Crystal structures of α-D and β-D anomeric 2′-Deoxycytidines decorated with octadiynyl side chains: Hydrogen bonding, crystal packing and impact of alkyne residues on physical properties

Publication date: Available online 13 April 2019Source: Journal of Molecular StructureAuthor(s): Xinglong Zhou, Sebastian Lars Müller, Peter Leonard, Constantin Daniliuc, Yingying Chai, Simone Budow-Busse, Frank SeelaAbstractSingle-crystal X-ray analyses and other physical properties of the anomeric nucleosides 1 and 2 are reported. The crystal of the β-D anomer 2 contains six conformers caused by the flexibility of the octadiynyl side chain. The conformers form layers and the crystal consists of a repetition of these layers in an alternating fashion. In case of the α-D anomer 1 only one conformer exits in the unit cell. It forms an uniform structure with nucleobase, sugar and side chain entities positioned above each other in a regular pillar-like fashion. Various hydrogen bonds are stabilizing the crystal structure but have influence on the electronic properties of nucleoside monomers; a phenomenon that has been verified by Hirshfeld surface analyses. A seldom CCH‧‧‧O hydrogen bond is formed by the terminal alkyne residue immobilizing the side chain of the α-D anomer 1 but not the β-D counterpart 2. The triple bonds of side chain affect UV, CD-spectra and pKa values with respect to the non-functionalized 2′-deoxycytidine but are similar for the α- and β-anomers. The observation made on anomeric nucleosides have the potential to be of general importance for the construction of bio-inspired materials based on nucleosides.Graphical abstract
Source: Journal of Molecular Structure - Category: Molecular Biology Source Type: research