Polymorph of (E)-N′-(4-chloro­benzyl­idene)isonicotinohydrazide monohydrate

Stondus, J.; Anthal, S.; Jayashree, A.; Narayana, B.; Sarojini, B.K.; Kant, R.

doi:10.1107/S2414314618016346

organic compounds

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ISSN: 2414-3146

Volume 3| Part 11| November 2018| x181634

https://doi.org/10.1107/S2414314618016346

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Polymorph of (E)-N′-(4-chlorobenzylidene)isonicotinohydrazide monohydrate

Jigmat Stondus,^a Sumati Anthal,^a A. Jayashree,^b B. Narayana,^b B. K. Sarojini ^c and Rajni Kant ^a ^*

^aX-ray Crystallography Laboratory, Department of Physics, University of Jammu, Jammu 180 006, India, ^bDepartment of Studies in Chemistry, Mangalore University, Mangalagangothri 574 199, India, and ^cDepartment of Industrial Chemistry, Mangalore University, Mangalagangothri 574 199, India
^*Correspondence e-mail: rkant.ju@gmail.com

Edited by A. J. Lough, University of Toronto, Canada (Received 14 November 2018; accepted 18 November 2018; online 30 November 2018)

The title hydrate, C₁₃H₁₀ClN₃O·H₂O, is the orthorhombic polymorph of the previously reported monoclinic compound [Fun et al. (2012 ). Acta Cryst. E68, o2303–o2304). In the title compound, the dihedral angle between the pyridine and benzene rings is 18.0 (2)°. In the crystal, the Schiff base molecules and water molecules are linked via O—H⋯O, N—H⋯O and O—H⋯N hydrogen bonds, forming a two-dimensional network parallel to (001). In addition, the Schiff base molecules are linked end-to-end by weak C—H⋯Cl hydrogen along the c-axis direction, forming an overall three-dimensional network. Weak C—H⋯π interactions are also observed.

Keywords: Schiff base; crystal structure; pyridine; dihedral angle; hydrogen bonding..

CCDC reference: 1871634

Structure description

Compounds that contain an azomethine group (–HC=N–), have gained increasing attention because of their broad spectrum of biological activities (da Silva et al., 2011 ; Kumar et al., 2011 ). Hydrazones derived from the reactions of aldehydes with hydrazides show potential biological properties (El-Tabl et al., 2008 ; Chen et al., 2008 ; Álvarez et al., 2008 ; Ventura & Martins, 2008 ) and have been reported to be anticancer, antifungal, antimicrobial, antiviral and antimalarial agents (Bhat et al., 2015 ; Maccari et al., 2005 ; Mallikarjuna et al., 2009 ; Bekhit et al., 2015 ). In recent years, a large number of hydrazones have been reported (e.g. Peng & Hou, 2008a ; Shan et al., 2008 ). As a part of our studies in this area, we describe herein the synthesis and crystal structure of the title compound (I).

The molecular structure of (I) is illustrated in Fig. 1. The monoclinic polymorph has already been reported (Fun et al., 2012). The C7=N1 bond length of 1.273 (7) Å indicates a typical C=N double bond. The Schiff base molecule has an E configuration with respect to the hydrazone bridge (C7=N1), as observed in similar compounds (Han et al., 2006 , Lu et al., 2008 , Peng & Hou 2008b ). The dihedral angle between the benzene (A) and pyridine (B) rings is 18.0 (2)°. The bond lengths are in normal ranges.

Figure 1
The molecular structure of the title compound with displacement ellipsoids drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.

In the crystal, the water molecules and Schiff base molecules are linked via O—H⋯O, N—H⋯O and O—H⋯N hydrogen bonds, forming a two-dimensional network parallel to (001) (Fig. 2). In addition, the Schiff base molecules are linked end-to-end along the c-axis direction by weak C—H⋯Cl hydrogen bonds (Fig. 3) to form an overall three-dimensional network. Weak C—H⋯π interactions are also observed (Table 1).

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the pyridine and benzene rings, respectively.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2⋯O2	0.86	2.01	2.814 (7)	156
O2—H1O⋯O1ⁱ	0.80 (7)	2.19 (7)	2.907 (7)	149 (6)
O2—H2O⋯N3ⁱⁱ	0.87 (8)	2.02 (9)	2.841 (8)	158 (8)
C4—H4⋯Cl1ⁱⁱⁱ	0.93	2.81	3.667 (7)	153
C5—H5⋯Cg1^iv	0.93	2.98	3.6350 (7)	129
C12—H12⋯Cg2^v	0.93	2.99	3.6489 (7)	129
Symmetry codes: (i) x+1, y, z; (ii) $[-x+3, y-{\script{1\over 2}}, -z-{\script{1\over 2}}]$ ; (iii) $[-x+{\script{3\over 2}}, -y+2, z-{\script{1\over 2}}]$ ; (iv) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (v) $[x-{\script{1\over 2}}, -y+{\script{3\over 2}}, -z]$ .

Figure 2
Part of the crystal structure with hydrogen bonds shown as dashed lines.

Figure 3
Part of the crystal structure showing weak C—H⋯Cl hydrogen bonds as dashed lines.

Synthesis and crystallization

A mixture of isoniazid (0.138 g, 1 mmol), 4-chlorobenzaldehyde (0.140 g, 1 mmol) and catalytic amount of ceric ammonium nitrate (2 mol %) in 5 ml of H₂O was sonicated at 60 W for 10 minutes. After completion of the reaction, as indicated by TLC, the reaction mixture was filtered and washed with distilled water. The pure title compound was obtained by recrystallization by a slow evaporation of an aqqueous alcohol solution (m.p. 455–457 K).

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₃H₁₀ClN₃O·H₂O
M_r	277.71
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	6.4405 (9), 7.2660 (14), 28.081 (4)
V (Å³)	1314.1 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.29
Crystal size (mm)	0.4 × 0.2 × 0.2

Data collection
Diffractometer	Oxford Diffraction Xcalibur Sapphire3
Absorption correction	Multi-scan (CrysAlis RED; Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ )
T_min, T_max	0.421, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	3321, 2323, 1471
R_int	0.034
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.067, 0.148, 1.02
No. of reflections	2323
No. of parameters	181
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.25
Absolute structure	Flack x determined using 359 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	−0.02 (14)
Computer programs: CrysAlis PRO (Oxford Diffraction, 2010 $[Oxford Diffraction (2010). CrysAlis PRO and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ), SHELXS97 (Sheldrick, 2008 ), SHELXL2016 (Sheldrick, 2015 ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2009 ).

Structural data

CCDC reference: 1871634

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314618016346/lh4041sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314618016346/lh4041Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314618016346/lh4041Isup3.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: PLATON (Spek, 2009).

(E)-N'-(4-Chlorobenzylidene)isonicotinohydrazide monohydrate top

Crystal data top

C₁₃H₁₀ClN₃O·H₂O	D_x = 1.404 Mg m⁻³
M_r = 277.71	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 945 reflections
a = 6.4405 (9) Å	θ = 3.8–27.0°
b = 7.2660 (14) Å	µ = 0.29 mm⁻¹
c = 28.081 (4) Å	T = 293 K
V = 1314.1 (4) Å³	Block, colourless
Z = 4	0.4 × 0.2 × 0.2 mm
F(000) = 576

Data collection top

Oxford Diffraction Xcalibur Sapphire3 diffractometer	2323 independent reflections
Radiation source: Enhance (Mo) X-ray Source	1471 reflections with I > 2σ(I)
Detector resolution: 16.1049 pixels mm^-1	R_int = 0.034
ω scans	θ_max = 26.0°, θ_min = 3.6°
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2010)	h = −4→7
T_min = 0.421, T_max = 1.000	k = −8→6
3321 measured reflections	l = −29→34

Refinement top

Refinement on F²	H atoms treated by a mixture of independent and constrained refinement
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.0492P)² + 0.2991P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.067	(Δ/σ)_max = 0.002
wR(F²) = 0.148	Δρ_max = 0.23 e Å⁻³
S = 1.02	Δρ_min = −0.25 e Å⁻³
2323 reflections	Extinction correction: SHELXL2016 (Sheldrick, 2015), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
181 parameters	Extinction coefficient: 0.007 (2)
0 restraints	Absolute structure: Flack x determined using 359 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Hydrogen site location: mixed	Absolute structure parameter: −0.02 (14)

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.

Refinement. H atoms (H1O and H2O) attached to O2 were located in a difference map and refined isotropically. The remaining H atoms were positioned geometrically and were treated as riding on their corresponding non hydrogen atoms with U_iso(H) = 1.2U_eq(C) and U_iso(H) = 1.2U_eq(N).

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

	x	y	z	U_iso*/U_eq
Cl1	0.7005 (3)	0.7850 (3)	0.11474 (6)	0.0706 (7)
O1	0.8317 (7)	1.3265 (8)	−0.16937 (15)	0.0632 (16)
O2	1.5258 (8)	1.0974 (9)	−0.12165 (18)	0.0489 (13)
N1	1.0024 (8)	1.1807 (7)	−0.09043 (16)	0.0386 (13)
N2	1.1179 (7)	1.2331 (8)	−0.12955 (15)	0.0380 (14)
H2	1.251082	1.224610	−0.129120	0.046*
N3	1.3838 (9)	1.3963 (9)	−0.29400 (19)	0.0555 (17)
C1	1.0203 (10)	1.2970 (10)	−0.1680 (2)	0.0406 (16)
C2	1.1515 (9)	1.3320 (9)	−0.2110 (2)	0.0376 (16)
C3	1.0683 (10)	1.2994 (11)	−0.2556 (2)	0.0527 (19)
H3	0.933810	1.254560	−0.258866	0.063*
C4	1.1891 (12)	1.3348 (11)	−0.2953 (2)	0.062 (2)
H4	1.130033	1.314197	−0.325006	0.074*
C5	1.4597 (10)	1.4252 (10)	−0.2506 (2)	0.0480 (18)
H5	1.593842	1.471847	−0.248316	0.058*
C6	1.3554 (9)	1.3914 (10)	−0.2087 (2)	0.0428 (17)
H6	1.420595	1.408204	−0.179516	0.051*
C7	1.1053 (10)	1.1320 (9)	−0.0539 (2)	0.0384 (16)
H7	1.248760	1.146679	−0.053660	0.046*
C8	1.0029 (9)	1.0537 (9)	−0.01233 (19)	0.0335 (15)
C9	1.1064 (10)	1.0381 (10)	0.0308 (2)	0.0443 (17)
H9	1.240781	1.083767	0.033398	0.053*
C10	1.0157 (12)	0.9569 (10)	0.0699 (2)	0.0464 (18)
H10	1.087477	0.947944	0.098500	0.056*
C11	0.8155 (11)	0.8887 (9)	0.0657 (2)	0.0439 (17)
C12	0.7077 (10)	0.9055 (9)	0.0242 (2)	0.0446 (17)
H12	0.571976	0.862446	0.022230	0.054*
C13	0.7993 (10)	0.9861 (9)	−0.0151 (2)	0.0404 (16)
H13	0.725653	0.995608	−0.043441	0.048*
H1O	1.626 (11)	1.161 (10)	−0.124 (2)	0.06 (3)*
H2O	1.531 (15)	1.017 (12)	−0.144 (3)	0.10 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Cl1	0.0999 (15)	0.0603 (13)	0.0515 (10)	−0.0130 (13)	0.0260 (11)	0.0058 (10)
O1	0.038 (3)	0.095 (5)	0.057 (3)	−0.002 (3)	0.004 (2)	0.019 (3)
O2	0.037 (3)	0.066 (4)	0.043 (3)	−0.008 (3)	0.006 (2)	−0.005 (3)
N1	0.036 (3)	0.045 (4)	0.035 (3)	0.001 (3)	0.008 (2)	0.002 (3)
N2	0.030 (2)	0.046 (4)	0.038 (3)	0.001 (3)	0.007 (2)	0.006 (3)
N3	0.061 (4)	0.068 (5)	0.037 (3)	−0.006 (4)	0.001 (3)	0.008 (3)
C1	0.034 (3)	0.045 (4)	0.043 (4)	−0.009 (4)	0.006 (3)	0.006 (3)
C2	0.033 (3)	0.045 (5)	0.034 (3)	−0.001 (3)	0.000 (3)	0.007 (3)
C3	0.043 (4)	0.067 (5)	0.047 (4)	−0.014 (4)	−0.005 (3)	0.003 (4)
C4	0.063 (5)	0.083 (7)	0.039 (4)	−0.009 (5)	−0.011 (4)	0.003 (4)
C5	0.044 (4)	0.054 (5)	0.046 (4)	−0.011 (4)	0.005 (4)	0.010 (4)
C6	0.040 (4)	0.051 (5)	0.038 (3)	−0.005 (4)	−0.003 (3)	0.003 (3)
C7	0.036 (3)	0.038 (4)	0.042 (3)	−0.001 (3)	0.008 (3)	−0.004 (3)
C8	0.035 (3)	0.031 (4)	0.035 (3)	−0.002 (3)	0.007 (3)	−0.005 (3)
C9	0.047 (4)	0.045 (4)	0.041 (4)	0.000 (3)	−0.001 (3)	−0.003 (3)
C10	0.063 (4)	0.042 (4)	0.034 (4)	0.001 (4)	0.006 (4)	−0.003 (3)
C11	0.057 (4)	0.035 (4)	0.040 (4)	0.001 (4)	0.020 (4)	−0.001 (3)
C12	0.041 (3)	0.042 (4)	0.051 (4)	−0.011 (4)	0.005 (4)	−0.004 (3)
C13	0.046 (4)	0.036 (4)	0.039 (3)	−0.004 (4)	0.000 (3)	0.003 (3)

Geometric parameters (Å, º) top

Cl1—C11	1.735 (6)	C5—C6	1.375 (8)
O1—C1	1.234 (7)	C5—H5	0.9300
O2—H1O	0.80 (7)	C6—H6	0.9300
O2—H2O	0.86 (8)	C7—C8	1.455 (8)
N1—C7	1.273 (7)	C7—H7	0.9300
N1—N2	1.380 (6)	C8—C9	1.387 (8)
N2—C1	1.333 (7)	C8—C13	1.402 (8)
N2—H2	0.8600	C9—C10	1.375 (8)
N3—C5	1.331 (8)	C9—H9	0.9300
N3—C4	1.332 (8)	C10—C11	1.387 (9)
C1—C2	1.494 (8)	C10—H10	0.9300
C2—C6	1.384 (8)	C11—C12	1.364 (8)
C2—C3	1.384 (8)	C12—C13	1.380 (8)
C3—C4	1.383 (9)	C12—H12	0.9300
C3—H3	0.9300	C13—H13	0.9300
C4—H4	0.9300

H1O—O2—H2O	108 (8)	C2—C6—H6	120.6
C7—N1—N2	116.0 (5)	N1—C7—C8	121.3 (5)
C1—N2—N1	119.1 (4)	N1—C7—H7	119.4
C1—N2—H2	120.4	C8—C7—H7	119.4
N1—N2—H2	120.4	C9—C8—C13	117.9 (6)
C5—N3—C4	115.0 (6)	C9—C8—C7	120.9 (6)
O1—C1—N2	123.4 (5)	C13—C8—C7	121.1 (5)
O1—C1—C2	120.1 (6)	C10—C9—C8	121.8 (6)
N2—C1—C2	116.5 (5)	C10—C9—H9	119.1
C6—C2—C3	117.5 (6)	C8—C9—H9	119.1
C6—C2—C1	123.6 (5)	C9—C10—C11	118.8 (7)
C3—C2—C1	118.9 (5)	C9—C10—H10	120.6
C4—C3—C2	118.7 (6)	C11—C10—H10	120.6
C4—C3—H3	120.7	C12—C11—C10	120.8 (6)
C2—C3—H3	120.7	C12—C11—Cl1	120.0 (5)
N3—C4—C3	124.8 (6)	C10—C11—Cl1	119.1 (5)
N3—C4—H4	117.6	C11—C12—C13	120.3 (6)
C3—C4—H4	117.6	C11—C12—H12	119.9
N3—C5—C6	125.1 (6)	C13—C12—H12	119.9
N3—C5—H5	117.4	C12—C13—C8	120.3 (6)
C6—C5—H5	117.4	C12—C13—H13	119.8
C5—C6—C2	118.8 (6)	C8—C13—H13	119.8
C5—C6—H6	120.6

C7—N1—N2—C1	−175.7 (6)	C1—C2—C6—C5	−177.9 (6)
N1—N2—C1—O1	6.1 (11)	N2—N1—C7—C8	−172.8 (5)
N1—N2—C1—C2	−173.5 (6)	N1—C7—C8—C9	−165.9 (7)
O1—C1—C2—C6	146.9 (7)	N1—C7—C8—C13	16.4 (10)
N2—C1—C2—C6	−33.4 (10)	C13—C8—C9—C10	0.9 (10)
O1—C1—C2—C3	−34.8 (11)	C7—C8—C9—C10	−177.0 (6)
N2—C1—C2—C3	144.9 (7)	C8—C9—C10—C11	0.1 (11)
C6—C2—C3—C4	−2.6 (11)	C9—C10—C11—C12	−1.6 (10)
C1—C2—C3—C4	179.0 (7)	C9—C10—C11—Cl1	179.7 (5)
C5—N3—C4—C3	−0.7 (12)	C10—C11—C12—C13	2.0 (10)
C2—C3—C4—N3	1.1 (12)	Cl1—C11—C12—C13	−179.3 (5)
C4—N3—C5—C6	2.0 (11)	C11—C12—C13—C8	−0.9 (10)
N3—C5—C6—C2	−3.7 (11)	C9—C8—C13—C12	−0.5 (9)
C3—C2—C6—C5	3.8 (10)	C7—C8—C13—C12	177.3 (6)

Hydrogen-bond geometry (Å, º) top

Cg1 and Cg2 are the centroids of the pyridine and benzene rings, respectively.

D—H···A	D—H	H···A	D···A	D—H···A
O2—H1O···O1ⁱ	0.80 (7)	2.19 (7)	2.907 (7)	149 (6)
N2—H2···O2	0.86	2.01	2.814 (7)	156
O2—H2O···N3ⁱⁱ	0.87 (8)	2.02 (9)	2.841 (8)	158 (8)
C4—H4···Cl1ⁱⁱⁱ	0.93	2.81	3.667 (7)	153
C5—H5···Cg1^iv	0.93	2.98	3.6350 (7)	129
C12—H12···Cg2^v	0.93	2.99	3.6489 (7)	129

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

Funding information

Rajni Kant acknowledges the Department of Science & Technology for the single-crystal X-ray diffractometer sanctioned as a National Facility under project No. SR/S2/CMP-47/2003 and for funding under grant No. EMR/204/000467. BN thanks the UGC for financial assistance through a BSR one-time grant for the purchase of chemicals. AJ thanks the UGC for a Senior Research Fellowship.

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