Home Crystal structure of 2-({[5-(adamantan-2-yl)-2-sulfanylidene-1,3,4-oxadiazolidin-3-yl]methyl}amino)benzonitrile, C20H22N4OS
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Crystal structure of 2-({[5-(adamantan-2-yl)-2-sulfanylidene-1,3,4-oxadiazolidin-3-yl]methyl}amino)benzonitrile, C20H22N4OS

  • Lamya H. Al-Wahaibi , Olivier Blacque , Nora H. Al-Shaalan , Edward R. T. Tiekink and Ali A. El-Emam ORCID logo EMAIL logo
Published/Copyright: December 19, 2022

Abstract

C20H22N4OS, triclinic, P 1 (no. 2), a = 6.8528(3) Å, b = 11.3498(5) Å, c = 13.3896(9) Å, α = 114.083(5)°, β = 104.326(4)°, γ = 90.369(3)°, V = 914.38(9) Å3, Z = 2, R gt (F) = 0.0844, wR ref (F2) = 0.2217, T = 160 K.

CCDC no.: 2216322

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 plate
Size: 0.19 × 0.10 × 0.02 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 1.70 mm−1
Diffractometer, scan mode: XtaLAB Synergy, ω
θmax, completeness: 74.6°, >99%
N(hkl)measured, N(hkl)unique, Rint: 24,423, 24,423
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 19,275
N(param)refined: 239
Programs: CrysAlisPRO [1], Shelx [2, 3], Olex2 [4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.3603 (6) 0.8333 (3) 0.6742 (3) 0.0283 (8)
C2 0.5068 (6) 0.7458 (3) 0.6457 (3) 0.0278 (8)
C3 0.5088 (7) 0.6359 (4) 0.6694 (4) 0.0350 (10)
H3 0.410156 0.619318 0.702435 0.042*
C4 0.6509 (8) 0.5528 (4) 0.6455 (4) 0.0372 (10)
H4 0.652854 0.479596 0.662962 0.045*
C5 0.7932 (7) 0.5761 (3) 0.5951 (4) 0.0340 (9)
H5 0.892182 0.518273 0.578294 0.041*
C6 0.7923 (6) 0.6827 (3) 0.5691 (3) 0.0292 (8)
H6 0.888634 0.696007 0.533294 0.035*
C7 0.6515 (6) 0.7703 (3) 0.5950 (3) 0.0248 (8)
C8 0.7895 (6) 0.9163 (3) 0.5261 (3) 0.0254 (8)
H8A 0.925414 0.896205 0.556915 0.031*
H8B 0.798008 1.011363 0.549199 0.031*
C9 0.8366 (6) 0.7691 (3) 0.3337 (3) 0.0233 (8)
C10 0.5462 (6) 0.7960 (3) 0.2346 (3) 0.0243 (8)
C11 0.3895 (6) 0.7742 (3) 0.1280 (3) 0.0235 (7)
C12 0.3016 (6) 0.6287 (3) 0.0660 (3) 0.0263 (8)
H12A 0.412221 0.574220 0.050279 0.032*
H12B 0.237979 0.604900 0.115127 0.032*
C13 0.1439 (6) 0.6038 (3) −0.0454 (3) 0.0293 (8)
H13 0.088109 0.509684 −0.085046 0.035*
C14 0.2442 (7) 0.6392 (4) −0.1220 (3) 0.0322 (9)
H14A 0.355671 0.585673 −0.138316 0.039*
H14B 0.143235 0.621426 −0.195166 0.039*
C15 0.3283 (7) 0.7839 (4) −0.0614 (4) 0.0307 (9)
H15 0.392055 0.807313 −0.111492 0.037*
C16 0.4882 (6) 0.8091 (3) 0.0495 (3) 0.0272 (8)
H16A 0.546063 0.901778 0.088068 0.033*
H16B 0.599666 0.755638 0.033004 0.033*
C17 0.1557 (7) 0.8665 (4) −0.0363 (4) 0.0339 (9)
H17A 0.052801 0.850609 −0.108288 0.041*
H17B 0.209495 0.959864 0.001956 0.041*
C18 0.0579 (6) 0.8306 (4) 0.0408 (4) 0.0310 (9)
H18 −0.054954 0.884468 0.057081 0.037*
C19 0.2158 (6) 0.8569 (3) 0.1524 (3) 0.0267 (8)
H19A 0.152323 0.835019 0.202494 0.032*
H19B 0.269868 0.950240 0.191907 0.032*
C20 −0.0282 (6) 0.6860 (4) −0.0208 (4) 0.0321 (9)
H20A −0.094507 0.662140 0.027267 0.038*
H20B −0.131178 0.669578 −0.093000 0.038*
N1 0.2453 (6) 0.9064 (3) 0.6983 (3) 0.0366 (8)
N2 0.6479 (5) 0.8798 (3) 0.5738 (3) 0.0275 (7)
H2 0.566 (6) 0.934 (3) 0.598 (4) 0.031 (11)*
N3 0.7322 (5) 0.8487 (3) 0.4011 (3) 0.0233 (7)
N4 0.5488 (5) 0.8661 (3) 0.3387 (3) 0.0242 (7)
O1 0.7161 (4) 0.7336 (2) 0.2254 (2) 0.0262 (6)
S1 1.06010 (15) 0.71962 (8) 0.36407 (9) 0.0295 (3)

Source of material

2–Aminobenzonitrile (0.59 g, 5.0 mmol) and 37% formaldehyde solution (0.5 mL) were added to a solution of 5-(adamantan-1-yl)-1,3,4-oxadiazole-2(3H)-thione [5] (1.18 g, 0.5 mmol) in ethanol (10 mL). The mixture was stirred at room temperature for 2 h and allowed to stand overnight. The precipitated crude product was filtered, washed with water, dried and crystallized from aqueous ethanol to yield 1.37 g (75%) of the title compound as colourless plates. M.pt: 447–449 K (uncorrected). IR ν (cm−1): 3374 (NH), 3021 (aromatic CH), 2911, 2850 (aliphatic CH), 2210 (CN), 1266 (C–O–C). 1 H NMR (CDCl3, 250 MHz): δ 1.72 (q, 6H, adamantane–H), 1.96 (s, 6H, adamantane–H), 2.10 (s, 3H, adamantane–H), 5.50 (d, 2H, NCH2N), 5.77 (t, 1H, NH), 6.86 (t, 1H, Ar–H), 7.31 (d, 1H, Ar–H), 7.47–7.51 (m, 2H, Ar–H). 13 C NMR (CDCl3, 62.9 MHz): δ 27.41, 34.55, 36.03, 39.02 (adamantane–C), 56.94 (NCH2N), 97.77 (CN), 112.72, 117.13, 119.35, 132.94. 134.50, 147.06 (Ar–C), 168.66 (oxadiazole C5), 176.94 (C=S). EI–MS m/z (Rel. Int.): 366 (M+, 8), 236 (100), 176 (29), 135 (97), 131 (58), 102 (42). Suitable single crystals for X-ray diffraction were obtained by slow evaporation of a solution of the title compound in ethanol:chloroform (1:1, v/v) held at room temperature.

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 N-bound H atom was located in a difference map and refined with N–H = 0.87 ± 0.01 Å. The crystal was refined as a two-component twin. The diffraction intensities were integrated according to a merohedral twin law: component two is rotated by 180° around [0.00 −0.00 1.00] in reciprocal space or [0.40 0.40 0.82] in direct space with respect to component one. The maximum and minimum residual electron density peaks of 1.29 and 0.29 e Å−3, respectively, were located 0.02 and 0.90 Å from the S1 and C8 atoms, respectively.

Comment

Adamantane derivatives have long been known for their diverse chemotherapeutic activities [6], [7], [8]. In addition, the 1,3,4-oxadiazole heterocycle represents an important scaffold in many chemotherapeutic agents [9, 10]. It was in this context that the title hybrid adamantanyl/oxadiazolidin-3-yl derivative, 1, was synthesised and its crystal and molecular structures studied.

The molecular structure of 1 is shown in the upper view of the figure (50% probability ellipsoids). The molecule is constructed about a strictly planar oxadiazolidin-3-yl ring appended at the N3 position by the methylene-bound substituent and at the C10 position by the adamantan-2-yl group. The substituted phenyl ring occupies a position almost perpendicular to the five-membered ring [dihedral angle = 72.2(2)°] so the molecule has the shape of the letter L. The amine–N–H and phenyl-nitrile groups project to the same side of the molecule as does the non-substituted ring-nitrogen atom. Within the five-membered ring, the short C10–N4 bond length [1.288(5) Å] as well as standard C9–N3 [1.343(5) Å] and C9, C10–O1 [1.368(5) & 1.373(5) Å] bond lengths are suggestive of limited delocalisation of π-electron density over ring.

There are five literature precedents for 1. Referring to the overlay diagram shown in the lower view of the figure, the molecule of 1 is shown in red; the molecules have been overlapped so the S, O and unsubstituted N atoms of the oxadiazolidin-3-yl fragment are coincident. The parent compound [11; aquamarine] and 4-fluorophenyl [12; pink], 4-chlorophenyl [13; yellow], 2-trifluoromethyl [14; black] and recently reported 4-trifluoromethyl [15; two independent molecules: green and blue] derivatives present very similar structural features with the exception of the relative orientations of the five- and six-membered rings. For example, the dihedral angle between the rings in the parent molecule, 2-trifluoromethyl derivative and 1 are 50.26(7), 66.80(6) and 72.2(2)°, respectively.

The most prominent intermolecular contact in the crystal of 1 is an amine–N–H…N(oxadiazolidin-3-yl) hydrogen bond [N2–H2…N4 i : H2…N4 i  = 2.30(4) Å, N2…N4 i  = 3.095(5) Å with angle at H2 = 156(4)° for symmetry operation (i): 1 − x, 2 − y, 1 − z] within a centrosymmetric aggregate and leading to a 10-membered synthon with the shape of an extended chair. The dimeric aggregates stack in columns along the a-axis with methylene–C–H…N(nitrile) [C8–H8a…N1 ii : H8a…N1 ii  = 2.48 Å, C8…N1 ii  = 3.426(6) Å with angle at H8a = 159° for (ii) 1 + x, y, z] and methylene–C–H…S(thione) [C8–H8b…S1 iii : H8b…S1 ii  = 2.85 Å, C8…S1 ii  = 3.813(4) Å with angle at H8b = 164° for (iii) 2 − x, 2 − y, 1 − z] contacts between them. Columns are connected into layers in the ab-plane by π(phenyl)…π(phenyl) [Cg(C2–C7)…Cg(C2–C7) iv  = 3.865(2) Å; slippage = 1.76 Å for (iv): 1 − x, 2 − y, 1 − z] contacts between centrosymmetrically related rings. The adamantan-2-yl groups project to either side of the supramolecular layer and inter-digitate along the c-axis with neighbouring layers.


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 Princess Nourah bint Abdulrahman University through the Research Group Program

Award Identifier / Grant number: RGP-1442-0010-5

  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 Princess Nourah bint Abdulrahman University through the Research Group Program (Grant No. RGP-1442-0010-5).

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

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Received: 2022-11-02
Accepted: 2022-12-05
Published Online: 2022-12-19
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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  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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