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Acta Crystallogr Sect E Struct Rep Online. 2008 February 1; 64(Pt 2): o365.
Published online 2008 January 4. doi:  10.1107/S1600536807068043
PMCID: PMC2960322

Redetermination of 5-iodo­uracil

Abstract

The title compound (systematic name: 2,4-dihydr­oxy-5-iodo­pyrimidine), C4H3IN2O2, which was first reported by Sternglanz, Freeman & Bugg [Acta Cryst. (1975 [triangle]), 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.

Related literature

For the previous structure determination, see: Sternglanz et al. (1975 [triangle]). For a general approach to the use of multiple-hydrogen-bonding DNA/RNA nucleobases as potential supra­molecular reagents, see: Portalone et al. (1999 [triangle]); Brunetti et al. (2000 [triangle], 2002 [triangle]); Portalone & Colapietro (2007 [triangle], and references therein). For computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990 [triangle]); Bernstein et al. (1995 [triangle]); Motherwell et al. (1999 [triangle]). the B25 boat confromation is defined by Cremer & Pople (1975 [triangle]).

For related literature, see: Portalone et al. (2002 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0o365-scheme1.jpg

Experimental

Crystal data

  • C4H3IN2O2
  • M r = 237.98
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o365-efi1.jpg
  • a = 4.89650 (18) Å
  • b = 4.45921 (13) Å
  • c = 14.2167 (2) Å
  • β = 92.341 (2)°
  • V = 310.16 (1) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 5.08 mm−1
  • T = 298 (2) K
  • 0.40 × 0.20 × 0.10 mm

Data collection

  • Oxford Diffraction Xcalibur S CCD diffractometer
  • Absorption correction: multi-scan (SCALE3 ABSPACK; Oxford Diffraction, 2006 [triangle]).T min = 0.252, T max = 0.602
  • 48636 measured reflections
  • 2127 independent reflections
  • 1803 reflections with I > 2σ(I)
  • R int = 0.049

Refinement

  • R[F 2 > 2σ(F 2)] = 0.025
  • wR(F 2) = 0.071
  • S = 1.04
  • 2127 reflections
  • 86 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.38 e Å−3
  • Δρmin = −0.03 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 934 Friedel pairs
  • Flack parameter: −0.01 (2)

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536807068043/tk2237sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807068043/tk2237Isup2.hkl

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

Acknowledgments

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

supplementary crystallographic information

Comment

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.

Experimental

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.

Refinement

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.

Figures

Fig. 1.
The molecular structure of (I), showing the atom-labelling scheme. Displacements ellipsoids are at the 50% probability level.
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.

Crystal data

C4H3IN2O2F000 = 220
Mr = 237.98Dx = 2.548 Mg m3
Monoclinic, P21Mo Kα radiation λ = 0.71069 Å
Hall symbol: P 2ybCell parameters from 29638 reflections
a = 4.89650 (18) Åθ = 2.9–32.4º
b = 4.45921 (13) ŵ = 5.08 mm1
c = 14.2167 (2) ÅT = 298 (2) K
β = 92.341 (2)ºTablets, colourless
V = 310.157 (15) Å30.40 × 0.20 × 0.10 mm
Z = 2

Data collection

Oxford Diffraction Xcalibur S CCD diffractometer2127 independent reflections
Radiation source: Enhance (Mo) X-ray source1803 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.049
Detector resolution: 16.0696 pixels mm-1θmax = 32.4º
T = 298(2) Kθmin = 2.9º
ω and [var phi] scansh = −7→7
Absorption correction: multi-scan(CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithmk = −6→6
Tmin = 0.252, Tmax = 0.602l = −21→21
48636 measured reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-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 = 1.04Δρmax = 0.38 e Å3
2127 reflectionsΔρmin = −0.03 e Å3
86 parametersExtinction correction: none
1 restraintAbsolute structure: Flack (1983), 934 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: −0.01 (2)
Secondary atom site location: difference Fourier map

Special details

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)

xyzUiso*/Ueq
I10.75060 (5)0.90920.595431 (10)0.05858 (9)
O10.7917 (3)0.3946 (8)0.99376 (14)0.0427 (4)
O20.4156 (4)1.0571 (5)0.78388 (17)0.0399 (4)
N10.9717 (4)0.4223 (8)0.84883 (14)0.0309 (3)
H11.0970.2890.86420.037 (9)*
C20.7939 (5)0.5077 (6)0.91511 (19)0.0295 (4)
N30.6128 (4)0.7269 (5)0.88650 (15)0.0291 (4)
H30.50250.78870.92790.058 (12)*
C40.5871 (4)0.8604 (5)0.79868 (16)0.0279 (5)
C50.7757 (5)0.7440 (6)0.73108 (17)0.0310 (4)
C60.9626 (5)0.5361 (6)0.75921 (19)0.0310 (4)
H61.09220.46630.71530.032 (8)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I10.09427 (18)0.05428 (13)0.02713 (9)0.00258 (15)0.00173 (8)0.00149 (12)
O10.0349 (8)0.0491 (11)0.0446 (9)0.0025 (12)0.0084 (6)0.0184 (14)
O20.0367 (10)0.0376 (10)0.0451 (11)0.0138 (8)−0.0008 (8)0.0023 (8)
N10.0250 (7)0.0282 (8)0.0396 (9)0.0038 (11)0.0016 (6)−0.0020 (13)
C20.0226 (9)0.0279 (9)0.0381 (12)−0.0016 (7)0.0017 (8)0.0041 (8)
N30.0260 (9)0.0294 (9)0.0322 (10)0.0052 (8)0.0058 (7)−0.0008 (8)
C40.0255 (9)0.0272 (14)0.0308 (9)0.0021 (8)−0.0004 (7)−0.0011 (8)
C50.0370 (11)0.0305 (12)0.0254 (10)0.0009 (9)0.0026 (8)−0.0041 (8)
C60.0295 (10)0.0306 (10)0.0333 (11)0.0000 (8)0.0042 (8)−0.0084 (9)

Geometric parameters (Å, °)

I1—C52.063 (2)C2—N31.370 (3)
O1—C21.227 (3)N3—C41.384 (3)
O2—C41.226 (3)N3—H30.8600
N1—C21.363 (3)C4—C51.456 (3)
N1—C61.370 (4)C5—C61.351 (4)
N1—H10.8762C6—H60.9600
C2—N1—C6122.8 (3)O2—C4—N3119.9 (2)
C2—N1—H1118.6O2—C4—C5126.2 (2)
C6—N1—H1118.6N3—C4—C5113.9 (2)
O1—C2—N1123.0 (3)C6—C5—C4119.3 (2)
O1—C2—N3122.3 (3)C6—C5—I1122.37 (19)
N1—C2—N3114.7 (2)C4—C5—I1118.33 (17)
C2—N3—C4127.5 (2)C5—C6—N1121.7 (2)
C2—N3—H3116.3C5—C6—H6119.2
C4—N3—H3116.3N1—C6—H6119.2
C6—N1—C2—O1175.9 (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—I1177.51 (16)
N1—C2—N3—C42.1 (4)C4—C5—C6—N12.8 (4)
C2—N3—C4—O2−179.3 (2)I1—C5—C6—N1−178.1 (2)
C2—N3—C4—C50.9 (3)C2—N1—C6—C50.5 (4)
O2—C4—C5—C6176.9 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.882.222.897 (3)133
N3—H3···O1ii0.861.922.767 (3)170

Symmetry codes: (i) x+1, y−1, z; (ii) −x+1, y+1/2, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2237).

References

  • 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.
  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Brunetti, B., Piacente, V. & Portalone, G. (2000). J. Chem. Eng. Data, 45, 242–246.
  • Brunetti, B., Piacente, V. & Portalone, G. (2002). J. Chem. Eng. Data, 47, 17–19..
  • Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc.97, 1354–1358.
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  • Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED, including ABSPACK Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
  • Portalone, G., Ballirano, P. & Maras, A. (2002). J. Mol. Struct.608, 35–39.
  • Portalone, G., Bencivenni, L., Colapietro, M., Pieretti, A. & Ramondo, F. (1999). Acta Chem. Scand.53, 57–68.
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  • Sternglanz, H., Freeman, G. R. & Bugg, C. E. (1975). Acta Cryst. B31, 1393–1395.

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