Theoretical Chemistry Accounts

, Volume 125, Issue 3–6, pp 253–268 | Cite as

Hydrogen bonding in the urea dimers and adenine–thymine DNA base pair: anharmonic effects in the intermolecular H-bond and intramolecular H-stretching vibrations

Regular Article

Abstract

The equilibrium structures, binding energies, vibrational harmonic frequencies, and the anharmonic corrections for two different (cyclic and asymmetric) urea dimers and for the adenine–thymine DNA base pair system have been studied using the second-order Møller–Plesset perturbation theory (MP2) method and different density functional theory (DFT) exchange–correlation (XC) functionals (BLYP, B3LYP, PBE, HCTH407, KMLYP, and BH and HLYP) with the D95V, D95V**, and D95V++** basis sets. The widely used a posteriori Boys–Bernardi or counterpoise correction scheme for basis set superposition error (BSSE) has been included in the calculations to take into account the BSSE effects during geometry optimization (on structure), on binding energies and on the different levels of approximation used for calculating the vibrational frequencies. The results obtained with the ab initio MP2 method are compared with those calculated with different DFT XC functionals; and finally the suitability of these DFT XC functionals to describe intermolecular hydrogen bonds as well as harmonic frequencies and the anharmonic corrections is assessed and discussed.

Keywords

Urea dimer Adenine–thymine base pairs Anharmonic corrections H-stretching vibration BSSE effect 

Notes

Acknowledgments

This work was supported by the Grant of Romanian Ministry of Education and Research for young researcher, No: CEEX ET-30/08.10.2005, for which A.B. is gratefully acknowledged. A. B. is also thankful for the Grant of German Cancer Research Center (DKFZ) and for its support during his visit to carrying out this work. The author thanks Prof. Dr. Sándor Suhai for helpful comments on the manuscript.

Supplementary material

214_2009_645_MOESM1_ESM.pdf (893 kb)
Supplementary material 1 (PDF 892 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Molecular and Biomolecular Physics DepartmentNational Institute for R&D of Isotopic and Molecular TechnologiesCluj-NapocaRomania
  2. 2.Molecular Biophysics DepartmentGerman Cancer Research CentreHeidelbergGermany

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