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Acta Crystallogr Sect E Struct Rep Online. 2009 December 1; 65(Pt 12): o3200–o3201.
Published online 2009 November 25. doi:  10.1107/S1600536809049654
PMCID: PMC2971864

5-(3-Nitro­benz­yl)-1,3,4-thia­diazol-2-amine

Abstract

In the title mol­ecule, C9H8N4O2S, the dihedral angle between the thia­diazole and benzene rings is 73.92 (8)° and the thia­diazole group S atom is orientated towards the benzene ring, the central S—C—C—C torsion angle being 45.44 (18)°. In the crystal, supra­molecular tapes mediated by N—H(...)N hydrogen bonds and comprising alternating eight-membered {(...)HNCN}2 and 10-membered {(...)HNH(...)NN}2 synthons are formed along [010]. The tapes are consolidated into a three-dimensional network by a combination of C—H(...)O, C—H(...)S and C—H(...)π inter­actions

Related literature

For background to the biological inter­est of 1,3,4-thia­diazo­les, see: Thomasco et al. (2003 [triangle]); Oruç et al. (2004 [triangle]); Moise et al. (2009 [triangle]); Amir et al. (2009 [triangle]). For the development of anti-trypanosomal compounds, see: Carvalho et al. (2004 [triangle]); Boechat et al. (2006 [triangle]); Boechat et al. (2008 [triangle]); Carvalho et al. (2008 [triangle]); Poorrajab et al. (2009 [triangle]) Riente et al. (2009 [triangle]). For the synthesis, see: Turner et al. (1988 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o3200-scheme1.jpg

Experimental

Crystal data

  • C9H8N4O2S
  • M r = 236.26
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o3200-efi1.jpg
  • a = 5.0878 (2) Å
  • b = 5.6213 (3) Å
  • c = 17.8035 (9) Å
  • α = 80.980 (3)°
  • β = 85.677 (3)°
  • γ = 79.855 (3)°
  • V = 494.42 (4) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.32 mm−1
  • T = 120 K
  • 0.38 × 0.20 × 0.09 mm

Data collection

  • Nonius KappaCCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003 [triangle]) T min = 0.639, T max = 0.746
  • 9074 measured reflections
  • 2256 independent reflections
  • 1973 reflections with I > 2σ(I)
  • R int = 0.040

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.086
  • S = 1.05
  • 2256 reflections
  • 151 parameters
  • 2 restraints
  • H-atom parameters constrained
  • Δρmax = 0.29 e Å−3
  • Δρmin = −0.33 e Å−3

Data collection: COLLECT (Hooft, 1998 [triangle]); cell refinement: DENZO (Otwinowski & Minor, 1997 [triangle]) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg, 2006 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809049654/lh2958sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809049654/lh2958Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The use of the EPSRC X-ray crystallographic service at the University of Southampton, England and the valuable assistance of the staff there is gratefully acknowledged. JLW acknowledges support from CAPES (Brazil).

supplementary crystallographic information

Comment

1,3,4-Thiadiazoles have attracted much attention due to their biological activities (Thomasco et al., 2003; Oruç et al., 2004; Moise et al., 2009; Amir et al., 2009), with particular attention being paid to the anti-trypanosomal activities of Megazol, and related compounds (Carvalho et al., 2004, 2008; Riente et al., 2009: Poorrajab et al., 2009). In continuation of our interests in 1,3,4-thiadiazoles (Boechat et al., 2006, 2008; Carvalho et al., 2004, 2008), we now report the structure of the title compound, (I), obtained by modification of a general procedure (Turner et al., 1988).

In the molecular structure of (I) atom S1 is orientated towards the benzene ring, Fig. 1. The dihedral angle between the thiadiazole (r.m.s. deviation = 0.005 Å) and benzene (r.m.s. deviation = 0.004 Å) rings of 73.92 (8) ° indicates a twist between planes as seen in the S1–C2–C3–C4 torsion angle of 45.44 (18) °. The nitro group is effectively co-planar with the benzene ring to which it is attached as seen in the O1–N4–C6–C5 torsion angle of 6.3 (2) °.

The crystal packing is dominated by N—H···N hydrogen bonds. Each of the amine-H atoms connects to a centrosymmetrically related molecule leading to eight-membered {···HNCN}2 and 10-membered {···HNH···NN}2 synthons. Each synthon is planar and alternate in a supramolecular tape orientated along [010], Table 1 and Fig. 2. Chains are consolidated into a 3-D network by a combination of C—H···O, C—H···S and C—H···π interactions, Table 1 and Fig. 3.

Experimental

A finely ground mixture of 2-nitrophenylacetic acid (0.49 g, 2.7 mmol) and thiosemicarbazide (0.25 g, 2.7 mmol) was added in portions over 0.5 h to polyphosphoric acid (5 g) at 353 K. The reaction mixture was maintained at 353 K for 5 h and cooled, water/ice was added, and the mixture was finally basified with NaOH 30% (aq.). The solids isolated by filtration were washed with water and air-dried to give (I), which was recrystallized from EtOH, m.p. 471–473 K; yield 72%. The sample used in the structure determination was obtained after a further recrystallization from EtOH. 1H NMR (d6-DMSO) δ: 4.47 (s, 2H, CH2), 7.05 (s, 2H, NH2), 7.55 (m, 2H, H4 and H5), 7.72 (m, 1H, H6), 8.03 (d, 1H, J = 8.0 Hz) p.p.m. 13C NMR (d6-DMSO) δ: 32.8, 124.7, 128.6, 132.0, 132.6, 133.8, 148.5, 155.1, 168.7 p.p.m.

Refinement

The C-bound H atoms were geometrically placed with C—H = 0.95–0.99 Å, and refined as riding with Uiso(H) = 1.2Ueq(C). The N-bound H atoms were located from a difference map and included in the model with N–H = 0.880±0.001 Å, and with Uiso(H) = 1.2Ueq(N).

Figures

Fig. 1.
Molecular structure of (I) showing atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Fig. 2.
Supramolecular chain along [010] in (I) mediated by N–H···N hydrogen bonds (blue dashed lines). Colour code: S, yellow; O, red; N, blue; C, grey; and H, green.
Fig. 3.
Unit-cell contents for (I) viewed in projection down the a axis. The N–H···N (blue), C—H···O (orange) and C—H···S (green) contacts are shown as dashed lines. ...

Crystal data

C9H8N4O2SZ = 2
Mr = 236.26F(000) = 244
Triclinic, P1Dx = 1.587 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 5.0878 (2) ÅCell parameters from 11753 reflections
b = 5.6213 (3) Åθ = 2.9–27.5°
c = 17.8035 (9) ŵ = 0.32 mm1
α = 80.980 (3)°T = 120 K
β = 85.677 (3)°Block, colourless
γ = 79.855 (3)°0.38 × 0.20 × 0.09 mm
V = 494.42 (4) Å3

Data collection

Nonius KappaCCD area-detector diffractometer2256 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode1973 reflections with I > 2σ(I)
10 cm confocal mirrorsRint = 0.040
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 3.5°
[var phi] and ω scansh = −6→5
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)k = −7→7
Tmin = 0.639, Tmax = 0.746l = −23→23
9074 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.086H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0347P)2 + 0.3167P] where P = (Fo2 + 2Fc2)/3
2256 reflections(Δ/σ)max = 0.001
151 parametersΔρmax = 0.29 e Å3
2 restraintsΔρmin = −0.33 e Å3

Special details

Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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)

xyzUiso*/Ueq
S10.39352 (8)0.87897 (7)0.63466 (2)0.01803 (12)
O1−0.3420 (3)0.5966 (2)0.79836 (7)0.0282 (3)
O2−0.2766 (3)0.4981 (2)0.91883 (7)0.0326 (3)
N10.7365 (3)1.1393 (2)0.56903 (8)0.0187 (3)
N20.5591 (3)1.2890 (2)0.61221 (8)0.0185 (3)
N30.8153 (3)0.7356 (2)0.54139 (8)0.0198 (3)
H1N0.75520.59590.54850.030*
H2N0.94450.76520.50730.030*
N4−0.2396 (3)0.6204 (2)0.85639 (8)0.0218 (3)
C10.6754 (3)0.9177 (3)0.57569 (9)0.0160 (3)
C20.3731 (3)1.1810 (3)0.64921 (9)0.0161 (3)
C30.1583 (3)1.2978 (3)0.70123 (9)0.0189 (3)
H3A−0.01311.33690.67540.023*
H3B0.20491.45280.71160.023*
C40.1235 (3)1.1329 (3)0.77600 (9)0.0167 (3)
C5−0.0430 (3)0.9582 (3)0.78225 (9)0.0164 (3)
H5−0.14110.94420.74030.020*
C6−0.0634 (3)0.8046 (3)0.85083 (9)0.0180 (3)
C70.0726 (3)0.8188 (3)0.91408 (10)0.0231 (4)
H70.05450.71170.96040.028*
C80.2360 (3)0.9947 (3)0.90746 (10)0.0249 (4)
H80.33091.00960.95000.030*
C90.2626 (3)1.1498 (3)0.83935 (10)0.0208 (3)
H90.37661.26840.83580.025*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0196 (2)0.0135 (2)0.0218 (2)−0.00748 (15)0.00547 (15)−0.00271 (14)
O10.0321 (7)0.0250 (6)0.0306 (7)−0.0141 (5)−0.0028 (5)−0.0022 (5)
O20.0328 (7)0.0306 (7)0.0307 (7)−0.0112 (6)0.0028 (6)0.0113 (5)
N10.0184 (7)0.0156 (6)0.0228 (7)−0.0061 (5)0.0044 (5)−0.0039 (5)
N20.0186 (7)0.0152 (6)0.0225 (7)−0.0061 (5)0.0034 (5)−0.0036 (5)
N30.0206 (7)0.0140 (6)0.0252 (8)−0.0067 (5)0.0064 (5)−0.0036 (5)
N40.0193 (7)0.0170 (7)0.0271 (8)−0.0029 (5)0.0029 (6)0.0012 (6)
C10.0156 (7)0.0165 (7)0.0162 (8)−0.0058 (6)−0.0008 (6)0.0001 (6)
C20.0188 (7)0.0130 (7)0.0174 (8)−0.0060 (6)−0.0006 (6)−0.0014 (6)
C30.0214 (8)0.0131 (7)0.0225 (8)−0.0052 (6)0.0035 (6)−0.0024 (6)
C40.0143 (7)0.0145 (7)0.0210 (8)−0.0018 (6)0.0046 (6)−0.0049 (6)
C50.0156 (7)0.0163 (7)0.0170 (8)−0.0020 (6)0.0006 (6)−0.0033 (6)
C60.0150 (7)0.0156 (7)0.0226 (8)−0.0024 (6)0.0025 (6)−0.0020 (6)
C70.0226 (8)0.0262 (9)0.0174 (8)0.0002 (7)0.0019 (6)−0.0001 (7)
C80.0228 (9)0.0325 (9)0.0209 (9)−0.0032 (7)−0.0041 (7)−0.0085 (7)
C90.0173 (8)0.0220 (8)0.0254 (9)−0.0052 (6)0.0017 (6)−0.0096 (7)

Geometric parameters (Å, °)

S1—C11.7373 (16)C3—H3A0.9900
S1—C21.7412 (15)C3—H3B0.9900
O1—N41.2271 (19)C4—C51.393 (2)
O2—N41.2321 (18)C4—C91.400 (2)
N1—C11.321 (2)C5—C61.389 (2)
N1—N21.3949 (19)C5—H50.9500
N2—C21.297 (2)C6—C71.385 (2)
N3—C11.342 (2)C7—C81.386 (2)
N3—H1N0.8800C7—H70.9500
N3—H2N0.8799C8—C91.391 (2)
N4—C61.472 (2)C8—H80.9500
C2—C31.506 (2)C9—H90.9500
C3—C41.516 (2)
C1—S1—C287.36 (7)H3A—C3—H3B107.9
C1—N1—N2111.82 (13)C5—C4—C9118.89 (15)
C2—N2—N1113.45 (12)C5—C4—C3120.45 (14)
C1—N3—H1N117.3C9—C4—C3120.64 (14)
C1—N3—H2N119.9C6—C5—C4118.95 (14)
H1N—N3—H2N122.0C6—C5—H5120.5
O1—N4—O2123.37 (14)C4—C5—H5120.5
O1—N4—C6118.11 (13)C7—C6—C5122.94 (15)
O2—N4—C6118.52 (14)C7—C6—N4118.81 (14)
N1—C1—N3124.39 (14)C5—C6—N4118.25 (14)
N1—C1—S1113.68 (12)C6—C7—C8117.65 (15)
N3—C1—S1121.93 (11)C6—C7—H7121.2
N2—C2—C3124.72 (13)C8—C7—H7121.2
N2—C2—S1113.68 (12)C9—C8—C7120.82 (15)
C3—C2—S1121.59 (11)C9—C8—H8119.6
C2—C3—C4112.03 (13)C7—C8—H8119.6
C2—C3—H3A109.2C8—C9—C4120.74 (15)
C4—C3—H3A109.2C8—C9—H9119.6
C2—C3—H3B109.2C4—C9—H9119.6
C4—C3—H3B109.2
C1—N1—N2—C2−0.19 (19)C3—C4—C5—C6177.85 (14)
N2—N1—C1—N3−178.79 (14)C4—C5—C6—C70.8 (2)
N2—N1—C1—S10.65 (17)C4—C5—C6—N4−179.81 (13)
C2—S1—C1—N1−0.70 (12)O1—N4—C6—C7−174.26 (14)
C2—S1—C1—N3178.76 (14)O2—N4—C6—C75.7 (2)
N1—N2—C2—C3178.85 (14)O1—N4—C6—C56.3 (2)
N1—N2—C2—S1−0.36 (17)O2—N4—C6—C5−173.78 (14)
C1—S1—C2—N20.59 (12)C5—C6—C7—C8−0.2 (2)
C1—S1—C2—C3−178.64 (14)N4—C6—C7—C8−179.63 (15)
N2—C2—C3—C4−133.70 (16)C6—C7—C8—C9−0.4 (3)
S1—C2—C3—C445.44 (18)C7—C8—C9—C40.5 (3)
C2—C3—C4—C5−85.79 (18)C5—C4—C9—C80.1 (2)
C2—C3—C4—C992.73 (17)C3—C4—C9—C8−178.44 (15)
C9—C4—C5—C6−0.7 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H1n···N2i0.882.253.0828 (19)157
N3—H2n···N1ii0.882.123.003 (2)175
C3—H3a···N2iii0.992.603.552 (2)162
C3—H3b···S1iv0.992.853.6687 (17)141
C7—H7···O2v0.952.533.355 (2)145
C9—H9···O1vi0.952.513.446 (2)168
C5—H5···Cgiii0.952.863.7708 (17)160

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH2958).

References

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