| Literature DB >> 26958404 |
Monirah A Al-Alshaikh1, Hatem A Abuelizz2, Ali A El-Emam2, Mohammed S M Abdelbaky3, Santiago Garcia-Granda3.
Abstract
The title compound, C18H20N4O2S2, is a new 1,3,4-oxa-diazole and a key pharmacophore of several biologically active agents. It is composed of a meth-yl(thio-phen-2-yl)-1,3,4-oxa-diazole-2(3H)-thione moiety linked to a 2-meth-oxy-phenyl unit via a piperazine ring that has a chair conformation. The thio-phene ring mean plane lies almost in the plane of the oxa-diazole ring, with a dihedral angle of 4.35 (9)°. The 2-meth-oxy-phenyl ring is almost normal to the oxa-diazole ring, with a dihedral angle of 84.17 (10)°. In the crystal, mol-ecules are linked by weak C-H⋯S hydrogen bonds and C-H⋯π inter-actions, forming layers parallel to the bc plane. The layers are linked via weak C-H⋯O hydrogen bonds and slipped parallel π-π inter-actions [inter-centroid distance = 3.6729 (10) Å], forming a three-dimensional structure. The thio-phene ring has an approximate 180° rotational disorder about the bridging C-C bond.Entities:
Keywords: 1,3,4-oxadiazole; crystal structure; disorder; hydrogen bonding; piperazine; thiophene
Year: 2016 PMID: 26958404 PMCID: PMC4770969 DOI: 10.1107/S2056989016000992
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The 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.
Hydrogen-bond geometry (Å, °)
Cg1 is the centroid of the S2A/C15/C16A/C17/C18 ring.
|
|
| H⋯ |
|
|
|---|---|---|---|---|
| C12—H12 | 0.97 | 2.95 | 3.860 (2) | 157 |
| C17—H17⋯O1ii | 0.93 | 2.69 | 3.475 (2) | 143 |
| C5—H5⋯ | 0.93 | 2.95 | 3.660 (2) | 135 |
Symmetry codes: (i) ; (ii) ; (iii) .
Figure 2Crystal 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.
Experimental details
| Crystal data | |
| Chemical formula | C18H20N4O2S2 |
|
| 388.5 |
| Crystal system, space group | Monoclinic, |
| Temperature (K) | 100 |
|
| 15.2925 (2), 10.0745 (1), 11.9726 (1) |
| β (°) | 93.413 (1) |
|
| 1841.28 (3) |
|
| 4 |
| Radiation type | Cu |
| 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 ( |
|
| 0.225, 0.315 |
| No. of measured, independent and observed [ | 13494, 3545, 3401 |
|
| 0.026 |
| (sin θ/λ)max (Å−1) | 0.612 |
| Refinement | |
|
| 0.045, 0.113, 1.04 |
| No. of reflections | 3494 |
| No. of parameters | 230 |
| H-atom treatment | H-atom parameters constrained |
| Δρmax, Δρmin (e Å−3) | 0.95, −0.65 |
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 ▸).
| C18H20N4O2S2 | |
| Monoclinic, | Cu |
| Hall symbol: -P 2ybc | Cell parameters from 11296 reflections |
| θ = 3.7–70.5° | |
| µ = 2.80 mm−1 | |
| β = 93.413 (1)° | Prism, colourless |
| 0.70 × 0.51 × 0.41 mm | |
| Agilent Xcalibur Ruby Gemini diffractometer | 3545 independent reflections |
| Radiation source: Enhance (Cu) X-ray Source | 3401 reflections with |
| Graphite monochromator | |
| Detector resolution: 10.2673 pixels mm-1 | θmax = 70.7°, θmin = 5.3° |
| ω scans | |
| Absorption correction: multi-scan ( | |
| 13494 measured reflections |
| Refinement on | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| Hydrogen site location: inferred from neighbouring sites | |
| H-atom parameters constrained | |
| 3494 reflections | (Δ/σ)max < 0.001 |
| 230 parameters | Δρmax = 0.95 e Å−3 |
| 0 restraints | Δρmin = −0.65 e Å−3 |
| 0 constraints |
| 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 |
| 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* |
| 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) |
| 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) |
| H··· | ||||
| C12—H12 | 0.97 | 2.95 | 3.860 (2) | 157 |
| C17—H17···O1ii | 0.93 | 2.69 | 3.475 (2) | 143 |
| C5—H5··· | 0.93 | 2.95 | 3.660 (2) | 135 |