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ISSN: 2056-9890

2-Chloro-6-methyl­pyrimidin-4-amine

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 ππ 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[Graceffa, R., Kaller, M. & La, D. (2010). US Patent No. 20100120774.]). For bond-length data, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C5H6ClN3

  • Mr = 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[North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351-359.]) Tmin = 0.935, Tmax = 0.944

  • 5910 measured reflections

  • 1157 independent reflections

  • 1103 reflections with I > 2σ(I)

  • Rint = 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

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.76 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA 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[Enraf-Nonius (1985). CAD-4 Software. Enraf-Nonius, Delft, The Netherlands.]); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo,1995[Harms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL.

Supporting information


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.

Refinement top

All H atoms were positioned geometrically and refined using a riding model: N-H = 0.86 Å, C—H = 0.93 and 0.96 Å for aromatic and CH3 H atoms, respectively, with Uiso(H) = k × Ueq(N,C), where k = 1.5 for CH3 H atoms and = 1.2 for other H atoms.

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
[Figure 1] Fig. 1. The molecular structure of the title compound, with the atom numbering. Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] 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
C5H6ClN3F(000) = 296
Mr = 143.58Dx = 1.446 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 5910 reflections
a = 7.1256 (8) Åθ = 3.2–25.0°
b = 7.8537 (8) ŵ = 0.48 mm1
c = 13.0769 (15) ÅT = 296 K
β = 115.678 (1)°Block, colourless
V = 659.54 (13) Å30.14 × 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 tubeRint = 0.077
Graphite monochromatorθmax = 25.0°, θmin = 3.2°
ω/2θ scansh = 88
Absorption correction: ψ scan
(North et al., 1968)
k = 89
Tmin = 0.935, Tmax = 0.944l = 1515
5910 measured reflections3 standard reflections every 200 reflections
1157 independent reflections intensity decay: 1%
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.057Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.143H-atom parameters constrained
S = 1.17 w = 1/[σ2(Fo2) + (0.0881P)2 + 0.2103P]
where P = (Fo2 + 2Fc2)/3
1157 reflections(Δ/σ)max = 0.004
83 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.76 e Å3
Crystal data top
C5H6ClN3V = 659.54 (13) Å3
Mr = 143.58Z = 4
Monoclinic, P21/cMo Kα radiation
a = 7.1256 (8) ŵ = 0.48 mm1
b = 7.8537 (8) ÅT = 296 K
c = 13.0769 (15) Å0.14 × 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)
Rint = 0.077
Tmin = 0.935, Tmax = 0.9443 standard reflections every 200 reflections
5910 measured reflections intensity decay: 1%
1157 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0570 restraints
wR(F2) = 0.143H-atom parameters constrained
S = 1.17Δρmax = 0.36 e Å3
1157 reflectionsΔρmin = 0.76 e Å3
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
xyzUiso*/Ueq
C10.6937 (3)0.4212 (2)0.33622 (15)0.0279 (4)
C20.9835 (3)0.2642 (2)0.42236 (17)0.0304 (5)
C30.9496 (3)0.2568 (2)0.51731 (17)0.0336 (5)
H31.04040.19800.58140.040*
C40.7729 (3)0.3408 (2)0.51565 (15)0.0286 (4)
C51.1670 (3)0.1823 (3)0.4147 (2)0.0463 (6)
H5A1.25510.13150.48630.069*
H5B1.24420.26690.39580.069*
H5C1.11930.09610.35690.069*
Cl10.51828 (9)0.52705 (8)0.21459 (4)0.0494 (3)
N10.8510 (2)0.34779 (19)0.32654 (13)0.0305 (4)
N20.6439 (2)0.42741 (19)0.42172 (13)0.0288 (4)
N30.7236 (3)0.3407 (3)0.60284 (15)0.0416 (5)
H3A0.61440.39390.59780.050*
H3B0.80090.28740.66420.050*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0323 (9)0.0294 (9)0.0252 (9)0.0011 (7)0.0154 (7)0.0003 (7)
C20.0321 (9)0.0291 (9)0.0321 (11)0.0023 (7)0.0158 (7)0.0051 (7)
C30.0348 (10)0.0346 (10)0.0300 (10)0.0008 (7)0.0126 (8)0.0023 (7)
C40.0340 (9)0.0300 (9)0.0250 (9)0.0042 (7)0.0159 (7)0.0013 (7)
C50.0422 (11)0.0513 (13)0.0525 (14)0.0096 (10)0.0271 (10)0.0002 (10)
Cl10.0559 (5)0.0652 (5)0.0326 (4)0.0224 (3)0.0245 (3)0.0176 (2)
N10.0348 (8)0.0331 (8)0.0289 (9)0.0021 (6)0.0187 (7)0.0044 (6)
N20.0332 (8)0.0315 (8)0.0267 (8)0.0006 (6)0.0177 (7)0.0003 (6)
N30.0466 (10)0.0571 (11)0.0284 (9)0.0088 (8)0.0232 (8)0.0095 (8)
Geometric parameters (Å, º) top
C1—N21.313 (3)C4—N31.331 (3)
C1—N11.315 (2)C4—N21.356 (2)
C1—Cl11.7494 (18)C5—H5A0.9600
C2—N11.366 (3)C5—H5B0.9600
C2—C31.365 (3)C5—H5C0.9600
C2—C51.499 (3)N3—H3A0.8600
C3—C41.413 (3)N3—H3B0.8600
C3—H30.9300
N2—C1—N1130.94 (17)C2—C5—H5A109.5
N2—C1—Cl1113.97 (13)C2—C5—H5B109.5
N1—C1—Cl1115.09 (14)H5A—C5—H5B109.5
N1—C2—C3122.03 (16)C2—C5—H5C109.5
N1—C2—C5114.88 (18)H5A—C5—H5C109.5
C3—C2—C5123.09 (19)H5B—C5—H5C109.5
C2—C3—C4118.28 (17)C1—N1—C2113.67 (16)
C2—C3—H3120.9C1—N2—C4115.17 (16)
C4—C3—H3120.9C4—N3—H3A120.0
N3—C4—N2116.70 (17)C4—N3—H3B120.0
N3—C4—C3123.43 (18)H3A—N3—H3B120.0
N2—C4—C3119.88 (17)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N2i0.862.243.090 (3)170
N3—H3B···N1ii0.862.263.045 (2)152
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H6ClN3
Mr143.58
Crystal system, space groupMonoclinic, P21/c
Temperature (K)296
a, b, c (Å)7.1256 (8), 7.8537 (8), 13.0769 (15)
β (°) 115.678 (1)
V3)659.54 (13)
Z4
Radiation typeMo Kα
µ (mm1)0.48
Crystal size (mm)0.14 × 0.12 × 0.12
Data collection
DiffractometerEnraf–Nonius CAD-4
diffractometer
Absorption correctionψ scan
(North et al., 1968)
Tmin, Tmax0.935, 0.944
No. of measured, independent and
observed [I > 2σ(I)] reflections
5910, 1157, 1103
Rint0.077
(sin θ/λ)max1)0.594
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.057, 0.143, 1.17
No. of reflections1157
No. of parameters83
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)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···AD—HH···AD···AD—H···A
N3—H3A···N2i0.862.243.090 (3)170
N3—H3B···N1ii0.862.263.045 (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

First citationAllen, 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
First citationEnraf–Nonius (1985). CAD-4 Software. Enraf–Nonius, Delft, The Netherlands.
First citationGraceffa, R., Kaller, M. & La, D. (2010). US Patent No. 20100120774.
First citationHarms, K. & Wocadlo, S. (1995). XCAD4. University of Marburg, Germany.
First citationNorth, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.  CrossRef IUCr Journals Web of Science
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals

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COMMUNICATIONS
ISSN: 2056-9890
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