Structures of the 1-(2-deoxy-2-fluoro-<script type="math/tex">\beta</script>-D-arabinopyranosyl)thymine-water complex and 1-(2-deoxy-2-fluoro-<script type="math/tex">\beta</script>-D-arabinopyranosyl)-5-ethyluracil

De Winter, H.L.; Blaton, N.M.; Peeters, O.M.; De Ranter, C.J.; Van Aerschot, A.; Herdewijn, P.

doi:10.1107/S0108270190014184

Title

Structures of the 1-(2-deoxy-2-fluoro- $\beta$ -D-arabinopyranosyl)thymine-water complex and 1-(2-deoxy-2-fluoro- $\beta$ -D-arabinopyranosyl)-5-ethyluracil

Author

De Winter, H.L.

Blaton, N.M.

Peeters, O.M.

De Ranter, C.J.

Van Aerschot, A.

Herdewijn, P.

Abstract

(I) 1-(2-Deoxy-2-fluoro-beta-D-arabinopyranosyl)thymine-water complex, C10H13FN2O5.H2O, M(r) = 278.24, monoclinic, P2(1), a = 8.669 (4), b = 6.395 (3), c = 10.713 (7) angstrom, beta = 103.73 (5)-degrees, V = 576.9 (6) angstrom 3, Z = 2, D(m) = 1.60, D(x) = 1.602 Mg m-3, graphite-monochromated Mo K-alpha radiation, lambda = 0.71069 angstrom, mu = 0.134 mm-1, F(000) = 292, room temperature, final R = 0.030 for 1307 unique observed [F greater-than-or-equal-to 4-sigma(F)] reflections. (II) 1-(2-Deoxy-2-fluoro-beta-D-arabinopyranosyl)-5-ethyluracil, C11H15FN2O5, M(r) = 274.25, hexagonal, P6(5), a = 10.108 (7), c = 19.48 (1) angstrom, V = 1724 (2) angstrom 3, Z = 6, D(m) = 1.54, D(x) = 1.585 Mg m-3 graphite-monochromated Mo K-alpha radiation, lambda = 0.71069 angstrom, mu = 0.127 mm-1, F(000) = 864, room temperature, final R = 0.026 for 694 unique observed [F greater-than-or-equal-to 4-sigma(F)] reflections. The geometries of molecules (I) and (II) show a close similarity. In both structures the sugar ring adopts a slightly distorted chair conformation and for both molecules the fluorine and one of the hydroxyl substituents are placed in an axial position on the ring. The N-glycosidic torsion angle chi between the pyranose ring and the pyrimidine base is oriented -ac for both molecules. The terminal C of the ethyl group in (II) deviates from the base least-squares plane. The packing in both crystals is determined by intermolecular hydrogen bonds and base-stacking forces. In (I) the solvent water is kept from being disordered by a dense network of strong hydrogen bonds. In (II) the molecules are packed in such a way that a single stranded left-handed helix is formed which resembles the structure of the 61 poly(2'-O-methylcytidine) single stranded helix. No intramolecular hydrogen bonds are present. The conformational parameters are in accordance with the IUPAC-IUB Joint Commission on Biochemical Nomenclature (1983) guidelines.

Language

English

Source (journal)

Acta crystallographica: section C: crystal structure communications. - Copenhagen

Publication

Copenhagen : 1991

ISSN

0108-2701

DOI

10.1107/S0108270190014184

Volume/pages

47 :8 (1991) , p. 1693-1697