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Acta Crystallogr Sect E Struct Rep Online. 2010 January 1; 66(Pt 1): o178–o179.
Published online 2009 December 16. doi:  10.1107/S1600536809053343
PMCID: PMC2980250

N′-[(E)-2,6-Dichloro­benzyl­idene]pyrazine-2-carbohydrazide

Abstract

The title compound, C12H8Cl2N4O, is non-planar, the dihedral angle formed between the pendant pyrazine and benzene rings being 12.55 (11)°. An intra­molecular N—H(...)N hydrogen bond occurs. The amide groups self-associate via N—H(...)O hydrogen bonding, forming supra­molecular chains with base vector [101], which are stabilized by C—H(...)O contacts. C—H(...)N inter­actions are formed orthogonal to the chains.

Related literature

For background to the biological activity of pyrazine derivatives, see: Barlin (1982 [triangle]); Dolezal et al. (2002 [triangle]); Krinkova et al. (2002 [triangle]); Özdemir et al. (2009 [triangle]); Chaisson et al. (2002 [triangle]); Gordin et al. (2000 [triangle]); de Souza et al. (2005 [triangle]). For related structures, see: Wardell et al. (2008 [triangle]); Baddeley et al. (2009 [triangle]).

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Object name is e-66-0o178-scheme1.jpg

Experimental

Crystal data

  • C12H8Cl2N4O
  • M r = 295.12
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o178-efi1.jpg
  • a = 6.9325 (3) Å
  • b = 24.5997 (13) Å
  • c = 7.6136 (4) Å
  • β = 111.709 (3)°
  • V = 1206.31 (10) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.53 mm−1
  • T = 120 K
  • 0.26 × 0.08 × 0.02 mm

Data collection

  • Nonius KappaCCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2007 [triangle]) T min = 0.760, T max = 1.000
  • 8211 measured reflections
  • 2108 independent reflections
  • 1858 reflections with I > 2σ(I)
  • R int = 0.052

Refinement

  • R[F 2 > 2σ(F 2)] = 0.052
  • wR(F 2) = 0.112
  • S = 1.14
  • 2108 reflections
  • 172 parameters
  • H-atom parameters constrained
  • Δρmax = 0.40 e Å−3
  • Δρmin = −0.34 e Å−3

Data collection: COLLECT (Hooft, 1998 [triangle]); cell refinement: DENZO (Otwinowski & Minor, 1997 [triangle]) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]) and DIAMOND (Brandenburg, 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809053343/lh2969sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809053343/lh2969Isup2.hkl

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

Acknowledgments

The use of the EPSRC X-ray crystallographic service at the University of Southampton, England and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from CAPES (Brazil).

supplementary crystallographic information

Comment

Pyrazine derivatives have various biological activities (Barlin, 1982; Dolezal et al., 2002; Krinkova et al., 2002; Özdemir et al., 2009; Chaisson, et al., 2002; Gordin et al., 2000; de Souza et al., 2005). We have studied the structures of N-arylpyrazinecarboxamides (Wardell et al., 2008) and (pyrazinecarbonyl)hydrazones derived from mono-substituted-benzaldehydes (Baddeley et al., 2009). We now report the structure of the title compound, (I).

The molecular structure of (I), Fig. 1, features a planar central C5–N3–N4–C6 core (torsion angle = 176.7 (3)°), but twists are evident in the molecule as evidenced in the O1–C5–C1–N2 and N4–C6–C7–C8 torsion angles of 155.9 (3) and -163.6 (3) °, respectively. This is reflected in the dihedral angle of 12.55 (11) ° formed between the pendant pyrazine and benzene rings. The most prominent intermolecular interactions in the crystal structure involve the amide functionality so that a supramolecular chain mediated by N3–H···O1i [see Table 1 for symmetry codes] interactions is formed, Fig. 2 and Table 1. The chain is stabilized by C6–H···O1i contacts and has base vector [1 0 1]. Interactions of the type C10–H···N1ii are formed orthogonal to the chains formed via hydrogen bonding, Table 1. Globally, the molecules pack into layers, in the ac plane, and stack along the b direction via the hydrogen bonding as well π···π interactions [the ring centroid(N1, N2, C1–C4)···ring centroid(C7–C12)iii distance is 3.630 (2) Å with a dihedral angle of 3.28 (17)° for symmetry operation iii: 1/2 + x, 1/2 - y, -1/2 + z], Fig. 3.

Experimental

Solutions of 2-[H2NN(H)C(=O)]-pyrazine (0.10 mg, 0.72 mmol) in water (10 ml) and 2,6-dichlorobenzaldehyde (0.125 mg, 0.79 mmol) in ethanol (10 ml) were mixed and the reaction mixture was stirred at ambient temperature until TLC indicated reaction was complete. The solvent was removed under reduced pressure and the residue was washed with cold diethyl ether (30 ml) and recrystallized from ethanol, yield 70%, m.p. 467–469 K. The crystal used in the X-ray structure determination was grown from EtOH solution. 1H NMR (400 MHz, DMSO-d6) δ: 12.66 (1H, s, NH), 9.28 (1H, s), 8.95 (1H, s, H6), 8.87 (1H, s, N=CH), 8.81 (1H, s), 7.58 (2H, d, J = 8.0 Hz), 7.47 (1H, t, J = 8.0 Hz) p.p.m.. 13C NMR (100 MHz, DMSO-d6) δ: 159.8, 147.9, 145.2, 144.5, 143.3, 134.0, 131.4, 130.6, 129.0 p.p.m.. MS/ESI: [M + Na] 317. IR (KBr, cm-1) ν: 3240 (N—H); 1675 (C=O).

Refinement

The N– and C-bound H atoms were geometrically placed (N–H = 0.88 Å and C–H = 0.95 Å) and refined as riding with Uiso(H) = 1.2Ueq(N, C). Owing to a large disparity between Fo and Fc, the 2 0 0 reflection was omitted in the final cycles of the refinement.

Figures

Fig. 1.
The molecular structure of (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Fig. 2.
A view of the supramolecular chain in (I) mediated by N–H···O hydrogen bonding (orange dashed lines). Colour code: Cl, cyan; O, red; N, blue; C, grey; and H, green.
Fig. 3.
A view of the global crystal packing in (I) with N–H···O hydrogen bonding and C–H···N contacts shown as orange and blue dashed lines, respectively. Colour code: Cl, cyan; O, red; N, blue; ...

Crystal data

C12H8Cl2N4OF(000) = 600
Mr = 295.12Dx = 1.625 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 11372 reflections
a = 6.9325 (3) Åθ = 2.9–27.5°
b = 24.5997 (13) ŵ = 0.53 mm1
c = 7.6136 (4) ÅT = 120 K
β = 111.709 (3)°Plate, colourless
V = 1206.31 (10) Å30.26 × 0.08 × 0.02 mm
Z = 4

Data collection

Enraf–Nonius KappaCCD area-detector diffractometer2108 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode1858 reflections with I > 2σ(I)
10 cm confocal mirrorsRint = 0.052
Detector resolution: 9.091 pixels mm-1θmax = 25.0°, θmin = 3.0°
[var phi] and ω scansh = −8→8
Absorption correction: multi-scan (SADABS; Sheldrick, 2007)k = −29→29
Tmin = 0.760, Tmax = 1.000l = −9→8
8211 measured reflections

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)] = 0.052Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.112H-atom parameters constrained
S = 1.14w = 1/[σ2(Fo2) + (0.0128P)2 + 2.8931P] where P = (Fo2 + 2Fc2)/3
2108 reflections(Δ/σ)max < 0.001
172 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = −0.34 e Å3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
Cl10.21383 (14)0.04241 (3)−0.00147 (12)0.0280 (2)
Cl20.35539 (13)0.19347 (3)0.56395 (11)0.0216 (2)
O10.4468 (3)0.31301 (9)0.2140 (3)0.0211 (5)
N10.2594 (4)0.41462 (11)−0.2597 (4)0.0229 (6)
N20.2914 (4)0.30126 (11)−0.2806 (4)0.0174 (6)
N30.2987 (4)0.24065 (10)0.0247 (4)0.0169 (6)
H3N0.23810.2284−0.09150.020*
N40.3326 (4)0.20678 (11)0.1769 (4)0.0177 (6)
C10.3138 (4)0.32651 (13)−0.1186 (4)0.0157 (7)
C20.2997 (5)0.38272 (13)−0.1084 (5)0.0195 (7)
H20.31950.39900.01020.023*
C30.2393 (5)0.38910 (14)−0.4200 (5)0.0216 (7)
H30.21270.4101−0.53120.026*
C40.2556 (5)0.33325 (13)−0.4310 (4)0.0202 (7)
H40.24090.3172−0.54880.024*
C50.3600 (5)0.29311 (12)0.0566 (4)0.0150 (6)
C60.2611 (5)0.15869 (13)0.1347 (4)0.0171 (7)
H60.19450.14920.00530.020*
C70.2784 (5)0.11748 (13)0.2801 (4)0.0170 (7)
C80.2472 (5)0.06223 (14)0.2280 (4)0.0191 (7)
C90.2446 (5)0.02134 (14)0.3508 (5)0.0231 (7)
H90.2212−0.01530.30840.028*
C100.2764 (5)0.03408 (14)0.5368 (5)0.0243 (8)
H100.27430.00630.62270.029*
C110.3110 (5)0.08741 (13)0.5960 (5)0.0198 (7)
H110.33300.09630.72340.024*
C120.3142 (5)0.12832 (13)0.4710 (5)0.0184 (7)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cl10.0433 (5)0.0230 (5)0.0214 (5)−0.0088 (4)0.0162 (4)−0.0058 (3)
Cl20.0286 (5)0.0192 (4)0.0173 (4)−0.0039 (3)0.0090 (3)−0.0028 (3)
O10.0247 (12)0.0195 (12)0.0159 (12)−0.0036 (10)0.0038 (10)−0.0034 (9)
N10.0225 (15)0.0208 (15)0.0239 (15)−0.0005 (12)0.0067 (12)0.0021 (12)
N20.0185 (14)0.0170 (14)0.0149 (13)−0.0019 (11)0.0042 (11)−0.0015 (11)
N30.0214 (14)0.0165 (14)0.0110 (13)−0.0020 (11)0.0036 (11)0.0011 (10)
N40.0210 (14)0.0170 (14)0.0150 (14)0.0006 (11)0.0066 (12)0.0035 (11)
C10.0103 (15)0.0203 (17)0.0128 (16)−0.0043 (13)−0.0002 (12)−0.0008 (12)
C20.0185 (16)0.0174 (16)0.0199 (17)0.0018 (13)0.0038 (14)0.0000 (13)
C30.0198 (17)0.0225 (18)0.0193 (17)−0.0004 (14)0.0036 (14)0.0046 (14)
C40.0231 (17)0.0234 (18)0.0149 (16)−0.0020 (14)0.0081 (14)−0.0027 (13)
C50.0150 (15)0.0174 (16)0.0120 (15)0.0017 (13)0.0044 (13)0.0008 (12)
C60.0174 (16)0.0203 (17)0.0106 (15)0.0001 (13)0.0018 (13)0.0020 (13)
C70.0133 (15)0.0187 (16)0.0188 (16)0.0006 (13)0.0056 (13)0.0026 (13)
C80.0196 (17)0.0232 (17)0.0161 (17)−0.0002 (14)0.0084 (14)0.0017 (13)
C90.0242 (18)0.0173 (17)0.0285 (19)0.0007 (14)0.0105 (15)0.0000 (14)
C100.0274 (18)0.0228 (19)0.0230 (18)0.0030 (15)0.0098 (15)0.0081 (14)
C110.0199 (17)0.0233 (18)0.0174 (16)0.0016 (14)0.0084 (14)0.0042 (13)
C120.0154 (15)0.0182 (17)0.0211 (17)−0.0012 (13)0.0060 (14)−0.0013 (13)

Geometric parameters (Å, °)

Cl1—C81.745 (3)C3—C41.384 (5)
Cl2—C121.732 (3)C3—H30.9500
O1—C51.227 (4)C4—H40.9500
N1—C31.333 (4)C6—C71.473 (4)
N1—C21.335 (4)C6—H60.9500
N2—C41.335 (4)C7—C121.407 (4)
N2—C11.338 (4)C7—C81.410 (5)
N3—C51.352 (4)C8—C91.378 (5)
N3—N41.375 (3)C9—C101.386 (5)
N3—H3N0.8800C9—H90.9500
N4—C61.277 (4)C10—C111.379 (5)
C1—C21.390 (4)C10—H100.9500
C1—C51.497 (4)C11—C121.391 (4)
C2—H20.9500C11—H110.9500
C3—N1—C2115.5 (3)N4—C6—C7122.2 (3)
C4—N2—C1116.0 (3)N4—C6—H6118.9
C5—N3—N4118.8 (3)C7—C6—H6118.9
C5—N3—H3N120.6C12—C7—C8115.0 (3)
N4—N3—H3N120.6C12—C7—C6125.5 (3)
C6—N4—N3114.8 (3)C8—C7—C6119.4 (3)
N2—C1—C2121.8 (3)C9—C8—C7123.5 (3)
N2—C1—C5118.7 (3)C9—C8—Cl1116.4 (3)
C2—C1—C5119.5 (3)C7—C8—Cl1120.0 (2)
N1—C2—C1122.2 (3)C8—C9—C10119.4 (3)
N1—C2—H2118.9C8—C9—H9120.3
C1—C2—H2118.9C10—C9—H9120.3
N1—C3—C4122.7 (3)C11—C10—C9119.5 (3)
N1—C3—H3118.7C11—C10—H10120.3
C4—C3—H3118.7C9—C10—H10120.3
N2—C4—C3121.8 (3)C10—C11—C12120.6 (3)
N2—C4—H4119.1C10—C11—H11119.7
C3—C4—H4119.1C12—C11—H11119.7
O1—C5—N3124.4 (3)C11—C12—C7121.9 (3)
O1—C5—C1121.2 (3)C11—C12—Cl2115.6 (2)
N3—C5—C1114.5 (3)C7—C12—Cl2122.5 (2)
C5—N3—N4—C6176.7 (3)N4—C6—C7—C1219.9 (5)
C4—N2—C1—C20.2 (4)N4—C6—C7—C8−163.6 (3)
C4—N2—C1—C5−178.4 (3)C12—C7—C8—C92.0 (5)
C3—N1—C2—C1−1.8 (5)C6—C7—C8—C9−174.9 (3)
N2—C1—C2—N11.3 (5)C12—C7—C8—Cl1−176.8 (2)
C5—C1—C2—N1179.9 (3)C6—C7—C8—Cl16.3 (4)
C2—N1—C3—C41.0 (5)C7—C8—C9—C10−0.8 (5)
C1—N2—C4—C3−1.1 (4)Cl1—C8—C9—C10178.1 (3)
N1—C3—C4—N20.5 (5)C8—C9—C10—C11−0.3 (5)
N4—N3—C5—O10.7 (5)C9—C10—C11—C120.0 (5)
N4—N3—C5—C1−179.4 (3)C10—C11—C12—C71.3 (5)
N2—C1—C5—O1155.9 (3)C10—C11—C12—Cl2179.0 (3)
C2—C1—C5—O1−22.7 (4)C8—C7—C12—C11−2.2 (4)
N2—C1—C5—N3−24.0 (4)C6—C7—C12—C11174.4 (3)
C2—C1—C5—N3157.4 (3)C8—C7—C12—Cl2−179.8 (2)
N3—N4—C6—C7−178.3 (3)C6—C7—C12—Cl2−3.1 (5)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3n···O1i0.882.263.003 (3)142
N3—H3n···N20.882.412.746 (4)103
C6—H6···O1i0.952.433.214 (4)140
C10—H10···N1ii0.952.533.448 (4)162

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2969).

References

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