2-Chloro-6-methyl­pyrimidin-4-amine

Dong, S.-L.; Cheng, X.

doi:10.1107/S1600536812047794

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 68| Part 12| December 2012| Page o3455

doi:10.1107/S1600536812047794

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2-Chloro-6-methylpyrimidin-4-amine

Su-Lan Dong ^a ^* and Xiaochun Cheng ^a

^aCollege of Life Science and Chemical Engineering, Huaiyin Institute of Technology, Huaiyin 223003, Jiangsu, People's Republic of China
^*Correspondence e-mail: dsl710221@163.com

(Received 13 November 2012; accepted 21 November 2012; online 28 November 2012)

In the crystal structure of the title compound, C₅H₆ClN₃, molecules are linked by pairs of N—H⋯N hydrogen bonds, forming inversion dimers. These dimers are linked via N—H⋯N hydrogen bonds, forming a two-dimensional network lying parallel to (100). Inversion-related molecules are also linked via a slipped π–π interaction, with a centroid–centroid distance of 3.5259 (11) Å, a normal separation of 3.4365 (7) Å and a slippage of 0.789 Å.

Related literature

The title compound is an important organic intermediate which has been used to synthesise a drug that has shown promising activity against, for example, inflammatory bowel disease. For the synthetic procedure, see: Graceffa et al. (2010 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₅H₆ClN₃
M_r = 143.58
Monoclinic, P 2₁ /c
a = 7.1256 (8) Å
b = 7.8537 (8) Å
c = 13.0769 (15) Å
β = 115.678 (1)°
V = 659.54 (13) Å³
Z = 4
Mo Kα radiation
μ = 0.48 mm⁻¹
T = 296 K
0.14 × 0.12 × 0.12 mm

Data collection

Enraf–Nonius CAD-4 diffractometer
Absorption correction: ψ scan (North et al., 1968 ) T_min = 0.935, T_max = 0.944
5910 measured reflections
1157 independent reflections
1103 reflections with I > 2σ(I)
R_int = 0.077
3 standard reflections every 200 reflections intensity decay: 1%

Refinement

R[F² > 2σ(F²)] = 0.057
wR(F²) = 0.143
S = 1.17
1157 reflections
83 parameters
H-atom parameters constrained
Δρ_max = 0.36 e Å⁻³
Δρ_min = −0.76 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N2ⁱ	0.86	2.24	3.090 (3)	170
N3—H3B⋯N1ⁱⁱ	0.86	2.26	3.045 (2)	152
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) $[x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: CAD-4 Software (Enraf–Nonius, 1985 ); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo,1995 ); 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: SHELXTL.

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536812047794/su2530sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812047794/su2530Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536812047794/su2530Isup3.cml

checkCIF report

Comment top

The title compound is an important organic intermediate which has been used to synthesis drugs which have show promising activity against diseases, such as asthma, inflammatory bowel disease, and Crohn's disease (Graceffa et al., 2010). Herein we report on the crystal structure of the title compound.

The molecular structure of the title molecule is shown in Fig. 1. The bond lengths (Allen et al., 1987) and angles are within normal ranges.

In the crystal, molecules are linked by pairs of N-H···N hydrogen bonds forming inversion dimers. These dimers are linked via N-H···N hydrogen bonds forming a two-dimensional network lying parallel to plane (100). See Table 1 and Fig. 2 for details. Inversion related molecules are also linked via a slipped π-π interaction with a centroid-to-centroid distance of 3.5259 (11) Å ; a normal separation of 3.4365 (7) Å; slippage of 0.789 Å (Cg1···Cg1ⁱ where Cg1 is the N1/C1/N2/C4/C3/C2 ring; symmetry code: (i) -x+2, -y+1, -z+1).

Related literature top

The title compound is an important organic intermediate which has been used to synthesise a drug that has shown promising activity against, for example, inflammatory bowel disease. For the synthetic procedure, see: Graceffa et al. (2010). For bond-length data, see: Allen et al. (1987).

Experimental top

The title compound was prepared by the method reported in the literature (Graceffa et al., 2010). A solution of 2-chloro-4-methyl-6-nitropyrimidine (5 g, 15.77 mmol) in dichloromethane (50 ml) was added slowly to a solution of iron powder and hydrochloric acid (10 g, 178 mmol). After being stirred for 6 h at room temperature, the solution was filtered and the organic phase was evaporated on a rotary evaporator and gave the title compound. Block-like colourless crystals were obtained by slow evaporation of a solution of the title compound (0.5 g, 3.5 mmol) in ethanol (25 ml), at room temperature after ca. 7 d.

Computing details top

Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell refinement: CAD-4 Software (Enraf–Nonius, 1985); data reduction: XCAD4 (Harms & Wocadlo,1995); 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: SHELXTL (Sheldrick, 2008).

Figures top

	Fig. 1. The molecular structure of the title compound, with the atom numbering. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. A view of the crystal packing of the title compound. The N—H···N hydrogen bonds are shown as dashed lines (see Table 1 for details).

2-Chloro-6-methylpyrimidin-4-amine top

Crystal data top

C₅H₆ClN₃	F(000) = 296
M_r = 143.58	D_x = 1.446 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 5910 reflections
a = 7.1256 (8) Å	θ = 3.2–25.0°
b = 7.8537 (8) Å	µ = 0.48 mm⁻¹
c = 13.0769 (15) Å	T = 296 K
β = 115.678 (1)°	Block, colourless
V = 659.54 (13) Å³	0.14 × 0.12 × 0.12 mm
Z = 4

Data collection top

Enraf–Nonius CAD-4 diffractometer	1103 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.077
Graphite monochromator	θ_max = 25.0°, θ_min = 3.2°
ω/2θ scans	h = −8→8
Absorption correction: ψ scan (North et al., 1968)	k = −8→9
T_min = 0.935, T_max = 0.944	l = −15→15
5910 measured reflections	3 standard reflections every 200 reflections
1157 independent reflections	intensity decay: 1%

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)] = 0.057	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.143	H-atom parameters constrained
S = 1.17	w = 1/[σ²(F_o²) + (0.0881P)² + 0.2103P] where P = (F_o² + 2F_c²)/3
1157 reflections	(Δ/σ)_max = 0.004
83 parameters	Δρ_max = 0.36 e Å⁻³
0 restraints	Δρ_min = −0.76 e Å⁻³

Crystal data top

C₅H₆ClN₃	V = 659.54 (13) Å³
M_r = 143.58	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 7.1256 (8) Å	µ = 0.48 mm⁻¹
b = 7.8537 (8) Å	T = 296 K
c = 13.0769 (15) Å	0.14 × 0.12 × 0.12 mm
β = 115.678 (1)°

Data collection top

Enraf–Nonius CAD-4 diffractometer	1103 reflections with I > 2σ(I)
Absorption correction: ψ scan (North et al., 1968)	R_int = 0.077
T_min = 0.935, T_max = 0.944	3 standard reflections every 200 reflections
5910 measured reflections	intensity decay: 1%
1157 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.057	0 restraints
wR(F²) = 0.143	H-atom parameters constrained
S = 1.17	Δρ_max = 0.36 e Å⁻³
1157 reflections	Δρ_min = −0.76 e Å⁻³
83 parameters

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
C1	0.6937 (3)	0.4212 (2)	0.33622 (15)	0.0279 (4)
C2	0.9835 (3)	0.2642 (2)	0.42236 (17)	0.0304 (5)
C3	0.9496 (3)	0.2568 (2)	0.51731 (17)	0.0336 (5)
H3	1.0404	0.1980	0.5814	0.040*
C4	0.7729 (3)	0.3408 (2)	0.51565 (15)	0.0286 (4)
C5	1.1670 (3)	0.1823 (3)	0.4147 (2)	0.0463 (6)
H5A	1.2551	0.1315	0.4863	0.069*
H5B	1.2442	0.2669	0.3958	0.069*
H5C	1.1193	0.0961	0.3569	0.069*
Cl1	0.51828 (9)	0.52705 (8)	0.21459 (4)	0.0494 (3)
N1	0.8510 (2)	0.34779 (19)	0.32654 (13)	0.0305 (4)
N2	0.6439 (2)	0.42741 (19)	0.42172 (13)	0.0288 (4)
N3	0.7236 (3)	0.3407 (3)	0.60284 (15)	0.0416 (5)
H3A	0.6144	0.3939	0.5978	0.050*
H3B	0.8009	0.2874	0.6642	0.050*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0323 (9)	0.0294 (9)	0.0252 (9)	−0.0011 (7)	0.0154 (7)	−0.0003 (7)
C2	0.0321 (9)	0.0291 (9)	0.0321 (11)	−0.0023 (7)	0.0158 (7)	−0.0051 (7)
C3	0.0348 (10)	0.0346 (10)	0.0300 (10)	0.0008 (7)	0.0126 (8)	0.0023 (7)
C4	0.0340 (9)	0.0300 (9)	0.0250 (9)	−0.0042 (7)	0.0159 (7)	−0.0013 (7)
C5	0.0422 (11)	0.0513 (13)	0.0525 (14)	0.0096 (10)	0.0271 (10)	−0.0002 (10)
Cl1	0.0559 (5)	0.0652 (5)	0.0326 (4)	0.0224 (3)	0.0245 (3)	0.0176 (2)
N1	0.0348 (8)	0.0331 (8)	0.0289 (9)	−0.0021 (6)	0.0187 (7)	−0.0044 (6)
N2	0.0332 (8)	0.0315 (8)	0.0267 (8)	−0.0006 (6)	0.0177 (7)	−0.0003 (6)
N3	0.0466 (10)	0.0571 (11)	0.0284 (9)	0.0088 (8)	0.0232 (8)	0.0095 (8)

Geometric parameters (Å, º) top

C1—N2	1.313 (3)	C4—N3	1.331 (3)
C1—N1	1.315 (2)	C4—N2	1.356 (2)
C1—Cl1	1.7494 (18)	C5—H5A	0.9600
C2—N1	1.366 (3)	C5—H5B	0.9600
C2—C3	1.365 (3)	C5—H5C	0.9600
C2—C5	1.499 (3)	N3—H3A	0.8600
C3—C4	1.413 (3)	N3—H3B	0.8600
C3—H3	0.9300

N2—C1—N1	130.94 (17)	C2—C5—H5A	109.5
N2—C1—Cl1	113.97 (13)	C2—C5—H5B	109.5
N1—C1—Cl1	115.09 (14)	H5A—C5—H5B	109.5
N1—C2—C3	122.03 (16)	C2—C5—H5C	109.5
N1—C2—C5	114.88 (18)	H5A—C5—H5C	109.5
C3—C2—C5	123.09 (19)	H5B—C5—H5C	109.5
C2—C3—C4	118.28 (17)	C1—N1—C2	113.67 (16)
C2—C3—H3	120.9	C1—N2—C4	115.17 (16)
C4—C3—H3	120.9	C4—N3—H3A	120.0
N3—C4—N2	116.70 (17)	C4—N3—H3B	120.0
N3—C4—C3	123.43 (18)	H3A—N3—H3B	120.0
N2—C4—C3	119.88 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2ⁱ	0.86	2.24	3.090 (3)	170
N3—H3B···N1ⁱⁱ	0.86	2.26	3.045 (2)	152

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

Experimental details

Crystal data
Chemical formula	C₅H₆ClN₃
M_r	143.58
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	296
a, b, c (Å)	7.1256 (8), 7.8537 (8), 13.0769 (15)
β (°)	115.678 (1)
V (Å³)	659.54 (13)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.48
Crystal size (mm)	0.14 × 0.12 × 0.12

Data collection
Diffractometer	Enraf–Nonius CAD-4 diffractometer
Absorption correction	ψ scan (North et al., 1968)
T_min, T_max	0.935, 0.944
No. of measured, independent and observed [I > 2σ(I)] reflections	5910, 1157, 1103
R_int	0.077
(sin θ/λ)_max (Å⁻¹)	0.594

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.057, 0.143, 1.17
No. of reflections	1157
No. of parameters	83
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.36, −0.76

Computer programs: CAD-4 Software (Enraf–Nonius, 1985), XCAD4 (Harms & Wocadlo,1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N2ⁱ	0.86	2.24	3.090 (3)	170
N3—H3B···N1ⁱⁱ	0.86	2.26	3.045 (2)	152

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

Acknowledgements

The authors thank the Center of Testing and Analysis, Nanjing University, for the data collection.

References

Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. CrossRef Web of Science Google Scholar
Enraf–Nonius (1985). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands. Google Scholar
Graceffa, R., Kaller, M. & La, D. (2010). US Patent No. 20100120774. Google Scholar
Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany. Google Scholar
North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359. CrossRef IUCr Journals Web of Science Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar