Conformation and structure of 9-alpha-D-arabinofuranoxyladenine

The crystal structure of the nucleoside 9-alpha-D-arabinofuranosyladenine (C10H13N5O4) has been determined by means of three-dimensional X-ray counter data. The adenosine analog crystallizes in space group P2(1)2(1)2(1) of the orthorhombic system with eight formula units in a cell of dimensions a, 6.720(5), b, 40.188(35), c, 8.357(8) A. Hence, there are two crystallographically independent molecules in the unit cell. The structure was solved by direct methods and refined by full-matrix least-squares techniques to a final value of the conventional R-factor of 0.076 using 1173 independent intensity data. In the crystal, both independent molecules (A and B) adopt the anti conformation (for an alpha-sugar), with glycosyl torsion angles, chi, of -73 degrees and -64 degrees; these are comparable to values found in other alpha-nucleosides. The conformation about the extracyclic C(4')-C(5') bond is gauche-gauche in both molecules. The sugar pucker is C(2'0-exo-C(3')-endo, 2T3, in molecule A and C(3')-endo, 3E, in molecule B. Conformational analysis of rotation about the N(9)-C(1') glycosyl bond has been performed by use of CNDO/2 molecular orbital calculations. These calculations suggest that the observed conformation may not be the global minimum, but that it lies only 0.4 kcal x mol-1 higher in energy than the global minimum. The highest energy barrier to rotation around the glycosyl bond is calculated to be only 1.1 kcal x mol-1, which is comparable to the value calculated for adenosine.