10-Methylisoalloxazine 5-oxide from synchrotron powder diffraction data

The title compound [systematic name: 10-methylbenzo[g]pteridine-2,4(3H,10H)-dione 5-oxide], C11H8N4O3, consists of a large rigid isoalloxazine group which is approximately planar (r.m.s. deviation = 0.037 Å). In the crystal, intermolecular N—H⋯O hydrogen bonds link the molecules into centrosymmetric dimers. Dimers related by translation along the c axis form stacks through π–π interactions [centroid–centroid distances = 3.560 (5) and 3.542 (5) Å]. Weak intermolecular C—H⋯O interactions further consolidate the crystal packing.

The asymmetric unit contains one molecule of the title compound, which is almost planar. The molecule consists of a isoalloxazine group which is formed by three connected rings -benzene, pyrazine and uracil ring. The most significant deviation from planarity occurs at the uracil ring, where the oxygen atom O12 is found to be out of the plane (torsion angle C10a-C4a-C4-O12 is app. 6.5°). The deviation of O12 atom is in accordance with the C4 carbon atom position which is slightly out of the plane and form the planar sp 2 hybridization. The next deviation from planarity is on the pyrazine ring where the nitrogen atom N10 leaves out of the plane and the connected methyl group follow the direction of sp 2 hybridization (torsion angle C4a-C10a-N10-C14 is app. 5.5°). Molecules of titled compound are connected together by several hydrogen bonds (Table 2) and by π-π interactions ( Table 1). The strongest hydrogen bond N3-H1N3···O11 connects always two molecules together into dimers, see Fig. 2. On the other hand, the other two hydrogen bonds C14-H1C14···O13 and C14-H2C14···O12 together with π-π interactions form molecules to the infinity layers which are parallel to (100). These layers are connected by the above mentioned N3-H1N3···O11 hydrogen bonds.
The survey in the CSD (Allen, 2002) found several crystal structures of similar molecules which are derived from isoalloxazine, but no crystal structure of isoalloxazine-5-oxide which we present here was found. The similar crystal structures of 10-Methylisoalloxazine (Wang & Fritchie, 1973) and 7,10-Dimethylisoalloxazine (Farrán et al., 2007) can be used for comparison. In both structures the isoalloxazine part is approximately planar and both structures form dimers which are connected by N-H···O hydrogen bonds. The occurrence of the π-π stacking is also evident.

Experimental
The title compound was prepared according to Yoneda et al. (1976). The 6-(N-Methylanilino)uracil (15.6 g; 65 mmol) was dissolved in acetic acid (130 ml) and sodium nitrite ( supplementary materials sup-2 The X-Ray diffraction data were collected on the Rossendorf Beamline BM20 at the ESRF in Grenoble. The energy was fixed at 14 keV which is equal to λ=0.8856 Å wavelength (the precise wavelength value was confirmed by the LaB 6 standard measurement). The beamline was equipped with double-crystal Si(111) monochromator and with two collimating/focusing mirrors (Si and Pt-coating). The sample was placed in the 1-mm-borosilicate glass capillary rotated during the measurement. The diffraction pattern was measured at room temperature from 4° 2θ to 36.5° 2θ with the 0.01° 2θ step size.
If the volume of the molecule is compared with the volume of the found unit, it is clear that there are four molecules in the unit cell. The space group P2 1 /a (Z = 4) was selected according to the peak extinction and the agreement of the Le-bail fit.
The crystal structure was solved by parallel tempering algorithm implemented in the program FOX (Favre-Nicolin & Černý, 2002). We decided to test the structure solution run for other space groups which had similar peak extinction to validate the selection of the P21/a space group. These two space groups P 2/m and P21/m were selected, but the solution was not found.
The final refinement was performed with GSAS (Larson & Von Dreele, 1994). The structure was restrained by soft bonds and angles restraints. Four planar groups restraints were added -one for the benzene ring (C5a-C9a) and remaining three for the sp 2 hybridization (C2/N1/N3/O11, C4a/C4/N3/O12 and C10a/C4a/C4/N5). At the final stage, positions and isotropic thermal parameters of all non-hydrogen atoms were refined to the low agreement R-factors (R p = 4.2%, R wp = 5.6%). During the refinement all hydrogen atoms were kept in their theoretical positions and were not refined. The final Rietveld plot is shown on the Fig. 3. Fig. 1. ORTEP plot of the title molecule with the displacement ellipsoids drawn at the 50% probability level. The H atoms are shown as spheres of arbitrary radius.