Acta Cryst. (2008). E64, o365 [ doi:10.1107/S1600536807068043 ]
The title compound (systematic name: 2,4-dihydroxy-5-iodopyrimidine), C4H3IN2O2, which was first reported by Sternglanz, Freeman & Bugg [Acta Cryst. (1975), B31, 1393-1395], has been redetermined, providing a significant increase in the precision of the derived geometric parameters. The asymmetric unit comprises a non-planar molecule in a slightly distorted B25 boat conformation. The molecules are associated in the crystal structure to form ribbons stabilized by N-H
O hydrogen bonds which involve NH groups and two carbonyl O atoms.
The title compound (0.1 mmol, Sigma Aldrich at 98% purity) was dissolved in water (6 ml) and heated under reflux for 1 h. After cooling the solution to ambient temperature, crystals suitable for single-crystal X-ray diffraction were grown by slow evaporation of the solvent.
The H atoms were included in the riding model approximation with C—H = 0.96 Å and N—H = 0.86–0.88 Å, and with refined isotropic displacement parameters.
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, 1997); molecular graphics: WinGX (Farrugia, 1999); software used to prepare material for publication: WinGX (Farrugia, 1999).
![[Figure 1]](./tk2237fig1thm.gif)
| Fig. 1. The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level. |
![[Figure 2]](./tk2237fig2thm.gif)
| Fig. 2. Crystal packing diagram for (I) viewed approximately down c. All atoms are shown as small spheres of arbitrary radii. For the sake of clarity, H atoms not involved in hydrogen bonding have been omitted. Hydrogen bonding is indicated by dashed lines. |
| C4H3IN2O2 | F000 = 220 |
| Mr = 237.98 | Dx = 2.548 Mg m−3 |
| Monoclinic, P21 | Mo Kα radiation λ = 0.71069 Å |
| Hall symbol: P 2yb | Cell parameters from 29638 reflections |
| a = 4.89650 (18) Å | θ = 2.9–32.4º |
| b = 4.45921 (13) Å | µ = 5.08 mm−1 |
| c = 14.2167 (2) Å | T = 298 (2) K |
| β = 92.341 (2)º | Tablets, colourless |
| V = 310.157 (15) Å3 | 0.40 × 0.20 × 0.10 mm |
| Z = 2 |
| Oxford Diffraction Xcalibur S CCD diffractometer | 2127 independent reflections |
| Radiation source: Enhance (Mo) X-ray source | 1803 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.049 |
| Detector resolution: 16.0696 pixels mm-1 | θmax = 32.4º |
| T = 298(2) K | θmin = 2.9º |
| ω and φ scans | h = −7→7 |
| Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm | k = −6→6 |
| Tmin = 0.252, Tmax = 0.602 | l = −21→21 |
| 48636 measured reflections |
| Refinement on F2 | Hydrogen site location: inferred from neighbouring sites |
| Least-squares matrix: full | H-atom parameters constrained |
| R[F2 > 2σ(F2)] = 0.025 | w = 1/[σ2(Fo2) + (0.0471P)2 + 0.0442P] where P = (Fo2 + 2Fc2)/3 |
| wR(F2) = 0.071 | (Δ/σ)max = 0.002 |
| S = 1.04 | Δρmax = 0.38 e Å−3 |
| 2127 reflections | Δρmin = −0.03 e Å−3 |
| 86 parameters | Extinction correction: none |
| 1 restraint | Absolute structure: Flack (1983), 934 Friedel pairs |
| Primary atom site location: structure-invariant direct methods | Flack parameter: −0.01 (2) |
| Secondary atom site location: difference Fourier map |
| C4H3IN2O2 | V = 310.157 (15) Å3 |
| Mr = 237.98 | Z = 2 |
| Monoclinic, P21 | Mo Kα |
| a = 4.89650 (18) Å | µ = 5.08 mm−1 |
| b = 4.45921 (13) Å | T = 298 (2) K |
| c = 14.2167 (2) Å | 0.40 × 0.20 × 0.10 mm |
| β = 92.341 (2)º |
| Oxford Diffraction Xcalibur S CCD diffractometer | 2127 independent reflections |
| Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm | 1803 reflections with I > 2σ(I) |
| Tmin = 0.252, Tmax = 0.602 | Rint = 0.049 |
| 48636 measured reflections |
| R[F2 > 2σ(F2)] = 0.025 | H-atom parameters constrained |
| wR(F2) = 0.071 | Δρmax = 0.38 e Å−3 |
| S = 1.04 | Δρmin = −0.03 e Å−3 |
| 2127 reflections | Absolute structure: Flack (1983), 934 Friedel pairs |
| 86 parameters | Flack parameter: −0.01 (2) |
| 1 restraint |
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. |
| x | y | z | Uiso*/Ueq | ||
| I1 | 0.75060 (5) | 0.9092 | 0.595431 (10) | 0.05858 (9) | |
| O1 | 0.7917 (3) | 0.3946 (8) | 0.99376 (14) | 0.0427 (4) | |
| O2 | 0.4156 (4) | 1.0571 (5) | 0.78388 (17) | 0.0399 (4) | |
| N1 | 0.9717 (4) | 0.4223 (8) | 0.84883 (14) | 0.0309 (3) | |
| H1 | 1.097 | 0.289 | 0.8642 | 0.037 (9)* | |
| C2 | 0.7939 (5) | 0.5077 (6) | 0.91511 (19) | 0.0295 (4) | |
| N3 | 0.6128 (4) | 0.7269 (5) | 0.88650 (15) | 0.0291 (4) | |
| H3 | 0.5025 | 0.7887 | 0.9279 | 0.058 (12)* | |
| C4 | 0.5871 (4) | 0.8604 (5) | 0.79868 (16) | 0.0279 (5) | |
| C5 | 0.7757 (5) | 0.7440 (6) | 0.73108 (17) | 0.0310 (4) | |
| C6 | 0.9626 (5) | 0.5361 (6) | 0.75921 (19) | 0.0310 (4) | |
| H6 | 1.0922 | 0.4663 | 0.7153 | 0.032 (8)* |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| I1 | 0.09427 (18) | 0.05428 (13) | 0.02713 (9) | 0.00258 (15) | 0.00173 (8) | 0.00149 (12) |
| O1 | 0.0349 (8) | 0.0491 (11) | 0.0446 (9) | 0.0025 (12) | 0.0084 (6) | 0.0184 (14) |
| O2 | 0.0367 (10) | 0.0376 (10) | 0.0451 (11) | 0.0138 (8) | −0.0008 (8) | 0.0023 (8) |
| N1 | 0.0250 (7) | 0.0282 (8) | 0.0396 (9) | 0.0038 (11) | 0.0016 (6) | −0.0020 (13) |
| C2 | 0.0226 (9) | 0.0279 (9) | 0.0381 (12) | −0.0016 (7) | 0.0017 (8) | 0.0041 (8) |
| N3 | 0.0260 (9) | 0.0294 (9) | 0.0322 (10) | 0.0052 (8) | 0.0058 (7) | −0.0008 (8) |
| C4 | 0.0255 (9) | 0.0272 (14) | 0.0308 (9) | 0.0021 (8) | −0.0004 (7) | −0.0011 (8) |
| C5 | 0.0370 (11) | 0.0305 (12) | 0.0254 (10) | 0.0009 (9) | 0.0026 (8) | −0.0041 (8) |
| C6 | 0.0295 (10) | 0.0306 (10) | 0.0333 (11) | 0.0000 (8) | 0.0042 (8) | −0.0084 (9) |
| I1—C5 | 2.063 (2) | C2—N3 | 1.370 (3) |
| O1—C2 | 1.227 (3) | N3—C4 | 1.384 (3) |
| O2—C4 | 1.226 (3) | N3—H3 | 0.8600 |
| N1—C2 | 1.363 (3) | C4—C5 | 1.456 (3) |
| N1—C6 | 1.370 (4) | C5—C6 | 1.351 (4) |
| N1—H1 | 0.8762 | C6—H6 | 0.9600 |
| C2—N1—C6 | 122.8 (3) | O2—C4—N3 | 119.9 (2) |
| C2—N1—H1 | 118.6 | O2—C4—C5 | 126.2 (2) |
| C6—N1—H1 | 118.6 | N3—C4—C5 | 113.9 (2) |
| O1—C2—N1 | 123.0 (3) | C6—C5—C4 | 119.3 (2) |
| O1—C2—N3 | 122.3 (3) | C6—C5—I1 | 122.37 (19) |
| N1—C2—N3 | 114.7 (2) | C4—C5—I1 | 118.33 (17) |
| C2—N3—C4 | 127.5 (2) | C5—C6—N1 | 121.7 (2) |
| C2—N3—H3 | 116.3 | C5—C6—H6 | 119.2 |
| C4—N3—H3 | 116.3 | N1—C6—H6 | 119.2 |
| C6—N1—C2—O1 | 175.9 (3) | N3—C4—C5—C6 | −3.4 (3) |
| C6—N1—C2—N3 | −2.9 (4) | O2—C4—C5—I1 | −2.2 (3) |
| O1—C2—N3—C4 | −176.7 (3) | N3—C4—C5—I1 | 177.51 (16) |
| N1—C2—N3—C4 | 2.1 (4) | C4—C5—C6—N1 | 2.8 (4) |
| C2—N3—C4—O2 | −179.3 (2) | I1—C5—C6—N1 | −178.1 (2) |
| C2—N3—C4—C5 | 0.9 (3) | C2—N1—C6—C5 | 0.5 (4) |
| O2—C4—C5—C6 | 176.9 (3) |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1—H1···O2i | 0.88 | 2.22 | 2.897 (3) | 133 |
| N3—H3···O1ii | 0.86 | 1.92 | 2.767 (3) | 170 |
| Symmetry codes: (i) x+1, y−1, z; (ii) −x+1, y+1/2, −z+2. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| N1—H1···O2i | 0.88 | 2.22 | 2.897 (3) | 133 |
| N3—H3···O1ii | 0.86 | 1.92 | 2.767 (3) | 170 |
| Symmetry codes: (i) x+1, y−1, z; (ii) −x+1, y+1/2, −z+2. |
The author thanks MIUR (Rome) for financial support in 2006 of the project 'X-ray diffractometry and spectrometry'.
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5-iodouracil, 5IUrac, was determined some 30 years ago (Sternglanz et al., 1975). In this study, 591 unique reflections were collected at ambient temperature on an automatic diffractometer, and the heavy-atom method was employed to solve the crystal structure. Only non-H atoms were localized and refined. The final refinement, carried out on a fairly small data set, led to R = 0.044, a data-to-parameter ratio of 7.2, S = 2.52 and standard deviations of 0.018Å in C—C bond lengths and 0.9° in bond angles, As a part of a more general study of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supramolecular reagents (Brunetti et al., 2000, 2002; Portalone et al., 1999; Portalone et al., 2002; 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) comprises a non-planar independent molecule (Fig. 1) in a slightly distorted B25 boat conformation (Cremer & Pople, 1975). Analysis of the crystal packing of (I), (Fig. 2), shows that the structure is stabilized by two intermolecular N—H···O interactions of descriptor C11(3) (Etter et al., 1990; Bernstein et al., 1995; Motherwell et al., 1999) (Table 1) between NH moieties and two carbonyl O atoms (O2i and O1ii) [symmetry code: (i) x + 1, y - 1, z; (ii) -x + 1, y + 1/2, -z + 2] which link the molecules into ribbons.