In the title compound, the dioxolane and cyclohexane rings adopt twist and chair conformations, respectively. In the crystal, intra- and intermolecular O—H⋯O hydrogen bonds are observed.
Keywords: crystal structure, hydrogen bonds, paclitaxel, cyclohexane, hydroxy groups
Abstract
In the title compound, C9H16O4, the five-membered dioxolane ring adopts a twist conformation; two adjacent C atoms deviate alternately from the mean plane of other atoms by −0.297 (4) and 0.288 (4) Å. The spiro-fused cyclohexane ring shows a chair form. The hydroxy group substituted in an axial position makes an intramolecular O—H⋯O hydrogen bond with one of the O atoms in the cyclic ether, forming an S(6) ring motif. In the crystal, the O—H⋯O hydrogen bond involving the equatorial hydroxy group connects the molecules into a zigzag chain with a C(5) motif running along the c axis.
Chemical context
Paclitaxel (systematic name: (1S,2S,3R,4S,7R,9S,10S,12R,15S)-4,12-diacetoxy-1,9-dihydroxy-15-{[(2R,3S)-3-benzoylamino-2-hydroxy-3-phenyl]propanoyl}oxy-10,14,17,17-tetramethyl-11-oxo-6-oxatetracyclo[11.3.1.03,10.04,7]heptadec-13-en-2-yl benzoate) is a well-known natural diterpenoid with a potent antitumor activity (Wall & Wani, 1995 ▸). Its rather complicated structure and significant bioactivity have attracted chemical and medicinal interests. While we recently reported several structures of the compounds (Oishi, Yamaguchi et al., 2015 ▸; Oishi, Fukaya et al., 2015a
▸,b
▸) obtained in the synthesis of paclitaxel (Fukaya, Tanaka et al., 2015 ▸; Fukaya, Kodama et al., 2015 ▸), the title compound has been prepared in an efficient synthetic approach to furnish the highly functionalized cyclohexane unit (Fukaya, Sugai et al., 2015 ▸). Although the title compound has been reported first with a different synthetic procedure, any stereochemical or conformational assignment was not mentioned (Li et al., 1981 ▸).
Structural commentary
The molecular structure of the title compound is shown in Fig. 1 ▸. The dioxolane ring (O1/C2/C3/O4/C5) adopts a twist form with puckering parameters of Q(2) = 0.3523 (16) Å and φ(2) = 233.8 (3)°. Atoms C2 and C3 deviate from the mean plane of the other three atoms by −0.297 (4) and 0.288 (4) Å, respectively. The cyclohexane ring (C5–C10) adopts a chair form with puckering parameters of Q = 0.5560 (18) Å, θ = 3.32 (18)°, φ = 193 (3)°, Q(2) = 0.0323 (17) Å and Q(3) = 0.5551 (18) Å. The C5—O1, C7—C11 and C8—O13 bonds of equatorially oriented substituents make angles of 68.30 (9), 69.85 (9) and 75.76 (9)°, respectively, with the normal to the Cremer and Pople plane of the cyclohexane ring. The axially oriented hydroxy group forms an intramolecular O—H⋯O hydrogen bond (O12—H12⋯O4; Table 1 ▸), generating an S(6) graph-set motif. In this ring motif, five atoms (C5—O4⋯H12—O12—O7) are nearly coplanar with a maximum deviation of 0.012 (5) Å for atom O4.
Figure 1.
The molecular structure of the title compound, showing the atom labels. Displacement ellipsoids are drawn at the 50% probability level. The yellow dotted line indicates the intramolecular O—H⋯O hydrogen bond. Only H atoms connected to O and chiral C atoms are shown for clarity.
Table 1. Hydrogen-bond geometry (, ).
| DHA | DH | HA | D A | DHA |
|---|---|---|---|---|
| O12H12O4 | 0.84 | 2.05 | 2.7838(16) | 146 |
| O13H13O12i | 0.84 | 1.99 | 2.8093(16) | 166 |
| C6H6BO1ii | 0.99 | 2.61 | 3.5631(19) | 162 |
Symmetry codes: (i) 
; (ii) 
.
Supramolecular features
The crystal packing features an intermolecular O—H⋯O hydrogen bond (O13—H13⋯O12i; Table 1 ▸) connecting enantiomers related by a glide plane to form a chain structure with a C(5) graph-set motif running along the c axis (Fig. 2 ▸). An intermolecular C—H⋯O interaction (C6—H6B⋯O1ii; Table 1 ▸) with a slightly longer distance, leading to form a sheet parallel to (100), is also observed (Fig. 3 ▸).
Figure 2.
A partial packing view showing the chain structure. Yellow lines indicate the intramolecular O—H⋯O hydrogen bonds. Purple dashed lines indicate the intermolecular O—H⋯O hydrogen bonds. Only H atoms involved in hydrogen bonds are shown for clarity. [Symmetry code: (i) x, −y + 
, z − 
.]
Figure 3.
A packing diagram viewed down the c axis. Black dotted lines indicate the intermolecular C—H⋯O interactions. Yellow lines and purple dashed lines indicate the intra- and intermolecular O—H⋯O hydrogen bonds, respectively. Only H atoms involved in hydrogen bonds are shown for clarity. [Symmetry code: (ii) −x, −y + 1, −z + 2.]
Database survey
In the Cambridge Structural Database (CSD, Version 5.36, November 2014; Groom & Allen, 2014 ▸), 266 structures containing a 7-methyl-1,4-dioxaspiro[4.5]decane skeleton, (a), are registered (Fig. 4 ▸). These include six compounds with 7,8-dioxy-substituents. Two of them (JIQFIY and JIQGAR; Collins et al., 1998 ▸), synthesized from d-glucose, are closely related to the title compound [(b); racemic, P21/c], which are its 9,10-dimethoxy-8-O-methyl [(c); chiral, P212121] and 9,10-dimethoxy-6-phenyl-8-O-methyl [(d); chiral, P212121] derivatives. In the crystal structures of (c) and (d), the dioxolane rings adopt twist forms and the cyclohexane rings show chair forms. The intramolecular O—H⋯O hydrogen bond is also observed in (c), but not in (d).
Figure 4.
(a) 7-Methyl-1,4-dioxaspiro[4.5]decane; as the core structure for database survey, (b) the title compound, and its (c) 9,10-dimethoxy-8-O-methyl and (d) 9,10-dimethoxy-6-phenyl-8-O-methyl derivatives.
Synthesis and crystallization
The title compound was afforded in an improved synthetic approach of paclitaxel from 3-methylanisole (Fukaya, Sugai et al., 2015 ▸). Purification was carried out by silica gel column chromatography, and colorless crystals were obtained from an ethyl acetate solution by slow evaporation at ambient temperature. M.p. 359–360 K. HRMS (ESI) m/z calculated for C9H16O4Na+ [M + Na]+: 211.0946; found: 211.0936. Analysis calculated for C9H16O4: C 57.43, H 8.57%; found: C 57.51, H 8.50%. It is noted that the crystals grown from a diethyl ether solution under a pentane-saturated atmosphere were non-merohedral twins, and the structure is essentially the same as that reported here.
Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. C-bound H atoms were positioned geometrically with C—H = 0.98–1.00 Å, and constrained to ride on their parent atoms with U iso(H) = 1.2U eq(C) or 1.5U eq(methyl C). The hydroxy H atoms were placed guided by difference maps, with O—H = 0.84 Å and with U iso(H) = 1.5U eq(O).
Table 2. Experimental details.
| Crystal data | |
| Chemical formula | C9H16O4 |
| M r | 188.22 |
| Crystal system, space group | Monoclinic, P21/c |
| Temperature (K) | 90 |
| a, b, c () | 7.7403(5), 18.1498(11), 6.7335(5) |
| () | 103.281(2) |
| V (3) | 920.66(11) |
| Z | 4 |
| Radiation type | Mo K |
| (mm1) | 0.11 |
| Crystal size (mm) | 0.28 0.27 0.25 |
| Data collection | |
| Diffractometer | Bruker D8 Venture |
| Absorption correction | Multi-scan (SADABS; Bruker, 2014 ▸) |
| T min, T max | 0.97, 0.97 |
| No. of measured, independent and observed [I > 2(I)] reflections | 8165, 1612, 1205 |
| R int | 0.037 |
| (sin /)max (1) | 0.595 |
| Refinement | |
| R[F 2 > 2(F 2)], wR(F 2), S | 0.036, 0.092, 1.01 |
| No. of reflections | 1612 |
| No. of parameters | 121 |
| H-atom treatment | H-atom parameters constrained |
| max, min (e 3) | 0.25, 0.27 |
Supplementary Material
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015016783/is5419sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015016783/is5419Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989015016783/is5419Isup3.cml
CCDC reference: 1422946
Additional supporting information: crystallographic information; 3D view; checkCIF report
Acknowledgments
This research was partially supported by the Keio Gijuku Fukuzawa Memorial Fund for the Advancement of Education and Research. We also thank Professor S. Ohba (Keio University, Japan) for his valuable advice.
supplementary crystallographic information
Crystal data
| C9H16O4 | Dx = 1.358 Mg m−3 |
| Mr = 188.22 | Melting point: 360.2 K |
| Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
| a = 7.7403 (5) Å | Cell parameters from 2733 reflections |
| b = 18.1498 (11) Å | θ = 2.7–24.7° |
| c = 6.7335 (5) Å | µ = 0.11 mm−1 |
| β = 103.281 (2)° | T = 90 K |
| V = 920.66 (11) Å3 | Prism, colorless |
| Z = 4 | 0.28 × 0.27 × 0.25 mm |
| F(000) = 408 |
Data collection
| Bruker D8 Venture diffractometer | 1612 independent reflections |
| Radiation source: fine-focus sealed tube | 1205 reflections with I > 2σ(I) |
| Multilayered confocal mirror monochromator | Rint = 0.037 |
| Detector resolution: 10.4167 pixels mm-1 | θmax = 25.0°, θmin = 2.7° |
| φ and ω scans | h = −9→8 |
| Absorption correction: multi-scan (SADABS; Bruker, 2014) | k = −21→21 |
| Tmin = 0.97, Tmax = 0.97 | l = −8→7 |
| 8165 measured reflections |
Refinement
| Refinement on F2 | Primary atom site location: structure-invariant direct methods |
| Least-squares matrix: full | Secondary atom site location: difference Fourier map |
| R[F2 > 2σ(F2)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
| wR(F2) = 0.092 | H-atom parameters constrained |
| S = 1.01 | w = 1/[σ2(Fo2) + (0.0407P)2 + 0.4103P] where P = (Fo2 + 2Fc2)/3 |
| 1612 reflections | (Δ/σ)max = 0.008 |
| 121 parameters | Δρmax = 0.25 e Å−3 |
| 0 restraints | Δρmin = −0.27 e Å−3 |
Special details
| Experimental. IR (KBr) 3476, 3398, 2986, 2950, 2931, 2895, 1448, 1419, 1397, 1356, 1229, 1120, 1083, 1060, 1013, 952, 840, 696 cm-1; 1H NMR (500 MHz, CDCl3) δ (p.p.m.) 4.02–3.91 (m, 4H), 3.73 (s, 1H), 3.33 (ddd, J = 10.7, 10.6, 4.9 Hz, 1H), 2.03 (d, J = 10.6 Hz, 1H), 1.94–1.86 (m, 2H), 1.78–1.56 (m, 4H), 1.25 (d, J = 0.9 Hz, 3H); 13C NMR (125 MHz, CDCl3) δ (p.p.m.) 108.7 (C), 74.0 (CH), 72.5 (C), 64.7 (CH2), 64.4 (CH2), 44.1 (CH2), 33.2 (CH2), 28.4 (CH2), 26.2 (CH3). |
| 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. |
| 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.Problematic one reflection with |I(obs)-I(calc)|/σW(I) greater than 10 (0 2 0) has been omitted in the final refinement. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
| x | y | z | Uiso*/Ueq | ||
| O1 | 0.27151 (15) | 0.55328 (6) | 1.12431 (17) | 0.0191 (3) | |
| C2 | 0.4342 (2) | 0.58896 (9) | 1.2186 (3) | 0.0209 (4) | |
| H2A | 0.5326 | 0.5725 | 1.158 | 0.025* | |
| H2B | 0.4662 | 0.5796 | 1.3675 | 0.025* | |
| C3 | 0.3914 (2) | 0.66886 (9) | 1.1734 (3) | 0.0204 (4) | |
| H3A | 0.327 | 0.6902 | 1.271 | 0.025* | |
| H3B | 0.5002 | 0.698 | 1.1772 | 0.025* | |
| O4 | 0.28135 (15) | 0.66576 (6) | 0.97209 (18) | 0.0177 (3) | |
| C5 | 0.1875 (2) | 0.59633 (9) | 0.9519 (2) | 0.0154 (4) | |
| C6 | −0.0045 (2) | 0.60871 (9) | 0.9585 (2) | 0.0139 (4) | |
| H6A | −0.0085 | 0.6365 | 1.0839 | 0.017* | |
| H6B | −0.0617 | 0.5603 | 0.9663 | 0.017* | |
| C7 | −0.1103 (2) | 0.65073 (8) | 0.7741 (3) | 0.0139 (4) | |
| C8 | −0.0926 (2) | 0.61203 (9) | 0.5774 (2) | 0.0141 (4) | |
| H8 | −0.1427 | 0.5614 | 0.5804 | 0.017* | |
| C9 | 0.1009 (2) | 0.60306 (9) | 0.5692 (3) | 0.0161 (4) | |
| H9A | 0.1551 | 0.6523 | 0.5649 | 0.019* | |
| H9B | 0.1079 | 0.5764 | 0.443 | 0.019* | |
| C10 | 0.2047 (2) | 0.56059 (9) | 0.7546 (3) | 0.0160 (4) | |
| H10A | 0.1598 | 0.5094 | 0.7496 | 0.019* | |
| H10B | 0.3315 | 0.5586 | 0.7499 | 0.019* | |
| C11 | −0.3033 (2) | 0.65735 (10) | 0.7850 (3) | 0.0209 (4) | |
| H11A | −0.3108 | 0.6838 | 0.9097 | 0.031* | |
| H11B | −0.3544 | 0.608 | 0.7868 | 0.031* | |
| H11C | −0.3692 | 0.6845 | 0.6658 | 0.031* | |
| O12 | −0.04355 (15) | 0.72524 (6) | 0.77185 (18) | 0.0170 (3) | |
| H12 | 0.0652 | 0.726 | 0.828 | 0.026* | |
| O13 | −0.19319 (15) | 0.64738 (6) | 0.40008 (17) | 0.0179 (3) | |
| H13 | −0.1446 | 0.6875 | 0.3825 | 0.027* |
Atomic displacement parameters (Å2)
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O1 | 0.0174 (6) | 0.0186 (7) | 0.0174 (7) | −0.0029 (5) | −0.0040 (5) | 0.0046 (5) |
| C2 | 0.0167 (9) | 0.0220 (10) | 0.0206 (10) | −0.0018 (8) | −0.0024 (7) | −0.0001 (8) |
| C3 | 0.0197 (10) | 0.0203 (10) | 0.0186 (10) | −0.0022 (8) | −0.0012 (8) | −0.0022 (8) |
| O4 | 0.0167 (6) | 0.0158 (6) | 0.0178 (7) | −0.0057 (5) | −0.0021 (5) | 0.0019 (5) |
| C5 | 0.0157 (9) | 0.0124 (8) | 0.0162 (9) | −0.0029 (7) | −0.0001 (7) | 0.0041 (7) |
| C6 | 0.0165 (9) | 0.0130 (9) | 0.0130 (9) | −0.0021 (7) | 0.0048 (7) | −0.0011 (7) |
| C7 | 0.0154 (9) | 0.0099 (8) | 0.0166 (10) | −0.0008 (7) | 0.0042 (7) | 0.0003 (7) |
| C8 | 0.0160 (9) | 0.0114 (9) | 0.0132 (9) | −0.0010 (7) | −0.0002 (7) | 0.0010 (7) |
| C9 | 0.0178 (9) | 0.0162 (9) | 0.0147 (9) | −0.0001 (7) | 0.0045 (7) | −0.0020 (7) |
| C10 | 0.0135 (9) | 0.0164 (9) | 0.0188 (10) | 0.0001 (7) | 0.0051 (7) | −0.0005 (7) |
| C11 | 0.0181 (9) | 0.0223 (10) | 0.0233 (10) | 0.0017 (8) | 0.0071 (8) | 0.0005 (8) |
| O12 | 0.0176 (6) | 0.0129 (6) | 0.0195 (7) | −0.0011 (5) | 0.0021 (5) | −0.0007 (5) |
| O13 | 0.0192 (7) | 0.0171 (6) | 0.0145 (7) | −0.0021 (5) | −0.0019 (5) | 0.0036 (5) |
Geometric parameters (Å, º)
| O1—C5 | 1.4265 (19) | C7—C11 | 1.517 (2) |
| O1—C2 | 1.428 (2) | C7—C8 | 1.532 (2) |
| C2—C3 | 1.503 (2) | C8—O13 | 1.4200 (19) |
| C2—H2A | 0.99 | C8—C9 | 1.520 (2) |
| C2—H2B | 0.99 | C8—H8 | 1.0 |
| C3—O4 | 1.427 (2) | C9—C10 | 1.529 (2) |
| C3—H3A | 0.99 | C9—H9A | 0.99 |
| C3—H3B | 0.99 | C9—H9B | 0.99 |
| O4—C5 | 1.4453 (19) | C10—H10A | 0.99 |
| C5—C10 | 1.512 (2) | C10—H10B | 0.99 |
| C5—C6 | 1.514 (2) | C11—H11A | 0.98 |
| C6—C7 | 1.526 (2) | C11—H11B | 0.98 |
| C6—H6A | 0.99 | C11—H11C | 0.98 |
| C6—H6B | 0.99 | O12—H12 | 0.84 |
| C7—O12 | 1.4491 (19) | O13—H13 | 0.84 |
| C5—O1—C2 | 107.70 (12) | O12—C7—C8 | 108.41 (13) |
| O1—C2—C3 | 102.52 (13) | C11—C7—C8 | 111.28 (14) |
| O1—C2—H2A | 111.3 | C6—C7—C8 | 109.66 (13) |
| C3—C2—H2A | 111.3 | O13—C8—C9 | 111.85 (13) |
| O1—C2—H2B | 111.3 | O13—C8—C7 | 112.27 (13) |
| C3—C2—H2B | 111.3 | C9—C8—C7 | 111.41 (13) |
| H2A—C2—H2B | 109.2 | O13—C8—H8 | 107.0 |
| O4—C3—C2 | 102.13 (13) | C9—C8—H8 | 107.0 |
| O4—C3—H3A | 111.3 | C7—C8—H8 | 107.0 |
| C2—C3—H3A | 111.3 | C8—C9—C10 | 111.21 (14) |
| O4—C3—H3B | 111.3 | C8—C9—H9A | 109.4 |
| C2—C3—H3B | 111.3 | C10—C9—H9A | 109.4 |
| H3A—C3—H3B | 109.2 | C8—C9—H9B | 109.4 |
| C3—O4—C5 | 107.54 (12) | C10—C9—H9B | 109.4 |
| O1—C5—O4 | 105.99 (12) | H9A—C9—H9B | 108.0 |
| O1—C5—C10 | 111.37 (13) | C5—C10—C9 | 111.42 (13) |
| O4—C5—C10 | 108.24 (13) | C5—C10—H10A | 109.3 |
| O1—C5—C6 | 108.93 (13) | C9—C10—H10A | 109.3 |
| O4—C5—C6 | 110.10 (13) | C5—C10—H10B | 109.3 |
| C10—C5—C6 | 112.02 (13) | C9—C10—H10B | 109.3 |
| C5—C6—C7 | 113.40 (13) | H10A—C10—H10B | 108.0 |
| C5—C6—H6A | 108.9 | C7—C11—H11A | 109.5 |
| C7—C6—H6A | 108.9 | C7—C11—H11B | 109.5 |
| C5—C6—H6B | 108.9 | H11A—C11—H11B | 109.5 |
| C7—C6—H6B | 108.9 | C7—C11—H11C | 109.5 |
| H6A—C6—H6B | 107.7 | H11A—C11—H11C | 109.5 |
| O12—C7—C11 | 106.50 (13) | H11B—C11—H11C | 109.5 |
| O12—C7—C6 | 110.42 (13) | C7—O12—H12 | 109.5 |
| C11—C7—C6 | 110.50 (14) | C8—O13—H13 | 109.5 |
| C5—O1—C2—C3 | 30.97 (17) | C5—C6—C7—C8 | 53.80 (17) |
| O1—C2—C3—O4 | −37.36 (16) | O12—C7—C8—O13 | −61.28 (17) |
| C2—C3—O4—C5 | 30.55 (17) | C11—C7—C8—O13 | 55.53 (17) |
| C2—O1—C5—O4 | −12.62 (16) | C6—C7—C8—O13 | 178.10 (12) |
| C2—O1—C5—C10 | 104.89 (15) | O12—C7—C8—C9 | 65.06 (16) |
| C2—O1—C5—C6 | −131.06 (14) | C11—C7—C8—C9 | −178.13 (13) |
| C3—O4—C5—O1 | −12.23 (16) | C6—C7—C8—C9 | −55.56 (17) |
| C3—O4—C5—C10 | −131.81 (14) | O13—C8—C9—C10 | −176.36 (12) |
| C3—O4—C5—C6 | 105.44 (15) | C7—C8—C9—C10 | 57.07 (18) |
| O1—C5—C6—C7 | −176.78 (12) | O1—C5—C10—C9 | 174.98 (12) |
| O4—C5—C6—C7 | 67.39 (16) | O4—C5—C10—C9 | −68.89 (16) |
| C10—C5—C6—C7 | −53.12 (18) | C6—C5—C10—C9 | 52.69 (18) |
| C5—C6—C7—O12 | −65.60 (17) | C8—C9—C10—C5 | −55.09 (18) |
| C5—C6—C7—C11 | 176.83 (13) |
Hydrogen-bond geometry (Å, º)
| D—H···A | D—H | H···A | D···A | D—H···A |
| O12—H12···O4 | 0.84 | 2.05 | 2.7838 (16) | 146 |
| O13—H13···O12i | 0.84 | 1.99 | 2.8093 (16) | 166 |
| C6—H6B···O1ii | 0.99 | 2.61 | 3.5631 (19) | 162 |
Symmetry codes: (i) x, −y+3/2, z−1/2; (ii) −x, −y+1, −z+2.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015016783/is5419sup1.cif
Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015016783/is5419Isup2.hkl
Supporting information file. DOI: 10.1107/S2056989015016783/is5419Isup3.cml
CCDC reference: 1422946
Additional supporting information: crystallographic information; 3D view; checkCIF report