2-Iodo-4,6-dimethyl­pyrimidine

Jiang, Q.-M.; Mao, G.-Y.; Hao, L.-Y.; Hao, X.-Q.; Song, M.-P.

doi:10.1107/S1600536810005660

organic compounds

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ISSN: 2056-9890

Volume 66| Part 3| March 2010| Page o686

doi:10.1107/S1600536810005660

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2-Iodo-4,6-dimethylpyrimidine

Qing-Min Jiang,^a,^b Gui-Yun Mao,^b ^* Lu-Ye Hao,^a Xin-Qi Hao ^b and Mao-Ping Song ^b

^aHenan Industrial University Chemical Technology Vocational College, Zhengzhou 450042, People's Republic of China, and ^bDepartment of Chemistry, Henan Key Laboratory of Chemical, Biology and Organic Chemistry, Zhengzhou University, Zhengzhou 450052, People's Republic of China
^*Correspondence e-mail: maopingsong@zzu.edu.cn

(Received 3 February 2010; accepted 10 February 2010; online 24 February 2010)

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

Experimental

Crystal data

C₆H₇IN₂
M_r = 234.04
Orthorhombic, P n m a
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 ) 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[F² > 2σ(F²)] = 0.026
wR(F²) = 0.066
S = 1.10
817 reflections
57 parameters
H-atom parameters constrained
Δρ_max = 0.81 e Å⁻³
Δρ_min = −0.21 e Å⁻³

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

Supporting information

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

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

checkCIF report

Comment top

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).

Related literature top

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

Experimental top

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.

Computing details top

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

Figures top

	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.

2-Iodo-4,6-dimethylpyrimidine top

Crystal data top

C₆H₇IN₂	D_x = 1.924 Mg m⁻³
M_r = 234.04	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pnma	Cell parameters from 2976 reflections
a = 7.930 (2) Å	θ = 2.8–24.9°
b = 7.0256 (19) Å	µ = 3.88 mm⁻¹
c = 14.499 (4) Å	T = 296 K
V = 807.8 (4) Å³	Block, colourless
Z = 4	0.32 × 0.25 × 0.21 mm
F(000) = 440

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	817 independent reflections
Radiation source: fine-focus sealed tube	739 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.029
phi and ω scans	θ_max = 25.5°, θ_min = 2.8°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −9→9
T_min = 0.370, T_max = 0.496	k = −8→8
5541 measured reflections	l = −17→17

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.026	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.066	H-atom parameters constrained
S = 1.10	w = 1/[σ²(F_o²) + (0.0375P)² + 0.259P] where P = (F_o² + 2F_c²)/3
817 reflections	(Δ/σ)_max = 0.001
57 parameters	Δρ_max = 0.81 e Å⁻³
0 restraints	Δρ_min = −0.21 e Å⁻³

Crystal data top

C₆H₇IN₂	V = 807.8 (4) Å³
M_r = 234.04	Z = 4
Orthorhombic, Pnma	Mo Kα radiation
a = 7.930 (2) Å	µ = 3.88 mm⁻¹
b = 7.0256 (19) Å	T = 296 K
c = 14.499 (4) Å	0.32 × 0.25 × 0.21 mm

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	817 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	739 reflections with I > 2σ(I)
T_min = 0.370, T_max = 0.496	R_int = 0.029
5541 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.026	0 restraints
wR(F²) = 0.066	H-atom parameters constrained
S = 1.10	Δρ_max = 0.81 e Å⁻³
817 reflections	Δρ_min = −0.21 e Å⁻³
57 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq	Occ. (<1)
C1	0.4205 (6)	0.2500	0.4216 (3)	0.0559 (10)
C2	0.4224 (8)	0.2500	0.5763 (3)	0.0708 (13)
C3	0.5963 (8)	0.2500	0.5741 (3)	0.0746 (14)
H3	0.6587	0.2500	0.6285	0.090*
C4	0.6751 (7)	0.2500	0.4899 (3)	0.0680 (12)
C5	0.3278 (11)	0.2500	0.6665 (5)	0.108 (2)
H5A	0.2299	0.1703	0.6612	0.162*	0.50
H5B	0.2935	0.3775	0.6812	0.162*	0.50
H5C	0.3996	0.2022	0.7145	0.162*	0.50
C6	0.8651 (8)	0.2500	0.4820 (5)	0.107 (2)
H6A	0.9047	0.1215	0.4761	0.161*	0.50
H6B	0.9132	0.3068	0.5361	0.161*	0.50
H6C	0.8980	0.3218	0.4286	0.161*	0.50
I1	0.27885 (5)	0.2500	0.29859 (2)	0.07396 (18)
N1	0.3314 (6)	0.2500	0.4980 (2)	0.0656 (9)
N2	0.5862 (5)	0.2500	0.4101 (2)	0.0616 (9)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.063 (3)	0.046 (2)	0.058 (2)	0.000	−0.002 (2)	0.000
C2	0.107 (4)	0.047 (2)	0.058 (3)	0.000	0.007 (3)	0.000
C3	0.106 (4)	0.059 (3)	0.059 (3)	0.000	−0.014 (3)	0.000
C4	0.076 (3)	0.064 (3)	0.064 (3)	0.000	−0.012 (2)	0.000
C5	0.158 (7)	0.098 (4)	0.068 (3)	0.000	0.022 (4)	0.000
C6	0.073 (4)	0.151 (6)	0.098 (4)	0.000	−0.014 (3)	0.000
I1	0.0685 (3)	0.0874 (3)	0.0660 (3)	0.000	−0.01043 (13)	0.000
N1	0.075 (2)	0.065 (2)	0.057 (2)	0.000	0.0106 (19)	0.000
N2	0.064 (2)	0.062 (2)	0.059 (2)	0.000	−0.0017 (17)	0.000

Geometric parameters (Å, º) top

C1—N1	1.314 (6)	C4—N2	1.356 (6)
C1—N2	1.325 (6)	C4—C6	1.511 (9)
C1—I1	2.108 (4)	C5—H5A	0.9600
C2—N1	1.345 (7)	C5—H5B	0.9600
C2—C3	1.380 (9)	C5—H5C	0.9600
C2—C5	1.507 (8)	C6—H6A	0.9600
C3—C4	1.371 (7)	C6—H6B	0.9600
C3—H3	0.9300	C6—H6C	0.9600

N1—C1—N2	129.8 (4)	C2—C5—H5B	109.5
N1—C1—I1	115.3 (3)	H5A—C5—H5B	109.5
N2—C1—I1	114.9 (3)	C2—C5—H5C	109.5
N1—C2—C3	121.1 (5)	H5A—C5—H5C	109.5
N1—C2—C5	117.7 (6)	H5B—C5—H5C	109.5
C3—C2—C5	121.2 (6)	C4—C6—H6A	109.5
C4—C3—C2	118.4 (5)	C4—C6—H6B	109.5
C4—C3—H3	120.8	H6A—C6—H6B	109.5
C2—C3—H3	120.8	C4—C6—H6C	109.5
N2—C4—C3	121.6 (5)	H6A—C6—H6C	109.5
N2—C4—C6	116.9 (4)	H6B—C6—H6C	109.5
C3—C4—C6	121.5 (5)	C1—N1—C2	115.1 (5)
C2—C5—H5A	109.5	C1—N2—C4	114.1 (4)

N1—C2—C3—C4	0.0	C3—C2—N1—C1	0.0
C5—C2—C3—C4	180.0	C5—C2—N1—C1	180.0
C2—C3—C4—N2	0.0	N1—C1—N2—C4	0.0
C2—C3—C4—C6	180.0	I1—C1—N2—C4	180.0
N2—C1—N1—C2	0.0	C3—C4—N2—C1	0.00
I1—C1—N1—C2	180.0	C6—C4—N2—C1	180.0

Experimental details

Crystal data
Chemical formula	C₆H₇IN₂
M_r	234.04
Crystal system, space group	Orthorhombic, Pnma
Temperature (K)	296
a, b, c (Å)	7.930 (2), 7.0256 (19), 14.499 (4)
V (Å³)	807.8 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	3.88
Crystal size (mm)	0.32 × 0.25 × 0.21

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 1996)
T_min, T_max	0.370, 0.496
No. of measured, independent and observed [I > 2σ(I)] reflections	5541, 817, 739
R_int	0.029
(sin θ/λ)_max (Å⁻¹)	0.606

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.026, 0.066, 1.10
No. of reflections	817
No. of parameters	57
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.81, −0.21

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Acknowledgements

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).

References

Bruker (2004). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Chinchilla, R., Najera, C. & Yus, M. (2004). Chem. Rev. 104, 2667–2722. Web of Science CrossRef PubMed CAS Google Scholar
Kosolapoff, G. M. & Roy, C. H. (1961). J. Org. Chem. 26, 1895–1898. CrossRef CAS Web of Science Google Scholar
Lommerse, J. P. M., Stone, A. J., Taylor, R. & Ottolenghi, M. (1996). J. Am. Chem. Soc. 118, 3108–3116. CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Xu, C., Wang, Z.-Q., Cen, F.-F., Cheng, L. & Ji, B.-M. (2009a). Acta Cryst. E65, o2785. Web of Science CrossRef IUCr Journals Google Scholar
Xu, C., Wang, Z. Q., Fu, W. J., Lou, X. H., Li, Y. F., Cen, F. F., Ma, H. J. & Ji, B. M. (2009b). Organometallics 28, 1909–1916. Web of Science CSD CrossRef CAS Google Scholar