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
Abstract
Single-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 alkyne-oxygen 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.
- Publication:
-
Journal of Molecular Structure
- Pub Date:
- August 2019
- DOI:
- 10.1016/j.molstruc.2019.04.056
- Bibcode:
- 2019JMoSt1190...37Z
- Keywords:
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- 5-Octadiynyl-2‧-deoxycytidine;
- Nucleoside;
- Anomer;
- Crystal structure;
- CD-Spectra;
- Hirshfeld surface analysis