organic compounds
5-(3-Nitrobenzyl)-1,3,4-thiadiazol-2-amine
aFundação Oswaldo Cruz, Instituto de Tecnologia em Fármacos - Far-Manguinhos, Laboratório de Síntese IV, 21041-250 Rio de Janeiro, RJ, Brazil, bInstituto de Química, Universidade Federal do Rio de Janeiro, 21949-900 Rio de Janeiro, RJ, Brazil, cDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia, dCentro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (FIOCRUZ), Casa Amarela, Campus de Manguinhos, Av. Brasil 4365, 21040-900, Rio de Janeiro, RJ, Brazil, and eCHEMSOL, 1 Harcourt Road, Aberdeen AB15 5NY, Scotland
*Correspondence e-mail: edward.tiekink@gmail.com
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); Oruç et al. (2004); Moise et al. (2009); Amir et al. (2009). For the development of anti-trypanosomal compounds, see: Carvalho et al. (2004); Boechat et al. (2006); Boechat et al. (2008); Carvalho et al. (2008); Poorrajab et al. (2009) Riente et al. (2009). For the synthesis, see: Turner et al. (1988).
Experimental
Crystal data
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Refinement
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Data collection: COLLECT (Hooft, 1998); cell DENZO (Otwinowski & Minor, 1997) and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2009).
Supporting information
10.1107/S1600536809049654/lh2958sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536809049654/lh2958Isup2.hkl
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 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.
was obtained after a further recrystallization from EtOH. 1H NMR (d6-DMSO)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).
Data collection: COLLECT (Hooft, 1998); cell
DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); data reduction: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: publCIF (Westrip, 2009).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. Colour code: S, yellow; O, red; N, blue; C, grey; and H, green. |
C9H8N4O2S | Z = 2 |
Mr = 236.26 | F(000) = 244 |
Triclinic, P1 | Dx = 1.587 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.0878 (2) Å | Cell parameters from 11753 reflections |
b = 5.6213 (3) Å | θ = 2.9–27.5° |
c = 17.8035 (9) Å | µ = 0.32 mm−1 |
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 |
Nonius KappaCCD area-detector diffractometer | 2256 independent reflections |
Radiation source: Enraf Nonius FR591 rotating anode | 1973 reflections with I > 2σ(I) |
10 cm confocal mirrors monochromator | Rint = 0.040 |
Detector resolution: 9.091 pixels mm-1 | θmax = 27.5°, θmin = 3.5° |
ϕ and ω scans | h = −6→5 |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | k = −7→7 |
Tmin = 0.639, Tmax = 0.746 | l = −23→23 |
9074 measured reflections |
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)] = 0.035 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.086 | H-atom parameters constrained |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0347P)2 + 0.3167P] where P = (Fo2 + 2Fc2)/3 |
2256 reflections | (Δ/σ)max = 0.001 |
151 parameters | Δρmax = 0.29 e Å−3 |
2 restraints | Δρmin = −0.33 e Å−3 |
C9H8N4O2S | γ = 79.855 (3)° |
Mr = 236.26 | V = 494.42 (4) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.0878 (2) Å | Mo Kα radiation |
b = 5.6213 (3) Å | µ = 0.32 mm−1 |
c = 17.8035 (9) Å | T = 120 K |
α = 80.980 (3)° | 0.38 × 0.20 × 0.09 mm |
β = 85.677 (3)° |
Nonius KappaCCD area-detector diffractometer | 2256 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 2003) | 1973 reflections with I > 2σ(I) |
Tmin = 0.639, Tmax = 0.746 | Rint = 0.040 |
9074 measured reflections |
R[F2 > 2σ(F2)] = 0.035 | 2 restraints |
wR(F2) = 0.086 | H-atom parameters constrained |
S = 1.05 | Δρmax = 0.29 e Å−3 |
2256 reflections | Δρmin = −0.33 e Å−3 |
151 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
S1 | 0.39352 (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) | |
N1 | 0.7365 (3) | 1.1393 (2) | 0.56903 (8) | 0.0187 (3) | |
N2 | 0.5591 (3) | 1.2890 (2) | 0.61221 (8) | 0.0185 (3) | |
N3 | 0.8153 (3) | 0.7356 (2) | 0.54139 (8) | 0.0198 (3) | |
H1N | 0.7552 | 0.5959 | 0.5485 | 0.030* | |
H2N | 0.9445 | 0.7652 | 0.5073 | 0.030* | |
N4 | −0.2396 (3) | 0.6204 (2) | 0.85639 (8) | 0.0218 (3) | |
C1 | 0.6754 (3) | 0.9177 (3) | 0.57569 (9) | 0.0160 (3) | |
C2 | 0.3731 (3) | 1.1810 (3) | 0.64921 (9) | 0.0161 (3) | |
C3 | 0.1583 (3) | 1.2978 (3) | 0.70123 (9) | 0.0189 (3) | |
H3A | −0.0131 | 1.3369 | 0.6754 | 0.023* | |
H3B | 0.2049 | 1.4528 | 0.7116 | 0.023* | |
C4 | 0.1235 (3) | 1.1329 (3) | 0.77600 (9) | 0.0167 (3) | |
C5 | −0.0430 (3) | 0.9582 (3) | 0.78225 (9) | 0.0164 (3) | |
H5 | −0.1411 | 0.9442 | 0.7403 | 0.020* | |
C6 | −0.0634 (3) | 0.8046 (3) | 0.85083 (9) | 0.0180 (3) | |
C7 | 0.0726 (3) | 0.8188 (3) | 0.91408 (10) | 0.0231 (4) | |
H7 | 0.0545 | 0.7117 | 0.9604 | 0.028* | |
C8 | 0.2360 (3) | 0.9947 (3) | 0.90746 (10) | 0.0249 (4) | |
H8 | 0.3309 | 1.0096 | 0.9500 | 0.030* | |
C9 | 0.2626 (3) | 1.1498 (3) | 0.83935 (10) | 0.0208 (3) | |
H9 | 0.3766 | 1.2684 | 0.8358 | 0.025* |
U11 | U22 | U33 | U12 | U13 | U23 | |
S1 | 0.0196 (2) | 0.0135 (2) | 0.0218 (2) | −0.00748 (15) | 0.00547 (15) | −0.00271 (14) |
O1 | 0.0321 (7) | 0.0250 (6) | 0.0306 (7) | −0.0141 (5) | −0.0028 (5) | −0.0022 (5) |
O2 | 0.0328 (7) | 0.0306 (7) | 0.0307 (7) | −0.0112 (6) | 0.0028 (6) | 0.0113 (5) |
N1 | 0.0184 (7) | 0.0156 (6) | 0.0228 (7) | −0.0061 (5) | 0.0044 (5) | −0.0039 (5) |
N2 | 0.0186 (7) | 0.0152 (6) | 0.0225 (7) | −0.0061 (5) | 0.0034 (5) | −0.0036 (5) |
N3 | 0.0206 (7) | 0.0140 (6) | 0.0252 (8) | −0.0067 (5) | 0.0064 (5) | −0.0036 (5) |
N4 | 0.0193 (7) | 0.0170 (7) | 0.0271 (8) | −0.0029 (5) | 0.0029 (6) | 0.0012 (6) |
C1 | 0.0156 (7) | 0.0165 (7) | 0.0162 (8) | −0.0058 (6) | −0.0008 (6) | 0.0001 (6) |
C2 | 0.0188 (7) | 0.0130 (7) | 0.0174 (8) | −0.0060 (6) | −0.0006 (6) | −0.0014 (6) |
C3 | 0.0214 (8) | 0.0131 (7) | 0.0225 (8) | −0.0052 (6) | 0.0035 (6) | −0.0024 (6) |
C4 | 0.0143 (7) | 0.0145 (7) | 0.0210 (8) | −0.0018 (6) | 0.0046 (6) | −0.0049 (6) |
C5 | 0.0156 (7) | 0.0163 (7) | 0.0170 (8) | −0.0020 (6) | 0.0006 (6) | −0.0033 (6) |
C6 | 0.0150 (7) | 0.0156 (7) | 0.0226 (8) | −0.0024 (6) | 0.0025 (6) | −0.0020 (6) |
C7 | 0.0226 (8) | 0.0262 (9) | 0.0174 (8) | 0.0002 (7) | 0.0019 (6) | −0.0001 (7) |
C8 | 0.0228 (9) | 0.0325 (9) | 0.0209 (9) | −0.0032 (7) | −0.0041 (7) | −0.0085 (7) |
C9 | 0.0173 (8) | 0.0220 (8) | 0.0254 (9) | −0.0052 (6) | 0.0017 (6) | −0.0096 (7) |
S1—C1 | 1.7373 (16) | C3—H3A | 0.9900 |
S1—C2 | 1.7412 (15) | C3—H3B | 0.9900 |
O1—N4 | 1.2271 (19) | C4—C5 | 1.393 (2) |
O2—N4 | 1.2321 (18) | C4—C9 | 1.400 (2) |
N1—C1 | 1.321 (2) | C5—C6 | 1.389 (2) |
N1—N2 | 1.3949 (19) | C5—H5 | 0.9500 |
N2—C2 | 1.297 (2) | C6—C7 | 1.385 (2) |
N3—C1 | 1.342 (2) | C7—C8 | 1.386 (2) |
N3—H1N | 0.8800 | C7—H7 | 0.9500 |
N3—H2N | 0.8799 | C8—C9 | 1.391 (2) |
N4—C6 | 1.472 (2) | C8—H8 | 0.9500 |
C2—C3 | 1.506 (2) | C9—H9 | 0.9500 |
C3—C4 | 1.516 (2) | ||
C1—S1—C2 | 87.36 (7) | H3A—C3—H3B | 107.9 |
C1—N1—N2 | 111.82 (13) | C5—C4—C9 | 118.89 (15) |
C2—N2—N1 | 113.45 (12) | C5—C4—C3 | 120.45 (14) |
C1—N3—H1N | 117.3 | C9—C4—C3 | 120.64 (14) |
C1—N3—H2N | 119.9 | C6—C5—C4 | 118.95 (14) |
H1N—N3—H2N | 122.0 | C6—C5—H5 | 120.5 |
O1—N4—O2 | 123.37 (14) | C4—C5—H5 | 120.5 |
O1—N4—C6 | 118.11 (13) | C7—C6—C5 | 122.94 (15) |
O2—N4—C6 | 118.52 (14) | C7—C6—N4 | 118.81 (14) |
N1—C1—N3 | 124.39 (14) | C5—C6—N4 | 118.25 (14) |
N1—C1—S1 | 113.68 (12) | C6—C7—C8 | 117.65 (15) |
N3—C1—S1 | 121.93 (11) | C6—C7—H7 | 121.2 |
N2—C2—C3 | 124.72 (13) | C8—C7—H7 | 121.2 |
N2—C2—S1 | 113.68 (12) | C9—C8—C7 | 120.82 (15) |
C3—C2—S1 | 121.59 (11) | C9—C8—H8 | 119.6 |
C2—C3—C4 | 112.03 (13) | C7—C8—H8 | 119.6 |
C2—C3—H3A | 109.2 | C8—C9—C4 | 120.74 (15) |
C4—C3—H3A | 109.2 | C8—C9—H9 | 119.6 |
C2—C3—H3B | 109.2 | C4—C9—H9 | 119.6 |
C4—C3—H3B | 109.2 | ||
C1—N1—N2—C2 | −0.19 (19) | C3—C4—C5—C6 | 177.85 (14) |
N2—N1—C1—N3 | −178.79 (14) | C4—C5—C6—C7 | 0.8 (2) |
N2—N1—C1—S1 | 0.65 (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—N3 | 178.76 (14) | O2—N4—C6—C7 | 5.7 (2) |
N1—N2—C2—C3 | 178.85 (14) | O1—N4—C6—C5 | 6.3 (2) |
N1—N2—C2—S1 | −0.36 (17) | O2—N4—C6—C5 | −173.78 (14) |
C1—S1—C2—N2 | 0.59 (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—C4 | 45.44 (18) | C7—C8—C9—C4 | 0.5 (3) |
C2—C3—C4—C5 | −85.79 (18) | C5—C4—C9—C8 | 0.1 (2) |
C2—C3—C4—C9 | 92.73 (17) | C3—C4—C9—C8 | −178.44 (15) |
C9—C4—C5—C6 | −0.7 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1n···N2i | 0.88 | 2.25 | 3.0828 (19) | 157 |
N3—H2n···N1ii | 0.88 | 2.12 | 3.003 (2) | 175 |
C3—H3a···N2iii | 0.99 | 2.60 | 3.552 (2) | 162 |
C3—H3b···S1iv | 0.99 | 2.85 | 3.6687 (17) | 141 |
C7—H7···O2v | 0.95 | 2.53 | 3.355 (2) | 145 |
C9—H9···O1vi | 0.95 | 2.51 | 3.446 (2) | 168 |
C5—H5···Cgiii | 0.95 | 2.86 | 3.7708 (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. |
Experimental details
Crystal data | |
Chemical formula | C9H8N4O2S |
Mr | 236.26 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 120 |
a, b, c (Å) | 5.0878 (2), 5.6213 (3), 17.8035 (9) |
α, β, γ (°) | 80.980 (3), 85.677 (3), 79.855 (3) |
V (Å3) | 494.42 (4) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.32 |
Crystal size (mm) | 0.38 × 0.20 × 0.09 |
Data collection | |
Diffractometer | Nonius KappaCCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 2003) |
Tmin, Tmax | 0.639, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9074, 2256, 1973 |
Rint | 0.040 |
(sin θ/λ)max (Å−1) | 0.650 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.035, 0.086, 1.05 |
No. of reflections | 2256 |
No. of parameters | 151 |
No. of restraints | 2 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.29, −0.33 |
Computer programs: , DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2006), publCIF (Westrip, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H1n···N2i | 0.88 | 2.25 | 3.0828 (19) | 157 |
N3—H2n···N1ii | 0.88 | 2.12 | 3.003 (2) | 175 |
C3—H3a···N2iii | 0.99 | 2.60 | 3.552 (2) | 162 |
C3—H3b···S1iv | 0.99 | 2.85 | 3.6687 (17) | 141 |
C7—H7···O2v | 0.95 | 2.53 | 3.355 (2) | 145 |
C9—H9···O1vi | 0.95 | 2.51 | 3.446 (2) | 168 |
C5—H5···Cgiii | 0.95 | 2.86 | 3.7708 (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
‡Additional correspondence author, e-mail: j.wardell@abdn.ac.uk.
Acknowledgements
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).
References
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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.