The alpha-D-anomer of 2 `-deoxycytidine: crystal structure, nucleoside conformation and Hirshfeld surface analysis

Autor(en): Budow-Busse, Simone
Chai, Yingying
Mueller, Sebastian Lars
Daniliuc, Constantin
Seela, Frank
Stichwörter: alpha-2 `-deoxycytidine; ALPHA-<D(CPAPTPGPCPG)>; anomer; Chemistry; Chemistry, Multidisciplinary; crystal packing; crystal structure; Crystallography; DISCOVERY; H-1-NMR; Hirshfeld surface analysis; MOLECULAR-STRUCTURE; nucleic acid chemistry; NUCLEOTIDES; STABILITY
Erscheinungsdatum: 2021
Herausgeber: INT UNION CRYSTALLOGRAPHY
Journal: ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY
Volumen: 77
Ausgabe: 5
Startseite: 202+
Zusammenfassung: 
beta-2'-Deoxyribonucleosides are the constituents of nucleic acids, whereas their anomeric alpha-analogues are rarely found in nature. Moreover, not much information is available on the structural and conformational parameters of alpha-2'-deoxyribonucleosides. This study reports on the single-crystal X-ray structure of alpha-2'-deoxycytidine, C9H13N3O4 (1), and the conformational parameters characterizing 1 were determined. The conformation at the glycosylic bond is anti, with chi = 173.4 (2)degrees, and the sugar residue adopts an almost symmetrical C2'-endo-C3'-exo twist ((2)(3) T; S-type), with P = 179.7 degrees. Both values lie outside the conformational range usually preferred by alpha-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 H-1 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 center dot center dot center dot O and O-H center dot center dot center dot O contacts between the nucleobase and sugar moieties. Moreover, two weak C-H center dot center dot center dot 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.
ISSN: 20532296
DOI: 10.1107/S2053229621003430

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