Conformational studies of N-(α-d-glucofuranurono-6,3-lactone)- and N-(methyl β-d-glucopyranuronate)-p-nitroanilines

Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).

Identification of the furanose ring conformations and the factors driving their adoption

Three groups of furanoses with restricted freedom of rotation on the C3-C4, C2-C3, and C1-C2 bonds, respectively, are presented. Conformational analysis of these furanoses is conducted based on the proton nuclear magnetic resonance (¹H NMR) spectroscopy, density functional theory (DFT) calculations, and X-ray analysis. It is shown that the particular group of the presented furanoses is locked in the specific conformation. These are the ¹T₂-like, the ⁰E-like, and the ³T₄-like conformation, respectively. Characteristic ¹H NMR spectra of these three conformations are presented and the factors influencing the conformational preferences of the analyzed furanoses are discussed.

Characteristic 1H NMR spectra of β-d-ribofuranosides and ribonucleosides: factors driving furanose ring conformations

A series of β-d-ribofuranosides and ribonucleosides fused with 2,3-O-isopropylidene ring was synthesized and studied in terms of their conformational preferences. Based on the 1H NMR spectra, DFT calculations, and X-ray analysis the E 0-like and E 4-like conformations adopted by these furanosides are identified. The 3 E-like and 2 E-like conformations are assigned to ribonucleosides without the 2,3-O-isopropylidene group. The studies are supported by analysis of the structural data of β-d-ribofuranosides and ribonucleosides deposited in the Cambridge Crystallographic Data Center (CCDC) database. Finally, the factors influencing the conformational preferences of the furanose ring with the β-d-ribo configuration are indicated. These are the unfavorable ecliptic orientation of the 2-OH and 3-OH groups, the 1,3-pseudodiaxial interaction of the aglycone and terminal hydroxymethyl group and the endo-anomeric effect. It is also proved that the exo-anomeric effect acts in β-d-ribofuranosides.