Redetermination of orotic acid monohydrate

Gustavo Portalone

doi:10.1107/S160053680800562X

. 2008 Mar 5;64(Pt 4):o656. doi: 10.1107/S160053680800562X

Redetermination of orotic acid monohydrate

Gustavo Portalone ^a,^*

PMCID: PMC2961056 PMID: 21202053

Abstract

The crystal structure of the title compound, which is also known as vitamin B₁₃ (systematic name: 2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid monohydrate), C₅H₄N₂O₄·H₂O, was reported for the first time by Takusagawa & Shimada [Bull. Chem. Soc. Jpn (1973 ▶), 46, 2011–2019]. The present redetermination provides more precise values of the molecular geometry. The asymmetric unit comprises a planar diketo tautomer and a solvent water molecule. In the crystal structure, molecules are connected by O—H⋯O, N—H⋯O and C—H⋯O hydrogen bonds involving NH groups, two carbonyl O atoms and the solvent water molecule.

Related literature

For the previous structure determination, see: Takusagawa & Shimada (1973 ▶). For a general approach to the use of multiple hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents, see: Portalone et al. (1999 ▶); Brunetti et al. (2000 ▶, 2002 ▶); Portalone & Colapietro (2007 ▶ and references therein). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990 ▶); Bernstein et al. (1995 ▶); Motherwell et al. (1999 ▶).

Experimental

Crystal data

C₅H₄N₂O₄·H₂O
M _r = 174.12
Triclinic,
a = 5.89854 (14) Å
b = 6.92921 (15) Å
c = 9.59160 (18) Å
α = 74.6778 (12)°
β = 72.3232 (16)°
γ = 68.447 (2)°
V = 342.21 (1) Å³
Z = 2
Mo Kα radiation
μ = 0.15 mm⁻¹
T = 298 (2) K
0.20 × 0.15 × 0.15 mm

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 ▶) T _min = 0.977, T _max = 0.985
64781 measured reflections
2340 independent reflections
2048 reflections with I > 2σ(I)
R _int = 0.017

Refinement

R[F ² > 2σ(F ²)] = 0.044
wR(F ²) = 0.133
S = 1.08
2340 reflections
133 parameters
All H-atom parameters refined
Δρ_max = 0.19 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP3 (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶).

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S160053680800562X/kp2160sup1.cif

e-64-0o656-sup1.cif^{(14.1KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S160053680800562X/kp2160Isup2.hkl

e-64-0o656-Isup2.hkl^{(112.6KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H4⋯O5	0.89 (3)	1.65 (3)	2.5231 (11)	166 (2)
N1—H1⋯O1ⁱ	0.85 (2)	2.03 (2)	2.8824 (11)	175.2 (19)
N3—H3⋯O2ⁱⁱ	0.94 (2)	1.87 (2)	2.8112 (11)	174.6 (18)
O5—H51⋯O2ⁱⁱⁱ	0.81 (3)	2.00 (3)	2.7786 (12)	161 (3)
O5—H52⋯O3^iv	0.82 (3)	1.98 (3)	2.7787 (12)	164 (2)
C5—H5⋯O4ⁱⁱⁱ	0.879 (19)	2.740 (19)	3.5922 (13)	163.7 (15)

Open in a new tab

Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

The author thanks MIUR (Rome) for financial support in 2006 of the project ‘X-ray diffractometry and spectrometry’.

supplementary crystallographic information

Comment

Orotic acid monohydrate, the only effective precursor in the biosynthesis of pyrimidine nucleobases, was determined some 35 years ago (Takusagawa & Shimada, 1973). In this study, 1488 unique reflections were collected at an ambient temperature by photographic techniques using Cu Kα radiation. 1344 of these, having values significantly above background, were estimated visually and no absorption correction was applied [µ(Cu Kα) = 15.4 cm^-1]. The final refinement led to R = 0.058 with standard deviations of 0.005Å in C—C bond lengths, As a part of a more general study of multiple hydrogen-bonded DNA/RNA-nucleobases as potential supramolecular reagents (Brunetti et al., 2000, 2002; Portalone et al., 1999; Portalone & Colapietro, 2007), this paper reports a redetermination of the crystal structure of the title compound, (I), with greater precision and accuracy. The asymmetric unit of (I) (Fig. 1) comprises a planar diketo tautomer and a crystal water molecule. The analysis of the crystal packing of (I) shows five N—H···O and O—H···O intermolecular hydrogen bonds (Table 1) which link the molecules into planar layers (Fig. 2). Two kinds of inversion-related N—H···O hydrogen bonds with graph-set motifs R²₂(8) (Etter et al., 1990; Bernstein et al., 1995; Motherwell et al., 1999) (Table 1) are formed between NH groups and two carbonyl O atoms (O1ⁱ and O2ⁱⁱ) [symmetry code: (i) -x, -y, z + 2; (ii) -x, -y + 1, -z + 1] to give a zigzag chain. Each chain is joined by three O—H···O intermolecular hydrogen bonds to form rings of descriptor R⁴₄(12), R⁴₃(13) and R⁴₄(18) through a water molecule (O4—H4···O5, O5—H51···O2ⁱⁱⁱ and O5—H52···O2^iv; symmetry code: (iii) -x + 2, -y, -z + 1; (iv) -x + 2, -y - 1, -z + 2). The hydrogen-bonded two-dimensional array involves the C5—H5···O4ⁱⁱⁱ intermolecular interaction.

Experimental

The title compound (0.1 mmol, Sigma Aldrich of 98% purity) was dissolved in water (9 ml) and heated under reflux for 2 h. After cooling the solution to ambient temperature, crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation.