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

Jiajaroen, S.; Chainok, K.; Kielar, F.

doi:10.1107/S2056989017009926

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ISSN: 2056-9890

Volume 73| Part 8| August 2017| Pages 1151-1153

https://doi.org/10.1107/S2056989017009926

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

Suwadee Jiajaroen,^a Kittipong Chainok ^b and Filip Kielar ^c ^*

^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 π–π interactions [centroid-to-centroid distance = 3.6887 (8) Å].

Keywords: crystal structure; iron chelator; isonicotinohydrazide; hydrogen bonding.

CCDC reference: 1560196

1. Chemical context

Hydrazone-based chelators of metal ions are interesting compounds that receive a significant amount of interest (Bendová et al., 2010 ; Jansová et al., 2014 ; Hrušková et al., 2016 ). 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 ). 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.

2. Structural commentary

The molecular structure of the title compound, with atom labelling, is presented in Fig. 1. 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
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

3. Supramolecular features

In the crystal, molecules are linked by bifurcated-acceptor N2—H2N⋯N1ⁱ and C4—H4⋯N1ⁱ hydrogen bonds (Table 1), leading to the formation of zigzag chains lying parallel to the b-axis direction, as shown in Fig. 2. Adjacent chains are further linked via C5—H5⋯O1ⁱⁱ hydrogen bonds, forming layers parallel to the ab plane, as shown in Fig. 3. Within the sheets, there are π–π 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	D⋯A	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
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

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 π–π interactions (dashed lines).

4. Database survey

A search of the Cambridge Structural Database (Version 5.38, latest update May 2017; Groom et al., 2016 ) 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 ), methoxy (CANCOK, Yu et al., 2005 ; CANCOK01, Yang, 2007 ; CANCOK02, Xu, 2013 ), and hydroxy (WAFVEG; Tecer et al., 2010 ) 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. 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 U_iso(H) = 1.5U_eq(O) and 1.2U_eq(N,C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₀FN₃O₂
M_r	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)
V (Å³)	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 )
T_min, T_max	0.700, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections	22872, 2475, 1769
R_int	0.045
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.16, −0.17
Computer programs: APEX3 and SAINT (Bruker, 2016), SHELXT (Sheldrick, 2015a ), SHELXL2016 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 1560196

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017009926/su5379sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017009926/su5379Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017009926/su5379Isup3.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2056989017009926/su5379Isup4.cml

checkCIF report

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

C₁₃H₁₀FN₃O₂	F(000) = 536
M_r = 259.24	D_x = 1.429 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 7.8555 (3) Å	Cell parameters from 5896 reflections
b = 10.2748 (5) Å	θ = 3.3–26.2°
c = 14.9390 (7) Å	µ = 0.11 mm⁻¹
β = 92.397 (2)°	T = 296 K
V = 1204.73 (9) Å³	Rod, light colourless
Z = 4	0.28 × 0.14 × 0.14 mm

Data collection top

Bruker D8 QUEST CMOS diffractometer	2475 independent reflections
Radiation source: microfocus sealed x-ray tube, Incoatec Iµus	1769 reflections with I > 2σ(I)
Graphite Double Bounce Multilayer Mirror monochromator	R_int = 0.045
Detector resolution: 10.5 pixels mm^-1	θ_max = 26.4°, θ_min = 3.3°
φ and ω scans	h = −9→9
Absorption correction: multi-scan (SADABS; Bruker, 2016)	k = −12→12
T_min = 0.700, T_max = 0.745	l = −18→18
22872 measured reflections

Refinement top

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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.100	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0468P)² + 0.1698P] where P = (F_o² + 2F_c²)/3
2475 reflections	(Δ/σ)_max < 0.001
173 parameters	Δρ_max = 0.16 e Å⁻³
0 restraints	Δρ_min = −0.17 e Å⁻³

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

	x	y	z	U_iso*/U_eq
F1	0.04982 (16)	0.68426 (11)	0.21940 (6)	0.0860 (4)
O1	0.42340 (15)	0.25717 (10)	0.46852 (6)	0.0554 (3)
O2	0.19539 (16)	0.52442 (11)	0.33911 (7)	0.0600 (3)
H2O	0.2346	0.4824	0.3818	0.090*
N1	0.63170 (16)	0.03844 (11)	0.75111 (8)	0.0441 (3)
N2	0.34254 (15)	0.40224 (11)	0.57234 (7)	0.0403 (3)
H2N	0.3409	0.4242	0.6279	0.048*
N3	0.27004 (15)	0.47948 (11)	0.50651 (8)	0.0399 (3)
C1	0.6525 (2)	0.01892 (14)	0.66412 (10)	0.0468 (4)
H1	0.7160	−0.0527	0.6473	0.056*
C2	0.58528 (18)	0.09868 (13)	0.59763 (9)	0.0412 (3)
H2B	0.6029	0.0803	0.5378	0.049*
C3	0.49156 (17)	0.20612 (12)	0.62066 (8)	0.0351 (3)
C4	0.4691 (2)	0.22719 (14)	0.71071 (9)	0.0446 (4)
H4	0.4061	0.2981	0.7293	0.054*
C5	0.5408 (2)	0.14213 (14)	0.77255 (9)	0.0463 (4)
H5	0.5248	0.1581	0.8329	0.056*
C6	0.41696 (18)	0.28991 (13)	0.54677 (9)	0.0386 (3)
C7	0.18964 (18)	0.58148 (13)	0.52892 (9)	0.0388 (3)
H7	0.1809	0.6025	0.5891	0.047*
C8	0.11173 (17)	0.66478 (13)	0.46000 (9)	0.0369 (3)
C9	0.11849 (19)	0.63208 (13)	0.36907 (9)	0.0415 (3)
C10	0.0421 (2)	0.71659 (16)	0.30725 (10)	0.0524 (4)
C11	−0.0379 (2)	0.82835 (16)	0.33089 (11)	0.0575 (5)
H11	−0.0862	0.8831	0.2872	0.069*
C12	−0.0460 (2)	0.85917 (15)	0.42025 (11)	0.0541 (4)
H12	−0.1014	0.9346	0.4374	0.065*
C13	0.02768 (19)	0.77830 (14)	0.48399 (10)	0.0468 (4)
H13	0.0214	0.7996	0.5443	0.056*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.1259 (10)	0.0961 (8)	0.0341 (5)	0.0010 (7)	−0.0206 (5)	0.0070 (5)
O1	0.0834 (8)	0.0553 (7)	0.0275 (5)	0.0052 (6)	0.0002 (5)	0.0019 (5)
O2	0.0887 (9)	0.0545 (7)	0.0356 (6)	0.0095 (6)	−0.0102 (6)	−0.0071 (5)
N1	0.0577 (8)	0.0394 (7)	0.0347 (6)	0.0017 (6)	−0.0025 (5)	0.0029 (5)
N2	0.0548 (7)	0.0375 (6)	0.0279 (6)	−0.0019 (5)	−0.0078 (5)	0.0044 (5)
N3	0.0493 (7)	0.0360 (6)	0.0336 (6)	−0.0058 (5)	−0.0088 (5)	0.0069 (5)
C1	0.0592 (10)	0.0391 (8)	0.0422 (8)	0.0079 (7)	0.0015 (7)	−0.0014 (6)
C2	0.0530 (9)	0.0413 (8)	0.0293 (7)	−0.0019 (7)	0.0027 (6)	−0.0033 (6)
C3	0.0411 (7)	0.0334 (7)	0.0304 (7)	−0.0078 (6)	−0.0014 (5)	0.0006 (5)
C4	0.0631 (10)	0.0387 (8)	0.0320 (7)	0.0094 (7)	0.0016 (6)	−0.0010 (6)
C5	0.0682 (10)	0.0433 (8)	0.0273 (7)	0.0049 (7)	0.0003 (7)	−0.0001 (6)
C6	0.0477 (8)	0.0391 (8)	0.0287 (7)	−0.0074 (6)	−0.0012 (6)	0.0042 (6)
C7	0.0472 (8)	0.0397 (7)	0.0291 (7)	−0.0090 (7)	−0.0049 (6)	0.0027 (6)
C8	0.0391 (7)	0.0361 (7)	0.0348 (7)	−0.0090 (6)	−0.0046 (6)	0.0042 (6)
C9	0.0498 (9)	0.0391 (7)	0.0347 (7)	−0.0084 (7)	−0.0069 (6)	0.0019 (6)
C10	0.0639 (10)	0.0603 (10)	0.0318 (7)	−0.0106 (8)	−0.0127 (7)	0.0084 (7)
C11	0.0568 (10)	0.0530 (10)	0.0610 (11)	−0.0064 (8)	−0.0178 (8)	0.0228 (8)
C12	0.0529 (9)	0.0446 (9)	0.0641 (11)	0.0022 (7)	−0.0057 (8)	0.0082 (8)
C13	0.0511 (9)	0.0451 (8)	0.0440 (8)	−0.0039 (7)	−0.0012 (7)	0.0001 (7)

Geometric parameters (Å, º) top

F1—C10	1.3576 (18)	C3—C6	1.4997 (18)
O1—C6	1.2195 (16)	C4—H4	0.9300
O2—H2O	0.8200	C4—C5	1.3753 (19)
O2—C9	1.3459 (18)	C5—H5	0.9300
N1—C1	1.3317 (19)	C7—H7	0.9300
N1—C5	1.3290 (18)	C7—C8	1.4541 (19)
N2—H2N	0.8600	C8—C9	1.4026 (19)
N2—N3	1.3692 (15)	C8—C13	1.394 (2)
N2—C6	1.3559 (18)	C9—C10	1.386 (2)
N3—C7	1.2756 (18)	C10—C11	1.362 (2)
C1—H1	0.9300	C11—H11	0.9300
C1—C2	1.376 (2)	C11—C12	1.376 (2)
C2—H2B	0.9300	C12—H12	0.9300
C2—C3	1.3784 (19)	C12—C13	1.373 (2)
C3—C4	1.3813 (18)	C13—H13	0.9300

C9—O2—H2O	109.5	N2—C6—C3	116.17 (11)
C5—N1—C1	116.42 (12)	N3—C7—H7	120.1
N3—N2—H2N	121.2	N3—C7—C8	119.74 (12)
C6—N2—H2N	121.2	C8—C7—H7	120.1
C6—N2—N3	117.53 (11)	C9—C8—C7	120.86 (13)
C7—N3—N2	118.90 (12)	C13—C8—C7	120.01 (12)
N1—C1—H1	118.1	C13—C8—C9	119.13 (13)
N1—C1—C2	123.77 (13)	O2—C9—C8	123.69 (12)
C2—C1—H1	118.1	O2—C9—C10	118.77 (13)
C1—C2—H2B	120.3	C10—C9—C8	117.54 (14)
C1—C2—C3	119.32 (12)	F1—C10—C9	117.07 (15)
C3—C2—H2B	120.3	F1—C10—C11	119.78 (14)
C2—C3—C4	117.38 (12)	C11—C10—C9	123.15 (14)
C2—C3—C6	118.19 (12)	C10—C11—H11	120.5
C4—C3—C6	124.40 (13)	C10—C11—C12	119.08 (14)
C3—C4—H4	120.4	C12—C11—H11	120.5
C5—C4—C3	119.28 (13)	C11—C12—H12	120.1
C5—C4—H4	120.4	C13—C12—C11	119.86 (15)
N1—C5—C4	123.83 (13)	C13—C12—H12	120.1
N1—C5—H5	118.1	C8—C13—H13	119.4
C4—C5—H5	118.1	C12—C13—C8	121.22 (14)
O1—C6—N2	122.72 (12)	C12—C13—H13	119.4
O1—C6—C3	121.11 (13)

F1—C10—C11—C12	179.40 (15)	C4—C3—C6—O1	−170.67 (14)
O2—C9—C10—F1	0.2 (2)	C4—C3—C6—N2	9.1 (2)
O2—C9—C10—C11	−179.55 (14)	C5—N1—C1—C2	−0.3 (2)
N1—C1—C2—C3	0.5 (2)	C6—N2—N3—C7	175.56 (12)
N2—N3—C7—C8	−179.99 (11)	C6—C3—C4—C5	178.64 (13)
N3—N2—C6—O1	1.1 (2)	C7—C8—C9—O2	−0.1 (2)
N3—N2—C6—C3	−178.64 (11)	C7—C8—C9—C10	−179.69 (13)
N3—C7—C8—C9	2.3 (2)	C7—C8—C13—C12	179.56 (13)
N3—C7—C8—C13	−178.24 (12)	C8—C9—C10—F1	179.79 (13)
C1—N1—C5—C4	0.2 (2)	C8—C9—C10—C11	0.1 (2)
C1—C2—C3—C4	−0.5 (2)	C9—C8—C13—C12	−1.0 (2)
C1—C2—C3—C6	−178.83 (13)	C9—C10—C11—C12	−0.9 (3)
C2—C3—C4—C5	0.4 (2)	C10—C11—C12—C13	0.8 (2)
C2—C3—C6—O1	7.5 (2)	C11—C12—C13—C8	0.1 (2)
C2—C3—C6—N2	−172.75 (12)	C13—C8—C9—O2	−179.55 (13)
C3—C4—C5—N1	−0.3 (2)	C13—C8—C9—C10	0.8 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+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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