organic compounds
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
In the 5H6ClN3, 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.
of the title compound, CRelated 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
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Refinement
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Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell 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
10.1107/S1600536812047794/su2530sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536812047794/su2530Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536812047794/su2530Isup3.cml
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.
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.
Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell
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).C5H6ClN3 | F(000) = 296 |
Mr = 143.58 | Dx = 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 |
Enraf–Nonius CAD-4 diffractometer | 1103 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.077 |
Graphite monochromator | θmax = 25.0°, θmin = 3.2° |
ω/2θ scans | h = −8→8 |
Absorption correction: ψ scan (North et al., 1968) | k = −8→9 |
Tmin = 0.935, Tmax = 0.944 | l = −15→15 |
5910 measured reflections | 3 standard reflections every 200 reflections |
1157 independent reflections | intensity decay: 1% |
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(Fo2) + (0.0881P)2 + 0.2103P] where P = (Fo2 + 2Fc2)/3 |
1157 reflections | (Δ/σ)max = 0.004 |
83 parameters | Δρmax = 0.36 e Å−3 |
0 restraints | Δρmin = −0.76 e Å−3 |
C5H6ClN3 | V = 659.54 (13) Å3 |
Mr = 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)° |
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 = 0.944 | 3 standard reflections every 200 reflections |
5910 measured reflections | intensity decay: 1% |
1157 independent reflections |
R[F2 > 2σ(F2)] = 0.057 | 0 restraints |
wR(F2) = 0.143 | H-atom parameters constrained |
S = 1.17 | Δρmax = 0.36 e Å−3 |
1157 reflections | Δρmin = −0.76 e Å−3 |
83 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
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* |
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) |
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) |
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 |
Mr | 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) |
Tmin, Tmax | 0.935, 0.944 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5910, 1157, 1103 |
Rint | 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 |
Δρmax, Δρmin (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).
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
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
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).