Redetermination of 5-iodo­uracil

Portalone, G.

doi:10.1107/S1600536807068043

organic compounds

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Volume 64| Part 2| February 2008| Page o365

doi:10.1107/S1600536807068043

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Redetermination of 5-iodouracil

Gustavo Portalone ^a ^*

^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 ), 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). 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 ). the B₂₅ boat confromation is defined by Cremer & Pople (1975 ).

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

Experimental

Crystal data

C₄H₃IN₂O₂
M_r = 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 $[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED, including ABSPACK. Versions 1.171.32.3. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]$ ).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[F² > 2σ(F²)] = 0.025
wR(F²) = 0.071
S = 1.04
2127 reflections
86 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.38 e Å⁻³
Δρ_min = −0.03 e Å⁻³
Absolute structure: Flack (1983 ), 934 Friedel pairs
Flack parameter: −0.01 (2)

Table 1
Hydrogen-bond geometry (Å, °)

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) $[-x+1, y+{\script{1\over 2}}, -z+2]$ .

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 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ); molecular graphics: WinGX (Farrugia, 1999 ); software used to prepare material for publication: WinGX.

Supporting information

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

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

checkCIF report

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.

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

	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.

2,4-dihydroxy-5-iodopyrimidine top

Crystal data top

C₄H₃IN₂O₂	F(000) = 220
M_r = 237.98	D_x = 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 = 2.9–32.4°
b = 4.45921 (13) Å	µ = 5.08 mm⁻¹
c = 14.2167 (2) Å	T = 298 K
β = 92.341 (2)°	Tablets, colourless
V = 310.16 (2) Å³	0.40 × 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 source	1803 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.049
Detector resolution: 16.0696 pixels mm^-1	θ_max = 32.4°, θ_min = 2.9°
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
T_min = 0.252, T_max = 0.602	l = −21→21
48636 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.025	H-atom parameters constrained
wR(F²) = 0.071	w = 1/[σ²(F_o²) + (0.0471P)² + 0.0442P] where P = (F_o² + 2F_c²)/3
S = 1.04	(Δ/σ)_max = 0.002
2127 reflections	Δρ_max = 0.38 e Å⁻³
86 parameters	Δρ_min = −0.03 e Å⁻³
1 restraint	Absolute structure: Flack (1983), 934 Friedel pairs
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.01 (2)

Crystal data top

C₄H₃IN₂O₂	V = 310.16 (2) Å³
M_r = 237.98	Z = 2
Monoclinic, P2₁	Mo Kα radiation
a = 4.89650 (18) Å	µ = 5.08 mm⁻¹
b = 4.45921 (13) Å	T = 298 K
c = 14.2167 (2) Å	0.40 × 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)
T_min = 0.252, T_max = 0.602	R_int = 0.049
48636 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.025	H-atom parameters constrained
wR(F²) = 0.071	Δρ_max = 0.38 e Å⁻³
S = 1.04	Δρ_min = −0.03 e Å⁻³
2127 reflections	Absolute structure: Flack (1983), 934 Friedel pairs
86 parameters	Absolute 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

	x	y	z	U_iso*/U_eq
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)*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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.

Experimental details

Crystal data
Chemical formula	C₄H₃IN₂O₂
M_r	237.98
Crystal system, space group	Monoclinic, P2₁
Temperature (K)	298
a, b, c (Å)	4.89650 (18), 4.45921 (13), 14.2167 (2)
β (°)	92.341 (2)
V (Å³)	310.16 (2)
Z	2
Radiation type	Mo Kα
µ (mm⁻¹)	5.08
Crystal size (mm)	0.40 × 0.20 × 0.10

Data collection
Diffractometer	Oxford Diffraction Xcalibur S CCD diffractometer
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2006), Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm
T_min, T_max	0.252, 0.602
No. of measured, independent and observed [I > 2σ(I)] reflections	48636, 2127, 1803
R_int	0.049
(sin θ/λ)_max (Å⁻¹)	0.754

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.025, 0.071, 1.04
No. of reflections	2127
No. of parameters	86
No. of restraints	1
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.03
Absolute structure	Flack (1983), 934 Friedel pairs
Absolute structure parameter	−0.01 (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···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.

Acknowledgements

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

References

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