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

Monirah A Al-Alshaikh; Hatem A Abuelizz; Ali A El-Emam; Mohammed S M Abdelbaky; Santiago Garcia-Granda

doi:10.1107/S2056989016000992

. 2016 Jan 30;72(Pt 2):269–272. doi: 10.1107/S2056989016000992

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

Monirah A Al-Alshaikh ^a, Hatem A Abuelizz ^b, Ali A El-Emam ^b,^‡, Mohammed S M Abdelbaky ^c, Santiago Garcia-Granda ^c,^*

PMCID: PMC4770969 PMID: 26958404

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.

Keywords: crystal structure; 1,3,4-oxadiazole; thiophene; piperazine; disorder; hydrogen bonding

Abstract

The title compound, C₁₈H₂₀N₄O₂S₂, 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—H⋯S hydrogen bonds and C—H⋯π interactions, forming layers parallel to the bc plane. The layers are linked via weak C—H⋯O hydrogen bonds and slipped parallel π–π interactions [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.

Chemical context

1,3,4-Oxadiazole derivatives are structural motifs of particular value in material sciences (Zhang et al., 2011 ▸) and agrochemistry (Shi et al., 2001 ▸; Milinkevich et al., 2009 ▸; Li et al., 2014 ▸). In addition, they occupy a unique situation in the field of medicinal chemistry as pharmacophores possessing diverse pharmacological activities including antibacterial (Ogata et al., 1971 ▸; Rane et al., 2012 ▸; Al-Omar, 2010 ▸), anticancer (Pinna et al., 2009 ▸; Gamal El-Din et al., 2015 ▸; Zhang et al., 2014 ▸; Du et al., 2013 ▸), antiviral (Summa et al., 2008 ▸; Wu et al., 2015 ▸; El-Emam et al., 2004 ▸), antihypertensive (Vardan et al., 1983 ▸; Schlecker & Thieme, 1988 ▸), anti-inflammatory (Bansal et al., 2014 ▸; Kadi et al., 2007 ▸) and anti-oxidant (Ma et al., 2013 ▸) activities. In continuation to our previous studies on 1,3,4-oxadiazoles (El-Emam et al., 2012 ▸), we report herein on the synthesis and crystal structure of the title compound.

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.

The molecular structure of the title compound, showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level. The thiophene ring has an approximate 180° rotational disorder about the bridging C—C bond.

Supramolecular features

In the crystal, molecules are linked by weak C—H⋯S hydrogen bonds and C—H⋯π interactions, forming layers in the bc plane (Table 1 ▸ and Fig. 2 ▸). The layers are linked via C—H⋯O hydrogen bonds and slipped parallel π–π interactions [Cg3⋯ Cg1ⁱ = 3.6729 (10) Å, inter-planar distance = 3.4757 (7) Å, slippage = 0.967 Å; Cg1 and Cg3 are the centroids of the S2A/C15/C16A/C17/C18 and O1/ N3/N4/C13/C14 rings, respectively; symmetry code (i): −x + 2, −y + 1, −z + 2], forming a three-dimensional structure (Table 1 ▸ and Fig. 2 ▸).

Table 1. Hydrogen-bond geometry (Å, °).

Cg1 is the centroid of the S2A/C15/C16A/C17/C18 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C12—H12A⋯S1ⁱ	0.97	2.95	3.860 (2)	157
C17—H17⋯O1ⁱⁱ	0.93	2.69	3.475 (2)	143
C5—H5⋯Cg1ⁱⁱⁱ	0.93	2.95	3.660 (2)	135

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) .

Crystal packing of the title compound, viewed along the b axis, showing the C—H⋯S and C—H⋯O hydrogen bonds (Table 1 ▸) as dashed lines. Only H atoms involved in intermolecular interactions have been included.

Database survey

A search of the Cambridge Structural Database (Version 5.37, last update November 2015; Groom & Allen, 2014 ▸) for the 3-methyl-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione moiety of the title compound gave three hits. Two of these compounds also contain a substituted piperazine ring, namely 3-[(4-phenylpiperazin-1-yl)methyl]-5-(2-thienyl)-1,3,4-oxadiazole-2(3H)-thione (IDOBUA; El-Emam et al., 2013 ▸) and 3-[(4-benzylpiperazin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4-oxadiazole-2-thione (VUBYUO; Al-Omary et al., 2015 ▸). In both of these molecules, the conformation is very similar to that of the title compound.

Synthesis and crystallization

To a solution of 5-(thiophen-2-yl)-1,3,4-oxadiazole-2-thiol (920 mg, 5 mmol), in ethanol (15 ml), 1-(2-methoxyphenyl)piperazine (960 mg, 5 mmol) and 37% formaldehyde solution (1.0 ml) were added and the mixture was stirred at room temperature for 3 h and then allowed to stand overnight at 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 CHCl₃:EtOH solution (1:1; 15 ml) at room temperature. ¹H NMR (CDCl₃, 500.13 MHz): δ 3.10 (s, 8H, piperazine-H), 3.85 (s, 3H, OCH₃), 5.15 (s, 2H, CH2), 6.85–6.87 (m, 1H, Ar-H), 6.92–6.95 (m, 2H, Ar-H), 7.01–7.03 (m, 1H, Ar-H), 7.18 (t, 1H, thiophene-H, J = 4.5 Hz), 7.59 (d, 1H, thiophene-H, J = 4.5 Hz), 7.75 (d, 1H, thiophene-H, J = 4.5 Hz). ¹³C NMR (CDCl₃, 125.76 MHz): δ 50.43, 50.64 (piperazine-C), 55.33 (OCH₃), 70.44 (CH2), 111.05, 118.28, 120.94, 123.17, 123.68, 128.32, 130.74, 130.95, 141.09, 152.23 (Ar & thiophene-C), 155.42 (C=N), 177.74 (C=S).

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.

Table 2. Experimental details.

Crystal data
Chemical formula	C₁₈H₂₀N₄O₂S₂
M _r	388.5
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	100
a, b, c (Å)	15.2925 (2), 10.0745 (1), 11.9726 (1)
β (°)	93.413 (1)
V (Å³)	1841.28 (3)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	2.80
Crystal size (mm)	0.70 × 0.51 × 0.41

Data collection
Diffractometer	Agilent Xcalibur Ruby Gemini
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2014 ▸)
T _min, T _max	0.225, 0.315
No. of measured, independent and observed [I > 2σ(I)] reflections	13494, 3545, 3401
R _int	0.026
(sin θ/λ)_max (Å⁻¹)	0.612

Refinement
R[F ² > 2σ(F ²)], wR(F ²), S	0.045, 0.113, 1.04
No. of reflections	3494
No. of parameters	230
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.95, −0.65

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Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2006 ▸), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▸), ORTEP-3 for Windows and WinGX (Farrugia, 2012 ▸), Mercury (Macrae et al., 2008 ▸) and publCIF (Westrip, 2010 ▸).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989016000992/su5269sup1.cif

e-72-00269-sup1.cif^{(478.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016000992/su5269Isup2.hkl

e-72-00269-Isup2.hkl^{(171.4KB, hkl)}

Click here for additional data file.^{(7.3KB, cml)}

Supporting information file. DOI: 10.1107/S2056989016000992/su5269Isup3.cml

CCDC reference: 1447823

Additional supporting information: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors extend their sincere appreciation to the Deanship of Scientific Research at King Saud University for funding this study through the Research Group Project No. PRG-1436–23. We also acknowledge financial support from the Spanish Ministerio de Economía y Competitividad (MINECO-13-MAT2013–40950-R, FPI grant BES-2011–046948 to MSMA).

supplementary crystallographic information

Crystal data

C₁₈H₂₀N₄O₂S₂	F(000) = 816
M_r = 388.5	D_x = 1.401 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54184 Å
Hall symbol: -P 2ybc	Cell parameters from 11296 reflections
a = 15.2925 (2) Å	θ = 3.7–70.5°
b = 10.0745 (1) Å	µ = 2.80 mm⁻¹
c = 11.9726 (1) Å	T = 100 K
β = 93.413 (1)°	Prism, colourless
V = 1841.28 (3) Å³	0.70 × 0.51 × 0.41 mm
Z = 4

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Data collection

Agilent Xcalibur Ruby Gemini diffractometer	3545 independent reflections
Radiation source: Enhance (Cu) X-ray Source	3401 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
Detector resolution: 10.2673 pixels mm^-1	θ_max = 70.7°, θ_min = 5.3°
ω scans	h = −18→17
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014)	k = −8→12
T_min = 0.225, T_max = 0.315	l = −14→14
13494 measured reflections

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Refinement

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)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.113	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0574P)² + 2.048P] where P = (F_o² + 2F_c²)/3
3494 reflections	(Δ/σ)_max < 0.001
230 parameters	Δρ_max = 0.95 e Å⁻³
0 restraints	Δρ_min = −0.65 e Å⁻³
0 constraints

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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	U_iso*/U_eq	Occ. (<1)
S1	0.89998 (3)	0.09896 (5)	0.99378 (4)	0.02414 (15)
S2A	0.87403 (4)	0.74266 (6)	1.04820 (5)	0.02497 (16)	0.7913 (14)
C16A	0.94021 (8)	0.57554 (13)	1.21094 (10)	0.02497 (16)	0.7913 (14)
H16A	0.9598	0.501	1.2508	0.03*	0.7913 (14)
S2B	0.94021 (8)	0.57554 (13)	1.21094 (10)	0.02497 (16)	0.2087 (14)
C16B	0.87403 (4)	0.74266 (6)	1.04820 (5)	0.02497 (16)	0.2087 (14)
H16B	0.8502	0.779	0.9817	0.03*	0.2087 (14)
O1	0.90631 (8)	0.35048 (13)	1.06190 (11)	0.0189 (3)
O2	0.43793 (9)	0.38449 (17)	0.90935 (12)	0.0312 (4)
N3	0.85646 (10)	0.33316 (16)	0.89001 (13)	0.0192 (3)
N1	0.55319 (10)	0.37224 (16)	0.74811 (13)	0.0198 (3)
N4	0.85770 (10)	0.46847 (16)	0.91387 (13)	0.0204 (3)
N2	0.73225 (10)	0.29806 (17)	0.75238 (13)	0.0210 (3)
C1	0.46191 (12)	0.37565 (18)	0.71654 (16)	0.0202 (4)
C15	0.90176 (11)	0.58606 (19)	1.08927 (15)	0.0183 (4)
C14	0.88737 (11)	0.47285 (19)	1.01696 (15)	0.0180 (4)
C13	0.88567 (12)	0.26006 (19)	0.97769 (15)	0.0187 (4)
C6	0.40227 (13)	0.3813 (2)	0.80197 (17)	0.0229 (4)
C9	0.67626 (13)	0.2461 (2)	0.83683 (17)	0.0237 (4)
H9A	0.6806	0.3025	0.9026	0.028*
H9B	0.6955	0.1577	0.8589	0.028*
C11	0.61058 (12)	0.4202 (2)	0.66366 (16)	0.0231 (4)
H11A	0.5908	0.5066	0.6368	0.028*
H11B	0.6088	0.3596	0.6007	0.028*
C4	0.28120 (13)	0.3853 (2)	0.66375 (19)	0.0278 (5)
H4	0.2211	0.3875	0.6463	0.033*
C3	0.33874 (14)	0.3826 (2)	0.57913 (18)	0.0284 (5)
H3	0.3177	0.3844	0.5046	0.034*
C2	0.42871 (13)	0.3770 (2)	0.60627 (17)	0.0249 (4)
H2	0.4672	0.3741	0.5491	0.03*
C10	0.70379 (12)	0.4304 (2)	0.71497 (16)	0.0228 (4)
H10A	0.7424	0.4638	0.66	0.027*
H10B	0.7058	0.4912	0.7779	0.027*
C8	0.58162 (13)	0.2411 (2)	0.78978 (18)	0.0240 (4)
H8A	0.5763	0.177	0.7292	0.029*
H8B	0.5441	0.2125	0.8478	0.029*
C5	0.31283 (13)	0.3849 (2)	0.77469 (18)	0.0275 (5)
H5	0.2738	0.3869	0.8313	0.033*
C12	0.82390 (12)	0.2821 (2)	0.77866 (15)	0.0224 (4)
H12A	0.8555	0.3268	0.7217	0.027*
H12B	0.8379	0.1883	0.7749	0.027*
C17	0.93757 (13)	0.7167 (2)	1.24746 (17)	0.0268 (4)
H17	0.9571	0.7421	1.3193	0.032*
C7	0.38537 (15)	0.4430 (3)	0.99152 (19)	0.0342 (5)
H7A	0.4167	0.4403	1.0634	0.051*
H7B	0.3316	0.3943	0.9947	0.051*
H7C	0.3726	0.5335	0.9715	0.051*
C18	0.90558 (13)	0.8060 (2)	1.1716 (2)	0.0297 (5)
H18	0.9016	0.8961	1.1874	0.036*

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Atomic displacement parameters (Å²)

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0282 (3)	0.0197 (3)	0.0246 (3)	0.00178 (18)	0.00181 (19)	0.00051 (18)
S2A	0.0229 (3)	0.0257 (3)	0.0265 (3)	−0.0011 (2)	0.0022 (2)	−0.0008 (2)
C16A	0.0229 (3)	0.0257 (3)	0.0265 (3)	−0.0011 (2)	0.0022 (2)	−0.0008 (2)
S2B	0.0229 (3)	0.0257 (3)	0.0265 (3)	−0.0011 (2)	0.0022 (2)	−0.0008 (2)
C16B	0.0229 (3)	0.0257 (3)	0.0265 (3)	−0.0011 (2)	0.0022 (2)	−0.0008 (2)
O1	0.0189 (6)	0.0199 (6)	0.0177 (6)	0.0015 (5)	0.0001 (5)	0.0003 (5)
O2	0.0213 (7)	0.0510 (10)	0.0218 (7)	−0.0010 (6)	0.0057 (6)	−0.0044 (6)
N3	0.0175 (7)	0.0216 (8)	0.0184 (8)	0.0028 (6)	0.0006 (6)	−0.0007 (6)
N1	0.0161 (8)	0.0234 (8)	0.0201 (8)	0.0005 (6)	0.0037 (6)	0.0027 (6)
N4	0.0196 (8)	0.0219 (8)	0.0197 (8)	0.0030 (6)	0.0022 (6)	0.0002 (6)
N2	0.0170 (8)	0.0260 (8)	0.0201 (8)	0.0035 (6)	0.0011 (6)	0.0002 (7)
C1	0.0175 (9)	0.0190 (9)	0.0244 (10)	−0.0012 (7)	0.0030 (7)	0.0003 (7)
C15	0.0141 (8)	0.0219 (9)	0.0191 (9)	0.0009 (7)	0.0019 (7)	0.0014 (7)
C14	0.0128 (8)	0.0209 (9)	0.0204 (9)	0.0022 (7)	0.0029 (7)	0.0023 (7)
C13	0.0143 (8)	0.0241 (10)	0.0182 (9)	0.0006 (7)	0.0031 (7)	−0.0016 (7)
C6	0.0216 (10)	0.0233 (10)	0.0239 (10)	−0.0022 (8)	0.0034 (8)	0.0000 (8)
C9	0.0218 (10)	0.0248 (10)	0.0245 (10)	0.0031 (8)	0.0021 (8)	0.0047 (8)
C11	0.0177 (9)	0.0309 (11)	0.0211 (9)	0.0008 (8)	0.0031 (7)	0.0060 (8)
C4	0.0163 (9)	0.0309 (11)	0.0360 (11)	−0.0025 (8)	0.0000 (8)	0.0014 (9)
C3	0.0228 (10)	0.0351 (12)	0.0267 (10)	−0.0024 (8)	−0.0019 (8)	0.0032 (9)
C2	0.0197 (9)	0.0309 (11)	0.0246 (10)	−0.0008 (8)	0.0042 (8)	0.0010 (8)
C10	0.0177 (9)	0.0284 (10)	0.0224 (9)	−0.0002 (8)	0.0024 (7)	0.0055 (8)
C8	0.0203 (9)	0.0228 (10)	0.0290 (10)	−0.0003 (7)	0.0030 (8)	0.0035 (8)
C5	0.0197 (10)	0.0331 (11)	0.0307 (11)	−0.0032 (8)	0.0087 (8)	−0.0001 (9)
C12	0.0204 (9)	0.0295 (10)	0.0174 (9)	0.0047 (8)	0.0017 (7)	−0.0042 (8)
C17	0.0173 (9)	0.0420 (12)	0.0211 (9)	−0.0069 (8)	0.0027 (7)	−0.0057 (9)
C7	0.0326 (11)	0.0442 (13)	0.0272 (11)	−0.0067 (10)	0.0117 (9)	−0.0083 (10)
C18	0.0240 (10)	0.0230 (10)	0.0432 (12)	−0.0017 (8)	0.0102 (9)	−0.0017 (9)

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Geometric parameters (Å, º)

S1—C13	1.647 (2)	C9—H9A	0.97
S2A—C18	1.655 (2)	C9—H9B	0.97
S2A—C15	1.6988 (19)	C11—C10	1.522 (3)
C16A—C17	1.489 (3)	C11—H11A	0.97
C16A—C15	1.542 (2)	C11—H11B	0.97
C16A—H16A	0.93	C4—C3	1.381 (3)
O1—C14	1.369 (2)	C4—C5	1.386 (3)
O1—C13	1.381 (2)	C4—H4	0.93
O2—C6	1.367 (3)	C3—C2	1.396 (3)
O2—C7	1.434 (3)	C3—H3	0.93
N3—C13	1.337 (2)	C2—H2	0.93
N3—N4	1.393 (2)	C10—H10A	0.97
N3—C12	1.487 (2)	C10—H10B	0.97
N1—C1	1.425 (2)	C8—H8A	0.97
N1—C11	1.460 (2)	C8—H8B	0.97
N1—C8	1.469 (2)	C5—H5	0.93
N4—C14	1.290 (2)	C12—H12A	0.97
N2—C12	1.427 (2)	C12—H12B	0.97
N2—C9	1.460 (2)	C17—C18	1.349 (3)
N2—C10	1.464 (3)	C17—H17	0.93
C1—C2	1.386 (3)	C7—H7A	0.96
C1—C6	1.412 (3)	C7—H7B	0.96
C15—C14	1.441 (3)	C7—H7C	0.96
C6—C5	1.388 (3)	C18—H18	0.93
C9—C8	1.522 (3)

C18—S2A—C15	92.58 (10)	C3—C4—C5	120.10 (19)
C17—C16A—C15	101.32 (13)	C3—C4—H4	120
C17—C16A—H16A	129.3	C5—C4—H4	120
C15—C16A—H16A	129.3	C4—C3—C2	119.49 (19)
C14—O1—C13	105.85 (14)	C4—C3—H3	120.3
C6—O2—C7	116.52 (17)	C2—C3—H3	120.3
C13—N3—N4	112.23 (15)	C1—C2—C3	121.48 (19)
C13—N3—C12	126.27 (17)	C1—C2—H2	119.3
N4—N3—C12	121.49 (15)	C3—C2—H2	119.3
C1—N1—C11	115.34 (15)	N2—C10—C11	108.46 (16)
C1—N1—C8	112.16 (15)	N2—C10—H10A	110
C11—N1—C8	110.80 (15)	C11—C10—H10A	110
C14—N4—N3	103.26 (15)	N2—C10—H10B	110
C12—N2—C9	114.55 (15)	C11—C10—H10B	110
C12—N2—C10	116.12 (16)	H10A—C10—H10B	108.4
C9—N2—C10	111.25 (15)	N1—C8—C9	110.57 (16)
C2—C1—C6	118.29 (18)	N1—C8—H8A	109.5
C2—C1—N1	123.40 (17)	C9—C8—H8A	109.5
C6—C1—N1	118.28 (17)	N1—C8—H8B	109.5
C14—C15—C16A	123.32 (15)	C9—C8—H8B	109.5
C14—C15—S2A	122.32 (14)	H8A—C8—H8B	108.1
C16A—C15—S2A	114.33 (12)	C4—C5—C6	120.56 (19)
N4—C14—O1	113.53 (16)	C4—C5—H5	119.7
N4—C14—C15	129.37 (18)	C6—C5—H5	119.7
O1—C14—C15	117.09 (16)	N2—C12—N3	115.51 (15)
N3—C13—O1	105.12 (16)	N2—C12—H12A	108.4
N3—C13—S1	132.09 (15)	N3—C12—H12A	108.4
O1—C13—S1	122.77 (14)	N2—C12—H12B	108.4
O2—C6—C5	123.60 (18)	N3—C12—H12B	108.4
O2—C6—C1	116.35 (17)	H12A—C12—H12B	107.5
C5—C6—C1	120.05 (19)	C18—C17—C16A	117.01 (18)
N2—C9—C8	109.84 (16)	C18—C17—H17	121.5
N2—C9—H9A	109.7	C16A—C17—H17	121.5
C8—C9—H9A	109.7	O2—C7—H7A	109.5
N2—C9—H9B	109.7	O2—C7—H7B	109.5
C8—C9—H9B	109.7	H7A—C7—H7B	109.5
H9A—C9—H9B	108.2	O2—C7—H7C	109.5
N1—C11—C10	109.26 (15)	H7A—C7—H7C	109.5
N1—C11—H11A	109.8	H7B—C7—H7C	109.5
C10—C11—H11A	109.8	C17—C18—S2A	114.76 (17)
N1—C11—H11B	109.8	C17—C18—H18	122.6
C10—C11—H11B	109.8	S2A—C18—H18	122.6
H11A—C11—H11B	108.3

C13—N3—N4—C14	−0.5 (2)	N1—C1—C6—O2	0.7 (3)
C12—N3—N4—C14	178.38 (15)	C2—C1—C6—C5	1.5 (3)
C11—N1—C1—C2	22.5 (3)	N1—C1—C6—C5	179.97 (18)
C8—N1—C1—C2	−105.7 (2)	C12—N2—C9—C8	−167.82 (16)
C11—N1—C1—C6	−155.90 (18)	C10—N2—C9—C8	58.0 (2)
C8—N1—C1—C6	76.0 (2)	C1—N1—C11—C10	171.49 (16)
C17—C16A—C15—C14	−177.76 (16)	C8—N1—C11—C10	−59.7 (2)
C17—C16A—C15—S2A	0.16 (15)	C5—C4—C3—C2	1.1 (3)
C18—S2A—C15—C14	177.79 (16)	C6—C1—C2—C3	−0.5 (3)
C18—S2A—C15—C16A	−0.16 (13)	N1—C1—C2—C3	−178.91 (19)
N3—N4—C14—O1	0.53 (19)	C4—C3—C2—C1	−0.8 (3)
N3—N4—C14—C15	−178.64 (17)	C12—N2—C10—C11	165.92 (15)
C13—O1—C14—N4	−0.4 (2)	C9—N2—C10—C11	−60.7 (2)
C13—O1—C14—C15	178.90 (15)	N1—C11—C10—N2	60.7 (2)
C16A—C15—C14—N4	−178.37 (16)	C1—N1—C8—C9	−172.53 (16)
S2A—C15—C14—N4	3.9 (3)	C11—N1—C8—C9	57.0 (2)
C16A—C15—C14—O1	2.5 (2)	N2—C9—C8—N1	−55.2 (2)
S2A—C15—C14—O1	−175.28 (13)	C3—C4—C5—C6	−0.2 (3)
N4—N3—C13—O1	0.29 (19)	O2—C6—C5—C4	178.1 (2)
C12—N3—C13—O1	−178.53 (15)	C1—C6—C5—C4	−1.2 (3)
N4—N3—C13—S1	−178.25 (15)	C9—N2—C12—N3	−52.8 (2)
C12—N3—C13—S1	2.9 (3)	C10—N2—C12—N3	79.1 (2)
C14—O1—C13—N3	0.03 (18)	C13—N3—C12—N2	110.8 (2)
C14—O1—C13—S1	178.74 (13)	N4—N3—C12—N2	−67.9 (2)
C7—O2—C6—C5	−24.0 (3)	C15—C16A—C17—C18	−0.1 (2)
C7—O2—C6—C1	155.31 (19)	C16A—C17—C18—S2A	0.0 (2)
C2—C1—C6—O2	−177.78 (18)	C15—S2A—C18—C17	0.11 (17)

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Hydrogen-bond geometry (Å, º)

Cg1 is the centroid of the S2A/C15/C16A/C17/C18 ring.

D—H···A	D—H	H···A	D···A	D—H···A
C12—H12A···S1ⁱ	0.97	2.95	3.860 (2)	157
C17—H17···O1ⁱⁱ	0.93	2.69	3.475 (2)	143
C5—H5···Cg1ⁱⁱⁱ	0.93	2.95	3.660 (2)	135

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Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x+2, y+1/2, −z+5/2; (iii) −x+1, −y+1, −z+2.

References

Agilent (2014). CrysAlis PRO. Agilent Technologies, Yarnton, England.
Al-Omar, M. A. (2010). Molecules, 15, 502–514. [DOI] [PMC free article] [PubMed]
Al-Omary, F. A. M., El-Emam, A. A., Ghabbour, H. A., Chidan Kumar, C. S., Quah, C. K. & Fun, H.-K. (2015). Acta Cryst. E71, o175–o176. [DOI] [PMC free article] [PubMed]
Bansal, S., Bala, M., Suthar, S. K., Choudhary, S., Bhattacharya, S., Bhardwaj, V., Singla, S. & Joseph, A. (2014). Eur. J. Med. Chem. 80, 167–174. [DOI] [PubMed]
Du, Q.-R., Li, D.-D., Pi, Y.-Z., Li, J.-R., Sun, J., Fang, F., Zhong, W.-Q., Gong, H.-B. & Zhu, H.-L. (2013). Eur. J. Med. Chem. 21, 2286–2297. [DOI] [PubMed]
El-Emam, A. A., Al-Deeb, O. A., Al-Omar, M. A. & Lehmann, J. (2004). Bioorg. Med. Chem. 12, 5107–5113. [DOI] [PubMed]
El-Emam, A. A., Al-Omar, M. A., Al-Obaid, A.-R. M., Ng, S. W. & Tiekink, E. R. T. (2013). Acta Cryst. E69, o684. [DOI] [PMC free article] [PubMed]
El-Emam, A. A., El-Brollosy, N. R., Attia, M. I., Said-Abdelbaky, M. & García-Granda, S. (2012). Acta Cryst. E68, o2172–o2173. [DOI] [PMC free article] [PubMed]
Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.
Gamal El-Din, M. M., El-Gamal, M. I., Abdel-Maksoud, M. S., Yoo, K. H. & Oh, C.-H. (2015). Eur. J. Med. Chem. 90, 45–52. [DOI] [PubMed]
Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662–671. [DOI] [PubMed]
Kadi, A. A., El-Brollosy, N. R., Al-Deeb, O. A., Habib, E. E., Ibrahim, T. M. & El-Emam, A. A. (2007). Eur. J. Med. Chem. 42, 235–242. [DOI] [PubMed]
Li, P., Shi, L., Yang, X., Yang, L., Chen, X.-W., Wu, F., Shi, Q.-C., Xu, W.-M., He, M., Hu, D.-Y. & Song, B.-A. (2014). Bioorg. Med. Chem. Lett. 24, 1677–1680. [DOI] [PubMed]
Ma, L., Xiao, Y., Li, C., Xie, Z.-L., Li, Z.-L., Wang, Y.-T., Ma, H.-T., Zhu, H.-L., Wang, M.-H. & Ye, Y.-H. (2013). Bioorg. Med. Chem. 21, 6763–6770. [DOI] [PubMed]
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.
Milinkevich, K. A., Yoo, C. L., Sparks, T. C., Lorsbach, B. A. & Kurth, M. J. (2009). Bioorg. Med. Chem. Lett. 19, 5796–5798. [DOI] [PubMed]
Ogata, M., Atobe, H., Kushida, H. & Yamamoto, K. (1971). J. Antibiot. 24, 443–451. [DOI] [PubMed]
Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.
Pinna, G. A., Murineddu, G., Murruzzu, C., Zuco, V., Zunino, F., Cappelletti, G., Artali, R., Cignarella, G., Solano, L. & Villa, S. (2009). ChemMedChem, 4, 998–1009. [DOI] [PubMed]
Rane, R. A., Gutte, S. W. & Sahu, N. U. (2012). Bioorg. Med. Chem. Lett. 22, 6429–6432. [DOI] [PubMed]
Schlecker, R. & Thieme, P. C. (1988). Tetrahedron, 44, 3289–3294.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]
Shi, W., Qian, X., Zhang, R. & Song, G. (2001). J. Agric. Food Chem. 49, 124–130. [DOI] [PubMed]
Summa, V., Petrocchi, A., Bonelli, F., Crescenzi, B., Donghi, M., Ferrara, M., Fiore, F., Gardelli, C., Gonzalez Paz, O., Hazuda, D. J., Jones, P., Kinzel, O., Laufer, R., Monteagudo, E., Muraglia, E., Nizi, E., Orvieto, F., Pace, P., Pescatore, G., Scarpelli, R., Stillmock, K., Witmer, M. V. & Rowley, M. (2008). J. Med. Chem. 51, 5843–5855. [DOI] [PubMed]
Vardan, S., Smulyan, H., Mookherjee, S. & Eich, R. (1983). Clin. Pharmacol. Ther. 34, 290–296. [DOI] [PubMed]
Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.
Wu, W., Chen, Q., Tai, A., Jiang, G. & Ouyang, G. (2015). Bioorg. Med. Chem. Lett. 25, 2243–2246. [DOI] [PubMed]
Zhang, K., Wang, P., Xuan, L.-N., Fu, X.-Y., Jing, F., Li, S., Liu, Y.-M. & Chen, B.-Q. (2014). Bioorg. Med. Chem. Lett. 24, 5154–5156. [DOI] [PubMed]
Zhang, Y., Zuniga, C., Kim, S.-J., Cai, D., Barlow, S., Salman, S., Coropceanu, V., Brédas, J.-L., Kippelen, B. & Marder, S. (2011). Chem. Mater. 23, 4002–4015.

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/S2056989016000992/su5269sup1.cif

e-72-00269-sup1.cif^{(478.8KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989016000992/su5269Isup2.hkl

e-72-00269-Isup2.hkl^{(171.4KB, hkl)}

Click here for additional data file.^{(7.3KB, cml)}

Supporting information file. DOI: 10.1107/S2056989016000992/su5269Isup3.cml

CCDC reference: 1447823

Additional supporting information: crystallographic information; 3D view; checkCIF report

[bb1] Agilent (2014). CrysAlis PRO. Agilent Technologies, Yarnton, England.

[bb2] Al-Omar, M. A. (2010). Molecules, 15, 502–514. [DOI] [PMC free article] [PubMed]

[bb3] Al-Omary, F. A. M., El-Emam, A. A., Ghabbour, H. A., Chidan Kumar, C. S., Quah, C. K. & Fun, H.-K. (2015). Acta Cryst. E71, o175–o176. [DOI] [PMC free article] [PubMed]

[bb4] Bansal, S., Bala, M., Suthar, S. K., Choudhary, S., Bhattacharya, S., Bhardwaj, V., Singla, S. & Joseph, A. (2014). Eur. J. Med. Chem. 80, 167–174. [DOI] [PubMed]

[bb5] Du, Q.-R., Li, D.-D., Pi, Y.-Z., Li, J.-R., Sun, J., Fang, F., Zhong, W.-Q., Gong, H.-B. & Zhu, H.-L. (2013). Eur. J. Med. Chem. 21, 2286–2297. [DOI] [PubMed]

[bb6] El-Emam, A. A., Al-Deeb, O. A., Al-Omar, M. A. & Lehmann, J. (2004). Bioorg. Med. Chem. 12, 5107–5113. [DOI] [PubMed]

[bb7] El-Emam, A. A., Al-Omar, M. A., Al-Obaid, A.-R. M., Ng, S. W. & Tiekink, E. R. T. (2013). Acta Cryst. E69, o684. [DOI] [PMC free article] [PubMed]

[bb8] El-Emam, A. A., El-Brollosy, N. R., Attia, M. I., Said-Abdelbaky, M. & García-Granda, S. (2012). Acta Cryst. E68, o2172–o2173. [DOI] [PMC free article] [PubMed]

[bb9] Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.

[bb10] Gamal El-Din, M. M., El-Gamal, M. I., Abdel-Maksoud, M. S., Yoo, K. H. & Oh, C.-H. (2015). Eur. J. Med. Chem. 90, 45–52. [DOI] [PubMed]

[bb11] Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662–671. [DOI] [PubMed]

[bb12] Kadi, A. A., El-Brollosy, N. R., Al-Deeb, O. A., Habib, E. E., Ibrahim, T. M. & El-Emam, A. A. (2007). Eur. J. Med. Chem. 42, 235–242. [DOI] [PubMed]

[bb13] Li, P., Shi, L., Yang, X., Yang, L., Chen, X.-W., Wu, F., Shi, Q.-C., Xu, W.-M., He, M., Hu, D.-Y. & Song, B.-A. (2014). Bioorg. Med. Chem. Lett. 24, 1677–1680. [DOI] [PubMed]

[bb14] Ma, L., Xiao, Y., Li, C., Xie, Z.-L., Li, Z.-L., Wang, Y.-T., Ma, H.-T., Zhu, H.-L., Wang, M.-H. & Ye, Y.-H. (2013). Bioorg. Med. Chem. 21, 6763–6770. [DOI] [PubMed]

[bb15] 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.

[bb16] Milinkevich, K. A., Yoo, C. L., Sparks, T. C., Lorsbach, B. A. & Kurth, M. J. (2009). Bioorg. Med. Chem. Lett. 19, 5796–5798. [DOI] [PubMed]

[bb17] Ogata, M., Atobe, H., Kushida, H. & Yamamoto, K. (1971). J. Antibiot. 24, 443–451. [DOI] [PubMed]

[bb18] Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.

[bb19] Pinna, G. A., Murineddu, G., Murruzzu, C., Zuco, V., Zunino, F., Cappelletti, G., Artali, R., Cignarella, G., Solano, L. & Villa, S. (2009). ChemMedChem, 4, 998–1009. [DOI] [PubMed]

[bb20] Rane, R. A., Gutte, S. W. & Sahu, N. U. (2012). Bioorg. Med. Chem. Lett. 22, 6429–6432. [DOI] [PubMed]

[bb21] Schlecker, R. & Thieme, P. C. (1988). Tetrahedron, 44, 3289–3294.

[bb22] Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [DOI] [PubMed]

[bb23] Shi, W., Qian, X., Zhang, R. & Song, G. (2001). J. Agric. Food Chem. 49, 124–130. [DOI] [PubMed]

[bb24] Summa, V., Petrocchi, A., Bonelli, F., Crescenzi, B., Donghi, M., Ferrara, M., Fiore, F., Gardelli, C., Gonzalez Paz, O., Hazuda, D. J., Jones, P., Kinzel, O., Laufer, R., Monteagudo, E., Muraglia, E., Nizi, E., Orvieto, F., Pace, P., Pescatore, G., Scarpelli, R., Stillmock, K., Witmer, M. V. & Rowley, M. (2008). J. Med. Chem. 51, 5843–5855. [DOI] [PubMed]

[bb25] Vardan, S., Smulyan, H., Mookherjee, S. & Eich, R. (1983). Clin. Pharmacol. Ther. 34, 290–296. [DOI] [PubMed]

[bb26] Westrip, S. P. (2010). J. Appl. Cryst. 43, 920–925.

[bb27] Wu, W., Chen, Q., Tai, A., Jiang, G. & Ouyang, G. (2015). Bioorg. Med. Chem. Lett. 25, 2243–2246. [DOI] [PubMed]

[bb28] Zhang, K., Wang, P., Xuan, L.-N., Fu, X.-Y., Jing, F., Li, S., Liu, Y.-M. & Chen, B.-Q. (2014). Bioorg. Med. Chem. Lett. 24, 5154–5156. [DOI] [PubMed]

[bb29] Zhang, Y., Zuniga, C., Kim, S.-J., Cai, D., Barlow, S., Salman, S., Coropceanu, V., Brédas, J.-L., Kippelen, B. & Marder, S. (2011). Chem. Mater. 23, 4002–4015.

PERMALINK

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

Monirah A Al-Alshaikh

Hatem A Abuelizz

Ali A El-Emam

Mohammed S M Abdelbaky

Santiago Garcia-Granda

Abstract

Chemical context

Structural commentary

Figure 1.