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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2012 Apr 13;68(Pt 5):o1345–o1346. doi: 10.1107/S1600536812014419

3-[(N-Methyl­anilino)meth­yl]-5-(thio­phen-2-yl)-1,3,4-oxadiazole-2(3H)-thione

Ali A El-Emam a, Mohamed A Al-Omar a, Hazem A Ghabbour a, Hoong-Kun Fun b,*,‡, Tze Shyang Chia b
PMCID: PMC3344480  PMID: 22590242

Abstract

In the title compound, C14H13N3OS2, the thio­phene ring is disordered over two orientations by ca 180° about the C—C bond axis linking the ring to the rest of the mol­ecule, with a site-occupancy ratio of 0.651 (5):0.349 (5). The central 1,3,4-oxadiazole-2(3H)-thione ring forms dihedral angles of 9.2 (5), 4.6 (11) and 47.70 (7)° with the major and minor parts of the disordered thio­phene ring and the terminal phenyl ring, respectively. In the crystal, no significant inter­molecular hydrogen bonds are observed. The crystal packing is stabilized by π–π inter­actions [centroid–centroid distance = 3.589 (2) Å].

Related literature  

For the biological activity of 1,3,4-oxadiazole derivatives, see: Navarrete-Vázquez et al. (2007 ▶); Kadi et al. (2007 ▶); Padmavathi et al. (2009 ▶); El-Emam et al. (2004 ▶); Al-Deeb et al. (2006 ▶). For the synthesis of the title compound, see: Al-Omar (2010 ▶). For related 1,3,4-oxadiazole structures, see: Fun et al. (2011 ▶); El-Emam et al. (2012 ▶).graphic file with name e-68-o1345-scheme1.jpg

Experimental  

Crystal data  

  • C14H13N3OS2

  • M r = 303.39

  • Monoclinic, Inline graphic

  • a = 11.9682 (8) Å

  • b = 7.4526 (5) Å

  • c = 17.0749 (14) Å

  • β = 108.072 (6)°

  • V = 1447.85 (18) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 3.32 mm−1

  • T = 296 K

  • 0.92 × 0.16 × 0.09 mm

Data collection  

  • Bruker SMART APEXII CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.150, T max = 0.754

  • 10021 measured reflections

  • 2676 independent reflections

  • 1516 reflections with I > 2σ(I)

  • R int = 0.066

Refinement  

  • R[F 2 > 2σ(F 2)] = 0.048

  • wR(F 2) = 0.156

  • S = 0.97

  • 2676 reflections

  • 220 parameters

  • H-atom parameters constrained

  • Δρmax = 0.16 e Å−3

  • Δρmin = −0.20 e Å−3

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812014419/is5107sup1.cif

e-68-o1345-sup1.cif (26KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812014419/is5107Isup2.hkl

e-68-o1345-Isup2.hkl (131.4KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812014419/is5107Isup3.cml

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

Acknowledgments

AAEE, MAAO and HAG thank the Deanship of Scientific Research and the Research Center of the College of Pharmacy, King Saud University, for financial support. HKF and TSC thank Universiti Sains Malaysia (USM) for the Research University Grant (1001/PFIZIK/811160). TSC also thanks the Malaysian Government and USM for the award of a research fellowship.

supplementary crystallographic information

Comment

Considerable attention has been devoted to 1,3,4-oxadiazole derivatives which have long been known for their diverse chemotherapeutic properties as antiviral agents against the HIV-1 viruses (El-Emam et al., 2004), antibacterial agents (Navarrete-Vázquez et al., 2007; Padmavathi et al., 2009) and anti-inflammatory agents (Kadi et al., 2007; Al-Deeb et al., 2006). The title compound (I) was synthesized among a series of 2-thienyl-1,3,4-oxadiazoles and related derivatives as potential antimicrobial agents (Al-Omar, 2010).

The molecular structure of the title compound is shown in Fig. 1. The thiophene ring is disordered by ca. 180° rotation about the C2—C3 bond axis with a site-occupancy ratio of 0.651 (5):0.349 (5). The central 1,3,4-oxadiazole-2(3H)-thione ring (N1/N2/C1/O1/C2/S2; maximum deviation = 0.0157 (12) Å at atom S2) forms dihedral angles of 9.23 (51), 4.6 (11) and 47.70 (7)° with the major and minor parts of the disordered thiophene ring [S1/C3–C6: maximum deviation = 0.024 (11) Å at atom C4 and S1A/C3/C4A–C6A: maximum deviation = 0.04 (3) Å at atom C6A] and the terminal phenyl ring (C9–C14), respectively.

In the crystal packing, no significant intermolecular hydrogen bondings are observed. The crystal packing is stabilized by a π–π interaction with Cg2···Cg4 distance = 3.589 (2) Å (symmetry code: 3/2-x, -1/2+y, 3/2-z), where Cg2 and Cg4 are the centroids of O1/C1/C2/N1/N2 and C9–C14 rings, respectively.

Experimental

N-Methylaniline (214 mg, 2 mmol) and 37% formaldehyde solution (0.5 ml) were added to a solution of 5-(thiophen-2-yl)-1,3,4-oxadiazole-2-thiol (369 mg, 2 mmol) in ethanol (8 ml). The mixture was stirred at room temperature for 2 h and allowed to stand overnight. The precipitated crude product was filtered, washed with cold ethanol, dried, and crystallized from ethanol to yield 558 mg (92%) of the title compound (I) as colorless needle crystals. M.p.: 112–114 °C. 1H NMR (CDCl3, 500.13 MHz): δ 3.28 (s, 3H, CH3), 5.64 (d, 2H, NCH2N), 6.83–7.36 (m, 6H, Ar—H & Thiophene-H), 7.55 (d, 1H, Thiophene-H, J = 5.0 Hz), 7.70 (d, 1H, Thiophene-H, J = 5.0 Hz). 13C NMR (CDCl3, 125.76 MHz): δ 39.54 (CH3), 66.80 (CH2), 113.72, 119.12, 123.65, 128.30, 129.36, 130.36, 131.07, 146.69 (Ar—C & Thiophene-C), 155.89 (Oxadiazole C-5), 176.32 (C=S).

Refinement

All H atoms were positioned geometrically (C—H = 0.93, 0.96 or 0.97 Å) and refined using a riding model with Uiso(H) = 1.2 or 1.5Ueq(C). A rotating group model was applied to the methyl group. Initially similarity and FLAT (only to the minor component) restraints were used. In the final refinement, these restraints were removed and the ratio of the refined site occupancies for the major and minor components of the disordered thiophene ring is 0.651 (5):0.349 (5).

Figures

Fig. 1.

Fig. 1.

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The molecular structure of the title compound with atom labels and 30% probability displacement ellipsoids. Atoms of the minor occupancy component are labelled with the suffix A.

Crystal data

C14H13N3OS2 F(000) = 632
Mr = 303.39 Dx = 1.392 Mg m−3
Monoclinic, P21/n Cu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2yn Cell parameters from 587 reflections
a = 11.9682 (8) Å θ = 4.0–45.3°
b = 7.4526 (5) Å µ = 3.32 mm−1
c = 17.0749 (14) Å T = 296 K
β = 108.072 (6)° Needle, colorless
V = 1447.85 (18) Å3 0.92 × 0.16 × 0.09 mm
Z = 4
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Data collection

Bruker SMART APEXII CCD area-detector diffractometer 2676 independent reflections
Radiation source: fine-focus sealed tube 1516 reflections with I > 2σ(I)
Graphite monochromator Rint = 0.066
φ and ω scans θmax = 69.5°, θmin = 4.0°
Absorption correction: multi-scan (SADABS; Bruker, 2009) h = −14→14
Tmin = 0.150, Tmax = 0.754 k = −8→7
10021 measured reflections l = −20→18
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Refinement

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)] = 0.048 H-atom parameters constrained
wR(F2) = 0.156 w = 1/[σ2(Fo2) + (0.0811P)2] where P = (Fo2 + 2Fc2)/3
S = 0.97 (Δ/σ)max = 0.001
2676 reflections Δρmax = 0.16 e Å−3
220 parameters Δρmin = −0.20 e Å−3
0 restraints Extinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods Extinction coefficient: 0.0019 (4)
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Special details

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

x y z Uiso*/Ueq Occ. (<1)
S2 0.86759 (10) 0.22270 (15) 1.02672 (6) 0.0941 (4)
O1 0.6522 (2) 0.3191 (3) 0.93576 (13) 0.0697 (6)
N1 0.6491 (2) 0.2726 (3) 0.80711 (15) 0.0627 (7)
N2 0.7564 (2) 0.2228 (3) 0.86200 (15) 0.0628 (6)
N3 0.8999 (2) 0.2802 (4) 0.79288 (16) 0.0707 (7)
C1 0.7617 (3) 0.2516 (4) 0.94048 (19) 0.0672 (8)
C2 0.5908 (3) 0.3288 (4) 0.85393 (19) 0.0620 (8)
C3 0.4743 (3) 0.4013 (4) 0.8291 (2) 0.0651 (8)
C4 0.413 (2) 0.451 (3) 0.8829 (15) 0.093 (8) 0.651 (5)
H4A 0.4370 0.4340 0.9396 0.111* 0.651 (5)
C5 0.2989 (18) 0.542 (3) 0.8296 (11) 0.083 (5) 0.651 (5)
H5A 0.2436 0.5951 0.8503 0.100* 0.651 (5)
C6 0.2904 (15) 0.533 (2) 0.7508 (13) 0.092 (5) 0.651 (5)
H6A 0.2254 0.5768 0.7096 0.110* 0.651 (5)
S1 0.4025 (5) 0.4400 (7) 0.7304 (4) 0.0799 (9) 0.651 (5)
S1A 0.4022 (12) 0.4715 (16) 0.8908 (8) 0.0785 (19) 0.349 (5)
C6A 0.293 (3) 0.522 (6) 0.825 (3) 0.125 (17) 0.349 (5)
H6AA 0.2263 0.5592 0.8375 0.150* 0.349 (5)
C5A 0.292 (3) 0.512 (4) 0.745 (2) 0.112 (13) 0.349 (5)
H5AA 0.2322 0.5508 0.6995 0.135* 0.349 (5)
C4A 0.416 (3) 0.420 (5) 0.745 (2) 0.090 (13) 0.349 (5)
H4AA 0.4405 0.3878 0.7008 0.108* 0.349 (5)
C7 0.8480 (3) 0.1488 (4) 0.83120 (19) 0.0694 (8)
H7A 0.9088 0.0953 0.8767 0.083*
H7B 0.8143 0.0545 0.7918 0.083*
C8 0.9964 (3) 0.3838 (6) 0.8467 (2) 0.0919 (12)
H8A 0.9945 0.5035 0.8255 0.138*
H8B 1.0697 0.3280 0.8492 0.138*
H8C 0.9887 0.3883 0.9010 0.138*
C9 0.8762 (3) 0.2882 (4) 0.70804 (19) 0.0638 (8)
C10 0.9562 (3) 0.3627 (4) 0.6735 (2) 0.0806 (10)
H10A 1.0280 0.4050 0.7073 0.097*
C11 0.9293 (5) 0.3740 (6) 0.5890 (3) 0.1074 (15)
H11A 0.9838 0.4249 0.5669 0.129*
C12 0.8256 (6) 0.3131 (7) 0.5371 (3) 0.1167 (17)
H12A 0.8090 0.3218 0.4803 0.140*
C13 0.7459 (4) 0.2383 (5) 0.5709 (3) 0.0997 (14)
H13A 0.6744 0.1965 0.5363 0.120*
C14 0.7697 (3) 0.2240 (4) 0.6550 (2) 0.0766 (9)
H14A 0.7150 0.1717 0.6764 0.092*
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Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
S2 0.0998 (8) 0.1138 (8) 0.0625 (6) 0.0053 (5) 0.0162 (5) −0.0036 (5)
O1 0.0771 (16) 0.0794 (14) 0.0594 (13) −0.0076 (10) 0.0311 (12) −0.0051 (9)
N1 0.0636 (17) 0.0670 (14) 0.0627 (15) −0.0058 (12) 0.0270 (14) −0.0015 (11)
N2 0.0631 (18) 0.0750 (15) 0.0545 (14) −0.0025 (12) 0.0245 (14) −0.0021 (11)
N3 0.0626 (17) 0.0918 (18) 0.0619 (16) −0.0176 (12) 0.0255 (14) −0.0119 (13)
C1 0.071 (2) 0.0719 (19) 0.0627 (19) −0.0063 (14) 0.0268 (18) −0.0024 (13)
C2 0.068 (2) 0.0644 (18) 0.0607 (18) −0.0118 (14) 0.0297 (17) −0.0054 (13)
C3 0.063 (2) 0.0739 (19) 0.065 (2) −0.0117 (14) 0.030 (2) −0.0079 (15)
C4 0.076 (11) 0.096 (9) 0.093 (13) −0.001 (6) 0.010 (8) −0.011 (6)
C5 0.092 (12) 0.080 (6) 0.099 (9) −0.013 (5) 0.059 (9) −0.012 (5)
C6 0.067 (9) 0.082 (6) 0.105 (11) 0.002 (5) −0.002 (7) 0.002 (6)
S1 0.071 (2) 0.1025 (17) 0.0634 (11) −0.0140 (14) 0.0171 (11) −0.0039 (14)
S1A 0.082 (4) 0.087 (3) 0.082 (3) −0.006 (3) 0.049 (3) −0.006 (3)
C6A 0.044 (17) 0.13 (3) 0.20 (3) 0.002 (14) 0.03 (2) −0.03 (2)
C5A 0.077 (18) 0.18 (3) 0.09 (2) −0.040 (14) 0.050 (15) 0.024 (17)
C4A 0.044 (12) 0.130 (18) 0.11 (3) 0.011 (9) 0.041 (15) 0.031 (12)
C7 0.070 (2) 0.0747 (19) 0.067 (2) 0.0020 (15) 0.0258 (17) 0.0004 (15)
C8 0.077 (3) 0.115 (3) 0.080 (2) −0.026 (2) 0.020 (2) −0.016 (2)
C9 0.065 (2) 0.0672 (17) 0.0646 (19) 0.0082 (14) 0.0283 (17) −0.0042 (13)
C10 0.088 (3) 0.078 (2) 0.090 (3) 0.0077 (17) 0.048 (2) 0.0057 (17)
C11 0.147 (4) 0.096 (3) 0.109 (4) 0.034 (3) 0.082 (3) 0.026 (3)
C12 0.175 (5) 0.110 (4) 0.072 (3) 0.050 (3) 0.049 (3) 0.013 (2)
C13 0.117 (4) 0.099 (3) 0.072 (2) 0.027 (2) 0.014 (3) −0.010 (2)
C14 0.080 (2) 0.080 (2) 0.070 (2) 0.0079 (17) 0.024 (2) −0.0098 (16)
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Geometric parameters (Å, º)

S2—C1 1.632 (3) C6A—C5A 1.35 (6)
O1—C2 1.364 (3) C6A—H6AA 0.9300
O1—C1 1.382 (4) C5A—C4A 1.63 (5)
N1—C2 1.283 (4) C5A—H5AA 0.9300
N1—N2 1.385 (3) C4A—H4AA 0.9300
N2—C1 1.339 (4) C7—H7A 0.9700
N2—C7 1.464 (4) C7—H7B 0.9700
N3—C9 1.388 (4) C8—H8A 0.9600
N3—C7 1.423 (4) C8—H8B 0.9600
N3—C8 1.455 (4) C8—H8C 0.9600
C2—C3 1.432 (4) C9—C10 1.386 (4)
C3—C4 1.388 (19) C9—C14 1.400 (5)
C3—C4A 1.39 (3) C10—C11 1.379 (5)
C3—S1A 1.641 (12) C10—H10A 0.9300
C3—S1 1.663 (6) C11—C12 1.360 (6)
C4—C5 1.55 (3) C11—H11A 0.9300
C4—H4A 0.9300 C12—C13 1.377 (6)
C5—C6 1.32 (3) C12—H12A 0.9300
C5—H5A 0.9300 C13—C14 1.378 (5)
C6—S1 1.641 (19) C13—H13A 0.9300
C6—H6A 0.9300 C14—H14A 0.9300
S1A—C6A 1.49 (5)
C2—O1—C1 106.2 (2) C6A—C5A—C4A 107 (3)
C2—N1—N2 103.6 (2) C6A—C5A—H5AA 126.3
C1—N2—N1 112.3 (3) C4A—C5A—H5AA 126.3
C1—N2—C7 127.7 (3) C3—C4A—C5A 102 (2)
N1—N2—C7 119.9 (2) C3—C4A—H4AA 128.9
C9—N3—C7 122.2 (3) C5A—C4A—H4AA 128.9
C9—N3—C8 120.1 (3) N3—C7—N2 112.9 (3)
C7—N3—C8 116.7 (3) N3—C7—H7A 109.0
N2—C1—O1 104.5 (3) N2—C7—H7A 109.0
N2—C1—S2 131.6 (3) N3—C7—H7B 109.0
O1—C1—S2 123.9 (2) N2—C7—H7B 109.0
N1—C2—O1 113.4 (3) H7A—C7—H7B 107.8
N1—C2—C3 127.3 (3) N3—C8—H8A 109.5
O1—C2—C3 119.3 (3) N3—C8—H8B 109.5
C4—C3—C4A 116.9 (19) H8A—C8—H8B 109.5
C4—C3—C2 124.6 (12) N3—C8—H8C 109.5
C4A—C3—C2 118.5 (15) H8A—C8—H8C 109.5
C4A—C3—S1A 115.5 (15) H8B—C8—H8C 109.5
C2—C3—S1A 126.0 (6) C10—C9—N3 121.1 (3)
C4—C3—S1 114.3 (12) C10—C9—C14 118.1 (3)
C2—C3—S1 121.0 (3) N3—C9—C14 120.7 (3)
S1A—C3—S1 112.7 (6) C11—C10—C9 120.1 (4)
C3—C4—C5 106.2 (16) C11—C10—H10A 119.9
C3—C4—H4A 126.9 C9—C10—H10A 119.9
C5—C4—H4A 126.9 C12—C11—C10 122.1 (4)
C6—C5—C4 110.7 (15) C12—C11—H11A 119.0
C6—C5—H5A 124.7 C10—C11—H11A 119.0
C4—C5—H5A 124.7 C11—C12—C13 118.2 (4)
C5—C6—S1 115.3 (13) C11—C12—H12A 120.9
C5—C6—H6A 122.4 C13—C12—H12A 120.9
S1—C6—H6A 122.4 C12—C13—C14 121.4 (5)
C6—S1—C3 93.3 (8) C12—C13—H13A 119.3
C6A—S1A—C3 96.2 (18) C14—C13—H13A 119.3
C5A—C6A—S1A 118 (3) C13—C14—C9 120.1 (4)
C5A—C6A—H6AA 120.8 C13—C14—H14A 120.0
S1A—C6A—H6AA 120.8 C9—C14—H14A 120.0
C2—N1—N2—C1 −0.7 (3) C2—C3—S1—C6 −175.1 (6)
C2—N1—N2—C7 179.4 (2) S1A—C3—S1—C6 −0.3 (8)
N1—N2—C1—O1 1.3 (3) C4A—C3—S1A—C6A 3 (3)
C7—N2—C1—O1 −178.9 (3) C2—C3—S1A—C6A −179.0 (19)
N1—N2—C1—S2 −177.7 (2) S1—C3—S1A—C6A 6 (2)
C7—N2—C1—S2 2.1 (5) C3—S1A—C6A—C5A −6 (4)
C2—O1—C1—N2 −1.3 (3) S1A—C6A—C5A—C4A 7 (5)
C2—O1—C1—S2 177.8 (2) C4—C3—C4A—C5A 4 (3)
N2—N1—C2—O1 −0.2 (3) C2—C3—C4A—C5A −177.8 (14)
N2—N1—C2—C3 178.2 (3) S1A—C3—C4A—C5A 1 (3)
C1—O1—C2—N1 1.0 (3) S1—C3—C4A—C5A −52 (19)
C1—O1—C2—C3 −177.6 (3) C6A—C5A—C4A—C3 −4 (4)
N1—C2—C3—C4 176.5 (11) C9—N3—C7—N2 −106.3 (3)
O1—C2—C3—C4 −5.2 (11) C8—N3—C7—N2 85.5 (4)
N1—C2—C3—C4A −2.0 (17) C1—N2—C7—N3 −107.6 (3)
O1—C2—C3—C4A 176.4 (17) N1—N2—C7—N3 72.2 (3)
N1—C2—C3—S1A 179.8 (5) C7—N3—C9—C10 −154.3 (3)
O1—C2—C3—S1A −1.9 (6) C8—N3—C9—C10 13.5 (4)
N1—C2—C3—S1 −6.1 (5) C7—N3—C9—C14 26.8 (4)
O1—C2—C3—S1 172.2 (3) C8—N3—C9—C14 −165.3 (3)
C4A—C3—C4—C5 −8 (2) N3—C9—C10—C11 −178.1 (3)
C2—C3—C4—C5 173.5 (10) C14—C9—C10—C11 0.8 (5)
S1A—C3—C4—C5 55 (29) C9—C10—C11—C12 −0.3 (6)
S1—C3—C4—C5 −4.1 (17) C10—C11—C12—C13 0.1 (6)
C3—C4—C5—C6 4 (2) C11—C12—C13—C14 −0.3 (6)
C4—C5—C6—S1 −3 (2) C12—C13—C14—C9 0.8 (5)
C5—C6—S1—C3 0.2 (15) C10—C9—C14—C13 −1.0 (5)
C4—C3—S1—C6 2.6 (12) N3—C9—C14—C13 177.9 (3)
C4A—C3—S1—C6 129 (20)
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Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS5107).

References

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536812014419/is5107sup1.cif

e-68-o1345-sup1.cif (26KB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812014419/is5107Isup2.hkl

e-68-o1345-Isup2.hkl (131.4KB, hkl)

Supplementary material file. DOI: 10.1107/S1600536812014419/is5107Isup3.cml

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

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography

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