Crystal structure of 3-{[4-(2-methoxyphenyl)piperazin-1-yl]methyl}-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione

In the crystal of the title compound, a novel biologically active agent based on 1,3,4-oxadiazole, molecules are linked by C—H⋯S hydrogen bonds and C—H⋯π interactions to form layers in the bc plane.

The title compound, C 18 H 20 N 4 O 2 S 2 , is a new 1,3,4-oxadiazole and a key pharmacophore of several biologically active agents. It is composed of a methyl(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione moiety linked to a 2-methoxyphenyl unit via a piperazine ring that has a chair conformation. The thiophene ring mean plane lies almost in the plane of the oxadiazole ring, with a dihedral angle of 4.35 (9) . The 2-methoxyphenyl ring is almost normal to the oxadiazole ring, with a dihedral angle of 84.17 (10) . In the crystal, molecules are linked by weak C-HÁ Á ÁS hydrogen bonds and C-HÁ Á Á interactions, forming layers parallel to the bc plane. The layers are linked via weak C-HÁ Á ÁO hydrogen bonds and slipped parallelinteractions [intercentroid distance = 3.6729 (10) Å ], forming a three-dimensional structure. The thiophene ring has an approximate 180 rotational disorder about the bridging C-C bond.

Structural commentary
The title compound, Fig. 1, is composed of a methyl(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione moiety linked to a 2-methoxyphenyl unit via a bridging piperazine ring. The molecule is V-shaped with the mean plane of the piperazine ring, that has a chair conformation, making dihedral angles of 51.2 (1) and 77.8 (1) with the 2-methoxyphenyl ring and the oxadiazole ring, respectively. The thiophene ring mean plane lies almost in the plane of the oxadiazole ring, with a dihedral angle of 4.35 (9) . The thiophene ring has an approximate 180 rotational disorder about the bridging C14-C15 bond.

Figure 2
Crystal packing of the title compound, viewed along the b axis, showing the C-HÁ Á ÁS and C-HÁ Á ÁO hydrogen bonds (Table 1)  room temperature. The precipitated crude product was filtered, washed with cold ethanol, dried, and crystallized from ethanol to yield the title compound as pale-yellow prismatic crystals(yield 1.67 g, 86%; m.p. 419-421 K). Single crystals suitable for X-ray analysis were obtained by slow evaporation of a CHCl 3 :EtOH solution (1:1; 15 ml) at room temperature.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. The C-bound H atoms were positioned geometrically and treated as riding atoms: C-H 0.95-0.97 Å with U iso (H) = 1.5U eq (C-methyl) and 1.2U eq (C) for other H atoms. The thienyl ring is disordered over two positions and in the final refinement cycles, the occupancy of atoms S2A and C16A, and S2B and C16B, were each fixed at 0.5.  ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: WinGX (Farrugia, 2012) and publCIF (Westrip, 2010).

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 F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.