Biopolym. Cell. 2008; 24(2):142-157.
http://dx.doi.org/10.7124/bc.00079C
Molecular Biophysics
Conformational possibilities of uridine: DFT quantum mechanical investigation
1Zhurakivsky R. O., 2Hovorun D. M.
  1. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01601
  2. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Complete conformational analysis of uridine is performed by density functional theory at MP2/6-311++G(d, p)//DFT B3LYP/6-31G(d, p) level. Main geometric, energetic, and polar characteristics of all 111 conformers were presented, along with conformational equilibria in temperature range of 298.15–420 K. At T = 298.15 K these are syn:anti = 10.6:89.4 %; S:N = 85.5:14.5 %, and at T = 420 K syn:anti = 16.6:83.4 %; S:N = 68.6:31.4 %. By quantum mechanical method (Bader’s atoms in molecules theory) as many as 17 types of intramolecular hydrogen bonds were established (total number is 313) in all possible conformers of uridine, namely, C1'H...O2, C2'H2...O5', C2'H2...O2, C3'H...O2, C5'H1...O2, C5'H2...O2, C6H...O4', C6H...O5', C3'H…HC6, C5'H1…HC6, C5'H2…HC6, O2'H...O2, O2'H...O3', O3'H...O2', O3'H...O5', O5'H...O2, and O5'H...O3'. Their conformational properties, geometric and electron topology characteristics were described.
Keywords: uridine, conformational analysis, quantum mechanical density functional theory method, intramolecular hydrogen bonds, electron density topology analysis
Full text: (PDF, in Ukrainian)

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