Home Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S
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Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S

  • Mohammad M. Al-Sanea , Mohammed S. M. Abdelbaky , Santiago Garcia-Granda , Ahmed A. B. Mohamed , Edward R. T. Tiekink ORCID logo and Ali A. El-Emam ORCID logo EMAIL logo
Published/Copyright: February 17, 2023

Abstract

C20H30N4O3S, orthorhombic, P212121 (no. 19), a = 7.7152(3) Å, b = 10.6132(2) Å, c = 25.5990(7) Å, V = 2096.12(11) Å3, Z = 4, Rgt(F) = 0.0579, wRref(F2) = 0.1216, T = 293 K.

CCDC no.: 2220806

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal: Colourless prism
Size: 0.15 × 0.08 × 0.06 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 1.60 mm−1
Diffractometer, scan mode: Xcalibur, ω
θmax, completeness: 75.5°, >99%
N(hkl)measured, N(hkl)unique, Rint: 11,877, 4126, 0.092
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 2199
N(param)refined: 255
Programs: CrysAlisPRO [1], SHELX [2, 3], WinGX/ORTEP [4]
Table 2:

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

Atom x y z Uiso*/Ueq
S1 0.1081 (3) 0.11839 (14) 0.50448 (7) 0.0644 (5)
O1 0.1475 (5) 0.3490 (3) 0.54356 (13) 0.0435 (11)
O2 0.6704 (7) 0.4683 (5) 0.2698 (2) 0.0857 (18)
O3 0.7237 (6) 0.2641 (4) 0.28874 (18) 0.0669 (14)
N1 0.0822 (7) 0.3523 (4) 0.46190 (17) 0.0432 (13)
N2 0.1013 (7) 0.4778 (4) 0.47689 (17) 0.0456 (13)
N3 0.1571 (7) 0.3257 (4) 0.36927 (17) 0.0448 (13)
N4 0.4768 (7) 0.3520 (5) 0.31556 (19) 0.0529 (14)
C1 0.1114 (8) 0.2735 (5) 0.5010 (2) 0.0457 (15)
C2 0.1381 (8) 0.4717 (5) 0.5254 (2) 0.0400 (15)
C3 0.1660 (9) 0.5765 (5) 0.5633 (2) 0.0430 (16)
C4 0.2404 (9) 0.6903 (5) 0.5339 (2) 0.0552 (18)
H4A 0.161796 0.715283 0.506199 0.066*
H4B 0.350728 0.668022 0.518220 0.066*
C5 −0.0089 (9) 0.6138 (5) 0.5865 (2) 0.0537 (17)
H5A −0.058813 0.542338 0.604743 0.064*
H5B −0.087601 0.637966 0.558710 0.064*
C6 0.2892 (9) 0.5392 (5) 0.6073 (2) 0.0587 (19)
H6A 0.401035 0.516182 0.592842 0.070*
H6B 0.243153 0.466755 0.625773 0.070*
C7 0.2658 (10) 0.8012 (6) 0.5726 (2) 0.065 (2)
H7 0.314267 0.873748 0.553936 0.078*
C8 0.0893 (10) 0.8362 (5) 0.5950 (2) 0.066 (2)
H8A 0.011529 0.859965 0.566865 0.079*
H8B 0.101189 0.907683 0.618311 0.079*
C9 0.0140 (10) 0.7244 (6) 0.6247 (3) 0.064 (2)
H9 −0.098563 0.747531 0.639595 0.077*
C10 0.1367 (10) 0.6851 (6) 0.6681 (2) 0.073 (2)
H10A 0.151016 0.754043 0.692656 0.088*
H10B 0.088607 0.613787 0.686872 0.088*
C11 0.3109 (11) 0.6497 (6) 0.6452 (3) 0.066 (2)
H11 0.389491 0.624909 0.673485 0.080*
C12 0.3879 (9) 0.7628 (6) 0.6160 (3) 0.073 (2)
H12A 0.404221 0.832555 0.639964 0.088*
H12B 0.499828 0.740318 0.601500 0.088*
C13 0.0261 (8) 0.3221 (5) 0.4087 (2) 0.0498 (17)
H13A −0.024324 0.238347 0.408910 0.060*
H13B −0.064828 0.380629 0.398907 0.060*
C14 0.2987 (8) 0.2351 (5) 0.3778 (2) 0.0508 (17)
H14A 0.250556 0.152735 0.385552 0.061*
H14B 0.367874 0.261554 0.407432 0.061*
C15 0.4125 (9) 0.2265 (5) 0.3296 (2) 0.0567 (19)
H15A 0.509597 0.170853 0.336447 0.068*
H15B 0.346406 0.191791 0.300770 0.068*
C16 0.2283 (9) 0.4503 (6) 0.3588 (2) 0.0539 (18)
H16A 0.296960 0.477898 0.388362 0.065*
H16B 0.134614 0.509982 0.353791 0.065*
C17 0.3405 (9) 0.4466 (6) 0.3103 (2) 0.0575 (19)
H17A 0.269224 0.427038 0.280196 0.069*
H17B 0.392417 0.528749 0.304798 0.069*
C18 0.6274 (10) 0.3705 (7) 0.2896 (2) 0.0591 (19)
C19 0.8821 (9) 0.2727 (7) 0.2597 (3) 0.074 (2)
H19A 0.954220 0.339919 0.273370 0.088*
H19B 0.858286 0.289490 0.223196 0.088*
C20 0.9707 (9) 0.1484 (6) 0.2658 (3) 0.079 (2)
H20A 1.078741 0.149615 0.247265 0.119*
H20B 0.898099 0.082937 0.251960 0.119*
H20C 0.992039 0.132635 0.302201 0.119*

Source of material

37% Formaldehyde solution (1.5 mL) and ethyl piperazine-1-carboxylate (1.58 g, 0.01 mole) were added to a solution of 5-(adamantan-1-yl)-1,3,4-oxadiazole-2(3H)-thione [5] (2.36 g, 0.01 mol), in ethanol (15 mL) and the mixture was stirred for 2 h at 298 K (room temperature) and allowed to stand overnight. Cold water (5 mL) was drop-wisely added with continuous stirring for an additional 30 min. at room temperature. The precipitated crude product was filtered, washed with cold water, dried and crystallised from EtOH/H2O to yield 3.09 g (76%) of the title compound as colourless prisms. Melting point: 391–393 K (uncorrected). IR, ν (cm−1): 1246 (C–O–C), 1362 (C=S), 1607, 1455 (C=N), 1692 (C=O), 2855, 2925, 2995 (CH3, CH2, CH). 1 H NMR (250 MHz, CDCl3): δ 4.99 (2H, NCH2N, s), 4.11 (CH2CH3, 2H, q), 3.49 (Piperazine-H, 4H, t), 2.77 (Piperazine-H, 4H, t), 2.11 (Adamantane-H, 3H, s), 1.99 (Adamantane-H, 6H, s), 1.74 (Adamantane-H, 6H, q), 1.25 (CH3, 3H, t). 13 C NMR (62.9 MHz, CDCl3): δ 178.56 (C=S), 167.96 (C=N), 155.41 (C=O), 70.01 (NCH2N), 61.45, 50.08 (Piperazine-C), 43.20 (CH2CH3), 39.09, 36.08, 34.40, 27.45 (Adamantane-C), 14.65 (CH3). Slow evaporation of a C2H5OH:CHCl3 (2:1, v/v) solution of the compound at room temperature afforded suitable single crystals which were used for the X-ray diffraction study.

Experimental details

The C-bound H atoms were geometrically placed (C–H = 0.96–0.98 Å) and refined as riding with Uiso(H) = 1.2–1.5Ueq(C). The sample was refined as a two-component inversion twin.

Comment

The 1,3,4-oxadiazole nucleus comprises the core pharmacophore of several bioactive compounds [6, 7] with marked chemotherapeutic properties such as antineoplastic [8] and anti-microbial [9] activities. Furthermore, adamantane-containing compounds have long been recognised for their chemotherapeutic activities, such as anti-viral, anti-bacterial and antineoplastic activities [10, 11]. Thus, the title oxadiazole/adamantane hybrid compound, (I), was studied in this context.

The molecular structure of (I) is shown in the figure (35% probability ellipsoids). The central 1,3,4-oxadiazolyl-2-thione ring is substituted at the N1-position by a methylene substituent bearing a ethyl piperazine-1-carboxylate group, and at the C2-position by a adamantanyl group. The five-membered ring is strictly planar with a r.m.s. deviation of the fitted atoms being 0.0051 Å; the maximum deviation from the least-squares plane is 0.007(4) Å for atom N1. The attached atoms, i.e. S1, C3 and C13. lie −0.010(9), 0.053(11) and 0.102(10) Å out of the plane, respectively. When the molecule of (I) is viewed side-on in line with the plane through the five-membered ring, the adamantyl atoms C5, C8, C9 and C10 clearly lie to one side of the plane, and the ethyl piperazine-1-carboxylate group to the other side. Within the central ring, the short C2–N2 bond length [1.275(6) Å] is indicative of significant double-bond character compared with C1–N1 [1.323(7) Å]. The N1–N2 [1.394(6) Å] as well as the experimentally equivalent C1–O1 and C2–O1 [1.381(6) & 1.385(6) Å] bond lengths are all consistent with limited delocalisation of π-electron density within the ring; the C1=S1 bond length is 1.649(5) Å.

While there are several examples of crystal structures where a central 1,3,4-oxadiazolyl-2-thione ring is substituted at the N1- and C2-positions, e.g. with (4-phenylpiperazin-1-yl)methylene and 2-thienyl groups [12], there is also a very closely related example bearing (4-phenylpiperazin-1-yl)methylene and adamantyl substituents [13]. In the latter, a very similar molecular conformation is found except the adamantyl substituent is disposed evenly about the plane through the central residue. Also, the bond lengths within the five-membered ring resembles closely those in (I), most notably the double-bond character of the C2–N2 bond [1.288(7) Å].

The molecular packing in the crystal of (I) is largely devoid of directional interactions. Side-on contacts between the thione-S1 atom approaching either side of the five-membered ring are apparent [C1=S1⋯Cg(O1,N1,N2,C1,C2) i : S1⋯Cg(O1,N1,N2,C1,C2) i  = 3.799(3) Å with angle at S1 = 91.3(2)° and C1=S1⋯Cg(O1,N1,N2,C1,C2) ii : S1⋯Cg(O1,N1,N2,C1,C2) ii  = 3.923(3) Å with angle at S1 = 89.5(2)° for symmetry operations (i) −1/2 + x, 1/2 − y, 1 − z and (ii) 1/2 + x, 1/2 − y, 1 − z]. Thus, the S1 atom bridges two rings. These contacts feature within a flat, supramolecular tape along the a-axis. The connections between the tapes within the three-dimensional architecture are close H⋯H contacts [C17–H17a⋯H20b iii –C20 iii  = 2.25 Å with angles at H17a and H20 of 117 and 179°, respectively, for (iii) 1 − x, 1/2 + y, 1/2 − z]. Globally, when viewed down the a-axis, the molecules are arranged to define columns in which reside the adamantanyl groups.

A further analysis of the molecular packing was conducted with the aid of the calculation of the Hirshfeld surfaces and fingerprint plots [14, 15]. As anticipated for molecules bearing adamantyl residues [16], there is a clear dominance of contacts involving H. In the present case, interactions involving H contribute 97.2% to the overall surface, i.e. 68.6% [H⋯H], 13.1% [O⋯H/H⋯O], 9.5% [S⋯H/H⋯S], 3.6% [N⋯H/H⋯N] and 2.4% [C⋯H/H⋯C]. The next most notable contribution is 1.2% for S⋯N/N⋯S contacts. The presence of a close H⋯H contact referred to above is evidenced by a pair of symmetric peaks at d i  + d e at ca 2.22 Å.


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

Funding source: Deanship of Scientific Research at Jouf University

Award Identifier / Grant number: DSR-2021-01-03116

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

  2. Research funding: Deanship of Scientific Research at Jouf University under grant no. DSR-2021-01-03116.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2022-11-20
Accepted: 2023-01-10
Published Online: 2023-02-17
Published in Print: 2023-04-25

© 2022 the author(s), published by De Gruyter, Berlin/Boston

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

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  46. Crystal structure of 1-(2-iodobenzoyl)-6-methoxy-1H-indole-3-carbaldehyde, C17H12INO3
  47. Crystal structure of bis(acridinium) tetrabromidomanganate(II), C26H20Br4MnN2
  48. The crystal structure of 6,6′-((1E,1′E)-hydrazine-1,2-diylidenebis(methanylylidene)) bis(2-(tert-butyl)phenol), C22H28N2O2
  49. The crystal structure of the cocrystal di-μ2-chlorido-tetramethyl-tetraphenyl-di-μ3-oxido-dichloridotetratin(IV) – diphenyl-methyl-chloridotin(IV)(1/2), C54H58Cl6O2Sn6
  50. Crystal structure of (3a7R,13bR)-3-((1R)-1-hydroxy-1-(5-methyl-6-oxo-3,6-dihydro-2H-pyran-2-yl)ethyl)-3a,11,11,13b-tetramethyl-2,3,3a,4,5,11,11a,12,13,13b-decahydroindeno[5′,4′:4,5] cyclohepta[1,2-c]oxepin-9(1H)-one, C30H40O5
  51. Crystal structure of 1-(4-methoxyphenyl)-2-phenoxyethan-1-one, C15H14O3
  52. Crystal structure of trans-tetrakis(3-phenylpyridine-κN)bis(thiocyanato-κN)nickel(II), C46H36N6NiS2
  53. Crystal structure of sodium catena-poly[bis(thiourea-κ1S)-tetrakis(μ2-thiourea-κ2S,S)tricopper(I)] difumarate, C14H29Cu3N12NaO8S6
  54. Crystal structure of bis(benzylamine-κ1N)-bis((E)-2-methyl-3-phenylacrylato-κ1O)copper(II), C34H36CuN2O4
  55. The crystal structure of 3,4-dihydroxybenzoic acid – 3-[7-{[2-(3,4-difluorophenyl)cyclopropyl]amino}-5-(propylsulfanyl)-3H-[1,2,3] triazolo[4,5-d]pyrimidin-3-yl]-5-(2-hydroxyethoxy)cyclopentane-1,2-diol – water (1/1/1), C30H36F2N6O9S
  56. Crystal structure of catena-poly[dipyridine-bis(pyridine-2-carboxylato-κ 2 N,O)-bis(μ 2-pyridine-2-carboxylato-κ 2 N,O)-dinickel(II)], C34H26N6Ni2O8
  57. The crystal structure of 1-((1-methyl-1H-1,2,4-triazol-3-yl) methyl)-3-(2,4,5-trifluorobenzyl)-1,3,5-triazinane-2,4,6-trione, C14H11F3N6O3
  58. Crystal structure of (E)-2-((Z)-2-((1S,4R)-3,3-dimethylbicyclo[2.2.1] heptan-2-ylidene)ethylidene)hydrazine-1-carbothioamide, C24H38N6S2
  59. Crystal structure of photochromic 3-(5-(2,5-dimethylthiophen-3-yl)-2,2,3,3,4,4-hexafluorocyclopentyl)-2-methylbenzo[b]-thiophene, C20H14F6S2
  60. Crystal structure of bis(2,5,5,7-tetramethyl-1,4-diazepane-1,4-diium) diaqua-bis(1,2-diaminopropane)copper(II) bis(μ6-oxido)tetrakis(μ3-oxido)-tetradecakis(μ2-oxido)-octaoxido-decavanadium(V) – water (1/4), C24H76CuN8V10O34
  61. Crystal structure of 1,2,3,5,13-pentamethoxy-6,7-dimethyl-1,2,3,4,4a,5,6,7,8,13b-decahydrobenzo[3′,4′]cycloocta[1′,2′:4,5]benzo[1,2-d][1,3]dioxole, C24H30O7
  62. Crystal structure of bis(6-carboxyhexyl)-4,4′-bipyridinium dibromide – 2,6-dihydroxynaphthalene (1/2), C42H46Br2N2O8
  63. Crystal structure of methyl 2-(2-chloroacetyl)-1-(4-(methoxycarbonyl)phenyl)-2,3,4,9-tetrahydro-1H-pyrido[3,4-b] indole-3-carboxylate, C23H21ClN2O5
  64. Crystal structure of bis(dimethylammonium) poly[{μ4-1,1ʹ-(1,4-phenylenebis(methylene))bis(1H-pyrazole-3,5-dicarboxylato)-κ6N4O2}zinc(II)], C22H26N6O8Zn
  65. Crystal structure of 2-(2-(4-methoxyphenyl)-2H-indazol-3-yl)acetonitrile, C16H13N3O
  66. Crystal structure of (E)-7-methoxy-2-(4-morpholinobenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H23NO3
  67. The crystal structure of N′1,N′2-bis((E)-3-(tert-butyl)-2-hydroxybenzylidene)oxalohydrazide, C24H30N4O4
  68. The crystal structure of trimethyl 2,2′,2′′-(benzene-1,3,5-triyltris(oxy))triacetate, C15H18O9
  69. Crystal structure of bis(N,N-dimethylformamide-κO)-bis(pyridine-2-carboxylato-κ2N,O)-bis(μ2-pyridine-2-carboxylato-κ2N,O)-dinickel(II), C30H30N6Ni2O10
  70. Crystal structure of bis(μ2-1-pyrenecarboxylato-κ3O,O′:O′)-bis(1-pyrenecarboxylato-κ2O,O′)-(benzimidazole-κ1N)dicadmium(II), C82H48Cd2N4O8
  71. One-pot synthesis and crystal structure of diethyl 2,6-dimethyl-4-(1-(2-nitrophenyl)-1H-1,2,3-triazol-4-yl)-1,4-dihydropyridine-3,5-dicarboxylate, C21H23N5O6
  72. The crystal structure of 1-(2-fluorobenzoyl)-5-methoxy-2-methyl-1H-indole-3-carbonitrile, C18H13FN2O2
  73. Crystal structure of bis(trimethylphenylammonium) aqua-oxido-octathiotritungstate, (Me3PhN)2[W3OS8(H2O)]
  74. The crystal structure of trichlorido[N-[(2-oxyphenyl)methylidene]phenylglycinemethylester-κ3O,N,O′]-tin(IV) – methylene chloride (1/1), C16H14Cl3NO3Sn·CH2Cl2
  75. The crystal structure of furan-2,5-diylbis((4-chlorophenyl)methanol), C18H14Cl2O3
  76. The crystal structure of hexalithium decavanadate hexadecahydrate, H32Li6O44V10
  77. Crystal structure of ethyl 4-{[5-(adamantan-1-yl)-2-sulfanylidene-2,3-dihydro-1,3,4-oxadiazol-3-yl]methyl}piperazine-1-carboxylate, C20H30N4O3S
  78. Crystal structure of aqua(μ2-2,2′,2″-((nitrilo)tris(ethane-2,1-diyl(nitrilo)methylylidene))tris (6-ethoxyphenolato))(pentane-2,4-dionato-κ2O,O′)-dinickel(II), C38H48N4Ni2O9
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