5-[(2-Methyl-4-nitro-1H-imidazol-1-yl)meth­yl]-1,3,4-thia­diazol-2-amine

Usha, M.K.; Madan Kumar, S.; Vidyashree Jois, H.S.; Kalluraya, B.; Lokanath, N.K.; Revannasiddaiah, D.

doi:10.1107/S1600536813030821

organic compounds

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ISSN: 2056-9890

Volume 69| Part 12| December 2013| Page o1825

doi:10.1107/S1600536813030821

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5-[(2-Methyl-4-nitro-1H-imidazol-1-yl)methyl]-1,3,4-thiadiazol-2-amine

M. K. Usha,^a S. Madan Kumar,^a H. S. Vidyashree Jois,^b B. Kalluraya,^b N. K. Lokanath ^a and D. Revannasiddaiah ^a ^*

^aDepartment of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570 006, India, and ^bDepartment of Studies in Chemistry, Mangalore University, Mangalagangotri, Mangalore 574 199, India
^*Correspondence e-mail: dr@physics.uni-mysore.ac.in

(Received 8 November 2013; accepted 9 November 2013; online 27 November 2013)

In the title compound, C₇H₈N₆O₂S, the dihedral angle between the imidazole and thiadiazole rings is 70.86 (15)°. In the crystal, molecules are linked into [10-1] chains by N—H⋯N hydrogen bonds, which incorporate centrosymmetric R₂²(8) and R₂²(18) loops. The chains are linked by C—H⋯O and C—H⋯N interactions, generating a three-dimensional network. Very weak π–π stacking [centroid–centroid distance = 3.901 (17) Å] is also observed.

CCDC reference: 971211

Related literature

For biological background, see: Dogan et al. (2002 ); Frank & Kalluraya (2005 ); Mullican et al. (1993 ). For related structures, see: Zama et al. (2013 ); Yin et al. (2012 ).

Experimental

Crystal data

C₇H₈N₆O₂S
M_r = 240.26
Triclinic, $[P \overline 1]$
a = 7.8030 (15) Å
b = 8.2750 (16) Å
c = 8.3596 (16) Å
α = 100.945 (8)°
β = 92.379 (8)°
γ = 105.911 (7)°
V = 507.15 (17) Å³
Z = 2
Cu Kα radiation
μ = 2.86 mm⁻¹
T = 296 K
0.23 × 0.22 × 0.21 mm

Data collection

Bruker X8 Proteum diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2013 ) T_min = 0.559, T_max = 0.585
5433 measured reflections
1640 independent reflections
1560 reflections with I > 2σ(I)
R_int = 0.038

Refinement

R[F² > 2σ(F²)] = 0.084
wR(F²) = 0.206
S = 1.10
1640 reflections
147 parameters
H-atom parameters constrained
Δρ_max = 0.80 e Å⁻³
Δρ_min = −0.65 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3A⋯N1ⁱ	0.86	2.15	2.996 (4)	169
N3—H3B⋯N5ⁱⁱ	0.86	2.26	3.033 (4)	150
C3—H3D⋯O1ⁱⁱⁱ	0.97	2.46	3.100 (4)	123
C4—H4⋯N2^iv	0.93	2.51	3.296 (4)	142
C7—H7C⋯O2^v	0.96	2.57	3.445 (4)	152
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) -x, -y+1, -z+2; (iii) x, y, z-1; (iv) -x, -y, -z+1; (v) x, y+1, z.

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008 ); software used to prepare material for publication: PLATON (Spek, 2009 ).

Supporting information

CCDC reference: 971211

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536813030821/hb7159sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813030821/hb7159Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813030821/hb7159Isup3.cml

checkCIF report

Comment top

Five-membered aromatic systems having three hetero atoms at symmetrical positions have been studied because of their interesting physiological properties (Dogan et al., 2002). It is also well established that various derivatives of 1,3,4-thiadiazoles exhibit broad spectrum of pharmacological properties such as antibacterial, antifungal (Frank & Kalluraya, 2005) and anti inflammatory (Mullican et al., 1993) activities. As part of our studies in this area, we now report the synthesis and structure of the title compound.

The bond distances in the title compound are comparable to related structures methyl 2-(2-methyl-4-nitro-1H-imidazol-1-yl)acetate (Zama et al., 2013) and 5-({[(E)-Benzylideneamino]oxy}methyl)-1,3,4-thiadiazol-2-amine (Yin et al., 2012). The ORTEP of the title compound is shown (Fig. 1) and the dihedral angle between imidazol and thiadiazol ring is 70.86 (15)°. In the crystal, the molecules are connected by hydrogen bonds (Table 2) N3—H3A···N1, N3—H3B···N5, C4—H4···N2 with R₂²(8), R₂²(18) and R₂²(12) ring motifs, respectively. The C3—H3D···O1 and C7—H7···O2 intermolecular hydrogen bonds generate continuous chains along c-axis and b-axis, respectively. Also, π–π interactions (Cg1···Cg1)[with minimum centroid-centroid distance 3.901 (17) Å] are observed. The centroid Cg1 is S1/C1/N1/N2/C2 and Cg2 is N4/C4/C5/N5/C6. The packing of the molecules show three-dimensional architecture (Fig. 2).

Related literature top

For biological background, see: Dogan et al. (2002); Frank & Kalluraya (2005); Mullican et al. (1993). For related structures, see: Zama et al. (2013); Yin et al. (2012).

Experimental top

A mixture of 2-methyl-4-nitro-1-imidazo thiosemicarbazide (1 mmol) and conc. sulfuric acid (1 ml) was heated under reflux for 2–3 h. The resulting solution was cooled, poured into crushed ice and treated with sodium carbonate to pH 6. The precipitate was collected by filtration and washed with water. The solid formed was filtered and recrystallized from ethanol-DMF mixture to yield red blocks (Melting point 251 °C).

Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top

	Fig. 1. ORTEP diagram of the title compound with 50% probability ellipsoids.
	Fig. 2. Packing diagram of molecule, viewed along b axis.

5-[(2-Methyl-4-nitro-1H-imidazol-1-yl)methyl]-1,3,4-thiadiazol-2-amine top

Crystal data top

C₇H₈N₆O₂S	Z = 2
M_r = 240.26	F(000) = 248
Triclinic, P1	D_x = 1.573 Mg m⁻³
Hall symbol: -P 1	Cu Kα radiation, λ = 1.54178 Å
a = 7.8030 (15) Å	Cell parameters from 1640 reflections
b = 8.2750 (16) Å	θ = 5.4–65.5°
c = 8.3596 (16) Å	µ = 2.86 mm⁻¹
α = 100.945 (8)°	T = 296 K
β = 92.379 (8)°	Block, red
γ = 105.911 (7)°	0.23 × 0.22 × 0.21 mm
V = 507.15 (17) Å³

Data collection top

Bruker X8 Proteum diffractometer	1640 independent reflections
Radiation source: Bruker MicroStar microfocus rotating anode	1560 reflections with I > 2σ(I)
Helios multilayer optics monochromator	R_int = 0.038
Detector resolution: 10.7 pixels mm^-1	θ_max = 64.5°, θ_min = 5.4°
ϕ and ω scans	h = −9→9
Absorption correction: multi-scan (SADABS; Bruker, 2013)	k = −9→9
T_min = 0.559, T_max = 0.585	l = −9→9
5433 measured reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.084	H-atom parameters constrained
wR(F²) = 0.206	w = 1/[σ²(F_o²) + (0.170P)² + 0.1569P] where P = (F_o² + 2F_c²)/3
S = 1.10	(Δ/σ)_max < 0.001
1640 reflections	Δρ_max = 0.80 e Å⁻³
147 parameters	Δρ_min = −0.65 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), FC^*=KFC[1+0.001XFC²Λ³/SIN(2Θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.128 (15)

Crystal data top

C₇H₈N₆O₂S	γ = 105.911 (7)°
M_r = 240.26	V = 507.15 (17) Å³
Triclinic, P1	Z = 2
a = 7.8030 (15) Å	Cu Kα radiation
b = 8.2750 (16) Å	µ = 2.86 mm⁻¹
c = 8.3596 (16) Å	T = 296 K
α = 100.945 (8)°	0.23 × 0.22 × 0.21 mm
β = 92.379 (8)°

Data collection top

Bruker X8 Proteum diffractometer	1640 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2013)	1560 reflections with I > 2σ(I)
T_min = 0.559, T_max = 0.585	R_int = 0.038
5433 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.084	0 restraints
wR(F²) = 0.206	H-atom parameters constrained
S = 1.10	Δρ_max = 0.80 e Å⁻³
1640 reflections	Δρ_min = −0.65 e Å⁻³
147 parameters

Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All su's are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F² for ALL reflections except those flagged by the user for potential systematic errors. Weighted R-factors wR and all goodnesses of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The observed criterion of F² > σ(F²) is used only for calculating -R-factor-obs 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
S1	0.07927 (9)	0.48240 (8)	0.72687 (8)	0.0272 (3)
O1	−0.3024 (4)	−0.0160 (4)	1.2300 (3)	0.0530 (10)
O2	−0.2117 (4)	−0.1962 (3)	1.0555 (4)	0.0520 (10)
N1	0.2714 (3)	0.3731 (3)	0.5159 (3)	0.0301 (8)
N2	0.1108 (3)	0.2446 (3)	0.4968 (3)	0.0292 (8)
N3	0.4148 (4)	0.6476 (3)	0.6733 (3)	0.0346 (9)
N4	−0.2299 (3)	0.1372 (3)	0.7565 (3)	0.0217 (7)
N5	−0.3183 (3)	0.1775 (3)	1.0046 (3)	0.0253 (8)
N6	−0.2558 (4)	−0.0653 (3)	1.0942 (3)	0.0327 (9)
C1	0.2758 (4)	0.5055 (4)	0.6315 (3)	0.0229 (8)
C2	−0.0004 (4)	0.2824 (3)	0.5963 (3)	0.0224 (8)
C3	−0.1855 (4)	0.1641 (4)	0.5939 (3)	0.0257 (9)
C4	−0.2020 (4)	0.0071 (3)	0.8234 (3)	0.0230 (8)
C5	−0.2577 (4)	0.0367 (3)	0.9743 (3)	0.0228 (8)
C6	−0.3017 (4)	0.2373 (3)	0.8694 (3)	0.0237 (8)
C7	−0.3577 (5)	0.3853 (4)	0.8382 (4)	0.0396 (11)
H3A	0.50960	0.65610	0.62280	0.0420*
H3B	0.40920	0.73040	0.75070	0.0420*
H3C	−0.27200	0.21210	0.54820	0.0310*
H3D	−0.19450	0.05410	0.52310	0.0310*
H4	−0.15570	−0.08100	0.77630	0.0280*
H7A	−0.48610	0.35570	0.82610	0.0600*
H7B	−0.31210	0.41570	0.73980	0.0600*
H7C	−0.31140	0.48100	0.92860	0.0600*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0282 (6)	0.0236 (6)	0.0256 (6)	0.0051 (4)	0.0134 (3)	−0.0037 (4)
O1	0.079 (2)	0.0551 (17)	0.0176 (12)	0.0078 (14)	0.0032 (11)	0.0072 (11)
O2	0.0665 (19)	0.0387 (15)	0.0623 (17)	0.0249 (13)	0.0124 (14)	0.0226 (13)
N1	0.0320 (14)	0.0244 (13)	0.0298 (14)	0.0055 (10)	0.0161 (10)	−0.0031 (10)
N2	0.0321 (14)	0.0231 (13)	0.0280 (13)	0.0044 (10)	0.0135 (11)	−0.0022 (10)
N3	0.0309 (15)	0.0277 (14)	0.0377 (16)	0.0028 (11)	0.0177 (11)	−0.0062 (11)
N4	0.0245 (12)	0.0199 (12)	0.0196 (12)	0.0057 (9)	0.0085 (9)	0.0012 (9)
N5	0.0274 (13)	0.0215 (13)	0.0225 (13)	0.0038 (10)	0.0102 (9)	−0.0031 (10)
N6	0.0326 (15)	0.0302 (15)	0.0294 (15)	−0.0002 (11)	−0.0024 (11)	0.0068 (11)
C1	0.0268 (15)	0.0227 (14)	0.0208 (14)	0.0090 (11)	0.0100 (11)	0.0040 (11)
C2	0.0298 (16)	0.0209 (14)	0.0169 (13)	0.0076 (12)	0.0079 (11)	0.0030 (10)
C3	0.0281 (16)	0.0284 (16)	0.0169 (14)	0.0037 (12)	0.0066 (11)	0.0013 (11)
C4	0.0233 (14)	0.0169 (14)	0.0263 (15)	0.0046 (11)	0.0043 (11)	0.0001 (11)
C5	0.0238 (14)	0.0194 (14)	0.0213 (14)	0.0018 (11)	0.0026 (11)	0.0015 (11)
C6	0.0234 (14)	0.0208 (14)	0.0256 (15)	0.0059 (11)	0.0116 (11)	0.0001 (11)
C7	0.046 (2)	0.0322 (17)	0.049 (2)	0.0214 (15)	0.0195 (16)	0.0104 (15)

Geometric parameters (Å, º) top

S1—C1	1.739 (3)	N6—C5	1.430 (3)
S1—C2	1.735 (3)	N3—H3A	0.8600
O1—N6	1.236 (4)	N3—H3B	0.8600
O2—N6	1.215 (4)	C2—C3	1.503 (4)
N1—N2	1.384 (3)	C4—C5	1.352 (4)
N1—C1	1.308 (4)	C6—C7	1.471 (4)
N2—C2	1.286 (4)	C3—H3C	0.9700
N3—C1	1.340 (4)	C3—H3D	0.9700
N4—C3	1.459 (4)	C4—H4	0.9300
N4—C4	1.366 (4)	C7—H7A	0.9600
N4—C6	1.376 (4)	C7—H7B	0.9600
N5—C5	1.358 (4)	C7—H7C	0.9600
N5—C6	1.315 (3)

C1—S1—C2	86.83 (14)	N4—C4—C5	103.6 (2)
N2—N1—C1	112.7 (2)	N6—C5—C4	125.5 (3)
N1—N2—C2	112.9 (2)	N5—C5—N6	121.4 (2)
C3—N4—C4	124.6 (2)	N5—C5—C4	113.1 (2)
C3—N4—C6	127.0 (2)	N4—C6—N5	110.2 (2)
C4—N4—C6	108.3 (2)	N4—C6—C7	124.1 (2)
C5—N5—C6	104.7 (2)	N5—C6—C7	125.7 (3)
O1—N6—O2	124.2 (3)	N4—C3—H3C	109.00
O1—N6—C5	117.7 (3)	N4—C3—H3D	109.00
O2—N6—C5	118.1 (3)	C2—C3—H3C	109.00
C1—N3—H3B	120.00	C2—C3—H3D	109.00
H3A—N3—H3B	120.00	H3C—C3—H3D	108.00
C1—N3—H3A	120.00	N4—C4—H4	128.00
N1—C1—N3	124.6 (3)	C5—C4—H4	128.00
S1—C1—N3	122.1 (2)	C6—C7—H7A	109.00
S1—C1—N1	113.3 (2)	C6—C7—H7B	109.00
S1—C2—N2	114.3 (2)	C6—C7—H7C	109.00
S1—C2—C3	123.6 (2)	H7A—C7—H7B	110.00
N2—C2—C3	122.1 (2)	H7A—C7—H7C	109.00
N4—C3—C2	112.6 (2)	H7B—C7—H7C	109.00

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N1ⁱ	0.86	2.15	2.996 (4)	169
N3—H3B···N5ⁱⁱ	0.86	2.26	3.033 (4)	150
C3—H3D···O1ⁱⁱⁱ	0.97	2.46	3.100 (4)	123
C4—H4···N2^iv	0.93	2.51	3.296 (4)	142
C7—H7C···O2^v	0.96	2.57	3.445 (4)	152

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3A···N1ⁱ	0.86	2.15	2.996 (4)	169
N3—H3B···N5ⁱⁱ	0.86	2.26	3.033 (4)	150
C3—H3D···O1ⁱⁱⁱ	0.97	2.46	3.100 (4)	123
C4—H4···N2^iv	0.93	2.51	3.296 (4)	142
C7—H7C···O2^v	0.96	2.57	3.445 (4)	152

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

Acknowledgements

The authors are thankful to the IOE, University of Mysore, for providing the single-crystal X-ray diffraction facility. MKU is grateful to the DST, New Delhi, for the award of an INSPIRE Fellowship. DR acknowledges the UGC, New Delhi, for financial support under the Major Research Project Scheme [No. F.41–882/2012 (SR)].

References

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