Empirical Correlations Between Conformational Parameters in β‐D‐Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters

TLDR: In this article, a data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives.

Abstract: A data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives. The variability in bond angles and torsion angles can be described by four conformational parameters; the kind and degree of ring puckering as expressed in phase angle of pseudorotation P and puckering amplitude vm, the conformation of the side-chain δ and the glycosidic torsion angle χ. Comparison between out-of-plane and torsion angle methods for calculation of pseudorotation parameters revealed that the latter method is better suited to describe the internal coordinates of the non-equilateral five-membered ring. Inspection of the distribution of phase angles and puckering amplitudes lends additional support to the hypothesis that conformational interconversion of the familiar N and S type ring conformers is a process of hindered pseudorotation, proceeding through the O4′endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of χ are correlated with furanose conformation in ribonucleosides; the distribution is also affected by the type of base, purines showing higher syn/anti ratios than pyrimidines. Three modes are observed for the backbone torsion angle δ(C4′–C5′); the most abundant rotamer is δ+, followed by δa. The δ− rotamer has so far been found only in S-type furanosides. Regressions based on existing or modified equations were used to express variations in internal coordinates in terms of the four parameters involved. As a consequence of its anomeric character, the glycosidic bond length can be described by a cyclic function of χ. Endocyclic bond angles' and torsion angles show small but systematic deviations from the pseudorotation equations derived for equilateral rings. Based on observed correlations with the four parameters, reasonably accurate coordinates for exocyclic atoms, including hydrogen atoms, could also be obtained. Coordinates for model β-D-furanoside fragments with preferred χ and δ orientations and variable pseudorotation parameters, covering a part of the N ⇌ S interconversion pathway, are presented. Their usefulness in future theoretical and experimental studies on nucleic acid conformations, both in the solid state and in solution, is discussed.