Biopolym. Cell. 1995; 11(5):21-23.
http://dx.doi.org/10.7124/bc.0003F6
Acidic-basic properties of pyrimidine, imidazole and purine in vacuum: calculation by AMI method
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

Abstract

The protonation energy of endocyclic nitrogen atoms, which is not bonded with hydrogen atoms, as well as the deprotonation energies of all NH- and OH-groups of the main molecular tautomers of pyrimidine (Pyr), imidazole (Im) and purine (Pur) were calculated in vacuum by means of semiempirical quantum mechanical AMI method with full optimization of all structural parameters. It was established, that the nitrogen Nl atom of pyrimidine ring is the most probable site of protonation, the acidic and basic properties of the pyrimidine fragment of Pur are more pronounced than the ones of Pyr. Imidazole fragment of Pur possesses the better acidic properties, than molecule of Im, but the significantly worse protofility of endocyclic nitrogen atom free of hydrogen. From the data obtained the next conclusions about the most probable mechanisms of Pyr and of Im homoassociations in vacuum has been drown: Pyr forms two cyclic cooperative H-bonds C2H...N1 (or C2...N3) and Im creates linear homoassociates through periodic cooperative H-bonds N1H...N3.
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