PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2009 June 1; 65(Pt 6): o1357.
Published online 2009 May 20. doi:  10.1107/S1600536809018443
PMCID: PMC2969760

rac-4,8-Divinyl­bicyclo­[3.3.1]nonane-2,6-dione

Abstract

The title compound, C13H16O2, is a chiral bicyclic structure composed of two fused cyclo­hexa­ne rings possessing both boat and chair conformations. The mol­ecules are packed in enantio­pure columns which are pairwise linked forming an overall racemic solid; within the column pairs the packing is governed by weak dipole–dipole inter­actions stemming from stacked carbonyl functionalities (COcentroid–COcentroid distance = 3.290 Å).

Related literature

For related structures, see: Orentas et al. (2007 [triangle]); Quast et al. (1994 [triangle], 1999 [triangle]); Wallentin et al. (2009 [triangle]). For a general background to non-covalent inter­actions, see: Desiraju & Steiner (1999 [triangle]); Aakeröy (1997 [triangle]), and references therein.

An external file that holds a picture, illustration, etc.
Object name is e-65-o1357-scheme1.jpg

Experimental

Crystal data

  • C13H16O2
  • M r = 204.26
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1357-efi1.jpg
  • a = 20.4254 (11) Å
  • b = 8.8913 (6) Å
  • c = 6.2570 (4) Å
  • V = 1136.32 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 293 K
  • 0.3 × 0.05 × 0.03 mm

Data collection

  • Oxford Diffraction Xcalibur diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006 [triangle]) T min = 0.827, T max = 1.000 (expected range = 0.825–0.998)
  • 8068 measured reflections
  • 1363 independent reflections
  • 811 reflections with I > 2σ(I)
  • R int = 0.031

Refinement

  • R[F 2 > 2σ(F 2)] = 0.044
  • wR(F 2) = 0.110
  • S = 1.02
  • 1363 reflections
  • 136 parameters
  • 1 restraint
  • H-atom parameters constrained
  • Δρmax = 0.32 e Å−3
  • Δρmin = −0.19 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2006 [triangle]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006 [triangle]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: DIAMOND (Brandenburg, 2000 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809018443/ng2580sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809018443/ng2580Isup2.hkl

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

Acknowledgments

Financial support from the Swedish Research Council, the Knut and Alice Wallenberg Foundation, The Swedish Foundation for Strategic Research, and the Royal Physiographic Society is gratefully acknowledged.

supplementary crystallographic information

Comment

The hydrocarbon backbone of the title compound is a common motif in many biologically active compounds and its unique molecular shape has been utilized in the construction of different types of supramolecular architectures and inclusion complexes. Diols from this category of structures has with great success been exploited within the field of crystal engineering. The title compound was obtained in the synthesis of a series of C2 -symmetrically derivatized bicyclo[3.3.1]nonane-2,6-diones as a part of an ongoing project with the aim to study various supramolecular features of this class of compounds. The chiral bicyclic structure is composed of two merged cyclohexanes possessing both boat and chair conformations similar to the previously reported phenyl-substituted bicyclo[3.3.1]nonane-2,6-dione (Quast et al., 1999). The molecules are packed in column pairs which propagate in a unidirectional manner along the c axis. The column pairs are homochiral and generated by a two fold screw axis. The glide plane generates an over-all racemic structure comprised of parallel columns with alternating absolute stereochemistry. The formation of column pairs is governed by dipole-dipole interactions stemming from stacked carbonyl functionalities: centroid C2O1···centroid C2O1, 3.290 Å.

Experimental

A solution of LiCl in THF ( 0.5M, 12.5 mL, 6.25 mmol) was added to a round-bottom flask charged with CuCN (0.272 g, 3.04 mmol) and the mixture was stirred under argon at room temperature until all solid dissolved. The solution was cooled down to -30 °C and a solution of vinyl magnesium bromide in THF (0.7 M, 4.34 mL, 3.04 mmol) was added dropwise. The resulting dark brown mixture was warmed to -20 °C and stirred at this temperature for 30 minutes and then cooled to -78 °C. A solution of bicyclo[3.3.1]nona-3,7-diene-2,6-dione (0.15g, 1.01 mmol) (Orentas et al., 2007) and trimethylsilylchloride (0.33 g, 3.04 mmol) in THF (3 mL) was added dropwise. The reaction mixture was stirred until the temperature reached -20 °C. The reaction was quenched with 10% HCl solution (20 mL) and stirred at room temperature until the intermediate silylenol ether was hydrolyzed (monitored by TLC). The mixture was diluted with water and extracted with EtOAc (3 x 20 mL). The combined organic phase was dried over Na2SO4 and evaporated to dryness. The residue was purified by flash chromatography (10% ethyl acetate/petroleum ether) to afford the title compound as a coluorless solid in 70 % yield (144.4 mg). The product was recrystallised from petroleum ether to give colourless crystals suitable for X-ray diffraction analysis; m.p. 65 °C; FTIR (KBr) 1700 (C=O) cm-1; 1H NMR (300 MHz, CDCl3) δ 5.83 (ddd, J1=17.0 Hz, J2=10.4 Hz, J3=6.0 Hz, 1H), 5.17 (dd, J1=10.4 Hz, J2=1.6 Hz, 1H), 5.10 (dd, J1=17.0 Hz,J2=1.6 Hz, 1H), 2.93-2.83 (m, 2H), 2.62-2.53 (m, 6H), 2.19-2.14 (m, 2H); 13C NMR (75 MHz, CDCl3) δ 211.86, 139.34, 116.01, 48.10, 39.46, 22.81; Anal. calcd for C13H16O2: C, 76.44; H, 7.90. Found: C, 76.57; H, 8.02.

Refinement

The H atoms were positioned geometrically and treated as riding on their parent atoms with C–H distances of 0.93–0.97 Å and Uiso(H) = 1.2Ueq - 1.5Ueq. Equivalent reflections including Friedel pairs were merged prior to the final refinement.

Figures

Fig. 1.
The molecular structure of the title compound with atom labels and 30% probability displacement ellipsoids.
Fig. 2.
A partial packing diagram of the title compound displaying the weak interactions that govern the formation of column pairs. Dipol-dipol interactions are visualized as yellow lines connecting the carbonyl O atoms.

Crystal data

C13H16O2F(000) = 440
Mr = 204.26Dx = 1.194 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 2363 reflections
a = 20.4254 (11) Åθ = 2.3–33.1°
b = 8.8913 (6) ŵ = 0.08 mm1
c = 6.2570 (4) ÅT = 293 K
V = 1136.32 (12) Å3Prism, colourless
Z = 40.3 × 0.05 × 0.03 mm

Data collection

Oxford Diffraction Xcalibur diffractometer1363 independent reflections
Radiation source: Enhance (Mo) X-ray Source811 reflections with I > 2σ(I)
graphiteRint = 0.031
ω scansθmax = 27.1°, θmin = 3.0°
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006)h = −24→26
Tmin = 0.827, Tmax = 1.000k = −11→11
8068 measured reflectionsl = −5→8

Refinement

Refinement on F21 restraint
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.044w = 1/[σ2(Fo2) + (0.06P)2] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.110(Δ/σ)max < 0.001
S = 1.02Δρmax = 0.32 e Å3
1363 reflectionsΔρmin = −0.19 e Å3
136 parameters

Special details

Experimental. The intensity data were collected on a Oxford Xcalibur 3 CCD diffractometer using an exposure time of 20 s/frame. A total of 552 frames were collected with a frame width of 0.5° covering up to θ = 27.09° with 99.9% completeness accomplished. The highest difference peak in the Fourier map is located 0.85 Å from H16.
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

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

xyzUiso*/Ueq
C60.60714 (11)0.5148 (3)0.2569 (5)0.0501 (7)
H60.59590.60850.18290.060*
O10.49120 (9)0.4888 (3)0.2890 (4)0.0684 (6)
C20.54437 (13)0.4308 (3)0.3065 (4)0.0522 (7)
C30.64496 (12)0.5550 (3)0.4657 (5)0.0490 (7)
H30.61620.53340.58720.059*
C40.70813 (12)0.4602 (3)0.4926 (5)0.0587 (8)
H4A0.74240.50280.40390.070*
H4B0.72250.46610.64020.070*
C50.69861 (13)0.2986 (4)0.4334 (6)0.0635 (8)
O70.71657 (11)0.1941 (3)0.5432 (5)0.0990 (10)
C80.60166 (13)0.1778 (3)0.2573 (6)0.0609 (8)
H80.61370.09120.34590.073*
C100.64888 (14)0.4191 (3)0.1080 (5)0.0592 (8)
H10A0.68910.47180.07300.071*
H10B0.62530.3995−0.02360.071*
C110.55214 (12)0.2721 (3)0.3865 (5)0.0571 (8)
H11A0.50990.22260.38210.069*
H11B0.56620.27520.53450.069*
C120.66464 (13)0.2711 (3)0.2209 (5)0.0607 (8)
H120.69420.21290.12940.073*
C150.66318 (14)0.7178 (3)0.4753 (6)0.0652 (9)
H150.68610.75690.35950.078*
C160.5761 (2)0.1174 (5)0.0507 (7)0.0924 (12)
H160.60530.0540−0.01950.111*
C130.64974 (18)0.8101 (4)0.6321 (7)0.0892 (12)
H13A0.62690.77580.75110.107*
H13B0.66300.91000.62470.107*
C140.5247 (3)0.1352 (5)−0.0434 (7)0.1147 (16)
H14A0.49250.19690.01450.138*
H14B0.51750.0872−0.17340.138*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C60.0477 (14)0.0546 (15)0.0480 (16)0.0009 (13)−0.0027 (14)0.0079 (14)
O10.0420 (10)0.1030 (15)0.0603 (12)0.0124 (11)−0.0049 (10)−0.0058 (11)
C20.0405 (15)0.076 (2)0.0406 (16)0.0009 (13)−0.0050 (12)−0.0052 (14)
C30.0443 (14)0.0523 (15)0.0504 (16)−0.0024 (13)0.0013 (12)−0.0010 (14)
C40.0489 (16)0.0657 (18)0.061 (2)−0.0011 (14)−0.0076 (14)−0.0050 (16)
C50.0429 (15)0.067 (2)0.080 (2)0.0088 (15)−0.0110 (16)−0.0021 (18)
O70.0928 (17)0.0737 (15)0.131 (2)0.0123 (12)−0.0493 (19)0.0152 (17)
C80.0605 (17)0.0593 (17)0.0628 (18)−0.0035 (14)−0.0097 (18)−0.0021 (17)
C100.0461 (15)0.081 (2)0.0507 (18)−0.0096 (15)0.0074 (14)−0.0017 (17)
C110.0464 (15)0.072 (2)0.0531 (16)−0.0107 (13)0.0031 (13)0.0032 (16)
C120.0449 (15)0.0669 (18)0.0702 (19)0.0079 (14)0.0060 (15)−0.0096 (18)
C150.0522 (16)0.064 (2)0.079 (2)−0.0059 (15)−0.0006 (16)0.0030 (19)
C160.074 (2)0.115 (3)0.088 (3)−0.022 (2)0.005 (3)−0.016 (3)
C130.080 (2)0.071 (2)0.116 (3)−0.0003 (19)−0.017 (2)−0.022 (2)
C140.140 (4)0.120 (3)0.084 (3)−0.049 (3)−0.011 (3)0.002 (3)

Geometric parameters (Å, °)

C6—C21.516 (4)C8—C121.548 (4)
C6—C101.522 (4)C8—H80.9800
C6—C31.560 (4)C10—C121.528 (4)
C6—H60.9800C10—H10A0.9700
O1—C21.207 (3)C10—H10B0.9700
C2—C111.506 (4)C11—H11A0.9700
C3—C151.496 (4)C11—H11B0.9700
C3—C41.550 (4)C12—H120.9800
C3—H30.9800C15—C131.308 (4)
C4—C51.497 (4)C15—H150.9300
C4—H4A0.9700C16—C141.215 (5)
C4—H4B0.9700C16—H160.9300
C5—O71.212 (4)C13—H13A0.9300
C5—C121.519 (5)C13—H13B0.9300
C8—C161.494 (5)C14—H14A0.9300
C8—C111.543 (4)C14—H14B0.9300
C2—C6—C10108.9 (2)C6—C10—C12108.4 (2)
C2—C6—C3111.1 (2)C6—C10—H10A110.0
C10—C6—C3111.3 (2)C12—C10—H10A110.0
C2—C6—H6108.5C6—C10—H10B110.0
C10—C6—H6108.5C12—C10—H10B110.0
C3—C6—H6108.5H10A—C10—H10B108.4
O1—C2—C11121.7 (2)C2—C11—C8113.8 (2)
O1—C2—C6122.1 (3)C2—C11—H11A108.8
C11—C2—C6116.1 (2)C8—C11—H11A108.8
C15—C3—C4108.3 (2)C2—C11—H11B108.8
C15—C3—C6112.3 (2)C8—C11—H11B108.8
C4—C3—C6112.2 (2)H11A—C11—H11B107.7
C15—C3—H3107.9C5—C12—C10111.3 (2)
C4—C3—H3107.9C5—C12—C8109.7 (3)
C6—C3—H3107.9C10—C12—C8110.8 (2)
C5—C4—C3112.8 (2)C5—C12—H12108.3
C5—C4—H4A109.0C10—C12—H12108.3
C3—C4—H4A109.0C8—C12—H12108.3
C5—C4—H4B109.0C13—C15—C3125.8 (3)
C3—C4—H4B109.0C13—C15—H15117.1
H4A—C4—H4B107.8C3—C15—H15117.1
O7—C5—C4123.8 (3)C14—C16—C8132.4 (4)
O7—C5—C12120.8 (3)C14—C16—H16113.8
C4—C5—C12115.5 (3)C8—C16—H16113.8
C16—C8—C11114.8 (3)C15—C13—H13A120.0
C16—C8—C12110.8 (3)C15—C13—H13B120.0
C11—C8—C12109.3 (2)H13A—C13—H13B120.0
C16—C8—H8107.2C16—C14—H14A120.0
C11—C8—H8107.2C16—C14—H14B120.0
C12—C8—H8107.2H14A—C14—H14B120.0
C10—C6—C2—O1−130.0 (3)C16—C8—C11—C2−79.0 (3)
C3—C6—C2—O1107.1 (3)C12—C8—C11—C246.2 (3)
C10—C6—C2—C1152.1 (3)O7—C5—C12—C10−177.9 (3)
C3—C6—C2—C11−70.9 (3)C4—C5—C12—C101.6 (3)
C2—C6—C3—C15−128.9 (3)O7—C5—C12—C859.1 (4)
C10—C6—C3—C15109.5 (3)C4—C5—C12—C8−121.3 (3)
C2—C6—C3—C4108.7 (2)C6—C10—C12—C5−56.8 (3)
C10—C6—C3—C4−12.8 (3)C6—C10—C12—C865.5 (3)
C15—C3—C4—C5−166.1 (3)C16—C8—C12—C5−166.2 (3)
C6—C3—C4—C5−41.6 (3)C11—C8—C12—C566.2 (3)
C3—C4—C5—O7−132.2 (3)C16—C8—C12—C1070.6 (3)
C3—C4—C5—C1248.3 (3)C11—C8—C12—C10−57.0 (3)
C2—C6—C10—C12−60.4 (3)C4—C3—C15—C13−109.0 (3)
C3—C6—C10—C1262.4 (3)C6—C3—C15—C13126.5 (3)
O1—C2—C11—C8136.2 (3)C11—C8—C16—C145.1 (6)
C6—C2—C11—C8−45.8 (3)C12—C8—C16—C14−119.3 (5)

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: NG2580).

References

  • Aakeröy, C. B. (1997). Acta Cryst. B53, 569–586.
  • Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst.32, 115–119.
  • Brandenburg, K. (2000). DIAMOND Crystal Impact GbR, Bonn, Germany.
  • Desiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond New York: Oxford University Press Inc.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Orentas, E., Bagdziunas, G., Berg, U., Zilinskas, A. & Butkus, E. (2007). Eur. J. Org. Chem. pp. 4251–4256.
  • Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
  • Quast, H., Becker, C., Geibler, E., Knoll, K., Peters, E.-M., Peters, K. & von Schnering, H. G. (1994). Liebigs Ann. Chem. pp. 109–120.
  • Quast, H., Seefelder, M., Peters, E.-M. & Peters, K. (1999). Eur. J. Org. Chem. pp. 1811–1823.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Wallentin, C.-J., Orentas, E., Johnson, M. T., Butkus, E., Wendt, O. F., Öhrström, L. & Wärnmark, K. (2009). CrystEngComm Submitted.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography