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

Morales-Rivera, K.F.; Piñero Cruz, D.M.; Prieto, J.A.

doi:10.1107/S2056989017009318

research communications

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Volume 73| Part 7| July 2017| Pages 1070-1072

https://doi.org/10.1107/S2056989017009318

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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

Keyla F. Morales-Rivera,^a Dalice M. Piñero Cruz ^a and Jose A. Prieto ^a ^*

^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)].

Keywords: crystal structure; polypropionate; 1,2-carbonate; stereotetrads; O—H⋯O hydrogen bonding.

CCDC reference: 1548935

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 ; Jiménez-Romero et al., 2012 ), 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 , 2009 ; Tirado et al., 2005 , Rodríguez et al., 2006 ). 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 ). Different methodologies for the synthesis of polypropionates have been developed, with aldol and aldol-related chemistry being the most used (Schetter & Mahrwald, 2006 ).

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) or Grignard reagent (Rodríguez et al., 2006), 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 ).

2. Structural commentary

The molecular structure of the title compound is illustrated in Fig. 1. 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
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). In the crystal, neighbouring molecules are linked by the O4—H4⋯O1ⁱ hydrogen bond, forming chains along [010]; see Fig. 2 and Table 1.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O4—H4⋯O1ⁱ	0.82	2.05	2.811 (2)	155
Symmetry code: (i) x, y+1, z.

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

4. Database survey

A search of the Cambridge Structural Database (Version 5.38, updated May 2017; Groom et al., 2016 ) 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 ) and erythronolides A and B (Lynch et al., 1989a ; 1989b ).

5. Synthesis and crystallization

The synthesis of the title compound, illustrated in Fig. 3, 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]²⁰_D = −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
Reaction scheme

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. 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 U_iso(H) = 1.5U_eq(O-hydroxyl and C-methyl) and 1.2U_eq(C) for other H atoms.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₁H₁₈O₄
M_r	214.25
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	100
a, b, c (Å)	5.0968 (1), 8.8153 (1), 25.6052 (3)
V (Å³)	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 $[Rigaku OD (2016). CrysAlis PRO. Rigaku Oxford Diffraction, Wroclaw, Poland.]$ )
T_min, T_max	0.739, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	17757, 2131, 2081
R_int	0.030
(sin θ/λ)_max (Å⁻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
Δρ_max, Δρ_min (e Å⁻³)	0.23, −0.17
Absolute structure	Flack x determined using 812 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
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 ), SHELXL2016 (Sheldrick, 2015b ), Mercury (Macrae et al., 2008 ) and OLEX2 (Dolomanov et al., 2009 ).

Supporting information

CCDC reference: 1548935

Crystal structure: contains datablocks Global, I. DOI: https://doi.org/10.1107/S2056989017009318/su5376sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017009318/su5376Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017009318/su5376Isup3.cml

checkCIF report

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

C₁₁H₁₈O₄	D_x = 1.237 Mg m⁻³
M_r = 214.25	Cu Kα radiation, λ = 1.54184 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 12810 reflections
a = 5.0968 (1) Å	θ = 3.5–68.8°
b = 8.8153 (1) Å	µ = 0.77 mm⁻¹
c = 25.6052 (3) Å	T = 100 K
V = 1150.44 (3) Å³	Block, colourless
Z = 4	0.23 × 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 Source	2081 reflections with I > 2σ(I)
Mirror monochromator	R_int = 0.030
ω scans	θ_max = 69.0°, θ_min = 3.5°
Absorption correction: gaussian (CrysAlis PRO; Rigaku OD, 2016)	h = −6→6
T_min = 0.739, T_max = 1.000	k = −10→10
17757 measured reflections	l = −30→31

Refinement top

Refinement on F²	H-atom parameters constrained
Least-squares matrix: full	w = 1/[σ²(F_o²) + (0.0367P)² + 0.4414P] where P = (F_o² + 2F_c²)/3
R[F² > 2σ(F²)] = 0.032	(Δ/σ)_max < 0.001
wR(F²) = 0.094	Δρ_max = 0.23 e Å⁻³
S = 1.26	Δρ_min = −0.17 e Å⁻³
2131 reflections	Extinction correction: (SHELXL2016; Sheldrick, 2015b), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
141 parameters	Extinction coefficient: 0.0032 (6)
0 restraints	Absolute structure: Flack x determined using 812 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
Primary atom site location: dual	Absolute 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

	x	y	z	U_iso*/U_eq
O1	0.9031 (4)	−0.13807 (18)	0.69895 (7)	0.0267 (4)
O2	0.6220 (3)	0.03761 (19)	0.72821 (6)	0.0234 (4)
O3	0.9752 (3)	0.10820 (18)	0.68416 (6)	0.0214 (4)
O4	0.8749 (4)	0.55481 (18)	0.66999 (6)	0.0241 (4)
H4	0.838292	0.644582	0.674153	0.036*
C1	0.8397 (5)	−0.0079 (3)	0.70337 (9)	0.0196 (5)
C2	0.6171 (5)	0.2019 (3)	0.73034 (9)	0.0208 (5)
H2A	0.653581	0.237855	0.765407	0.025*
H2B	0.447987	0.240857	0.719285	0.025*
C3	0.8339 (5)	0.2503 (2)	0.69242 (9)	0.0182 (5)
H3	0.949859	0.323486	0.709691	0.022*
C4	0.7482 (5)	0.3135 (2)	0.63967 (8)	0.0164 (5)
H4A	0.904016	0.316110	0.617275	0.020*
C5	0.6564 (5)	0.4780 (2)	0.64684 (9)	0.0179 (5)
H5	0.509516	0.479338	0.671547	0.021*
C6	0.5674 (5)	0.5528 (3)	0.59550 (8)	0.0188 (5)
H6	0.418322	0.494773	0.581917	0.023*
C7	0.7832 (5)	0.5488 (3)	0.55492 (9)	0.0224 (5)
H7	0.947944	0.581376	0.565794	0.027*
C8	0.7641 (5)	0.5043 (3)	0.50573 (9)	0.0266 (5)
H8	0.916088	0.510563	0.485756	0.032*
C9	0.5243 (6)	0.4446 (4)	0.47858 (10)	0.0394 (7)
H9A	0.492138	0.503209	0.447625	0.059*
H9B	0.375977	0.452228	0.501530	0.059*
H9C	0.551540	0.340378	0.469213	0.059*
C10	0.5456 (5)	0.2129 (3)	0.61247 (9)	0.0208 (5)
H10A	0.379257	0.222893	0.629735	0.031*
H10B	0.601834	0.109062	0.613932	0.031*
H10C	0.528349	0.243598	0.576661	0.031*
C11	0.4749 (6)	0.7165 (3)	0.60482 (10)	0.0268 (6)
H11A	0.343748	0.717439	0.631719	0.040*
H11B	0.401916	0.756573	0.573128	0.040*
H11C	0.621298	0.777709	0.615420	0.040*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0337 (10)	0.0144 (8)	0.0319 (9)	0.0021 (7)	−0.0088 (8)	−0.0007 (7)
O2	0.0230 (8)	0.0183 (8)	0.0289 (8)	−0.0017 (7)	0.0033 (7)	0.0048 (7)
O3	0.0198 (8)	0.0151 (7)	0.0292 (8)	0.0029 (7)	0.0022 (7)	0.0037 (6)
O4	0.0278 (9)	0.0128 (7)	0.0316 (9)	0.0000 (7)	−0.0107 (7)	−0.0023 (7)
C1	0.0218 (11)	0.0181 (11)	0.0189 (10)	−0.0010 (10)	−0.0052 (9)	0.0004 (9)
C2	0.0244 (12)	0.0166 (11)	0.0215 (11)	0.0024 (11)	0.0028 (10)	0.0003 (9)
C3	0.0180 (11)	0.0134 (10)	0.0231 (11)	0.0004 (9)	−0.0006 (9)	−0.0017 (8)
C4	0.0159 (10)	0.0128 (10)	0.0205 (10)	0.0007 (9)	0.0012 (9)	−0.0006 (8)
C5	0.0175 (11)	0.0146 (10)	0.0214 (11)	−0.0010 (9)	−0.0012 (9)	−0.0014 (9)
C6	0.0158 (11)	0.0181 (11)	0.0224 (11)	−0.0002 (9)	−0.0019 (9)	0.0013 (9)
C7	0.0164 (11)	0.0230 (11)	0.0277 (11)	0.0002 (10)	−0.0008 (9)	0.0054 (10)
C8	0.0217 (12)	0.0331 (13)	0.0251 (11)	0.0042 (11)	0.0026 (10)	0.0053 (10)
C9	0.0310 (15)	0.0616 (19)	0.0258 (13)	−0.0003 (15)	−0.0020 (11)	−0.0064 (13)
C10	0.0218 (12)	0.0182 (11)	0.0224 (11)	−0.0015 (10)	−0.0008 (9)	−0.0013 (9)
C11	0.0314 (14)	0.0192 (12)	0.0299 (12)	0.0065 (11)	−0.0050 (11)	0.0029 (10)

Geometric parameters (Å, º) top

O1—C1	1.198 (3)	C6—H6	0.9800
O2—C1	1.340 (3)	C6—C7	1.513 (3)
O2—C2	1.450 (3)	C6—C11	1.536 (3)
O3—C1	1.329 (3)	C7—H7	0.9300
O3—C3	1.461 (3)	C7—C8	1.323 (3)
O4—H4	0.8200	C8—H8	0.9300
O4—C5	1.432 (3)	C8—C9	1.501 (4)
C2—H2A	0.9700	C9—H9A	0.9600
C2—H2B	0.9700	C9—H9B	0.9600
C2—C3	1.532 (3)	C9—H9C	0.9600
C3—H3	0.9800	C10—H10A	0.9600
C3—C4	1.525 (3)	C10—H10B	0.9600
C4—H4A	0.9800	C10—H10C	0.9600
C4—C5	1.535 (3)	C11—H11A	0.9600
C4—C10	1.529 (3)	C11—H11B	0.9600
C5—H5	0.9800	C11—H11C	0.9600
C5—C6	1.539 (3)

C1—O2—C2	109.32 (19)	C5—C6—H6	107.9
C1—O3—C3	110.52 (17)	C7—C6—C5	111.25 (19)
C5—O4—H4	109.5	C7—C6—H6	107.9
O1—C1—O2	123.7 (2)	C7—C6—C11	110.58 (19)
O1—C1—O3	124.2 (2)	C11—C6—C5	111.11 (18)
O3—C1—O2	112.07 (19)	C11—C6—H6	107.9
O2—C2—H2A	111.0	C6—C7—H7	116.3
O2—C2—H2B	111.0	C8—C7—C6	127.4 (2)
O2—C2—C3	104.01 (18)	C8—C7—H7	116.3
H2A—C2—H2B	109.0	C7—C8—H8	116.4
C3—C2—H2A	111.0	C7—C8—C9	127.2 (2)
C3—C2—H2B	111.0	C9—C8—H8	116.4
O3—C3—C2	102.04 (17)	C8—C9—H9A	109.5
O3—C3—H3	109.4	C8—C9—H9B	109.5
O3—C3—C4	109.03 (18)	C8—C9—H9C	109.5
C2—C3—H3	109.4	H9A—C9—H9B	109.5
C4—C3—C2	117.2 (2)	H9A—C9—H9C	109.5
C4—C3—H3	109.4	H9B—C9—H9C	109.5
C3—C4—H4A	107.1	C4—C10—H10A	109.5
C3—C4—C5	109.04 (18)	C4—C10—H10B	109.5
C3—C4—C10	112.68 (18)	C4—C10—H10C	109.5
C5—C4—H4A	107.1	H10A—C10—H10B	109.5
C10—C4—H4A	107.1	H10A—C10—H10C	109.5
C10—C4—C5	113.36 (19)	H10B—C10—H10C	109.5
O4—C5—C4	105.02 (18)	C6—C11—H11A	109.5
O4—C5—H5	108.7	C6—C11—H11B	109.5
O4—C5—C6	112.33 (18)	C6—C11—H11C	109.5
C4—C5—H5	108.7	H11A—C11—H11B	109.5
C4—C5—C6	113.11 (18)	H11A—C11—H11C	109.5
C6—C5—H5	108.7	H11B—C11—H11C	109.5

O2—C2—C3—O3	−13.8 (2)	C2—C3—C4—C10	−49.2 (3)
O2—C2—C3—C4	105.2 (2)	C3—O3—C1—O1	175.2 (2)
O3—C3—C4—C5	−167.31 (18)	C3—O3—C1—O2	−4.5 (2)
O3—C3—C4—C10	65.9 (2)	C3—C4—C5—O4	56.7 (2)
O4—C5—C6—C7	61.8 (2)	C3—C4—C5—C6	179.52 (19)
O4—C5—C6—C11	−61.9 (3)	C4—C5—C6—C7	−56.9 (3)
C1—O2—C2—C3	12.2 (2)	C4—C5—C6—C11	179.4 (2)
C1—O3—C3—C2	11.6 (2)	C5—C6—C7—C8	131.2 (3)
C1—O3—C3—C4	−113.0 (2)	C6—C7—C8—C9	−1.0 (4)
C2—O2—C1—O1	174.9 (2)	C10—C4—C5—O4	−176.93 (18)
C2—O2—C1—O3	−5.3 (2)	C10—C4—C5—C6	−54.1 (3)
C2—C3—C4—C5	77.5 (2)	C11—C6—C7—C8	−104.8 (3)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O4—H4···O1ⁱ	0.82	2.05	2.811 (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).

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