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Crystal structure of (−)-(S)-4-[(2S,3S,4S,Z)-3-hy­droxy-4-methyl­hept-5-en-2-yl]-1,3-dioxolan-2-one

aDepartment of Chemistry, University of Puerto Rico-Rio Piedras Campus, PO Box 23346, San Juan, 00931-3346, Puerto Rico
*Correspondence e-mail: jose.prieto2@upr.edu

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 1 June 2017; accepted 20 June 2017; online 27 June 2017)

The title compound, C11H18O4, consists of an anti,anti,anti-stereo­tetrad with a 1,2-carbonate and an alkene motif. The mol­ecule displays a common zigzag conformation. The five-membered ring has a twisted conformation on the C—C bond. In the crystal, a strong inter­molecular hydrogen bond between the hy­droxy group and the carboxyl­ate moiety from an adjacent mol­ecule forms chains propagating along the b-axis direction. The absolute structure of the mol­ecule in the crystal was determined by resonant scattering [Flack parameter = 0.05 (6)].

1. Chemical context

The title compound was obtained as part of our studies toward the synthesis of (−)-dolabriferol and (−)-dolabriferol B (Ciavatta et al., 1996[Ciavatta, M. L., Gavagnin, M., Puliti, R., Cimino, G., Martinez, E., Ortea, J. & Mattia, C. A. (1996). Tetrahedron, 52, 12831-12838.]; Jiménez-Romero et al., 2012[Jiménez-Romero, C., González, K. & Rodríguez, A. (2012). Tetrahedron Lett. 53, 6641-6645.]), using an epoxide-based approach for the stereo­tetrad construction. Polypropionate chains are structural motifs consisting of alternating methyl and hy­droxy groups within an aliphatic framework (Torres et al., 2004[Torres, G., Torres, W. & Prieto, J. A. (2004). Tetrahedron, 60, 10245-10251.], 2009[Torres, W., Rodríguez, R. & Prieto, J. (2009). J. Org. Chem. 74, 2447-2451.]; Tirado et al., 2005[Tirado, R., Torres, G., Torres, W. & Prieto, J. A. (2005). Tetrahedron Lett. 46, 797-801.], Rodríguez et al., 2006[Rodríguez, D., Mulero, M. & Prieto, J. A. (2006). J. Org. Chem. 71, 5826-5829.]). Their structure is found in various natural products, many of them possessing a wide range of biological activity, typically anti­biotic, anti­tumor, anti­fungal, anti­parasitic, among others (Rohr, 2000[Rohr, J. (2000). Angew. Chem. Int. Ed. 39, 2847-2849.]). Different method­ologies for the synthesis of polypropionates have been developed, with aldol and aldol-related chemistry being the most used (Schetter & Mahrwald, 2006[Schetter, B. & Mahrwald, R. (2006). Angew. Chem. Int. Ed. 45, 7506-7525.]).

[Scheme 1]

In our laboratory, we have developed an epoxide-based methodology for the construction of polypropionates, consisting of a reiterative sequence of three steps. Our approach involves a regioselect­ive epoxide cleavage with an alkynyl aluminium reagent (Torres et al., 2005[Tirado, R., Torres, G., Torres, W. & Prieto, J. A. (2005). Tetrahedron Lett. 46, 797-801.]) or Grignard reagent (Rodríguez et al., 2006[Rodríguez, D., Mulero, M. & Prieto, J. A. (2006). J. Org. Chem. 71, 5826-5829.]), cis or trans reduction of the alkyne (if needed), and the stereoselective epoxidation of the resulting alkenol for the elaboration of each propionate unit. In this approach, the configuration of the hydroxyl group is derived from the absolute configuration of the epoxide precursor, while the syn/anti relative configuration of the methyl and hydroxyl groups is derived from the epoxide geometry. One of the advantages of this methodology is that it is a substrate-controlled synthesis; the only enanti­omeric step in this sequence is the first epoxidation (Katsuki & Sharpless, 1980[Katsuki, T. & Sharpless, K. B. (1980). J. Am. Chem. Soc. 102, 5974-5976.]).

2. Structural commentary

The mol­ecular structure of the title compound is illustrated in Fig. 1[link]. The alkyl back bone has a typical zigzag conformation with two of the three methyl groups, those located on C4 and C6, anti to one another. Likewise, the hy­droxy group located on C5 is in an anti relative conformation with respect to the methyl groups. The five-membered ring (O2/O3/C1–C3) has a twisted conformation on bond C2–C3 [puckering parameters Q(2) = 0.137 (2) Å and φ(2) = 307.4 (10)°].

[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling. Displacement ellipsoids are drawn at the 50% probability level.

3. Supra­molecular features

The conformational distance between the hydroxyl group and the carbonyl moiety does not allow intra­molecular hydrogen-bond formation, therefore, hydrogen bonding is observed through inter­molecular inter­actions alone (Table 1[link]). In the crystal, neighbouring mol­ecules are linked by the O4—H4⋯O1i hydrogen bond, forming chains along [010]; see Fig. 2[link] and Table 1[link].

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H4⋯O1i 0.82 2.05 2.811 (2) 155
Symmetry code: (i) x, y+1, z.
[Figure 2]
Figure 2
A view along the a axis of crystal packing of the title compound, with hydrogen bonds shown as dashed lines (see Table 1[link]).

4. Database survey

A search of the Cambridge Structural Database (Version 5.38, updated May 2017; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) revealed no related compounds with the 3-hy­droxy-2-methyl-1,2-carbonate substructure. However, a search for the 2,4-di­methyl­hex-5-en-3-ol fragment revealed more than 120 hits. Many of these involve reactants for the synthesis of natural products, such as superotolide A (Yakelis & Roush, 2003[Yakelis, N. A. & Roush, W. R. (2003). J. Org. Chem. 68, 3838-3843.]) and erythronolides A and B (Lynch et al., 1989a[Lynch, V. M., Pacofsky, G. J., Martin, S. F. & Davis, B. E. (1989a). Acta Cryst. C45, 973-975.]; 1989b[Lynch, V. M., Pacofsky, G. J., Martin, S. F. & Davis, B. E. (1989b). Acta Cryst. C45, 1641-1643.]).

5. Synthesis and crystallization

The synthesis of the title compound, illustrated in Fig. 3[link], was performed through the selective protection of the 1,2-diol of (+)-(2S,3S,4S,5S,Z)-3,5-di­methyl­oct-6-ene-1,2,4-triol with a carbonate using N,N′-carbonyl­diimidazole (CDI) in CH2Cl2 as solvent, favouring formation of the 1,2-carbonate over the 1,3-carbonate. This reaction afforded the optically active anti,anti,anti-polypropionate unit with the correct absolute configuration. To a dry round-bottom flask containing the 1,2-diol of (+)-(2S,3S,4S,5S,Z)-3,5-di­methyl­oct-6-ene-1,2,4-triol (0.04 g, 0.212 mmol) in dry CH2Cl2 (1.07 ml, 0.2 M) was added N,N′-carbonyl­diimidazole (0.048 g, 0.30 mmol). The reaction mixture was stirred at 298 K for 2.5 h, then saturated aqueous NaCl was added. The resulting mixture was then extracted with ethyl acetate (three times). The combined organic layer was dried over MgSO4 and concentrated at reduced pressure. The crude product was purified by flash chromatography (2:1, ethyl acetate:hexa­ne) to yield 0.027 g (62%) of the pure title carbonate product as a white solid (m.p. 360–363 K). Block-like clear crystals suitable for X-ray diffraction, were obtained by slow diffusion of a 1:1 (v:v) ethyl acetate:hexa­nes solution of the title compound at room temperature over a period of two days. NMR analyses were performed on a Bruker AV-500 spectrometer using Chloro­form-d as solvent (CDCl3). The solvent signal at 7.26 and 77.00 ppm were used as inter­nal standards for proton and carbon respectively. 1H NMR (500 MHz, CDCl3) δ 5.69 (dq, J = 10.9, 6.8 Hz, 1H), 5.23 (ddt, J = 11.2, 9.8, 1.8 Hz, 1H), 4.99 (td, J = 8.2, 5.0 Hz, 1H), 4.44 (t, J = 8.6 Hz, 1H), 4.37 (t, J = 8.6 Hz, 1H), 3.26 (dd, J = 7.5, 4.2 Hz, 1H), 2.72 (ddq, J = 6.9, 6.7, 3.1 Hz, 1H), 2.29 (ddq, J = 6.6, 4.5, 2.4 Hz, 1H), 2.00 (s, 1H, -OH), 1.65 (dd, J = 6.8, 1.9 Hz, 3H), 1.05 (d, J = 6.9 Hz, 3H), 1.00 (d, J = 6.6 Hz, 3H). 13C NMR (125 MHz, CDCl3) δ 155.3, 131.3, 127.4, 77.5, 77.3, 66.9, 36.8, 35.3, 17.1, 13.3, 11.7. [α]20D = −2.0 (c = 1.0, CHCl3). Analysis calculated for C11H18O4: C, 61.66, H, 8.47%. Found: C, 61.74, H, 8.44%. IR data: C=O: 1761.32 cm−1, C—O: 1061.01 cm−1.

[Figure 3]
Figure 3
Reaction scheme

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. H atoms were included in geometrically calculated positions and refined as riding: O—H = 0.82 Å, C—H = 0.93–0.98 Å with Uiso(H) = 1.5Ueq(O-hydroxyl and C-meth­yl) and 1.2Ueq(C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula C11H18O4
Mr 214.25
Crystal system, space group Orthorhombic, P212121
Temperature (K) 100
a, b, c (Å) 5.0968 (1), 8.8153 (1), 25.6052 (3)
V3) 1150.44 (3)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.77
Crystal size (mm) 0.23 × 0.13 × 0.06
 
Data collection
Diffractometer Rigaku OD SuperNova, single source at offset/far, HyPix3000
Absorption correction Gaussian (CrysAlis PRO; Rigaku OD, 2016[Rigaku OD (2016). CrysAlis PRO. Rigaku Oxford Diffraction, Wroclaw, Poland.])
Tmin, Tmax 0.739, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 17757, 2131, 2081
Rint 0.030
(sin θ/λ)max−1) 0.606
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.094, 1.26
No. of reflections 2131
No. of parameters 141
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.23, −0.17
Absolute structure Flack x determined using 812 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 0.05 (6)
Computer programs: CrysAlis PRO (Rigaku OD, 2016[Rigaku OD (2016). CrysAlis PRO. Rigaku Oxford Diffraction, Wroclaw, Poland.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL2016 (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]), 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.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Computing details top

Data collection: CrysAlis PRO (Rigaku OD, 2016); cell refinement: CrysAlis PRO (Rigaku OD, 2016); data reduction: CrysAlis PRO (Rigaku OD, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2016 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

(-)-(S)-4-[(2S,3S,4S,Z)-3-hydroxy-4-methylhept-5-en-2-yl]-1,3-dioxolan-2-one top
Crystal data top
C11H18O4Dx = 1.237 Mg m3
Mr = 214.25Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, P212121Cell parameters from 12810 reflections
a = 5.0968 (1) Åθ = 3.5–68.8°
b = 8.8153 (1) ŵ = 0.77 mm1
c = 25.6052 (3) ÅT = 100 K
V = 1150.44 (3) Å3Block, colourless
Z = 40.23 × 0.13 × 0.06 mm
F(000) = 464
Data collection top
Rigaku OD SuperNova, Single source at offset/far, HyPix3000
diffractometer
2131 independent reflections
Radiation source: micro-focus sealed X-ray tube, SuperNova (Cu) X-ray Source2081 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.030
ω scansθmax = 69.0°, θmin = 3.5°
Absorption correction: gaussian
(CrysAlis PRO; Rigaku OD, 2016)
h = 66
Tmin = 0.739, Tmax = 1.000k = 1010
17757 measured reflectionsl = 3031
Refinement top
Refinement on F2H-atom parameters constrained
Least-squares matrix: full w = 1/[σ2(Fo2) + (0.0367P)2 + 0.4414P]
where P = (Fo2 + 2Fc2)/3
R[F2 > 2σ(F2)] = 0.032(Δ/σ)max < 0.001
wR(F2) = 0.094Δρmax = 0.23 e Å3
S = 1.26Δρmin = 0.17 e Å3
2131 reflectionsExtinction correction: (SHELXL2016; Sheldrick, 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
141 parametersExtinction coefficient: 0.0032 (6)
0 restraintsAbsolute structure: Flack x determined using 812 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
Primary atom site location: dualAbsolute structure parameter: 0.05 (6)
Hydrogen site location: inferred from neighbouring sites
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
xyzUiso*/Ueq
O10.9031 (4)0.13807 (18)0.69895 (7)0.0267 (4)
O20.6220 (3)0.03761 (19)0.72821 (6)0.0234 (4)
O30.9752 (3)0.10820 (18)0.68416 (6)0.0214 (4)
O40.8749 (4)0.55481 (18)0.66999 (6)0.0241 (4)
H40.8382920.6445820.6741530.036*
C10.8397 (5)0.0079 (3)0.70337 (9)0.0196 (5)
C20.6171 (5)0.2019 (3)0.73034 (9)0.0208 (5)
H2A0.6535810.2378550.7654070.025*
H2B0.4479870.2408570.7192850.025*
C30.8339 (5)0.2503 (2)0.69242 (9)0.0182 (5)
H30.9498590.3234860.7096910.022*
C40.7482 (5)0.3135 (2)0.63967 (8)0.0164 (5)
H4A0.9040160.3161100.6172750.020*
C50.6564 (5)0.4780 (2)0.64684 (9)0.0179 (5)
H50.5095160.4793380.6715470.021*
C60.5674 (5)0.5528 (3)0.59550 (8)0.0188 (5)
H60.4183220.4947730.5819170.023*
C70.7832 (5)0.5488 (3)0.55492 (9)0.0224 (5)
H70.9479440.5813760.5657940.027*
C80.7641 (5)0.5043 (3)0.50573 (9)0.0266 (5)
H80.9160880.5105630.4857560.032*
C90.5243 (6)0.4446 (4)0.47858 (10)0.0394 (7)
H9A0.4921380.5032090.4476250.059*
H9B0.3759770.4522280.5015300.059*
H9C0.5515400.3403780.4692130.059*
C100.5456 (5)0.2129 (3)0.61247 (9)0.0208 (5)
H10A0.3792570.2228930.6297350.031*
H10B0.6018340.1090620.6139320.031*
H10C0.5283490.2435980.5766610.031*
C110.4749 (6)0.7165 (3)0.60482 (10)0.0268 (6)
H11A0.3437480.7174390.6317190.040*
H11B0.4019160.7565730.5731280.040*
H11C0.6212980.7777090.6154200.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0337 (10)0.0144 (8)0.0319 (9)0.0021 (7)0.0088 (8)0.0007 (7)
O20.0230 (8)0.0183 (8)0.0289 (8)0.0017 (7)0.0033 (7)0.0048 (7)
O30.0198 (8)0.0151 (7)0.0292 (8)0.0029 (7)0.0022 (7)0.0037 (6)
O40.0278 (9)0.0128 (7)0.0316 (9)0.0000 (7)0.0107 (7)0.0023 (7)
C10.0218 (11)0.0181 (11)0.0189 (10)0.0010 (10)0.0052 (9)0.0004 (9)
C20.0244 (12)0.0166 (11)0.0215 (11)0.0024 (11)0.0028 (10)0.0003 (9)
C30.0180 (11)0.0134 (10)0.0231 (11)0.0004 (9)0.0006 (9)0.0017 (8)
C40.0159 (10)0.0128 (10)0.0205 (10)0.0007 (9)0.0012 (9)0.0006 (8)
C50.0175 (11)0.0146 (10)0.0214 (11)0.0010 (9)0.0012 (9)0.0014 (9)
C60.0158 (11)0.0181 (11)0.0224 (11)0.0002 (9)0.0019 (9)0.0013 (9)
C70.0164 (11)0.0230 (11)0.0277 (11)0.0002 (10)0.0008 (9)0.0054 (10)
C80.0217 (12)0.0331 (13)0.0251 (11)0.0042 (11)0.0026 (10)0.0053 (10)
C90.0310 (15)0.0616 (19)0.0258 (13)0.0003 (15)0.0020 (11)0.0064 (13)
C100.0218 (12)0.0182 (11)0.0224 (11)0.0015 (10)0.0008 (9)0.0013 (9)
C110.0314 (14)0.0192 (12)0.0299 (12)0.0065 (11)0.0050 (11)0.0029 (10)
Geometric parameters (Å, º) top
O1—C11.198 (3)C6—H60.9800
O2—C11.340 (3)C6—C71.513 (3)
O2—C21.450 (3)C6—C111.536 (3)
O3—C11.329 (3)C7—H70.9300
O3—C31.461 (3)C7—C81.323 (3)
O4—H40.8200C8—H80.9300
O4—C51.432 (3)C8—C91.501 (4)
C2—H2A0.9700C9—H9A0.9600
C2—H2B0.9700C9—H9B0.9600
C2—C31.532 (3)C9—H9C0.9600
C3—H30.9800C10—H10A0.9600
C3—C41.525 (3)C10—H10B0.9600
C4—H4A0.9800C10—H10C0.9600
C4—C51.535 (3)C11—H11A0.9600
C4—C101.529 (3)C11—H11B0.9600
C5—H50.9800C11—H11C0.9600
C5—C61.539 (3)
C1—O2—C2109.32 (19)C5—C6—H6107.9
C1—O3—C3110.52 (17)C7—C6—C5111.25 (19)
C5—O4—H4109.5C7—C6—H6107.9
O1—C1—O2123.7 (2)C7—C6—C11110.58 (19)
O1—C1—O3124.2 (2)C11—C6—C5111.11 (18)
O3—C1—O2112.07 (19)C11—C6—H6107.9
O2—C2—H2A111.0C6—C7—H7116.3
O2—C2—H2B111.0C8—C7—C6127.4 (2)
O2—C2—C3104.01 (18)C8—C7—H7116.3
H2A—C2—H2B109.0C7—C8—H8116.4
C3—C2—H2A111.0C7—C8—C9127.2 (2)
C3—C2—H2B111.0C9—C8—H8116.4
O3—C3—C2102.04 (17)C8—C9—H9A109.5
O3—C3—H3109.4C8—C9—H9B109.5
O3—C3—C4109.03 (18)C8—C9—H9C109.5
C2—C3—H3109.4H9A—C9—H9B109.5
C4—C3—C2117.2 (2)H9A—C9—H9C109.5
C4—C3—H3109.4H9B—C9—H9C109.5
C3—C4—H4A107.1C4—C10—H10A109.5
C3—C4—C5109.04 (18)C4—C10—H10B109.5
C3—C4—C10112.68 (18)C4—C10—H10C109.5
C5—C4—H4A107.1H10A—C10—H10B109.5
C10—C4—H4A107.1H10A—C10—H10C109.5
C10—C4—C5113.36 (19)H10B—C10—H10C109.5
O4—C5—C4105.02 (18)C6—C11—H11A109.5
O4—C5—H5108.7C6—C11—H11B109.5
O4—C5—C6112.33 (18)C6—C11—H11C109.5
C4—C5—H5108.7H11A—C11—H11B109.5
C4—C5—C6113.11 (18)H11A—C11—H11C109.5
C6—C5—H5108.7H11B—C11—H11C109.5
O2—C2—C3—O313.8 (2)C2—C3—C4—C1049.2 (3)
O2—C2—C3—C4105.2 (2)C3—O3—C1—O1175.2 (2)
O3—C3—C4—C5167.31 (18)C3—O3—C1—O24.5 (2)
O3—C3—C4—C1065.9 (2)C3—C4—C5—O456.7 (2)
O4—C5—C6—C761.8 (2)C3—C4—C5—C6179.52 (19)
O4—C5—C6—C1161.9 (3)C4—C5—C6—C756.9 (3)
C1—O2—C2—C312.2 (2)C4—C5—C6—C11179.4 (2)
C1—O3—C3—C211.6 (2)C5—C6—C7—C8131.2 (3)
C1—O3—C3—C4113.0 (2)C6—C7—C8—C91.0 (4)
C2—O2—C1—O1174.9 (2)C10—C4—C5—O4176.93 (18)
C2—O2—C1—O35.3 (2)C10—C4—C5—C654.1 (3)
C2—C3—C4—C577.5 (2)C11—C6—C7—C8104.8 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···O1i0.822.052.811 (2)155
Symmetry code: (i) x, y+1, z.
 

Acknowledgements

The authors thank NIH RISE (5R25GM061151–15) and SCORE (2S06GM-08102–29) for the financial support. This material is based upon work supported by the National Science Foundation under Grant No. 1626103.

Funding information

Funding for this research was provided by: National Institutes of Health (award No. 5R25GM061151-15); National Institutes of General Medical Sciences (award No. 2S06GM-08102-29); National Science Foundation (award No. 1626103).

References

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