Crystal structure and Hirshfeld surface analysis of 3,3′-[ethane-1,2-diylbis(­oxy)]bis­(5,5-di­methyl­cyclo­hex-2-en-1-one) including an unknown solvate

Sadikhova, N.D.; Akkurt, M.; Ismayilov, V.M.; Yusubov, N.N.; Hasanov, K.I.; Bhattarai, A.

doi:10.1107/S2056989024004286

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Volume 80| Part 6| June 2024| Pages 615-619

https://doi.org/10.1107/S2056989024004286

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Crystal structure and Hirshfeld surface analysis of 3,3′-[ethane-1,2-diylbis(oxy)]bis(5,5-dimethylcyclohex-2-en-1-one) including an unknown solvate

Nurlana D. Sadikhova,^a Mehmet Akkurt,^b Valeh M. Ismayilov,^a Niftali N. Yusubov,^a Khudayar I. Hasanov ^c,^d and Ajaya Bhattarai ^e ^*

^aDepartment of Chemistry, Baku State University, Z. Khalilov Str. 23, Az 1148 Baku, Azerbaijan, ^bDepartment of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Türkiye, ^cWestern Caspian University, Istiqlaliyyat Street 31, AZ1001, Baku, Azerbaijan, ^dAzerbaijan Medical University, Scientific Research Centre (SRC), A. Kasumzade St. 14. AZ 1022, Baku, Azerbaijan, and ^eDepartment of Chemistry, M.M.A.M.C (Tribhuvan University) Biratnagar, Nepal
^*Correspondence e-mail: ajaya.bhattarai@mmamc.tu.edu.np

Edited by X. Hao, Institute of Chemistry, Chinese Academy of Sciences (Received 3 May 2024; accepted 8 May 2024; online 17 May 2024)

The title molecule, C₁₈H₂₆O₄, consists of two symmetrical halves related by the inversion centre at the mid-point of the central –C—C– bond. The hexene ring adopts an envelope conformation. In the crystal, the molecules are connected into dimers by C—H⋯O hydrogen bonds with R²₂(8) ring motifs, forming zigzag ribbons along the b-axis direction. According to a Hirshfeld surface analysis, H⋯H (68.2%) and O⋯H/H⋯O (25.9%) interactions are the most significant contributors to the crystal packing. The contribution of some disordered solvent to the scattering was removed using the SQUEEZE routine [Spek (2015 ). Acta Cryst. C71, 9–18] in PLATON. The solvent contribution was not included in the reported molecular weight and density.

Keywords: crystal structure; β-diketones; dimers; weak interactions; Hirshfeld surface analysis.

CCDC reference: 2354123

1. Chemical context

β-Diketones have been employed as versatile synthetic precursors for the synthesis of new functional materials, such as catalysts, ionophores, heterocycles, organic conductors as well as pharmaceuticals (Abdelhamid et al., 2011 ; Afkhami et al., 2017 ; Khalilov et al., 2021 ; Maharramov et al., 2010 ; Martins et al., 2017 ; Safavora et al., 2019 ). For example, arylhydrazones of β-diketones have been widely used in coordination chemistry for a long time and have recently been the object of increasing attention as constituents of polydentate ligands in metallo-supramolecular chemistry (Gurbanov et al., 2018 , 2020 ; Kopylovich et al., 2012a ,b ; Mac Leod et al., 2012 ; Mahmoudi et al., 2017a ,b , 2019 ). The reactivity of β-diketones as enols or ketones can also be used as a synthetic strategy to access new organic materials (Yamabe et al., 2004 ). Moreover, bridging of two β-diketone moieties into one molecule can improve their properties as well as the number of coordination and non-covalent sites (Shixaliyev et al., 2019 ).

We have bridged two dimedone molecules into 3,3′-[ethane-1,2-diylbis(oxy)]bis(5,5-dimethylcyclohex-2-en-1-one) via reaction with dichloroethane, and undertaken a full characterization, including X-ray analysis.

2. Structural commentary

The title compound (Fig. 1) consists of two symmetrical halves related by the inversion centre at the mid-point of the central –C—C– bond. The hexene ring (C2–C7) in the molecule adopts an envelope conformation [the puckering parameters (Cremer & Pople, 1975 ) are Q_T = 0.4488 (15) Å, θ = 127.49 (19)°, φ = 60.6 (2)°]. The geometric parameters of the title compound are normal and comparable to those of the related compound listed in the Database survey section.

Figure 1
The molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level.

3. Supramolecular features and Hirshfeld surface analysis

In the crystal, the molecules are connected into dimers by C—H⋯O hydrogen bonds with $[R_{2}^{2}]$ (8) ring motifs, forming zigzag ribbons along the b-axis direction (Bernstein et al., 1995 ; Table 1; Figs. 2, 3 and 4). These ribbons are connected via van der Waals interactions, ensuring crystal cohesion.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3⋯O2ⁱ	0.95	2.46	3.391 (2)	168
Symmetry code: (i) .

Figure 2
A partial view down the a axis of the C—H⋯O hydrogen bonds (dashed lines) in the title compound.

Figure 3
Partial packing of the title compound, viewed down the b axis, showing C—H⋯O hydrogen-bonded inversion-dimers with R²₂(8) graph-set motifs; H-atoms not involved in hydrogen bonds have been excluded for clarity.

Figure 4
A partial view down the c axis of the C—H⋯O hydrogen bonds (dashed lines) in the title compound.

In order to visualize and quantify the intermolecular interactions, a Hirshfeld surface analysis was performed using Crystal Explorer 17.5 (Spackman et al., 2021 ), which was also used to generate the associated two-dimensional fingerprint plots. The Hirshfeld surfaces were mapped over d_norm in the range −0.2098 (red) to +1.6767 (blue) a.u. (Fig. 5). The most important interatomic contact is H⋯H as it makes the highest contribution to the crystal packing (68.2%, Fig. 6b). The other major contributor is the O⋯H/H⋯O (25.9%, Fig. 6c) interaction. Other smaller contributions are made by C⋯H/H⋯C (5.5%) and O⋯O (0.4%) interactions.

Figure 5
Front and back views of the three-dimensional Hirshfeld surfaces of the title compound.

Figure 6
The full two-dimensional fingerprint plots for of the title compound, showing (a) all interactions, and delineated into (b) H⋯H and (c) O⋯H / H⋯O interactions. The d_i and d_e values are the closest internal and external distances (in Å) from given points on the Hirshfeld surface.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.43, last update November 2022; Groom et al., 2016 ) for the six-membered cyclohexene ring yielded nine compounds related to the title compound, viz. CSD refcodes WOMWUU (Naghiyev et al., 2024 ), UPOMOE (Naghiyev et al., 2021 ), ZOMDUD (Gein et al., 2019 ), PEWJUZ (Fatahpour et al., 2018 ), OZUKAX (Tkachenko et al., 2014 ), IFUDOD (Gein et al., 2007 ), IWEVOV (Mohan et al., 2003 ), IWEVUB (Mohan et al., 2003) and HALROB (Ravikumar & Mehdi, 1993 ).

WOMWUU, UPOMOE and ZOMDUD crystallize in the monoclinic space group P2₁/c, with Z = 4, PEWJUZ in I2/c with Z = 4, IFUDOD, HALROB and IWEVUB in P2₁/n with Z = 4, and IWEVOV and OZUKAX in the orthorhombic space group Pbca with Z = 8. In WOMWUU, molecules are connected by intermolecular C—H⋯S hydrogen bonds with $[R_{2}^{2}]$ (10) ring motifs, forming ribbons along the b-axis direction. C—H⋯π interactions consolidate the ribbon structure while van der Waals forces between the ribbons ensure the cohesion of the crystal structure. In UPOMOE, the central cyclohexane ring adopts a chair conformation. In the crystal, molecules are linked by N—H⋯O, C—H⋯O and C—H⋯N hydrogen bonds, forming molecular layers parallel to the bc plane, which are connected by van der Waals interactions between them. In ZOMDUD, molecules are linked by intermolecular N—H⋯O and C—H⋯O hydrogen bonds, forming a three-dimensional network. C—H⋯π interactions are also observed. In PEWJUZ, molecules are linked by intermolecular N—H⋯O and C—H⋯O hydrogen bonds, forming sheets parallel to the bc plane. C—H⋯π interactions are also observed. In OZUKAX, molecules are linked by intermolecular N—H⋯O and C—H⋯O hydrogen bonds, forming sheets parallel to the ac plane. C—H⋯π interactions are also observed. Intermolecular O—H⋯O hydrogen bonds consolidate the crystal structure. There are no classical hydrogen bonds in the crystal of IFUDOD where intermolecular C—H⋯O contacts and weak C—H⋯π interactions lead to the formation of a three-dimensional network. In the crystal of IWEVOV, the molecules pack such that both carbonyl O atoms participate in hydrogen-bond formation with symmetry-related amide nitrogen atoms present in the carbamoyl substituents, forming N—H⋯O hydrogen bonds in a helical arrangement. In the crystal, the phenyl rings are positioned so as to favour edge-to-edge aromatic stacking. When the crystal packing is viewed normal to the ac plane, it reveals a `wire-mesh' type hydrogen-bond network. In the crystal of IWEVUB, unlike in IWEVOV where both carbonyl O atoms participate in hydrogen bonding, only one of the carbonyl oxygen atoms participates in intermolecular N—H⋯O hydrogen bonding while the other carbonyl oxygen participates in a weak C—H⋯O interaction. In addition, one of the amide nitrogen atoms participates in N—H⋯O hydrogen bonding with the hydroxyl oxygen atom, linking the molecules in a helical arrangement, which is similar to that in the structure of IWEVOV. As observed in the structure of IWEVOV, the packing of the molecules viewed normal to the ab plane resembles a `wire-mesh' arrangement of the molecules. In the crystal of HALROB, the amide carbonyl groups are oriented in different directions with respect to the cyclohexanone ring. These orientations of the carboxamide groups facilitate the formation of an intramolecular O—H⋯O hydrogen bond. The molecules are packed such that chains are formed along the b-axis direction. These chains are held together by N—H⋯O hydrogen bonds.

5. Synthesis and crystallization

0.12 mol of dichloroethane were added drop by drop to a mixture of 0.12 mol of dimedone and 0.25 mol of K₂CO₃ in 50 mL of DMSO. The reaction mixture was held for 12 h at 353 K then cooled to room temperature, water added and extracted with ethyl ether. The extract was dried with MgSO₄, the solvent was distilled off, and the residue was distilled under vacuum. Crystals suitable for X-ray analysis were obtained by evaporation of a dimethylformamide solution. Colourless solid (65%); m.p. 416–418 K. Analysis calculated for C₁₈H₂₆O₄ (M = 306.40): C 70.56, H 8.55; found: C 70.52, H 8.49%. ¹H NMR (300 MHz, DMSO-d₆) δ 0.99 (12H, 4CH₃), 2.12 and 2.30 (8H, 4CH₂), 4.16 (4H, 2CH₂) and 5.36 (2H, 2CH). ¹³C NMR (75 MHz, DMSO-d₆) δ 27.72 (4CH₃), 32.12 (2C_ipso), 41.78 (2CH₂), 50.25 (2CH₂), 66.37 (2CH₂), 101.44 (2CH), 175.18 (2C—O) and 197.89 (2C=O).

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. All H atoms were placed in calculated positions (C—H = 0.95–0.99 Å) and allowed to ride on their carrier atoms, with U_iso= 1.2 or 1.5U_eq(C). The residual electron density was difficult to model and therefore the SQUEEZE routine (Spek, 2015) in PLATON (Spek, 2020 ) was used to remove the contribution of the electron density in the solvent region from the intensity data and the solvent-free model was employed for the final refinement. The solvent formula mass and unit-cell characteristics were not taken into account during refinement. The cavity of volume ca 77 Å³ (ca 4.4% of the unit-cell volume) contains approximately 11 electrons. A suitable solvent with this electron number may be about four dimethylformamide molecules per unit cell.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₈H₂₆O₄
M_r	306.39
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	150
a, b, c (Å)	16.9184 (13), 6.5230 (5), 17.2645 (11)
β (°)	111.822 (4)
V (Å³)	1768.8 (2)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.08
Crystal size (mm)	0.33 × 0.29 × 0.18

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.966, 0.980
No. of measured, independent and observed [I > 2σ(I)] reflections	10346, 2111, 1559
R_int	0.046
(sin θ/λ)_max (Å⁻¹)	0.659

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.045, 0.118, 1.04
No. of reflections	2111
No. of parameters	102
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.20
Computer programs: APEX4 and SAINT (Bruker, 2018 ), SHELXT (Sheldrick, 2015a ), SHELXL2018 (Sheldrick, 2015b ), ORTEP-3 for Windows (Farrugia, 2012 ) and PLATON (Spek, 2020).

Supporting information

CCDC reference: 2354123

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989024004286/nx2010sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024004286/nx2010Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989024004286/nx2010Isup3.cml

checkCIF report

Computing details top

3,3'-[Ethane-1,2-diylbis(oxy)]bis(5,5-dimethylcyclohex-2-en-1-one) top

Crystal data top

C₁₈H₂₆O₄	F(000) = 664
M_r = 306.39	D_x = 1.151 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.9184 (13) Å	Cell parameters from 2235 reflections
b = 6.5230 (5) Å	θ = 2.5–27.7°
c = 17.2645 (11) Å	µ = 0.08 mm⁻¹
β = 111.822 (4)°	T = 150 K
V = 1768.8 (2) Å³	Prism, colourless
Z = 4	0.33 × 0.29 × 0.18 mm

Data collection top

Bruker APEXII CCD diffractometer	1559 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.046
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 27.9°, θ_min = 2.5°
T_min = 0.966, T_max = 0.980	h = −22→22
10346 measured reflections	k = −8→8
2111 independent reflections	l = −22→22

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.045	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.118	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0456P)² + 1.1303P] where P = (F_o² + 2F_c²)/3
2111 reflections	(Δ/σ)_max < 0.001
102 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

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

	x	y	z	U_iso*/U_eq
O1	0.44150 (6)	0.32631 (17)	0.28986 (6)	0.0333 (3)
O2	0.42054 (9)	0.1572 (2)	0.54805 (7)	0.0545 (4)
C6	0.30515 (9)	0.5396 (2)	0.39219 (8)	0.0252 (3)
C2	0.41732 (8)	0.3534 (2)	0.35542 (8)	0.0264 (3)
C3	0.43558 (8)	0.2261 (2)	0.42109 (8)	0.0276 (3)
H3	0.468878	0.106836	0.424213	0.033*
C7	0.36773 (9)	0.5477 (2)	0.34683 (9)	0.0311 (3)
H7A	0.335662	0.575102	0.286885	0.037*
H7B	0.407869	0.662711	0.369541	0.037*
C5	0.35360 (9)	0.4640 (2)	0.48148 (8)	0.0296 (3)
H5A	0.392750	0.573764	0.513085	0.036*
H5B	0.312185	0.439501	0.508610	0.036*
C4	0.40447 (9)	0.2706 (2)	0.48729 (8)	0.0299 (3)
C1	0.49293 (9)	0.1495 (3)	0.29054 (9)	0.0316 (4)
H1A	0.463346	0.022376	0.295832	0.038*
H1B	0.548105	0.157036	0.338214	0.038*
C8	0.23173 (9)	0.3930 (3)	0.34703 (10)	0.0350 (4)
H8A	0.201336	0.441546	0.289903	0.052*
H8B	0.192439	0.388104	0.376769	0.052*
H8C	0.254452	0.255480	0.345518	0.052*
C9	0.26825 (12)	0.7527 (3)	0.39343 (10)	0.0429 (4)
H9A	0.314317	0.847356	0.423877	0.064*
H9B	0.227197	0.745890	0.421145	0.064*
H9C	0.239567	0.801562	0.336078	0.064*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0318 (5)	0.0481 (7)	0.0280 (5)	0.0114 (5)	0.0202 (4)	0.0110 (5)
O2	0.0716 (9)	0.0690 (9)	0.0366 (6)	0.0442 (7)	0.0362 (6)	0.0280 (6)
C6	0.0289 (7)	0.0247 (7)	0.0238 (7)	0.0061 (6)	0.0121 (6)	0.0007 (5)
C2	0.0206 (6)	0.0374 (8)	0.0251 (7)	0.0023 (6)	0.0130 (5)	0.0031 (6)
C3	0.0255 (7)	0.0352 (8)	0.0259 (7)	0.0101 (6)	0.0141 (6)	0.0058 (6)
C7	0.0341 (8)	0.0309 (8)	0.0319 (7)	0.0035 (6)	0.0163 (6)	0.0082 (6)
C5	0.0342 (8)	0.0323 (8)	0.0244 (7)	0.0065 (6)	0.0134 (6)	−0.0016 (6)
C4	0.0291 (7)	0.0393 (8)	0.0237 (7)	0.0107 (6)	0.0124 (6)	0.0056 (6)
C1	0.0259 (7)	0.0468 (9)	0.0274 (7)	0.0067 (6)	0.0160 (6)	0.0036 (6)
C8	0.0247 (7)	0.0441 (9)	0.0355 (8)	0.0049 (6)	0.0106 (6)	−0.0037 (7)
C9	0.0584 (11)	0.0332 (9)	0.0406 (9)	0.0173 (8)	0.0223 (8)	0.0045 (7)

Geometric parameters (Å, º) top

O1—C2	1.3507 (16)	C5—C4	1.5096 (19)
O1—C1	1.4423 (17)	C5—H5A	0.9900
O2—C4	1.2284 (17)	C5—H5B	0.9900
C6—C9	1.527 (2)	C1—C1ⁱ	1.505 (3)
C6—C8	1.532 (2)	C1—H1A	0.9900
C6—C5	1.5336 (19)	C1—H1B	0.9900
C6—C7	1.5340 (19)	C8—H8A	0.9800
C2—C3	1.3454 (19)	C8—H8B	0.9800
C2—C7	1.496 (2)	C8—H8C	0.9800
C3—C4	1.4543 (18)	C9—H9A	0.9800
C3—H3	0.9500	C9—H9B	0.9800
C7—H7A	0.9900	C9—H9C	0.9800
C7—H7B	0.9900

C2—O1—C1	117.88 (10)	C6—C5—H5B	108.6
C9—C6—C8	108.50 (12)	H5A—C5—H5B	107.6
C9—C6—C5	110.31 (11)	O2—C4—C3	121.41 (13)
C8—C6—C5	109.89 (12)	O2—C4—C5	119.97 (12)
C9—C6—C7	109.84 (12)	C3—C4—C5	118.59 (12)
C8—C6—C7	110.15 (11)	O1—C1—C1ⁱ	107.24 (10)
C5—C6—C7	108.15 (11)	O1—C1—H1A	110.3
C3—C2—O1	125.39 (13)	C1ⁱ—C1—H1A	110.3
C3—C2—C7	123.44 (12)	O1—C1—H1B	110.3
O1—C2—C7	111.17 (11)	C1ⁱ—C1—H1B	110.3
C2—C3—C4	120.14 (13)	H1A—C1—H1B	108.5
C2—C3—H3	119.9	C6—C8—H8A	109.5
C4—C3—H3	119.9	C6—C8—H8B	109.5
C2—C7—C6	112.86 (11)	H8A—C8—H8B	109.5
C2—C7—H7A	109.0	C6—C8—H8C	109.5
C6—C7—H7A	109.0	H8A—C8—H8C	109.5
C2—C7—H7B	109.0	H8B—C8—H8C	109.5
C6—C7—H7B	109.0	C6—C9—H9A	109.5
H7A—C7—H7B	107.8	C6—C9—H9B	109.5
C4—C5—C6	114.46 (11)	H9A—C9—H9B	109.5
C4—C5—H5A	108.6	C6—C9—H9C	109.5
C6—C5—H5A	108.6	H9A—C9—H9C	109.5
C4—C5—H5B	108.6	H9B—C9—H9C	109.5

C1—O1—C2—C3	−1.6 (2)	C9—C6—C5—C4	−170.57 (13)
C1—O1—C2—C7	177.57 (12)	C8—C6—C5—C4	69.86 (16)
O1—C2—C3—C4	−178.91 (13)	C7—C6—C5—C4	−50.42 (16)
C7—C2—C3—C4	2.0 (2)	C2—C3—C4—O2	−179.70 (15)
C3—C2—C7—C6	−28.0 (2)	C2—C3—C4—C5	−1.5 (2)
O1—C2—C7—C6	152.85 (12)	C6—C5—C4—O2	−154.38 (15)
C9—C6—C7—C2	170.39 (13)	C6—C5—C4—C3	27.4 (2)
C8—C6—C7—C2	−70.16 (15)	C2—O1—C1—C1ⁱ	177.15 (12)
C5—C6—C7—C2	49.95 (16)

Symmetry code: (i) −x+1, y, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O2ⁱⁱ	0.95	2.46	3.391 (2)	168

Symmetry code: (ii) −x+1, −y, −z+1.

Acknowledgements

This work was been supported by Baku State University (Azerbaijan), Western Caspian University (Azerbaijan) and Azerbaijan Medical University. The authors′ contributions are as follows. Conceptualization, MA and AB; synthesis, NDS, VMI and NNY; X-ray analysis, NDS and KIH; writing (review and editing of the manuscript) NDS and MA; funding acquisition, NDS, VMI, NNY and KIH; supervision, MA and AB.

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