Abstract
β-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric α-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of α-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of α-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with χ = 173.4 (2)°, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist (23T; S-type), with P = 179.7°. Both values lie outside the conformational range usually preferred by α-nucleosides. In addition, the amino group at the nucleobase shows partial double-bond character. This is supported by two separated signals for the amino protons in the 1H NMR spectrum, indicating a hindered rotation around the C4-N4 bond and a relatively short C-N bond in the solid state. Crystal packing is controlled by N-H...O and O-H...O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H...N contacts (C1'-H1' and C3'-H3'A) are observed. A Hirshfeld surface analysis was carried out and the results support the intermolecular interactions observed by the X-ray analysis.
Highlights
Nucleosides with an -configuration at the anomeric carbon are seldom found in nature (Ni et al, 2019). -Nucleosides are not building blocks of naturally occurring DNA or RNA
-nucleosides have been isolated as constituents of small molecules in living cells, such as vitamin B12 (Bonnett, 1963) or a nicotinamide adenine dinucleotide (NAD) derivative isolated from Azobacter vinelandii (Suzuki et al, 1965)
Strong interactions are found for OÁ Á ÁH/HÁ Á ÁO (31.2%) and NÁ Á ÁH/HÁ Á ÁN (13.4%), which agrees with the fact that the crystal packing of -dC (1) is largely controlled by N—HÁ Á ÁO and O—HÁ Á ÁO hydrogen bonds (Table 3)
Summary
Nucleosides with an -configuration at the anomeric carbon are seldom found in nature (Ni et al, 2019). -Nucleosides are not building blocks of naturally occurring DNA or RNA. Protocols were developed for the stereoselective synthesis of -d nucleosides or by anomerization of -d anomers. This topic has been reviewed recently by Ni et al (2019). We reported on the stability and recognition of silver-mediated heterochiral DNA with complementary / strands (Chai et al, 2020). Conformational studies on -nucleosides revealed distinct differences compared to their -anomeric counterparts (Sundaralingam, 1971; Latha & Yathindra, 1992). The different conformational properties of the / -anomers were attributed to the differences in the steric interactions between the nucleobase and the sugar moiety (Sundaralingam, 1971; Latha & Yathindra, 1992). Computer programs: SAINT (Bruker, 2015), SHELXS2014 (Sheldrick, 2015a), SHELXL2014 (Sheldrick, 2015b), APEX3 (Bruker, 2016) and XP (Bruker, 1998)
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