Simulation of the interconversion path between stable conformations of the furanose ring: methyl β-D-2-deoxyribofuranoside and simpler ribose and deoxyribose analogues

Abstract

The results of simulation of the pseudorotation path in methyl β-D-2-deoxyribofuranoside, cyclopentane, tetrahydrofuran, 3-hydroxytetrahydrofuran, and 2,3-dihydroxytetrahydrofuran by using a geometrical ring-puckering model and an empirical all-atom force-field method are presented. For all these molecules energetic and geometric profiles of the N–S interconversion pathway are presented for various exocyclic group orientations. The difference in the simulated conformational behaviour of certain model compounds in the vapour state and in polar-solution conditions is discussed. The influence of the orientation and presence of exocyclic groups and the role of C- and O-ring structure on the conformational behaviour of the compounds examined is investigated. Conformational analysis of the furanose ring in several model compounds of increasing structure complexity reveals great diversity in their conformational behaviour in both geometric and energetic respects. The only features of conformational behaviour attributed to ring structure are: (a) the existence of energy minima in wide N and S regions of pseudorotation wheel; (b) the existence of N–S interconversion path via puckered-ring conformations. The puckering amplitude q varies considerably during N–S interconversion path and is no longer a quantitative feature of furanosering structure.