Crystal structure and computational study of 2,4-di­chloro-N-[(E)-(5-nitro­thio­phen-2-yl)methyl­idene]aniline

Köysal, Y.; Bülbül, H.; Gümüş, S.; Ağar, E.; Soylu, M.S.

doi:10.1107/S2056989016011816

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ISSN: 2056-9890

Volume 72| Part 8| August 2016| Pages 1187-1189

https://doi.org/10.1107/S2056989016011816

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Crystal structure and computational study of 2,4-dichloro-N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline

Yavuz Köysal,^a Hakan Bülbül,^b ^* Sümeyye Gümüş,^c Erbil Ağar ^c and Mustafa Serkan Soylu ^d

^aYesilyurt Demir Celik Vocational School, Ondokuz Mayıs University, TR-55139 Samsun, Turkey, ^bDepartment of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, TR-55139 Samsun, Turkey, ^cDepartment of Chemistry, Faculty of Arts and Sciences, Ondokuz Mayıs University, Kurupelit, 55139 Samsun, Turkey, and ^dDepartment of Physics, Faculty of Arts and Sciences, Giresun University, Giresun, Turkey
^*Correspondence e-mail: hbulbul@omu.edu.tr

Edited by S. Parkin, University of Kentucky, USA (Received 9 July 2016; accepted 19 July 2016; online 22 July 2016)

The title compound, C₁₁H₆Cl₂N₂O₂S, is a Schiff base that incorporates an N-bound 2,4-dichlorophenyl and a C-bound 5-nitrothiophene ring. The molecule is approximately planar, the maximum deviation from the mean plane being 0.233 (4) Å for the C=N N atom. The dihedral angle between the benzene and thiophene rings is 9.7 (2)°. The C=N double bond has an E configuration. The crystal structure features C—H⋯O hydrogen bonds,forming sheets parallel to (10-1), and π–π stacking interactions between symmetry-related thiophene and benzene rings, in which the distance between adjacent ring centroids is 3.707 (4) Å, forming a three-dimensional supramolecular structure. Geometric parameters from quantum-chemical calculations are in good agreement with experimental X-ray diffraction results.

Keywords: crystal structure; Schiff base; nitrothiophene; π–π interactions; quantum-chemical calculations.

CCDC reference: 1494850

1. Chemical context

Schiff bases, which contain C=N double bonds, are well known starting materials for the synthesis of many drugs (Aydoğan et al., 2001 ) and often possess very important biological activities, such as anti-inflammatory and analgesic properties (Sondhi et al., 2006 ). In addition, nitrothiophene and its derivatives also exhibit many biological activities, including antibacterial and antifungal (Kalluraya et al., 1994 ; Kalluraya & Shetty, 1997 ) properties. We report the synthesis, structural analysis and theoretical calculations of the title compound, C₁₁H₆Cl₂N₂O₂S (I), which is a new Schiff base that includes a nitrothiophene group.

2. Structural commentary

The title compound (Fig. 1) is nearly planar, the maximum deviation from the mean plane of 0.233 (4) Å is for atom N2. Schiff bases that are derived from salicylaldehyde show thermochromism and photochromism properties that are dependent upon planarity or non-planarity of the molecules (Cohen et al., 1964 ; Hadjoudis et al., 1987 ). Since the dihedral angle between the benzene and thiophene rings is 9.7 (2)°, the title compound may exhibit thermochromic features. The slight twist of the molecule is caused by a steric repulsion of atoms H5 and H7. The C7=N2 double-bond distance is 1.267 (6)Å, which is comparable to those of reported structures (Özdemir Tarı & Işık, 2012 ; Ceylan et al., 2012 ). The C8—C7—N2—C6 torsion angle is 178.5 (5)°.

Figure 1
A view of (I)

, with the atom-numbering scheme and 50% probability displacement ellipsoids.

3. Supramolecular features

In the crystal structure there are weak C—H⋯O hydrogen bonds (Fig. 2 and Table 1) with atom O1 acting as a bifurcated acceptor from both C5 and C7 (x − 1, y, z − 1), creating an R₂¹(7) motif, and forming sheets parallel to (10 $[\overline1]$ ). π–π stacking interactions are present between the benzene (centroid Cg2) and thiophene (centroid Cg1) rings of symmetry-related molecules [Cg1⋯Cg2(x, $[{3\over 2}]$ − y, $[{1\over 2}]$ + z) = 3.707 (4) Å, forming a three-dimensional supramolecular structure.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C5—H5⋯O1ⁱ	0.93	2.59	3.508 (8)	171
C7—H7⋯O1ⁱ	0.93	2.55	3.300 (8)	138
C2—H2⋯O2ⁱⁱ	0.93	2.56	3.360 (7)	144
Symmetry codes: (i) x-1, y, z-1; (ii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 2
A partial packing view of (I)

. Dashed lines indicate the C—H⋯O hydrogen-bonding interactions

4. Theoretical Calculations

Quantum-chemical calculations were performed to compare with the experimental analysis. Ab initio Hartree–Fock (HF) and density functional DFT(B3LYP) methods were used with the standard basis set of 6-31+G(d) (Becke, 1993 ; Lee et al., 1988 ; Schlegel, 1982 ; Peng et al., 1996 ) using the Gaussian 03 software package (Frisch et al., 2004 ; Dennington et al., 2007 ) to obtain the optimized molecular structure. The computational results are consistent with experimental crystallographic data. The C7=N2 bond length was calculated to be 1.25 and 1.28 Å using HF and DFT(B3LYP) methods, respectively. The torsion angle C8—C7—N2—C6 was calculated to be −177.98 and −176.09° by HF and DFT(B3LYP) methods, respectively.

5. Synthesis and crystallization

The compound 2,4-dichloro-N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline was prepared by refluxing a mixture of a solution containing 5-nitro-2-thiophenecarboxaldehyde (0.0180 g, 0.114 mmol) in 20 ml ethanol and a solution containing 2,4-dichloroaniline (0.0185 g, 0.114 mmol) in 20 ml ethanol. The reaction mixture was stirred for 1h under reflux. Crystals suitable for X-ray analysis were obtained from a solution in ethanol by slow evaporation (yield 65%; m.p 443–445 K).

IR (KBr/cm⁻¹): 3102.59 (C—H), 1602.71 (C=N), 1503.00 (NO₂), 1231.00 (C—N, methylene), 1192.05 (C—N, thiophene), 1039.60 (C—H, thiophene), 1124.10 (C—H, methylene), 957.96 (C—H, methylene), 787.73 (C—H, 957.96)

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were positioned geometrically with C—H = 0.93 Å and refined with using a riding model with U_iso(H) = 1.2U_eq(C).

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₆Cl₂N₂O₂S
M_r	301.14
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	7.5731 (9), 22.1795 (16), 8.3093 (16)
β (°)	117.967 (10)
V (Å³)	1232.7 (3)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.69
Crystal size (mm)	0.18 × 0.15 × 0.10

Data collection
Diffractometer	Agilent SuperNova (Single source at offset) Eos
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2011)
T_min, T_max	0.712, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	3059, 2201, 1119
R_int	0.033
(sin θ/λ)_max (Å⁻¹)	0.617

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.063, 0.138, 1.09
No. of reflections	2201
No. of parameters	163
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.38, −0.32
Computer programs: CrysAlis PRO (Oxford Diffraction, 2007 $[Oxford Diffraction (2007). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.]$ ), SHELXS97 (Sheldrick, 2008 ), SHELXL2014 (Sheldrick, 2015 ) and ORTEP-3 for Windows and WinGX (Farrugia, 2012 ).

Supporting information

CCDC reference: 1494850

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989016011816/pk2586sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016011816/pk2586Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989016011816/pk2586Isup3.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2007); cell refinement: CrysAlis PRO (Oxford Diffraction, 2007); data reduction: CrysAlis PRO (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012); software used to prepare material for publication: WinGX (Farrugia, 2012).

2,4-Dichloro-N-[(E)-(5-nitrothiophen-2-yl)methylidene]aniline top

Crystal data top

C₁₁H₆Cl₂N₂O₂S	F(000) = 608
M_r = 301.14	D_x = 1.623 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
a = 7.5731 (9) Å	Cell parameters from 612 reflections
b = 22.1795 (16) Å	θ = 3.2–28.4°
c = 8.3093 (16) Å	µ = 0.69 mm⁻¹
β = 117.967 (10)°	T = 293 K
V = 1232.7 (3) Å³	Block, red
Z = 4	0.18 × 0.15 × 0.10 mm

Data collection top

Agilent SuperNova (Single source at offset) Eos diffractometer	2201 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	1119 reflections with I > 2σ(I)
Detector resolution: 16.0454 pixels mm^-1	R_int = 0.033
ω scans	θ_max = 26.0°, θ_min = 3.2°
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2011)	h = −7→9
T_min = 0.712, T_max = 1.000	k = −27→12
3059 measured reflections	l = −10→5

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.063	H-atom parameters constrained
wR(F²) = 0.138	w = 1/[σ²(F_o²) + (0.019P)²] where P = (F_o² + 2F_c²)/3
S = 1.09	(Δ/σ)_max < 0.001
2201 reflections	Δρ_max = 0.38 e Å⁻³
163 parameters	Δρ_min = −0.32 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
S1	0.4933 (2)	0.69183 (7)	0.38617 (19)	0.0450 (4)
Cl1	0.3105 (3)	0.89412 (7)	0.2025 (2)	0.0612 (5)
Cl2	−0.2711 (3)	0.95859 (7)	−0.4521 (2)	0.0720 (6)
C6	0.0675 (8)	0.8117 (2)	−0.0461 (7)	0.0369 (14)
C7	0.1939 (9)	0.7153 (3)	0.0411 (7)	0.0473 (16)
H7	0.1199	0.7042	−0.0806	0.057*
C5	−0.0926 (8)	0.7988 (3)	−0.2169 (7)	0.0443 (15)
H5	−0.1307	0.7588	−0.2472	0.053*
C2	0.0113 (9)	0.9185 (3)	−0.1289 (7)	0.0468 (16)
H2	0.0445	0.9588	−0.0990	0.056*
C4	−0.1955 (9)	0.8429 (3)	−0.3414 (7)	0.0446 (15)
H4	−0.3005	0.8328	−0.4545	0.053*
O1	0.8046 (7)	0.6438 (2)	0.7224 (6)	0.0768 (15)
N2	0.1847 (7)	0.7692 (2)	0.0870 (6)	0.0429 (12)
C10	0.4560 (10)	0.5791 (3)	0.3021 (8)	0.0499 (16)
H10	0.4750	0.5376	0.3102	0.060*
N1	0.7237 (8)	0.6023 (2)	0.6127 (7)	0.0538 (14)
C1	0.1141 (8)	0.8726 (2)	−0.0056 (7)	0.0395 (14)
O2	0.7734 (7)	0.5493 (2)	0.6444 (6)	0.0761 (15)
C9	0.3146 (9)	0.6094 (3)	0.1475 (7)	0.0495 (17)
H9	0.2288	0.5902	0.0393	0.059*
C11	0.5608 (9)	0.6182 (3)	0.4372 (8)	0.0450 (15)
C8	0.3165 (9)	0.6706 (3)	0.1730 (7)	0.0445 (15)
C3	−0.1422 (9)	0.9020 (3)	−0.2976 (7)	0.0436 (15)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0440 (10)	0.0394 (9)	0.0480 (9)	0.0004 (8)	0.0184 (8)	0.0007 (7)
Cl1	0.0617 (12)	0.0609 (11)	0.0451 (9)	−0.0060 (9)	0.0118 (9)	−0.0096 (8)
Cl2	0.0749 (15)	0.0527 (10)	0.0616 (11)	0.0061 (10)	0.0096 (11)	0.0135 (9)
C6	0.041 (4)	0.038 (3)	0.036 (3)	0.004 (3)	0.022 (3)	0.004 (3)
C7	0.051 (4)	0.050 (4)	0.037 (3)	0.000 (3)	0.017 (3)	0.002 (3)
C5	0.037 (4)	0.039 (3)	0.046 (3)	0.003 (3)	0.009 (3)	0.002 (3)
C2	0.051 (4)	0.042 (4)	0.053 (4)	−0.009 (3)	0.029 (4)	−0.003 (3)
C4	0.041 (4)	0.047 (4)	0.033 (3)	0.001 (3)	0.007 (3)	0.001 (3)
O1	0.069 (4)	0.067 (3)	0.060 (3)	−0.008 (3)	0.001 (3)	−0.003 (3)
N2	0.042 (3)	0.037 (3)	0.045 (3)	−0.005 (2)	0.016 (3)	−0.001 (2)
C10	0.064 (5)	0.036 (3)	0.060 (4)	0.006 (3)	0.038 (4)	0.003 (3)
N1	0.049 (4)	0.055 (4)	0.061 (4)	0.004 (3)	0.029 (3)	0.007 (3)
C1	0.037 (4)	0.044 (4)	0.036 (3)	−0.006 (3)	0.016 (3)	−0.004 (3)
O2	0.086 (4)	0.053 (3)	0.082 (3)	0.028 (3)	0.033 (3)	0.021 (2)
C9	0.052 (5)	0.053 (4)	0.036 (3)	−0.001 (3)	0.014 (3)	−0.001 (3)
C11	0.049 (4)	0.039 (3)	0.049 (4)	−0.004 (3)	0.025 (4)	0.002 (3)
C8	0.042 (4)	0.042 (3)	0.046 (4)	0.003 (3)	0.018 (3)	0.003 (3)
C3	0.041 (4)	0.049 (4)	0.033 (3)	0.003 (3)	0.011 (3)	0.005 (3)

Geometric parameters (Å, º) top

S1—C11	1.703 (6)	C2—C1	1.394 (7)
S1—C8	1.711 (6)	C2—H2	0.9300
Cl1—C1	1.737 (5)	C4—C3	1.370 (7)
Cl2—C3	1.732 (6)	C4—H4	0.9300
C6—C5	1.397 (7)	O1—N1	1.237 (6)
C6—C1	1.398 (7)	C10—C11	1.344 (7)
C6—N2	1.407 (6)	C10—C9	1.399 (7)
C7—N2	1.267 (6)	C10—H10	0.9300
C7—C8	1.446 (7)	N1—O2	1.226 (6)
C7—H7	0.9300	N1—C11	1.445 (7)
C5—C4	1.371 (7)	C9—C8	1.372 (7)
C5—H5	0.9300	C9—H9	0.9300
C2—C3	1.386 (7)

C11—S1—C8	89.5 (3)	C9—C10—H10	124.6
C5—C6—C1	116.3 (5)	O2—N1—O1	124.1 (6)
C5—C6—N2	126.1 (5)	O2—N1—C11	118.8 (5)
C1—C6—N2	117.6 (5)	O1—N1—C11	117.1 (5)
N2—C7—C8	121.7 (5)	C2—C1—C6	122.5 (5)
N2—C7—H7	119.2	C2—C1—Cl1	117.0 (4)
C8—C7—H7	119.2	C6—C1—Cl1	120.4 (4)
C4—C5—C6	122.5 (6)	C8—C9—C10	112.6 (5)
C4—C5—H5	118.8	C8—C9—H9	123.7
C6—C5—H5	118.8	C10—C9—H9	123.7
C3—C2—C1	117.8 (5)	C10—C11—N1	125.2 (6)
C3—C2—H2	121.1	C10—C11—S1	114.8 (5)
C1—C2—H2	121.1	N1—C11—S1	120.0 (4)
C3—C4—C5	119.3 (5)	C9—C8—C7	127.2 (6)
C3—C4—H4	120.3	C9—C8—S1	112.2 (4)
C5—C4—H4	120.3	C7—C8—S1	120.6 (5)
C7—N2—C6	119.9 (5)	C4—C3—C2	121.6 (5)
C11—C10—C9	110.8 (6)	C4—C3—Cl2	120.2 (4)
C11—C10—H10	124.6	C2—C3—Cl2	118.2 (5)

C1—C6—C5—C4	2.0 (8)	O1—N1—C11—C10	−179.9 (6)
N2—C6—C5—C4	−177.9 (5)	O2—N1—C11—S1	−177.9 (5)
C6—C5—C4—C3	−0.7 (9)	O1—N1—C11—S1	2.2 (7)
C8—C7—N2—C6	178.5 (5)	C8—S1—C11—C10	−0.3 (5)
C5—C6—N2—C7	22.1 (9)	C8—S1—C11—N1	177.9 (5)
C1—C6—N2—C7	−157.7 (5)	C10—C9—C8—C7	178.5 (5)
C3—C2—C1—C6	−0.2 (8)	C10—C9—C8—S1	0.6 (7)
C3—C2—C1—Cl1	178.2 (4)	N2—C7—C8—C9	168.4 (6)
C5—C6—C1—C2	−1.5 (8)	N2—C7—C8—S1	−13.8 (8)
N2—C6—C1—C2	178.4 (5)	C11—S1—C8—C9	−0.2 (5)
C5—C6—C1—Cl1	−179.9 (3)	C11—S1—C8—C7	−178.3 (5)
N2—C6—C1—Cl1	0.0 (7)	C5—C4—C3—C2	−1.2 (9)
C11—C10—C9—C8	−0.8 (8)	C5—C4—C3—Cl2	−179.6 (4)
C9—C10—C11—N1	−177.4 (5)	C1—C2—C3—C4	1.6 (8)
C9—C10—C11—S1	0.6 (7)	C1—C2—C3—Cl2	−180.0 (4)
O2—N1—C11—C10	0.0 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···O1ⁱ	0.93	2.59	3.508 (8)	171
C7—H7···O1ⁱ	0.93	2.55	3.300 (8)	138
C2—H2···O2ⁱⁱ	0.93	2.56	3.360 (7)	144

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

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