2'-Deoxycytidine-N(3)-cyanoborane Monohydrate

Abstract

The structure of the title compound, [4-amino-l-(2-deoxy-fl-D-ribofuranosyl)-2-oxo-1H-3-pyrimidinio]-(cyano)borate, C10H15BNnOa.H20, features an interaction of 2.05 (4)/k between an H atom of the --BH2CN group and an H atom of the --NH2 group. The ~N group does not lie in the cytosine plane, the N atom being 2.24 ,~ away from the plane. The cytosine tings are stacked with almost complete overlap along the twofold screw axis with an interplanar separation of 4.03/~. The sugar is in the ~T puckering mode, the C(5')--O(5') bond has the gg conformation and the relative orientation of the sugar and the base is anti.In order to provide more insight into the structureactivity relationships of cyanoborane nucleosides we have started a program of research on the structure of these nucleosides using X-ray diffraction and ab initio molecular-orbital (MO) calculations. The title nucleoside has been crystallized in a different crystal system by Gao, Sood, Shaw & Williams (1996). Some of the X-ray results described here have been used recently in theoretical computations on intramolecular non-bonded H...H interactions between the mNH2 and mBH2CN group H atoms (Zottola, Pedersen, Singh & Shaw, 1994).The The pyrimidine ring is planar, although the deviations of the atoms from the mean plane are somewhat CommentCyanoborane analogs of 2'-deoxynucleosides such as the title compound, (I), show in vivo antineoplastic activity against various tumors (Sood, Spielvogel & Shaw, 1989;Sood, Spielvogel, Shaw, Carlton, Burnham, Hall & Hall, 1992). In addition, the title compound has potential use in boron neutron-capture therapy (BNCT) since it tends to concentrate quite effectively in rapidly divid'.mg cancer cells (Sood et al., 1992). The BNCT technique has been used recently in the treatment of brain cancer (see, for example, Science, 17 February 1995, Vol. 267, p. 956 and 23 September 1994, Vol. 265, p. 1799). (Johnson, 1965) drawing of the nucleoside showing 50% probability displacement ellipsoids and the atom-numbering scheme. H atoms are shown as small circles of arbitrary size.

Dihydrogen Bonding: Structures, Energetics, and Dynamics

“…The N−H···H−B dihydrogen bonding can also form intramolecularly, as found in the crystal structure of the 2‘-deoxycytidine- N (3)-cyanoborane ( 1 ), which shows a close H···H contact of 2.05 Å. ,

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“…26 The N-H‚‚‚H-B dihydrogen bonding can also form intramolecularly, as found in the crystal structure of the 2′-deoxycytidine-N(3)-cyanoborane (1), which shows a close H‚‚‚H contact of 2.05 Å. 27,28 Intramolecular C-H‚‚‚H-B close contacts are present in the aminoboron hydrides 2-6, which could be responsible for the stabilization against disproportionation in these complexes. 29 Their X-ray crystal structures show multiple H-H distances below 2.65 Å, which was considered the threshold intermolecular distance for H‚‚‚H interactions in this study.…”