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Crystal structure of (E)-N′-(3-fluoro-2-hy­dr­oxy­benzyl­­idene)isonicotinohydrazide

aDepartment of Chemistry, Faculty of Science and Technology, Thammasat University, Khlong Luang, Pathum Thani 12121, Thailand, bMaterials and Textile Technology, Faculty of Science and Technology, Thammasat University, Khlong Luang, Pathum Thani 12121, Thailand, and cDepartment of Chemistry and Center of Excellence in Biomaterials, Faculty of Science, Naresuan University, Muang, Phitsanulok 65000, Thailand
*Correspondence e-mail: filipkielar@nu.ac.th

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 19 June 2017; accepted 4 July 2017; online 11 July 2017)

In the title compound, C13H10FN3O2, the mol­ecule has an E conformation with respect to the C=N bond of the hydrazone bridge. The dihedral angle between the isonicotinoyl and fluoro­phenol moieties is 4.03 (4)°, and an intra­molecular O—H⋯N hydrogen bond generates an S(6) ring motif. In the crystal, mol­ecules are linked by N—H⋯N and C—H⋯N hydrogen bonds, forming chains propagating along the a-axis direction. The chains are linked by C—H⋯O hydrogen bonds, resulting in the formation of layers lying parallel to the ab plane. The crystal structure also features ππ inter­actions [centroid-to-centroid distance = 3.6887 (8) Å].

1. Chemical context

Hydrazone-based chelators of metal ions are inter­esting compounds that receive a significant amount of inter­est (Bendová et al., 2010[Bendová, P., Macková, E., Hašková, P., Vávrová, A., Jirkovský, E., Štěrba, M., Popelová, O., Kalinowski, D. S., Kovaříková, P., Vávrová, K., Richardson, D. R. & Šimůnek, T. (2010). Chem. Res. Toxicol. 23, 1105-1114.]; Jansová et al., 2014[Jansová, H., Macháček, M., Wang, Q., Hašková, P., Jirkovská, A., Potůčková, E., Kielar, F., Franz, K. J. & Šimůnek, T. (2014). Free Radical Biol. Med. 74, 210-221.]; Hrušková et al., 2016[Hrušková, K., Potůčková, E., Hergeselová, T., Liptáková, L., Hašková, P., Mingas, P., Kovaříková, P., Šimůnek, T. & Vávrová, K. (2016). Eur. J. Med. Chem. 120, 97-110.]). We have recently published the structures of two derivatives of the prototypical chelator from this class, salicyl aldehyde isonicotinoyl hydrazide (SIH), which were synthesized as potential sensors for metal ions (Chainok et al., 2016[Chainok, K., Makmuang, S. & Kielar, F. (2016). Acta Cryst. E72, 980-983.]). The structures reported have fluorine and methyl substitution in position 5 on the benzene ring. Herein, we report the crystal structure of a further analogue in this series bearing a fluorine substituent in position 3 of the benzene ring, which was synthesized in order to investigate the effect of the distance between the reporting fluorine atom and the metal chelating unit.

[Scheme 1]

2. Structural commentary

The mol­ecular structure of the title compound, with atom labelling, is presented in Fig. 1[link]. The mol­ecule has an E conformation with respect to the hydrazone bridge (C7=N3). The C6—N2 and C7—N3 bond lengths differ by 0.08 Å hence; these two bonds are formally double and single bonds, respectively. The mol­ecule deviates slightly from planarity with an r.m.s deviation for the fitted non-hydrogen atoms of 0.062 Å. There is an intra­molecular O2—H2O⋯N3 hydrogen bond with an S(6) ring motif present in the pyridine carboxamide moiety, and the pyridine ring (N1/C1–C5) is approximately coplanar with the amide group (C6(=O1)N2) [dihedral angle = 8.25 (6)°]. The isonicotinoyl moiety (N1/C1–C6/O1/N2) is inclined to the fluoro­phenol moiety (C8-C13/O2/F1) by 4.03 (4)°.

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling and 50% probability displacement ellipsoids. The intra­molecular hydrogen bond is shown as a dashed line (see Table 1[link]).

3. Supra­molecular features

In the crystal, mol­ecules are linked by bifurcated-acceptor N2—H2N⋯N1i and C4—H4⋯N1i hydrogen bonds (Table 1[link]), leading to the formation of zigzag chains lying parallel to the b-axis direction, as shown in Fig. 2[link]. Adjacent chains are further linked via C5—H5⋯O1ii hydrogen bonds, forming layers parallel to the ab plane, as shown in Fig. 3[link]. Within the sheets, there are ππ stacking inter­actions involving inversion-related mol­ecules [Cg1⋯Cg2i = 3.6887 (8) Å; Cg1 and Cg2 are the centroids of the pyridine (N1/C1–C5) and phenyl (C8–C13) rings, respectively; symmetry code: (i) −x + 1, −y + 1, −z + 1].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2O⋯N3 0.82 1.87 2.5862 (14) 145
N2—H2N⋯N1i 0.86 2.16 2.9851 (16) 161
C4—H4⋯N1i 0.93 2.51 3.3492 (18) 151
C5—H5⋯O1ii 0.93 2.37 3.2738 (17) 163
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x, -y+{\script{1\over 2}}, z+{\script{1\over 2}}].
[Figure 2]
Figure 2
A view of the hydrogen-bonded chains, formed in the crystal structure of the title compound via bifurcated-acceptor N—H⋯N and C—H⋯N hydrogen bonds (dashed lines; Table 1[link]).
[Figure 3]
Figure 3
Part of the crystal structure of the title compound, showing the formation of the layers, parallel to the ab plane, formed via C—H⋯O hydrogen bonds, and the ππ inter­actions (dashed lines).

4. Database survey

A search of the Cambridge Structural Database (Version 5.38, latest update May 2017; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) for compounds with the (E)-N-(2-hy­droxy­benzyl­idene)isonicotinohydrazide skeleton revealed 86 hits. They include the isotypic crystal structures with bromide (PORYEC; Xiong & Li, 2014[Xiong, Y. & Li, W.-H. (2014). J. Coord. Chem. 67, 3279-3287.]), meth­oxy (CANCOK, Yu et al., 2005[Yu, M., Chen, X. & Jing, Z.-L. (2005). Acta Cryst. E61, o1345-o1346.]; CANCOK01, Yang, 2007[Yang, D.-S. (2007). J. Chem. Crystallogr. 37, 343-348.]; CANCOK02, Xu, 2013[Xu, J. (2013). Synth. React. Inorg. Met.-Org. Nano-Met. Chem. 43, 1329-1333.]), and hy­droxy (WAFVEG; Tecer et al., 2010[Tecer, E., Dege, N., Zülfikaroğlu, A., Şenyüz, N. & Batı, H. (2010). Acta Cryst. E66, o3369-o3370.]) groups substituted at the 3-position of the phenyl ring.

5. Synthesis and crystallization

Isonicotinic acid hydrazide (301 mg, 2.19 mmol) and 3-fluoro­salicyl­aldehyde (338 mg, 2.69 mmol) were suspended in a 1:1 mixture of water and ethanol (6 ml). The reaction mixture was stirred at 363 K for 24 h and formation of a precipitate was observed. The reaction mixture was allowed to cool to room temperature and then filtered. The isolated solid was washed with water to give the product as a white solid (510 mg, 1.97 mmol, 90%). Colourless rod-like crystals, suitable for X-ray diffraction analysis, were grown by slow evaporation of a solution in methanol of the title compound. 1H NMR (400 MHz, DMSO-d6) d 6.94 (1H, m, CH-Ph), 7.32 (1H, dd, J = 8.8, J = 10.4 CH-Ph), 7.44 (1H, d, J = 8.4, CH-Ph), 7.85 (2H, d, J = 5.6, CH-Py), 8.70 (1H, s, CH=N), 8.81 (2H, d, J = 5.6, CH-Py), 11.40 (1H, s, NH), 12.39 (1H, s, OH). HR–MS (ES+) C13H11FN3O2 requires 260.0835 [M + H]+; found 260.0830.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms bonded to C, N, and O atoms were placed at calculated positions and refined using a riding-model approximation: N—H = 0.86 Å, O—H = 0.82 Å and C—H = 0.93 Å with Uiso(H) = 1.5Ueq(O) and 1.2Ueq(N,C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula C13H10FN3O2
Mr 259.24
Crystal system, space group Monoclinic, P21/c
Temperature (K) 296
a, b, c (Å) 7.8555 (3), 10.2748 (5), 14.9390 (7)
β (°) 92.397 (2)
V3) 1204.73 (9)
Z 4
Radiation type Mo Kα
μ (mm−1) 0.11
Crystal size (mm) 0.28 × 0.14 × 0.14
 
Data collection
Diffractometer Bruker D8 QUEST CMOS
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.700, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections 22872, 2475, 1769
Rint 0.045
(sin θ/λ)max−1) 0.625
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.100, 1.04
No. of reflections 2475
No. of parameters 173
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.16, −0.17
Computer programs: APEX3 and SAINT (Bruker, 2016[Bruker (2016). APEX3, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2016 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Computing details top

Data collection: APEX3 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

(E)-N'-(3-Fluoro-2-hydroxybenzylidene)isonicotinohydrazide top
Crystal data top
C13H10FN3O2F(000) = 536
Mr = 259.24Dx = 1.429 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 7.8555 (3) ÅCell parameters from 5896 reflections
b = 10.2748 (5) Åθ = 3.3–26.2°
c = 14.9390 (7) ŵ = 0.11 mm1
β = 92.397 (2)°T = 296 K
V = 1204.73 (9) Å3Rod, light colourless
Z = 40.28 × 0.14 × 0.14 mm
Data collection top
Bruker D8 QUEST CMOS
diffractometer
2475 independent reflections
Radiation source: microfocus sealed x-ray tube, Incoatec Iµus1769 reflections with I > 2σ(I)
Graphite Double Bounce Multilayer Mirror monochromatorRint = 0.045
Detector resolution: 10.5 pixels mm-1θmax = 26.4°, θmin = 3.3°
φ and ω scansh = 99
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
k = 1212
Tmin = 0.700, Tmax = 0.745l = 1818
22872 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.100H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0468P)2 + 0.1698P]
where P = (Fo2 + 2Fc2)/3
2475 reflections(Δ/σ)max < 0.001
173 parametersΔρmax = 0.16 e Å3
0 restraintsΔρmin = 0.17 e Å3
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
F10.04982 (16)0.68426 (11)0.21940 (6)0.0860 (4)
O10.42340 (15)0.25717 (10)0.46852 (6)0.0554 (3)
O20.19539 (16)0.52442 (11)0.33911 (7)0.0600 (3)
H2O0.23460.48240.38180.090*
N10.63170 (16)0.03844 (11)0.75111 (8)0.0441 (3)
N20.34254 (15)0.40224 (11)0.57234 (7)0.0403 (3)
H2N0.34090.42420.62790.048*
N30.27004 (15)0.47948 (11)0.50651 (8)0.0399 (3)
C10.6525 (2)0.01892 (14)0.66412 (10)0.0468 (4)
H10.71600.05270.64730.056*
C20.58528 (18)0.09868 (13)0.59763 (9)0.0412 (3)
H2B0.60290.08030.53780.049*
C30.49156 (17)0.20612 (12)0.62066 (8)0.0351 (3)
C40.4691 (2)0.22719 (14)0.71071 (9)0.0446 (4)
H40.40610.29810.72930.054*
C50.5408 (2)0.14213 (14)0.77255 (9)0.0463 (4)
H50.52480.15810.83290.056*
C60.41696 (18)0.28991 (13)0.54677 (9)0.0386 (3)
C70.18964 (18)0.58148 (13)0.52892 (9)0.0388 (3)
H70.18090.60250.58910.047*
C80.11173 (17)0.66478 (13)0.46000 (9)0.0369 (3)
C90.11849 (19)0.63208 (13)0.36907 (9)0.0415 (3)
C100.0421 (2)0.71659 (16)0.30725 (10)0.0524 (4)
C110.0379 (2)0.82835 (16)0.33089 (11)0.0575 (5)
H110.08620.88310.28720.069*
C120.0460 (2)0.85917 (15)0.42025 (11)0.0541 (4)
H120.10140.93460.43740.065*
C130.02768 (19)0.77830 (14)0.48399 (10)0.0468 (4)
H130.02140.79960.54430.056*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
F10.1259 (10)0.0961 (8)0.0341 (5)0.0010 (7)0.0206 (5)0.0070 (5)
O10.0834 (8)0.0553 (7)0.0275 (5)0.0052 (6)0.0002 (5)0.0019 (5)
O20.0887 (9)0.0545 (7)0.0356 (6)0.0095 (6)0.0102 (6)0.0071 (5)
N10.0577 (8)0.0394 (7)0.0347 (6)0.0017 (6)0.0025 (5)0.0029 (5)
N20.0548 (7)0.0375 (6)0.0279 (6)0.0019 (5)0.0078 (5)0.0044 (5)
N30.0493 (7)0.0360 (6)0.0336 (6)0.0058 (5)0.0088 (5)0.0069 (5)
C10.0592 (10)0.0391 (8)0.0422 (8)0.0079 (7)0.0015 (7)0.0014 (6)
C20.0530 (9)0.0413 (8)0.0293 (7)0.0019 (7)0.0027 (6)0.0033 (6)
C30.0411 (7)0.0334 (7)0.0304 (7)0.0078 (6)0.0014 (5)0.0006 (5)
C40.0631 (10)0.0387 (8)0.0320 (7)0.0094 (7)0.0016 (6)0.0010 (6)
C50.0682 (10)0.0433 (8)0.0273 (7)0.0049 (7)0.0003 (7)0.0001 (6)
C60.0477 (8)0.0391 (8)0.0287 (7)0.0074 (6)0.0012 (6)0.0042 (6)
C70.0472 (8)0.0397 (7)0.0291 (7)0.0090 (7)0.0049 (6)0.0027 (6)
C80.0391 (7)0.0361 (7)0.0348 (7)0.0090 (6)0.0046 (6)0.0042 (6)
C90.0498 (9)0.0391 (7)0.0347 (7)0.0084 (7)0.0069 (6)0.0019 (6)
C100.0639 (10)0.0603 (10)0.0318 (7)0.0106 (8)0.0127 (7)0.0084 (7)
C110.0568 (10)0.0530 (10)0.0610 (11)0.0064 (8)0.0178 (8)0.0228 (8)
C120.0529 (9)0.0446 (9)0.0641 (11)0.0022 (7)0.0057 (8)0.0082 (8)
C130.0511 (9)0.0451 (8)0.0440 (8)0.0039 (7)0.0012 (7)0.0001 (7)
Geometric parameters (Å, º) top
F1—C101.3576 (18)C3—C61.4997 (18)
O1—C61.2195 (16)C4—H40.9300
O2—H2O0.8200C4—C51.3753 (19)
O2—C91.3459 (18)C5—H50.9300
N1—C11.3317 (19)C7—H70.9300
N1—C51.3290 (18)C7—C81.4541 (19)
N2—H2N0.8600C8—C91.4026 (19)
N2—N31.3692 (15)C8—C131.394 (2)
N2—C61.3559 (18)C9—C101.386 (2)
N3—C71.2756 (18)C10—C111.362 (2)
C1—H10.9300C11—H110.9300
C1—C21.376 (2)C11—C121.376 (2)
C2—H2B0.9300C12—H120.9300
C2—C31.3784 (19)C12—C131.373 (2)
C3—C41.3813 (18)C13—H130.9300
C9—O2—H2O109.5N2—C6—C3116.17 (11)
C5—N1—C1116.42 (12)N3—C7—H7120.1
N3—N2—H2N121.2N3—C7—C8119.74 (12)
C6—N2—H2N121.2C8—C7—H7120.1
C6—N2—N3117.53 (11)C9—C8—C7120.86 (13)
C7—N3—N2118.90 (12)C13—C8—C7120.01 (12)
N1—C1—H1118.1C13—C8—C9119.13 (13)
N1—C1—C2123.77 (13)O2—C9—C8123.69 (12)
C2—C1—H1118.1O2—C9—C10118.77 (13)
C1—C2—H2B120.3C10—C9—C8117.54 (14)
C1—C2—C3119.32 (12)F1—C10—C9117.07 (15)
C3—C2—H2B120.3F1—C10—C11119.78 (14)
C2—C3—C4117.38 (12)C11—C10—C9123.15 (14)
C2—C3—C6118.19 (12)C10—C11—H11120.5
C4—C3—C6124.40 (13)C10—C11—C12119.08 (14)
C3—C4—H4120.4C12—C11—H11120.5
C5—C4—C3119.28 (13)C11—C12—H12120.1
C5—C4—H4120.4C13—C12—C11119.86 (15)
N1—C5—C4123.83 (13)C13—C12—H12120.1
N1—C5—H5118.1C8—C13—H13119.4
C4—C5—H5118.1C12—C13—C8121.22 (14)
O1—C6—N2122.72 (12)C12—C13—H13119.4
O1—C6—C3121.11 (13)
F1—C10—C11—C12179.40 (15)C4—C3—C6—O1170.67 (14)
O2—C9—C10—F10.2 (2)C4—C3—C6—N29.1 (2)
O2—C9—C10—C11179.55 (14)C5—N1—C1—C20.3 (2)
N1—C1—C2—C30.5 (2)C6—N2—N3—C7175.56 (12)
N2—N3—C7—C8179.99 (11)C6—C3—C4—C5178.64 (13)
N3—N2—C6—O11.1 (2)C7—C8—C9—O20.1 (2)
N3—N2—C6—C3178.64 (11)C7—C8—C9—C10179.69 (13)
N3—C7—C8—C92.3 (2)C7—C8—C13—C12179.56 (13)
N3—C7—C8—C13178.24 (12)C8—C9—C10—F1179.79 (13)
C1—N1—C5—C40.2 (2)C8—C9—C10—C110.1 (2)
C1—C2—C3—C40.5 (2)C9—C8—C13—C121.0 (2)
C1—C2—C3—C6178.83 (13)C9—C10—C11—C120.9 (3)
C2—C3—C4—C50.4 (2)C10—C11—C12—C130.8 (2)
C2—C3—C6—O17.5 (2)C11—C12—C13—C80.1 (2)
C2—C3—C6—N2172.75 (12)C13—C8—C9—O2179.55 (13)
C3—C4—C5—N10.3 (2)C13—C8—C9—C100.8 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O2—H2O···N30.821.872.5862 (14)145
N2—H2N···N1i0.862.162.9851 (16)161
C4—H4···N1i0.932.513.3492 (18)151
C5—H5···O1ii0.932.373.2738 (17)163
Symmetry codes: (i) x+1, y+1/2, z+3/2; (ii) x, y+1/2, z+1/2.
 

Acknowledgements

The authors thank the Faculty of Science and Technology, Thammasat University, for funds to purchase the X-ray diffractometer.

Funding information

This work was supported by a National Research Council of Thailand grant provided by the Naresuan University Division of Research Administration (R2559B060).

References

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