Startseite Crystal structure of 2-(adamantan-1-yl)-5-(3,5-dinitrophenyl)-1,3,4-oxadiazole, C18H18N4O5
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Crystal structure of 2-(adamantan-1-yl)-5-(3,5-dinitrophenyl)-1,3,4-oxadiazole, C18H18N4O5

  • Lamya H. Al-Wahaibi , Olivier Blacque , Edward R. T. Tiekink und Ali A. El-Emam ORCID logo EMAIL logo
Veröffentlicht/Copyright: 5. Juli 2022

Abstract

C18H18N4O5, monoclinic, P21/c (no. 14), a = 11.7553(8) Å, b = 6.4876(4) Å, c = 22.3442(15) Å, β = 91.263(7)°, V = 1703.64(19) Å3, Z = 4, Rgt (F) = 0.0531, wRref (F 2) = 0.1376, T = 160 K.

CCDC no.: 2173380

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 plate
Size: 0.12 × 0.07 × 0.01 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.90 mm−1
Diffractometer, scan mode: XtaLAB Synergy, ω
θ max, completeness: 74.6°, >99%
N(hkl)measured, N(hkl)unique, R int: 6232, 6232
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 4033
N(param)refined: 245
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 U iso*/U eq
C1 0.8577 (2) 0.7819 (4) 0.69232 (10) 0.0333 (6)
C2 0.8024 (2) 0.9481 (4) 0.71731 (10) 0.0353 (6)
H2 0.842743 1.053385 0.738362 0.042*
C3 0.6859 (2) 0.9527 (4) 0.71004 (10) 0.0323 (5)
C4 0.6242 (2) 0.8020 (4) 0.68018 (10) 0.0324 (5)
H4 0.543881 0.812750 0.675324 0.039*
C5 0.6827 (2) 0.6341 (4) 0.65740 (10) 0.0325 (6)
C6 0.8009 (2) 0.6237 (4) 0.66345 (10) 0.0340 (6)
H6 0.841465 0.509658 0.647932 0.041*
C7 0.6221 (2) 0.4643 (4) 0.62800 (10) 0.0317 (5)
C8 0.4828 (2) 0.2888 (4) 0.59284 (10) 0.0330 (6)
C9 0.3623 (2) 0.2453 (4) 0.57540 (11) 0.0328 (6)
C10 0.2827 (2) 0.2846 (5) 0.62800 (11) 0.0385 (6)
H10A 0.304942 0.195270 0.662224 0.046*
H10B 0.289245 0.430014 0.641056 0.046*
C11 0.1596 (3) 0.2382 (5) 0.60835 (12) 0.0418 (6)
H11 0.108048 0.262139 0.642671 0.050*
C12 0.1254 (3) 0.3810 (5) 0.55639 (12) 0.0422 (6)
H12A 0.045432 0.353884 0.543939 0.051*
H12B 0.131343 0.526470 0.569435 0.051*
C13 0.2035 (3) 0.3437 (5) 0.50361 (11) 0.0392 (6)
H13 0.180847 0.436678 0.469698 0.047*
C14 0.3271 (2) 0.3877 (4) 0.52273 (11) 0.0371 (6)
H14A 0.334896 0.533664 0.535099 0.045*
H14B 0.377670 0.363704 0.488570 0.045*
C15 0.1504 (3) 0.0140 (5) 0.58816 (13) 0.0456 (7)
H15A 0.172820 −0.078254 0.621692 0.055*
H15B 0.070632 −0.017583 0.576332 0.055*
C16 0.2277 (3) −0.0235 (5) 0.53526 (12) 0.0424 (6)
H16 0.220315 −0.170242 0.521993 0.051*
C17 0.3513 (3) 0.0192 (4) 0.55500 (12) 0.0381 (6)
H17A 0.402608 −0.006822 0.521266 0.046*
H17B 0.373608 −0.073891 0.588344 0.046*
C18 0.1941 (3) 0.1192 (5) 0.48338 (12) 0.0434 (7)
H18A 0.244738 0.094967 0.449281 0.052*
H18B 0.114952 0.089406 0.469918 0.052*
N1 0.9822 (2) 0.7726 (4) 0.69664 (9) 0.0386 (5)
N2 0.6232 (2) 1.1268 (4) 0.73577 (9) 0.0366 (5)
N3 0.6651 (2) 0.2948 (4) 0.60817 (9) 0.0364 (5)
N4 0.5728 (2) 0.1799 (4) 0.58514 (9) 0.0361 (5)
O1 1.03085 (17) 0.6403 (3) 0.66813 (8) 0.0434 (5)
O2 1.0322 (2) 0.8980 (4) 0.72841 (11) 0.0627 (7)
O3 0.6754 (2) 1.2451 (4) 0.76899 (10) 0.0551 (6)
O4 0.52210 (17) 1.1428 (3) 0.72273 (8) 0.0429 (5)
O5 0.50776 (16) 0.4750 (3) 0.62007 (7) 0.0334 (4)

Source of material

A mixture of adamantane-1-carboxylic acid (1.8 g, 0.01 mol), 3,5-dinitrobenzoyl chloride (2.3 g, 0.01 mol) and phosphorus oxychloride (8 mL) was heated under reflux for 1 h. On cooling, crushed ice (50 g) was added cautiously and the mixture stirred for 30 min. The precipitated crude product was filtered, washed with saturated sodium hydrogen carbonate solution and finally with water, dried and crystallised from ethanol to yield 3.41 g (92%) of the title compound (I) as colourless plates. M.pt.: 473–475 K (uncorrected). Anal. Calcd. for C18H18N4O5: C, 58.37; H, 4.90; N, 15.13%. Found: C, 58.33; H, 4.92; N, 15.09%. 1 H NMR (DMSO-d6, 700.17 MHz): δ 1.80–1.82 (m, 6H, Adamantane–H), 2.01–2.13 (m, 9H, Adamantane–H), 8.99 (s, 1H, Ar–H), 9.02 (s, 2H, Ar–H). 13 C{1 H} NMR (DMSO-d6, 176.08 MHz): δ 27.61, 34.53, 36.12, 39.63 (Adamantane–C), 121.34, 126.82, 126.86, 149.21 (Ar–C), 161.55, 173.81 (Oxadiazole–C). Single crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution of (I) in EtOH/CHCl3 (1:1) 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 Uiso (H) = 1.2Ueq (C). The crystal was refined as a twin with a 180° rotation about [0 0 1]; the major component of the twin was refined to 0.5597(14).

Comment

Adamantane-containing derivatives were recognized early for their diverse chemotherapeutic properties and several adamantane derivatives are currently used in efficient therapies as anti-viral, anti-cancer and anti-microbial agents [5, 6]. On the other hand, the 1,3,4-oxadiazole heterocycle represents the core pharmacophore of several marketed drugs [7, 8]. In the present study, the crystal structure of an adamantane-1,3,4-oxadiazole hybrid molecule, (I), is described and its features compared to literature precedents [9], [10], [11], [12], [13], [14].

The molecular structure of (I) is shown in Figure (50% probability ellipsoids). The molecule comprises a central 1,3,4-oxadiazole ring connected at the C1-position to an adamantan-1-yl residue and at the C2-position to a 3,5-dinitrophenyl ring. Within the ring, the C7–N3 [1.292(4) Å] and C8–N4 [1.287(4) Å] bond lengths are consistent with substantial double-bond character with the N3–N4 bond length being 1.405(3) Å. The small elongation and shortening of the C–N and N–N bonds from their standard values is indicative of delocalisation of π-electron density in the ring; the r.m.s. deviation of the five atoms comprising the ring is 0.002 Å, consistent with strict planarity. The substituted phenyl ring forms a dihedral angle of 4.73(13)° with the five-membered ring. The N1- and N2-nitro groups are twisted out of the phenyl ring they are connected to, as seen in the dihedral angles between the respective least-squares planes of 9.38(12)° and 9.94(16)°. The dihedral angle between the nitro substituents [10.3(3)°] is indicative of a conrotatory relationship.

There are five literature precedents for (I) which differ only in the nature of the phenyl-bound substituents. These are the 4-fluoro [9], 4-chloro [9], 4-bromo [10], 4-nitro [11] and 3-fluoro [12] derivatives. The molecules adopt approximately the same conformations to that seen in (I) but with a range of nearly 21° in the dihedral angles formed between the five- and six-membered rings. Thus, for the 4-substituted molecules, the dihedral angles are 20.79(15)°, 9.48(7)°, 10.41(5)° and 0° [the molecule is bisected by a mirror plane], respectively. For the two independent molecules comprising the asymmetric-unit of the 3-fluoro species, the independent dihedral angles are 3.0(3)° and 3.3(3)°. Two other molecules worthy of mention are those where the adamantan-1-yl residue of (I) is substituted by a second 3,5-dinitrophenyl substituent [13] and a 2-(4-chlorophenyl)-1H-1,3-benzodiazole [14]. The bond lengths in the 1,3,4-oxadiazole ring of both structures match those noted for (I).

In the molecular packing of (I), helical chains along the 21-screw axis along the b-direction feature phenyl–C–H⃛O(nitro) contacts [C2–H2⃛O1i: H6⃛O2i = 2.60 Å, C6⃛O2i = 3.425(3) Å with angle at H6 = 146° for symmetry operation i: 2 − x, 1/2 + y, 3/2 − z]. Within the individual stacks comprising the chain, there are additional nitro-O⃛π(oxadiazole) interactions whereby the nitro-group is approximately parallel to a translationally related five-membered ring, forming a dihedral angle of 12.2(2)° [O4⃛Cg(oxadiazole)ii = 2.955(2) Å with angle at O4 = 92.42(14)° for ii: x, −1 + y, z]. Centrosymmetrically related helical chains are connected into a double layer by methylene–C—H⃛π(oxadiazole) interactions [C14–H14b⃛Cg(oxadiazole)iii = 2.94° with angle at H10 = 126° for iii: 1 − x, 1 − y, 1 − z]. The layers stack along the c-axis without directional interactions between them.

Given all of the specified interactions identified from a geometric-based analysis of the molecular packing are relatively weak. It was thought worthwhile to conduct a complimentary analysis of the calculated Hirshfeld surfaces, encompassing the full and decomposed two-dimensional fingerprint plots, employing Crystal Explorer 17.5 [15] and following established procedures [16]. Despite their being only one H⃛O contact less than the sum of the van der Waals radii, O⃛H/H⃛O contacts make up 30.3% of all surface contacts. This contribution is only exceeded by H⃛H contacts at 33.4%. The next two most important percentage contributions come from N⃛H/H⃛N [11.5%] and C⃛H/H⃛C [10.1%] contacts. The next two significant surface contacts are O⃛C/C⃛O [5.0%] and O⃛O [4.2%]. The remaining contacts are due to N⃛C/C⃛N [2.5%], O⃛N/N⃛O [2.2%] and N⃛N [0.9%].


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

Funding source: Princess Nourah bint Abdulrahman University

Award Identifier / Grant number: PNURSP2022R3

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

  2. Research funding: Princess Nourah bint Abdulrahman University Researchers Supporting Project No. PNURSP2022R3, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.

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

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Received: 2022-05-21
Accepted: 2022-06-20
Published Online: 2022-07-05
Published in Print: 2022-10-26

© 2022 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. The crystal structure of 3-(1-(2-((5-methylthiophen-2-yl)methylene)hydrazinyl)ethylidene)chroman-2,4-dione, C17H14N2O3S
  4. Crystal structure of chlorido-(η 6-toluene)(5,5′-dimethyl-2,2′-bipyridine-κ2 N,N′)ruthenium(II) hexafluoridophosphate(V) ─ acetone (1/1) C22H26ClN2ORuPF6
  5. Crystal structure of 4-(((2-(3-(1-(3-(3-cyanophenyl)-6-oxopyridazin-1(6H)-yl)ethyl)phenyl) pyrimidin-5-yl)oxy)methyl)-1-methylpiperidin-1-ium chloride monohydrate, C30H33N6O2Cl
  6. The crystal structure of 2-chloro-N-((2-chlorophenyl)carbamoyl)nicotinamide, C13H9Cl2N3O2
  7. Crystal structure of 9-(t-butyl)-3,11-dihydro-6H-pyrazolo [1,5-a]pyrrolo[3′,2′:5,6]pyrido[4,3-d]pyrimidin-6-one hemihydrate, C30H32N10O3
  8. Crystal structure of di-μ2-hydroxido-tetrakis(6-methylpyridine-2-carboxylato-k2 N,O) diiron(III) trihydrate C28H32Fe2N4O13
  9. Crystal structure of catena-poly[qua-(μ2-2-aminoisophthalat-κ3 O,O′:O′′)(1,10-phenanthroline-κ2 N,N′)manganese(II)] C20H15MnN3O5
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  11. Crystal structure of (E)-N′-(1-(5-chloro-2-hydroxyphenyl)propylidene)-4-hydroxybenzohydrazide, C16H15ClN2O3
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  14. Synthesis and crystal structure of 1-((3R,10S,13R,17S)-10,13-dimethyl-3- (phenylamino)hexadecahydro-1H-cyclopenta[α] phenanthren-17-yl)ethan-1-one, C27H39NO
  15. Crystal structre of 1,4-bis(bromomethyl)-2,3,5,6-tetramethylbenzene, C12H16Br2
  16. Crystal structure of 2-(adamantan-1-yl)-5-(3,5-dinitrophenyl)-1,3,4-oxadiazole, C18H18N4O5
  17. Crystal structure of (E)-N′-benzylidene-4-nitrobenzohydrazide – methanol (1/1), C15H15N3O4
  18. The crystal structure of 3-(2-bromophenyl)-1,5-di-p-tolylpentane-1,5-dione, C25H23BrO2
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  29. Crystal structure of poly[μ2-aqua-aqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2 N:N′)-(μ2-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ2 O:O′)-(μ4-4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ5 O,O′:O″:O′″:O′″)dicobalt(II)] – water – dimethylformamide (1/1/1) C44H43N11O12Co2
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  33. Synthesis and crystal structure of (E)-1-(4-(((E)-3-(tert-butyl)-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-methyl oxime, C20H24N2O2
  34. The crystal structure of 4,4′-dichloro-6,6′-dimethoxy-2,2′,3,3′,5,5′- hexanitroazobenzene, C14H6N8O14Cl2
  35. Crystal structure of N 2,N 4-dimesitylpentane-2,4-diamine, C23H34N2
  36. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ 6O6)potassium(2-methylphenylamino)ethyl-2-methylphenylamide ammoniate (1/3.5), [K(18-crown-6)](o-CH3C6H4)NH(CH2)2N(o-CH3C6H4) 3.5 NH3, C28H53.5KN5.5O6
  37. The crystal structure of N′,N″,2-tris((E)-5-chloro-2-hydroxybenzylidene)hydrazine-1-carbohydrazonhydrazide hydrochloride – methanol (1/3), C25H30Cl4N6O6
  38. Crystal structure of (E)-7-bromo-2-(3,5-dimethoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C19H17BrO3
  39. Crystal structure of (E)-N′-(1-(5-chloro-2-hydroxyphenyl) ethylidene)-4-hydroxybenzohydrazide, C15H13ClN2O3
  40. {2-(((2-aminoethyl)imino)methyl)-6-bromophenolato-κ3 N,N′,O}iron(III) nitrate, C18H20Br2FeN5O5
  41. Crystal structure of 2-(tert-pentyl)anthracene-9,10-dione, C19H18O2
  42. Crystal structure of 5,5′-(1,4-phenylene)bis(1H-imidazol-3-ium) bis(2-(2-(carboxymethyl)phenyl)acetate), C32H30N4O8
  43. Crystal structure of N 2,N 6-bis(2-(((E)-naphthalen-1-ylmethylene)amino)phenyl)pyridine-2,6-dicarboxamide, C41H29N5O2
  44. The crystal structure of 3-amino-1,2,4-triazolium 2,4,5-trinitroimidazolate, C5H5O6N9
  45. Hydrogen bonded dimers in the crystal structure of 2-chloro-N-(phenylcarbamoyl)nicotinamide, C26H20Cl2N6O4
  46. The crystal structure of 4,4′-bipyridine-5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one-water(1/2/2), C40H32N2O12
  47. Crystal structure of N,N'-bis(4-fluoro-salicylaldehyde)-3,6-dioxa-1,8-diaminooctane, C20H22F2N2O4
  48. Crystal structure of 3-(1,3-dinitropropan-2-yl)-4H-chromen-4-one, C12H10N2O6
  49. The crystal structure of (4-(2-bromoethoxy)-phenyl)(phenyl)methanone, C15H13BrO2
  50. Crystal structure of (E)-7-bromo-2-(4-methoxybenzylidene)-3,4-dihydronaphthalen-1(2H)-one, C18H15BrO2
  51. Crystal structure of dichlorido-tetrakis((E)-(RS)-1-(2,4-dichlorophenyl)-4,4-dimethyl-2-(1,2,4-triazol-1-yl)pent-1-en-3-ol-κ 1 N)cadmium(II), C60H68O4N12Cl10Cd
  52. Crystal structure of diaqua-diphenanthroline-κ2 N,N′-bis(μ2-2-carboxy-3,4,5,6-tetrafluorobenzoato-κ2 O:O′)-bis(μ2-tetrafluorophthalato-κ3 O,O′:O′)didysprosium(III) – phenanthroline (1/2), C80H38Dy2F16N8O18
  53. Crystal structure of bis(μ2-2-oxido-2-phenylacetato-κ3 O,O′:O′)-bis(N-oxido-benzamide-κ2 O,O′)-bis(propan-2-olato-κ1 O)dititanium(IV), C36H38N2O12Ti2
  54. Crystal structure of poly[diaqua-(μ2-1H-benzo[d][1,2,3]triazole-5-carboxylato-κ2 O:O′)(μ2-oxalato-κ4O,O:O″,O′″)europium(III)] monohydrate, C9H10N3O9Eu
  55. Crystal structure of bis((N-methyl-2-oxyethyl)amine)-bis(μ 2-N,N,N-tris(2-oxoethyl)amine)-bis(isopropoxy)-bis(μ 3-oxo)tetratitanium(IV)– isopropanol (1/2), C34H76N4O16Ti4
  56. Synthesis and crystal structure of ethyl 4-((4-iodobenzyl)amino)benzoate, C16H16INO2
  57. Crystal structure of (Z)-2-(tert-butyl)-5-((5-(tert- butyl)-2H-pyrrol-2-ylidene)(mesityl)methyl)-1H-pyrrole, C26H34N2
  58. Crystal structure of dimethylammonium poly[μ4-1,1′-(1,4- phenylenebis(methylene))bis(1H-pyrazole-3,5-dicarboxylato-κ6 N,O:O′:N′,O″:O‴) manganese(II)], C22H26MnN6O8
Heruntergeladen am 7.9.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2022-0263/html
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