The structures of 19 alpha-helical alanine-based peptides, 13 amino acids in length, have been fully optimized using density functional theory and analyzed by means of the quantum theory of atoms in molecules. Two types of N-H...O bonds and one type of C-H...O bond have been identified. The value of the electron density at hydrogen bond critical points corresponding to N-H...O interactions is higher than that of C-H...O interactions. The effect of amino acid substitution at the central position of the peptide on the hydrogen bond network of the alpha-helix has been assessed. The strength of the hydrogen bond network, measured as the summation of the electron density over the hydrogen bond critical points, may be used to explain experimental relative helix propensities of amino acids in cases where solvation and entropic effects cannot.

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Density functional theory (DFT) is used to study the properties of a series of azole carboxamides in attempts to better understand why these molecules do not have an equal affinity for all natural DNA (RNA) nucleobases, which is an important criterion for universal bases. The thermodynamics and kinetics for bond rotations that afford four azole carboxamide conformers, which each bind to a different natural (DNA) base, are studied. It is concluded that a particular conformer of some azole carboxamides is favorably stabilized; therefore, these molecules will likely preferentially bind to a particular natural base. The geometries and binding energies are calculated for complexes formed between azole carboxamides and natural bases. Our calculations indicate that some complexes are highly distorted and therefore likely reduce the stability of duplexes. Our calculations also indicate that azole carboxamides bind to natural bases with varying affinities. Furthermore, the azole carboxamide binding interactions are generally significantly less than those in the corresponding natural base pair, with the exception of the thymine (or uracil) azole carboxamide complexes. Our calculations provide insight into interactions between azole carboxamides and the natural bases and allow suggestions to be made regarding why these compounds do not function as universal nucleobases.

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