Investigation of conformational structures of gemcitabine and its 2′,2′-difluoro 2′-deoxy derivatives: A computational study

Abstract

This study investigates the electronic structure of natural DNA nucleosides and their 2′-difoluoro analogues to assess the possible substitution effects of two hydrogen atoms with fluorine ones in the positions of sugar moiety. Gemcitabine representing an analogue with specific features was utilized in this study. To conduct proper calculations, DFT method at the B3LYP/6-31+G* level was accordingly used. In terms of conformational characteristics of gemcitabine and other analogues, full geometry optimizations, atomic charges, dipole moments, NBO, and HOMO & LUMO were duly made. PROSIT was also used to calculate the pseudorotational parameters of gemcitabine and the DNA analogues. The outcome proved that all the 2-difoluoro DNA nucleosides have slight differences in geometrical parameters with natural nucleosides.