Abstract
The title compound, C13H9ClN4O3, was synthesized by the condensation reaction of 2-chloro-5-nitrobenzaldehyde with isonicotinohydrazide in a methanol solution. The molecule of the compound displays a trans configuration with respect to the C=N and C—N bonds. The dihedral angle between the benzene and pyridine rings is 12.1 (2)°. In the crystal structure, adjacent molecules are linked through intermolecular N—H⋯O hydrogen bonds, forming dimers.
Related literature
For Schiff base compounds, see: Fan et al. (2007 ▶); Kim et al. (2005 ▶); Nimitsiriwat et al. (2004 ▶). For the biological activity of Schiff base compounds, see: Chen et al. (1997 ▶); Ren et al. (2002 ▶). For similar structures, see: Mohd Lair et al. (2009 ▶); Fun et al. (2008 ▶); Yang (2008 ▶); Zhi (2008 ▶); Zhi & Yang (2007 ▶).
Experimental
Crystal data
C13H9ClN4O3
M r = 304.69
Tetragonal,
a = 18.586 (3) Å
c = 15.183 (3) Å
V = 5244.9 (15) Å3
Z = 16
Mo Kα radiation
μ = 0.31 mm−1
T = 298 K
0.12 × 0.10 × 0.10 mm
Data collection
Bruker SMART 1000 CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▶) T min = 0.964, T max = 0.970
16616 measured reflections
2869 independent reflections
1685 reflections with I > 2σ(I)
R int = 0.083
Refinement
R[F 2 > 2σ(F 2)] = 0.054
wR(F 2) = 0.131
S = 1.03
2869 reflections
194 parameters
1 restraint
H atoms treated by a mixture of independent and constrained refinement
Δρmax = 0.17 e Å−3
Δρmin = −0.21 e Å−3
Data collection: SMART (Bruker, 2002 ▶); cell refinement: SAINT (Bruker, 2002 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97.
Supplementary Material
Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809006588/hg2481sup1.cif
Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006588/hg2481Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report
Table 1. Hydrogen-bond geometry (Å, °).
| D—H⋯A | D—H | H⋯A | D⋯A | D—H⋯A |
|---|---|---|---|---|
| N2—H2⋯O3i | 0.892 (10) | 2.187 (13) | 3.055 (3) | 164 (3) |
Symmetry code: (i)
.
Acknowledgments
Financial support from the Third Affiliated Hospital of Suzhou University is acknowledged.
supplementary crystallographic information
Comment
Schiff base compounds have been widely investigated over a century (Fan et al., 2007; Kim et al., 2005; Nimitsiriwat et al., 2004). Some of the compounds have been found to have pharmacological and antibacterial activity (Chen et al., 1997; Ren et al., 2002). In this paper, the crystal structure of a new Schiff base compound, (I), Fig. 1, derived from the condensation reaction of 2-chloro-5-nitrobenzaldehyde with isonicotinohydrazide is reported.
In (I), the molecular structure of the compound displays a trans configuration with respect to the C=N and C-N bonds. The dihedral angle between the benzene ring and the pyridine ring is 12.1 (2)°. The dihedral angle between the O1/N4/O2 plane and the benzene ring is 8.1 (2)°. All the bond lengths are within normal ranges and comparable to those in other similar compounds (Mohd Lair et al., 2009; Fun et al., 2008; Yang, 2008; Zhi, 2008; Zhi & Yang, 2007).
In the crystal structure, adjacent molecules are linked through intermolecular N—H···O hydrogen bonds (Table 1), forming dimers (Fig. 2).
Experimental
2-Chloro-5-nitrobenzaldehyde (0.01 mol, 1.85 g) and isonicotinohydrazide (0.01 mol, 1.37 g) were dissolved in a methanol solution (50 ml). The mixture was stirred at room temperature to give a clear colorless solution. Crystals of the title compound were formed by gradual evaporation of the solvent for a week at room temperature.
Refinement
The N proton H2 was located in a difference map and refined with N–H distance restrained to 0.90 (1) Å. All other H atoms were positioned geometrically [C–H = 0.93 Å] and refined using a riding model, with Uiso(H) = 1.2Ueq(C).
Figures
Fig. 1.
The structure of (I) at the 30% probability level.
Fig. 2.
Molecular packing of (I), viewed along the b axis. Intermolecular hydrogen bonds are shown as dashed lines.
Crystal data
| C13H9ClN4O3 | Dx = 1.543 Mg m−3 |
| Mr = 304.69 | Mo Kα radiation, λ = 0.71073 Å |
| Tetragonal, I41/a | Cell parameters from 1528 reflections |
| Hall symbol: -I 4ad | θ = 2.2–24.5° |
| a = 18.586 (3) Å | µ = 0.31 mm−1 |
| c = 15.183 (3) Å | T = 298 K |
| V = 5244.9 (15) Å3 | Block, colorless |
| Z = 16 | 0.12 × 0.10 × 0.10 mm |
| F(000) = 2496 |
Data collection
| Bruker SMART 1000 CCD area-detector diffractometer | 2869 independent reflections |
| Radiation source: fine-focus sealed tube | 1685 reflections with I > 2σ(I) |
| graphite | Rint = 0.083 |
| ω scans | θmax = 27.0°, θmin = 1.7° |
| Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −23→22 |
| Tmin = 0.964, Tmax = 0.970 | k = −21→23 |
| 16616 measured reflections | l = −19→19 |
Refinement
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.054 | H atoms treated by a mixture of independent and constrained refinement |
| wR(F2) = 0.131 | w = 1/[σ2(Fo2) + (0.0346P)2 + 2.6778P] where P = (Fo2 + 2Fc2)/3 |
| S = 1.03 | (Δ/σ)max < 0.001 |
| 2869 reflections | Δρmax = 0.17 e Å−3 |
| 194 parameters | Δρmin = −0.21 e Å−3 |
| 1 restraint | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
| Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.00084 (18) |
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)
| x | y | z | Uiso*/Ueq | ||
| Cl1 | 0.14870 (5) | 0.28558 (6) | 0.06873 (6) | 0.0950 (4) | |
| O1 | 0.24702 (14) | 0.38109 (14) | 0.46884 (14) | 0.0866 (7) | |
| O2 | 0.17681 (13) | 0.29247 (14) | 0.49968 (15) | 0.0980 (8) | |
| O3 | 0.36910 (10) | 0.56885 (10) | 0.18178 (11) | 0.0646 (5) | |
| N1 | 0.29514 (11) | 0.44612 (12) | 0.16009 (13) | 0.0507 (5) | |
| N2 | 0.33431 (12) | 0.47740 (12) | 0.09354 (12) | 0.0520 (6) | |
| N3 | 0.50947 (13) | 0.62326 (13) | −0.09159 (15) | 0.0627 (6) | |
| N4 | 0.20600 (15) | 0.33277 (15) | 0.44731 (16) | 0.0674 (7) | |
| C1 | 0.21758 (13) | 0.35202 (14) | 0.20311 (17) | 0.0497 (6) | |
| C2 | 0.16520 (15) | 0.30249 (16) | 0.17913 (19) | 0.0624 (8) | |
| C3 | 0.12506 (16) | 0.26504 (17) | 0.2413 (3) | 0.0767 (10) | |
| H3 | 0.0893 | 0.2333 | 0.2231 | 0.092* | |
| C4 | 0.13799 (16) | 0.27471 (16) | 0.3291 (2) | 0.0723 (9) | |
| H4 | 0.1120 | 0.2494 | 0.3713 | 0.087* | |
| C5 | 0.19049 (14) | 0.32300 (14) | 0.35332 (18) | 0.0540 (7) | |
| C6 | 0.22899 (13) | 0.36163 (14) | 0.29285 (16) | 0.0505 (6) | |
| H6 | 0.2632 | 0.3947 | 0.3120 | 0.061* | |
| C7 | 0.25958 (14) | 0.39094 (15) | 0.13746 (17) | 0.0544 (7) | |
| H7 | 0.2603 | 0.3753 | 0.0793 | 0.065* | |
| C8 | 0.37206 (13) | 0.53777 (14) | 0.11106 (15) | 0.0471 (6) | |
| C9 | 0.41915 (13) | 0.56487 (13) | 0.03806 (15) | 0.0446 (6) | |
| C10 | 0.41588 (15) | 0.54180 (14) | −0.04791 (15) | 0.0543 (7) | |
| H10 | 0.3836 | 0.5060 | −0.0645 | 0.065* | |
| C11 | 0.46139 (17) | 0.57273 (16) | −0.10915 (17) | 0.0643 (8) | |
| H11 | 0.4580 | 0.5568 | −0.1671 | 0.077* | |
| C12 | 0.51235 (15) | 0.64389 (16) | −0.00807 (19) | 0.0632 (8) | |
| H12 | 0.5459 | 0.6789 | 0.0070 | 0.076* | |
| C13 | 0.46919 (15) | 0.61719 (15) | 0.05767 (17) | 0.0588 (7) | |
| H13 | 0.4737 | 0.6343 | 0.1150 | 0.071* | |
| H2 | 0.3334 (16) | 0.4566 (14) | 0.0406 (10) | 0.080* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cl1 | 0.0684 (6) | 0.1253 (8) | 0.0914 (6) | 0.0108 (5) | −0.0135 (4) | −0.0546 (6) |
| O1 | 0.1009 (18) | 0.1033 (19) | 0.0558 (13) | −0.0094 (15) | −0.0011 (12) | 0.0119 (12) |
| O2 | 0.1027 (18) | 0.1125 (19) | 0.0787 (15) | 0.0079 (15) | 0.0333 (13) | 0.0459 (14) |
| O3 | 0.0837 (14) | 0.0749 (13) | 0.0351 (10) | −0.0072 (11) | 0.0146 (9) | −0.0096 (9) |
| N1 | 0.0517 (13) | 0.0618 (14) | 0.0385 (11) | 0.0045 (11) | 0.0075 (10) | 0.0043 (10) |
| N2 | 0.0645 (14) | 0.0606 (15) | 0.0308 (11) | 0.0020 (12) | 0.0090 (10) | −0.0004 (10) |
| N3 | 0.0636 (16) | 0.0770 (17) | 0.0476 (15) | 0.0023 (13) | 0.0087 (11) | 0.0066 (12) |
| N4 | 0.0682 (17) | 0.0753 (18) | 0.0588 (16) | 0.0173 (15) | 0.0191 (13) | 0.0226 (14) |
| C1 | 0.0445 (15) | 0.0519 (16) | 0.0526 (15) | 0.0061 (12) | 0.0028 (12) | −0.0037 (12) |
| C2 | 0.0493 (17) | 0.0646 (19) | 0.073 (2) | 0.0108 (14) | 0.0018 (15) | −0.0201 (15) |
| C3 | 0.0525 (19) | 0.062 (2) | 0.116 (3) | −0.0120 (15) | 0.0152 (19) | −0.0258 (19) |
| C4 | 0.064 (2) | 0.0575 (19) | 0.095 (3) | −0.0031 (16) | 0.0257 (18) | −0.0006 (17) |
| C5 | 0.0489 (16) | 0.0497 (16) | 0.0635 (18) | 0.0065 (13) | 0.0140 (13) | 0.0059 (13) |
| C6 | 0.0469 (15) | 0.0528 (16) | 0.0519 (16) | 0.0001 (12) | 0.0037 (12) | 0.0029 (12) |
| C7 | 0.0588 (17) | 0.0681 (19) | 0.0364 (14) | 0.0076 (15) | 0.0028 (12) | −0.0043 (13) |
| C8 | 0.0546 (16) | 0.0541 (16) | 0.0325 (13) | 0.0091 (13) | 0.0035 (11) | 0.0015 (11) |
| C9 | 0.0470 (15) | 0.0507 (15) | 0.0359 (13) | 0.0129 (12) | 0.0034 (11) | 0.0023 (11) |
| C10 | 0.0679 (18) | 0.0570 (16) | 0.0378 (14) | −0.0026 (14) | 0.0091 (12) | −0.0018 (12) |
| C11 | 0.081 (2) | 0.074 (2) | 0.0377 (15) | 0.0014 (18) | 0.0124 (14) | −0.0056 (14) |
| C12 | 0.0542 (17) | 0.078 (2) | 0.0572 (18) | −0.0075 (15) | −0.0030 (14) | 0.0078 (15) |
| C13 | 0.0644 (18) | 0.0738 (19) | 0.0383 (14) | −0.0027 (15) | −0.0019 (13) | −0.0018 (13) |
Geometric parameters (Å, °)
| Cl1—C2 | 1.733 (3) | C3—H3 | 0.9300 |
| O1—N4 | 1.222 (3) | C4—C5 | 1.376 (4) |
| O2—N4 | 1.220 (3) | C4—H4 | 0.9300 |
| O3—C8 | 1.221 (3) | C5—C6 | 1.368 (3) |
| N1—C7 | 1.268 (3) | C6—H6 | 0.9300 |
| N1—N2 | 1.374 (3) | C7—H7 | 0.9300 |
| N2—C8 | 1.350 (3) | C8—C9 | 1.499 (3) |
| N2—H2 | 0.892 (10) | C9—C10 | 1.375 (3) |
| N3—C11 | 1.324 (4) | C9—C13 | 1.378 (3) |
| N3—C12 | 1.326 (3) | C10—C11 | 1.382 (4) |
| N4—C5 | 1.467 (4) | C10—H10 | 0.9300 |
| C1—C2 | 1.388 (4) | C11—H11 | 0.9300 |
| C1—C6 | 1.391 (3) | C12—C13 | 1.373 (4) |
| C1—C7 | 1.458 (4) | C12—H12 | 0.9300 |
| C2—C3 | 1.390 (4) | C13—H13 | 0.9300 |
| C3—C4 | 1.367 (4) | ||
| C7—N1—N2 | 114.8 (2) | C5—C6—H6 | 119.6 |
| C8—N2—N1 | 118.8 (2) | C1—C6—H6 | 119.6 |
| C8—N2—H2 | 123 (2) | N1—C7—C1 | 119.7 (2) |
| N1—N2—H2 | 118 (2) | N1—C7—H7 | 120.2 |
| C11—N3—C12 | 115.2 (2) | C1—C7—H7 | 120.2 |
| O2—N4—O1 | 123.7 (3) | O3—C8—N2 | 122.9 (2) |
| O2—N4—C5 | 118.1 (3) | O3—C8—C9 | 121.2 (2) |
| O1—N4—C5 | 118.3 (2) | N2—C8—C9 | 115.9 (2) |
| C2—C1—C6 | 116.7 (2) | C10—C9—C13 | 117.1 (2) |
| C2—C1—C7 | 121.7 (3) | C10—C9—C8 | 124.8 (2) |
| C6—C1—C7 | 121.6 (2) | C13—C9—C8 | 118.1 (2) |
| C1—C2—C3 | 122.0 (3) | C9—C10—C11 | 118.8 (3) |
| C1—C2—Cl1 | 119.9 (2) | C9—C10—H10 | 120.6 |
| C3—C2—Cl1 | 118.1 (2) | C11—C10—H10 | 120.6 |
| C4—C3—C2 | 120.1 (3) | N3—C11—C10 | 124.9 (3) |
| C4—C3—H3 | 119.9 | N3—C11—H11 | 117.5 |
| C2—C3—H3 | 119.9 | C10—C11—H11 | 117.5 |
| C3—C4—C5 | 118.1 (3) | N3—C12—C13 | 124.6 (3) |
| C3—C4—H4 | 120.9 | N3—C12—H12 | 117.7 |
| C5—C4—H4 | 120.9 | C13—C12—H12 | 117.7 |
| C6—C5—C4 | 122.3 (3) | C12—C13—C9 | 119.5 (2) |
| C6—C5—N4 | 119.0 (3) | C12—C13—H13 | 120.3 |
| C4—C5—N4 | 118.7 (3) | C9—C13—H13 | 120.3 |
| C5—C6—C1 | 120.7 (3) |
Hydrogen-bond geometry (Å, °)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H2···O3i | 0.89 (1) | 2.19 (1) | 3.055 (3) | 164 (3) |
Symmetry codes: (i) y−1/4, −x+3/4, z−1/4.
Footnotes
Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2481).
References
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809006588/hg2481sup1.cif
Structure factors: contains datablocks I. DOI: 10.1107/S1600536809006588/hg2481Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report


