Redetermination of 5-iodo-uracil.

THE TITLE COMPOUND (SYSTEMATIC NAME: 2,4-dihydr-oxy-5-iodo-pyrimidine), C(4)H(3)IN(2)O(2), 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 mol-ecule in a slightly distorted B(25) boat conformation. The mol-ecules 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 = 237.98

Monoclinic,

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 ▶).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 ▶), 934 Friedel pairs

Flack parameter: −0.01 (2)

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 ▶); 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.

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

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

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

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) ; (ii) .