Journal of Molecular Modeling

, Volume 12, Issue 5, pp 665–672

Probing the nature of hydrogen bonds in DNA base pairs

Original Paper

DOI: 10.1007/s00894-005-0021-y

Cite this article as:
Mo, Y. J Mol Model (2006) 12: 665. doi:10.1007/s00894-005-0021-y


Energy decomposition analyses based on the block-localized wave-function (BLW-ED) method are conducted to explore the nature of the hydrogen bonds in DNA base pairs in terms of deformation, Heitler–London, polarization, electron-transfer and dispersion-energy terms, where the Heitler–London energy term is composed of electrostatic and Pauli-exchange interactions. A modest electron-transfer effect is found in the Watson–Crick adenine–thymine (AT), guanine–cytosine (GC) and Hoogsteen adenine-thymine (H-AT) pairs, confirming the weak covalence in the hydrogen bonds. The electrostatic attraction and polarization effects account for most of the binding energies, particularly in the GC pair. Both theoretical and experimental data show that the GC pair has a binding energy (−25.4 kcal mol−1 at the MP2/6-31G** level) twice that of the AT (−12.4 kcal mol−1) and H-AT (−12.8 kcal mol−1) pairs, compared with three conventional N-H···O(N) hydrogen bonds in the GC pair and two in the AT or H-AT pair. Although the remarkably strong binding between the guanine and cytosine bases benefits from the opposite orientations of the dipole moments in these two bases assisted by the π-electron delocalization from the amine groups to the carbonyl groups, model calculations demonstrate that π-resonance has very limited influence on the covalence of the hydrogen bonds. Thus, the often adopted terminology “resonance-assisted hydrogen bonding (RHAB)” may be replaced with “resonance-assisted binding” which highlights the electrostatic rather than electron-transfer nature of the enhanced stabilization, as hydrogen bonds are usually regarded as weak covalent bonds.


Electron density difference (EDD) maps for the GC pair: a shows the polarization effect (isodensity 1.2×10−3 a.u.); b shows the charge transfer effect (isodensity 2×10−4 a.u.)


Hydrogen bond DNA base pair Charge transfer Electrostatic interaction Resonance-assisted hydrogen bonding (RAHB) 

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  1. 1.Department of ChemistryWestern Michigan UniversityKalamazooUSA

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