Redetermination of germacrone type II based on single-crystal X-ray data

Meurer, F.; Bodensteiner, M.; Kolev, I.

doi:10.1107/S2414314624003468

organic compounds

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ISSN: 2414-3146

Volume 9| Part 4| April 2024| x240346

https://doi.org/10.1107/S2414314624003468

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Redetermination of germacrone type II based on single-crystal X-ray data

Florian Meurer,^a Michael Bodensteiner ^a and Iliyan Kolev ^b ^*

^aFaculty of Chemistry and Pharmacy, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany, and ^bFaculty of Pharmacy, Department of Pharmaceutical Chemistry, Medical University `Prof. Dr. Paraskev Stoyanov' – Varna, 84 "Tzar Osvoboditel" Blvd, 9000 Varna, Bulgaria
^*Correspondence e-mail: ilian.kolev@mu-varna.bg

Edited by M. Weil, Vienna University of Technology, Austria (Received 11 March 2024; accepted 18 April 2024; online 26 April 2024)

The extraction and purification procedures, crystallization and crystal structure refinement (single-crystal X-ray data) of germacrone type II, C₁₅H₂₂O, are presented. The structural results are compared with a previous powder X-ray synchrotron study [Kaduk et al. (2022 ). Powder Diffr. 37, 98–104], revealing significant improvements in terms of accuracy and precision. Hirshfeld atom refinement (HAR), as well as Hirshfeld surface analysis, give insight into the intermolecular interactions of germacrone type II.

Keywords: crystal structure; germacrone; Hirshfeld atom refinement; Hirsfeld surface analysis; synthesis; extraction.

CCDC reference: 2349265

Structure description

(3E,7E)-3,7-Dimethyl-10-propan-2-ylidenecyclodeca-3,7-dien-1-one (1), also called germacrone, is dimorphic. The first polymorph was reported in 1999 based on single-crystal X-ray data (Clardy & Lobkovsky, 1999 ), and the second polymorph (germacrone type II) in 2022 based on synchrotron powder X-ray diffraction data (Kaduk et al., 2022). Herein we compare the results of our single-crystal X-ray study with the molecular structure refined with the Rietveld method (Kaduk et al., 2022).

We confirm that (1) crystallizes in the monoclinic space group C2/c. The unit-cell volume of 2579.78 (10) Å³ at a temperature of 100 K is about 4% smaller than that of 2684.06 (4) Å³ determined at room temperature. Fig. 1 shows the molecular structure of (1) and Fig. 2 the packing of the molecules along the crystallographic b direction. The most prominent feature with respect to the crystal packing aspects of (1) is the carbonyl group (C1=O1) next to the C=CMe₂ entity [C2=C13(C14H₃)(C15H₃)]. A Hirshfeld surface analysis using CrystalExplorer (Spackman et al., 2021 ) reveals that the carbonyl group is responsible for the only contacts of (1) with its periodic environment, with distances below the sum of the van der Waals radii (Fig. 3, red contacts). Numerical details of the contacts involving H atoms below 5 Å are listed in Table 1. In comparison with the room-temperature powder study, we found longer hydrogen–acceptor (H⋯A) distances, e.g. with one of the shortest H⋯A contacts being 2.59 (1) Å, while it was reported at 2.473 Å by Kaduk et al. (2022). A possible reason for this difference may be that we refined C—H distances directly based on the single-crystal X-ray diffraction data, employing Hirshfeld Atom Refinement (HAR). It has been reported that HAR yields C—H bond lengths that are as accurate as neutron data (Woińska et al., 2016 ), so we are confident that these distances for germacrone type II are improved compared to the previous powder study.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C8—H8⋯O1ⁱ	1.076 (10)	2.590 (10)	3.6245 (10)	161.0 (8)
C10—H10B⋯O1ⁱ	1.105 (9)	2.695 (10)	3.7028 (10)	151.3 (7)
C14—H14B⋯O1ⁱ	1.072 (11)	2.552 (12)	3.2434 (10)	121.5 (9)
C4—H4⋯O1ⁱ	1.104 (9)	3.356 (10)	4.1760 (9)	132.0 (6)
C11—H11C⋯O1ⁱⁱ	1.073 (13)	3.177 (12)	4.1177 (11)	146.9 (9)
Symmetry codes: (i) $[x, -y+1, z+{\script{1\over 2}}]$ ; (ii) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 1
The molecular structure of (1) with the atomic labelling scheme. Anisotropic displacement ellipsoids are drawn at the 50% probability level. Bond lengths (Å), except for C(sp³)—C(sp³) and C(sp²)—C(sp²) bonds, are indicated.

Figure 2
Crystal packing of (1) along the crystallographic b direction. Anisotropic displacement ellipsoids are drawn at the 50% probability level.

Figure 3
Hirshfeld fingerprint plots (left) of (1), showing the contacts on the Hirshfeld surface (right).

In Table 2, the bond lengths between all atoms heavier than hydrogen are compared between the current single-crystal X-ray study and the previous powder study by Kaduk et al. (2022). The accuracy of the bond lengths differs by an entire order of magnitude and some distances differ strongly. For example, the C5—C12 bond to the methyl group of C12 is heavily underestimated [1.395 (12) Å] compared to 1.5017 (10) Å determined in the current study. The higher accuracy and precision of the current model results from the single-crystal X-ray data and the use of a successful non-spherical description of the atoms, but also from the low-temperature data. The overlap of both molecular structures (Fig. 4) underlines the difference between the two structure refinements.

Table 2
Comparison of bond lengths (Å) determined from the current single-crystal X-ray study and from the powder study by Kaduk et al. (2022)

Atom	Atom	Current single-crystal X-ray study.	Previous powder study*
O1	C1	1.2144 (9)	1.212 (10)
C1	C2	1.5035 (10)	1.558 (10)
C2	C3	1.5221 (10)	1.516 (11)
C4	C3	1.5069 (11)	1.513 (12)
C5	C4	1.3387 (11)	1.314 (11)
C5	C12	1.5017 (10)	1.395 (12)
C5	C6	1.5121 (11)	1.497 (12)
C7	C6	1.5597 (12)	1.518 (15)
C1	C10	1.5292 (10)	1.514 (12)
C9	C8	1.3391 (10)	1.326 (13)
C9	C10	1.5207 (10)	1.576 (12)
C9	C11	1.5005 (10)	1.537 (13)
C8	C7	1.5002 (10)	1.484 (13)
C13	C2	1.3460 (10)	1.405 (10)
C13	C14	1.5015 (11)	1.601 (11)
C13	C15	1.5015 (11)	1.574 (11)
Note: (*) atom labels were adopted from the current single-crystal X-ray study for better comparison.

Figure 4
Overlayed molecular structures of germacrone type II determined in this work (ellipsoids connected by orange bonds) and from previous powder data (Kaduk et al., 2022

; blue spheres). Ellipsoids and spheres are drawn at the 50% probability level.

However, the Hirshfeld surface analysis (Fig. 3) is in close agreement with the results by Kaduk et al. (2022). The intermolecular interaction in germacrone type II is of primarily dispersion character of H⋯H contacts (81.1%), with the remainder mostly consisting of O⋯H contacts (9.5%) and O⋯C contacts (0.8%).

Synthesis and crystallization

The essential oil (EO) from the leaves of Geranium macrorrhizum L. was obtained by steam distillation, using a conventional distillation vessel with a capacity of 2.5 m³. The target terpenoid was isolated from the resulting EO. For this purpose, approximately 1.0 g of EO was dissolved in 5.0 ml of 99% vol. ethanol. To this solution, distilled water was subsequently added dropwise until a faint opalescence appeared. The homogeneity of the latter was restored by adding 200 µl of ethanol. The resulting solution was allowed to stand in a refrigerator for several hours. The crystals formed were separated from the remaining solution and purified twice by the same methodology. Approximately 200 mg of thin acicular crystals were thus obtained.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. Refinement of the initial structure solution as determined by SHELXT (Sheldrick, 2015 ) was performed using olex2.refine (Dolomanov et al., 2009 ; Bourhis et al., 2015 ). The refined structure was used as an input to perform an iterative Hirshfeld atom refinement (HAR) using NoSpherA2 (Kleemiss et al., 2021 ) at the R2SCAN/cc-pVDZ level of theory until convergence was reached after eight cycles. This allowed us to model all atoms, including H atoms anisotropically without any constraints or restraints on the structural model.

Table 3
Experimental details

Crystal data
Chemical formula	C₁₅H₂₂O
M_r	218.34
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	100
a, b, c (Å)	25.6112 (6), 9.7565 (2), 10.3664 (2)
β (°)	95.169 (2)
V (Å³)	2579.78 (10)
Z	8
Radiation type	Cu Kα
μ (mm⁻¹)	0.52
Crystal size (mm)	0.35 × 0.10 × 0.01

Data collection
Diffractometer	XtaLAB Synergy R, DW system, HyPix-Arc 150
Absorption correction	Gaussian (CrysAlis PRO; Rigaku OD, 2023 )
T_min, T_max	0.601, 1.000
No. of measured, independent and observed [I ≥ 2u(I)] reflections	13789, 2579, 2244
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.624

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.029, 0.077, 1.07
No. of reflections	2579
No. of parameters	343
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.15, −0.19
Computer programs: CrysAlis PRO (Rigaku OD, 2023), SHELXT (Sheldrick, 2015), olex2.refine (Bourhis et al., 2015) and OLEX2 (Dolomanov et al., 2009).

The final model was used to generate the input file for CrystalExplorer (Spackman et al., 2021).

Structural data

CCDC reference: 2349265

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314624003468/wm4211sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624003468/wm4211Isup2.hkl

checkCIF report

Computing details top

(3E,7E)-3,7-Dimethyl-10-propan-2-ylidenecyclodeca-3,7-dien-1-one top

Crystal data top

C₁₅H₂₂O	F(000) = 962.722
M_r = 218.34	D_x = 1.124 Mg m⁻³
Monoclinic, C2/c	Cu Kα radiation, λ = 1.54184 Å
a = 25.6112 (6) Å	Cell parameters from 7327 reflections
b = 9.7565 (2) Å	θ = 3.5–73.5°
c = 10.3664 (2) Å	µ = 0.52 mm⁻¹
β = 95.169 (2)°	T = 100 K
V = 2579.78 (10) Å³	Plate, colourless
Z = 8	0.35 × 0.10 × 0.01 mm

Data collection top

XtaLAB Synergy R, DW system, HyPix-Arc 150 diffractometer	2244 reflections with I ≥ 2u(I)
Detector resolution: 10.0000 pixels mm^-1	R_int = 0.026
ω scans	θ_max = 74.2°, θ_min = 3.5°
Absorption correction: gaussian (CrysAlis PRO; Rigaku OD, 2023)	h = −31→31
T_min = 0.601, T_max = 1.000	k = −12→11
13789 measured reflections	l = −12→7
2579 independent reflections

Refinement top

Refinement on F²	0 restraints
Least-squares matrix: full	0 constraints
R[F² > 2σ(F²)] = 0.029	All H-atom parameters refined
wR(F²) = 0.077	w = 1/[σ²(F_o²) + (0.055P)² + 0.0128P] where P = (F_o² + 2F_c²)/3
S = 1.07	(Δ/σ)_max = 0.0002
2579 reflections	Δρ_max = 0.15 e Å⁻³
343 parameters	Δρ_min = −0.19 e Å⁻³

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

	x	y	z	U_iso*/U_eq
O1	0.33333 (3)	0.41200 (6)	0.20570 (5)	0.03252 (17)
C9	0.31211 (3)	0.25885 (7)	0.45034 (7)	0.02028 (17)
C8	0.34076 (3)	0.24944 (8)	0.56458 (7)	0.02222 (18)
C13	0.36790 (3)	0.66412 (8)	0.42455 (6)	0.02161 (18)
C1	0.33372 (3)	0.45137 (7)	0.31692 (6)	0.02148 (17)
C2	0.37771 (3)	0.54035 (8)	0.37471 (6)	0.02055 (17)
C10	0.29269 (3)	0.39910 (8)	0.40343 (7)	0.02205 (18)
C14	0.31393 (3)	0.72500 (9)	0.42034 (8)	0.02466 (18)
C5	0.44323 (3)	0.24947 (8)	0.49580 (7)	0.02413 (18)
C4	0.44050 (3)	0.38643 (8)	0.49131 (7)	0.02410 (18)
C3	0.43197 (3)	0.47697 (8)	0.37352 (7)	0.02458 (18)
C11	0.30102 (4)	0.14357 (9)	0.35603 (8)	0.02775 (19)
C7	0.37470 (4)	0.13211 (9)	0.61428 (8)	0.02777 (19)
C15	0.40994 (4)	0.75499 (9)	0.48836 (9)	0.02842 (19)
C12	0.44745 (4)	0.15866 (10)	0.38024 (8)	0.0297 (2)
C6	0.43328 (4)	0.17738 (9)	0.62037 (8)	0.0290 (2)
H8	0.3460 (4)	0.3411 (11)	0.6219 (9)	0.041 (3)
H10A	0.2546 (4)	0.3942 (11)	0.3461 (10)	0.038 (3)
H10B	0.2903 (4)	0.4685 (10)	0.4870 (9)	0.034 (2)
H14A	0.2841 (4)	0.6658 (11)	0.3672 (10)	0.048 (3)
H14B	0.3025 (5)	0.7431 (14)	0.5158 (11)	0.061 (4)
H14C	0.3145 (5)	0.8231 (12)	0.3739 (11)	0.049 (3)
H4	0.4366 (4)	0.4415 (10)	0.5829 (9)	0.038 (3)
H3A	0.4331 (4)	0.4181 (11)	0.2840 (10)	0.040 (3)
H3B	0.4618 (4)	0.5565 (11)	0.3739 (10)	0.043 (3)
H11A	0.3154 (5)	0.1660 (13)	0.2629 (10)	0.051 (3)
H11B	0.3178 (5)	0.0496 (12)	0.3891 (10)	0.053 (3)
H7A	0.3659 (5)	0.1001 (11)	0.7122 (10)	0.049 (3)
H7B	0.3688 (4)	0.0424 (12)	0.5518 (9)	0.044 (3)
H15A	0.4471 (5)	0.7088 (14)	0.5030 (12)	0.064 (4)
H15B	0.4128 (6)	0.8482 (12)	0.4331 (12)	0.060 (4)
H15C	0.3996 (5)	0.7869 (14)	0.5819 (11)	0.060 (4)
H12A	0.4126 (5)	0.0982 (14)	0.3561 (11)	0.058 (4)
H12B	0.4554 (6)	0.2159 (12)	0.2938 (11)	0.065 (4)
H12C	0.4805 (5)	0.0899 (13)	0.3954 (11)	0.064 (4)
H6A	0.4579 (5)	0.0867 (12)	0.6382 (10)	0.049 (3)
H6B	0.4410 (4)	0.2496 (12)	0.7012 (10)	0.040 (3)
H11C	0.2595 (5)	0.1274 (12)	0.3405 (11)	0.050 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0470 (4)	0.0323 (3)	0.0186 (3)	−0.0112 (3)	0.0049 (2)	−0.0026 (2)
C9	0.0235 (4)	0.0174 (4)	0.0201 (3)	−0.0011 (3)	0.0027 (3)	0.0002 (3)
C8	0.0269 (4)	0.0204 (4)	0.0195 (4)	0.0022 (3)	0.0032 (3)	0.0005 (3)
C13	0.0258 (4)	0.0187 (4)	0.0205 (3)	−0.0003 (3)	0.0028 (3)	0.0001 (3)
C1	0.0274 (4)	0.0184 (3)	0.0187 (3)	−0.0019 (3)	0.0022 (3)	0.0008 (3)
C2	0.0237 (4)	0.0180 (4)	0.0203 (3)	−0.0009 (3)	0.0039 (3)	0.0002 (3)
C10	0.0220 (4)	0.0202 (4)	0.0240 (4)	−0.0005 (3)	0.0023 (3)	0.0021 (3)
C14	0.0283 (5)	0.0213 (4)	0.0242 (4)	0.0036 (3)	0.0018 (3)	0.0009 (3)
C5	0.0242 (4)	0.0231 (4)	0.0249 (4)	0.0054 (3)	0.0015 (3)	−0.0018 (3)
C4	0.0228 (4)	0.0239 (4)	0.0253 (4)	0.0028 (3)	0.0008 (3)	−0.0031 (3)
C3	0.0245 (4)	0.0218 (4)	0.0284 (4)	−0.0008 (3)	0.0070 (3)	−0.0013 (3)
C11	0.0350 (5)	0.0218 (4)	0.0264 (4)	−0.0035 (4)	0.0023 (3)	−0.0035 (3)
C7	0.0366 (5)	0.0245 (4)	0.0227 (4)	0.0066 (3)	0.0052 (3)	0.0043 (3)
C15	0.0300 (5)	0.0225 (4)	0.0323 (5)	−0.0033 (4)	0.0008 (4)	−0.0055 (3)
C12	0.0353 (5)	0.0254 (4)	0.0294 (4)	0.0043 (4)	0.0085 (4)	−0.0033 (3)
C6	0.0328 (5)	0.0296 (4)	0.0243 (4)	0.0107 (4)	0.0006 (3)	0.0028 (3)
H8	0.052 (8)	0.040 (7)	0.030 (5)	0.002 (6)	0.000 (5)	−0.006 (5)
H10A	0.021 (6)	0.045 (7)	0.048 (6)	0.001 (5)	−0.004 (5)	0.012 (5)
H10B	0.045 (7)	0.024 (6)	0.035 (5)	0.000 (5)	0.018 (5)	−0.003 (5)
H14A	0.040 (7)	0.036 (7)	0.063 (7)	−0.002 (6)	−0.018 (6)	0.000 (6)
H14B	0.065 (9)	0.083 (11)	0.036 (7)	0.021 (8)	0.010 (6)	−0.003 (6)
H14C	0.045 (8)	0.046 (8)	0.057 (7)	0.007 (6)	0.008 (6)	0.020 (6)
H4	0.056 (8)	0.027 (6)	0.031 (6)	0.010 (5)	−0.005 (5)	−0.012 (5)
H3A	0.049 (7)	0.038 (7)	0.037 (6)	−0.002 (6)	0.017 (5)	−0.005 (5)
H3B	0.021 (6)	0.042 (7)	0.067 (8)	−0.003 (5)	0.005 (5)	0.002 (6)
H11A	0.074 (10)	0.059 (9)	0.024 (6)	−0.011 (7)	0.015 (6)	−0.012 (5)
H11B	0.074 (9)	0.037 (7)	0.044 (7)	0.000 (7)	−0.018 (6)	−0.008 (6)
H7A	0.066 (9)	0.043 (7)	0.041 (7)	0.006 (6)	0.011 (6)	0.022 (5)
H7B	0.051 (8)	0.045 (7)	0.036 (6)	0.016 (6)	0.004 (5)	0.000 (6)
H15A	0.034 (8)	0.059 (9)	0.098 (10)	0.006 (7)	−0.012 (7)	−0.023 (7)
H15B	0.086 (11)	0.032 (7)	0.060 (8)	−0.021 (7)	−0.008 (7)	0.003 (6)
H15C	0.056 (9)	0.081 (10)	0.044 (7)	−0.013 (8)	0.011 (6)	−0.037 (7)
H12A	0.047 (8)	0.076 (10)	0.053 (7)	−0.037 (7)	0.023 (6)	−0.029 (7)
H12B	0.119 (13)	0.032 (7)	0.045 (7)	−0.005 (8)	0.018 (7)	0.008 (6)
H12C	0.072 (10)	0.061 (9)	0.058 (8)	0.041 (8)	0.001 (7)	−0.013 (6)
H6A	0.054 (8)	0.042 (7)	0.053 (7)	0.022 (6)	0.009 (6)	0.007 (6)
H6B	0.041 (7)	0.049 (7)	0.031 (6)	0.000 (6)	0.006 (5)	0.002 (5)
H11C	0.046 (8)	0.050 (8)	0.052 (7)	−0.007 (6)	−0.005 (6)	−0.013 (6)

Geometric parameters (Å, º) top

O1—C1	1.2144 (9)	C5—C6	1.5121 (11)
C9—C8	1.3391 (10)	C4—C3	1.5069 (11)
C9—C10	1.5207 (10)	C4—H4	1.104 (9)
C9—C11	1.5005 (10)	C3—H3A	1.094 (10)
C8—C7	1.5002 (10)	C3—H3B	1.089 (11)
C8—H8	1.076 (10)	C11—H11A	1.086 (11)
C13—C2	1.3460 (10)	C11—H11B	1.056 (12)
C13—C14	1.5015 (11)	C11—H11C	1.073 (13)
C13—C15	1.5015 (11)	C7—C6	1.5597 (12)
C1—C2	1.5035 (10)	C7—H7A	1.105 (10)
C1—C10	1.5292 (10)	C7—H7B	1.091 (11)
C2—C3	1.5221 (10)	C15—H15A	1.052 (12)
C10—H10A	1.096 (10)	C15—H15B	1.081 (12)
C10—H10B	1.105 (9)	C15—H15C	1.074 (11)
C14—H14A	1.069 (11)	C12—H12A	1.081 (11)
C14—H14B	1.072 (11)	C12—H12B	1.091 (11)
C14—H14C	1.072 (11)	C12—H12C	1.080 (12)
C5—C4	1.3387 (11)	C6—H6A	1.093 (11)
C5—C12	1.5017 (10)	C6—H6B	1.099 (11)

C10—C9—C8	118.81 (7)	H3A—C3—C4	111.5 (6)
C11—C9—C8	125.55 (7)	H3B—C3—C2	110.6 (6)
C11—C9—C10	115.40 (6)	H3B—C3—C4	111.4 (6)
C7—C8—C9	127.62 (7)	H3B—C3—H3A	107.7 (8)
H8—C8—C9	117.5 (5)	H11A—C11—C9	111.7 (6)
H8—C8—C7	113.9 (5)	H11B—C11—C9	113.1 (5)
C14—C13—C2	123.16 (7)	H11B—C11—H11A	107.7 (10)
C15—C13—C2	123.20 (7)	H11C—C11—C9	109.5 (6)
C15—C13—C14	113.64 (7)	H11C—C11—H11A	107.8 (9)
C2—C1—O1	120.18 (7)	H11C—C11—H11B	106.8 (9)
C10—C1—O1	120.26 (7)	C6—C7—C8	108.86 (7)
C10—C1—C2	119.26 (6)	H7A—C7—C8	111.8 (6)
C1—C2—C13	120.78 (7)	H7A—C7—C6	108.6 (6)
C3—C2—C13	124.74 (7)	H7B—C7—C8	111.3 (5)
C3—C2—C1	114.46 (6)	H7B—C7—C6	109.4 (6)
C1—C10—C9	105.39 (6)	H7B—C7—H7A	106.8 (8)
H10A—C10—C9	112.6 (6)	H15A—C15—C13	114.5 (7)
H10A—C10—C1	108.7 (5)	H15B—C15—C13	110.1 (7)
H10B—C10—C9	109.9 (5)	H15B—C15—H15A	109.4 (11)
H10B—C10—C1	110.1 (5)	H15C—C15—C13	110.1 (7)
H10B—C10—H10A	110.1 (8)	H15C—C15—H15A	106.7 (9)
H14A—C14—C13	114.5 (6)	H15C—C15—H15B	105.6 (10)
H14B—C14—C13	111.5 (7)	H12A—C12—C5	112.9 (6)
H14B—C14—H14A	108.8 (10)	H12B—C12—C5	112.7 (6)
H14C—C14—C13	108.4 (6)	H12B—C12—H12A	107.5 (9)
H14C—C14—H14A	106.8 (8)	H12C—C12—C5	111.2 (6)
H14C—C14—H14B	106.4 (9)	H12C—C12—H12A	108.4 (11)
C12—C5—C4	124.64 (7)	H12C—C12—H12B	103.6 (10)
C6—C5—C4	118.79 (7)	C7—C6—C5	109.43 (6)
C6—C5—C12	115.89 (7)	H6A—C6—C5	112.5 (6)
C3—C4—C5	128.07 (7)	H6A—C6—C7	108.4 (6)
H4—C4—C5	117.7 (5)	H6B—C6—C5	108.7 (6)
H4—C4—C3	113.2 (5)	H6B—C6—C7	108.6 (6)
C4—C3—C2	107.30 (6)	H6B—C6—H6A	109.2 (8)
H3A—C3—C2	108.4 (6)

O1—C1—C2—C13	123.05 (8)	C8—C7—C6—C5	−46.11 (7)
O1—C1—C2—C3	−58.17 (8)	C13—C2—C1—C10	−63.20 (8)
O1—C1—C10—C9	80.30 (8)	C13—C2—C3—C4	94.67 (8)
C9—C8—C7—C6	110.92 (9)	C1—C2—C3—C4	−84.06 (6)
C9—C10—C1—C2	−93.45 (6)	C2—C3—C4—C5	110.80 (7)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C8—H8···O1ⁱ	1.076 (10)	2.590 (10)	3.6245 (10)	161.0 (8)
C10—H10B···O1ⁱ	1.105 (9)	2.695 (10)	3.7028 (10)	151.3 (7)
C14—H14B···O1ⁱ	1.072 (11)	2.552 (12)	3.2434 (10)	121.5 (9)
C4—H4···O1ⁱ	1.104 (9)	3.356 (10)	4.1760 (9)	132.0 (6)
C11—H11C···O1ⁱⁱ	1.073 (13)	3.177 (12)	4.1177 (11)	146.9 (9)

Symmetry codes: (i) x, −y+1, z+1/2; (ii) −x+1/2, y−1/2, −z+1/2.

Comparison of bond lengths (Å) determined from the current single-crystal X-ray study and from the powder study by Kaduk et al. (2022) top

Atom	Atom	Current single-crystal X-ray study	Previous powder study*
O1	C1	1.2144 (9)	1.212 (10)
C1	C2	1.5035 (10)	1.558 (10)
C2	C3	1.5221 (10)	1.516 (11)
C4	C3	1.5069 (11)	1.513 (12)
C5	C4	1.3387 (11)	1.314 (11)
C5	C12	1.5017 (10)	1.395 (12)
C5	C6	1.5121 (11)	1.497 (12)
C7	C6	1.5597 (12)	1.518 (15)
C1	C10	1.5292 (10)	1.514 (12)
C9	C8	1.3391 (10)	1.326 (13)
C9	C10	1.5207 (10)	1.576 (12)
C9	C11	1.5005 (10)	1.537 (13)
C8	C7	1.5002 (10)	1.484 (13)
C13	C2	1.3460 (10)	1.405 (10)
C13	C14	1.5015 (11)	1.601 (11)
C13	C15	1.5015 (11)	1.574 (11)

Note: (*) atom labels were adopted from the current single-crystal X-ray study for better comparison.

Acknowledgements

The European Union-NextGenerationEU provided funding through the National Recovery and Resilience Plan of the Republic of Bulgaria. The Studienstiftung des Deutschen Volkes is thanked for the award of a PhD fellowship to FM.

Funding information

Funding for this research was provided by: European Union-NextGenerationEU (grant No. BG-RRP-2.004-0009-C02).

References

Bourhis, L. J., Dolomanov, O. V., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2015). Acta Cryst. A71, 59–75. Web of Science CrossRef IUCr Journals Google Scholar
Clardy, J. C. & Lobkovsky, E. (1999). CCDC 102883: Experimental Crystal Structure Determination. Google Scholar
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341. Web of Science CrossRef CAS IUCr Journals Google Scholar
Kaduk, J. A., Gates-Rector, S. & Blanton, T. N. (2022). Powder Diffr. 37, 98–104. CrossRef CAS Google Scholar
Kleemiss, F., Dolomanov, O. V., Bodensteiner, M., Peyerimhoff, N., Midgley, L., Bourhis, L. J., Genoni, A., Malaspina, L. A., Jayatilaka, D., Spencer, J. L., White, F., Grundkötter-Stock, B., Steinhauer, S., Lentz, D., Puschmann, H. & Grabowsky, S. (2021). Chem. Sci. 12, 1675–1692. Web of Science CSD CrossRef CAS Google Scholar
Rigaku OD (2023). CrysAlis PRO. Agilent Technologies Ltd, Yarnton, Oxfordshire, England. Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006–1011. Web of Science CrossRef CAS IUCr Journals Google Scholar
Woińska, M., Grabowsky, S., Dominiak, P. M., Woźniak, K. & Jayatilaka, D. (2016). Sci. Adv. 2, e1600192. Web of Science PubMed Google Scholar

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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Redetermination of germacrone type II based on single-crystal X-ray data

Structure description

Synthesis and crystallization

Refinement

Structural data

Acknowledgements

Funding information

References

organic compounds