Ukr.Biochem.J. 2011; Volume 83, Issue 3, May-Jun, pp. 106-112

The simplest molecular model of 2′-deoxyribopolinucleotides sugar-phosphate backbone: quantum-chemical adequacy check

I. S. Voiteshenko1, R. O. Zhurakivsky2, L. A. Bulavin1, D. M. Hovorun2,3

1Taras Shevchenko Kyiv National University, Kyiv, Ukraine;
2Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv;
3Institute of High Technologies, Taras Shevchenko Kyiv National University, Ukraine;

The physical adequacy of the simplest molecular model “sugar residue (SR) – phosphate group (PG) – SR” of 2′-deoxyribopolinucleotides sugar-phosphate backbone is confirmed at DFT B3LYP/6-31++G(d,p) and DFT B3LYP/6-31G(d,p) of quantum-chemical methods. It is proved that complicacy of the model to the “SR-PG-SR-PG-SR” and higher levels does not noticeably change the numerical values of torsion angles. Also these angles depend negligibly on counterion nature (e.g. Na+ to Li+, K+ or Cs+ change) and transition from vacuum to continuum approximation with medium dielectrical values of 1.4, 24.9, and 78.4. It is shown that model loses its adequacy when PG is the end link.

Keywords: , , ,

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