organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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Crystal structure of 4,6-di­chloro-5-methyl­pyrimidine

aLaboratory of Crystallography, Department of Physics, University Mentouri Brothers Constantine, 25000 Constantine, Algeria, and bUMR 6226 CNRS University of Rennes 1 `Chemical Sciences Rennes', `Team Systems and Synthetic Condensed Electroactive', 263 Avenue du General Leclerc, F-35042 Rennes, France
*Correspondence e-mail: medjanimeriem@yahoo.fr

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 11 December 2015; accepted 14 December 2015; online 19 December 2015)

The title compound, C5H4Cl2N2, is essentially planar with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for an N atom. In the crystal, mol­ecules are linked by pairs of C—H⋯N hydrogen bonds, forming inversion dimers, enclosing an R22(6) ring motif.

1. Related literature

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993[Condon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Prot. Conf. Weeds, pp. 41-46 Alton, Hampshire, England: BCPC Publications.]); as agrochemicals, see: Maeno et al. (1990[Maeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415-422 Alton, Hampshire, England: BCPC Publications.]); as anti­viral agents, see: Gilchrist (1997[Gilchrist, T. L. (1997). Heterocycl. Chem. 3rd ed., pp. 261-276. Singapore: Addison Wesley Longman.]); as herbicides, see: Selby et al. (2002[Selby, T. P., Drumm, J. E., Coats, R. A., Coppo, F. T., Gee, S. K., Hay, J. V., Pasteris, R. J. & Stevenson, T. M. (2002). ACS Symposium Series, Vol. 800, Synthesis and Chemistry of Agrochemicals VI, pp. 74-84. Washington DC: American Chemical Society.]); Zhu et al. (2007[Zhu, Y.-Q., Zou, X.-M., Li, G.-C., Yao, C.-S. & Yang, H.-Z. (2007). Chin. J. Org. Chem. 27, 753-757.]); and for applications of organoselenide compounds, see: Ip et al. (1997[Ip, C., Lisk, D. J., Ganther, H. & Thompson, H. J. (1997). Anticancer Res. 17, 3195-3199.]). For the crystal structure of 5-methyl­pyrimidine, see: Furberg et al. (1979[Furberg, S., Grøgaard, J. & Smedsrud, B. (1979). Acta Chem. Scand. 33b, 715-724.]).

[Scheme 1]

2. Experimental

2.1. Crystal data

  • C5H4Cl2N2

  • Mr = 163.00

  • Monoclinic, P 21 /n

  • a = 7.463 (5) Å

  • b = 7.827 (5) Å

  • c = 11.790 (5) Å

  • β = 93.233 (5)°

  • V = 687.6 (7) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.85 mm−1

  • T = 293 K

  • 0.11 × 0.10 × 0.08 mm

2.2. Data collection

  • Oxford Diffraction Xcalibur, Eos diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2013[Oxford Diffraction (2013). CrysAlis PRO. Oxford Diffraction Ltd., Abingdon, UK.]) Tmin = 0.922, Tmax = 0.934

  • 2347 measured reflections

  • 1228 independent reflections

  • 791 reflections with I > 2σ(I)

  • Rint = 0.099

2.3. Refinement

  • R[F2 > 2σ(F2)] = 0.068

  • wR(F2) = 0.173

  • S = 1.01

  • 1228 reflections

  • 83 parameters

  • H-atom parameters constrained

  • Δρmax = 0.39 e Å−3

  • Δρmin = −0.38 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯N3i 0.93 2.66 3.468 (6) 146
Symmetry code: (i) -x, -y+1, -z+1.

Data collection: CrysAlis PRO (Oxford Diffraction, 2013[Oxford Diffraction (2013). CrysAlis PRO. Oxford Diffraction Ltd., Abingdon, UK.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL2014/6 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]); software used to prepare material for publication: SHELXL2014/6 and PLATON.

Supporting information


Comments top

Pyrimidines have inter­esting biological properties with applications as pesticides, pharmaceutical agents (Condon et al., 1993; Maeno et al., 1990) and are also inter­esting from a biochemical pint of view and applications of organoselenide compounds (Ip et al., 1997). Pyrimidine derivatives have been developed as anti­viral agents, such as AZT, which is the anti-AIDS drug most widely used (Gilchrist, 1997). Recently, a new series of highly substituted pyrimidine herbicides have been reported (Selby et al., 2002; Zhu et al., 2007). In the present study, we were inter­ested in examining a derivative of pyrimidine with a methyl substituent surrounded by two chlorine atoms.

The molecular structure of the title compound is shown in Fig. 1. The molecule is planar, as is typical in benzenes substituted by halogen atoms and methyl groups, with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for atom N3. The bond distances and bond angles in the molecule are similar to those reported for 5-methyl­pyrimidine (Furberg et al., 1979).

In the crystal, molecules are linked by a pair of C—H···N hydrogen bonds forming inversion dimers (Table 1 and Fig. 2), enclosing an R22(6) ring motif.

Synthesis and crystallization top

The commercially available title compound (Sigma-Aldrich) was recrystallized from ethanol giving colourless prismatic crystals.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were localized in a difference Fourier map but introduced in calculated positions and treated as riding: C—H = 0.93-0.96 Å with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other H atoms.

Related literature top

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993); as agrochemicals, see: Maeno et al. (1990); as antiviral agents, see: Gilchrist (1997); as herbicides, see: Selby et al. (2002); Zhu et al. (2007); and for applications of organoselenide compounds, see: Ip et al. (1997). For the crystal structure of 5-methylpyrimidine, see: Furberg et al. (1979).

Structure description top

Pyrimidines have inter­esting biological properties with applications as pesticides, pharmaceutical agents (Condon et al., 1993; Maeno et al., 1990) and are also inter­esting from a biochemical pint of view and applications of organoselenide compounds (Ip et al., 1997). Pyrimidine derivatives have been developed as anti­viral agents, such as AZT, which is the anti-AIDS drug most widely used (Gilchrist, 1997). Recently, a new series of highly substituted pyrimidine herbicides have been reported (Selby et al., 2002; Zhu et al., 2007). In the present study, we were inter­ested in examining a derivative of pyrimidine with a methyl substituent surrounded by two chlorine atoms.

The molecular structure of the title compound is shown in Fig. 1. The molecule is planar, as is typical in benzenes substituted by halogen atoms and methyl groups, with an r.m.s. deviation for all non-H atoms of 0.009 Å. The largest deviation from the mean plane is 0.016 (4) Å for atom N3. The bond distances and bond angles in the molecule are similar to those reported for 5-methyl­pyrimidine (Furberg et al., 1979).

In the crystal, molecules are linked by a pair of C—H···N hydrogen bonds forming inversion dimers (Table 1 and Fig. 2), enclosing an R22(6) ring motif.

For the applications of pyrimidine derivatives as pesticides and pharmaceutical agents, see: Condon et al. (1993); as agrochemicals, see: Maeno et al. (1990); as antiviral agents, see: Gilchrist (1997); as herbicides, see: Selby et al. (2002); Zhu et al. (2007); and for applications of organoselenide compounds, see: Ip et al. (1997). For the crystal structure of 5-methylpyrimidine, see: Furberg et al. (1979).

Synthesis and crystallization top

The commercially available title compound (Sigma-Aldrich) was recrystallized from ethanol giving colourless prismatic crystals.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were localized in a difference Fourier map but introduced in calculated positions and treated as riding: C—H = 0.93-0.96 Å with Uiso(H) = 1.5Ueq(C-methyl) and 1.2Ueq(C) for other H atoms.

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2013); cell refinement: CrysAlis PRO (Oxford Diffraction, 2013); data reduction: CrysAlis PRO (Oxford Diffraction, 2013); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL2014/6 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014/6 (Sheldrick, 2015) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labelling. Displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed along the b axis. Hydrogen bonds are shown as dashed lines (see Table 1).
4,6-Dichloro-5-methylpyrimidine top
Crystal data top
C5H4Cl2N2F(000) = 328
Mr = 163.00Dx = 1.575 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
a = 7.463 (5) ÅCell parameters from 776 reflections
b = 7.827 (5) Åθ = 4.2–27.8°
c = 11.790 (5) ŵ = 0.85 mm1
β = 93.233 (5)°T = 293 K
V = 687.6 (7) Å3Prism, colourless
Z = 40.11 × 0.10 × 0.08 mm
Data collection top
Oxford Diffraction Xcalibur, Eos
diffractometer
1228 independent reflections
Radiation source: Enhance (Mo) X-ray Source791 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.099
CCD rotation images, thin slices ω scansθmax = 25.2°, θmin = 3.1°
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2013)
h = 88
Tmin = 0.922, Tmax = 0.934k = 94
2347 measured reflectionsl = 1410
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)] = 0.068Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.173H-atom parameters constrained
S = 1.01 w = 1/[σ2(Fo2) + (0.0729P)2]
where P = (Fo2 + 2Fc2)/3
1228 reflections(Δ/σ)max < 0.001
83 parametersΔρmax = 0.39 e Å3
0 restraintsΔρmin = 0.38 e Å3
Crystal data top
C5H4Cl2N2V = 687.6 (7) Å3
Mr = 163.00Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.463 (5) ŵ = 0.85 mm1
b = 7.827 (5) ÅT = 293 K
c = 11.790 (5) Å0.11 × 0.10 × 0.08 mm
β = 93.233 (5)°
Data collection top
Oxford Diffraction Xcalibur, Eos
diffractometer
1228 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2013)
791 reflections with I > 2σ(I)
Tmin = 0.922, Tmax = 0.934Rint = 0.099
2347 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0680 restraints
wR(F2) = 0.173H-atom parameters constrained
S = 1.01Δρmax = 0.39 e Å3
1228 reflectionsΔρmin = 0.38 e Å3
83 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cl140.47393 (16)0.21816 (17)0.57181 (8)0.0686 (5)
Cl160.45631 (17)0.4430 (2)0.13763 (9)0.0853 (6)
N10.2066 (5)0.4832 (6)0.2775 (3)0.0604 (11)
N30.2153 (5)0.3882 (5)0.4695 (3)0.0579 (10)
C20.1383 (6)0.4657 (7)0.3784 (4)0.0661 (14)
H20.02510.51230.38650.079*
C40.3744 (5)0.3225 (5)0.4544 (3)0.0458 (10)
C50.4659 (5)0.3309 (6)0.3546 (3)0.0458 (10)
C60.3650 (6)0.4175 (6)0.2685 (3)0.0514 (11)
C510.6464 (6)0.2553 (7)0.3426 (4)0.0666 (14)
H51A0.70410.31210.28230.100*
H51B0.63440.13590.32520.100*
H51C0.71750.26920.41240.100*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl140.0846 (9)0.0601 (9)0.0604 (6)0.0009 (7)0.0019 (6)0.0089 (5)
Cl160.0934 (11)0.1053 (14)0.0592 (7)0.0109 (9)0.0219 (6)0.0116 (6)
N10.057 (2)0.061 (3)0.063 (2)0.005 (2)0.0033 (16)0.0012 (19)
N30.057 (2)0.057 (3)0.0602 (19)0.000 (2)0.0160 (15)0.0040 (17)
C20.050 (2)0.074 (4)0.075 (3)0.008 (3)0.005 (2)0.008 (3)
C40.045 (2)0.039 (3)0.0537 (19)0.003 (2)0.0041 (16)0.0034 (18)
C50.042 (2)0.039 (3)0.057 (2)0.005 (2)0.0089 (16)0.0056 (17)
C60.054 (2)0.053 (3)0.0475 (18)0.004 (2)0.0070 (16)0.0023 (18)
C510.051 (3)0.070 (4)0.081 (3)0.007 (3)0.016 (2)0.002 (2)
Geometric parameters (Å, º) top
Cl14—C41.737 (4)C4—C51.395 (5)
Cl16—C61.733 (4)C5—C61.403 (6)
N1—C61.299 (6)C5—C511.486 (6)
N1—C21.327 (5)C51—H51A0.9600
N3—C41.315 (5)C51—H51B0.9600
N3—C21.335 (5)C51—H51C0.9600
C2—H20.9300
C6—N1—C2115.4 (3)C6—C5—C51125.2 (4)
C4—N3—C2114.8 (3)N1—C6—C5125.9 (3)
N1—C2—N3126.8 (4)N1—C6—Cl16115.6 (3)
N1—C2—H2116.6C5—C6—Cl16118.5 (3)
N3—C2—H2116.6C5—C51—H51A109.5
N3—C4—C5125.7 (4)C5—C51—H51B109.5
N3—C4—Cl14115.1 (3)H51A—C51—H51B109.5
C5—C4—Cl14119.2 (3)C5—C51—H51C109.5
C4—C5—C6111.4 (4)H51A—C51—H51C109.5
C4—C5—C51123.4 (4)H51B—C51—H51C109.5
C6—N1—C2—N30.2 (8)Cl14—C4—C5—C510.2 (6)
C4—N3—C2—N10.7 (8)C2—N1—C6—C50.5 (8)
C2—N3—C4—C51.3 (7)C2—N1—C6—Cl16179.0 (4)
C2—N3—C4—Cl14178.9 (4)C4—C5—C6—N10.1 (7)
N3—C4—C5—C61.1 (6)C51—C5—C6—N1179.5 (5)
Cl14—C4—C5—C6179.2 (3)C4—C5—C6—Cl16179.6 (3)
N3—C4—C5—C51179.5 (4)C51—C5—C6—Cl161.0 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···N3i0.932.663.468 (6)146
Symmetry code: (i) x, y+1, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···N3i0.932.663.468 (6)146
Symmetry code: (i) x, y+1, z+1.
 

Acknowledgements

This work is supported by the Laboratoire de Cristallographie, Département de Physique, Université Mentouri-Constantine, Algeria, and the UMR 6226 CNRS-Université Rennes 1 `Sciences Chimiques de Rennes', France. We would also like to thank Mr F. Saidi, Engineer at the Université Mentouri-Constantine, for assistance with the data collection.

References

First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationCondon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Prot. Conf. Weeds, pp. 41–46 Alton, Hampshire, England: BCPC Publications.  Google Scholar
First citationFurberg, S., Grøgaard, J. & Smedsrud, B. (1979). Acta Chem. Scand. 33b, 715–724.  CrossRef Web of Science Google Scholar
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First citationOxford Diffraction (2013). CrysAlis PRO. Oxford Diffraction Ltd., Abingdon, UK.  Google Scholar
First citationSelby, T. P., Drumm, J. E., Coats, R. A., Coppo, F. T., Gee, S. K., Hay, J. V., Pasteris, R. J. & Stevenson, T. M. (2002). ACS Symposium Series, Vol. 800, Synthesis and Chemistry of Agrochemicals VI, pp. 74–84. Washington DC: American Chemical Society.  Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
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