organic compounds
N′-[(E)-2-Methoxybenzylidene]pyrazine-2-carbohydrazide
aFundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos – Farmanguinhos, R. Sizenando Nabuco, 100, Manguinhos, 21041-250 Rio de Janeiro, RJ, Brazil, bCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brazil, cCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland, and dDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: edward.tiekink@gmail.com
In the title compound, C13H12N4O2, all the non-H atoms lie on a crystallographic mirror plane and an intramolecular N—H⋯N hydrogen bond generates an S(5) ring; the conformation about the imine bond [1.280 (3) Å] is E. In the crystal, molecules assemble into a two-dimensional array via C—H⋯O(carbonyl) and C—H⋯N(pyrazine) contacts. Layers stack along the b-axis direction via weak π–π interactions between pyrazine rings [ring centroid distance = 3.8028 (8) Å].
Related literature
For background to the anti-mycobacterial activity of pyrazinamide derivatives, see: Chaisson et al. (2002); Gordin et al. (2000); de Souza (2006); Pinheiro et al. (2007). For related structures of pyrazinecarbonylhydrazones, see: Baddeley et al. (2009); Howie et al. (2010a,b).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997), DIAMOND (Brandenburg, 2006); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).
Supporting information
10.1107/S1600536811022938/hb5910sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811022938/hb5910Isup2.hkl
Solutions of 2-pyrazinehydrazide (0.72 mmol) in water (10 ml), and 2-methoxybenzaldehyde (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 to yield colourless plates of (I). Yield: 52%; M.pt.: 453–454 K. 1H NMR (400 MHz, DMSO-d6) δ: 12.35 (1H, s, NH), 9.26 (1H, s, H3), 9.00 (1H, s, H6), 8.92 (1H, s, H5), 8.80 (1H, s, N═CH), 7.91 (1H, d, J=7.5 Hz, H60), 7.45 (1H, t, J=7.5, H40), 7.12 (1H, d, J=7.5 Hz, H3'), 7.04 (1H, t, J=7.5 Hz, H5'), 3.87 (3H, s, OCH3) p.p.m.. 13C NMR (100 MHz, DMSO-d6) δ: 160.5, 148.8, 148.2, 144.7, 144.4, 143.7, 133.5, 133.2, 132.2, 128.4, 127.8, 124.1, 55.4 p.p.m. MS/ESI: [M—H]: 255. IR (KBr pellets): \v 3300 (N—H); 1680 (C═O) cm-1.
The C-bound H atoms were geometrically placed (C—H = 0.95–0.98 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The N-bound atom was refined with N—H = 0.88±0.01 Å, and with Uiso(H) = 1.2Ueq(N). One reflection, i.e. (011), was omitted from the final
owing to poor agreement.Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997), DIAMOND (Brandenburg, 2006); software used to prepare material for publication: PLATON (Spek, 2009) and publCIF (Westrip, 2010).C13H12N4O2 | F(000) = 268 |
Mr = 256.27 | Dx = 1.397 Mg m−3 |
Monoclinic, P21/m | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2yb | Cell parameters from 6063 reflections |
a = 7.7615 (6) Å | θ = 2.9–27.5° |
b = 6.4257 (4) Å | µ = 0.10 mm−1 |
c = 12.2480 (9) Å | T = 120 K |
β = 93.893 (3)° | Plate, colourless |
V = 609.44 (8) Å3 | 0.46 × 0.24 × 0.01 mm |
Z = 2 |
Nonius KappaCCD area-detector diffractometer | 1481 independent reflections |
Radiation source: Enraf Nonius FR591 rotating anode | 1032 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.074 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.4°, θmin = 3.0° |
ϕ and ω scans | h = −9→9 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | k = −8→8 |
Tmin = 0.594, Tmax = 0.746 | l = −14→15 |
7850 measured reflections |
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)] = 0.052 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.147 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | w = 1/[σ2(Fo2) + (0.087P)2] where P = (Fo2 + 2Fc2)/3 |
1481 reflections | (Δ/σ)max = 0.006 |
122 parameters | Δρmax = 0.31 e Å−3 |
4 restraints | Δρmin = −0.29 e Å−3 |
C13H12N4O2 | V = 609.44 (8) Å3 |
Mr = 256.27 | Z = 2 |
Monoclinic, P21/m | Mo Kα radiation |
a = 7.7615 (6) Å | µ = 0.10 mm−1 |
b = 6.4257 (4) Å | T = 120 K |
c = 12.2480 (9) Å | 0.46 × 0.24 × 0.01 mm |
β = 93.893 (3)° |
Nonius KappaCCD area-detector diffractometer | 1481 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2007) | 1032 reflections with I > 2σ(I) |
Tmin = 0.594, Tmax = 0.746 | Rint = 0.074 |
7850 measured reflections |
R[F2 > 2σ(F2)] = 0.052 | 4 restraints |
wR(F2) = 0.147 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.03 | Δρmax = 0.31 e Å−3 |
1481 reflections | Δρmin = −0.29 e Å−3 |
122 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.1276 (2) | 0.2500 | 0.91441 (14) | 0.0329 (5) | |
O2 | 0.0786 (2) | 0.2500 | 0.36159 (13) | 0.0288 (5) | |
N1 | 0.5591 (2) | 0.2500 | 0.83175 (16) | 0.0220 (5) | |
N2 | 0.6293 (3) | 0.2500 | 1.06050 (16) | 0.0240 (5) | |
N3 | 0.2321 (2) | 0.2500 | 0.74474 (15) | 0.0200 (5) | |
H3N | 0.327 (2) | 0.2500 | 0.7099 (19) | 0.024* | |
N4 | 0.0712 (2) | 0.2500 | 0.68916 (15) | 0.0193 (4) | |
C1 | 0.4324 (3) | 0.2500 | 0.90152 (18) | 0.0185 (5) | |
C2 | 0.7208 (3) | 0.2500 | 0.87780 (19) | 0.0227 (5) | |
H2 | 0.8148 | 0.2500 | 0.8320 | 0.027* | |
C3 | 0.7549 (3) | 0.2500 | 0.99078 (19) | 0.0235 (5) | |
H3 | 0.8717 | 0.2500 | 1.0195 | 0.028* | |
C4 | 0.4676 (3) | 0.2500 | 1.01421 (18) | 0.0206 (5) | |
H4 | 0.3738 | 0.2500 | 1.0602 | 0.025* | |
C5 | 0.2483 (3) | 0.2500 | 0.85506 (18) | 0.0199 (5) | |
C6 | 0.0729 (3) | 0.2500 | 0.58476 (18) | 0.0210 (5) | |
H6 | 0.1803 | 0.2500 | 0.5519 | 0.025* | |
C7 | −0.0876 (3) | 0.2500 | 0.51541 (19) | 0.0203 (5) | |
C8 | −0.0819 (3) | 0.2500 | 0.40041 (19) | 0.0214 (5) | |
C9 | −0.2344 (3) | 0.2500 | 0.3333 (2) | 0.0265 (6) | |
H9 | −0.2304 | 0.2500 | 0.2560 | 0.032* | |
C10 | −0.3910 (3) | 0.2500 | 0.3800 (2) | 0.0362 (7) | |
H10 | −0.4949 | 0.2500 | 0.3343 | 0.043* | |
C11 | −0.3992 (3) | 0.2500 | 0.4929 (2) | 0.0440 (8) | |
H11 | −0.5078 | 0.2500 | 0.5243 | 0.053* | |
C12 | −0.2482 (3) | 0.2500 | 0.5589 (2) | 0.0325 (6) | |
H12 | −0.2542 | 0.2500 | 0.6361 | 0.039* | |
C13 | 0.088612 (1) | 0.2500 | 0.244660 (1) | 0.0341 (6) | |
H13A | 0.2108 | 0.2500 | 0.2292 | 0.051* | |
H13B | 0.0328 | 0.3754 | 0.2135 | 0.051* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0181 (9) | 0.0612 (11) | 0.0196 (9) | 0.000 | 0.0021 (7) | 0.000 |
O2 | 0.0280 (10) | 0.0415 (10) | 0.0168 (9) | 0.000 | 0.0011 (7) | 0.000 |
N1 | 0.0167 (10) | 0.0290 (10) | 0.0200 (10) | 0.000 | −0.0011 (8) | 0.000 |
N2 | 0.0238 (11) | 0.0287 (10) | 0.0190 (11) | 0.000 | −0.0020 (8) | 0.000 |
N3 | 0.0144 (10) | 0.0297 (10) | 0.0154 (10) | 0.000 | −0.0028 (7) | 0.000 |
N4 | 0.0164 (10) | 0.0217 (9) | 0.0191 (10) | 0.000 | −0.0041 (8) | 0.000 |
C1 | 0.0175 (12) | 0.0199 (11) | 0.0180 (12) | 0.000 | 0.0003 (9) | 0.000 |
C2 | 0.0170 (11) | 0.0301 (12) | 0.0207 (12) | 0.000 | −0.0017 (9) | 0.000 |
C3 | 0.0166 (12) | 0.0312 (12) | 0.0221 (13) | 0.000 | −0.0039 (10) | 0.000 |
C4 | 0.0192 (12) | 0.0261 (11) | 0.0164 (11) | 0.000 | 0.0002 (9) | 0.000 |
C5 | 0.0176 (12) | 0.0234 (11) | 0.0184 (12) | 0.000 | −0.0004 (9) | 0.000 |
C6 | 0.0205 (12) | 0.0227 (11) | 0.0194 (12) | 0.000 | −0.0008 (9) | 0.000 |
C7 | 0.0218 (12) | 0.0200 (11) | 0.0182 (11) | 0.000 | −0.0049 (9) | 0.000 |
C8 | 0.0257 (13) | 0.0188 (11) | 0.0192 (12) | 0.000 | −0.0015 (9) | 0.000 |
C9 | 0.0339 (14) | 0.0244 (12) | 0.0195 (12) | 0.000 | −0.0102 (11) | 0.000 |
C10 | 0.0234 (13) | 0.0512 (16) | 0.0317 (15) | 0.000 | −0.0145 (11) | 0.000 |
C11 | 0.0200 (14) | 0.079 (2) | 0.0323 (16) | 0.000 | −0.0017 (12) | 0.000 |
C12 | 0.0262 (14) | 0.0484 (15) | 0.0227 (13) | 0.000 | −0.0003 (11) | 0.000 |
C13 | 0.0406 (16) | 0.0459 (15) | 0.0160 (13) | 0.000 | 0.0030 (11) | 0.000 |
O1—C5 | 1.224 (3) | C4—H4 | 0.9500 |
O2—C8 | 1.363 (3) | C6—C7 | 1.459 (3) |
O2—C13 | 1.4395 (16) | C6—H6 | 0.9500 |
N1—C2 | 1.341 (3) | C7—C12 | 1.388 (3) |
N1—C1 | 1.346 (3) | C7—C8 | 1.412 (3) |
N2—C3 | 1.339 (3) | C8—C9 | 1.394 (3) |
N2—C4 | 1.342 (3) | C9—C10 | 1.378 (4) |
N3—C5 | 1.348 (3) | C9—H9 | 0.9500 |
N3—N4 | 1.381 (2) | C10—C11 | 1.388 (4) |
N3—H3N | 0.875 (10) | C10—H10 | 0.9500 |
N4—C6 | 1.280 (3) | C11—C12 | 1.377 (4) |
C1—C4 | 1.389 (3) | C11—H11 | 0.9500 |
C1—C5 | 1.502 (3) | C12—H12 | 0.9500 |
C2—C3 | 1.391 (3) | C13—H13A | 0.9800 |
C2—H2 | 0.9500 | C13—H13B | 0.9800 |
C3—H3 | 0.9500 | ||
C8—O2—C13 | 117.35 (16) | N4—C6—H6 | 119.5 |
C2—N1—C1 | 115.86 (19) | C7—C6—H6 | 119.5 |
C3—N2—C4 | 115.54 (19) | C12—C7—C8 | 118.2 (2) |
C5—N3—N4 | 120.89 (17) | C12—C7—C6 | 122.0 (2) |
C5—N3—H3N | 117.6 (17) | C8—C7—C6 | 119.8 (2) |
N4—N3—H3N | 121.5 (17) | O2—C8—C9 | 123.6 (2) |
C6—N4—N3 | 114.97 (17) | O2—C8—C7 | 116.0 (2) |
N1—C1—C4 | 121.9 (2) | C9—C8—C7 | 120.3 (2) |
N1—C1—C5 | 118.47 (19) | C10—C9—C8 | 119.5 (2) |
C4—C1—C5 | 119.63 (19) | C10—C9—H9 | 120.2 |
N1—C2—C3 | 121.9 (2) | C8—C9—H9 | 120.2 |
N1—C2—H2 | 119.1 | C9—C10—C11 | 121.0 (2) |
C3—C2—H2 | 119.1 | C9—C10—H10 | 119.5 |
N2—C3—C2 | 122.5 (2) | C11—C10—H10 | 119.5 |
N2—C3—H3 | 118.8 | C12—C11—C10 | 119.3 (2) |
C2—C3—H3 | 118.8 | C12—C11—H11 | 120.4 |
N2—C4—C1 | 122.4 (2) | C10—C11—H11 | 120.4 |
N2—C4—H4 | 118.8 | C11—C12—C7 | 121.7 (2) |
C1—C4—H4 | 118.8 | C11—C12—H12 | 119.1 |
O1—C5—N3 | 124.9 (2) | C7—C12—H12 | 119.1 |
O1—C5—C1 | 121.5 (2) | O2—C13—H13A | 108.1 |
N3—C5—C1 | 113.65 (18) | O2—C13—H13B | 109.6 |
N4—C6—C7 | 121.02 (19) | H13A—C13—H13B | 109.4 |
C5—N3—N4—C6 | 180.0 | N4—C6—C7—C12 | 0.0 |
C2—N1—C1—C4 | 0.000 (1) | N4—C6—C7—C8 | 180.0 |
C2—N1—C1—C5 | 180.0 | C13—O2—C8—C9 | 0.0 |
C1—N1—C2—C3 | 0.000 (1) | C13—O2—C8—C7 | 180.0 |
C4—N2—C3—C2 | 0.000 (1) | C12—C7—C8—O2 | 180.0 |
N1—C2—C3—N2 | 0.000 (1) | C6—C7—C8—O2 | 0.0 |
C3—N2—C4—C1 | 0.000 (1) | C12—C7—C8—C9 | 0.0 |
N1—C1—C4—N2 | 0.000 (1) | C6—C7—C8—C9 | 180.0 |
C5—C1—C4—N2 | 180.0 | O2—C8—C9—C10 | 180.0 |
N4—N3—C5—O1 | 0.0 | C7—C8—C9—C10 | 0.0 |
N4—N3—C5—C1 | 180.0 | C8—C9—C10—C11 | 0.0 |
N1—C1—C5—O1 | 180.0 | C9—C10—C11—C12 | 0.0 |
C4—C1—C5—O1 | 0.0 | C10—C11—C12—C7 | 0.0 |
N1—C1—C5—N3 | 0.0 | C8—C7—C12—C11 | 0.0 |
C4—C1—C5—N3 | 180.0 | C6—C7—C12—C11 | 180.0 |
N3—N4—C6—C7 | 180.0 |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3n···N1 | 0.88 (2) | 2.27 (2) | 2.685 (3) | 109 (2) |
C2—H2···O1i | 0.95 | 2.57 | 3.160 (3) | 121 |
C3—H3···O1i | 0.95 | 2.44 | 3.103 (3) | 127 |
C9—H9···N2ii | 0.95 | 2.56 | 3.437 (3) | 153 |
Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z−1. |
Experimental details
Crystal data | |
Chemical formula | C13H12N4O2 |
Mr | 256.27 |
Crystal system, space group | Monoclinic, P21/m |
Temperature (K) | 120 |
a, b, c (Å) | 7.7615 (6), 6.4257 (4), 12.2480 (9) |
β (°) | 93.893 (3) |
V (Å3) | 609.44 (8) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.46 × 0.24 × 0.01 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2007) |
Tmin, Tmax | 0.594, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7850, 1481, 1032 |
Rint | 0.074 |
(sin θ/λ)max (Å−1) | 0.647 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.052, 0.147, 1.03 |
No. of reflections | 1481 |
No. of parameters | 122 |
No. of restraints | 4 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.31, −0.29 |
Computer programs: , DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), DIAMOND (Brandenburg, 2006), PLATON (Spek, 2009) and publCIF (Westrip, 2010).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3n···N1 | 0.882 (18) | 2.27 (2) | 2.685 (3) | 108.9 (19) |
C2—H2···O1i | 0.95 | 2.57 | 3.160 (3) | 121 |
C3—H3···O1i | 0.95 | 2.44 | 3.103 (3) | 127 |
C9—H9···N2ii | 0.95 | 2.56 | 3.437 (3) | 153 |
Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z−1. |
Footnotes
‡Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.
Acknowledgements
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).
References
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Pyrazinamide has well known anti-mycobacterial activity and it is the one of the most important drugs used in tuberculosis treatment (Chaisson et al., 2002; Gordin et al., 2000; de Souza, 2006). Various derivatives have been prepared and their anti-tuberculosis properties studied (Pinheiro et al., 2007). Among the reported crystal structures of pyrazinamide derivatives are those of pyrazinecarbonylhydrazones (Baddeley et al., 2009; Howie et al. 2010a, 2010b). In continuation of previous work, we now wish to report on the crystal structure of the title compound, (I).
All non-hydrogen atoms in (I) lie on a crystallographic mirror plane, Fig. 1. The formation of intramolecular N3—H···N1 and C6—H···O2 contacts, Table 1, contributes to the stability of the planar conformation. The configuration about the N4═C6 bond [1.280 (3) Å] is E. The most prominent contacts in the crystal packing are of the type C—H···O and C—H···N, Table 1. The C—H···O contacts lead to chains along the a direction and involve the bifurcated carbonyl-O1 atom. Chains are linked in the c direction by C—H···N2(pyrazinyl) contacts with the result that a two-dimensional array is formed in the ac plane, Fig. 2. Layers stack along the b direction stabilized by weak π–π interactions formed between pyrazinyl rings [ring centroid(N1,N2,C1–C4)···ring centroid(N1,N2,C1—C4)i = 3.8028 (8) Å for i: 1 - x, -1/2 + y, 2 - z], Fig. 3.