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Acta Crystallogr Sect E Struct Rep Online. 2010 June 1; 66(Pt 6): o1464.
Published online 2010 May 26. doi:  10.1107/S1600536810019124
PMCID: PMC2979631

5-Iodo­pyrimidin-2-amine

Abstract

The mol­ecule of the title compound, C4H4IN3, has crystallographic mirror plane symmetry. In the crystal, the mol­ecules are connected through N—H(...)N hydrogen bonds into polymeric tapes extended along the a axis, which are typical of 2-amino­pyrimidines. Each mol­ecule acts as a double donor and a double acceptor in the hydrogen bonding.

Related literature

For coordination polymers formed with the title compound, see: Lin et al. (2006 [triangle]).

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Object name is e-66-o1464-scheme1.jpg

Experimental

Crystal data

  • C4H4IN3
  • M r = 221.00
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1464-efi1.jpg
  • a = 7.9088 (7) Å
  • b = 8.3617 (10) Å
  • c = 18.3821 (16) Å
  • V = 1215.6 (2) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 5.16 mm−1
  • T = 295 K
  • 0.6 × 0.4 × 0.2 mm

Data collection

  • Bruker P4 diffractometer
  • Absorption correction: multi-scan (XSCANS; Siemens, 1995 [triangle]) T min = 0.332, T max = 1.000
  • 800 measured reflections
  • 573 independent reflections
  • 535 reflections with I > 2σ(I)
  • R int = 0.032
  • 3 standard reflections every 97 reflections intensity decay: none

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.089
  • S = 1.10
  • 573 reflections
  • 48 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.93 e Å−3
  • Δρmin = −0.83 e Å−3

Data collection: XSCANS (Siemens, 1995 [triangle]); cell refinement: XSCANS; data reduction: XSCANS; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: XP in SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810019124/gk2275sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810019124/gk2275Isup2.hkl

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

Acknowledgments

We are grateful to the National Science Council of the Republic of China for support. This research was also supported by the project of specific research fields in Chung-Yuan Christian University, Taiwan, under grant No. CYCU-98-CR—CH.

supplementary crystallographic information

Comment

A series of Ag(I) coordination polymers containg 2-amino-5-iodopyrimidine have been prepared, which show metallocycles and one-dimensional helical chains (Lin, et al., 2006). Within this project the crystal structure of 2-amino-5-iodopyrimidine was determined to investigate its weak interactions.

In its crystal structure weak intermolecular N—H···N hydrogen bonding is found (Tab. 1) and the molecules are almost planar (Fig. 1).

Experimental

The title compound was purchased from Acros Chemical Co. and used as received. Coloress plate crystals suitable for X-ray crystallography were obtained by dissolving the title compound in THF, followed by allowing the solution to evaporate slowly under air.

Refinement

The pyrimidyl hydrogen atoms were placed into idealized positions and constrained by the riding atom approximation with C—H = 0.93 Å, and Uiso(H) = 1.2 Ueq(C). The amine hydrogen atoms were located from difference Fourier maps..

Figures

Fig. 1.
Crystal structure of the title compound with labeling and displacement ellipsoids drawn at the 30% probability level.Symmetry codes: (i) -x, y, z.

Crystal data

C4H4IN3F(000) = 816
Mr = 221.00Dx = 2.415 Mg m3
Orthorhombic, CmcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2bc 2Cell parameters from 31 reflections
a = 7.9088 (7) Åθ = 4.9–12.6°
b = 8.3617 (10) ŵ = 5.16 mm1
c = 18.3821 (16) ÅT = 295 K
V = 1215.6 (2) Å3Plate, colorless
Z = 80.6 × 0.4 × 0.2 mm

Data collection

Bruker P4 diffractometer535 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.032
graphiteθmax = 25.0°, θmin = 2.2°
ω scansh = −1→9
Absorption correction: multi-scan (XSCANS; Siemens, 1995)k = −1→9
Tmin = 0.332, Tmax = 1.000l = −21→1
800 measured reflections3 standard reflections every 97 reflections
573 independent reflections intensity decay: none

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.032H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.089w = 1/[σ2(Fo2) + (0.055P)2 + 3.1925P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max = 0.001
573 reflectionsΔρmax = 0.93 e Å3
48 parametersΔρmin = −0.83 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0148 (9)

Special details

Experimental. 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.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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
I0.00000.25315 (4)0.72128 (2)0.0462 (4)
N1−0.1515 (4)0.6239 (4)0.57261 (16)0.0378 (8)
N20.00000.8038 (8)0.5044 (4)0.0456 (13)
C10.00000.4412 (6)0.6466 (3)0.0345 (11)
C2−0.1488 (5)0.5037 (4)0.6200 (2)0.0367 (9)
H2C−0.25070.46040.63580.044*
C30.00000.6791 (7)0.5508 (3)0.0343 (11)
H2N−0.085 (7)0.831 (7)0.485 (3)0.061 (15)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I0.0388 (4)0.0504 (5)0.0495 (5)0.0000.0000.01869 (14)
N10.0321 (17)0.0427 (17)0.0385 (16)0.0031 (14)0.0005 (12)0.0041 (13)
N20.039 (3)0.053 (3)0.045 (3)0.0000.0000.017 (3)
C10.038 (3)0.033 (2)0.032 (2)0.0000.0000.002 (2)
C20.0329 (19)0.0406 (19)0.036 (2)−0.0011 (16)0.0016 (15)0.0034 (14)
C30.041 (3)0.035 (3)0.027 (2)0.0000.0000.000 (2)

Geometric parameters (Å, °)

I—C12.088 (5)N2—H2N0.79 (5)
N1—C21.331 (4)C1—C21.377 (4)
N1—C31.346 (4)C2—H2C0.9300
N2—C31.346 (10)
C2—N1—C3116.1 (3)N1—C2—H2C118.9
C3—N2—H2N120 (4)C1—C2—H2C118.9
C2i—C1—C2117.4 (5)N1i—C3—N1125.9 (5)
C2—C1—I121.3 (2)N1i—C3—N2117.0 (2)
N1—C2—C1122.2 (4)

Symmetry codes: (i) −x, y, z.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2N···N1ii0.79 (5)2.37 (5)3.157 (4)173 (6)

Symmetry codes: (ii) −x−1/2, −y+3/2, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GK2275).

References

  • Lin, C.-Y., Chan, Z.-K., Yeh, C.-W., Wu, C.-J., Chen, J.-D. & Wang, J.-C. (2006). CrystEngComm, 8, 841–846.
  • Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [PubMed]
  • Siemens (1995). XSCANS Siemens Analytical X-ray Instruments Inc., Madison, Wisconsin, USA.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography