Biopolym. Cell. 2007; 23(4):363-367.
http://dx.doi.org/10.7124/bc.000774
Molecular Biophysics
Which intramolecular hygrogen bonds stabilize conformers of deoxyadenosine? The results of quantum-chemical analysis of electron density topology
1Zhurakivsky R. O., 2Hovorun D. M.
  1. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01033
  2. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

As many as 18 types of intramolecular hydrogen bonds are determined over 88 conformers of 2'-deoxyadenosine nucleoside by means of quantum-chemical analysis (at DFT B3LYP/6-31G(d, p) theory level) of electron density topology with Bader’s Atoms-in-Molecules theory. The total number of H-bonds is 129 and their types are C2'H2...O5' (11 H-bonds), C2'H2…N3 (32), C2'H1…N3 (1), C3'H…N3 (16), C5'H1…N3 (12), C5'H1…C8 (1), C5'H2…C8 (1), C5'H2…N3 (11), C8H…O5' (19), C3'H...HC8 (3), C8H…HC3' (2), C8H…H1C5' (2), C8H…H2C5' (1), O5'H...HC8 (2), O3'H...O5' (4), O5'H...O3' (4), O5'H…N3 (6), and O5'H…N9 (1). Conformational, geometric, and electron-topological properties of H-bonds are presented.
Keywords: deoxyadenosine, stable conformers, intramolecular hydrogen bonds, electron density topology analysis
Full text: (PDF, in Ukrainian)

References

[1] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[2] Michelson M. The Chemistry of Nucleosides and Nucleotides. Academic Press. 1963; 622 p.
[3] Zhurakivs'kyi RO, Yurenko EP, Hovorun DM. Conformational properties of 1',2'-deoxyribose - the model sugar residue of 2'-deoxyribonucleosides: results of a nonempiric quantum mechanical study. Dopovidi Nats Akad Nauk Ukrainy. 2006; (8):207-13.
[4] Zhurakivsky RO, Hovorun DM. Comprehensive conformational analysis of 2'-deoxyuridine by quantum-chemical density functional method. Biopolym Cell. 2006; 22(5):384-9.
[5] Zhurakivsky RO, Hovorun DM. Comprehensive conformational analyses of 2’-deoxythymidine by quantum-chemical density functional method. Ukr Bioorg Acta. 2006; 4(2):30-8.
[6] Zhurakivsky RO, Hovorun DM. Exhaustive conformational analysis of canonical nucleoside 2'-deoxycytidine quantum mechanical density functional method. Physics of Alive. 2006; 14(3):35–48.
[7] Zhurakivsky RO, Hovorun DM. Complete conformational analysis of 2'-deoxycytidine molecule by density functional theory. Dopovidi Nats Akad Nauk Ukrainy. 2007; (4):187-95.
[8] Zhurakivsky RO, Hovorun DM. Complete conformational analysis of deoxyadenosine by density functional theory. Biopolym Cell. 2007; 23(1):45-53.
[9] Krasnokutskiy SA monomer molecular structure of nucleic acid fragments isolated in low temperature inert matrices: Author. Thesis. ... kand. biol. nauk. Kharkiv. University. VN Karazina. Kharkov, 2004. 19 p
[10] Bader R. Atoms in Molecules: A Quantum Theory (International Series of Monographs on Chemistry. Oxford University Press. 1994. 458 p.
[11] Bilobrov VM. Hydrogen bond. Intramolecular interactions Kiev. Naukova dumka, 1991 320 p.
[12] Hocquet A. Intramolecular hydrogen bonding in 2?-deoxyribonucleosides: an AIM topological study of the electronic density. Phys Chem Chem Phys. 2001;3(15):3192–9.
[13] Zhurakivsky RO, Hovorun DM. Intramolecular hydrogen bonds in 2'-deoxyuridine conformers: results of non-empirical quantum chemical analysis of electron density topology. Ukr Bioorg Acta. 2006; 4(1):34-41.
[14] Matta CF, Bader RF. An atoms-in-molecules study of the genetically-encoded amino acids: I. Effects of conformation and of tautomerization on geometric, atomic, and bond properties. Proteins. 2000;40(2):310-29.
[15] Pinchuk VM, Tsybulyov PN, Parkhomenko VD. Quantum Chemistry intermolecular and ion-molecule interactions solvation and adsorption. Kiev. Naukova Dumka, 1994. 392 p.
[16] Grabowski SJ. Ab initio calculations on conventional and unconventional hydrogen bonds – study of the hydrogen bond strength. J. Phys. Chem. A. 2001. 105(47):10739–46.
[17] Zefirov YuV, Zorkii PM. Van der Waals radii and their application in chemistry. Russ Chem Rev. 1989; 58(5):421–40.