB.53.R10441
  22. 22.
    Soler JM, Artacho E, Gale JD, García A, Junquera P, Ordejón P, Sánchez-Portal D (2002) The SIESTA method for ab initio order-N materials simulation. J Phys Cond Mat 14(11):2745–2779. doi:10.1088/0953-8984/14/11/302 Google Scholar
  23. 23.
    Gaussian 03, Revision C.02, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr., Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, 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 JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels A. D, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian, Inc., WallingfordGoogle Scholar
  24. 24.
    Dion M, Rydberg H, Schröder E, Langreth DC, Lundqvist BI (2004) van der Waals density functional for general geometries. Phys Rev Lett 92(2):246401. doi:10.1103/PhysRevLett.92.246401 Google Scholar
  25. 25.
    Román-Pérez G, Soler JM (2009) Efficient implementation of a van der Waals density functional: application to double-wall carbon nanotubes. Phys Rev Lett 103(9):096102. doi:10.1103/PhysRevLett.103.096102 Google Scholar
  26. 26.
    Becke AD (1988) Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A38(6):3098–3100. doi:10.1103/PhysRevA.38.3098
  27. 27.
    Perdew JP, Burke K, Wang Y (1996) Generalized gradient approximation for the exchange-correlation hole of a many-electron system. Phys Rev B54(16):16533–16539. doi:10.1103/PhysRevB.54.16533
  28. 28.
    Schaefer A, Horn H, Ahlrichs R (1992) Fully optimized contracted Gaussian-basis sets for atoms Li to Kr. J Chem Phys 97(4):2571–2577. doi:10.1063/1.463096 Google Scholar
  29. 29.
    Guerra CF, Bickelhaupt FM, Snijders JG, Baerends EJ (2000) Hydrogen bonding in DNA base pairs: reconciliation of theory and experiment. J Am Chem Soc 122:4117–4128. doi:10.1021/ja993262d Google Scholar
  30. 30.
    Allouche AR (2011) Gabedit—a graphical user interface for computational chemistry software. J Comp Chem 32:174–182. doi:10.1002/jcc.21600 Google Scholar
  31. 31.
    Clabo DA Jr, Allen WD, Remington RB, Yamaguchi Y, Schaefer HF III (1988) A systematic study of molecular vibrational anharmonicity and vibration-rotation interaction by self-consistent-field higher-derivative methods. Asymmetric top molecules. Chem Phys 123:187–239. doi:10.1016/0301-0104(88)87271-9
  32. 32.
    Barone V (2005) Anharmonic vibrational properties by a fully automated second-order perturbative approach. J Chem Phys 122(01):014108. doi:10.1063/1.1824881 CrossRefGoogle Scholar
  33. 33.
    Christiansen O (2003) Møller–Plesset perturbation theory for vibrational wavefunctions. J Chem Phys 119(12):5773–5781. doi:10.1063/1.1601593 Google Scholar
  34. 34.
    Neugebauer J, Hess BA (2003) Fundamental vibrational frequencies of small polyatomic molecules from density-functional calculations and vibrational perturbation theory. J Chem Phys 118:7215–7225. doi:10.1063/1.1561045 CrossRefGoogle Scholar
  35. 35.
    Herzberg G (1945) Molecular spectra and molecular structure. II. Infrared and Raman spectra of polyatomic molecules. D. Van Nostrand Co. Inc., New YorkGoogle Scholar
  36. 36.
    Wilson EB, Decius JC, Cross PC (1955) Molecular vibrations. McGraw–Hill, New York (reprinted by Dover in 1980)Google Scholar
  37. 37.
    Postnikov AV, Pagés O, Hugel J (2005) Lattice dynamics of the mixed semiconductors (Be, Zn)Se from first-principles calculations. Phys Rev B 71:115206. doi:10.1103/PhysRevB.71.115206 CrossRefGoogle Scholar
  38. 38.
    Špirko V, Šponer J, Hobza P (1997) Anharmonic and harmonic intermolecular vibrational modes of the DNA base pairs. J Chem Phys 106:1472–1479. doi:10.1063/1.473296 CrossRefGoogle Scholar
  39. 39.
    Brauer B, Gerber RB, Kabeláč M, Hobza P, Bakker JM, Riziq AGA, de Vries MS (2005) Vibrational spectroscopy of the G-C base pair: experiment, harmonic and anharmonic calculations, and the nature of the anharmonic couplings. J Phys Chem A 109:6974–6984. doi:10.1021/jp051767m CrossRefGoogle Scholar
  40. 40.
    Bende A (2010) Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations. Theor Chem Acc 125(3–6):253–268. doi:10.1007/s00214-009-0645-6 CrossRefGoogle Scholar
  41. 41.
    Wang G-X, Ma X-Y, Wang J-P (2009) Anharmonic vibrational signatures of DNA bases and Watson–Crick base pairs. Chin J Chem Phys 22(6):563–570. doi:10.1088/1674-0068/22/06/563-570 Google Scholar
  42. 42.
    Del Bene JE, Jordan MJT (1998) A comparative study of anharmonicity and matrix effects on the complexes XH:NH3, X = F, Cl, and Br. J Chem Phys 108(8):3205–3212. doi:10.1063/1.476370 Google Scholar
  43. 43.
    Brisker D, Peskin U (2006) Vibrational anharmonicity effects in electronic tunneling through molecular bridges. J Chem Phys 125(11):111103. doi:10.1063/1.2353148 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Attila Bende
    • 1
  • Diana Bogdan
    • 1
  • Cristina M. Muntean
    • 1
  • Cristian Morari
    • 1
  1. 1.Molecular and Biomolecular Physics DepartmentNational Institute for Research and Development of Isotopic and Molecular TechnologiesCluj-NapocaRomania

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