organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

Redetermination of orotic acid monohydrate

aChemistry Department, `Sapienza' University of Rome, P. le A. Moro 5, I-00185 Rome, Italy
*Correspondence e-mail: g.portalone@caspur.it

(Received 26 February 2008; accepted 27 February 2008; online 5 March 2008)

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[Takusagawa, F. & Shimada, A. (1973). Bull. Chem. Soc. Jpn, 46, 2011-2019.]), 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[Takusagawa, F. & Shimada, A. (1973). Bull. Chem. Soc. Jpn, 46, 2011-2019.]). For a general approach to the use of multiple hydrogen-bonding DNA/RNA nucleobases as potential supra­molecular reagents, see: Portalone et al. (1999[Portalone, G., Bencivenni, L., Colapietro, M., Pieretti, A. & Ramondo, F. (1999). Acta Chem. Scand. 53, 57-68.]); Brunetti et al. (2000[Brunetti, B., Piacente, V. & Portalone, G. (2000). J. Chem. Eng. Data, 45, 242-246.], 2002[Brunetti, B., Piacente, V. & Portalone, G. (2002). J. Chem. Eng. Data, 47, 17-19.]); Portalone & Colapietro (2007[Portalone, G. & Colapietro, M. (2007). Acta Cryst. C63, o650-o654.] and references therein). For the computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]); Motherwell et al. (1999[Motherwell, W. D. S., Shields, G. P. & Allen, F. H. (1999). Acta Cryst. B55, 1044-1056.]).

[Scheme 1]

Experimental

Crystal data
  • C5H4N2O4·H2O

  • Mr = 174.12

  • Triclinic, [P \overline 1]

  • 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[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.977, Tmax = 0.985

  • 64781 measured reflections

  • 2340 independent reflections

  • 2048 reflections with I > 2σ(I)

  • Rint = 0.017

Refinement
  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.133

  • S = 1.08

  • 2340 reflections

  • 133 parameters

  • All H-atom parameters refined

  • Δρmax = 0.19 e Å−3

  • Δρmin = −0.22 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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⋯O3iv 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)
Symmetry codes: (i) -x, -y, -z+2; (ii) -x, -y+1, -z+1; (iii) -x+2, -y, -z+1; (iv) -x+2, -y-1, -z+2.

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

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···O2iv; 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.

Related literature top

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 top

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.

Refinement top

All H atoms were found in a difference map and refined isotropically.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level. Hydrogen bonding is indicated by dashed lines.
[Figure 2] Fig. 2. Crystal packing diagram of (I). All atoms are shown as small spheres of arbitrary radii. Hydrogen bonding is indicated by dashed lines.
2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid monohydrate top
Crystal data top
C5H4N2O4·H2OZ = 2
Mr = 174.12F(000) = 180
Triclinic, P1Dx = 1.690 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.89854 (14) ÅCell parameters from 64781 reflections
b = 6.92921 (15) Åθ = 3.2–32.0°
c = 9.59160 (18) ŵ = 0.15 mm1
α = 74.6778 (12)°T = 298 K
β = 72.3232 (16)°Plate, colourless
γ = 68.447 (2)°0.20 × 0.15 × 0.15 mm
V = 342.21 (1) Å3
Data collection top
Oxford Diffraction Xcalibur S CCD
diffractometer
2340 independent reflections
Radiation source: Enhance (Mo) X-ray source2048 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.017
Detector resolution: 16.0696 pixels mm-1θmax = 32.0°, θmin = 3.2°
ω and ϕ scansh = 88
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
k = 1010
Tmin = 0.977, Tmax = 0.985l = 1414
64781 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.044Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133All H-atom parameters refined
S = 1.08 w = 1/[σ2(Fo2) + (0.0846P)2 + 0.0376P]
where P = (Fo2 + 2Fc2)/3
2340 reflections(Δ/σ)max < 0.001
133 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.22 e Å3
Crystal data top
C5H4N2O4·H2Oγ = 68.447 (2)°
Mr = 174.12V = 342.21 (1) Å3
Triclinic, P1Z = 2
a = 5.89854 (14) ÅMo Kα radiation
b = 6.92921 (15) ŵ = 0.15 mm1
c = 9.59160 (18) ÅT = 298 K
α = 74.6778 (12)°0.20 × 0.15 × 0.15 mm
β = 72.3232 (16)°
Data collection top
Oxford Diffraction Xcalibur S CCD
diffractometer
2340 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
2048 reflections with I > 2σ(I)
Tmin = 0.977, Tmax = 0.985Rint = 0.017
64781 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0440 restraints
wR(F2) = 0.133All H-atom parameters refined
S = 1.08Δρmax = 0.19 e Å3
2340 reflectionsΔρmin = 0.22 e Å3
133 parameters
Special details top

Experimental. Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.14403 (15)0.19593 (14)0.87497 (9)0.0437 (2)
O20.33017 (14)0.40869 (13)0.43298 (8)0.0402 (2)
O30.67729 (18)0.25757 (17)0.92057 (11)0.0575 (3)
O40.94015 (16)0.17721 (14)0.70790 (10)0.0430 (2)
H41.045 (5)0.276 (4)0.759 (3)0.072 (6)*
N10.27952 (15)0.03091 (13)0.83018 (9)0.03108 (19)
H10.248 (4)0.038 (3)0.918 (2)0.052 (4)*
C20.06502 (18)0.17428 (15)0.79307 (10)0.0302 (2)
N30.09988 (15)0.29328 (13)0.65310 (8)0.03059 (19)
H30.050 (4)0.391 (3)0.630 (2)0.054 (5)*
C40.32531 (17)0.28849 (14)0.55477 (10)0.0284 (2)
C50.54286 (17)0.13666 (14)0.60218 (10)0.0295 (2)
H50.689 (3)0.127 (3)0.540 (2)0.042 (4)*
C60.51057 (17)0.01317 (13)0.73716 (9)0.02706 (19)
C70.72006 (19)0.15575 (15)0.79814 (11)0.0325 (2)
O51.28887 (17)0.45822 (16)0.81521 (11)0.0523 (3)
H511.421 (5)0.460 (4)0.757 (3)0.080 (7)*
H521.313 (5)0.528 (4)0.896 (3)0.082 (7)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0285 (4)0.0499 (5)0.0329 (4)0.0054 (3)0.0022 (3)0.0094 (3)
O20.0291 (4)0.0447 (4)0.0298 (4)0.0065 (3)0.0079 (3)0.0154 (3)
O30.0390 (5)0.0612 (6)0.0449 (5)0.0062 (4)0.0138 (4)0.0266 (4)
O40.0302 (4)0.0449 (4)0.0385 (4)0.0003 (3)0.0112 (3)0.0054 (3)
N10.0289 (4)0.0311 (4)0.0247 (3)0.0063 (3)0.0080 (3)0.0067 (3)
C20.0277 (4)0.0308 (4)0.0252 (4)0.0071 (3)0.0065 (3)0.0037 (3)
N30.0245 (4)0.0319 (4)0.0258 (3)0.0047 (3)0.0077 (3)0.0070 (3)
C40.0260 (4)0.0289 (4)0.0244 (4)0.0064 (3)0.0078 (3)0.0041 (3)
C50.0243 (4)0.0308 (4)0.0258 (4)0.0045 (3)0.0072 (3)0.0029 (3)
C60.0268 (4)0.0251 (4)0.0257 (4)0.0045 (3)0.0106 (3)0.0014 (3)
C70.0306 (4)0.0297 (4)0.0322 (4)0.0049 (3)0.0137 (3)0.0038 (3)
O50.0287 (4)0.0598 (6)0.0426 (5)0.0010 (4)0.0082 (3)0.0118 (4)
Geometric parameters (Å, º) top
O1—C21.2241 (12)N3—C41.3716 (12)
O2—C41.2418 (10)N3—H30.94 (2)
O3—C71.2056 (13)C4—C51.4387 (12)
O4—C71.3040 (13)C5—C61.3525 (12)
O4—H40.89 (3)C5—H50.879 (19)
N1—C61.3656 (12)C6—C71.5012 (12)
N1—C21.3702 (12)O5—H510.81 (3)
N1—H10.85 (2)O5—H520.82 (3)
C2—N31.3772 (11)
C7—O4—H4104.3 (16)N3—C4—C5115.74 (8)
C6—N1—C2122.36 (8)C6—C5—C4118.56 (8)
C6—N1—H1126.4 (14)C6—C5—H5124.1 (11)
C2—N1—H1111.2 (14)C4—C5—H5117.3 (11)
O1—C2—N1123.81 (8)C5—C6—N1122.13 (8)
O1—C2—N3121.35 (8)C5—C6—C7124.03 (9)
N1—C2—N3114.83 (8)N1—C6—C7113.84 (8)
C4—N3—C2126.29 (7)O3—C7—O4125.70 (9)
C4—N3—H3120.3 (12)O3—C7—C6120.28 (10)
C2—N3—H3113.3 (12)O4—C7—C6114.02 (8)
O2—C4—N3119.61 (8)H51—O5—H52110 (2)
O2—C4—C5124.64 (9)
C6—N1—C2—O1178.86 (10)C4—C5—C6—N11.20 (15)
C6—N1—C2—N32.20 (15)C4—C5—C6—C7178.02 (9)
O1—C2—N3—C4177.12 (10)C2—N1—C6—C50.18 (16)
N1—C2—N3—C43.91 (15)C2—N1—C6—C7179.11 (9)
C2—N3—C4—O2178.17 (10)C5—C6—C7—O3178.85 (12)
C2—N3—C4—C52.97 (15)N1—C6—C7—O31.87 (15)
O2—C4—C5—C6179.05 (10)C5—C6—C7—O41.13 (15)
N3—C4—C5—C60.26 (14)N1—C6—C7—O4178.15 (9)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···O50.89 (3)1.65 (3)2.5231 (11)166 (2)
N1—H1···O1i0.85 (2)2.03 (2)2.8824 (11)175.2 (19)
N3—H3···O2ii0.94 (2)1.87 (2)2.8112 (11)174.6 (18)
O5—H51···O2iii0.81 (3)2.00 (3)2.7786 (12)161 (3)
O5—H52···O3iv0.82 (3)1.98 (3)2.7787 (12)164 (2)
C5—H5···O4iii0.879 (19)2.740 (19)3.5922 (13)163.7 (15)
Symmetry codes: (i) x, y, z+2; (ii) x, y+1, z+1; (iii) x+2, y, z+1; (iv) x+2, y1, z+2.

Experimental details

Crystal data
Chemical formulaC5H4N2O4·H2O
Mr174.12
Crystal system, space groupTriclinic, P1
Temperature (K)298
a, b, c (Å)5.89854 (14), 6.92921 (15), 9.59160 (18)
α, β, γ (°)74.6778 (12), 72.3232 (16), 68.447 (2)
V3)342.21 (1)
Z2
Radiation typeMo Kα
µ (mm1)0.15
Crystal size (mm)0.20 × 0.15 × 0.15
Data collection
DiffractometerOxford Diffraction Xcalibur S CCD
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2006)
Tmin, Tmax0.977, 0.985
No. of measured, independent and
observed [I > 2σ(I)] reflections
64781, 2340, 2048
Rint0.017
(sin θ/λ)max1)0.745
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.133, 1.08
No. of reflections2340
No. of parameters133
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.19, 0.22

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···O50.89 (3)1.65 (3)2.5231 (11)166 (2)
N1—H1···O1i0.85 (2)2.03 (2)2.8824 (11)175.2 (19)
N3—H3···O2ii0.94 (2)1.87 (2)2.8112 (11)174.6 (18)
O5—H51···O2iii0.81 (3)2.00 (3)2.7786 (12)161 (3)
O5—H52···O3iv0.82 (3)1.98 (3)2.7787 (12)164 (2)
C5—H5···O4iii0.879 (19)2.740 (19)3.5922 (13)163.7 (15)
Symmetry codes: (i) x, y, z+2; (ii) x, y+1, z+1; (iii) x+2, y, z+1; (iv) x+2, y1, z+2.
 

Acknowledgements

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

References

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