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Acta Crystallogr Sect E Struct Rep Online. 2010 October 1; 66(Pt 10): o2638.
Published online 2010 September 25. doi:  10.1107/S160053681003758X
PMCID: PMC2983305

2,6-Dichloro­pyridine-3,5-dicarbonitrile

Abstract

In the crystal, essentially planar (r.m.s. deviation = 0.003 Å) mol­ecules of the title compound, C7HCl2N3, form chains along the b axis by means of C—H(...)N inter­actions. These chains are further linked into layers parallel to the ab plane by C—Cl(...)N inter­actions.

Related literature

For the structures of related pyridine derivatives, see: Boer et al. (1972 [triangle]); Clegg et al. (1997 [triangle]); Julia et al. (1983 [triangle]); Schlosser et al. (2006 [triangle]); Schmidt et al. (2005 [triangle]); Smith et al. (2008 [triangle]). For more information on the synthesis of 2,6-dichloro­pyridine-3,5-dicarbonitrile, see: Duindam et al. (1993 [triangle]). For compounds obtained from 2,6-dichloro­pyridine-3,5-dicarbonitrile, see: Katz et al. (2005 [triangle]); Vilarelle et al. (2004 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-o2638-scheme1.jpg

Experimental

Crystal data

  • C7HCl2N3
  • M r = 198.01
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2638-efi1.jpg
  • a = 6.8473 (9) Å
  • b = 12.1307 (15) Å
  • c = 19.430 (3) Å
  • V = 1613.9 (4) Å3
  • Z = 8
  • Mo Kα radiation
  • μ = 0.74 mm−1
  • T = 297 K
  • 0.41 × 0.39 × 0.39 mm

Data collection

  • Bruker SMART APEX CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2000 [triangle]) T min = 0.751, T max = 0.761
  • 10614 measured reflections
  • 1420 independent reflections
  • 1328 reflections with I > 2σ(I)
  • R int = 0.049

Refinement

  • R[F 2 > 2σ(F 2)] = 0.067
  • wR(F 2) = 0.133
  • S = 1.29
  • 1420 reflections
  • 109 parameters
  • H-atom parameters constrained
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.33 e Å−3

Data collection: SMART (Bruker, 2000 [triangle]); cell refinement: SAINT-Plus (Bruker, 2001 [triangle]); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg & Putz, 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Intermolecular interactions (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, New_Global_Publ_Block. DOI: 10.1107/S160053681003758X/ya2129sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S160053681003758X/ya2129Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the National University Research Council of Romania (CNCSIS–UEFISCSU); project number PNII–IDEI 570/2007. We thank Dr Ciprian Rat for helpful disussions and advice.

supplementary crystallographic information

Comment

Some pyridine derivatives are known to be important intermediates in pharmaceutical and medicinal chemistry. They can be used for the synthesis of various compounds having antibacterial, antianaphilactic, antipyretic, antiallergic or anticancer properties (Vilarelle et al., 2004). Lately, pyridine derivatives were used in the synthesis of cage molecules, supramolecular structures which are important as tools for the study of molecular encapsulation and host–guest interactions (Katz et al., 2005).

Relatively few crystal structures of pyridines substituted in positions 2 and 6 with chlorine atoms were published (Boer et al., 1972; Clegg et al., 1997; Julia et al., 1983; Schlosser et al., 2006; Schmidt et al., 2005; Smith et al., 2008). The synthesis of the title compound has been reported some years ago (Duindam et al., 1993), however its crystal structure has not yet been determined, even though electron withdrawing CN groups, causing considerable acidity of the H atom in position 4, as well as chlorine substituents at the pyridine atoms adjacent to the endocyclic N atom, may give rise to important non-conventional intermolecular interactions. Therefore, one may expect that structural study of the title compound may provide some non-trivial information.

Molecule of the title compound (Fig. 1) is essentially planar; the N2 and N3 atoms deviate from the pyridine plane by 0.060 (4) Å and 0.026 (4) Å respectively.

The molecules are linked by means of C3—H3···N1i ineractions (Table 1) into infinite chains running along the b axis. The pyridine rings in the adjacent molecules of these chains are not coplanar, but rather form substantial dihedral angle with one another [56.5 (1)°]. The chains are further linked via C1—Cl1···N2ii and C5—Cl2···N3iii interactions into layers parallel to the ab-plane (Table 1; Fig. 2).

Experimental

A mixture of malononitrile (5 g, 75.69 mmol, 2 equiv.), triethyl orthoformate (5.61 g, 37.84 mmol, 1 equiv.) and pyridine (2.99 g, 37.84 mmol, 1 equiv.) was allowed to reflux for 20 minutes, then concentrated HCl was added at 80°C. The mixture was cooled to room temperature and water (20 ml) was added. The formed precipitate was collected by filtration, washed successively with water, ethanol and diethylether to afford the intermediate 2-amino-6-chloropyridine-3,5-dicarbonitrile (9.74 g, 96%). To a solution of 2-amino-6-chloropyridine-3,5-dicarbonitrile (3 g, 16.8 mmol, 1 equiv.) and CuCl2 (3.39 g, 25.2 mmol, 1.5 equiv.) in dry CH3CN (150 ml), isopentyl nitrite was added (2.95 g, 25.2 mmol, 1.5 equiv.). The mixture was heated at 65°C for 5 h. The solution was acidified (HCl, 2 N) to pH=3, extracted with CH2Cl2 (3×50 ml) and dried with Na2SO4. The solvent was removed under reduced pressure and the crude product was purified by flash chromatography using CH2Cl2 as eluent to yield 2,6-dichloropyridine-3,5-dicarbonitrile as a colourless solid (2.97 g, 89%). The crystals were obtained by slow evaporation of the solvent from solution of the title compound in dichloromethane.

Refinement

The H3 atom was placed in calculated position (C—H = 0.93 Å) and treated in the subsequent refinement using the riding model approximation with Uiso= 1.2Ueq(C).

Figures

Fig. 1.
Molecular structure of the title compound; displacement ellipsoids are drawn at the 50% probability level, and the H3 atom is shown as a circle of arbitrary small radius.
Fig. 2.
Packing diagram for the crystal of the title compound viewed down the b axis. The C—H···N and Cl···N interactions are shown as dashed lines.

Crystal data

C7HCl2N3F(000) = 784
Mr = 198.01Dx = 1.630 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 4078 reflections
a = 6.8473 (9) Åθ = 3.1–26.1°
b = 12.1307 (15) ŵ = 0.74 mm1
c = 19.430 (3) ÅT = 297 K
V = 1613.9 (4) Å3Block, colourless
Z = 80.41 × 0.39 × 0.39 mm

Data collection

Bruker SMART APEX CCD area-detector diffractometer1420 independent reflections
Radiation source: fine-focus sealed tube1328 reflections with I > 2σ(I)
graphiteRint = 0.049
phi and ω scansθmax = 25.0°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2000)h = −8→8
Tmin = 0.751, Tmax = 0.761k = −14→14
10614 measured reflectionsl = −23→23

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.067Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.133H-atom parameters constrained
S = 1.29w = 1/[σ2(Fo2) + (0.0317P)2 + 2.8365P] where P = (Fo2 + 2Fc2)/3
1420 reflections(Δ/σ)max < 0.001
109 parametersΔρmax = 0.25 e Å3
0 restraintsΔρmin = −0.33 e Å3

Special details

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)

xyzUiso*/Ueq
C10.9151 (5)0.3589 (3)0.4007 (2)0.0375 (9)
C20.8734 (5)0.2479 (3)0.40946 (19)0.0364 (9)
C30.7015 (5)0.2084 (3)0.38179 (18)0.0368 (9)
H30.66870.13430.38610.044*
C40.5791 (5)0.2801 (3)0.34764 (18)0.0332 (8)
C50.6383 (6)0.3884 (3)0.34168 (19)0.0390 (9)
C61.0034 (6)0.1770 (4)0.4467 (2)0.0474 (10)
C70.3992 (6)0.2425 (3)0.3184 (2)0.0438 (10)
Cl11.12351 (16)0.41416 (10)0.43512 (6)0.0578 (4)
Cl20.49486 (18)0.48205 (10)0.29881 (6)0.0604 (4)
N10.8014 (5)0.4280 (3)0.36795 (16)0.0404 (8)
N21.1049 (6)0.1222 (3)0.4775 (2)0.0683 (12)
N30.2550 (6)0.2128 (4)0.29590 (19)0.0630 (11)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.033 (2)0.040 (2)0.039 (2)−0.0043 (18)0.0058 (17)−0.0067 (17)
C20.035 (2)0.0368 (19)0.0372 (19)0.0031 (18)−0.0002 (16)−0.0039 (17)
C30.042 (2)0.0271 (18)0.041 (2)−0.0021 (17)0.0037 (18)−0.0046 (16)
C40.0343 (19)0.0314 (19)0.0339 (19)0.0003 (16)0.0020 (16)−0.0033 (15)
C50.041 (2)0.037 (2)0.039 (2)0.0048 (18)0.0058 (18)0.0025 (17)
C60.048 (2)0.047 (2)0.048 (2)0.003 (2)−0.003 (2)−0.009 (2)
C70.048 (2)0.041 (2)0.042 (2)−0.001 (2)−0.003 (2)−0.0012 (18)
Cl10.0412 (6)0.0622 (7)0.0699 (8)−0.0128 (5)−0.0045 (5)−0.0138 (6)
Cl20.0611 (7)0.0487 (6)0.0714 (8)0.0081 (6)−0.0105 (6)0.0191 (5)
N10.0417 (19)0.0334 (17)0.0461 (19)−0.0030 (15)0.0061 (16)−0.0011 (15)
N20.067 (3)0.064 (3)0.074 (3)0.025 (2)−0.020 (2)−0.007 (2)
N30.054 (2)0.075 (3)0.060 (2)−0.014 (2)−0.013 (2)0.002 (2)

Geometric parameters (Å, °)

C1—N11.309 (5)C4—C51.380 (5)
C1—C21.387 (5)C4—C71.430 (5)
C1—Cl11.713 (4)C5—N11.319 (5)
C2—C31.380 (5)C5—Cl21.717 (4)
C2—C61.434 (6)C6—N21.133 (5)
C3—C41.378 (5)C7—N31.139 (5)
C3—H30.9300
N1—C1—C2124.0 (4)C3—C4—C5117.6 (3)
N1—C1—Cl1115.8 (3)C3—C4—C7120.9 (3)
C2—C1—Cl1120.2 (3)C5—C4—C7121.6 (3)
C3—C2—C1117.7 (3)N1—C5—C4124.3 (4)
C3—C2—C6121.2 (4)N1—C5—Cl2115.5 (3)
C1—C2—C6121.1 (4)C4—C5—Cl2120.2 (3)
C4—C3—C2119.1 (3)N2—C6—C2178.4 (5)
C4—C3—H3120.4N3—C7—C4179.2 (5)
C2—C3—H3120.4C1—N1—C5117.3 (3)
N1—C1—C2—C30.1 (6)C3—C4—C5—N1−1.8 (6)
Cl1—C1—C2—C3178.7 (3)C7—C4—C5—N1179.4 (4)
N1—C1—C2—C6−179.2 (4)C3—C4—C5—Cl2179.1 (3)
Cl1—C1—C2—C6−0.6 (5)C7—C4—C5—Cl20.3 (5)
C1—C2—C3—C4−0.6 (5)C2—C1—N1—C5−0.3 (6)
C6—C2—C3—C4178.7 (4)Cl1—C1—N1—C5−179.0 (3)
C2—C3—C4—C51.4 (5)C4—C5—N1—C11.2 (6)
C2—C3—C4—C7−179.8 (3)Cl2—C5—N1—C1−179.6 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C3—H3···N1i0.932.543.412 (5)157
C1—Cl1···N2ii1.713 (4)3.241 (4)4.820 (5)151.9 (2)
C5—Cl2···N3iii1.717 (4)3.281 (5)4.851 (6)150.6 (2)

Symmetry codes: (i) −x+3/2, y−1/2, z; (ii) −x+5/2, y+1/2, z; (iii) −x+1/2, y+1/2, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: YA2129).

References

  • Boer, F. P., Turley, J. W. & Van Remoortere, F. P. (1972). Chem. Commun. pp. 573–574.
  • Brandenburg, K. & Putz, H. (2006). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Bruker (2000). SMART and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruker (2001). SAINT-Plus Bruker AXS Inc., Madison, Wisconsin, USA.
  • Clegg, W., Elsegood, M. R. J., Jackson, R. F. W., Fraser, J. L. & Emsden, L. J. (1997). Acta Cryst. C53, 797–799.
  • Duindam, A., Lishinsky, V. L. & Sikkema, D. J. (1993). Synth. Commun.23, 2605–2609.
  • Julia, L., Suschitzky, H., Barnes, J. C. & Tomlin, C. D. S. (1983). J. Chem. Soc. Perkin Trans. 1, pp. 2507–2511.
  • Katz, J. L., Selby, K. J. & Conry, R. R. (2005). Org. Lett.7, 3505–3507. [PubMed]
  • Schlosser, M., Heiss, C., Marzi, E. & Scopelliti, R. (2006). Eur. J. Org. Chem. pp. 4398–4404.
  • Schmidt, A., Mordhorst, T. & Nieger, M. (2005). Org. Biomol. Chem.3, 3788–3793. [PubMed]
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Smith, A. E., Clapham, K. M., Batsanov, A. S., Bryce, M. R. & Tarbit, B. (2008). Eur. J. Org. Chem. pp. 1458–1463.
  • Vilarelle, D. V., Veira, C. P. & Quintela Lopez, J. M. (2004). Tetrahedron, 60, 275–283.
  • Westrip, S. P. (2010). J. Appl. Cryst.43, 920–925.

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