Biopolym. Cell. 1996; 12(1):42-48.
http://dx.doi.org/10.7124/bc.000410
The quantum mechanical calculations evidence molecular-zwitterionic features of prototropfc tautomerism of canonical nucleotide bases. 1. Pyrimidines
1Govorun D. M., 1Kondratyuk I. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

A prototroplc zwitterionic tautomerism of free uracil (Ura) and cytosine (Cyt) was Investigated by the semi-empirical quantum-mechanical AMI method at the full optimization of structural parameters. The prototropic tautomerism of canonical pyrimidine nucleotide bases was show to be molecular-zwitterionic in nature, rather high CH-acidity in combination with the pronounced basicity being of the root of this phenomenon. It was found that the higher energetically subfamilies of zwitterionic tautomers Ura and Cyt are separated from the lower energetically subfamilies of molecular tautomers by the significant energetical gap (21,4 kcal/mol for Uraand 12,6 kcal/molforCyt). Inthis case, relative energy (42,3 kcal/moLfor Ura and 29, / kcall mol for Cyt) of the lowest energetically zwitterionic tautomers, formed by migration of C6H carboproton to Cyt N3 nitrogen atom and Ura O4 oxygen atom with the cis-position to C5H6 bond of resulting hydroxylbond exceed significantly suchvalues of mainylidic forms ofpurine nucleotide bases and imidazole. It makes clear why there is practically no hydrogen-tritium exchange of Ura and Cyt C6H6 groups with water under favourable pH values, unlike situation in the case of purine bases and imidazol, if one takes in consideration that it is just the lowest energetically zwitterionic tautomer which is an intermediate state of such reaction, water proton participating information of it by profanation of Ura O4 and CytNS atoms accompaning deprotonation ofC6H6 bonds.
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