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Issue 12, 2010
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Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

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Abstract

The self-organized adenine ribbon is studied theoretically. The experimental evidence for the formation of such a ribbon has been found in the crystal structure of the supramolecular system [Dobrzyńska and Jerzykiewicz, J. Am. Chem. Soc., 2004, 126, 11118], and the striking structural feature is the fact that both the Watson–Crick and Hoogsteen faces of adenine are involved in the hydrogen bonding within the ribbon. The structure and physical properties of the monomer and five clusters of adenine (Ade)n (where n = 2, 3, 4, 5, 6) with AA22 configuration have been studied by means of the B3LYP, RI-TPSS, RI-TPSS-D (augmented with the dispersion term) and RI-MP2 methods using the 6-311+G(d,p), cc-pVTZ and TZVP basis sets. It is shown that among the investigated adenine clusters only the dimer has the planar structure. The evaluation of the three-body contribution to the total binding energy of adenine trimer has been performed at different levels of theory. All the methods consistently indicate that this term is positive and small (less than 0.5 kcal mol−1) which corresponds to a weak anti-cooperative effect, in adenine trimer. The differences between the total electronic energies obtained at the RI-TPSS/TZVP-D and RI-TPSS/TZVP levels of theory have shown that the London dispersion forces stabilize the adenine cluster containing 12 or more molecules by about −8 kcal mol−1 per molecule. The results from the DFT symmetry adapted perturbation theory analysis have revealed that the contribution of dispersion to the binding energy of the adenine ribbon is about 25%.

Graphical abstract: Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

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Publication details

The article was received on 30 Sep 2009, accepted on 24 Dec 2009 and first published on 29 Jan 2010


Article type: Paper
DOI: 10.1039/B920433D
Citation: Phys. Chem. Chem. Phys., 2010,12, 2888-2894
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    Adenine ribbon stabilized by Watson–Crick and Hoogsteen hydrogen Bonds: WFT and DFT study

    W. Zierkiewicz, D. Michalska and P. Hobza, Phys. Chem. Chem. Phys., 2010, 12, 2888
    DOI: 10.1039/B920433D

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