Crystal structure of N′-hydroxypyrimidine-2-carboximidamide

The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The molecule adopts an E configuration about the C=N double bond. In the crystal, adjacent molecules are linked by pairs of N—H⋯O hydrogen bonds, forming inversion dimers with an R 2 2(10) ring motif. The dimers are further linked via N—H⋯N and O—H⋯N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N—H⋯O and weak C—H⋯O hydrogen bonds and offset π–π stacking interactions between adjacent pyrimidine rings [centroid–centroid distance = 3.622 (1) Å].


Crystal structure of N′-hydroxypyrimidine-2-carboximidamide
Nithianantham Jeeva Jasmine, Packianathan Thomas Muthiah and Nithianantham Stanley S1. Comment Supramolecular architectures assembled via various delicate noncovalent interactions such as hydrogen bonds, π-π stacking and electrostatic interactions, have attracted intense interest in recent years because of their fascinating structural diversity and potential applications for functional materials (Desiraju, 2007). In particular, the application of intermolecular hydrogen bonding is a well known and efficient tool in the field of organic crystal design owing to their strength and directional properties (Aakeroy & Seddon, 1993). Substituted N′-hydroxybenzamidines are important intermediates obtained during the synthesis of pharmaceuticaly important 1,2,4-oxadiazole derivatives (Kundu et al., 2012). 1,2,4-oxadiazole derivatives are well known for their biological activities such as for anti-HIV (Sakamoto et al., 2007) and anti-microbial applications (Tyrkov & Sukhenko, 2004). Herein, we report the crystal structure determination of the title compound, (I).
The asymmetric unit of the title compound is shown in Fig. 1. The essentially planar pyrimidine ring [N1/N2/C1-C4, maximum deviation of 0.009 (2) Å at atom C4] forms a dihedral angle of 11.04 (15)° with the hydroxyacetimidamide (N4/C5/N3/O1). The compound adopts an E configuration across the C5═N3 double bond, as the OH group and benzene ring are on opposite sides of the double bond while the hydrogen atom of the hydroxy group is directed away from the NH 2 group. The bond lengths and angles are within normal ranges.

S2. Experimental
A hot methanol solution (20 ml) of N′-hydroxypyrimidine-2-carboximidamide (69 mg, Aldrich) was warmed over a magnetic stirrer hotplate for a few minutes. The resulting solution was allowed to cool slowly at room temperature.
Single crystals of the title compound (I) appeared from the mother liquor after a few days.  The molecular structure of the title compound with atom labels. Displacement ellipsoids are shown at the 50% probability level.

Figure 2
The crystal packing of the title compound viewed along the b axis die=rection. H atoms not involved in intermolecular interactions (dashed lines) have been omitted for clarity. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger. Symmetry codes: (i) −x+2, −y+1, −z; (ii) x, −y+1/2, z−1/2; (iii) −x+2, y+1/2, −z+1/2; (iv) x, y−1, z.