Biopolym. Cell. 2007; 23(1):45-53.
http://dx.doi.org/10.7124/bc.000755
Molecular Biophysics
Complete conformational analysis of deoxyadenosine by density functional theory
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

For the first time the comprehensive conformational analysis of 2'-deoxyadenosine is performed by means of the quantum-chemical density functional method on MP2/6-311++G(d, p)//DFT B3LYP/6-31G(d, p) theory level. Main geometric, energetic, and polar characteristics for all of its 88 stable conformers as well as conformational equilibrium at normal conditions are presented.
Keywords: deoxyadenosine, conformational analysis, quantumchemical calculations
Full text: (PDF, in Ukrainian)

References

[1] Structure and Stability of Biological Macromolecules. Ed MB Volkenshtein. M. Mir, 1973. 584 p.
[2] 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.
[3] Zhurakivsky RO, Hovorun DM. Comprehensive conformational analysis of 2'-deoxyuridine by quantum-chemical density functional method. Biopolym Cell. 2006; 22(5):384-389.
[4] Zhurakivsky RO, Hovorun DM. Comprehensive conformational analyses of 2'-deoxythymidine by quantum-chemical density functional method. Ukr Bioorg Acta. 2006; 4(2):56–63.
[5] 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.
[6] Zhurakivsky RO, Hovorun DM. Complete conformational analysis of 2'-deoxycytidine molecule by density functional theory. Dopovidi Nats Akad Nauk Ukrainy. 2007; (4):187-95.
[7] Michelson M. The Chemistry of Nucleosides and Nucleotides. Academic Press. 1963; 622 p.
[8] Chemistry of biologically active natural compounds. Ed Preobrazhenskiy NA, Evstigneeva RP. M.: Khimiia, 1970; 512 p.
[9] Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[10] Kitamura K, Wakahara A, Mizuno H, Baba Y, Tomita K. Conformationally 'concerted' changes in nucleotide structures. A new description using circular correlation and regression analyses. J Am Chem Soc. 1981; 103(13):3899–904.
[11] Preobrazhenskaya NN, Shabarova ZA. The steric structure of nucleosides, nucleotides, and their derivatives. Russ Chem Rev. 1969; 38 (2):111–125.
[12] Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr, JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar S. S., Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian 03, Revision C.02. Wallingford: Gaussian Inc., 2004.