Crystal structures of (E)-N′-(2-hy­droxy-5-methyl­benzyl­idene)isonicotinohydrazide and (E)-N′-(5-fluoro-2-hy­droxy­benzyl­idene)isonicotinohydrazide

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

doi:10.1107/S2056989016009762

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ISSN: 2056-9890

Volume 72| Part 7| July 2016| Pages 980-983

https://doi.org/10.1107/S2056989016009762

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Crystal structures of (E)-N′-(2-hydroxy-5-methylbenzylidene)isonicotinohydrazide and (E)-N′-(5-fluoro-2-hydroxybenzylidene)isonicotinohydrazide

Kittipong Chainok,^a Sureerat Makmuang ^b and Filip Kielar ^b ^*

^aDepartment of Physics, Faculty of Science and Technology, Thammasat University, Khlong Luang, Pathum Thani, 12120, Thailand, and ^bDepartment of Chemistry and Center of Excellence in Biomaterials, Faculty of Science, Naresuan University, Muang, Phitsanulok, 65000, Thailand
^*Correspondence e-mail: filipk@nu.ac.th

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 20 May 2016; accepted 15 June 2016; online 17 June 2016)

Two derivatives of the well-known iron chelator, (E)-N′-(2-hydroxybenzylidene)isonicotinohydrazide (SIH), substituted in the 5-position of the 2-hydroxybenzene ring by a methyl and a fluorine group viz. (E)-N′-(2-hydroxy-5-methylbenzylidene)isonicotinohydrazide, C₁₄H₁₃N₃O₂, (I), and (E)-N′-(5-fluoro-2-hydroxybenzylidene)isonicotinohydrazide, C₁₃H₁₀FN₃O₂, (II), have been prepared and characterized by single-crystal X-ray diffraction, ¹H NMR and mass spectrometry. The molecules of both compounds deviate slightly from planarity [r.m.s. deviations are 0.145 and 0.110 Å for (I) and (II), respectively] and adopt an E conformation with respect to the double bond of the hydrazone bridge. In each molecule, there is an intramolecular O—H⋯N hydrogen bond forming an S(6) ring motif. The dihedral angles between the mean planes of the isonicotinoyl ring and the cresol ring in (I) or the fluorophenol ring in (II) are 10.49 (6) and 9.43 (6)°, respectively. In the crystals of both compounds, zigzag chains are formed via N—H⋯N hydrogen bonds, in the [10-1] direction for (I) and [010] for (II). In (I), the chains are linked by weak C—H⋯π and π–π stacking interactions [centroid-to-centroid distances = 3.6783 (8) Å; inter-planar angle = 10.94 (5)°], leading to the formation of a three-dimensional supramolecular architecture. In (II), adjacent chains are connected through C—H⋯O hydrogen bonds to form sheets parallel to (100), which enclose R₄⁴(30) ring motifs. The sheets are linked by weak C—H⋯π and π–π [centroid-to-centroid distance = 3.7147 (8) Å; inter-planar angle = 10.94 (5)°] interactions, forming a three-dimensional supramolecular architecture.

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

CCDC references: 1485834; 1485833

1. Chemical context

Hydrazone-based chelators for metal ions have received a significant amount of attention (Bendova et al., 2010 ; Hrušková et al., 2016 ). Compounds from this class, such as salicyl aldehyde isonicotinoyl hydrazide (SIH), have been studied as potential metal chelators in biological systems (Hrušková et al., 2011 ). These compounds have also been shown to be effective in protecting against metal-based oxidative stress (Jansová et al., 2014 ). In our research we are interested in developing probes for metal ions (Carter et al., 2014 ). We have therefore synthesized the title compounds, which are derivatives of the chelator SIH containing a signalling unit.

2. Structural commentary

The molecular structures of the title compounds, (I) and (II), are illustrated in Figs. 1 and 2, respectively. They consist of an isonicotinoyl moiety linked by a –C7=N3–N2– linkage to a cresol unit in (I) and a fluorophenol ring in (II). The molecules deviate slightly from planarity with the r.m.s deviations for the fitted atoms being 0.145 for (I) and 0.110 Å for (II). In each molecule, there is an intramolecular O—H⋯N hydrogen bond forming an S(6) ring motif. Both compounds have an E conformation with respect to the double bond of the hydrazone bridge (C7=N3) with the C8—C7=N3—N2 torsion angles being −179.03 (12) and −177.61 (11)° for (I) and (II), respectively. The dihedral angles between the mean planes of the isonicotinoyl moiety and the cresol moiety in (I), or the fluorophenol moiety in (II) are 10.49 (6) and 9.43 (6)°, respectively. The bond lengths and angles in the title molecules agree reasonably well with those found in closely related structures (Chumakov et al., 2001 ; Yang, 2006a ,b ; Kargar et al., 2010 ; Sedaghat et al., 2014 )

Figure 1
The molecular structure of compound (I)

, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level. The intramolecular O—H⋯N hydrogen bond is shown as a dashed line (see Table 1

Figure 2
The molecular structure of compound (II)

, showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 40% probability level. The intramolecular O—H⋯N hydrogen bond is shown as a dashed line (see Table 2

3. Supramolecular features

In the crystals of both compounds, zigzag chains are formed via N—H⋯N hydrogen bonds (Tables 1 and 2), in direction [10 $[\overline{1}]$ ] for (I) and [010] for (II). In (I), the chains are linked by weak C—H⋯π and π–π stacking interactions [centroid-to-centroid distances = 3.6783 (8) Å; inter-planar angle = 10.94 (5)°], leading to the formation of a three-dimensional supramolecular architecture (Fig. 3). In (II), adjacent chains are connected through C—H⋯O hydrogen bonds to form sheets parallel to (100), which enclose R₄⁴(30) ring motifs. Weak C—H⋯π and π—π [centroid-to-centroid distance = 3.7147 (8) Å, inter-planar angle = 10.94 (5)°] interactions link the sheets, forming a three-dimensional supramolecular architecture (Fig. 4).

Table 1
Hydrogen-bond geometry (Å, °) for (I)

Cg1 is the centroid of the N1/C1–C5 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2O⋯N3	0.82	1.87	2.5857 (16)	145
N2—H2N⋯N1ⁱ	0.86	2.19	3.0232 (17)	164
C10—H10⋯Cg1ⁱⁱ	0.93	2.85	3.5259 (17)	130
Symmetry codes: (i) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Table 2
Hydrogen-bond geometry (Å, °) for (II)

Cg1 is the centroid of the N1/C1–C5 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2⋯N3	0.82	1.92	2.6329 (15)	145
N2—H2A⋯N1ⁱ	0.86	2.19	2.8889 (15)	138
C10—H10⋯O1ⁱⁱ	0.93	2.51	3.2573 (18)	138
C11—H11⋯Cg1ⁱⁱⁱ	0.93	2.98	3.8917 (18)	168
Symmetry codes: (i) $[-x+2, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) $[-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iii) $[x-1, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ .

Figure 3
Partial view along the a axis of the crystal packing of compound (I)

, showing the hydrogen-bonded (dashed lines; see Table 1

) zigzag chains parallel to [10 $[\overline{1}]$ ].

Figure 4
Partial view along the a axis of the crystal packing of compound (II)

, showing the N—H⋯N and C—H⋯O hydrogen-bonded (dashed lines; see Table 2

) sheet propagating in the bc plane.

4. Database survey

A search of the Cambridge Structural Database (Version 5.37, last update November 2015; Groom et al., 2016 ) indicated the presence of 40 structures containing the (E)-N-(2-hydroxybezylydene)isonicotinohydrazide substructure. They include the isotypic crystal structures with chloride (UCAREV, Chumakov et al., 2001; UCAREV01, Yang, 2006a), bromide (XENDOK, Yang, 2006b; XENDOK01, Sedaghat et al., 2014) and methoxy (VACHAK, Kargar et al., 2010) groups substituted at the 5-position of the phenyl ring. In the crystals of all three compounds, the N—H⋯N hydrogen bond involving the hydrazone hydrogen and the pyridine nitrogen atoms organize the molecules into a herringbone motif, while in the crystal of the methoxy compound there are also weak N—H⋯O and C—H⋯O hydrogen bonds present forming R₁²(6) ring motifs.

5. Synthesis and crystallization

A solution of isonicotinic acid hydrazide (0.184 g, 1.34 mmol) and the appropriately substituted salicyl aldehyde (1.47 mmol) in a mixture of ethanol (3 ml) and water (1 ml) containing a catalytic amount of acetic acid was heated to reflux for 5 h. The reaction mixture was allowed to cool to room temperature, resulting in the formation of a white precipitate. The reaction mixture was filtered and the isolated solid was washed with diethyl ether and dried in vacuo. The compounds were isolated as white crystalline solids in 73% and 66% yield for the methyl (I) and fluoro (II) derivatives, respectively. Single crystals suitable for X-ray diffraction were grown by slow evaporation of methanolic solutions of the title compounds.

Spectroscopic data for (I): ¹H NMR (400 MHz, DMSO-d₆) d 2.25 (1H, s, CH₃), 6.84 (1H, d, J = 8.4, CH—Ph), 7.12 (1H, dd, J = 2.0, J = 8.4, CH—Ph), 7.40 (1H, d, J = 1.6, CH—Ph), 7.84 (2H, d, J = 6.0, CH—Py), 8.63 (1H, s, CH=N), 8.79 (2H, d, J = 6.0, CH—Py), 10.82 (1H, s, NH), 12.26 (1H, s, OH). HR–MS (ES⁺) C₁₄H₁₄N₃O₂ requires 256.1086 [M+H]⁺; found 256.1051.

Spectroscopic data for (II): ¹H NMR (400 MHz, DMSO-d₆) d 6.94 (1H, dd, J = 4.4, J = 8.8, CH—Ph), 7.16 (1H, td, J = 3.2, J = 8.8, CH—Ph), 7.46 (1H, dd, J = 3.2, J = 9.6, CH—Ph), 7.84 (2H, d, J = 6.0, CH—Py), 8.67 (1H, s, CH=N), 8.80 (2H, d, J = 6.0, CH—Py), 10.84 (1H, s, NH), 12.35 (1H, s, OH). HR–MS (ES⁺) C₁₃H₁₁FN₃O₂ requires 260.0835 [M+H]⁺; found 260.0831.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. 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 = 0.93–0.96 Å with U_iso(H) = 1.5U_eq(C-methyl,O) and 1.2U_eq(N,C) for other H atoms.

Table 3
Experimental details

	(I)	(II)
Crystal data
Chemical formula	C₁₄H₁₃N₃O₂	C₁₃H₁₀FN₃O₂
M_r	255.27	259.24
Crystal system, space group	Monoclinic, P2₁/n	Monoclinic, P2₁/c
Temperature (K)	296	296
a, b, c (Å)	8.5318 (4), 15.9973 (8), 9.4637 (5)	8.9195 (3), 10.1128 (3), 13.6254 (4)
β (°)	102.738 (2)	103.481 (1)
V (Å³)	1259.87 (11)	1195.16 (6)
Z	4	4
Radiation type	Mo Kα	Mo Kα
μ (mm⁻¹)	0.09	0.11
Crystal size (mm)	0.30 × 0.22 × 0.22	0.32 × 0.26 × 0.26

Data collection
Diffractometer	Bruker D8 QUEST CMOS	Bruker APEX2 D8 QUEST CMOS
Absorption correction	Multi-scan (SADABS; Bruker, 2014 )	Multi-scan (SADABS; Bruker, 2014)
T_min, T_max	0.685, 0.746	0.685, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	26052, 2996, 2111	31833, 2848, 2128
R_int	0.045	0.039
(sin θ/λ)_max (Å⁻¹)	0.659	0.658

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.126, 1.01	0.042, 0.124, 1.03
No. of reflections	2996	2848
No. of parameters	174	174
H-atom treatment	H-atom parameters constrained	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.20, −0.22	0.26, −0.29
Computer programs: APEX2 and SAINT (Bruker, 2014), SHELXT (Sheldrick, 2015a ), SHELXL2014 (Sheldrick, 2015b ), OLEX2 (Dolomanov et al., 2009 ), ORTEP-3 for Windows (Farrugia, 2012 ), DIAMOND (Brandenburg, 2006 ), publCIF (Westrip, 2010 ) and enCIFer (Allen et al., 2004 ).

Supporting information

CCDC references: 1485834; 1485833

Crystal structure: contains datablocks Global, I, II. DOI: https://doi.org/10.1107/S2056989016009762/su5301sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016009762/su5301Isup2.hkl

Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989016009762/su5301IIsup3.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016009762/su5301Isup4.cdx

Supporting information file. DOI: https://doi.org/10.1107/S2056989016009762/su5301Isup5.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989016009762/su5301IIsup6.cml

checkCIF report

Computing details top

For both compounds, data collection: APEX2 (Bruker, 2014); cell refinement: SAINT (Bruker, 2014); data reduction: SAINT (Bruker, 2014); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015b); molecular graphics: OLEX2 (Dolomanov et al., 2009), ORTEP-3 for Windows (Farrugia, 2012) and DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2010) and enCIFer (Allen et al., 2004).

(I) (E)-N'-(2-Hydroxy-5-methylbenzylidene)isonicotinohydrazide top

Crystal data top

C₁₄H₁₃N₃O₂	F(000) = 536
M_r = 255.27	D_x = 1.346 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 8.5318 (4) Å	Cell parameters from 6456 reflections
b = 15.9973 (8) Å	θ = 2.9–27.3°
c = 9.4637 (5) Å	µ = 0.09 mm⁻¹
β = 102.738 (2)°	T = 296 K
V = 1259.87 (11) Å³	Block, colourless
Z = 4	0.30 × 0.22 × 0.22 mm

Data collection top

Bruker D8 QUEST CMOS diffractometer	2996 independent reflections
Radiation source: microfocus sealed x-ray tube, Incoatec Iµus	2111 reflections with I > 2σ(I)
GraphiteDouble Bounce Multilayer Mirror monochromator	R_int = 0.045
Detector resolution: 10.5 pixels mm^-1	θ_max = 27.9°, θ_min = 2.9°
φ and ω scans	h = −11→11
Absorption correction: multi-scan (SADABS; Bruker, 2014)	k = −21→21
T_min = 0.685, T_max = 0.746	l = −12→12
26052 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.046	H-atom parameters constrained
wR(F²) = 0.126	w = 1/[σ²(F_o²) + (0.0596P)² + 0.2954P] where P = (F_o² + 2F_c²)/3
S = 1.01	(Δ/σ)_max < 0.001
2996 reflections	Δρ_max = 0.20 e Å⁻³
174 parameters	Δρ_min = −0.22 e Å⁻³
0 restraints

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
O1	0.55036 (17)	0.49610 (7)	0.82618 (13)	0.0710 (4)
O2	0.21987 (15)	0.36743 (7)	0.62695 (11)	0.0575 (3)
H2O	0.2779	0.4085	0.6481	0.086*
N1	0.84669 (14)	0.76238 (8)	0.96854 (13)	0.0422 (3)
N2	0.43283 (14)	0.57825 (7)	0.63975 (12)	0.0390 (3)
H2N	0.4281	0.6255	0.5957	0.047*
N3	0.33377 (14)	0.51301 (7)	0.58586 (13)	0.0392 (3)
C1	0.81205 (18)	0.69573 (9)	1.04127 (15)	0.0430 (4)
H1	0.8580	0.6923	1.1398	0.052*
C2	0.71232 (18)	0.63196 (9)	0.97872 (15)	0.0418 (4)
H2	0.6922	0.5868	1.0340	0.050*
C3	0.64217 (16)	0.63598 (8)	0.83192 (15)	0.0362 (3)
C4	0.67688 (16)	0.70444 (9)	0.75506 (15)	0.0377 (3)
H4	0.6321	0.7096	0.6565	0.045*
C5	0.77918 (17)	0.76509 (9)	0.82720 (15)	0.0406 (3)
H5	0.8025	0.8106	0.7741	0.049*
C6	0.53873 (18)	0.56378 (9)	0.76673 (16)	0.0415 (3)
C7	0.23407 (16)	0.51994 (8)	0.46483 (14)	0.0365 (3)
H7	0.2291	0.5691	0.4116	0.044*
C8	0.12838 (16)	0.45084 (8)	0.41038 (14)	0.0336 (3)
C9	0.12462 (17)	0.37797 (9)	0.49306 (15)	0.0393 (3)
C10	0.02068 (19)	0.31395 (9)	0.43625 (17)	0.0463 (4)
H10	0.0153	0.2664	0.4914	0.056*
C11	−0.07485 (18)	0.31991 (10)	0.29884 (17)	0.0453 (4)
H11	−0.1419	0.2755	0.2622	0.054*
C12	−0.07365 (16)	0.39037 (10)	0.21364 (15)	0.0409 (4)
C13	0.02749 (17)	0.45510 (9)	0.27258 (15)	0.0378 (3)
H13	0.0283	0.5034	0.2182	0.045*
C14	−0.1769 (2)	0.39481 (12)	0.06279 (18)	0.0601 (5)
H14A	−0.1905	0.3397	0.0218	0.090*
H14B	−0.1260	0.4299	0.0039	0.090*
H14C	−0.2800	0.4176	0.0664	0.090*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0903 (10)	0.0412 (7)	0.0624 (8)	−0.0114 (6)	−0.0244 (7)	0.0126 (6)
O2	0.0751 (8)	0.0487 (7)	0.0403 (6)	−0.0108 (6)	−0.0055 (5)	0.0119 (5)
N1	0.0409 (7)	0.0425 (7)	0.0401 (7)	0.0010 (5)	0.0022 (5)	−0.0074 (5)
N2	0.0408 (7)	0.0309 (6)	0.0400 (7)	−0.0020 (5)	−0.0022 (5)	−0.0019 (5)
N3	0.0409 (7)	0.0332 (6)	0.0404 (7)	−0.0023 (5)	0.0021 (5)	−0.0041 (5)
C1	0.0457 (8)	0.0465 (9)	0.0320 (7)	0.0056 (7)	−0.0018 (6)	−0.0044 (6)
C2	0.0475 (8)	0.0376 (8)	0.0368 (8)	0.0037 (6)	0.0019 (6)	0.0009 (6)
C3	0.0341 (7)	0.0348 (7)	0.0368 (7)	0.0065 (6)	0.0018 (6)	−0.0044 (6)
C4	0.0371 (8)	0.0406 (8)	0.0323 (7)	0.0043 (6)	0.0011 (6)	−0.0025 (6)
C5	0.0419 (8)	0.0392 (8)	0.0391 (8)	0.0003 (6)	0.0057 (6)	−0.0022 (6)
C6	0.0446 (8)	0.0357 (8)	0.0395 (8)	0.0018 (6)	−0.0007 (6)	−0.0010 (6)
C7	0.0411 (8)	0.0301 (7)	0.0368 (7)	0.0008 (6)	0.0053 (6)	0.0005 (6)
C8	0.0354 (7)	0.0314 (7)	0.0339 (7)	0.0027 (6)	0.0076 (5)	−0.0027 (5)
C9	0.0439 (8)	0.0386 (8)	0.0350 (7)	−0.0010 (6)	0.0076 (6)	0.0011 (6)
C10	0.0547 (9)	0.0361 (8)	0.0491 (9)	−0.0080 (7)	0.0136 (7)	0.0034 (6)
C11	0.0411 (8)	0.0418 (8)	0.0531 (9)	−0.0100 (7)	0.0107 (7)	−0.0105 (7)
C12	0.0348 (7)	0.0454 (8)	0.0406 (8)	0.0022 (6)	0.0046 (6)	−0.0080 (6)
C13	0.0408 (8)	0.0344 (7)	0.0362 (7)	0.0032 (6)	0.0041 (6)	0.0012 (6)
C14	0.0527 (10)	0.0672 (11)	0.0513 (10)	−0.0003 (9)	−0.0081 (8)	−0.0085 (8)

Geometric parameters (Å, º) top

O1—C6	1.2140 (17)	C5—H5	0.9300
O2—H2O	0.8200	C7—H7	0.9300
O2—C9	1.3566 (17)	C7—C8	1.4476 (19)
N1—C1	1.3371 (19)	C8—C9	1.4083 (19)
N1—C5	1.3353 (18)	C8—C13	1.3969 (18)
N2—H2N	0.8600	C9—C10	1.383 (2)
N2—N3	1.3687 (16)	C10—H10	0.9300
N2—C6	1.3547 (17)	C10—C11	1.377 (2)
N3—C7	1.2720 (17)	C11—H11	0.9300
C1—H1	0.9300	C11—C12	1.387 (2)
C1—C2	1.376 (2)	C12—C13	1.384 (2)
C2—H2	0.9300	C12—C14	1.505 (2)
C2—C3	1.3878 (19)	C13—H13	0.9300
C3—C4	1.382 (2)	C14—H14A	0.9600
C3—C6	1.5011 (19)	C14—H14B	0.9600
C4—H4	0.9300	C14—H14C	0.9600
C4—C5	1.3808 (19)

C9—O2—H2O	109.5	C8—C7—H7	120.2
C5—N1—C1	116.49 (12)	C9—C8—C7	121.54 (12)
N3—N2—H2N	122.1	C13—C8—C7	120.15 (12)
C6—N2—H2N	122.1	C13—C8—C9	118.31 (12)
C6—N2—N3	115.88 (12)	O2—C9—C8	122.64 (13)
C7—N3—N2	120.30 (12)	O2—C9—C10	118.14 (13)
N1—C1—H1	118.1	C10—C9—C8	119.21 (13)
N1—C1—C2	123.76 (13)	C9—C10—H10	119.6
C2—C1—H1	118.1	C11—C10—C9	120.72 (14)
C1—C2—H2	120.5	C11—C10—H10	119.6
C1—C2—C3	119.05 (14)	C10—C11—H11	119.1
C3—C2—H2	120.5	C10—C11—C12	121.76 (13)
C2—C3—C6	117.42 (13)	C12—C11—H11	119.1
C4—C3—C2	117.92 (13)	C11—C12—C14	120.79 (14)
C4—C3—C6	124.62 (12)	C13—C12—C11	117.23 (13)
C3—C4—H4	120.6	C13—C12—C14	121.98 (15)
C5—C4—C3	118.81 (13)	C8—C13—H13	118.6
C5—C4—H4	120.6	C12—C13—C8	122.74 (13)
N1—C5—C4	123.95 (14)	C12—C13—H13	118.6
N1—C5—H5	118.0	C12—C14—H14A	109.5
C4—C5—H5	118.0	C12—C14—H14B	109.5
O1—C6—N2	122.27 (13)	C12—C14—H14C	109.5
O1—C6—C3	121.01 (13)	H14A—C14—H14B	109.5
N2—C6—C3	116.73 (12)	H14A—C14—H14C	109.5
N3—C7—H7	120.2	H14B—C14—H14C	109.5
N3—C7—C8	119.63 (13)

O2—C9—C10—C11	−177.73 (14)	C5—N1—C1—C2	−0.3 (2)
N1—C1—C2—C3	−0.2 (2)	C6—N2—N3—C7	−177.70 (13)
N2—N3—C7—C8	−179.03 (12)	C6—C3—C4—C5	−177.39 (13)
N3—N2—C6—O1	3.1 (2)	C7—C8—C9—O2	−0.7 (2)
N3—N2—C6—C3	−176.69 (12)	C7—C8—C9—C10	179.63 (13)
N3—C7—C8—C9	4.8 (2)	C7—C8—C13—C12	178.65 (13)
N3—C7—C8—C13	−174.87 (13)	C8—C7—N3—N2	−179.03 (12)
C1—N1—C5—C4	0.7 (2)	C8—C9—C10—C11	1.9 (2)
C1—C2—C3—C4	0.2 (2)	C9—C8—C13—C12	−1.0 (2)
C1—C2—C3—C6	177.94 (13)	C9—C10—C11—C12	−1.5 (2)
C2—C3—C4—C5	0.1 (2)	C10—C11—C12—C13	−0.2 (2)
C2—C3—C6—O1	−19.9 (2)	C10—C11—C12—C14	178.89 (15)
C2—C3—C6—N2	159.99 (13)	C11—C12—C13—C8	1.5 (2)
C3—C4—C5—N1	−0.6 (2)	C13—C8—C9—O2	178.91 (14)
C4—C3—C6—O1	157.69 (16)	C13—C8—C9—C10	−0.7 (2)
C4—C3—C6—N2	−22.5 (2)	C14—C12—C13—C8	−177.64 (14)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the N1/C1–C5 ring.

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2O···N3	0.82	1.87	2.5857 (16)	145
N2—H2N···N1ⁱ	0.86	2.19	3.0232 (17)	164
C10—H10···Cg1ⁱⁱ	0.93	2.85	3.5259 (17)	130

Symmetry codes: (i) x−1/2, −y+3/2, z−1/2; (ii) −x+1/2, y−1/2, −z+3/2.

(II) (E)-N'-(5-Fluoro-2-hydroxybenzylidene)isonicotinohydrazide top

Crystal data top

C₁₃H₁₀FN₃O₂	F(000) = 536
M_r = 259.24	D_x = 1.441 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 8.9195 (3) Å	Cell parameters from 9934 reflections
b = 10.1128 (3) Å	θ = 3.1–28.5°
c = 13.6254 (4) Å	µ = 0.11 mm⁻¹
β = 103.481 (1)°	T = 296 K
V = 1195.16 (6) Å³	Block, colourless
Z = 4	0.32 × 0.26 × 0.26 mm

Data collection top

Bruker APEX2 D8 QUEST CMOS diffractometer	2848 independent reflections
Radiation source: microfocus sealed x-ray tube, Incoatec Iµus	2128 reflections with I > 2σ(I)
GraphiteDouble Bounce Multilayer Mirror monochromator	R_int = 0.039
Detector resolution: 10.5 pixels mm^-1	θ_max = 27.9°, θ_min = 3.1°
φ and ω scans	h = −11→11
Absorption correction: multi-scan (SADABS; Bruker, 2014)	k = −13→13
T_min = 0.685, T_max = 0.746	l = −17→17
31833 measured reflections

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.042	w = 1/[σ²(F_o²) + (0.0595P)² + 0.282P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.124	(Δ/σ)_max < 0.001
S = 1.03	Δρ_max = 0.26 e Å⁻³
2848 reflections	Δρ_min = −0.29 e Å⁻³
174 parameters	Extinction correction: SHELXL2014 (Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.020 (3)
Primary atom site location: structure-invariant direct methods

Special details top

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
F1	0.20524 (13)	−0.04313 (11)	0.46463 (10)	0.0868 (4)
O1	0.82356 (13)	0.59703 (11)	0.44402 (7)	0.0572 (3)
O2	0.53778 (15)	0.31773 (13)	0.30688 (8)	0.0650 (3)
H2	0.5959	0.3608	0.3508	0.097*
N1	1.11088 (14)	0.82083 (13)	0.75798 (9)	0.0497 (3)
N2	0.75299 (13)	0.47336 (11)	0.56431 (8)	0.0404 (3)
H2A	0.7633	0.4582	0.6276	0.048*
N3	0.65442 (13)	0.39828 (11)	0.49277 (8)	0.0410 (3)
C1	1.12858 (18)	0.81537 (17)	0.66408 (12)	0.0553 (4)
H1	1.2031	0.8689	0.6466	0.066*
C2	1.04204 (17)	0.73427 (16)	0.59110 (11)	0.0497 (4)
H2B	1.0577	0.7346	0.5260	0.060*
C3	0.93237 (14)	0.65288 (12)	0.61510 (9)	0.0355 (3)
C4	0.91374 (17)	0.65656 (14)	0.71277 (10)	0.0429 (3)
H4	0.8417	0.6026	0.7327	0.052*
C5	1.00507 (19)	0.74261 (15)	0.78056 (10)	0.0502 (4)
H5	0.9910	0.7455	0.8460	0.060*
C6	0.83297 (15)	0.57142 (13)	0.53241 (9)	0.0376 (3)
C7	0.57486 (15)	0.31041 (13)	0.52504 (10)	0.0413 (3)
H7	0.5825	0.3020	0.5940	0.050*
C8	0.47255 (15)	0.22351 (13)	0.45483 (10)	0.0408 (3)
C9	0.46263 (16)	0.22688 (15)	0.35051 (11)	0.0457 (3)
C10	0.37199 (18)	0.13466 (17)	0.28799 (13)	0.0569 (4)
H10	0.3694	0.1346	0.2194	0.068*
C11	0.28665 (18)	0.04408 (16)	0.32564 (14)	0.0597 (4)
H11	0.2260	−0.0174	0.2834	0.072*
C12	0.29224 (18)	0.04568 (15)	0.42667 (15)	0.0567 (4)
C13	0.38397 (17)	0.13144 (15)	0.49236 (12)	0.0499 (4)
H13	0.3870	0.1282	0.5610	0.060*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0769 (7)	0.0678 (7)	0.1118 (9)	−0.0293 (6)	0.0143 (7)	0.0139 (6)
O1	0.0767 (7)	0.0616 (7)	0.0271 (5)	−0.0163 (6)	−0.0006 (5)	−0.0004 (4)
O2	0.0697 (8)	0.0754 (8)	0.0453 (6)	−0.0252 (6)	0.0041 (5)	−0.0007 (6)
N1	0.0495 (7)	0.0494 (7)	0.0426 (7)	0.0033 (6)	−0.0048 (5)	−0.0125 (5)
N2	0.0452 (6)	0.0399 (6)	0.0297 (5)	−0.0020 (5)	−0.0040 (4)	−0.0007 (4)
N3	0.0404 (6)	0.0380 (6)	0.0379 (6)	0.0007 (5)	−0.0044 (5)	−0.0031 (5)
C1	0.0519 (9)	0.0616 (10)	0.0502 (9)	−0.0136 (8)	0.0077 (7)	−0.0123 (7)
C2	0.0530 (8)	0.0598 (9)	0.0356 (7)	−0.0099 (7)	0.0092 (6)	−0.0088 (6)
C3	0.0382 (7)	0.0351 (6)	0.0291 (6)	0.0058 (5)	−0.0007 (5)	−0.0021 (5)
C4	0.0532 (8)	0.0409 (7)	0.0324 (6)	0.0015 (6)	0.0051 (6)	−0.0022 (5)
C5	0.0662 (9)	0.0509 (8)	0.0294 (6)	0.0075 (8)	0.0026 (6)	−0.0066 (6)
C6	0.0418 (7)	0.0377 (7)	0.0285 (6)	0.0027 (6)	−0.0011 (5)	−0.0016 (5)
C7	0.0413 (7)	0.0394 (7)	0.0393 (7)	0.0042 (6)	0.0013 (6)	−0.0011 (6)
C8	0.0348 (7)	0.0358 (7)	0.0475 (7)	0.0039 (5)	0.0008 (5)	−0.0004 (6)
C9	0.0396 (7)	0.0462 (8)	0.0469 (8)	−0.0005 (6)	0.0016 (6)	−0.0020 (6)
C10	0.0514 (9)	0.0605 (10)	0.0525 (9)	−0.0037 (8)	−0.0006 (7)	−0.0119 (7)
C11	0.0464 (8)	0.0472 (9)	0.0759 (12)	−0.0042 (7)	−0.0051 (8)	−0.0132 (8)
C12	0.0435 (8)	0.0398 (8)	0.0824 (12)	−0.0038 (6)	0.0060 (8)	0.0060 (7)
C13	0.0452 (8)	0.0445 (8)	0.0572 (9)	0.0022 (6)	0.0060 (7)	0.0051 (7)

Geometric parameters (Å, º) top

F1—C12	1.3651 (19)	C3—C6	1.5061 (17)
O1—C6	1.2154 (15)	C4—H4	0.9300
O2—H2	0.8200	C4—C5	1.387 (2)
O2—C9	1.3537 (18)	C5—H5	0.9300
N1—C1	1.3263 (19)	C7—H7	0.9300
N1—C5	1.322 (2)	C7—C8	1.4537 (18)
N2—H2A	0.8600	C8—C9	1.404 (2)
N2—N3	1.3783 (15)	C8—C13	1.393 (2)
N2—C6	1.3513 (17)	C9—C10	1.388 (2)
N3—C7	1.2775 (18)	C10—H10	0.9300
C1—H1	0.9300	C10—C11	1.365 (2)
C1—C2	1.378 (2)	C11—H11	0.9300
C2—H2B	0.9300	C11—C12	1.366 (2)
C2—C3	1.375 (2)	C12—C13	1.372 (2)
C3—C4	1.3796 (18)	C13—H13	0.9300

C9—O2—H2	109.5	N2—C6—C3	115.07 (11)
C5—N1—C1	116.85 (12)	N3—C7—H7	119.7
N3—N2—H2A	120.8	N3—C7—C8	120.53 (13)
C6—N2—H2A	120.8	C8—C7—H7	119.7
C6—N2—N3	118.31 (11)	C9—C8—C7	122.23 (13)
C7—N3—N2	116.98 (11)	C13—C8—C7	119.03 (13)
N1—C1—H1	118.4	C13—C8—C9	118.72 (13)
N1—C1—C2	123.25 (15)	O2—C9—C8	122.70 (13)
C2—C1—H1	118.4	O2—C9—C10	117.61 (14)
C1—C2—H2B	120.2	C10—C9—C8	119.68 (14)
C3—C2—C1	119.64 (13)	C9—C10—H10	119.5
C3—C2—H2B	120.2	C11—C10—C9	121.06 (15)
C2—C3—C4	117.76 (12)	C11—C10—H10	119.5
C2—C3—C6	118.48 (11)	C10—C11—H11	120.7
C4—C3—C6	123.65 (12)	C10—C11—C12	118.57 (14)
C3—C4—H4	120.8	C12—C11—H11	120.7
C3—C4—C5	118.37 (14)	F1—C12—C11	118.92 (15)
C5—C4—H4	120.8	F1—C12—C13	118.30 (16)
N1—C5—C4	124.13 (13)	C11—C12—C13	122.77 (15)
N1—C5—H5	117.9	C8—C13—H13	120.5
C4—C5—H5	117.9	C12—C13—C8	119.09 (15)
O1—C6—N2	123.74 (12)	C12—C13—H13	120.5
O1—C6—C3	121.15 (12)

F1—C12—C13—C8	−179.45 (13)	C4—C3—C6—N2	−18.13 (18)
O2—C9—C10—C11	−176.72 (15)	C5—N1—C1—C2	0.6 (2)
N1—C1—C2—C3	−0.8 (3)	C6—N2—N3—C7	−176.78 (12)
N2—N3—C7—C8	−177.61 (11)	C6—C3—C4—C5	−175.40 (12)
N3—N2—C6—O1	−0.3 (2)	C7—C8—C9—O2	−5.4 (2)
N3—N2—C6—C3	177.26 (10)	C7—C8—C9—C10	174.98 (13)
N3—C7—C8—C9	3.5 (2)	C7—C8—C13—C12	−177.30 (13)
N3—C7—C8—C13	−178.08 (12)	C8—C7—N3—N2	−177.61 (11)
C1—N1—C5—C4	0.2 (2)	C8—C9—C10—C11	2.9 (2)
C1—C2—C3—C4	0.1 (2)	C9—C8—C13—C12	1.1 (2)
C1—C2—C3—C6	176.36 (13)	C9—C10—C11—C12	−0.1 (2)
C2—C3—C4—C5	0.6 (2)	C10—C11—C12—F1	178.91 (14)
C2—C3—C6—O1	−16.5 (2)	C10—C11—C12—C13	−2.3 (2)
C2—C3—C6—N2	165.85 (12)	C11—C12—C13—C8	1.7 (2)
C3—C4—C5—N1	−0.8 (2)	C13—C8—C9—O2	176.21 (13)
C4—C3—C6—O1	159.53 (14)	C13—C8—C9—C10	−3.4 (2)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the N1/C1–C5 ring.

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2···N3	0.82	1.92	2.6329 (15)	145
N2—H2A···N1ⁱ	0.86	2.19	2.8889 (15)	138
C10—H10···O1ⁱⁱ	0.93	2.51	3.2573 (18)	138
C11—H11···Cg1ⁱⁱⁱ	0.93	2.98	3.8917 (18)	168

Symmetry codes: (i) −x+2, y−1/2, −z+3/2; (ii) −x+1, y−1/2, −z+1/2; (iii) x−1, −y+1/2, z−1/2.

Acknowledgements

This work was supported by a National Research Councils of Thailand grant provided by the Naresuan University Division of Research Administration (R2558B106). The authors thank the Faculty of Science and Technology, Thammasat University, for funds to purchase the X-ray diffractometer.

References

Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). J. Appl. Cryst. 37, 335–338. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Bendova, P., Mackova, E., Haskova, P., Vavrova, A., Jirkovsky, E., Sterba, M., Popelova, O., Kalinowski, D. S., Kovarikova, P., Vavrova, K., Richardson, D. R. & Simunek, T. (2010). Chem. Res. Toxicol. 23, 1105–1114. CrossRef CAS PubMed Google Scholar
Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
Bruker (2014). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Carter, K. P., Young, A. M. & Palmer, A. E. (2014). Chem. Rev. 114, 4564–4601. CrossRef CAS PubMed Google Scholar
Chumakov, Y. M., Antosyak, B. Y., Tsapkov, V. I. & Samus, N. M. (2001). J. Struct. Chem. 42, 335–339. CrossRef CAS Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854. Web of Science CrossRef CAS IUCr Journals Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Hrušková, K., Kovaříková, P., Bendová, P., Hašková, P., Macková, E., Stariat, J., Vávrová, A., Vávrová, K. & Šimůnek, T. (2011). Chem. Res. Toxicol. 24, 290–302. PubMed Google Scholar
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. PubMed Google Scholar
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. Google Scholar
Kargar, H., Kia, R., Akkurt, M. & Büyükgüngör, O. (2010). Acta Cryst. E66, o2982. Web of Science CSD CrossRef IUCr Journals Google Scholar
Sedaghat, T., Yousefi, M., Bruno, G., Rudbari, H. A., Motamedi, H. & Nobakht, V. (2014). Polyhedron, 79, 88–96. CSD CrossRef CAS Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925. Web of Science CrossRef CAS IUCr Journals Google Scholar
Yang, D.-S. (2006a). Acta Cryst. E62, o3755–o3756. CSD CrossRef IUCr Journals Google Scholar
Yang, D.-S. (2006b). Acta Cryst. E62, o3792–o3793. CSD CrossRef IUCr Journals Google Scholar

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Volume 72| Part 7| July 2016| Pages 980-983

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Crystal structures of (E)-N′-(2-hy­dr­oxy-5-methyl­benzyl­­idene)isonicotinohydrazide and (E)-N′-(5-fluoro-2-hy­dr­oxy­benzyl­­idene)isonicotinohydrazide

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement

Supporting information

Acknowledgements

References

research communications

Crystal structures of (E)-N′-(2-hydroxy-5-methylbenzylidene)isonicotinohydrazide and (E)-N′-(5-fluoro-2-hydroxybenzylidene)isonicotinohydrazide

3. Supramolecular features