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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2012 Apr 21;68(Pt 5):o1484. doi: 10.1107/S1600536812016716

N′-(2,6-Difluoro­benzyl­idene)pyridine-4-carbohydrazide

Hoong-Kun Fun a,*,, Ching Kheng Quah a,§, Divya N Shetty b, B Narayana b, B K Sarojini c
PMCID: PMC3344594  PMID: 22590356

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).graphic file with name e-68-o1484-scheme1.jpg

Experimental  

Crystal data  

  • C13H9F2N3O

  • M r = 261.23

  • Monoclinic, Inline graphic

  • 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

e-68-o1484-sup1.cif (22.4KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812016716/bv2204Isup2.hkl

e-68-o1484-Isup2.hkl (222KB, 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 DA 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) Inline graphic; (ii) Inline graphic.

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.

Fig. 1.

The molecular structure of the title compound showing 50% probability displacement ellipsoids for non-H atoms.

Fig. 2.

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 m3
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 mm1
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 Å3
0 restraints Δρmin = −0.23 e Å3

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

  1. 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.
  2. Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  3. Chen, S.-K. (2006). Acta Cryst. E62, o5352–o5353.
  4. Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107.
  5. Nie, A., Ghosh, S. & Huang, Z. (2006). Acta Cryst. E62, o1824–o1825.
  6. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
  7. 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

e-68-o1484-sup1.cif (22.4KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812016716/bv2204Isup2.hkl

e-68-o1484-Isup2.hkl (222KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812016716/bv2204Isup3.cml

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


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