Biopolym. Cell. 2006; 22(5):384-389.
Molecular Biophysics
Comprehensive conformational analysis of 2'-deoxyuridine by quantum-chemical density functional method
- Taras Shevchenko National University of Kyiv
64, Volodymyrska Str., Kyiv, Ukraine, 01033 - Institute of Molecular Biology and Genetics, NAS of Ukraine
150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
Abstract
The comprehensive conformational analysis of minor nucleoside 2'-deoxyuridine is first performed by means of quantum-chemical density functional method on MP2/6-311++G(d, p)//DFT B3LYP/6-31G(d, p) theory level. The main geometric, energetic, and polar characteristics are presented for all of its 94 stable conformers as well as conformational equilibriums at normal conditions
Keywords: conformational analysis, nucleosides, deoxyuridine, quantum-chemical method
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]
Michelson M. The Chemistry of Nucleosides and Nucleotides. Academic Press. 1963; 622 p.
[4]
Chemistry of biologically active natural compounds. Eds Preobrazhenskiy NA, Evstigneeva RP. M.: Khimiia, 1970; 512 p.
[5]
Lehninger AL. Biochemistry: The Molecular Basis of Cell Structure and Function. Worth Publishers, 1970 833 p
[6]
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.
[7]
Bader R. Atoms in Molecules: A Quantum Theory (International Series of Monographs on Chemistry. Oxford University Press. 1994. 458 p.
[8]
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.
[9]
Saenger W. Principles of nucleic acid structure. New York: Springer, 1984; 556 p.
[10]
Kitamura K, Wakahara A, Mizuno 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]
Shishkin OV, Pelmenschikov A, Hovorun DM, Leszczynski J. Molecular structure of free canonical 2?-deoxyribonucleosides: a density functional study. J Mol Struct. 2000;526(1-3):329–41.