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Acta Crystallogr Sect E Struct Rep Online. 2009 March 1; 65(Pt 3): o643.
Published online 2009 February 28. doi:  10.1107/S1600536809006783
PMCID: PMC2968665

2-(3-Chloro-1,2-dihydro­pyrazin-2-yl­idene)malononitrile

Abstract

In the crystal structure of the title compound, C7H3ClN4, neighbouring mol­ecules are linked via pairs of N—H(...)N hydrogen bonds into inversion dimers, thereby forming an R 2 2(12) ring motif. With respective average deviations from planarity of 0.009 (1) and 0.006 (1) Å, the pyrazine skeleton and the malononitrile fragment are oriented at an angle of 6.0 (1)° with respect to each other. The mean planes of the pyrazine ring lie either parallel or are inclined at an angle of 68.5 (1)° in the crystal structure.

Related literature

For applications of this class of compounds, see: Daniel et al. (1947 [triangle]); Dutcher (1947 [triangle], 1958 [triangle]); Matter et al. (2005 [triangle]); Kaliszan et al. (1985 [triangle]); Lampen & Jones (1946 [triangle]); Petrusewicz et al. (1993 [triangle], 1995 [triangle]); White (1940 [triangle]); White & Hill (1943 [triangle]). For related structures, see: Vishweshwar et al. (2000 [triangle]); Wardell et al. (2006 [triangle]). For the synthesis, see: Pilarski & Foks (1981 [triangle], 1982 [triangle]). For the analysis of inter­molecular inter­actions, see: Spek (2009 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o643-scheme1.jpg

Experimental

Crystal data

  • C7H3ClN4
  • M r = 178.58
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o643-efi1.jpg
  • a = 5.7612 (2) Å
  • b = 8.1457 (2) Å
  • c = 16.2296 (5) Å
  • β = 94.116 (3)°
  • V = 759.67 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.44 mm−1
  • T = 295 K
  • 0.40 × 0.10 × 0.08 mm

Data collection

  • Oxford Diffraction Ruby CCD diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008 [triangle]) T min = 0.946, T max = 0.967
  • 6880 measured reflections
  • 1335 independent reflections
  • 1060 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.084
  • S = 1.10
  • 1335 reflections
  • 109 parameters
  • H-atom parameters constrained
  • Δρmax = 0.15 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2008 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2008 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPII (Johnson, 1976 [triangle]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809006783/xu2486sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006783/xu2486Isup2.hkl

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

Acknowledgments

This scientific work has been supported by Funds for Science in Year 2009 as a research project (DS/8410–4–0139–9).

supplementary crystallographic information

Comment

The pyrazine ring is found in many physiologically active compounds, including natural products such as folic acid (Lampen & Jones, 1946), aspergillic acid (Dutcher, 1947), pterins (Daniel et al., 1947; Matter et al., 2005). Important group of natural compounds are derivatives which posses antibiotic activities, for examples aspegillic acid isolated from Aspergillus flavus (Dutcher, 1958; White, 1940; White & Hill, 1943). Some of pyrazine-acetonitrile compounds also posses biological activities. Some of them show anti-inflammatory (Petrusewicz et al., 1995) and analgesic activities (Kaliszan et al., 1985; Petrusewicz et al., 1993). We decided to synthesis some of this derivatives. 2-(3-Chloropyrazin-2(1H)-ylidene)malononitrile belongs to pyrazine-acetonitrile derivatives. We report here crystal structure of the title compound, 2-(3-chloropyrazin-2(1H)-ylidene)malononitrile.

In the molecule of the title compound (Fig. 1) the bond lengths and angles characterizing the geometry of the pyrazines skeleton are typical for this group compounds (Vishweshwar et al., 2000; Wardell et al., 2006). With respective average deviations from planarity of 0.009 (1) and 0.006 (1) Å, the pyrazine skeleton and malononitrile fragment are oriented at an angle 6.0 (1)° to each other. The mean planes of the pyrazine skeleton lie either parallel or are inclined at an angle of 68.5 (1)° in the lattice. One of the nitrile fragment (delineated by C7, C8 and N9 atoms) is nearly in the plane of the heterocyclic ring (the angle between the mean planes of the pyrazine skeleton and nitrile fragment is equal 178.4 (2)°) while the other (involving C7, C10 and N11 atoms) is out of plane the pyrazine skeleton (the angle between the mean planes of the pyrazine skeleton and nitrile fragment is equal 172.8 (2)°).

In the crystal structure, neighbouring molecules are linked through N–H···N hydrogen bond forming R22(12) ring motif (Table 1 and Fig. 2). The interactions demonstrated were found by PLATON (Spek, 2009).

Experimental

2-[3-Chloropyrazin-2(1H)-ylidene)malononitrile was obtained by the aromatic nucleophilic substitution of chlorine in 2,3-dichloropyrazine with malononitrile (Pilarski & Foks, 1981 and 1982). A mixture of 2,3-dichloropyrazine, malononitrile and potassium carbonate was dissolved in DMSO. The mixture was stirred for 4 h in 333 K to give an orange solution. After cooling the reaction mixture to room temperature, water was added. Then mixture was acidified with hydrochloric acid. Single crystals suitable for X-ray analysis were grown in methanol solution [m.p. = 436 K].

Refinement

All H atoms were positioned geometrically and refined using a riding model, with C–H = 0.93 Å and Uiso(H) = 1.2Ueq(C) and N–H = 0.86 Å and Uiso(H) = 1.2Ueq(N).

Figures

Fig. 1.
The molecular structure of the title compound showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 25% probability level and H atoms are shown as small spheres of arbitrary radius.
Fig. 2.
The arrangement of the molecules in the crystal structure viewed approximately along a axis. The N—H···N interactions are represented by dashed lines. H atoms not involved in the interactions have been omitted. [Symmetry ...

Crystal data

C7H3ClN4F(000) = 360
Mr = 178.58Dx = 1.561 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1335 reflections
a = 5.7612 (2) Åθ = 3.0–25.0°
b = 8.1457 (2) ŵ = 0.44 mm1
c = 16.2296 (5) ÅT = 295 K
β = 94.116 (3)°Needle, orange
V = 759.67 (4) Å30.40 × 0.10 × 0.08 mm
Z = 4

Data collection

Oxford Diffraction Ruby CCD diffractometer1335 independent reflections
Radiation source: Enhance (Mo) X-ray Source1060 reflections with I > 2σ(I)
graphiteRint = 0.026
Detector resolution: 10.4002 pixels mm-1θmax = 25.0°, θmin = 3.6°
ω scansh = −6→6
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008)k = −9→9
Tmin = 0.946, Tmax = 0.967l = −18→19
6880 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.084w = 1/[σ2(Fo2) + (0.0481P)2 + 0.0305P] where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
1335 reflectionsΔρmax = 0.14 e Å3
109 parametersΔρmin = −0.19 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008)
Primary atom site location: structure-invariant direct methods

Special details

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.
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
N10.6636 (3)0.11965 (16)0.38343 (8)0.0365 (4)
H10.77970.07220.40980.044*
C20.5179 (3)0.20873 (19)0.42756 (10)0.0313 (4)
C30.3266 (3)0.2760 (2)0.37691 (10)0.0373 (4)
N40.2971 (3)0.25960 (19)0.29792 (10)0.0523 (5)
C50.4568 (4)0.1719 (3)0.25856 (12)0.0611 (6)
H50.43950.16130.20140.073*
C60.6386 (4)0.1004 (2)0.30035 (11)0.0508 (5)
H60.74520.03890.27300.061*
C70.5634 (3)0.22285 (19)0.51338 (9)0.0327 (4)
C80.7584 (3)0.13941 (19)0.55144 (10)0.0343 (4)
N90.9152 (3)0.0691 (2)0.58089 (9)0.0467 (4)
C100.4414 (3)0.3217 (2)0.56834 (11)0.0383 (4)
N110.3624 (3)0.3981 (2)0.61843 (11)0.0568 (5)
Cl120.11485 (8)0.38509 (6)0.42290 (3)0.0490 (2)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0352 (9)0.0416 (8)0.0323 (8)0.0067 (7)0.0001 (6)0.0014 (6)
C20.0292 (9)0.0286 (8)0.0364 (9)−0.0016 (7)0.0034 (7)0.0010 (7)
C30.0358 (10)0.0344 (9)0.0413 (10)0.0015 (8)−0.0009 (8)0.0016 (7)
N40.0591 (12)0.0544 (10)0.0416 (9)0.0133 (9)−0.0099 (8)−0.0002 (7)
C50.0793 (17)0.0700 (14)0.0324 (10)0.0224 (13)−0.0072 (11)−0.0037 (9)
C60.0608 (14)0.0565 (11)0.0351 (10)0.0137 (10)0.0041 (9)−0.0041 (8)
C70.0303 (10)0.0330 (8)0.0348 (9)0.0012 (7)0.0017 (7)0.0013 (7)
C80.0379 (11)0.0348 (9)0.0302 (9)−0.0012 (8)0.0037 (8)−0.0034 (7)
N90.0460 (11)0.0536 (9)0.0397 (9)0.0108 (8)−0.0029 (8)−0.0034 (7)
C100.0341 (11)0.0440 (10)0.0366 (10)0.0007 (8)0.0016 (8)0.0025 (8)
N110.0539 (11)0.0717 (11)0.0456 (10)0.0135 (9)0.0088 (8)−0.0075 (8)
Cl120.0368 (3)0.0530 (3)0.0568 (3)0.0114 (2)0.0017 (2)0.0011 (2)

Geometric parameters (Å, °)

N1—C21.353 (2)C5—C61.339 (3)
N1—C61.355 (2)C5—H50.9300
N1—H10.8600C6—H60.9300
C2—C71.403 (2)C7—C81.416 (2)
C2—C31.436 (2)C7—C101.424 (2)
C3—N41.288 (2)C8—N91.145 (2)
C3—Cl121.7219 (18)C10—N111.144 (2)
N4—C51.360 (3)
C2—N1—C6124.28 (15)C6—C5—H5119.3
C2—N1—H1117.9N4—C5—H5119.3
C6—N1—H1117.9C5—C6—N1118.50 (18)
N1—C2—C7119.36 (15)C5—C6—H6120.8
N1—C2—C3112.43 (15)N1—C6—H6120.8
C7—C2—C3128.20 (16)C2—C7—C8118.66 (14)
N4—C3—C2124.83 (17)C2—C7—C10127.03 (15)
N4—C3—Cl12116.00 (14)C8—C7—C10114.20 (14)
C2—C3—Cl12119.16 (13)N9—C8—C7178.40 (18)
C3—N4—C5118.48 (16)N11—C10—C7172.83 (19)
C6—C5—N4121.43 (18)
C6—N1—C2—C7−178.76 (16)C3—N4—C5—C61.5 (3)
C6—N1—C2—C32.4 (2)N4—C5—C6—N1−1.2 (3)
N1—C2—C3—N4−2.1 (3)C2—N1—C6—C5−0.9 (3)
C7—C2—C3—N4179.14 (17)N1—C2—C7—C8−1.6 (2)
N1—C2—C3—Cl12176.92 (11)C3—C2—C7—C8177.09 (16)
C7—C2—C3—Cl12−1.8 (3)N1—C2—C7—C10174.39 (16)
C2—C3—N4—C50.3 (3)C3—C2—C7—C10−6.9 (3)
Cl12—C3—N4—C5−178.77 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1···N9i0.862.102.896 (2)154

Symmetry codes: (i) −x+2, −y, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2486).

References

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