Crystal Structure, Infrared Spectra and DFT Study of Benzyl 2,3-Anhydro-β-d-Ribopyranoside

Abstract

The crystal structure of benzyl 2,3-anhydro-β-d-ribopyranoside is orthorhombic, P2₁2₁2₁, Z = 4. The pyranose ring adopts the E _O conformation distorted considerably to the ⁵ H _O direction. The molecules of the title compound are linked into infinite chains running along the a-axis by bifurcated O–H···O hydrogen bonds. Interaction energies of these hydrogen bonds are significantly different, ~−5.4 for the bond with the smaller and ~−1.1 kcal/mol for the bond with the larger O···O separation. The hydrogen-bond pattern is completed by the two weaker C–H···O intermolecular hydrogen bonds, aiming at the epoxy oxygen atom. IR vibrational spectrum was interpreted by means of comparison with the full list of vibrational modes predicted using DFT method in the solid state. While till 1495 cm⁻¹ the individual bands can be reconciled with single calculated modes, the region below this limit is populated by heavily overlapped HCH, HCO, HOC, COC and HCC bending modes merged with few ν(CC) and ν(CO) modes. The respective “red” shifts of the positions of the ν(OH) bands correlate well with the size of the O···O separation.

Graphical Abstract

The crystal structure and the analysis of electronic structure and vibrational modes of an important precursor for preparation of model branched oligosaccharides related to xylan, arabinoxylan and 4-O-methylglucuronoxylan have been established and discussed.