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Nucleic Acids Research, 1977, Vol. 4, No. 4 929-937
© 1977

Articles

5-Nitrouridine-monohydrate: crystal structure and conformation

Ernst Egert*, Hans-Jorg Lindner*, Wolfgang Hillen+ and Hans Gunter Gassen+

*Fachgebiet Organische Chemie I Technische Hochschule Darmstadt Petersenstr. 22, D-6100 Darmstadt, GFR +Technische Hochschule Darmstadt Petersenstr. 22, D-6100 Darmstadt, GFR

Received February 4, 1977. The crystal structure of 5-nitrouridine was determined by X-ray analysis. The pyrimidine ring is slightly non-planar, showing a shallow boat conformation. The nitro group has no influence on the C4 - 04 bond length as compared to uridine. The ribose shows the C3'-endo conformation and the base is in the anti orientation to the sugar with a torsion angle of 25.6°. This conformation is stabilized by a hydrogen bond from the base to the ribosyl moiety (H6 ... 05'). Stacking interactions between neighboring bases are almost negligible in the crystal. A water molecule is involved in a bifurcated donating hydrogen bond to 04 and to 052 of the nitro group of the one base and an accepting bond from the H3 of the other base. Two- more hydrogen bonds are formed between the water molecule and the ribose. The structural aspects of 5-nitrouridine are discussed with respect to the special stacking features found for 5-ni-tro-1-(ß-D-ribosyluronic acid)-uracil monohydrate in the crystal (1).


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