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


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.


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



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)


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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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