Startseite Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2
Artikel Open Access

Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2

  • Lamya H. Al-Wahaibi ORCID logo , Olivier Blacque ORCID logo , Edward R.T. Tiekink ORCID logo und Ali A. El-Emam ORCID logo EMAIL logo
Veröffentlicht/Copyright: 23. April 2025

Abstract

C18H19N3OS2, orthorhombic, Pca21 (no. 29), a = 14.8852(2) Å, b = 5.23480(10) Å, c = 44.1008(7) Å, V = 3436.38(10) Å3, Z = 8, R gt(F) = 0.0554, wR ref(F 2) = 0.1501, T = 160 K.

CCDC no.: 2440381

The molecular structure is shown in the figure. Table 1 contains the crystallographic data. The list of the atoms including atomic coordinates and displacement parameters can be found in the cif-file attached to this article.

1 Source of material

4–Phenylpiperidine (1.6 g, 0.01 mol) and 37 % formaldehyde solution (0.5 mL) were added to a solution of 5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione (1.8 g, 0.01 mol) in ethanol (10 mL), and the mixture was stirred at room temperature for 3 h then allowed to stand overnight. The precipitated crude product was filtered, washed with cold ethanol, dried and crystallised from ethanol to yield 3.15 g (88 %) of the title compound as colourless needles. M. pt.: 407–409 K (uncorrected). 1H NMR (CDCl3, 700.17 MHz): δ 1.76–1.78 (m, 4H, Piperidine–H), 2.40–2.62 (m, 4H, Piperidine–H), 2.66–2.68 (m, 1H, Piperidine–H), 5.12 (s, 2H, NCH2N), 6.96–7.08 (m, 3H, Ar–H), 7.20–7.26 (m, 3H, Ar–H & Thiophene–H), 7.82 (d, 1H, Thiophene–H, J = 4.2 Hz), 7.88 (d, 1H, Thiophene–H, J = 4.2 Hz). 13C NMR (CDCl3, 176.06 MHz): δ 32.88, 41.20, 50.02 (Piperidine–C), 69.04 (NCH2N), 121.40, 124.22, 127.80, 128.33, 129.08, 130.02, 130.96, 146.46 (Ar–C & Thiophene–C), 156.20 (Oxadiazole C-5), 175.46 (C=S). Analysis for C18H19N3OS2 (357.49): Found C, 60.36; H, 5.38; N, 11.70 %. Calc. C, 60.48; H, 5.36; N, 11.75 %.

Table 1:

Data collection and handling.

Crystal: colourless needle
Size: 0.16 × 0.03 × 0.02 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 2.89 mm−1
Diffractometer, scan mode: Rigaku Synergy, ω scans
θ max, completeness: 68.3°, 100 %
N(hkl)measured , N(hkl)unique, R int: 34854, 6292, 0.047
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 6010
N(param)refined: 434
Programs: Rigaku, 1 SHELX 2 , 3 and ORTEP for Windows 4

2 Experimental details

The C-bound H atoms were geometrically placed (C–H = 0.95–1.00 Å) and refined as riding with U iso (H) = 1.2U eq(C). The data were modelled as a twin with a ratio 0.53(3):0.47(3).

3 Discussion

The heterocyclic 1,2,4-triazole scaffold was recognised early as an essential pharmacophore of numerous therapeutically interesting drugs which exhibit a wide spectrum of chemotherapeutic activities. 5 , 6 , 7 In the same way, the thiophene ring constitutes a key component of many drugs. 8 , 9 In this connection, the title thiophenyl-linked oxadiazolyl hybrid molecule, (I), was synthesised and its crystal structure investigated by X-ray crystallography.

The molecular structures of the two independent molecules comprising the asymmetric-unit of (I) are shown in the upper two images of the figure (50 % probability ellipsoids). From the overlay diagram shown in the lower view of the figure the conformation of the S1-containing molecule (red image) overlaps to a first approximation with the inverted conformation of the S3-containing molecule (blue image). Thus, the two independent molecules are close to being an enantiomeric pair. The S1-containing molecule comprises a (4-phenylpiperidin-1-yl)methyl group connected at the N2 atom and a thiophen-2-yl ring linked at C5. The dihedral angle between the oxadiazolyl and the thiophen-2-yl rings is 4.1(3) indicating a co-planar relationship but, overall the molecule adopts a splayed L-shape as seen in the dihedral angles formed between the oxadiazolyl ring and each of the thiophen-2-yl ring and the terminal phenyl group of 84.1(3) and 87.9(3), respectively. The equivalent dihedral angles for the S3-containing molecule are comparable, being 3.8(3), 86.1(3) and 89.4(3), respectively. Globally, the oxadiazolyl–S1 and thiophen-2-yl–S2 atoms lie to opposite sides of the molecule. The piperidin-1-yl rings adopt chair-conformations.

In the crystallographic literature, there is a closely related molecule whereby the bridging piperidin-1-yl ring in (I) is substituted by a piperazin-1-yl residue; 10 the thiophen-2-yl ring is disordered over two co-planar orientations in the ratio 0.684(2):0.316(2). As illustrated by the green image of the lower view of the figure, the conformation is relatively close to those of the molecules in (I). Thus, the dihedral angles between the oxadiazolyl and the thiophen-2-yl (main disorder component) rings and terminal phenyl group are 4.59(10) and 67.58(6), respectively, and between the thiophen-2-yl and phenyl rings, 72.16(9). All geometric parameters are in the expected ranges. 11

In the molecular packing, thiophen-2-yl–C–H···S(thione) [C1–H1···S2 i : H1···S2 i  = 2.84 Å, C1···S2 i  = 3.781(6) Å with angle at H1 = 172°; C19–H19···S4 ii : H19···S4 ii  = 2.84 Å, C19···S4 ii  = 3.790(6) Å with angle at H19 = 173° for symmetry operations: (i) −1/2+x, 1−y, z and (ii) 1/2+x, −y, z] and π(oxadiazolyl)···π(thiophen-2-yl) [Cg(S1,C1–C4)···Cg(O1,N1,N2,C5,C6) iii  = 3.667(3) Å with angle of inclination = 4.1(3); Cg(S3,C19–C22)···Cg(O2,N4,N5,C23,C24) iv  = 3.653(3) Å with angle of inclination = 3.8(3) for symmetry operations: (iii) x, 1+y, z and (iv) x, −1+y, z] interactions occur between like molecules. In addition, phenyl–C–H···π(phenyl) [C34–H34···Cg(C13–C18 v ) = 2.90 Å with angle at H34 = 154° for symmetry operation (v) 1/2-x, y, 1/2+z] occur between the independent molecules. The aforementioned interactions occur within supramolecular layers in the ab-plane. The most notable interactions between the layers which are interdigitated along the c-axis are long thiophen-2-yl–C–H···O(thiophen-2-yl) contacts > 2.73 Å.

A further analysis of the molecular packing was conducted by calculating the contributions to the Hirshfeld surfaces for (I) and the associated two-dimensional fingerprint plots employing CrystalExplorer 12 and standard procedures. 13 The percentage contributions to the Hirshfeld surface contacts are similar for both independent molecules; values for the S3-containing molecule are given in square brackets. For the S1-containing molecule, the most significant contributions to the surface are H···H contacts at 47.9 % [48.2 %] followed by nearly equal contributions by S···H/H···S and C···H/H···C contacts of 15.9 and 15.8 % [15.8 and 15.7 %], respectively. Significant contributions to the surface are also made N···H/H···N, S···C/C···S and O···H/H···O contacts of 6.3, 4.5 and 4.1 % [5.9, 4.6 and 4.1 %], respectively.

The different contributions to the surfaces by N···H/H···N contacts represents the most significant difference in Hirshfeld surface contacts between the independent molecules.


Corresponding author: Ali A. El–Emam, Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt, E-mail:

  1. Author contributions: All authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Conflict of interest: The authors declare no conflicts of interest.

  3. Research funding: This study was financially supported by the the Princess Nourah bint Abdulrahman University Researchers Supporting Project No. PNURSP2025R3, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.

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Received: 2025-02-14
Accepted: 2025-04-02
Published Online: 2025-04-23
Published in Print: 2025-06-26

© 2025 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of 5,5′-bis(2,4,6-trinitrophenyl)-2,2′-bi(1,3,4-oxadiazole), C16H4N10O14
  4. Crystal structure of catena-poly[(μ3-4,4′-oxydibenzoato- κ5 O,O: O,O:O)-bis(2,4,6-tri(3-pyridine)-1,3,5-triazine-κ1 N)cadmium(II)], C50H32CdN12O5
  5. The crystal structure of 1,4-diazepane-1,4-diium potassium trinitrate, C5H14KN5O9
  6. The crystal structure of benzyl 2,2,5,5-tetramethylthiazolidine-4-carboxylate, C15H21NO2S
  7. Crystal structure of 2-hydroxyethyl-triphenylphosphonium tetracyanidoborate, C24H20BN4OP
  8. The crystal structure of 1-methyl-3-(N-methylnitrous amide–N-methylene) imidazolidine-2,4,5-trione
  9. Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S
  10. Crystal structure of 5-(2,2-difluoropropyl)-5-methylbenzo[4,5]imidazo[2,1-a] isoquinolin-6(5H)-one, C20H18F2N2O
  11. The crystal structure of N′,N″-[1,2-bis(4-chlorophenyl)ethane-1,2-diylidene]bis(furan-2- carbohydrazide), C24H16Cl2N4O4
  12. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromoantimony(III), [C25H21BrP]+[SbBr4]
  13. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromidoindium(III), [C25H21BrP]+[InBr4]
  14. The crystal structure of 4-carboxy-2-oxobutan-1-aminium chloride, C5H10ClNO3
  15. Crystal structure of (4-(4-chlorophenyl)-1H-pyrrole-3-carbonyl)ferrocene, C21H16ClFeNO
  16. The crystal structure of dichlorido(η6-p-cymene)(triphenylarsine)ruthenium(II), C28H29AsCl2Ru
  17. Crystal structure of (Z)-2-hydroxy-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H16N2O2
  18. The crystal structure of 10-(1-bromoethyl)-14-(bromomethyl)dibenzo[a, c]acridine, C24H17NBr2
  19. Synthesis and crystal structure of 6-methoxy-7-[(4-methoxyphenyl)methoxy]-2H-1-benzopyran-2-one, C18H16O5
  20. Synthesis and crystal structure of ethyl 4-((4-trifluoromethylbenzyl)amino)benzo, C17H16F3NO2
  21. The crystal structure of (Z)-2-(tert-butyl)-6-(7-(tert-butyl)-5-methylbenzo[d][1,3]oxathiol-2-ylidene)-4-methylcyclohexa-2,4-dien-1-one, C23H28O2S
  22. The crystal structure of (R)-2-aminobutanamide hydrochloride, C4H11ClN2O
  23. Crystal structure of bromido[hydridotris(3-tert-butyl-5-isopropylpyrazolyl)borato-κ3 N,N′,N″]copper(II), C30H52BBrCuN6
  24. Crystal structure of chlorido{hydridotris[3-mesityl-5-methyl-1H-pyrazol-1-yl-κN3]borato}-copper(II) dichloromethane monosolvate
  25. Crystal structure of 4-[3,5-bis(propan-2-yl)-1H-pyrazol-4-yl]pyridine, C14H19N3
  26. Crystal structure of ((4-(4-bromophenyl)-1H-pyrrol-3-yl)methyl)ferrocene, C21H16BrFeNO
  27. Crystal structure of [(4-chlorobenzyl)triphenylphosphonium] dichloridocopper(I), {[C25H21ClP]+[CuCl2]}n
  28. The crystal structure of {Cu(2,9-diisopropyl-4,7-diphenyl-1,10-phenanthroline)[4,5-bis(diphenylphosphino)-9,9-dimethylxanthene]}+ PF6·1.5(EtOAC)
  29. Crystal structure of 3,5-bis(t-butyl)-1H-pyrazol-4-amine, C11H21N3
  30. Crystal structure of [(2,4-dichlorobenzyl)triphenylphosphonium] trichloridocopper(II), [C25H20Cl2P]+[CuCl3]
  31. The crystal structure of dipotassium sulfide, K2S
  32. Crystal structure of (4-(4-methoxyphenyl)-1H-pyrrole-3-carbonyl)ferrocene, C22H19FeNO2
  33. Crystal structure of (E)-6-(4-methylpiperazin-1-yl)-2-(4-(trifluoromethyl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one, C23H23F3N2O
  34. Crystal structure of (E)-6-morpholino-2-(4-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H20F3NO2
  35. Crystal structure of Ce9Ir37Ge25
  36. The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S
  37. Crystal structure of (4-(4-isopropylphenyl)-1H-pyrrol-3-yl)(ferrocenyl)methanone, C24H23FeNO
  38. Crystal structure of bis(methylammonium) tetrathiotungstate(VI), (CH3NH3)2[WS4]
  39. Crystal structure of 6,11-dihydro-12H-benzo[e]indeno[1,2-b]oxepin-12-one, C17H12O2
  40. Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2
  41. Crystal structure of N-isopropyl-1,8-naphthalimide C15H13NO2
  42. TiNiSi-type EuPdBi
  43. Crystal structure of 1-(p-tolylphenyl)-4-(2-thienoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O2S
  44. The crystal structure of 3-(3-carboxypropyl)-2-nitro-1H-pyrrole 1-oxide, C7H9N3O5
  45. The crystal structure of tetraaqua-bis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k2O:N)-tetrakis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k1N)trizinc(II) hexahydrate C36H52N18O32Zn3
  46. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 4-hydroxy-3,5-dimethoxybenzoate monohydrate, C25H30FN3O9
  47. Crystal structure of bis(DL-1-carboxy-2-(1H-indol-3-yl)ethan-1-aminium) oxalate — acetic acid (1/2)
  48. Crystal structure of methyl (E)-4-((4-methylphenyl)sulfonamido)but-2-enoate, C12H15NO4S
  49. The crystal structure of actarit, C10H11NO3
  50. The crystal structure of bicyclol, C19H18O9
  51. The crystal structure of topiroxostat, C13H8N6
  52. Crystal structure of 2,2-dichloro-N-methyl-N-(4-p-tolylthiazol-2-yl)acetamide, C13H12Cl2N2OS
  53. Crystal structure of 4-(trifluoromethyl)-7-coumarinyl trifluoromethanesulfonate C11H4F6O5S
  54. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ6O6)-((Z)-N,N′-bis(2-(dimethylamino)phenyl)carbamimidato-κ1N)potassium(I)
  55. Crystal structure of (Z)-2-(5-((4-(dimethylamino)naphthalen-1-yl)methylene)-4-oxo-2-thioxothiazolidin-3-yl)acetic acid, C18H16N2O3S2
  56. Crystal structure of (4-fluorobenzyl)triphenylphosphonium bromide, C25H21BrFP
  57. The crystal structure of dichlorido-[6-(pyridin-2-yl)phenanthridine-κ2N, N′]zinc(II)-chloroform (1/1), C19H13N2ZnCl5
  58. Crystal structure of (E)-(3-(2,4-dichlorophenyl)acryloyl)ferrocene, C19H14Cl2FeO
  59. The crystal structure of (E)-7-chloro-1-cyclopropyl-6-fluoro-3-((2-hydroxybenzylidene)amino)quinolin-4(1H)-one, C19H14ClFN2O2
  60. Crystal structure of 2-bromo-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13BrFNO4S2
  61. Crystal structure of 2-chloro-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13ClFNO4S2
  62. Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O
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