Detection and evaluation of hydrogen bond strength in nucleic acid base pairs.

J Phys Chem A 2008 Jan 18;112(2):281-95. Epub 2007 Dec 18.

Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454, Iran.

The strengths of N-H---N and N-H---O hydrogen bonds in 15 nucleic acid base pairs have been investigated using different descriptors. Geometrical and energetic criteria, atoms in molecules topological parameters, natural bond orbital analysis, and spectroscopic measurements have been used to detect the H-bonds and evaluate their strengths in the intermolecular interactions between five nucleic acid bases. Different correlations have been obtained between many of these descriptors to provide a global view of H-bond interaction. We found good linear correlations for the dependence of some descriptors such as atomic interpenetration and hyperconjugation energy on density at bond critical point, while others like destabilization of H-atom energy, variation in N-H frequency, and NMR parameters correlate in a much worse fashion. The calculations suggest that almost all H-bonds in different base pairs belong to medium strength H-bonds. We found in thymine the H-bond interaction is more likely through the amide-type oxygen while the situation is reverse for uracil in which the urea-type oxygen is more accessible to form an H-bond. Cytosine and guanine can also form H-bonds via their amine-type or amide-type nitrogens. In cytosine, the amine-type nitrogen is involved in an N-H---O bond interaction, while, in guanine, the amide-type nitrogen has a greater contribution to H-bond interaction.

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http://dx.doi.org/10.1021/jp075992aDOI Listing
January 2008

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