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Crystal structure and absolute configuration of (3aS,4S,5R,7aR)-2,2,7-tri­methyl-3a,4,5,7a-tetra­hydro-1,3-benzodioxole-4,5-diol

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aCryssmat-Lab/Cátedra de Física/DETEMA, Facultad de Química, Universidad de la República, Montevideo, Uruguay, bGrupo INTERFASE, Universidad Industrial de Santander, Carrera 27, Calle 9, Ciudad Universitaria, Bucaramanga, Colombia, and cDepartamento de Química Orgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
*Correspondence e-mail: leopoldo@fq.edu.uy

Edited by M. Gdaniec, Adam Mickiewicz University, Poland (Received 30 July 2015; accepted 3 August 2015; online 6 August 2015)

The absolute configuration of the title compound, C10H16O4, determined as 3aS,4S,5R,7aR on the basis of the synthetic pathway, was confirmed by X-ray diffraction. The mol­ecule contains a five- and a six-membered ring that adopt twisted and envelope conformations, respectively. The dihedral angle between the mean planes of the rings is 76.80 (11)° as a result of their cis-fusion. In the crystal, mol­ecules are linked by two pairs of O—H⋯O hydrogen bonds, forming chains along [010]. These chains are further connected by weaker C—H⋯O inter­actions along [100], creating (001) sheets that inter­act only by weak van der Waals forces.

1. Chemical context

Compounds containing an ep­oxy­cyclo­hexenone skeleton are very inter­esting, not only because of their wide spectrum of biological activities, but also because of their synthetically challenging chemical structures (Pandolfi et al., 2013[Pandolfi, E., Schapiro, V., Heguaburu, V. & Labora, M. (2013). Curr. Org. Synth. 71, 2-42.]). A biotransformation of toluene leads to a chiral diol (see Fig. 1[link]) which is used as a precursor in enanti­oselective syntheses of ep­oxy­cyclo­hexenone compounds. Model compounds of the central core of ambuic acid (Labora et al., 2008[Labora, M., Heguaburu, V., Pandolfi, E. & Schapiro, V. (2008). Tetrahedron Asymmetry, 19, 893-895.]), (+)- and (−)-bromoxone (Labora et al., 2010[Labora, M., Pandolfi, E. & Schapiro, V. (2010). Tetrahedron Asymmetry, 21, 153-155.]), an ep­oxy­quinol analog (Heguaburu et al., 2010[Heguaburu, V., Schapiro, V. & Pandolfi, E. (2010). Tetrahedron Lett. 51, 6921-6923.]), gabosine A, ent-epoformin and ent-epiepoformin (Labora et al., 2011[Labora, M., Schapiro, V. & Pandolfi, E. (2011). Tetrahedron Asymmetry, 22, 1705-1707.]) have been prepared starting from the same precursor. The title compound, diol (3) (see Fig. 1[link]) has been prepared from iodo­hydrin (1), which, as indicated earlier, can be easily synthesized via biotransformation of toluene (Carrera et al., 2007[Carrera, I., Brovetto, M. & Seoane, G. (2007). Tetrahedron, 63, 4095-4107.]).

[Scheme 1]
[Figure 1]
Figure 1
Synthesis pathway and structural scheme of the chiral C10H16O4 compound.

2. Structural commentary

Fig. 2[link] shows the mol­ecule of the title compound. The absolute configuration of the title compound, determined as 3aS,4S,5R,7aR on the basis of the synthetic pathway, was confirmed by X-ray diffraction on the basis of anomalous dispersion of light atoms only. The five-membered ring (O1–C2–O3–C3A–C7A) adopts a twisted conformation with puckering parameters Q(2) = 0.342 (2) Å and φ = 122.1 (3)°. The six-membered ring (C3A–C4–C5–C6–C7–C7A) adopts an envelope conformation with atom C4 as the flap. In this case, the puckering parameters are Q = 0.466 (2) Å, θ = 52.1 (2) and φ = 50.8 (3)°. The fused rings are nearly perpendicular with a dihedral angle of 76.20 (11)° as a result of their cis-fusion.

[Figure 2]
Figure 2
The mol­ecular structure of the title compound, showing the anisotropic displacement ellipsoids drawn at the 50% probability level.

3. Supra­molecular features

In the crystal structure, the mol­ecules are connected in the three crystallographic directions by inter­molecular inter­actions of different strengths (Table 1[link]). In the [010] direction hydrogen bonds O41—H41⋯O3i and O51—H51⋯O41i [symmetry code: (i) −x, y + [{1\over 2}], −z + [{3\over 2}]] join mol­ecules into chains that are further connected by weaker C7A—H7A⋯O51ii [symmetry code: (ii) x + 1, y, z] hydrogen bonds along [100], forming (001) sheets. Hydrogen bonds of the O—H⋯O type generate R22(10) motifs (Fig. 3[link]). There are only weak van der Waals forces acting between neighbouring (001) sheets.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O41—H41⋯O3i 0.82 (3) 2.04 (3) 2.849 (2) 171 (3)
O51—H51⋯O41i 0.80 (3) 2.04 (3) 2.826 (2) 167 (2)
C7A—H7A⋯O51ii 0.98 2.44 3.299 (3) 146
Symmetry codes: (i) [-x, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) x+1, y, z.
[Figure 3]
Figure 3
Packing of the title compound, viewed along [100], showing hydrogen-bonded chains of mol­ecules

4. Database survey

A search of the Cambridge Structural Database (CSD Version 5.36 with one update; Groom & Allen, 2014[Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662-671.]) of the 3a,4,5,7a-tetra­hydro-1,3-benzodioxole skeleton gave 30 hits, of which only 20 had no additional fused rings. In all cases, the six-membered ring displays an envelope conformation with atom C4 as a flap. The orientation of the flap with respect to the plane of the envelope can be determined from the C7—C7A—C3A—C4 or the H7A—C7A—C3A—H3A torsion angles (with very similar values due to the geometry of the cis-fused rings). The C7—C7A—C3A—C4 torsion angle is positive if the flap atom is located on the opposite side of the plane (defined by the remaining five atoms of the cyclo­hexene ring) to O1 and O3 of the 1,3-dioxole ring, as observed in the title compound [33.5 (2)°]. 12 of the 20 mentioned structures, show a positive torsion angle with minimum and maximum values of 17.2 and 36.4°, respectively. From analysis of the above-mentioned torsion angle and the equatorial/axial orientation of the C4 and C5 substituents in the 20 structures, there is no clear trend that allows the relative orientation of the flap to be predicted based only on the size or kind of the substituents.

5. Synthesis and crystallization

The synthesis of the title compound was carried out through the inter­mediate epoxide (2) (see Fig. 1[link]). Iodo­hydrin (1) (0.6 mmol, 0.18 g) was dissolved in dry di­chloro­methane (5 mL) and 1,8-di­aza­bicyclo[5.4.0]undec-7-en (DBU) (0.8 mmol, 0.12 g) was added at room temperature. The reaction was stirred for 24 h After completion of the reaction, the mixture was diluted with saturated NH4Cl solution (20 mL) and extracted with di­chloro­methane (3 x 10 mL). The combined organic layers were washed with saturated NaCl solution (10 mL), dried (Na2SO4) and filtered. Concentration of the filtrate, followed by flash chromatography (hexa­nes:ethyl acetate 93:7) yielded (2) (0.063 g, 60%). FT–IR (KBr): 2983, 2926, 2856, 1672, 1371. 1H-NMR (400 MHz, CDCl3) δ: 6.01 (m, 1H), 4.40 (m, 2H), 3.58 (m, 1H), 3.42 (t, J = 4.0 Hz, 1H), 1.91 (s, 3H), 1.53 (s, 3H), 1.41 (s, 1H). For the synthesis of diol (3), epoxide (2) (0.27 mmol, 0.05 g) was dissolved in THF (25 mL) and 10% KOH (aq., 25 mL) was added. This mixture was refluxed for 4 h. After completion of the reaction, the mixture was diluted with di­chloro­methane (20 mL) and the organic phase was washed with 10% HCl until neutralization, washed with saturated NaCl solution (10 mL), dried with (Na2SO4) and filtered. Concentration of the filtrate, followed by flash chromatography (ethyl acetate:hexa­nes 4:6) yielded (3) (0.02g, 52%). Crystals suitable for X-ray structure analysis were obtained by dissolving (3) in the minimum volume of ethyl acetate, adding hexa­nes until the solution became slightly turbid and slowly evaporating the solvent at room temperature. (m.p. = 385–386 K). FT–IR (KBr): 3402, 1637, 1371. 1H NMR (400 MHz, CDCl3) δ: 5.45 (s, 1H), 4.48 (m, 2H), 4.33 (m, 1H), 3.59 (m, 1H), 2.52 (bs, 1H), 2.30 (bs, 1H), 1.79 (s, 3H), 1.38 (s, 3H), 1.35 (s, 3H).

6. Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms bonded to C were placed in calculated positions (C—H = 0.95–1.00 Å) and included as riding contributions with isotropic displacement parameters set to 1.2–1.5 times of the Ueq of the parent atom. H atoms belonging to OH groups were located in ΔF maps and freely refined.

Table 2
Experimental details

Crystal data
Chemical formula C10H16O4
Mr 200.23
Crystal system, space group Orthorhombic, P212121
Temperature (K) 293
a, b, c (Å) 6.1230 (13), 7.5163 (17), 23.347 (5)
V3) 1074.5 (4)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.79
Crystal size (mm) 0.28 × 0.18 × 0.14
 
Data collection
Diffractometer Bruker D8 Venture/Photon 100 CMOS
Absorption correction Multi-scan (SADABS; Bruker, 2013[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.643, 0.752
No. of measured, independent and observed [I > 2σ(I)] reflections 29451, 1967, 1951
Rint 0.030
(sin θ/λ)max−1) 0.603
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.029, 0.078, 1.18
No. of reflections 1967
No. of parameters 139
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.14, −0.11
Absolute structure Flack x determined using 782 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.])
Absolute structure parameter 0.01 (3)
Computer programs: APEX2 and SAINT (Bruker, 2013[Bruker (2013). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]).

Supporting information


Computing details top

Data collection: APEX2 (Bruker, 2013); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).

(3aS,4S,5R,7aR)-2,2,7-Trimethyl-3a,4,5,7a-tetrahydro-1,3-benzodioxole-4,5-diol top
Crystal data top
C10H16O4F(000) = 432
Mr = 200.23Dx = 1.238 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abθ = 3.8–66.7°
a = 6.1230 (13) ŵ = 0.79 mm1
b = 7.5163 (17) ÅT = 293 K
c = 23.347 (5) ÅParallelepiped, colorless
V = 1074.5 (4) Å30.28 × 0.18 × 0.14 mm
Z = 4
Data collection top
Bruker D8 Venture/Photon 100 CMOS
diffractometer
1967 independent reflections
Radiation source: Cu Incoatec microsource1951 reflections with I > 2σ(I)
Helios X-ray optical focusing and monochromatization moduleRint = 0.030
Detector resolution: 10.4167 pixels mm-1θmax = 68.4°, θmin = 3.8°
π and ω scansh = 76
Absorption correction: multi-scan
(SADABS; Bruker, 2013)
k = 99
Tmin = 0.643, Tmax = 0.752l = 2828
29451 measured reflections
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.029 w = 1/[σ2(Fo2) + (0.0278P)2 + 0.2133P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.078(Δ/σ)max < 0.001
S = 1.18Δρmax = 0.14 e Å3
1967 reflectionsΔρmin = 0.11 e Å3
139 parametersExtinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0063 (9)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack x determined using 782 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.01 (3)
Special details top

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) top
xyzUiso*/Ueq
O30.1718 (2)0.02424 (17)0.83031 (6)0.0431 (4)
C3A0.2609 (3)0.1964 (3)0.81761 (8)0.0379 (4)
H3A0.38680.18500.79190.045*
O10.4078 (3)0.0973 (2)0.90222 (7)0.0562 (5)
C7A0.3342 (3)0.2591 (3)0.87622 (8)0.0405 (5)
H7A0.45830.34030.87190.049*
H410.026 (5)0.337 (4)0.7201 (12)0.066 (9)*
H510.197 (5)0.545 (4)0.8006 (10)0.051 (8)*
O410.0349 (3)0.2538 (2)0.73585 (6)0.0499 (4)
O510.2609 (3)0.4552 (2)0.80767 (7)0.0488 (4)
C70.1596 (4)0.3484 (3)0.91126 (8)0.0403 (5)
C60.0366 (3)0.3793 (3)0.88973 (8)0.0415 (5)
H60.13870.43440.91330.050*
C230.4527 (6)0.1837 (4)0.85765 (13)0.0778 (9)
H23A0.53760.22480.88960.117*
H23B0.54750.13070.82970.117*
H23C0.37690.28240.84070.117*
C20.2898 (4)0.0479 (3)0.87792 (9)0.0484 (5)
C40.0914 (3)0.3159 (3)0.79142 (8)0.0358 (4)
H40.15570.43470.78730.043*
C50.1064 (3)0.3320 (2)0.83012 (9)0.0370 (4)
H50.17710.21520.83170.044*
C710.2246 (5)0.3979 (4)0.97104 (10)0.0621 (7)
H71A0.10420.45540.98980.093*
H71B0.34710.47750.96980.093*
H71C0.26390.29250.99190.093*
C220.1246 (6)0.1199 (4)0.91968 (12)0.0762 (9)
H22A0.19850.16460.95300.114*
H22B0.04370.21450.90190.114*
H22C0.02630.02660.93080.114*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O30.0525 (8)0.0324 (7)0.0444 (8)0.0017 (6)0.0105 (7)0.0019 (6)
C3A0.0346 (9)0.0391 (10)0.0400 (10)0.0008 (8)0.0044 (8)0.0027 (8)
O10.0621 (10)0.0478 (9)0.0587 (9)0.0118 (8)0.0243 (8)0.0051 (7)
C7A0.0353 (9)0.0407 (10)0.0455 (10)0.0020 (9)0.0032 (9)0.0026 (9)
O410.0668 (11)0.0458 (8)0.0372 (7)0.0157 (8)0.0080 (7)0.0020 (7)
O510.0369 (8)0.0452 (9)0.0643 (10)0.0056 (7)0.0024 (7)0.0124 (7)
C70.0482 (12)0.0349 (10)0.0377 (10)0.0064 (9)0.0036 (9)0.0010 (8)
C60.0428 (11)0.0414 (11)0.0405 (10)0.0022 (9)0.0124 (9)0.0014 (9)
C230.083 (2)0.0651 (17)0.0857 (19)0.0354 (16)0.0191 (16)0.0160 (15)
C20.0605 (14)0.0390 (11)0.0456 (11)0.0103 (10)0.0116 (10)0.0022 (9)
C40.0408 (10)0.0323 (9)0.0343 (9)0.0000 (8)0.0034 (8)0.0004 (7)
C50.0323 (9)0.0323 (9)0.0465 (10)0.0003 (8)0.0031 (8)0.0047 (8)
C710.0779 (17)0.0649 (15)0.0436 (12)0.0032 (15)0.0050 (12)0.0076 (11)
C220.102 (2)0.0665 (17)0.0599 (15)0.0030 (18)0.0010 (15)0.0110 (13)
Geometric parameters (Å, º) top
O3—C21.433 (2)C6—H60.9300
O3—C3A1.435 (2)C23—C21.503 (3)
C3A—C41.503 (3)C23—H23A0.9600
C3A—C7A1.515 (3)C23—H23B0.9600
C3A—H3A0.9800C23—H23C0.9600
O1—C21.427 (3)C2—C221.505 (4)
O1—C7A1.432 (3)C4—C51.516 (3)
C7A—C71.504 (3)C4—H40.9800
C7A—H7A0.9800C5—H50.9800
O41—C41.421 (2)C71—H71A0.9600
O41—H410.82 (3)C71—H71B0.9600
O51—C51.424 (2)C71—H71C0.9600
O51—H510.80 (3)C22—H22A0.9600
C7—C61.323 (3)C22—H22B0.9600
C7—C711.498 (3)C22—H22C0.9600
C6—C51.499 (3)
C2—O3—C3A108.04 (16)O1—C2—C23108.0 (2)
O3—C3A—C4111.11 (16)O3—C2—C23110.34 (19)
O3—C3A—C7A101.91 (15)O1—C2—C22111.0 (2)
C4—C3A—C7A112.71 (16)O3—C2—C22107.4 (2)
O3—C3A—H3A110.3C23—C2—C22113.9 (2)
C4—C3A—H3A110.3O41—C4—C3A110.06 (15)
C7A—C3A—H3A110.3O41—C4—C5112.08 (17)
C2—O1—C7A108.78 (15)C3A—C4—C5110.92 (15)
O1—C7A—C7111.85 (17)O41—C4—H4107.9
O1—C7A—C3A102.24 (16)C3A—C4—H4107.9
C7—C7A—C3A114.80 (16)C5—C4—H4107.9
O1—C7A—H7A109.2O51—C5—C6112.15 (17)
C7—C7A—H7A109.2O51—C5—C4111.30 (16)
C3A—C7A—H7A109.2C6—C5—C4110.18 (16)
C4—O41—H41105.6 (19)O51—C5—H5107.7
C5—O51—H51107.4 (19)C6—C5—H5107.7
C6—C7—C71123.5 (2)C4—C5—H5107.7
C6—C7—C7A121.16 (18)C7—C71—H71A109.5
C71—C7—C7A115.4 (2)C7—C71—H71B109.5
C7—C6—C5124.75 (18)H71A—C71—H71B109.5
C7—C6—H6117.6C7—C71—H71C109.5
C5—C6—H6117.6H71A—C71—H71C109.5
C2—C23—H23A109.5H71B—C71—H71C109.5
C2—C23—H23B109.5C2—C22—H22A109.5
H23A—C23—H23B109.5C2—C22—H22B109.5
C2—C23—H23C109.5H22A—C22—H22B109.5
H23A—C23—H23C109.5C2—C22—H22C109.5
H23B—C23—H23C109.5H22A—C22—H22C109.5
O1—C2—O3105.92 (16)H22B—C22—H22C109.5
C2—O3—C3A—C4151.43 (16)C7A—O1—C2—C23127.8 (2)
C2—O3—C3A—C7A31.14 (19)C7A—O1—C2—C22106.6 (2)
C2—O1—C7A—C795.1 (2)C3A—O3—C2—O114.5 (2)
C2—O1—C7A—C3A28.2 (2)C3A—O3—C2—C23102.1 (2)
O3—C3A—C7A—O135.64 (18)C3A—O3—C2—C22133.2 (2)
C4—C3A—C7A—O1154.80 (17)O3—C3A—C4—O4168.3 (2)
O3—C3A—C7A—C785.7 (2)C7A—C3A—C4—O41178.01 (16)
C4—C3A—C7A—C733.5 (2)O3—C3A—C4—C556.3 (2)
O1—C7A—C7—C6120.5 (2)C7A—C3A—C4—C557.4 (2)
C3A—C7A—C7—C64.6 (3)C7—C6—C5—O51147.6 (2)
O1—C7A—C7—C7159.4 (2)C7—C6—C5—C423.0 (3)
C3A—C7A—C7—C71175.29 (19)O41—C4—C5—O5160.8 (2)
C71—C7—C6—C5179.8 (2)C3A—C4—C5—O51175.69 (16)
C7A—C7—C6—C50.3 (3)O41—C4—C5—C6174.10 (15)
C7A—O1—C2—O39.6 (2)C3A—C4—C5—C650.6 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O41—H41···O3i0.82 (3)2.04 (3)2.849 (2)171 (3)
O51—H51···O41i0.80 (3)2.04 (3)2.826 (2)167 (2)
C7A—H7A···O51ii0.982.443.299 (3)146
Symmetry codes: (i) x, y+1/2, z+3/2; (ii) x+1, y, z.
 

Acknowledgements

The authors wish to thank ANII (EQC_2012_07), CSIC and the Facultad de Química for funds to purchase the diffractometer and the financial support of OPCW and PEDECIBA. MM and GT also thank ANII for their respective postdoctoral contracts (PD_NAC_2014_1_102409 and PD_NAC_2014_1_102498).

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