Abstract
In the title compound, C13H9F2N3O, the pyridine ring forms a dihedral angle of 16.92 (7)° with the benzene ring. In the crystal, molecules are linked via N—H⋯O, C—H⋯O and C—H⋯F, with the same O atom accepting two bonds.
Related literature
For related structures, see: Chen (2006 ▶); Nie et al. (2006 ▶). For standard bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).
Experimental
Crystal data
C13H9F2N3O
M r = 261.23
Monoclinic,
a = 6.8462 (1) Å
b = 24.7903 (5) Å
c = 8.3719 (1) Å
β = 125.249 (1)°
V = 1160.36 (3) Å3
Z = 4
Mo Kα radiation
μ = 0.12 mm−1
T = 100 K
0.68 × 0.26 × 0.10 mm
Data collection
Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.923, T max = 0.988
22044 measured reflections
4531 independent reflections
3819 reflections with I > 2σ(I)
R int = 0.029
Refinement
R[F 2 > 2σ(F 2)] = 0.045
wR(F 2) = 0.117
S = 1.06
4531 reflections
176 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρmax = 0.50 e Å−3
Δρmin = −0.23 e Å−3
Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).
Supplementary Material
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812016716/bv2204sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812016716/bv2204Isup2.hkl
Supplementary material file. DOI: 10.1107/S1600536812016716/bv2204Isup3.cml
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—H1N2⋯O1i | 0.88 (2) | 2.00 (2) | 2.8554 (12) | 163.4 (16) |
| C1—H1A⋯F1ii | 0.93 | 2.54 | 3.4622 (13) | 169 |
| C7—H7A⋯O1i | 0.93 | 2.45 | 3.2253 (13) | 141 |
Symmetry codes: (i)
; (ii)
.
Acknowledgments
The authors would like to thank Universiti Sains Malaysia (USM) for the Research University Grant (No. 1001/PFIZIK/811160). BN thanks the UGC SAP for financial assistance for the purchase of chemicals. DNS thanks Mangalore University for research facilities.
supplementary crystallographic information
Comment
In view of the importance of isoniazid and its various Schiff base derivatives (Chen, 2006; Nie et al., 2006), the synthesis and crystal structure of the title Schiff base is reported.
In the title molecule (Fig. 1), the pyridine ring (N1/C1-C5) forms a dihedral angle of 16.92 (7)° with the benzene ring (C8-C13). Bond lengths (Allen et al., 1987) and angles are within normal ranges and are comparable with related structures (Chen, 2006; Nie et al., 2006).
In the crystal structure, Fig. 2, molecules are linked via intermolecular C1–H1A···F1 and bifurcated N2–H1N2···O1 and C7–H7A···O1 hydrogen bonds (Table 1) into two-dimensional planes parallel to (010).
Experimental
A mixture of isoniazid (1.4 g, 0.01 mol) and 2,6-difluorobenzaldehyde (1.4 ml, 0.01 mol) in 15 ml of absolute alcohol containing 2 drops of hydrochloric acid was refluxed for about 3 h. On cooling, the solid was separated, which was then filtered and recrystallized from DMF. The single crystal was grown from DMF by the slow evaporation method. (m.p. > 523 K).
Refinement
Atom H1N2 was located in a difference Fourier map and refined freely with N2-H1N2 = 0.884 (18) Å. The remaining H atoms were positioned geometrically and refined using a riding model with C–H = 0.93 Å and Uiso(H) = 1.2 Ueq(C).
Figures
Fig. 1.
The molecular structure of the title compound showing 50% probability displacement ellipsoids for non-H atoms.
Fig. 2.
The crystal structure of the title compound, viewed along the a axis. H atoms not involved in hydrogen bonds (dashed lines) have been omitted for clarity.
Crystal data
| C13H9F2N3O | F(000) = 536 |
| Mr = 261.23 | Dx = 1.495 Mg m−3 |
| Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
| Hall symbol: -P 2ybc | Cell parameters from 8606 reflections |
| a = 6.8462 (1) Å | θ = 3.1–33.5° |
| b = 24.7903 (5) Å | µ = 0.12 mm−1 |
| c = 8.3719 (1) Å | T = 100 K |
| β = 125.249 (1)° | Plate, colourless |
| V = 1160.36 (3) Å3 | 0.68 × 0.26 × 0.10 mm |
| Z = 4 |
Data collection
| Bruker SMART APEXII CCD area-detector diffractometer | 4531 independent reflections |
| Radiation source: fine-focus sealed tube | 3819 reflections with I > 2σ(I) |
| Graphite monochromator | Rint = 0.029 |
| φ and ω scans | θmax = 33.5°, θmin = 3.1° |
| Absorption correction: multi-scan (SADABS; Bruker, 2009) | h = −10→10 |
| Tmin = 0.923, Tmax = 0.988 | k = −38→38 |
| 22044 measured reflections | l = −12→12 |
Refinement
| 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)] = 0.045 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.117 | H atoms treated by a mixture of independent and constrained refinement |
| S = 1.06 | w = 1/[σ2(Fo2) + (0.0562P)2 + 0.3643P] where P = (Fo2 + 2Fc2)/3 |
| 4531 reflections | (Δ/σ)max = 0.001 |
| 176 parameters | Δρmax = 0.50 e Å−3 |
| 0 restraints | Δρmin = −0.23 e Å−3 |
Special details
| Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. |
| 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 > 2sigma(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 | ||
| F1 | 0.41487 (12) | 0.82429 (3) | −0.46332 (9) | 0.02284 (14) | |
| F2 | 0.74397 (12) | 0.94647 (3) | 0.06279 (9) | 0.02428 (15) | |
| O1 | 0.88240 (14) | 0.69293 (3) | −0.10748 (11) | 0.01802 (15) | |
| N1 | 1.26302 (17) | 0.60373 (4) | 0.54592 (13) | 0.02081 (18) | |
| N2 | 0.85867 (15) | 0.75837 (3) | 0.07264 (12) | 0.01533 (15) | |
| N3 | 0.73916 (15) | 0.79285 (3) | −0.08611 (12) | 0.01499 (15) | |
| C1 | 1.20146 (17) | 0.69340 (4) | 0.41379 (14) | 0.01558 (17) | |
| H1A | 1.2365 | 0.7300 | 0.4362 | 0.019* | |
| C2 | 1.30695 (18) | 0.65690 (4) | 0.56804 (15) | 0.01889 (18) | |
| H2A | 1.4143 | 0.6701 | 0.6940 | 0.023* | |
| C3 | 1.11063 (19) | 0.58554 (4) | 0.36284 (16) | 0.01903 (19) | |
| H3A | 1.0787 | 0.5487 | 0.3448 | 0.023* | |
| C4 | 0.99779 (17) | 0.61841 (4) | 0.19868 (15) | 0.01578 (17) | |
| H4A | 0.8951 | 0.6039 | 0.0741 | 0.019* | |
| C5 | 1.04182 (16) | 0.67368 (4) | 0.22471 (13) | 0.01332 (16) | |
| C6 | 0.92010 (16) | 0.70905 (4) | 0.04740 (14) | 0.01366 (16) | |
| C7 | 0.71196 (16) | 0.84069 (4) | −0.04226 (14) | 0.01461 (16) | |
| H7A | 0.7767 | 0.8489 | 0.0877 | 0.018* | |
| C8 | 0.58232 (16) | 0.88247 (4) | −0.19069 (14) | 0.01341 (16) | |
| C9 | 0.43387 (17) | 0.87443 (4) | −0.39305 (14) | 0.01554 (17) | |
| C10 | 0.30493 (19) | 0.91512 (4) | −0.52600 (15) | 0.01971 (19) | |
| H10A | 0.2063 | 0.9079 | −0.6594 | 0.024* | |
| C11 | 0.3256 (2) | 0.96720 (4) | −0.45622 (16) | 0.0218 (2) | |
| H11A | 0.2382 | 0.9950 | −0.5441 | 0.026* | |
| C12 | 0.47472 (19) | 0.97845 (4) | −0.25729 (16) | 0.02061 (19) | |
| H12A | 0.4914 | 1.0134 | −0.2107 | 0.025* | |
| C13 | 0.59696 (17) | 0.93600 (4) | −0.13148 (14) | 0.01623 (17) | |
| H1N2 | 0.870 (3) | 0.7667 (7) | 0.180 (3) | 0.034 (4)* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| F1 | 0.0293 (3) | 0.0157 (3) | 0.0164 (3) | 0.0010 (2) | 0.0091 (3) | −0.0034 (2) |
| F2 | 0.0308 (3) | 0.0188 (3) | 0.0156 (3) | 0.0007 (2) | 0.0089 (3) | −0.0043 (2) |
| O1 | 0.0264 (4) | 0.0163 (3) | 0.0134 (3) | 0.0014 (3) | 0.0126 (3) | −0.0004 (2) |
| N1 | 0.0226 (4) | 0.0217 (4) | 0.0176 (4) | 0.0037 (3) | 0.0113 (3) | 0.0052 (3) |
| N2 | 0.0211 (4) | 0.0142 (3) | 0.0117 (3) | 0.0042 (3) | 0.0100 (3) | 0.0025 (3) |
| N3 | 0.0182 (3) | 0.0143 (3) | 0.0135 (3) | 0.0027 (3) | 0.0097 (3) | 0.0029 (3) |
| C1 | 0.0165 (4) | 0.0160 (4) | 0.0139 (4) | 0.0004 (3) | 0.0086 (3) | −0.0003 (3) |
| C2 | 0.0183 (4) | 0.0226 (4) | 0.0133 (4) | 0.0022 (3) | 0.0077 (4) | 0.0013 (3) |
| C3 | 0.0222 (4) | 0.0154 (4) | 0.0204 (5) | 0.0021 (3) | 0.0128 (4) | 0.0037 (3) |
| C4 | 0.0175 (4) | 0.0146 (4) | 0.0158 (4) | 0.0003 (3) | 0.0100 (3) | 0.0003 (3) |
| C5 | 0.0154 (4) | 0.0135 (3) | 0.0130 (4) | 0.0014 (3) | 0.0093 (3) | 0.0011 (3) |
| C6 | 0.0154 (4) | 0.0136 (3) | 0.0127 (4) | 0.0001 (3) | 0.0085 (3) | 0.0004 (3) |
| C7 | 0.0162 (4) | 0.0149 (4) | 0.0131 (4) | 0.0010 (3) | 0.0086 (3) | 0.0009 (3) |
| C8 | 0.0155 (4) | 0.0124 (3) | 0.0138 (4) | 0.0007 (3) | 0.0093 (3) | 0.0005 (3) |
| C9 | 0.0180 (4) | 0.0139 (4) | 0.0149 (4) | −0.0001 (3) | 0.0096 (3) | −0.0009 (3) |
| C10 | 0.0225 (4) | 0.0199 (4) | 0.0143 (4) | 0.0025 (3) | 0.0092 (4) | 0.0032 (3) |
| C11 | 0.0269 (5) | 0.0168 (4) | 0.0210 (5) | 0.0048 (3) | 0.0135 (4) | 0.0061 (4) |
| C12 | 0.0266 (5) | 0.0135 (4) | 0.0224 (5) | 0.0020 (3) | 0.0146 (4) | 0.0015 (3) |
| C13 | 0.0192 (4) | 0.0146 (4) | 0.0150 (4) | −0.0003 (3) | 0.0099 (3) | −0.0012 (3) |
Geometric parameters (Å, º)
| F1—C9 | 1.3488 (11) | C4—C5 | 1.3928 (13) |
| F2—C13 | 1.3550 (12) | C4—H4A | 0.9300 |
| O1—C6 | 1.2334 (11) | C5—C6 | 1.4963 (13) |
| N1—C3 | 1.3399 (14) | C7—C8 | 1.4601 (13) |
| N1—C2 | 1.3410 (14) | C7—H7A | 0.9300 |
| N2—C6 | 1.3485 (12) | C8—C9 | 1.3983 (13) |
| N2—N3 | 1.3826 (11) | C8—C13 | 1.3998 (13) |
| N2—H1N2 | 0.884 (18) | C9—C10 | 1.3790 (14) |
| N3—C7 | 1.2864 (12) | C10—C11 | 1.3901 (15) |
| C1—C2 | 1.3897 (14) | C10—H10A | 0.9300 |
| C1—C5 | 1.3936 (13) | C11—C12 | 1.3897 (16) |
| C1—H1A | 0.9300 | C11—H11A | 0.9300 |
| C2—H2A | 0.9300 | C12—C13 | 1.3783 (14) |
| C3—C4 | 1.3872 (14) | C12—H12A | 0.9300 |
| C3—H3A | 0.9300 | ||
| C3—N1—C2 | 116.95 (9) | N2—C6—C5 | 114.91 (8) |
| C6—N2—N3 | 118.36 (8) | N3—C7—C8 | 121.88 (9) |
| C6—N2—H1N2 | 121.3 (11) | N3—C7—H7A | 119.1 |
| N3—N2—H1N2 | 119.4 (11) | C8—C7—H7A | 119.1 |
| C7—N3—N2 | 113.49 (8) | C9—C8—C13 | 114.68 (8) |
| C2—C1—C5 | 118.26 (9) | C9—C8—C7 | 126.14 (8) |
| C2—C1—H1A | 120.9 | C13—C8—C7 | 119.14 (9) |
| C5—C1—H1A | 120.9 | F1—C9—C10 | 117.80 (9) |
| N1—C2—C1 | 123.84 (9) | F1—C9—C8 | 118.65 (8) |
| N1—C2—H2A | 118.1 | C10—C9—C8 | 123.55 (9) |
| C1—C2—H2A | 118.1 | C9—C10—C11 | 118.53 (10) |
| N1—C3—C4 | 123.81 (9) | C9—C10—H10A | 120.7 |
| N1—C3—H3A | 118.1 | C11—C10—H10A | 120.7 |
| C4—C3—H3A | 118.1 | C12—C11—C10 | 121.09 (9) |
| C3—C4—C5 | 118.45 (9) | C12—C11—H11A | 119.5 |
| C3—C4—H4A | 120.8 | C10—C11—H11A | 119.5 |
| C5—C4—H4A | 120.8 | C13—C12—C11 | 117.68 (9) |
| C4—C5—C1 | 118.67 (9) | C13—C12—H12A | 121.2 |
| C4—C5—C6 | 118.35 (8) | C11—C12—H12A | 121.2 |
| C1—C5—C6 | 122.96 (8) | F2—C13—C12 | 118.28 (9) |
| O1—C6—N2 | 124.30 (9) | F2—C13—C8 | 117.29 (8) |
| O1—C6—C5 | 120.79 (8) | C12—C13—C8 | 124.43 (9) |
| C6—N2—N3—C7 | −172.82 (9) | N3—C7—C8—C9 | 14.15 (15) |
| C3—N1—C2—C1 | 1.03 (16) | N3—C7—C8—C13 | −167.93 (9) |
| C5—C1—C2—N1 | −0.46 (15) | C13—C8—C9—F1 | 178.07 (8) |
| C2—N1—C3—C4 | −0.28 (16) | C7—C8—C9—F1 | −3.93 (15) |
| N1—C3—C4—C5 | −0.99 (15) | C13—C8—C9—C10 | −1.87 (14) |
| C3—C4—C5—C1 | 1.52 (14) | C7—C8—C9—C10 | 176.13 (10) |
| C3—C4—C5—C6 | 179.93 (9) | F1—C9—C10—C11 | −178.93 (9) |
| C2—C1—C5—C4 | −0.85 (14) | C8—C9—C10—C11 | 1.00 (16) |
| C2—C1—C5—C6 | −179.18 (9) | C9—C10—C11—C12 | 0.75 (17) |
| N3—N2—C6—O1 | 2.02 (14) | C10—C11—C12—C13 | −1.46 (17) |
| N3—N2—C6—C5 | −178.14 (8) | C11—C12—C13—F2 | 179.64 (9) |
| C4—C5—C6—O1 | −34.71 (13) | C11—C12—C13—C8 | 0.49 (16) |
| C1—C5—C6—O1 | 143.63 (10) | C9—C8—C13—F2 | −178.05 (9) |
| C4—C5—C6—N2 | 145.45 (9) | C7—C8—C13—F2 | 3.79 (13) |
| C1—C5—C6—N2 | −36.22 (13) | C9—C8—C13—C12 | 1.10 (15) |
| N2—N3—C7—C8 | −177.64 (8) | C7—C8—C13—C12 | −177.05 (9) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| N2—H1N2···O1i | 0.88 (2) | 2.00 (2) | 2.8554 (12) | 163.4 (16) |
| C1—H1A···F1ii | 0.93 | 2.54 | 3.4622 (13) | 169 |
| C7—H7A···O1i | 0.93 | 2.45 | 3.2253 (13) | 141 |
Symmetry codes: (i) x, −y+3/2, z+1/2; (ii) x+1, y, z+1.
Footnotes
Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BV2204).
References
- Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
- Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
- Chen, S.-K. (2006). Acta Cryst. E62, o5352–o5353.
- Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.
- Nie, A., Ghosh, S. & Huang, Z. (2006). Acta Cryst. E62, o1824–o1825.
- Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
- Spek, A. L. (2009). Acta Cryst. D65, 148–155. [DOI] [PMC free article] [PubMed]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812016716/bv2204sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812016716/bv2204Isup2.hkl
Supplementary material file. DOI: 10.1107/S1600536812016716/bv2204Isup3.cml
Additional supplementary materials: crystallographic information; 3D view; checkCIF report


