organic compounds Acta Crystallographica Section E
(2005); Xu et al. (2010); Yu et al. (2007). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986).
Structure Reports Online ISSN 1600-5368
Absolute configuration of xerophenone A Hoong-Kun Fun,a*‡ Cholpisut Tantapakul,b Surat Laphookhieo,b Nawong Boonnakc and Suchada Chantraprommac§ a
X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, bNatural Products Research Laboratory, School of Science, Mae Fah Luang University, Tasud, Muang Chiang Rai 57100, Thailand, and cCrystal Materials Research Unit, Department of Chemistry, Faculty of Science, Prince of Songkla University, Hat-Yai, Songkhla 90112, Thailand Correspondence e-mail:
[email protected] Received 31 March 2012; accepted 7 April 2012 ˚; Key indicators: single-crystal X-ray study; T = 100 K; mean (C–C) = 0.003 A disorder in main residue; R factor = 0.037; wR factor = 0.099; data-to-parameter ratio = 12.9.
The title compound, C33H42O5, known as xerophenone A {systematic name: (1R,3R,4R,6S,8E,10R)-10-hydroxy-8-[hydroxy(phenyl)methylene]-4-methyl-1,6-bis(3-methylbut-2-en1-yl)-3-(3-methylbut-3-en-1-yl)-11-oxatricyclo[4.3.1.1 4,10 ]undecane-7,9-dione} is a naturally occurring rearranged benzophenone compound which was isolated from the twigs of Garcinia propinqua. The absolute configuration was determined by refining the Flack parameter to 0.18 (16). The absolute configurations at positions 1, 3, 4, 6 and 10 of the xerophenone A are R, R, R, S and R. In the molecule, the cyclohexane-1,3-dione, tetrahydro-2H-pyran and tetrahydrofuran rings adopt twisted boat, standard chair and envelope conformations, respectively. The 3-methylbut-3-en-1-yl substituent is disordered over two sets of sites in a 0.771 (11):0.229 (11) ratio. An intramolecular O—H O hydrogen bond generates an S(6) ring motif. In the crystal, molecules are linked by O—H O and weak C—H O interactions into a chain along the a axis. A very weak C— ˚ ] are H interaction and C O short contact [2.989 (2) A also present.
Related literature For bond-length data, see: Allen et al. (1987). For ring conformations, see: Cremer & Pople (1975). For hydrogenbond motifs, see: Bernstein et al. (1995). For background to plants in the Clusiaceae family, bioactive metabolites and their biological and pharmacological activities, see: Castardo et al. (2008); Henry & Jacobs (1995); Nguyen et al. (2011); Phongpaichit et al. (1994); Suksamrarn et al. (2006); Thoison et al. ‡ Thomson Reuters ResearcherID: A-3561-2009. § Additional correspondence author, e-mail:
[email protected]. Thomson Reuters ResearcherID: A-5085-2009. Acta Cryst. (2012). E68, o1451–o1452
Experimental Crystal data ˚3 V = 1451.92 (7) A Z=2 Cu K radiation = 0.62 mm1 T = 100 K 0.31 0.13 0.09 mm
C33H42O5 Mr = 518.67 Monoclinic, P21 ˚ a = 6.1984 (2) A ˚ b = 17.0998 (4) A ˚ c = 13.7007 (3) A = 91.036 (1)
Data collection 11622 measured reflections 4746 independent reflections 4661 reflections with I > 2(I) Rint = 0.023
Bruker APEX Duo CCD area detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009) Tmin = 0.830, Tmax = 0.944
Refinement R[F 2 > 2(F 2)] = 0.037 wR(F 2) = 0.099 S = 1.07 4746 reflections 369 parameters 7 restraints
H-atom parameters constrained ˚ 3 max = 0.24 e A ˚ 3 min = 0.20 e A Absolute structure: Flack (1983), 2079 Friedel pairs Flack parameter: 0.18 (16)
Table 1 ˚ , ). Hydrogen-bond geometry (A Cg4 is the centroid of the C28–C33 ring. D—H A
D—H
H A
D A
D—H A
O1—H1O1 O2 O4—H1O4 O3i C21—H21B O3i C25—H25B Cg4ii
0.82 0.82 0.97 0.96
1.70 1.97 2.48 2.99
2.4446 (19) 2.7499 (18) 3.283 (2) 3.786 (3)
151 159 139 142
Symmetry codes: (i) x þ 1; y; z; (ii) x; y 12; z.
Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009).
doi:10.1107/S1600536812015267
Fun et al.
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organic compounds SL and CT are grateful to the Thailand Research Fund and Mae Fah Luang University for financial support. The authors thank Prince of Songkla University for financial support through the Crystal Materials Research Unit and Universiti Sains Malaysia for the Research University Grant No. 1001/ PFIZIK/811160. We thank Assoc. Professor Dr Chatchanok Karalai for useful discussions. Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS5112).
References Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19. Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
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Castardo, J. C., Prudente, A. S., Ferreira, J., Guimaraes, C. L., Monache, F. D., Filho, V. C., Otuki, M. F. & Cabrini, D. A. (2008). J. Ethnopharmacol. 118, 405–411. Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107. Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354–1358. Flack, H. D. (1983). Acta Cryst. A39, 876–881. Henry, G. E. & Jacobs, H. (1995). Tetrahedron Lett. 36, 4575–4578. Nguyen, H. D., Trinh, B. T. D., Tran, Q. N., Nguyen, H. D., Pham, H. D., Hansen, P. E., Duus, F., Connolly, J. D. & Nguyen, L.-H. D. (2011). Phytochemistry, 72, 290–295. Phongpaichit, S., Ongsakul, M., Nilrat, L., Tharavichitkul, P., Bunchoo, S., Chauprapaisilp, T. & Wiriyachitra, P. (1994). Songklanakarin J. Sci. Technol. 16, 399–405. Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Spek, A. L. (2009). Acta Cryst. D65, 148–155. Suksamrarn, S., Komutiban, O., Ratananukul, P., Chimnoi, N., Lartpornmatulee, N. & Suksamrarn, A. (2006). Chem. Pharm. Bull. 54, 301–305. Thoison, O., Cuong, D. D., Gramain, A., Chiaroni, A., Hung, N. V. & Sevenet, T. (2005). Tetrahedron, 61, 8529–8535. Xu, G., Kan, W. L. T., Zhou, Y., Song, J. Z., Han, Q. B., Qiao, C. F., Cho, C. H., Rudd, J. A., Lin, G. & Xu, H. X. (2010). J. Nat. Prod. 73, 104–108. Yu, L., Zhao, M., Yang, B., Zhao, Q. & Jiang, Y. (2007). Food Chem. 104, 176– 181.
Acta Cryst. (2012). E68, o1451–o1452
supplementary materials
supplementary materials Acta Cryst. (2012). E68, o1451–o1452
[doi:10.1107/S1600536812015267]
Absolute configuration of xerophenone A Hoong-Kun Fun, Cholpisut Tantapakul, Surat Laphookhieo, Nawong Boonnak and Suchada Chantrapromma Comment Garcinia belongs to the Clusiaceae family which is well recognized to produce a variety of biological active metabolites including xanthones (Phongpaichit et al., 1994), flavanones (Castardo et al., 2008), terpenoids (Nguyen et al., 2011) and benzophenones (Thoison et al., 2005; Xu et al., 2010). Several of these compounds possess interesting biological and pharmacological activities, such as antimicrobial (Xu et al., 2010), antidepressant and anti-HIV (Xu et al., 2010), antioxidant (Yu et al., 2007) and also cytotoxic (Suksamrarn et al., 2006) activities. During the course of our study of bioactive compounds from medicinal plants, the title compound (I), known as xerophenone A (Henry & Jacobs, 1995) was isolated from the twigs of G. propinqua which were collected from Chiang Rai province in the northern part of Thailand. Herein the crystal structure and absolute configuration of (I) was reported. The title compound (I), C33H42O5, is a rearranged benzophenone and an isoprenylated derivative of 11-oxatricyclo[4.3.1.14,10]undecane-7,9-dione. Figure 1 shows that (I) exists in an E configuration with respect to the C8═C27 double bond [1.402 (3) Å] with a C9–C8–C27–C28 torsion angle 177.48 (17)°. In order to view more clearly and gain more information of the ring conformations and the orientations of the rings and how each substituent is in respect to the bound rings, Figure 2 is also shown. It can be clearly seen that the cyclohexane-1,3-dione ring is in a twisted boat with the puckering parameters Q = 0.616 (2) Å, θ = 101.86 (19)° and φ = 157.84 (19)° (Cremer & Pople, 1975), the tetrahydro-2H-pyran ring (C1–C4/C10/O5) is in a standard chair conformation and the tetrahydrofuran ring (C4–C6/C10/O5) is in an envelope conformation with the puckering atom O5 of 0.283 (1) Å, and puckering parameter Q = 0.4223 (18) Å and φ = 1.0 (3)°. The two 3-methyl-2-buten-1-yl substituents (C11–C15 and C21–C15) are attached to the cyclohexane-1,3-dione moiety at atoms C1 and C6 with the torsion angles C1—C11—C12–C13 = 153.3 (2)° and C6–C21– C22–C23 = -161.87 (19)°, indicating a (+)-anti-periplanar and (-)-anti-periplanar conformations, respectively. The 3methyl-3-buten-1-yl substituent (C16–C20) is disordered over two positions in a 0.771 (11): 0.229 (11) ratio, and attached to the tetrahydro-2H-pyran ring at atom C3 with the torsion angles C3–C16–C17–C18 = 179.6 (3)° for the major component (A) and -168.3 (8)° for the minor component (B) (Fig. 1). An intramolecular O1—H1O1···O2 hydrogen bond (Table 1) generates an S(6) ring motif (Bernstein et al., 1995). The bond distances in (I) are within normal ranges (Allen et al., 1987). The absolute configuration at atoms C1, C3, C4, C6 and C10 or at positions 1, 3, 4, 6 and 10 of the xerophenone A are R,R,R,S,R configurations. In the crystal (Fig. 3), molecules are linked by O—H···O hydrogen bonds and weak C—H···O interactions (Table 1) forming an R21(7) motif which connected the molecules into a chain along the a axis. A C—H···π interaction (Table 1) and a C27···O4i short contact [2.989 (2) Å] are observed.
Acta Cryst. (2012). E68, o1451–o1452
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supplementary materials Experimental Twigs of G. propinqua (1.90 Kg) were successively extracted with acetone over the period of 3 days at room temperature to provide the crude acetone extract (183.72g) which was subjected to quick column chromatography over silica gel and eluted by gradients of EtOAc-hexanes (100% hexanes to 100% EtOAc) to yield fourteen fractions (A-N). Fraction B (268.0 mg) was subjected to sephadex LH-20 using CH3OH as eluent to afford compound (I) (21.8 mg) as white solid. Colorless plate-shaped single crystals of the title compound suitable for x-ray structure determination were recrystallized from CH2Cl2:acetone (1:1 v/v) by the slow evaporation of the solvent at room temperature after several days, m.p. 451.0-452.4 K [[α]D29 -21.2 (c 0.400, CH3OH)]. Refinement H atoms were placed in calculated positions with d(O—H) = 0.82 Å, and d(C—H) = 0.93 Å for aromatic and CH, 0.97 Å for CH2 and 0.96 Å for CH3 atoms. The Uiso(H) values were constrained to be 1.5Ueq of the carrier atom for methyl H atoms and 1.2Ueq for the remaining H atoms. A rotating group model was used for the methyl groups. The 3-methyl-3buten-1-yl substituent was found to be disordered over two sites in a 0.771 (11): 0.229 (11) occupancy ratio. In the final refinement, distance restraints were used for the disordered components. 2079 Friedel pairs were used to determine the absolute configuration. Computing details Data collection: APEX2 (Bruker, 2009); cell refinement: SAINT (Bruker, 2009); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).
Acta Cryst. (2012). E68, o1451–o1452
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supplementary materials
Figure 1 The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. Open bond is a minor component. The intramolecular O—H···O hydrogen bond is shown as a dashed line.
Acta Cryst. (2012). E68, o1451–o1452
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supplementary materials
Figure 2 The molecular structure of the title compound, showing 40% probability displacement ellipsoids and the atom-numbering scheme. The intramolecular O—H···O hydrogen bond was shown as a dashed line. Only H atoms of the hydroxy groups and the disordered side chain substituent are shown for clarity.
Acta Cryst. (2012). E68, o1451–o1452
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supplementary materials
Figure 3 The crystal packing diagram of the major component of the title compound, viewed along the c axis. Only H atoms involving in the hydrogen bonds (dashed lines) are shown. (1R,3R,4R,6S,8E,10R)-10-hydroxy-8- [hydroxy(phenyl)methylene]-4-methyl-1,6-bis(3-methylbut-2-en-1-yl)-3-(3methylbut-3-en-1-yl)-11-oxatricyclo[4.3.1.14,10]undecane-7,9-dione Crystal data C33H42O5 Mr = 518.67 Monoclinic, P21 Hall symbol: P 2yb a = 6.1984 (2) Å b = 17.0998 (4) Å c = 13.7007 (3) Å
Acta Cryst. (2012). E68, o1451–o1452
β = 91.036 (1)° V = 1451.92 (7) Å3 Z=2 F(000) = 560 Dx = 1.186 Mg m−3 Melting point = 451.0–452.4 K Cu Kα radiation, λ = 1.54178 Å
sup-5
supplementary materials Cell parameters from 4746 reflections θ = 3.2–67.5° µ = 0.62 mm−1
T = 100 K Plate, colorless 0.31 × 0.13 × 0.09 mm
Data collection 11622 measured reflections 4746 independent reflections 4661 reflections with I > 2σ(I) Rint = 0.023 θmax = 67.5°, θmin = 3.2° h = −6→7 k = −19→20 l = −16→16
Bruker APEX Duo CCD area detector diffractometer Radiation source: sealed tube Graphite monochromator φ and ω scans Absorption correction: multi-scan (SADABS; Bruker, 2009) Tmin = 0.830, Tmax = 0.944 Refinement Refinement on F2 Least-squares matrix: full R[F2 > 2σ(F2)] = 0.037 wR(F2) = 0.099 S = 1.07 4746 reflections 369 parameters 7 restraints Primary atom site location: structure-invariant direct methods Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites H-atom parameters constrained w = 1/[σ2(Fo2) + (0.0526P)2 + 0.4822P] where P = (Fo2 + 2Fc2)/3 (Δ/σ)max = 0.001 Δρmax = 0.24 e Å−3 Δρmin = −0.20 e Å−3 Absolute structure: Flack (1983), 2079 Friedel pairs Flack parameter: 0.18 (16)
Special details Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. 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. Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
O1 H1O1 O2 O3 O4 H1O4 O5 C1 C2 H2A
x
y
z
Uiso*/Ueq
−0.2134 (2) −0.1378 0.0272 (2) −0.2215 (2) 0.4496 (2) 0.5236 0.4021 (2) 0.1716 (3) 0.0072 (3) −0.0471
0.52353 (8) 0.5351 0.50870 (8) 0.27900 (8) 0.36790 (8) 0.3382 0.26998 (8) 0.38478 (11) 0.33858 (11) 0.3725
0.24048 (11) 0.2881 0.38262 (10) 0.24870 (9) 0.32243 (9) 0.2901 0.43398 (9) 0.43458 (13) 0.49672 (13) 0.5474
0.0296 (3) 0.084 (13)* 0.0262 (3) 0.0200 (3) 0.0208 (3) 0.031* 0.0198 (3) 0.0191 (4) 0.0191 (4) 0.023*
Acta Cryst. (2012). E68, o1451–o1452
Occ. (
