Biopolym. Cell. 1996; 12(5):5-12.
On a quantum-chemical nature of a stereochemical nonrigidity of canonical nucleotide bases
1Hovorun D. M., 1Mishchuk Ya. R., 1Kondratyuk I. V.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

An interconversion of canonical nucleotide bases adenine, guanine and cytosine, exactly an inversion about a plane, and anisotropic inner rotation around exocyclic C-N bonds, and structural perturbations and the bases' profanation as well, have AMI and MNDO/H methods with an optimization of full structural parameters and agradient norm < 0.01.An mutually coordinated relaxational behaviour of essential structural parameters which describe valence bond configurations of amino group N atoms and neighbouring double C–N bonds were analysed. It was found that pπ-conjugation of an electron lone pair of an amino group nitrogen atom with a ring π-electron system is a main factor to determine structural-dynamical properties of exocyclic amino groups of canonical nucleotide bases, and moreover, of the bases themselves. Besides appreciable effects of other intramolecular interactions, namely intramolecular H-bonds (first of all of NH...N type), steric factors, and an electrostatic repulsion of electron lone pairs of neighbouring (endo- and exocyclic) nitrogen atoms as well, were estimated. They determine both nonequivalence of amino group NH bonds (as well as amino group ground-state orientation about a ring plane) and an anisotropy ofamino group inner rotation.

References

[1] Govorun DN, Danchuk VD, Mishchuk YaR, Kondratyuk IV, Radomsky NF, Zheltovsky NV. Mirror symmetrical conformational states of canonical nucleic acid bases. Doklady Akad Nauk Ukrainy. 1992; (2):66-9.
[2] Govorun DM, Danchuk VD, Mishchuk YaR, Kondratyuk IV, Zheltovsky MV. About nonplanarity and dipole nonstability of canonical nucleotide bases methylated at the glycoside nitrogen. Dopovidi Nats Akad Nauk Ukrainy. 1995; (6):117-9.
[3] Spiridonov VP, Ishchenko AA, Zasorin EZ. Electron diffraction studies on stereochemically non-rigid molecules. Russ Chem Rev. 1978; 47(1):54–68.
[4] Govorun DM, Kondratyuk IV, Mishchuk YaR, Zheltovskyi MV. The nonequavalence of amine hydrogens in canonical nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1995; (8):130-2.
[5] Govorun DM, Kondratyuk IV. Anisotropic rotation of amino groups in canonical nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1996:(10):151-4.
[6] Romm IP, Gur'yanova EN. p?-Conjugation in aromatic compounds of group V and VI elements. Russ Chem Rev. 1986; 55 (2):83–98.
[7] Shorygin PP, Burshtein KYa. Conjugation and the periodic system of the elements. Russ Chem Rev. 1991; 60 (1):1–24.
[8] Tsvetkov EN, Bochvar DA, Kabachnik MI. Hybridization of the of a nonbonding pair of electrons and?? conjugation. Theor Exp Chem. 1969;3(1):1–3.
[9] Sadova NI, Khaikin LS, Vilkov LV. Some problems in the stereochemistry of nitrogen compounds in the gas phase. Russ Chem Rev. 1992; 61(12): 1169–93.
[10] Shustov GV, Kachanov AV, Denisenko SN, Kostyanovsky RG. Asymmetrical nitrogen. Part 76. Quantum-chemical study of geometry and cobfigural stability of keteimines. Izv Akad Nauk, Ser Khim. 1992; (11):2572-8.
[11] Krueger PJ, Smith DW. Amino group stretching vibrations in primary aliphatic amines. Can J Chem. 1967;45(14):1605–10.
[12] Radchenko ED, Plokhotnichenko AM, Ivanov AYu, Sheina GG, Blagoy YuP. Ketoenole tautomeria of guanine and isocytosine molecules. Biofizika. 1986; 31(3):373-81.
[13] Szczepaniak K, Szczesniak M, Person WB. Infrared studies and the effect of ultraviolet irradiation on the tautomers of 9-methylguanine isolated in an argon matrix. Chem Phys Lett. 1988;153(1):39–44.
[14] Govorun DM, Mischuk YaR, Kondratyuk IV, Zheltovs'kyi MV. Dynamic stereo isomerism of the Watson-Crick nucleotide bases pairs. Dopovidi Nats Akad Nauk Ukrainy. 1995;(11):121-3.
[15] Govorun DM, Kondratyuk IV, Misjichuk YaR, Zheltovsky MV. The manifestation of Jahn-Teller effect in electronic absorption spectra of nucleic acids and their constituents. Intern. scientific. Conf. "Physics and chemistry of organic phosphors": Proc. Kharkov, 1995;126.
[16] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[17] Antipin MYu. Low-temperature X-ray diffraction analysis: possibilities in the solution of chemical problems. Russ Chem Rev. 1990; 59(7):607-26.
[18] Govorun DM, Mishchuk YaR, Kondratyuk IV, Zheltovsky MV. Intramolecular cooperative hydrogen bonds in nucleotide bases. Dopovidi Nats Akad Nauk Ukrainy. 1996;(8):141-4.