Biopolym. Cell. 1995; 11(5):15-20.
Nucleotide bases as CH-Acids
1Govorun D. M., 1Kondratyuk I. V., 1Zheltovsky N. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680


The CH-acidity of some purine (Ade, Gua, Xan, Hyp and Pur) and pyrimidine (Ura, Thy, Cyt and Pyr) nucleotide bases and of imidazole was investigated in vacuum by means of semiempirical quantum mechanical AMI method with full optimization of all parameters. The consideration of CH bond deprotonation energies which determine the:r ability to donate protons and are situated in the 350,8 kcal/mol (Hyp C2H2) – 403,4 kcal/mol (Im C4H4) interval and correlation with the charges of CH group hydrogen atoms, equilibrium CH bond length and frequencies of strething -v (CH) vibration bring as about the conclusion that unlike «usual» organic CH-acids and physico-chemical parameters, which caused it. This may be explained by considerable (if main) contribution of conjugation effects (on the background of inductive mechanism) to the stabilization of carbanion of nucleotide bases, which is confirmed by significant change delocalization involving all the atoms under deprotonation of CH group. The obtained quantitative information on the vacuum CH-acidity of nucleotide bases may be useful to predict contributions of H-bond involving C–H groups of nucleotide bases to high specific protein-nucleic acid contacts.


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