Redetermination of 3-deazauracil

The crystal structure of the title compound, 4-hydroxy-2-pyridone, C5H5NO2, which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, 1688–1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of π-electron density through the molecule. In the crystal structure, the molecules are connected into chains by two strong O—H⋯O and N—H⋯O hydrogen bonds between the OH and NH groups and the carbonyl O atom.

The crystal structure of the title compound, 4-hydroxy-2pyridone, C 5 H 5 NO 2 , which has been the subject of several determinations using X-rays and neutron diffraction, was first reported by Low & Wilson [Acta Cryst. (1983). C39, [1688][1689][1690]. It has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a planar 4-enol tautomer having some degree of delocalization of -electron density through the molecule. In the crystal structure, the molecules are connected into chains by two strong O-HÁ Á ÁO and N-HÁ Á ÁO hydrogen bonds between the OH and NH groups and the carbonyl O atom.

Comment
The crystal structure of the modified nucleic acid base 3-deazauracil, 3deazur, has been the subject of several structural studies using XD and ND techniques in order to localise the H atoms as accurately as possible and to define their functions; the very strong hydrogen bond is found in the structure, as also observed in the parent nucleoside (3-deazauridine) (Schwalbe & Saenger, 1973). This interaction might play a relevant role in the powerful cytostatic properties of the nucleoside (Robins et al., 1969). In the first crystal structure determination (XRD, Low & Wilson, 1983) 713 unique reflections were collected at ambient temperature on an automatic diffractometer. H atoms were localized by a difference Fourier map with the exception of the hydroxyl H2, and all but H1, which was fixed at its position as obtained from the difference map, were included as riding atoms at calculated positions. The final refinement led to R = 0.065, and standard deviations of 0.004Å in C-C bond lengths and 0.3° in bond angles. Subsequently, a joint X-ray and neutron diffraction blocked-matrix refinement, based on limited neutron single-crystal data (80) combined with 674 X-ray data, was reported (X-N, Wilson et al., 1992). This calculation, involving 94 refined parameters with all but the H atoms treated anisotropically, led to R = 0.075. Two years later, in a pulsed neutron single-crystal study (PND, Wilson, 1994), 119 parameters and 447 unique reflections [with I > 5σ(I)] yielded an R = 0.071, with a poor agreement between the geometrical parameters obtained from this and the previous experiments (e.g. the N1-C2 bond distance is 1.332 (6) in PND, 1.362 (6) in X-N and 1.360 (4) in XRD, Table 2). Finally, in a neutron single-crystal diffraction experiment at 100 K using a sample containing one crystal of 3-deazauracil and one of lead hydrogen arsenate (LTND, Wilson, 2001). 118 parameters and 1426 unique reflections [with I > 2σ(I)] yielded an R = 0.078. Again, some discrepancies between the geometrical parameters from this study and those from the previous structural determinations remain unsolved (e.g. the C4-O2 bond distance is 1.322 (4) in LTND, 1.345 (8) in PND, 1.346 (5) in X-N and 1.319 (3) in XRD, Table 2). and it was suggested the presence of tautomeric mixing.
As a part of a more general study of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents (Portalone et al., 1999;Portalone & Colapietro, 2004, 2007, and in view of the importance of the title compound, this paper reports a redetermination of the crystal structure with greater precision and accuracy. The asymmetric unit of (I) comprises a planar independent molecule as 4-enol tautomer (Fig. 1). A comparison of the molecular geometry of 3-deazur (high θ refinement) with that reported for uracil (Stewart & Jensen, 1967), in conjunction with a detailed examination of Fourier maps, exclude the presence of tautomeric mixing (4-enol and 2-enol tautomers) and suggests some degree of delocalization of π-electron density through the 4-enol tautomer, which in turn strengthens the existing intermolecular hydrogen bonds (Portalone et al., 1999). Analysis of the crystal packing of (I) shows (Table 1) that the structure is stabilized by two strong independent intermolecular O-H···O and N-H···O interactions of descriptor C 1 1 (3) (Etter et al., 1990;Bernstein et al., 1995;Motherwell et al., 1999) between OH and NH moieties and the carbonyl O atom (O1 i and O1 ii ) [symmetry code: (i) -x + 1, y -1/2, -z + 3/2; (ii) x + 1/2, -y + 1/2, -z + 2] which link the molecules into chains (Fig. 2).
supplementary materials sup-2 Experimental 3-deazauracil (0.1 mmol, Sigma Aldrich at 97% purity) was dissolved in water (9 mL) and heated under reflux for 3 h. After cooling the solution to an ambient temperature, crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of a solvent after a few days.
H atoms were kept fixed at values deduced from the conventional refinement. In the absence of significant anomalous scattering in this light-atom study, Friedel pairs were merged.
Figures Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level.