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

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ISSN: 2056-9890

Redetermination of 5-iodo­uracil

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

(Received 18 December 2007; accepted 21 December 2007; online 4 January 2008)

The title compound (systematic name: 2,4-dihydr­oxy-5-iodo­pyrimidine), C4H3IN2O2, which was first reported by Sternglanz, Freeman & Bugg [Acta Cryst. (1975[Sternglanz, H., Freeman, G. R. & Bugg, C. E. (1975). Acta Cryst. B31, 1393-1395.]), 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[Sternglanz, H., Freeman, G. R. & Bugg, C. E. (1975). Acta Cryst. B31, 1393-1395.]). 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 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.]). the B25 boat confromation is defined by Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358.]).

For related literature, see: Portalone et al. (2002[Portalone, G., Ballirano, P. & Maras, A. (2002). J. Mol. Struct. 608, 35-39.]).

[Scheme 1]

Experimental

Crystal data
  • C4H3IN2O2

  • Mr = 237.98

  • Monoclinic, P 21

  • 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[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED, including ABSPACK. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]).Tmin = 0.252, Tmax = 0.602

  • 48636 measured reflections

  • 2127 independent reflections

  • 1803 reflections with I > 2σ(I)

  • Rint = 0.049

Refinement
  • R[F2 > 2σ(F2)] = 0.025

  • wR(F2) = 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[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 934 Friedel pairs

  • Flack parameter: −0.01 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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+{\script{1\over 2}}, -z+2].

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED, including ABSPACK. 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, including ABSPACK. 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, 1997[Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.]); molecular graphics: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]); software used to prepare material for publication: WinGX.

Supporting information


Comment top

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.

Related literature top

For the previous structure determination, see: Sternglanz et al. (1975). 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 computation of ring patterns formed by hydrogen bonds in crystal structures, see: Etter et al. (1990); Bernstein et al. (1995); Motherwell et al. (1999).

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

Experimental top

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 top

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.

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, 1997); 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.
[Figure 2] 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.
2,4-dihydroxy-5-iodopyrimidine top
Crystal data top
C4H3IN2O2F(000) = 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 = 2.9–32.4°
b = 4.45921 (13) ŵ = 5.08 mm1
c = 14.2167 (2) ÅT = 298 K
β = 92.341 (2)°Tablets, colourless
V = 310.16 (2) Å30.40 × 0.20 × 0.10 mm
Z = 2
Data collection top
Oxford Diffraction Xcalibur S CCD
diffractometer
2127 independent reflections
Radiation source: Enhance (Mo) X-ray source1803 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.049
Detector resolution: 16.0696 pixels mm-1θmax = 32.4°, θmin = 2.9°
ω and ϕ scansh = 77
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
k = 66
Tmin = 0.252, Tmax = 0.602l = 2121
48636 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.071 w = 1/[σ2(Fo2) + (0.0471P)2 + 0.0442P]
where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max = 0.002
2127 reflectionsΔρmax = 0.38 e Å3
86 parametersΔρmin = 0.03 e Å3
1 restraintAbsolute structure: Flack (1983), 934 Friedel pairs
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0.01 (2)
Crystal data top
C4H3IN2O2V = 310.16 (2) Å3
Mr = 237.98Z = 2
Monoclinic, P21Mo Kα radiation
a = 4.89650 (18) ŵ = 5.08 mm1
b = 4.45921 (13) ÅT = 298 K
c = 14.2167 (2) Å0.40 × 0.20 × 0.10 mm
β = 92.341 (2)°
Data collection top
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 = 0.602Rint = 0.049
48636 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.071Δρmax = 0.38 e Å3
S = 1.04Δρmin = 0.03 e Å3
2127 reflectionsAbsolute structure: Flack (1983), 934 Friedel pairs
86 parametersAbsolute structure parameter: 0.01 (2)
1 restraint
Special details top

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
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) top
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, º) top
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—C63.4 (3)
C6—N1—C2—N32.9 (4)O2—C4—C5—I12.2 (3)
O1—C2—N3—C4176.7 (3)N3—C4—C5—I1177.51 (16)
N1—C2—N3—C42.1 (4)C4—C5—C6—N12.8 (4)
C2—N3—C4—O2179.3 (2)I1—C5—C6—N1178.1 (2)
C2—N3—C4—C50.9 (3)C2—N1—C6—C50.5 (4)
O2—C4—C5—C6176.9 (3)
Hydrogen-bond geometry (Å, º) top
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, y1, z; (ii) x+1, y+1/2, z+2.

Experimental details

Crystal data
Chemical formulaC4H3IN2O2
Mr237.98
Crystal system, space groupMonoclinic, P21
Temperature (K)298
a, b, c (Å)4.89650 (18), 4.45921 (13), 14.2167 (2)
β (°) 92.341 (2)
V3)310.16 (2)
Z2
Radiation typeMo Kα
µ (mm1)5.08
Crystal size (mm)0.40 × 0.20 × 0.10
Data collection
DiffractometerOxford Diffraction Xcalibur S CCD
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
Tmin, Tmax0.252, 0.602
No. of measured, independent and
observed [I > 2σ(I)] reflections
48636, 2127, 1803
Rint0.049
(sin θ/λ)max1)0.754
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.025, 0.071, 1.04
No. of reflections2127
No. of parameters86
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.38, 0.03
Absolute structureFlack (1983), 934 Friedel pairs
Absolute structure parameter0.01 (2)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) top
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, y1, z; (ii) x+1, y+1/2, z+2.
 

Acknowledgements

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

References

First citationAltomare, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBrunetti, B., Piacente, V. & Portalone, G. (2000). J. Chem. Eng. Data, 45, 242–246.  Web of Science CrossRef CAS Google Scholar
First citationBrunetti, B., Piacente, V. & Portalone, G. (2002). J. Chem. Eng. Data, 47, 17–19..  Web of Science CrossRef CAS Google Scholar
First citationCremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358.  CrossRef CAS Web of Science Google Scholar
First citationEtter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262.  CrossRef CAS Web of Science IUCr Journals Google Scholar
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First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationMotherwell, W. D. S., Shields, G. P. & Allen, F. H. (1999). Acta Cryst. B55, 1044–1056.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationOxford Diffraction (2006). CrysAlis CCD and CrysAlis RED, including ABSPACK. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.  Google Scholar
First citationPortalone, G., Ballirano, P. & Maras, A. (2002). J. Mol. Struct. 608, 35–39.  Web of Science CSD CrossRef CAS Google Scholar
First citationPortalone, G., Bencivenni, L., Colapietro, M., Pieretti, A. & Ramondo, F. (1999). Acta Chem. Scand. 53, 57–68.  Web of Science CrossRef CAS Google Scholar
First citationPortalone, G. & Colapietro, M. (2007). Acta Cryst. C63, o650–o654.  Web of Science CSD CrossRef IUCr Journals Google Scholar
First citationSheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.  Google Scholar
First citationSternglanz, H., Freeman, G. R. & Bugg, C. E. (1975). Acta Cryst. B31, 1393–1395.  CSD CrossRef CAS IUCr Journals Web of Science Google Scholar

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