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

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

doi:10.1107/S2414314624003468

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

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.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S2414314624003468/wm4211sup1.cif Contains datablock I
	Structure factor file (CIF format) https://doi.org/10.1107/S2414314624003468/wm4211Isup2.hkl Contains datablock I

CCDC reference: 2349265

checkCIF report

Key indicators

Structure: I

Single-crystal X-ray study
T = 100 K
R factor = 0.029
wR factor = 0.077
Data-to-parameter ratio = 7.5

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT088_ALERT_3_B Poor Data / Parameter Ratio ....................       7.52 Note

Alert level C
PLAT351_ALERT_3_C Long   C-H (X0.96,N1.08A)  C7       - H7A      .       1.11 Ang.
PLAT351_ALERT_3_C Long   C-H (X0.96,N1.08A)  C10      - H10B     .       1.11 Ang.
PLAT481_ALERT_4_C Long D...A H-Bond Reported C4       ..O1       .       4.18 Ang.
PLAT481_ALERT_4_C Long D...A H-Bond Reported C11      ..O1       .       4.12 Ang.
PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          7 Report
                0 10  0, -22  0  4,  -4  0 12,  -2  0 12,   0  0 12,   2  0 12,
                4  0 12,

Alert level G
PLAT068_ALERT_1_G Reported F000 Differs from Calcd (or Missing)...     Please Check
PLAT480_ALERT_4_G Long H...A H-Bond Reported H10B     ..O1       .       2.69 Ang.
PLAT480_ALERT_4_G Long H...A H-Bond Reported H4       ..O1       .       3.36 Ang.
PLAT480_ALERT_4_G Long H...A H-Bond Reported H11C     ..O1       .       3.18 Ang.
PLAT795_ALERT_4_G C-Atom in CIF Coordinate List Out-of-Sequence ..         C8 Note
PLAT802_ALERT_4_G CIF Input Record(s) with more than 80 Characters          2 Info
PLAT883_ALERT_1_G No Info/Value for _atom_sites_solution_primary .     Please Do !
PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         40 Note
PLAT960_ALERT_3_G Number of Intensities with I  <   - 2*sig(I) ...          1 Check
PLAT969_ALERT_5_G The 'Henn et al.' R-Factor-gap value ...........       3.15 Note
              Predicted wR2: Based on SigI   2  2.43 or SHELX Weight  7.70       
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.         10 Info
PLAT979_ALERT_1_G NoSpherA2 Scattering Factors Used ..............     Please Note

   0 ALERT level A = Most likely a serious problem - resolve or explain
   1 ALERT level B = A potentially serious problem, consider carefully
   5 ALERT level C = Check. Ensure it is not caused by an omission or oversight
  12 ALERT level G = General information/check it is not something unexpected

   3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   5 ALERT type 3 Indicator that the structure quality may be low
   8 ALERT type 4 Improvement, methodology, query or suggestion
   1 ALERT type 5 Informative message, check

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.

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