3aH,4H,5H,8H,9H,9aH-Cyclo­octa­[d][1,3]dioxole-2-thione

Schollmeyer, D.; Kammler, C.; Detert, H.

doi:10.1107/S2414314624010198

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 9| Part 11| November 2024| x241019

https://doi.org/10.1107/S2414314624010198

Open

access

3aH,4H,5H,8H,9H,9aH-Cycloocta[d][1,3]dioxole-2-thione

Dieter Schollmeyer,^a Claudia Kammler ^a and Heiner Detert ^a ^*

^aUniversity of Mainz, Department of Chemistry, Duesbergweg 10-14, 55099 Mainz, Germany
^*Correspondence e-mail: detert@uni-mainz.de

Edited by M. Bolte, Goethe-Universität Frankfurt, Germany (Received 4 October 2024; accepted 18 October 2024; online 8 November 2024)

The thionocarbonate of trans-cyclooctenediol, C₉H₁₂O₂S, crystallizes with a 9/1 disorder in the position of the R,R and S,S-enantiomers. As a result of trans-annulation, both rings adopt a twist conformation.

Keywords: crystal structure; sulfur; heterocycles.

CCDC reference: 2391879

Structure description

Cyclic thionocarbonates, 1,3-dioxolan-2-thiones, are important intermediates for several transformations (Klein et al., 2022 ; Rizzo & Trauner, 2018 ). Outstanding in this context is the Corey–Winter reaction, a reductive desulfuration with fragmentation of the heterocycle leading to alkenes (Corey et al. 1965 ). This method allows cis–trans isomerizations of alkenes and the synthesis of strained compounds (Paquette et al., 1975 ; Daub et al., 1972 ). As part of our interest in strained hydrocarbons (Detert & Meier, 1997a ,b ), the title compound was prepared as a precursor for the ‘labile’ 1,5-cyclooctadiene (Ziegler & Wilms, 1950 ). The racemate crystallizes with disorder, the positions of the title molecule are filled in a 9/1 ratio with S,S- and R,R-enantiomers (Fig. 1). As a result of trans-annulation located on C3,C10, both rings adopt a twist conformation. Furthermore, the eight-membered ring forms two planes, the olefinic unit (C5,C6,C7,C8) with maximum deviation of 0.008 (7) Å from the mean plane and the aliphatic part (C4,C5,C8,C9), maximum deviation 0.051 (8) Å. Then angle between the mean planes amounts to 67.5 (5)°. The cyclic thionocarbonate is nearly planar, C3 lies slightly above the mean plane [0.092 (8) Å] and C10 similarly below [0.094 (2) Å]. The exocyclic sulfur atom deviates from this plane by just 0.01 (2) Å. The packing is shown in Fig. 2.

Figure 1
View of the title compound. Displacement ellipsoids are drawn at the 50% probability level. Bonds involving the lower occupied sites are drawn with broken tubes.

Figure 2
Part of the packing diagram. View along the c-axis. Minor occupied sites are omitted for clarity.

Synthesis and crystallization

(5Z-1,2-trans)-Cyclooct-5-ene-1,2-diol (3.00 g, 0.02 mol, 1.00 eq), 4-dimethylaminopyridine (DMAP; 5.86 g, 0.05 mol, 2.40 eq), pyridine (32.24 ml, 0.40 mol) and dichloromethane (40.00 ml) were placed in a flask with a magnetic stirrer under a nitrogen atmosphere. The mixture was cooled in ice–water, while a solution of thiophosgene (2.76 g, 0.02 mol, 1.20 eq) in dichloromethane (20.00 ml) was added over 1 h, after one additional hour the reaction mixture was allowed to warm up to room temperature and was stirred for 16 h. The solvent was removed by distillation. The reaction mixture was diluted with a saturated sodium chloride solution (40.00 ml). The aqueous phase was separated and extracted with ethyl acetate (4 × 50.00 ml). The combined organic phases were dried over magnesium sulfate. The mixture was filtered to remove the magnesium sulfate and the solvent was removed under reduced pressure. The crude product was purified by column chromatography (EtOAc:cyclohexane = 1:3). The light-orange solid obtained was recrystallized from cyclohexane solution. (Z)-3a,4,5,8,9,9a-Hexahydrocycloocta[d][1,3]dioxole-2-thione (0.38 g, 2.00 mmol, 10%) was obtained as colorless crystals. TLC: R_f = 0.46 (EtOAc:Cyclohexane = 1:3). Melting range: (EtOAc) = 127–132°C. ESI–HRMS (pos.): calc. [C₉H₁₂O₂S]⁺: m/z = 185.0631, found: m/z = 185.0632. ¹H-NMR: (300 MHz, CDCl₃); δ [p.p.m.] = 5.70–5.58 (m, 2H, 5-CH, 6-CH), 4.72–4.62 (m, 2H, 2-CH, 9-CH), 2.36–2.23 (m, 4H, 4-CH₂, 7-CH₂), 2.23–2.13 (m, 2H, 3-CH₂, 8-CH₂), 1.77–1.61 (m, 2H, 3-CH₂, 8-CH₂). ¹³C-NMR: (75 MHz, CDCl₃); δ [p.p.m.] = 191.51 (1 C, C=S), 129.21 (2 C, 5-CH, 6-CH), 87.27 (2 C, 2-CH, 9-CH), 29.23 (2 C, 3-CH₂, 8-CH₂), 20.66 (2 C, 4-CH₂, 7-CH₂). The assignment of H- and C-signals is based on HH-Cosy, HMBC– and HSQC– experiments. IR: 3018 (w), 2952 (w), 1449 (w), 1322 (s), 1257 (s), 1039 (s), 965 (s), 878 (w), 783 (m), 595 (w) cm⁻¹.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 1. Hydrogen atoms were placed at calculated positions and were refined in the riding-model approximation with C_aromatic–H = 0.95 Å, C_methylene–H = 0.99 Å, and with U_iso(H) = 1.2 U_eq(C). The site occupation factors were kept fixed at 0.9 and 0.1 for the disordered sites. The displacement parameters of the disordered C and O atoms were constrained to be equal for the corresponding sites. The absolute structure could not be determined reliably.

Table 1
Experimental details

Crystal data
Chemical formula	C₉H₁₂O₂S
M_r	184.25
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	120
a, b, c (Å)	7.5555 (9), 15.7119 (17), 7.4892 (8)
V (Å³)	889.05 (17)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.32
Crystal size (mm)	0.57 × 0.09 × 0.03

Data collection
Diffractometer	Stoe IPDS 2T
Absorption correction	Integration
T_min, T_max	0.898, 0.989
No. of measured, independent and observed [I > 2σ(I)] reflections	3713, 1963, 1439
R_int	0.055
(sin θ/λ)_max (Å⁻¹)	0.660

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.070, 0.159, 1.10
No. of reflections	1963
No. of parameters	121
No. of restraints	6
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.32, −0.29
Absolute structure	Classical Flack method preferred over Parsons because s.u. lower.
Absolute structure parameter	0.3 (3)
Computer programs: X-AREA WinXpose, Recipe and Integrate (Stoe & Cie, 2020 ), SHELXT2014 (Sheldrick, 2015a ), SHELXL2019/2 (Sheldrick, 2015b ) and PLATON (Spek, 2020 ).

Structural data

CCDC reference: 2391879

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S2414314624010198/bt4155sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314624010198/bt4155Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314624010198/bt4155Isup3.cml

checkCIF report

Computing details top

3aH,4H,5H,8H,9H,9aH-Cycloocta[d][1,3]dioxole-2-thione top

Crystal data top

C₉H₁₂O₂S	D_x = 1.377 Mg m⁻³
M_r = 184.25	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pna2₁	Cell parameters from 3621 reflections
a = 7.5555 (9) Å	θ = 3.0–28.2°
b = 15.7119 (17) Å	µ = 0.32 mm⁻¹
c = 7.4892 (8) Å	T = 120 K
V = 889.05 (17) Å³	Needle, colorless
Z = 4	0.57 × 0.09 × 0.03 mm
F(000) = 392

Data collection top

Stoe IPDS 2T diffractometer	1963 independent reflections
Radiation source: sealed X-ray tube, 12x0.4mm long-fine focus	1439 reflections with I > 2σ(I)
Detector resolution: 6.67 pixels mm^-1	R_int = 0.055
rotation method, ω scans	θ_max = 28.0°, θ_min = 3.0°
Absorption correction: integration	h = −9→9
T_min = 0.898, T_max = 0.989	k = −20→20
3713 measured reflections	l = −9→8

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.070	w = 1/[σ²(F_o²) + (0.0349P)² + 2.2293P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.159	(Δ/σ)_max = 0.002
S = 1.10	Δρ_max = 0.32 e Å⁻³
1963 reflections	Δρ_min = −0.29 e Å⁻³
121 parameters	Absolute structure: Classical Flack method preferred over Parsons because s.u. lower.
6 restraints	Absolute structure parameter: 0.3 (3)
Primary atom site location: dual

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	Occ. (<1)
C1	0.5985 (9)	0.3473 (4)	0.6938 (9)	0.0291 (14)
O2	0.5867 (7)	0.3159 (3)	0.5280 (6)	0.0292 (12)	0.9
C3	0.4227 (10)	0.3437 (5)	0.4437 (10)	0.0267 (15)	0.9
H3	0.335024	0.296075	0.443307	0.032*	0.9
C4	0.4633 (10)	0.3704 (5)	0.2539 (10)	0.0324 (16)
H4A	0.495129	0.319495	0.183013	0.039*	0.9
H4B	0.566653	0.409199	0.254135	0.039*	0.9
H4C	0.448687	0.307895	0.247867	0.039*	0.1
H4D	0.575352	0.386047	0.193598	0.039*	0.1
C5	0.3070 (9)	0.4151 (5)	0.1658 (9)	0.0350 (16)
H5A	0.293459	0.472383	0.219282	0.042*
H5B	0.332900	0.422742	0.037191	0.042*
C6	0.1361 (10)	0.3678 (4)	0.1850 (10)	0.0357 (17)
H6	0.107377	0.326913	0.096048	0.043*
C7	0.0227 (9)	0.3789 (4)	0.3170 (11)	0.0334 (16)
H7	−0.080012	0.344029	0.318413	0.040*
C8	0.0442 (10)	0.4430 (4)	0.4663 (10)	0.0349 (16)
H8A	−0.073915	0.455640	0.517033	0.042*
H8B	0.091387	0.496579	0.415429	0.042*
C9	0.1672 (9)	0.4140 (5)	0.6185 (9)	0.0335 (17)
H9A	0.150571	0.452070	0.722425	0.040*	0.9
H9B	0.133462	0.355718	0.655515	0.040*	0.9
H9C	0.094452	0.382082	0.705681	0.040*	0.1
H9D	0.211017	0.465622	0.679986	0.040*	0.1
C10	0.3590 (11)	0.4144 (5)	0.5659 (10)	0.0307 (17)	0.9
H10	0.390122	0.470873	0.512854	0.037*	0.9
O11	0.4647 (7)	0.4000 (4)	0.7264 (6)	0.0317 (13)	0.9
S12	0.7542 (3)	0.32268 (11)	0.8348 (3)	0.0398 (4)
O2A	0.635 (6)	0.375 (3)	0.523 (6)	0.0292 (12)	0.1
C3A	0.465 (6)	0.400 (4)	0.446 (4)	0.0267 (15)	0.1
H3A	0.449620	0.463421	0.452080	0.032*	0.1
C10A	0.335 (7)	0.357 (4)	0.570 (6)	0.0307 (17)	0.1
H10A	0.297608	0.300001	0.521916	0.037*	0.1
O11A	0.430 (3)	0.347 (3)	0.740 (5)	0.0317 (13)	0.1

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.037 (4)	0.032 (3)	0.018 (3)	−0.007 (3)	0.000 (3)	0.001 (3)
O2	0.031 (3)	0.035 (3)	0.021 (3)	0.005 (2)	0.000 (2)	−0.001 (2)
C3	0.027 (4)	0.027 (3)	0.027 (4)	0.000 (3)	0.000 (3)	0.004 (3)
C4	0.040 (4)	0.035 (4)	0.022 (4)	0.003 (3)	0.005 (3)	0.003 (3)
C5	0.046 (4)	0.043 (4)	0.016 (3)	0.005 (4)	0.001 (3)	0.000 (3)
C6	0.046 (4)	0.033 (3)	0.028 (4)	0.002 (3)	−0.013 (4)	−0.002 (3)
C7	0.034 (3)	0.029 (3)	0.038 (5)	0.000 (3)	−0.005 (4)	0.001 (3)
C8	0.036 (4)	0.035 (3)	0.034 (4)	0.010 (3)	0.004 (3)	0.001 (3)
C9	0.040 (4)	0.036 (4)	0.025 (4)	0.006 (3)	0.003 (3)	−0.001 (3)
C10	0.045 (5)	0.029 (4)	0.019 (4)	0.005 (4)	−0.001 (3)	0.000 (3)
O11	0.041 (3)	0.037 (3)	0.017 (3)	0.004 (3)	−0.003 (2)	−0.005 (2)
S12	0.0412 (8)	0.0489 (9)	0.0293 (8)	−0.0041 (10)	−0.0065 (9)	0.0080 (10)
O2A	0.031 (3)	0.035 (3)	0.021 (3)	0.005 (2)	0.000 (2)	−0.001 (2)
C3A	0.027 (4)	0.027 (3)	0.027 (4)	0.000 (3)	0.000 (3)	0.004 (3)
C10A	0.045 (5)	0.029 (4)	0.019 (4)	0.005 (4)	−0.001 (3)	0.000 (3)
O11A	0.041 (3)	0.037 (3)	0.017 (3)	0.004 (3)	−0.003 (2)	−0.005 (2)

Geometric parameters (Å, º) top

C1—O11A	1.32 (3)	C6—H6	0.9500
C1—O11	1.330 (8)	C7—C8	1.515 (10)
C1—O2	1.339 (8)	C7—H7	0.9500
C1—O2A	1.38 (5)	C8—C9	1.539 (10)
C1—S12	1.627 (7)	C8—H8A	0.9900
O2—C3	1.458 (8)	C8—H8B	0.9900
C3—C4	1.514 (10)	C9—C10	1.502 (10)
C3—C10	1.517 (10)	C9—C10A	1.60 (7)
C3—H3	1.0000	C9—H9A	0.9900
C4—C3A	1.51 (3)	C9—H9B	0.9900
C4—C5	1.524 (10)	C9—H9C	0.9900
C4—H4A	0.9900	C9—H9D	0.9900
C4—H4B	0.9900	C10—O11	1.461 (8)
C4—H4C	0.9900	C10—H10	1.0000
C4—H4D	0.9900	O2A—C3A	1.46 (3)
C5—C6	1.497 (10)	C3A—C10A	1.52 (3)
C5—H5A	0.9900	C3A—H3A	1.0000
C5—H5B	0.9900	C10A—O11A	1.47 (3)
C6—C7	1.320 (10)	C10A—H10A	1.0000

O11—C1—O2	110.5 (6)	C7—C8—H8A	108.6
O11A—C1—O2A	116 (3)	C9—C8—H8A	108.6
O11A—C1—S12	122 (2)	C7—C8—H8B	108.6
O11—C1—S12	125.4 (5)	C9—C8—H8B	108.6
O2—C1—S12	124.2 (5)	H8A—C8—H8B	107.6
O2A—C1—S12	122.2 (17)	C10—C9—C8	112.8 (6)
C1—O2—C3	110.3 (5)	C8—C9—C10A	118.6 (17)
O2—C3—C4	108.5 (6)	C10—C9—H9A	109.0
O2—C3—C10	103.2 (6)	C8—C9—H9A	109.0
C4—C3—C10	115.3 (6)	C10—C9—H9B	109.0
O2—C3—H3	109.8	C8—C9—H9B	109.0
C4—C3—H3	109.8	H9A—C9—H9B	107.8
C10—C3—H3	109.8	C8—C9—H9C	107.7
C3—C4—C5	112.2 (6)	C10A—C9—H9C	107.7
C3A—C4—C5	105.9 (18)	C8—C9—H9D	107.7
C3—C4—H4A	109.2	C10A—C9—H9D	107.7
C5—C4—H4A	109.2	H9C—C9—H9D	107.1
C3—C4—H4B	109.2	O11—C10—C9	108.1 (5)
C5—C4—H4B	109.2	O11—C10—C3	102.1 (6)
H4A—C4—H4B	107.9	C9—C10—C3	117.5 (7)
C3A—C4—H4C	110.5	O11—C10—H10	109.6
C5—C4—H4C	110.5	C9—C10—H10	109.6
C3A—C4—H4D	110.5	C3—C10—H10	109.6
C5—C4—H4D	110.5	C1—O11—C10	111.1 (5)
H4C—C4—H4D	108.7	C1—O2A—C3A	106 (3)
C6—C5—C4	113.4 (6)	O2A—C3A—C4	107 (3)
C6—C5—H5A	108.9	O2A—C3A—C10A	102 (4)
C4—C5—H5A	108.9	C4—C3A—C10A	116 (4)
C6—C5—H5B	108.9	O2A—C3A—H3A	110.4
C4—C5—H5B	108.9	C4—C3A—H3A	110.4
H5A—C5—H5B	107.7	C10A—C3A—H3A	110.4
C7—C6—C5	124.5 (7)	O11A—C10A—C3A	105 (4)
C7—C6—H6	117.8	O11A—C10A—C9	104 (4)
C5—C6—H6	117.8	C3A—C10A—C9	113 (4)
C6—C7—C8	124.9 (6)	O11A—C10A—H10A	111.2
C6—C7—H7	117.6	C3A—C10A—H10A	111.2
C8—C7—H7	117.6	C9—C10A—H10A	111.2
C7—C8—C9	114.5 (6)	C1—O11A—C10A	104 (3)

O11—C1—O2—C3	−5.2 (7)	S12—C1—O11—C10	174.4 (5)
S12—C1—O2—C3	174.1 (5)	C9—C10—O11—C1	138.8 (6)
C1—O2—C3—C4	136.5 (6)	C3—C10—O11—C1	14.3 (8)
C1—O2—C3—C10	13.7 (7)	O11A—C1—O2A—C3A	2 (5)
O2—C3—C4—C5	−169.9 (6)	S12—C1—O2A—C3A	−173 (3)
C10—C3—C4—C5	−54.7 (9)	C1—O2A—C3A—C4	−140 (3)
C3—C4—C5—C6	−49.4 (8)	C1—O2A—C3A—C10A	−17 (5)
C3A—C4—C5—C6	−87 (2)	C5—C4—C3A—O2A	−167 (3)
C4—C5—C6—C7	91.1 (8)	C5—C4—C3A—C10A	80 (4)
C5—C6—C7—C8	2.1 (11)	O2A—C3A—C10A—O11A	26 (6)
C6—C7—C8—C9	−81.3 (9)	C4—C3A—C10A—O11A	142 (4)
C7—C8—C9—C10	72.8 (8)	O2A—C3A—C10A—C9	139 (4)
C7—C8—C9—C10A	35 (3)	C4—C3A—C10A—C9	−105 (4)
C8—C9—C10—O11	170.6 (6)	C8—C9—C10A—O11A	175 (3)
C8—C9—C10—C3	−74.7 (9)	C8—C9—C10A—C3A	61 (4)
O2—C3—C10—O11	−15.9 (7)	O2A—C1—O11A—C10A	15 (5)
C4—C3—C10—O11	−134.1 (6)	S12—C1—O11A—C10A	−170 (3)
O2—C3—C10—C9	−134.0 (6)	C3A—C10A—O11A—C1	−25 (6)
C4—C3—C10—C9	107.9 (7)	C9—C10A—O11A—C1	−144 (3)
O2—C1—O11—C10	−6.3 (8)

References

Corey, E. J., Carey, F. A. & Winter, R. A. E. (1965). J. Am. Chem. Soc. 87, 934–935. CrossRef CAS Web of Science Google Scholar
Daub, J. & Erhardt, U. (1972). Tetrahedron, 28, 181–186. CrossRef CAS Web of Science Google Scholar
Detert, H. & Meier, H. (1997). Liebigs Ann. Recl, pp. 1557–1563. Google Scholar
Detert, H. & Meier, H. (1997). Liebigs Ann. Recl, pp. 1565–1570. Google Scholar
Klein, M. T., Krause, B. M., Neudörfl, J.-M., Kühne, R. & Schmalz, H.-G. (2022). Org. Biomol. Chem. 20, 9368–9377. Web of Science CSD CrossRef CAS PubMed Google Scholar
Paquette, L. A., Itoh, I. & Farnham, W. B. (1975). J. Am. Chem. Soc. 97, 7280–7285. CrossRef CAS Web of Science Google Scholar
Rizzo, A. & Trauner, D. (2018). Org. Lett. 20, 1841–1844. Web of Science CSD CrossRef CAS PubMed Google Scholar
Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Spek, A. L. (2020). Acta Cryst. E76, 1–11. Web of Science CrossRef IUCr Journals Google Scholar
Stoe & Cie (2020). X-RED and X-AREA. Stoe & Cie, Darmstadt, Germany. Google Scholar
Ziegler, K. & Wilms, H. (1950). Justus Liebigs Ann. Chem. 567, 1–43. CrossRef CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.