4-(5-Chloro­thio­phen-2-yl)-1,2,3-selenadiazole

Sugumar, P.; Sankari, S.; Manisankar, P.; Ponnuswamy, M.N.G.

doi:10.1107/S1600536812049549

organic compounds

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ISSN: 2056-9890

Volume 69| Part 1| January 2013| Page o65

https://doi.org/10.1107/S1600536812049549

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4-(5-Chlorothiophen-2-yl)-1,2,3-selenadiazole

Paramasivam Sugumar,^a Subramaniyan Sankari,^b Paramasivam Manisankar ^c and Mondikalipudur Nanjappa Gounder Ponnuswamy ^a ^*

^aCentre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India, ^bDepartment of Chemistry, Sri Sarada College for Women (Autonomus), Fairlands, Salem 636 016, India, and ^cDepartment of Industrial Chemistry, Alagappa University, Karaikudi 630 003, India
^*Correspondence e-mail: mnpsy2004@yahoo.com

(Received 10 November 2012; accepted 3 December 2012; online 12 December 2012)

In the title compound, C₆H₃ClN₂SSe, the selenadiazole and chlorothiophene rings are almost coplanar [dihedral angle = 5.24 (15)°]. In the crystal, C—H⋯N interactions link the molecules into chains extending along the b-axis direction. C—H⋯π interactions also occur.

Related literature

For the biological activity of selenadiazole derivatives, see: El-Bahaie et al. (1990 ); El-Kashef et al. (1986 ); Padmavathi et al. (2002 ); Plano et al. (2010 ); Stadtman (1991 ); Velusamy et al. (2005 ). For bond-length data, see: Allen et al. (1987 ).

Experimental

Crystal data

C₆H₃ClN₂SSe
M_r = 249.57
Monoclinic, P 2₁ /c
a = 6.0412 (3) Å
b = 19.5870 (11) Å
c = 7.2010 (4) Å
β = 110.257 (3)°
V = 799.38 (7) Å³
Z = 4
Mo Kα radiation
μ = 5.22 mm⁻¹
T = 293 K
0.22 × 0.20 × 0.18 mm

Data collection

Bruker SMART APEX CCD detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ) T_min = 0.330, T_max = 0.391
7064 measured reflections
1978 independent reflections
1558 reflections with I > 2σ(I)
R_int = 0.044

Refinement

R[F² > 2σ(F²)] = 0.039
wR(F²) = 0.121
S = 1.01
1978 reflections
100 parameters
H-atom parameters constrained
Δρ_max = 0.44 e Å⁻³
Δρ_min = −0.52 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1⋯N1ⁱ	0.93	2.62	3.545 (5)	171
Symmetry code: (i) x+1, y, z.

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012 ); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812049549/bt6854sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812049549/bt6854Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812049549/bt6854Isup3.cml

checkCIF report

Comment top

Selenium containing compounds, like 1,2,3-selenadiazoles are of increasing interest because of their chemical properties and biological applications such as anti-bacterial (El-Kashef et al., 1986), anti-microbial (El-Bahaie et al., 1990),anti-cancer (Plano et al., 2010) and insecticidal (Padmavathi et al., 2002) activities. It has been found that the introduction of 1,2,3-selenadiazole ring system increase the biological activity. Selenium atom has a much larger size and less electronegativity than the sulfur atom, selenium containig compounds influence the electro-optical properties of the small molecules (Velusamy et al., 2005).

Glutathione peroxidases(GPx) are the antioxidant selenoenzymes protecting various organisms from oxidative stress by catalyzing the reduction of hydroperoxides at the expense of glutathione(GSH) (Stadtman, 1991). In view of the growing importance of selenium containing compounds, the crystal structure of the title compound has been carried out.

The ORTEP plot of the molecule is shown in Fig. 1. The bond lengths [Se1—N1] 1.870 (3) Å and [Se1—C1] 1.825 (4) Å are comparable with the values reported in the literature (Allen et al., 1987). The selenadiazole ring is planar [with the maximum deviation for atom C2 of 0.004 (3)°]. Both the selenadiazole ring and chlorothiophene ring are lie in a common plane, the corresponding torsion angle is [C4—C3—C2—N2] 175.5 (3)°.

The packing of the molecules is shown in Fig. 2. The crystal packing is stabilized by C—H···N intermolecular interactions, linking the molecules to chains extending along the b axis.

Related literature top

For the biological activity of selenadiazole derivatives, see: El-Bahaie et al. (1990); El-Kashef et al. (1986); Padmavathi et al. (2002); Plano et al. (2010); Stadtman (1991); Velusamy et al. (2005). For bond-length data, see: Allen et al. (1987).

Experimental top

A mixture of 2-acetyl-5-chlorothiophene (1 mmol), semicarbazide hydrochloride (2 mmol) and sodium acetate (3 mmol) in ethanol (10 ml) was refluxed for 4 hrs. After completion of the reaction as monitored by TLC, the mixture was poured into ice cold water and the resulting semicarbazone was filtered off. Then, a mixture of semicarbazone (1 mmol) and SeO₂ (2 mmol) in tetrahydrofuran (10 ml) were refluxed on a water bath for 1 h. The selenium deposited on cooling was removed by filtration, and the filtrate was poured into crushed ice, extracted with dichloromethane, and purified by column chromatography using silica gel (60–120 mesh) with 97:3 petroleum ether: ethyl acetate as eluent to give 4-(5-chloro-2,5-dihydrothiophen-2-yl)-1,2,3-selenadiazole.

Structure description top

The packing of the molecules is shown in Fig. 2. The crystal packing is stabilized by C—H···N intermolecular interactions, linking the molecules to chains extending along the b axis.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 2012); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top

	Fig. 1. The molecular structure of the title compound, showing the atomic numbering and displacement ellipsoids drawn at 30% probability level.
	Fig. 2. The crystal packing.

4-(5-Chlorothiophen-2-yl)-1,2,3-selenadiazole top

Crystal data top

C₆H₃ClN₂SSe	F(000) = 480
M_r = 249.57	D_x = 2.074 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1558 reflections
a = 6.0412 (3) Å	θ = 2.1–28.3°
b = 19.5870 (11) Å	µ = 5.22 mm⁻¹
c = 7.2010 (4) Å	T = 293 K
β = 110.257 (3)°	Black, white crystalline
V = 799.38 (7) Å³	0.22 × 0.20 × 0.18 mm
Z = 4

Data collection top

Bruker SMART APEX CCD detector diffractometer	1978 independent reflections
Radiation source: fine-focus sealed tube	1558 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.044
ω scans	θ_max = 28.3°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −8→6
T_min = 0.330, T_max = 0.391	k = −25→26
7064 measured reflections	l = −9→9

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)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.121	H-atom parameters constrained
S = 1.01	w = 1/[σ²(F_o²) + (0.0716P)² + 0.3075P] where P = (F_o² + 2F_c²)/3
1978 reflections	(Δ/σ)_max = 0.001
100 parameters	Δρ_max = 0.44 e Å⁻³
0 restraints	Δρ_min = −0.52 e Å⁻³

Crystal data top

C₆H₃ClN₂SSe	V = 799.38 (7) Å³
M_r = 249.57	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.0412 (3) Å	µ = 5.22 mm⁻¹
b = 19.5870 (11) Å	T = 293 K
c = 7.2010 (4) Å	0.22 × 0.20 × 0.18 mm
β = 110.257 (3)°

Data collection top

Bruker SMART APEX CCD detector diffractometer	1978 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	1558 reflections with I > 2σ(I)
T_min = 0.330, T_max = 0.391	R_int = 0.044
7064 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.121	H-atom parameters constrained
S = 1.01	Δρ_max = 0.44 e Å⁻³
1978 reflections	Δρ_min = −0.52 e Å⁻³
100 parameters

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
C1	0.3771 (6)	0.60797 (19)	0.2132 (5)	0.0397 (7)
H1	0.5288	0.6078	0.2081	0.048*
C2	0.2578 (6)	0.55180 (18)	0.2343 (4)	0.0333 (7)
C3	0.3344 (6)	0.48114 (17)	0.2494 (5)	0.0328 (7)
C4	0.5358 (6)	0.45391 (19)	0.2353 (5)	0.0412 (8)
H4	0.6532	0.4799	0.2134	0.049*
C5	0.5478 (6)	0.38256 (19)	0.2573 (5)	0.0413 (8)
H5	0.6726	0.3562	0.2502	0.050*
C6	0.3579 (6)	0.35688 (18)	0.2896 (5)	0.0376 (7)
Cl1	0.29911 (17)	0.27326 (5)	0.32523 (15)	0.0529 (3)
N1	−0.0347 (5)	0.62617 (17)	0.2239 (5)	0.0482 (8)
N2	0.0334 (5)	0.56419 (16)	0.2406 (4)	0.0428 (7)
S1	0.15880 (15)	0.41890 (5)	0.29606 (14)	0.0408 (2)
Se1	0.19762 (7)	0.684213 (19)	0.19625 (6)	0.04757 (18)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0304 (16)	0.0409 (19)	0.0469 (18)	0.0004 (14)	0.0120 (14)	−0.0018 (15)
C2	0.0271 (15)	0.0379 (18)	0.0349 (15)	−0.0008 (12)	0.0107 (12)	−0.0014 (13)
C3	0.0286 (15)	0.0333 (16)	0.0368 (15)	−0.0044 (13)	0.0120 (13)	−0.0002 (13)
C4	0.0325 (17)	0.0404 (19)	0.056 (2)	−0.0015 (14)	0.0216 (15)	0.0038 (16)
C5	0.0336 (17)	0.042 (2)	0.055 (2)	0.0011 (14)	0.0232 (16)	−0.0024 (16)
C6	0.0353 (17)	0.0351 (18)	0.0427 (17)	−0.0030 (14)	0.0138 (14)	−0.0027 (14)
Cl1	0.0501 (6)	0.0375 (5)	0.0727 (6)	−0.0066 (4)	0.0234 (5)	0.0031 (4)
N1	0.0335 (15)	0.0461 (19)	0.068 (2)	0.0029 (13)	0.0221 (15)	0.0005 (15)
N2	0.0308 (14)	0.0443 (18)	0.0577 (18)	−0.0008 (13)	0.0208 (13)	−0.0007 (14)
S1	0.0289 (4)	0.0409 (5)	0.0559 (5)	−0.0041 (3)	0.0190 (4)	0.0004 (4)
Se1	0.0375 (2)	0.0371 (3)	0.0659 (3)	0.00047 (14)	0.01514 (19)	0.00089 (16)

Geometric parameters (Å, º) top

C1—C2	1.352 (5)	C4—H4	0.9300
C1—Se1	1.825 (4)	C5—C6	1.345 (5)
C1—H1	0.9300	C5—H5	0.9300
C2—N2	1.394 (4)	C6—Cl1	1.714 (4)
C2—C3	1.451 (5)	C6—S1	1.721 (4)
C3—C4	1.364 (5)	N1—N2	1.274 (4)
C3—S1	1.724 (3)	N1—Se1	1.870 (3)
C4—C5	1.406 (5)

C2—C1—Se1	110.2 (3)	C5—C4—H4	123.4
C2—C1—H1	124.9	C6—C5—C4	112.2 (3)
Se1—C1—H1	124.9	C6—C5—H5	123.9
C1—C2—N2	115.1 (3)	C4—C5—H5	123.9
C1—C2—C3	128.0 (3)	C5—C6—Cl1	128.1 (3)
N2—C2—C3	116.9 (3)	C5—C6—S1	112.7 (3)
C4—C3—C2	129.5 (3)	Cl1—C6—S1	119.2 (2)
C4—C3—S1	111.3 (3)	N2—N1—Se1	111.1 (2)
C2—C3—S1	119.2 (2)	N1—N2—C2	116.7 (3)
C3—C4—C5	113.1 (3)	C3—S1—C6	90.63 (17)
C3—C4—H4	123.4	C1—Se1—N1	86.89 (15)

Se1—C1—C2—N2	−0.7 (4)	C4—C5—C6—S1	−0.4 (4)
Se1—C1—C2—C3	178.8 (3)	Se1—N1—N2—C2	−0.3 (4)
C1—C2—C3—C4	−4.0 (6)	C1—C2—N2—N1	0.7 (5)
N2—C2—C3—C4	175.4 (3)	C3—C2—N2—N1	−178.8 (3)
C1—C2—C3—S1	174.7 (3)	C4—C3—S1—C6	−1.4 (3)
N2—C2—C3—S1	−5.8 (4)	C2—C3—S1—C6	179.7 (3)
C2—C3—C4—C5	−179.7 (3)	C5—C6—S1—C3	1.0 (3)
S1—C3—C4—C5	1.4 (4)	Cl1—C6—S1—C3	−179.5 (2)
C3—C4—C5—C6	−0.7 (5)	C2—C1—Se1—N1	0.4 (3)
C4—C5—C6—Cl1	−179.8 (3)	N2—N1—Se1—C1	−0.1 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···N1ⁱ	0.93	2.62	3.545 (5)	171

Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formula	C₆H₃ClN₂SSe
M_r	249.57
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	6.0412 (3), 19.5870 (11), 7.2010 (4)
β (°)	110.257 (3)
V (Å³)	799.38 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	5.22
Crystal size (mm)	0.22 × 0.20 × 0.18

Data collection
Diffractometer	Bruker SMART APEX CCD detector
Absorption correction	Multi-scan (SADABS; Bruker, 2008)
T_min, T_max	0.330, 0.391
No. of measured, independent and observed [I > 2σ(I)] reflections	7064, 1978, 1558
R_int	0.044
(sin θ/λ)_max (Å⁻¹)	0.667

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.121, 1.01
No. of reflections	1978
No. of parameters	100
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.44, −0.52

Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 2012), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···N1ⁱ	0.93	2.62	3.545 (5)	170.7

Symmetry code: (i) x+1, y, z.

Acknowledgements

The authors thank the TBI Consultancy, University of Madras, India, for the data collection.

References

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