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Acta Crystallogr Sect E Struct Rep Online. 2010 March 1; 66(Pt 3): o686.
Published online 2010 February 24. doi:  10.1107/S1600536810005660
PMCID: PMC2983557

2-Iodo-4,6-dimethyl­pyrimidine

Abstract

In the title compound, C6H7IN2, the non-H atoms of the mol­ecule are located on a crystallographic mirror plane; the H atoms of the methyl groups are therefore disordered over two positions of equal occupancy. In the crystal structure, short inter­molecular I(...)N contacts [3.390 (3) Å] are found, linking the mol­ecules into zigzag chains. In addition, there are inter­molecular π–π stacking inter­actions between the pyrimidine rings of adjacent mol­ecules [centroid–centroid distance = 3.5168 (10) Å], resulting in a two-dimensional supra­molecular architecture.

Related literature

For applications of pyrimidine derivatives, see: Chinchilla et al. (2004 [triangle]); Xu et al. (2009a [triangle],b [triangle]). For halogen–electronegative atom inter­actions, see: Lommerse et al. (1996 [triangle]). For the synthesis of 4,6-dimethyl-2-chloro­pyrimidine, see: Kosolapoff & Roy (1961 [triangle]) and literature cited therein.

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Object name is e-66-0o686-scheme1.jpg

Experimental

Crystal data

  • C6H7IN2
  • M r = 234.04
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o686-efi1.jpg
  • a = 7.930 (2) Å
  • b = 7.0256 (19) Å
  • c = 14.499 (4) Å
  • V = 807.8 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 3.88 mm−1
  • T = 296 K
  • 0.32 × 0.25 × 0.21 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.370, T max = 0.496
  • 5541 measured reflections
  • 817 independent reflections
  • 739 reflections with I > 2σ(I)
  • R int = 0.029

Refinement

  • R[F 2 > 2σ(F 2)] = 0.026
  • wR(F 2) = 0.066
  • S = 1.10
  • 817 reflections
  • 57 parameters
  • H-atom parameters constrained
  • Δρmax = 0.81 e Å−3
  • Δρmin = −0.21 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810005660/si2242sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810005660/si2242Isup2.hkl

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

Acknowledgments

This work was sponsored by the National Natural Science Foundation of China (No. 20872133) and the Natural Science Foundation of Henan Education Department (No. 2009 A150027).

supplementary crystallographic information

Comment

Some derivatives of pyrimidine are important chemical materials (Chinchilla et al., 2004). Among them, 4,6-dimethyl-2-iodopyrimidine is a good partner in cross-coupling reaction giving a variety of pyrimidine ligands (Xu et al., 2009a, b). The molecular structure of the related title compound is shown in Fig. 1. The molecule is located on a crystallographic mirror plane, thus the H atoms of the methyl groups are disordered over two positions, with site-occupation factors fixed at 0.5. The interesting feature of the crystal structure is short intermolecular I···N contacts [3.390 (3) Å] (Lommerse et al., 1996), which is obviously shorter than the sum of the van der Waals radii of the relevant atoms. In addtion, there are strong intermolecular π—π stacking interactions between the pyrimidine rings of adjacent molecules [centroid-centroid distance = 3.5168 (10) Å], resulting in a two-dimensional supramolecular architecture (Fig.2).

Experimental

The title compound was prepared as described in literature (Kosolapoff & Roy 1961) and recrystallized from dichloromethane-petroleum ether solution at room temperature to give the desired product as colourless crystals suitable for single-crystal X-ray diffraction.

Refinement

H atoms attached to C atoms of the title compound were placed in geometrically idealized positions and treated as riding with C—H distances constrained to 0.93–0.96 Å, and with Uiso(H) = 1.2Ueq(C) and (1.5Ueq for methyl H).

Figures

Fig. 1.
The molecular structure of the title compound with displacement ellipsoids at the 30% probability level, the disordered H atoms are omitted.
Fig. 2.
Partial view of the crystal packing showing the short intermolecular I···N contacts and π—π stacking interactions.

Crystal data

C6H7IN2Dx = 1.924 Mg m3
Mr = 234.04Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, PnmaCell parameters from 2976 reflections
a = 7.930 (2) Åθ = 2.8–24.9°
b = 7.0256 (19) ŵ = 3.88 mm1
c = 14.499 (4) ÅT = 296 K
V = 807.8 (4) Å3Block, colourless
Z = 40.32 × 0.25 × 0.21 mm
F(000) = 440

Data collection

Bruker SMART APEXII CCD area-detector diffractometer817 independent reflections
Radiation source: fine-focus sealed tube739 reflections with I > 2σ(I)
graphiteRint = 0.029
phi and ω scansθmax = 25.5°, θmin = 2.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −9→9
Tmin = 0.370, Tmax = 0.496k = −8→8
5541 measured reflectionsl = −17→17

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.026Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.066H-atom parameters constrained
S = 1.10w = 1/[σ2(Fo2) + (0.0375P)2 + 0.259P] where P = (Fo2 + 2Fc2)/3
817 reflections(Δ/σ)max = 0.001
57 parametersΔρmax = 0.81 e Å3
0 restraintsΔρmin = −0.21 e Å3

Special details

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 takeninto account individually in the estimation of esds in distances, anglesand torsion angles; correlations between esds in cell parameters are onlyused 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 andgoodness of fit S are based on F2, conventional R-factors R are basedon F, with F set to zero for negative F2. The threshold expression ofF2 > σ(F2) is used only for calculating R-factors(gt) etc. and isnot relevant to the choice of reflections for refinement. R-factors basedon 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*/UeqOcc. (<1)
C10.4205 (6)0.25000.4216 (3)0.0559 (10)
C20.4224 (8)0.25000.5763 (3)0.0708 (13)
C30.5963 (8)0.25000.5741 (3)0.0746 (14)
H30.65870.25000.62850.090*
C40.6751 (7)0.25000.4899 (3)0.0680 (12)
C50.3278 (11)0.25000.6665 (5)0.108 (2)
H5A0.22990.17030.66120.162*0.50
H5B0.29350.37750.68120.162*0.50
H5C0.39960.20220.71450.162*0.50
C60.8651 (8)0.25000.4820 (5)0.107 (2)
H6A0.90470.12150.47610.161*0.50
H6B0.91320.30680.53610.161*0.50
H6C0.89800.32180.42860.161*0.50
I10.27885 (5)0.25000.29859 (2)0.07396 (18)
N10.3314 (6)0.25000.4980 (2)0.0656 (9)
N20.5862 (5)0.25000.4101 (2)0.0616 (9)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.063 (3)0.046 (2)0.058 (2)0.000−0.002 (2)0.000
C20.107 (4)0.047 (2)0.058 (3)0.0000.007 (3)0.000
C30.106 (4)0.059 (3)0.059 (3)0.000−0.014 (3)0.000
C40.076 (3)0.064 (3)0.064 (3)0.000−0.012 (2)0.000
C50.158 (7)0.098 (4)0.068 (3)0.0000.022 (4)0.000
C60.073 (4)0.151 (6)0.098 (4)0.000−0.014 (3)0.000
I10.0685 (3)0.0874 (3)0.0660 (3)0.000−0.01043 (13)0.000
N10.075 (2)0.065 (2)0.057 (2)0.0000.0106 (19)0.000
N20.064 (2)0.062 (2)0.059 (2)0.000−0.0017 (17)0.000

Geometric parameters (Å, °)

C1—N11.314 (6)C4—N21.356 (6)
C1—N21.325 (6)C4—C61.511 (9)
C1—I12.108 (4)C5—H5A0.9600
C2—N11.345 (7)C5—H5B0.9600
C2—C31.380 (9)C5—H5C0.9600
C2—C51.507 (8)C6—H6A0.9600
C3—C41.371 (7)C6—H6B0.9600
C3—H30.9300C6—H6C0.9600
N1—C1—N2129.8 (4)C2—C5—H5B109.5
N1—C1—I1115.3 (3)H5A—C5—H5B109.5
N2—C1—I1114.9 (3)C2—C5—H5C109.5
N1—C2—C3121.1 (5)H5A—C5—H5C109.5
N1—C2—C5117.7 (6)H5B—C5—H5C109.5
C3—C2—C5121.2 (6)C4—C6—H6A109.5
C4—C3—C2118.4 (5)C4—C6—H6B109.5
C4—C3—H3120.8H6A—C6—H6B109.5
C2—C3—H3120.8C4—C6—H6C109.5
N2—C4—C3121.6 (5)H6A—C6—H6C109.5
N2—C4—C6116.9 (4)H6B—C6—H6C109.5
C3—C4—C6121.5 (5)C1—N1—C2115.1 (5)
C2—C5—H5A109.5C1—N2—C4114.1 (4)
N1—C2—C3—C40.0C3—C2—N1—C10.0
C5—C2—C3—C4180.0C5—C2—N1—C1180.0
C2—C3—C4—N20.0N1—C1—N2—C40.0
C2—C3—C4—C6180.0I1—C1—N2—C4180.0
N2—C1—N1—C20.0C3—C4—N2—C10.00
I1—C1—N1—C2180.0C6—C4—N2—C1180.0

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: SI2242).

References

  • Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
  • Chinchilla, R., Najera, C. & Yus, M. (2004). Chem. Rev.104, 2667–2722. [PubMed]
  • Kosolapoff, G. M. & Roy, C. H. (1961). J. Org. Chem.26, 1895–1898.
  • Lommerse, J. P. M., Stone, A. J., Taylor, R. & Ottolenghi, M. (1996). J. Am. Chem. Soc.118, 3108–3116.
  • Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Xu, C., Wang, Z.-Q., Cen, F.-F., Cheng, L. & Ji, B.-M. (2009a). Acta Cryst. E65, o2785. [PMC free article] [PubMed]
  • Xu, C., Wang, Z. Q., Fu, W. J., Lou, X. H., Li, Y. F., Cen, F. F., Ma, H. J. & Ji, B. M. (2009b). Organometallics28, 1909–1916.

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