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.

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

Conformational analysis of furanoside-containing mono- and oligosaccharides.

Publisher Summary This chapter discusses the results of the quantum-mechanical computations of the conformational properties of nucleic acids and their constituents, comparing the results obtained by different methods among themselves with the results of the empirical computations, and with the available experimental data as obtained by different techniques, both in the solid state and in solution. It reviews that “empirical” procedures consist of partitioning the potential energy of the system into several discrete contributions such as nonbonded interactions, electrostatic interactions; barriers to internal rotations, hydrogen-bonding, which are then evaluated with the help of empirical formulas deduced from studies on model compounds of small molecular weight. In the simplest approximation of these procedures, the problem is limited to the evaluation of allowed or forbidden contacts, with the help of van der Wads radii. The quantum-mechanical methods also aim at a direct evaluation of the total molecular energy, associated with the different atomic configurations of the system, and thus at a direct prediction of the preferred molecular conformations. The practical realization of this scheme became possible only recently, owing to the development of the all-valence-electrons and all-electron-molecular-orbital methods. The chapter reviews that quantum mechanics have been extensively used in the field of the conformational properties of the nucleic acid and their constituents, and that yielded the most complete and the most satisfactory description of the subject.

Quantum-mechanical studies on the conformation of nucleic acids and their constituents.

Conformation of non-aromatic ring compounds—XLVII

The diastereomeric 16-bromo- and 16-azido-17-alcohols 5−8, 11, 12, 16, and 17 and 17-ketones 3, 4, 9, and 10 of the 13α-estra-1,3,5(10)-triene series were synthesized as precursors for biologically active compounds and chiral ligands for metal complexation. Conformational investigations of these and some other compounds via X-ray analysis and 1H NMR spectroscopy show the existence of compounds with the classical steroid conformation (ring C chair, restricted conformation of ring D) and such with an atypical ring C twist-boat and a flexible ring D conformation. It could be shown that 17β-substituents or flattening of the D-ring are responsible for the twist-boat conformation, whereas compounds containing a 17α-substituent or 17-keto group possess the classical conformation. By varying the substituents, compounds with either of these conformations can be intentionally synthesized. MO calculations confirmed the relative stability of the twist-boat conformation.

H.J. Geise

Papers

The relations between torsional and valency angles of cyclopentane