supplementary materials


hb7159 scheme

Acta Cryst. (2013). E69, o1825    [ doi:10.1107/S1600536813030821 ]

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

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

Abstract top

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 [pi]-[pi] stacking [centroid-centroid distance = 3.901 (17) Å] is also observed.

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, ππ 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).

Refinement top

The H atoms were placed in calculated positions (C–H = 0.93-0.97Å and N–H = 0.86 Å), and refined as riding on their parent C and N atoms with Uiso(H) = 1.2 Ueq(C,N).

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
[Figure 1] Fig. 1. ORTEP diagram of the title compound with 50% probability ellipsoids.
[Figure 2] 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
C7H8N6O2SZ = 2
Mr = 240.26F(000) = 248
Triclinic, P1Dx = 1.573 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.54178 Å
a = 7.8030 (15) ÅCell parameters from 1640 reflections
b = 8.2750 (16) Åθ = 5.4–65.5°
c = 8.3596 (16) ŵ = 2.86 mm1
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 anode1560 reflections with I > 2σ(I)
Helios multilayer optics monochromatorRint = 0.038
Detector resolution: 10.7 pixels mm-1θmax = 64.5°, θmin = 5.4°
φ and ω scansh = 99
Absorption correction: multi-scan
(SADABS; Bruker, 2013)
k = 99
Tmin = 0.559, Tmax = 0.585l = 99
5433 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.084H-atom parameters constrained
wR(F2) = 0.206 w = 1/[σ2(Fo2) + (0.170P)2 + 0.1569P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
1640 reflectionsΔρmax = 0.80 e Å3
147 parametersΔρmin = 0.65 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), FC*=KFC[1+0.001XFC2Λ3/SIN(2Θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.128 (15)
Crystal data top
C7H8N6O2Sγ = 105.911 (7)°
Mr = 240.26V = 507.15 (17) Å3
Triclinic, P1Z = 2
a = 7.8030 (15) ÅCu Kα radiation
b = 8.2750 (16) ŵ = 2.86 mm1
c = 8.3596 (16) ÅT = 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)
Tmin = 0.559, Tmax = 0.585Rint = 0.038
5433 measured reflectionsθmax = 64.5°
Refinement top
R[F2 > 2σ(F2)] = 0.084H-atom parameters constrained
wR(F2) = 0.206Δρmax = 0.80 e Å3
S = 1.10Δρmin = 0.65 e Å3
1640 reflectionsAbsolute structure: ?
147 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
S10.07927 (9)0.48240 (8)0.72687 (8)0.0272 (3)
O10.3024 (4)0.0160 (4)1.2300 (3)0.0530 (10)
O20.2117 (4)0.1962 (3)1.0555 (4)0.0520 (10)
N10.2714 (3)0.3731 (3)0.5159 (3)0.0301 (8)
N20.1108 (3)0.2446 (3)0.4968 (3)0.0292 (8)
N30.4148 (4)0.6476 (3)0.6733 (3)0.0346 (9)
N40.2299 (3)0.1372 (3)0.7565 (3)0.0217 (7)
N50.3183 (3)0.1775 (3)1.0046 (3)0.0253 (8)
N60.2558 (4)0.0653 (3)1.0942 (3)0.0327 (9)
C10.2758 (4)0.5055 (4)0.6315 (3)0.0229 (8)
C20.0004 (4)0.2824 (3)0.5963 (3)0.0224 (8)
C30.1855 (4)0.1641 (4)0.5939 (3)0.0257 (9)
C40.2020 (4)0.0071 (3)0.8234 (3)0.0230 (8)
C50.2577 (4)0.0367 (3)0.9743 (3)0.0228 (8)
C60.3017 (4)0.2373 (3)0.8694 (3)0.0237 (8)
C70.3577 (5)0.3853 (4)0.8382 (4)0.0396 (11)
H3A0.509600.656100.622800.0420*
H3B0.409200.730400.750700.0420*
H3C0.272000.212100.548200.0310*
H3D0.194500.054100.523100.0310*
H40.155700.081000.776300.0280*
H7A0.486100.355700.826100.0600*
H7B0.312100.415700.739800.0600*
H7C0.311400.481000.928600.0600*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0282 (6)0.0236 (6)0.0256 (6)0.0051 (4)0.0134 (3)0.0037 (4)
O10.079 (2)0.0551 (17)0.0176 (12)0.0078 (14)0.0032 (11)0.0072 (11)
O20.0665 (19)0.0387 (15)0.0623 (17)0.0249 (13)0.0124 (14)0.0226 (13)
N10.0320 (14)0.0244 (13)0.0298 (14)0.0055 (10)0.0161 (10)0.0031 (10)
N20.0321 (14)0.0231 (13)0.0280 (13)0.0044 (10)0.0135 (11)0.0022 (10)
N30.0309 (15)0.0277 (14)0.0377 (16)0.0028 (11)0.0177 (11)0.0062 (11)
N40.0245 (12)0.0199 (12)0.0196 (12)0.0057 (9)0.0085 (9)0.0012 (9)
N50.0274 (13)0.0215 (13)0.0225 (13)0.0038 (10)0.0102 (9)0.0031 (10)
N60.0326 (15)0.0302 (15)0.0294 (15)0.0002 (11)0.0024 (11)0.0068 (11)
C10.0268 (15)0.0227 (14)0.0208 (14)0.0090 (11)0.0100 (11)0.0040 (11)
C20.0298 (16)0.0209 (14)0.0169 (13)0.0076 (12)0.0079 (11)0.0030 (10)
C30.0281 (16)0.0284 (16)0.0169 (14)0.0037 (12)0.0066 (11)0.0013 (11)
C40.0233 (14)0.0169 (14)0.0263 (15)0.0046 (11)0.0043 (11)0.0001 (11)
C50.0238 (14)0.0194 (14)0.0213 (14)0.0018 (11)0.0026 (11)0.0015 (11)
C60.0234 (14)0.0208 (14)0.0256 (15)0.0059 (11)0.0116 (11)0.0001 (11)
C70.046 (2)0.0322 (17)0.049 (2)0.0214 (15)0.0195 (16)0.0104 (15)
Geometric parameters (Å, º) top
S1—C11.739 (3)N6—C51.430 (3)
S1—C21.735 (3)N3—H3A0.8600
O1—N61.236 (4)N3—H3B0.8600
O2—N61.215 (4)C2—C31.503 (4)
N1—N21.384 (3)C4—C51.352 (4)
N1—C11.308 (4)C6—C71.471 (4)
N2—C21.286 (4)C3—H3C0.9700
N3—C11.340 (4)C3—H3D0.9700
N4—C31.459 (4)C4—H40.9300
N4—C41.366 (4)C7—H7A0.9600
N4—C61.376 (4)C7—H7B0.9600
N5—C51.358 (4)C7—H7C0.9600
N5—C61.315 (3)
C1—S1—C286.83 (14)N4—C4—C5103.6 (2)
N2—N1—C1112.7 (2)N6—C5—C4125.5 (3)
N1—N2—C2112.9 (2)N5—C5—N6121.4 (2)
C3—N4—C4124.6 (2)N5—C5—C4113.1 (2)
C3—N4—C6127.0 (2)N4—C6—N5110.2 (2)
C4—N4—C6108.3 (2)N4—C6—C7124.1 (2)
C5—N5—C6104.7 (2)N5—C6—C7125.7 (3)
O1—N6—O2124.2 (3)N4—C3—H3C109.00
O1—N6—C5117.7 (3)N4—C3—H3D109.00
O2—N6—C5118.1 (3)C2—C3—H3C109.00
C1—N3—H3B120.00C2—C3—H3D109.00
H3A—N3—H3B120.00H3C—C3—H3D108.00
C1—N3—H3A120.00N4—C4—H4128.00
N1—C1—N3124.6 (3)C5—C4—H4128.00
S1—C1—N3122.1 (2)C6—C7—H7A109.00
S1—C1—N1113.3 (2)C6—C7—H7B109.00
S1—C2—N2114.3 (2)C6—C7—H7C109.00
S1—C2—C3123.6 (2)H7A—C7—H7B110.00
N2—C2—C3122.1 (2)H7A—C7—H7C109.00
N4—C3—C2112.6 (2)H7B—C7—H7C109.00
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N1i0.862.152.996 (4)169
N3—H3B···N5ii0.862.263.033 (4)150
C3—H3D···O1iii0.972.463.100 (4)123
C4—H4···N2iv0.932.513.296 (4)142
C7—H7C···O2v0.962.573.445 (4)152
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+2; (iii) x, y, z1; (iv) x, y, z+1; (v) x, y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3A···N1i0.862.152.996 (4)169
N3—H3B···N5ii0.862.263.033 (4)150
C3—H3D···O1iii0.972.463.100 (4)123
C4—H4···N2iv0.932.513.296 (4)142
C7—H7C···O2v0.962.573.445 (4)152
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1, z+2; (iii) x, y, z1; (iv) x, y, z+1; (v) x, y+1, z.
Acknowledgements top

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
References top

Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Dogan, H. N., Duran, A., Rollas, S., Sener, G., Uysal, M. K. & Gülen, D. (2002). Bioorg. Med. Chem. 10, 2893–2898.

Frank, P. V. & Kalluraya, B. (2005). J. Indian J. Chem. Sect. B, 44, 1456–1459.

Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.

Mullican, M. D., Wilson, M. W., Conner, D. T., Kostlan, C. R., Schrier, D. J. & Dyer, R. D. (1993). J. Med. Chem. 36, 1090–1099.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Yin, W., Wang, Z. & Yang, Z.-W. (2012). Acta Cryst. E68, o769.

Zama, S., Bouraiou, A., Bouacida, S., Roisnel, T. & Belfaitah, A. (2013). Acta Cryst. E69, o837–o838.