(−)-(1S,5R)-2-Oxabicyclo­[3.3.1]nonan-3-one

Olejniczak, T.; Białońska, A.

doi:10.1107/S1600536810014339

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 66| Part 5| May 2010| Page o1163

https://doi.org/10.1107/S1600536810014339

Open

access

(−)-(1S,5R)-2-Oxabicyclo[3.3.1]nonan-3-one

Teresa Olejniczak ^a and Agata Białońska ^b ^*

^aDepartment of Chemistry, Wrocław University of Environmental and Life Sciences, 25. Norwida, 50-375 Wrocław, Poland, and ^bFaculty of Chemistry, University of Wrocław, 14. F. Joliot-Curie, 50-383 Wrocław, Poland
^*Correspondence e-mail: bialonsk@eto.wchuwr.pl

(Received 29 March 2010; accepted 19 April 2010; online 24 April 2010)

In the title compound, C₈H₁₂O₂, the cyclohexane ring exhibits a chair conformation and the δ-lactone ring is axially bonded to the cyclohexane ring. In the crystal, molecules are linked by C—H⋯O hydrogen bonds, resulting in ribbons extending along [010].

Related literature

For the synthesis and confirmation of the absolute configuration of the title compound, see Olejniczak (2010 ); Wascholowski et al. (2008 ); Tzvetkov et al. (2006 ); Xu et al. (2002 ). For related structures see: Yokoyama et al. (2003 ); Schmidt et al. (1998 ); Finet et al. (2007 ); Militsina et al. (2005 ).

Experimental

Crystal data

C₈H₁₂O₂
M_r = 140.18
Orthorhombic, P 2₁ 2₁ 2₁
a = 6.793 (2) Å
b = 7.467 (2) Å
c = 14.170 (4) Å
V = 718.7 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 100 K
0.30 × 0.14 × 0.10 mm

Data collection

Kuma KM-4-CCD diffractometer
4925 measured reflections
935 independent reflections
685 reflections with I > 2σ(I)
R_int = 0.051

Refinement

R[F² > 2σ(F²)] = 0.043
wR(F²) = 0.096
S = 1.04
935 reflections
92 parameters
H-atom parameters constrained
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C1—H1⋯O2ⁱ	1.00	2.58	3.224 (3)	122
Symmetry code: (i) $[-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Bruker, 1999 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810014339/hg2667sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810014339/hg2667Isup2.hkl

checkCIF report

Comment top

The titled compound, C₈H₁₂O₂, was prepared in a three step synthesis (Fig. 2). Racemic diethyl 2-(3-oxocyclohexyl)malonate (1) was synthesized as a product of Michael addition of diethyl malonate to cyclohex-2-en-1-one. (-)-Diethyl 2-((S)-3-oxocyclohexyl)malonate ((-)-1) (ee=98%) and (+)-diethyl 2-((1R, 3R)-3-hydroxycyclohexyl)malonate ((+)-2) (ee=99%) were isolated by micriobial bioreduction using Absidia coerulea AM 93. Hydroxydiester-(+)-2 was subjected to chemical lactonization, leading to (-)-(1S, 5R)-2-oxabicyclo[3.3.1]nonan-3-one ((-)-3) [for more details see Olejniczak, 2010].

The molecular structure of the title compound is shown in Fig. 1. Bond lengths and angles in (-)-3 are similar to those observed in related structures [Yokoyama et al., 2003; Schmidt et al., 1998; Finet et al., 2007]. As in these related structures, in (-)-3 the cyclohexane ring reveals chair conformation (Fig. 1) and the δ-lactone ring is axially bonded to the cyclohexane ring.

It is worth mentioning that the conformation of the δ-lactone ring differs a little from those observed in the related structures. According to the numbering scheme employed in this paper, the torsion angles C1 O2 C3 C4 and O2 C3 C4 C5 in the related structures are in the range -7.1 - 0.4 ° and 0.0 - 8.8 °, respectively, and in (-)-3 values of suitable torsion angles are equal to -18.1 (3) and 23.3 (4) °. However, the values of the torsion angles are similar to those, -17.5 and 25.5 °, observed in one of crystallographically unrelated molecules of 3,9,12a-trimethyl-5-oxotetradecahydro-3,6a- methanonaphtho[2,1-d]oxocine-9-carboxylic acid, in which δ-lactone ring axially bonded to cyclohexane ring is observed [Militsina et al., 2005].

The structure of (-)-3 is stabilized by weak intermolecular C—H···O hydrogen bonds and van der Waals contacts. Molecules of (-)-3 are linked by the C1—H1···O2(2-x, 0.5+y, 0.5-z) hydrogen bonds, resulting in ribbons extended along the [010] direction (Table 1, Fig. 3).

Related literature top

For the synthesis and conformation of the absolute configuration of the title compound, see Olejniczak (2010); Wascholowski et al. (2008); Tzvetkov et al. (2006); Xu et al. (2002). For related structures see: Yokoyama et al. (2003); Schmidt et al. (1998); Finet et al. (2007); Militsina et al., (2005).

Experimental top

Crystals suitable for X-ray structure analysis were obtained directly after purification by column chromatography by slow evaporation of the eluent (petroleum ether : aceton : iso-propanol : ethyl acetate (40:1:3:1) v/v) at room temperature.

Structure description top

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: XP (Bruker, 1999); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. Selected view of (-)-3 (30% probability thermal ellipsoids).
	Fig. 2. Scheme of a three step synthesis of (-)-3.
	Fig. 3. Packing of (-)-3.

(-)-(1S,5R)-2-Oxabicyclo[3.3.1]nonan-3-one top

Crystal data top

C₈H₁₂O₂	F(000) = 304
M_r = 140.18	D_x = 1.295 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1754 reflections
a = 6.793 (2) Å	θ = 3.0–28.8°
b = 7.467 (2) Å	µ = 0.09 mm⁻¹
c = 14.170 (4) Å	T = 100 K
V = 718.7 (4) Å³	Needle, colorless
Z = 4	0.30 × 0.14 × 0.10 mm

Data collection top

Kuma KM-4-CCD diffractometer	685 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	R_int = 0.051
Graphite monochromator	θ_max = 27.0°, θ_min = 3.1°
ω scan	h = −8→8
4925 measured reflections	k = −9→9
935 independent reflections	l = −15→18

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)] = 0.043	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.096	H-atom parameters constrained
S = 1.04	w = 1/[σ²(F_o²) + (0.0507P)²] where P = (F_o² + 2F_c²)/3
935 reflections	(Δ/σ)_max = 0.004
92 parameters	Δρ_max = 0.35 e Å⁻³
0 restraints	Δρ_min = −0.16 e Å⁻³

Crystal data top

C₈H₁₂O₂	V = 718.7 (4) Å³
M_r = 140.18	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.793 (2) Å	µ = 0.09 mm⁻¹
b = 7.467 (2) Å	T = 100 K
c = 14.170 (4) Å	0.30 × 0.14 × 0.10 mm

Data collection top

Kuma KM-4-CCD diffractometer	685 reflections with I > 2σ(I)
4925 measured reflections	R_int = 0.051
935 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.043	0 restraints
wR(F²) = 0.096	H-atom parameters constrained
S = 1.04	Δρ_max = 0.35 e Å⁻³
935 reflections	Δρ_min = −0.16 e Å⁻³
92 parameters

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.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
C1	0.9078 (4)	0.4787 (3)	0.29810 (17)	0.0293 (6)
H1	1.0256	0.4916	0.2564	0.035*
O2	0.8893 (3)	0.2882 (2)	0.32719 (12)	0.0331 (5)
C3	0.7920 (4)	0.2414 (4)	0.40668 (17)	0.0302 (6)
O3	0.7539 (3)	0.0838 (2)	0.41770 (13)	0.0389 (5)
C4	0.7539 (4)	0.3815 (3)	0.48057 (18)	0.0300 (6)
H4A	0.8553	0.3693	0.5304	0.036*
H4B	0.6247	0.3561	0.5100	0.036*
C5	0.7535 (4)	0.5754 (3)	0.44672 (17)	0.0287 (6)
H5	0.7674	0.6561	0.5027	0.034*
C6	0.5660 (4)	0.6256 (4)	0.39356 (19)	0.0347 (7)
H6B	0.4509	0.6041	0.4349	0.042*
H6A	0.5695	0.7549	0.3782	0.042*
C7	0.5413 (4)	0.5192 (4)	0.30310 (17)	0.0344 (7)
H7B	0.4290	0.5683	0.2669	0.041*
H7A	0.5108	0.3931	0.3189	0.041*
C8	0.7258 (4)	0.5254 (4)	0.24230 (17)	0.0334 (6)
H8B	0.7115	0.4402	0.1892	0.040*
H8A	0.7407	0.6471	0.2155	0.040*
C9	0.9334 (4)	0.5985 (4)	0.38359 (19)	0.0302 (7)
H9B	0.9457	0.7250	0.3635	0.036*
H9A	1.0542	0.5648	0.4184	0.036*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0333 (15)	0.0256 (14)	0.0290 (14)	0.0004 (12)	0.0060 (13)	0.0044 (12)
O2	0.0360 (11)	0.0311 (10)	0.0322 (10)	0.0031 (8)	0.0082 (9)	−0.0003 (9)
C3	0.0285 (15)	0.0334 (16)	0.0286 (14)	0.0022 (12)	−0.0040 (12)	0.0043 (12)
O3	0.0434 (11)	0.0284 (10)	0.0451 (11)	−0.0025 (10)	−0.0047 (11)	0.0059 (9)
C4	0.0245 (14)	0.0393 (15)	0.0261 (12)	−0.0021 (14)	0.0014 (13)	0.0003 (11)
C5	0.0291 (14)	0.0297 (14)	0.0273 (13)	−0.0034 (13)	−0.0009 (13)	−0.0068 (11)
C6	0.0268 (15)	0.0336 (16)	0.0435 (17)	0.0048 (12)	0.0036 (13)	−0.0038 (13)
C7	0.0284 (14)	0.0368 (16)	0.0381 (17)	−0.0040 (12)	−0.0047 (12)	0.0040 (14)
C8	0.0429 (17)	0.0314 (14)	0.0259 (13)	−0.0055 (14)	−0.0033 (13)	0.0012 (11)
C9	0.0242 (14)	0.0312 (15)	0.0353 (16)	−0.0039 (12)	−0.0012 (12)	0.0037 (12)

Geometric parameters (Å, º) top

C1—O2	1.486 (3)	C5—H5	1.0000
C1—C8	1.509 (3)	C6—C7	1.517 (4)
C1—C9	1.516 (4)	C6—H6B	0.9900
C1—H1	1.0000	C6—H6A	0.9900
O2—C3	1.352 (3)	C7—C8	1.522 (3)
C3—O3	1.215 (3)	C7—H7B	0.9900
C3—C4	1.502 (4)	C7—H7A	0.9900
C4—C5	1.526 (3)	C8—H8B	0.9900
C4—H4A	0.9900	C8—H8A	0.9900
C4—H4B	0.9900	C9—H9B	0.9900
C5—C9	1.524 (3)	C9—H9A	0.9900
C5—C6	1.526 (4)

O2—C1—C8	107.3 (2)	C7—C6—H6B	109.1
O2—C1—C9	110.7 (2)	C5—C6—H6B	109.1
C8—C1—C9	112.1 (2)	C7—C6—H6A	109.1
O2—C1—H1	108.9	C5—C6—H6A	109.1
C8—C1—H1	108.9	H6B—C6—H6A	107.9
C9—C1—H1	108.9	C6—C7—C8	111.8 (2)
C3—O2—C1	121.32 (19)	C6—C7—H7B	109.3
O3—C3—O2	117.5 (2)	C8—C7—H7B	109.3
O3—C3—C4	123.2 (2)	C6—C7—H7A	109.3
O2—C3—C4	119.0 (2)	C8—C7—H7A	109.3
C3—C4—C5	116.2 (2)	H7B—C7—H7A	107.9
C3—C4—H4A	108.2	C1—C8—C7	111.8 (2)
C5—C4—H4A	108.2	C1—C8—H8B	109.3
C3—C4—H4B	108.2	C7—C8—H8B	109.3
C5—C4—H4B	108.2	C1—C8—H8A	109.3
H4A—C4—H4B	107.4	C7—C8—H8A	109.3
C9—C5—C4	106.9 (2)	H8B—C8—H8A	107.9
C9—C5—C6	110.59 (19)	C1—C9—C5	108.1 (2)
C4—C5—C6	112.9 (2)	C1—C9—H9B	110.1
C9—C5—H5	108.8	C5—C9—H9B	110.1
C4—C5—H5	108.8	C1—C9—H9A	110.1
C6—C5—H5	108.8	C5—C9—H9A	110.1
C7—C6—C5	112.4 (2)	H9B—C9—H9A	108.4

C8—C1—O2—C3	−85.9 (3)	C4—C5—C6—C7	−63.5 (3)
C9—C1—O2—C3	36.8 (3)	C5—C6—C7—C8	−50.9 (3)
C1—O2—C3—O3	167.8 (2)	O2—C1—C8—C7	65.6 (3)
C1—O2—C3—C4	−18.1 (3)	C9—C1—C8—C7	−56.1 (3)
O3—C3—C4—C5	−162.9 (3)	C6—C7—C8—C1	50.3 (3)
O2—C3—C4—C5	23.3 (4)	O2—C1—C9—C5	−59.8 (3)
C3—C4—C5—C9	−46.0 (3)	C8—C1—C9—C5	60.0 (3)
C3—C4—C5—C6	75.9 (3)	C4—C5—C9—C1	64.0 (2)
C9—C5—C6—C7	56.2 (3)	C6—C5—C9—C1	−59.3 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O2ⁱ	1.00	2.58	3.224 (3)	122

Symmetry code: (i) −x+2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₈H₁₂O₂
M_r	140.18
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	100
a, b, c (Å)	6.793 (2), 7.467 (2), 14.170 (4)
V (Å³)	718.7 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.30 × 0.14 × 0.10

Data collection
Diffractometer	Kuma KM-4-CCD
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	4925, 935, 685
R_int	0.051
(sin θ/λ)_max (Å⁻¹)	0.639

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.043, 0.096, 1.04
No. of reflections	935
No. of parameters	92
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.16

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), XP (Bruker, 1999).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···O2ⁱ	1.00	2.58	3.224 (3)	122

Symmetry code: (i) −x+2, y+1/2, −z+1/2.

Acknowledgements

This work was supported by the Polish State Committee for Scientific Research, grant No. 2200/B/P01/2007/33.

References

Bruker (1999). XP. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Finet, L., Dakir, M., Chiaroni, A. & Arseniyadis, S. (2007). Eur. J. Org. Chem. pp. 342–350. Web of Science CSD CrossRef Google Scholar
Militsina, O. I., Kovyljaeva, G. I., Bakaleynik, G. A., Strobykina, I. Yu., Kataev, V. E., Alfonsov, V. A., Musin, R. Z., Beskrovny, D. V. & Litvinov, I. A. (2005). Mendeleev Commun. pp. 27–29. Web of Science CSD CrossRef Google Scholar
Olejniczak, T. (2010). J. Mol. Cat. B, 63, 1–10. Web of Science CrossRef CAS Google Scholar
Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England. Google Scholar
Schmidt, T. J., Schmidt, H. M., Muller, E., Peters, W., Fronczek, F. R., Truesdale, A. & Fischer, N. H. (1998). J. Nat. Prod. 61, 230–236. Web of Science CSD CrossRef CAS PubMed Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Tzvetkov, N. T., Schmoldt, P., Neumann, B., Stammler, H.-G. & Mattay, J. (2006). Tetrahedron Asymmetry, 17, 993–998. Web of Science CSD CrossRef CAS Google Scholar
Wascholowski, V., Knudsen, K. R., Mitchell, C. E. T. & Ley, S. V. (2008). Chem. Eur. J. 14, 6155–6165. Web of Science CrossRef PubMed CAS Google Scholar
Xu, Y., Ohori, K. & Shibasaki, M. (2002). Tetrahedron, 58, 2585–2588. Web of Science CrossRef CAS Google Scholar
Yokoyama, R., Huang, J. M., Hosoda, A., Kino, K., Yang, C. S. & Fukuyama, Y. (2003). J. Nat. Prod. 66, 799–803. Web of Science CrossRef PubMed CAS Google Scholar