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Acta Crystallogr Sect E Struct Rep Online. 2010 May 1; 66(Pt 5): o1163.
Published online 2010 April 24. doi:  10.1107/S1600536810014339
PMCID: PMC2979232

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

Abstract

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 [triangle]); Wascholowski et al. (2008 [triangle]); Tzvetkov et al. (2006 [triangle]); Xu et al. (2002 [triangle]). For related structures see: Yokoyama et al. (2003 [triangle]); Schmidt et al. (1998 [triangle]); Finet et al. (2007 [triangle]); Militsina et al. (2005 [triangle]).

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Object name is e-66-o1163-scheme1.jpg

Experimental

Crystal data

  • C8H12O2
  • M r = 140.18
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o1163-efi1.jpg
  • 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[F 2 > 2σ(F 2)] = 0.043
  • wR(F 2) = 0.096
  • S = 1.04
  • 935 reflections
  • 92 parameters
  • H-atom parameters constrained
  • Δρmax = 0.35 e Å−3
  • Δρmin = −0.16 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810014339/hg2667Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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

supplementary crystallographic information

Comment

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).

Experimental

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.

Refinement

All H atoms were placed at calculated positions and were treated as riding atoms, with C—H distances of 0.99 - 1.00 Å. The absolute configuration of (-)-3 was choosen on the basis of known absolute configuration of particular substrates: The absolute configuration of (-)-1 was confirmed by comparison of its optical rotation with the literature data [Wascholowski et al., 2008; Tzvetkov et al., 2006; Xu et al., 2002]. The absolute configuration of the carbon atom bearing hydroxyl group in product (+)-2 was determined using the Mosher's ester [Olejniczak, 2010].

Figures

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.

Crystal data

C8H12O2F(000) = 304
Mr = 140.18Dx = 1.295 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 1754 reflections
a = 6.793 (2) Åθ = 3.0–28.8°
b = 7.467 (2) ŵ = 0.09 mm1
c = 14.170 (4) ÅT = 100 K
V = 718.7 (4) Å3Needle, colorless
Z = 40.30 × 0.14 × 0.10 mm

Data collection

Kuma KM-4-CCD diffractometer685 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.051
graphiteθmax = 27.0°, θmin = 3.1°
ω scanh = −8→8
4925 measured reflectionsk = −9→9
935 independent reflectionsl = −15→18

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.043Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H-atom parameters constrained
S = 1.04w = 1/[σ2(Fo2) + (0.0507P)2] where P = (Fo2 + 2Fc2)/3
935 reflections(Δ/σ)max = 0.004
92 parametersΔρmax = 0.35 e Å3
0 restraintsΔρmin = −0.16 e Å3

Special details

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)

xyzUiso*/Ueq
C10.9078 (4)0.4787 (3)0.29810 (17)0.0293 (6)
H11.02560.49160.25640.035*
O20.8893 (3)0.2882 (2)0.32719 (12)0.0331 (5)
C30.7920 (4)0.2414 (4)0.40668 (17)0.0302 (6)
O30.7539 (3)0.0838 (2)0.41770 (13)0.0389 (5)
C40.7539 (4)0.3815 (3)0.48057 (18)0.0300 (6)
H4A0.85530.36930.53040.036*
H4B0.62470.35610.51000.036*
C50.7535 (4)0.5754 (3)0.44672 (17)0.0287 (6)
H50.76740.65610.50270.034*
C60.5660 (4)0.6256 (4)0.39356 (19)0.0347 (7)
H6B0.45090.60410.43490.042*
H6A0.56950.75490.37820.042*
C70.5413 (4)0.5192 (4)0.30310 (17)0.0344 (7)
H7B0.42900.56830.26690.041*
H7A0.51080.39310.31890.041*
C80.7258 (4)0.5254 (4)0.24230 (17)0.0334 (6)
H8B0.71150.44020.18920.040*
H8A0.74070.64710.21550.040*
C90.9334 (4)0.5985 (4)0.38359 (19)0.0302 (7)
H9B0.94570.72500.36350.036*
H9A1.05420.56480.41840.036*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0333 (15)0.0256 (14)0.0290 (14)0.0004 (12)0.0060 (13)0.0044 (12)
O20.0360 (11)0.0311 (10)0.0322 (10)0.0031 (8)0.0082 (9)−0.0003 (9)
C30.0285 (15)0.0334 (16)0.0286 (14)0.0022 (12)−0.0040 (12)0.0043 (12)
O30.0434 (11)0.0284 (10)0.0451 (11)−0.0025 (10)−0.0047 (11)0.0059 (9)
C40.0245 (14)0.0393 (15)0.0261 (12)−0.0021 (14)0.0014 (13)0.0003 (11)
C50.0291 (14)0.0297 (14)0.0273 (13)−0.0034 (13)−0.0009 (13)−0.0068 (11)
C60.0268 (15)0.0336 (16)0.0435 (17)0.0048 (12)0.0036 (13)−0.0038 (13)
C70.0284 (14)0.0368 (16)0.0381 (17)−0.0040 (12)−0.0047 (12)0.0040 (14)
C80.0429 (17)0.0314 (14)0.0259 (13)−0.0055 (14)−0.0033 (13)0.0012 (11)
C90.0242 (14)0.0312 (15)0.0353 (16)−0.0039 (12)−0.0012 (12)0.0037 (12)

Geometric parameters (Å, °)

C1—O21.486 (3)C5—H51.0000
C1—C81.509 (3)C6—C71.517 (4)
C1—C91.516 (4)C6—H6B0.9900
C1—H11.0000C6—H6A0.9900
O2—C31.352 (3)C7—C81.522 (3)
C3—O31.215 (3)C7—H7B0.9900
C3—C41.502 (4)C7—H7A0.9900
C4—C51.526 (3)C8—H8B0.9900
C4—H4A0.9900C8—H8A0.9900
C4—H4B0.9900C9—H9B0.9900
C5—C91.524 (3)C9—H9A0.9900
C5—C61.526 (4)
O2—C1—C8107.3 (2)C7—C6—H6B109.1
O2—C1—C9110.7 (2)C5—C6—H6B109.1
C8—C1—C9112.1 (2)C7—C6—H6A109.1
O2—C1—H1108.9C5—C6—H6A109.1
C8—C1—H1108.9H6B—C6—H6A107.9
C9—C1—H1108.9C6—C7—C8111.8 (2)
C3—O2—C1121.32 (19)C6—C7—H7B109.3
O3—C3—O2117.5 (2)C8—C7—H7B109.3
O3—C3—C4123.2 (2)C6—C7—H7A109.3
O2—C3—C4119.0 (2)C8—C7—H7A109.3
C3—C4—C5116.2 (2)H7B—C7—H7A107.9
C3—C4—H4A108.2C1—C8—C7111.8 (2)
C5—C4—H4A108.2C1—C8—H8B109.3
C3—C4—H4B108.2C7—C8—H8B109.3
C5—C4—H4B108.2C1—C8—H8A109.3
H4A—C4—H4B107.4C7—C8—H8A109.3
C9—C5—C4106.9 (2)H8B—C8—H8A107.9
C9—C5—C6110.59 (19)C1—C9—C5108.1 (2)
C4—C5—C6112.9 (2)C1—C9—H9B110.1
C9—C5—H5108.8C5—C9—H9B110.1
C4—C5—H5108.8C1—C9—H9A110.1
C6—C5—H5108.8C5—C9—H9A110.1
C7—C6—C5112.4 (2)H9B—C9—H9A108.4
C8—C1—O2—C3−85.9 (3)C4—C5—C6—C7−63.5 (3)
C9—C1—O2—C336.8 (3)C5—C6—C7—C8−50.9 (3)
C1—O2—C3—O3167.8 (2)O2—C1—C8—C765.6 (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—C150.3 (3)
O2—C3—C4—C523.3 (4)O2—C1—C9—C5−59.8 (3)
C3—C4—C5—C9−46.0 (3)C8—C1—C9—C560.0 (3)
C3—C4—C5—C675.9 (3)C4—C5—C9—C164.0 (2)
C9—C5—C6—C756.2 (3)C6—C5—C9—C1−59.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C1—H1···O2i1.002.583.224 (3)122

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2667).

References

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