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Acta Crystallogr Sect E Struct Rep Online. 2009 November 1; 65(Pt 11): o2798.
Published online 2009 October 23. doi:  10.1107/S1600536809039348
PMCID: PMC2971388

2-Hydr­oxy-1-methoxyxanthen-9-one monohydrate

Abstract

In the title compound, C14H10O4·H2O, isolated from the roots of Calophyllum membranaceum, the xanthene ring system is almost planar (r.m.s. deviation = 0.008 Å). In the crystal structure, inter­molecular O—H(...)O and O—H(...)(O,O) hydrogen bonds connect the mol­ecules.

Related literature

For medicinal and botanical background, see: Zou et al. (2005 [triangle]); Chen et al. (2008 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2798-scheme1.jpg

Experimental

Crystal data

  • C14H10O4·H2O
  • M r = 260.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2798-efi1.jpg
  • a = 8.8008 (6) Å
  • b = 7.0856 (4) Å
  • c = 19.4596 (9) Å
  • β = 102.402 (4)°
  • V = 1185.16 (12) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.11 mm−1
  • T = 295 K
  • 0.38 × 0.26 × 0.24 mm

Data collection

  • Bruker SMART CCD diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1997 [triangle]) T min = 0.959, T max = 0.974
  • 8151 measured reflections
  • 2919 independent reflections
  • 2269 reflections with I > 2σ(I)
  • R int = 0.080

Refinement

  • R[F 2 > 2σ(F 2)] = 0.053
  • wR(F 2) = 0.164
  • S = 1.04
  • 2919 reflections
  • 181 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.26 e Å−3
  • Δρmin = −0.36 e Å−3

Data collection: SMART (Bruker, 1997 [triangle]); cell refinement: SAINT (Bruker, 1997 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809039348/hb5095sup1.cif

Structure factors: contains datablocks . DOI: 10.1107/S1600536809039348/hb5095Isup2.hkl

Click here to view.(2 bytes, hkl)

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

This work was supported by the National Natural Science Foundation of China (20862005), the Program for New Century Excellent Talents in Universities (NCET-08–0656) and the Natural Science Foundation of Hainan Province, China (No. 070207). We thank Bingjing Xin and Tingting Zhang for collecting the crystal data.

supplementary crystallographic information

Comment

Secondary metabolites in the plants of Calophyllum membranaceum are mainly xanthones, coumarins and flavonids (Zou et al., 2005; Chen et al., 2008). The plants in this family were used in folk medicine such as, for rheumatism, arthritis, lumbago and wounds (Zou et al., 2005). The title xanthones was isolated from the 75% EtOH extract of the roots of Calophyllum membranaceum which were collected from Lingshui County, Hainan Province, P. R. China. We have undertaken the X-ray crystal structure analysis of the title xanthone in order to establish its molecular structure and relative stereochemistry.

The xanthene ring system of (I) (C1-C13/O1) is almost planar, with all atoms lying within 0.008 (8)Å of the mean plane.

In the crystal, molecules are linked by intermolecular O–H···O hydrogen bonds into chains (Fig.2). The hydrogen bonds and angles are listed in Table 1.

Experimental

Air-dried roots of Calophyllum membranaceum (15.00 kg) were ground and percolated (3 × 2.5 h) with 75% EtOH at 333 K, which was suspended in 1.5 l water and then partitioned with petroleum ether, chloroform, ethyl acetate and n-hexane, successively, yielding a petroleum ether extract, a chloroform extract, an ethyl acetate extract and a n-BuOH extract, respectively. The chloroform extract was subjected to a silica gel CC column using petroleum ether as first eluent and then increasing the polarity with EtOAc, to afford 15 fractions (A—N). Fraction C was further separated by column chromatography with a gradient of CHCl3—CH3OH to give the title xanthone. The crude product was dissolved in small amount of anhydrous methanol to obtain colourless blocks of (I) by slow evaporation of a methanol solution at 298 K.

Refinement

H atoms bonded to C atoms were palced in geometrically calculated position and were refined using a riding model, with Uiso(H) = 1.2 Ueq(C). H atoms attached to O atoms were found in a difference Fourier synthesis and were refined using a riding model, with the O—H distances fixed as initially found and with Uiso(H) values set at 1.5 Ueq(O).

Figures

Fig. 1.
View of (I): displacement ellipsoids are drawn at the 30% probability level.
Fig. 2.
A view of the molecular packing. Dashed lines indicate hydrogen bonds.

Crystal data

C14H10O4·H2OF(000) = 544
Mr = 260.24Dx = 1.458 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2919 reflections
a = 8.8008 (6) Åθ = 2.1–28.2°
b = 7.0856 (4) ŵ = 0.11 mm1
c = 19.4596 (9) ÅT = 295 K
β = 102.402 (4)°Block, colourless
V = 1185.16 (12) Å30.38 × 0.26 × 0.24 mm
Z = 4

Data collection

Bruker SMART CCD diffractometer2919 independent reflections
Radiation source: fine-focus sealed tube2269 reflections with I > 2σ(I)
graphiteRint = 0.080
Detector resolution: 0 pixels mm-1θmax = 28.2°, θmin = 2.1°
ω scansh = −6→11
Absorption correction: multi-scan (SADABS; Bruker, 1997)k = −8→9
Tmin = 0.959, Tmax = 0.974l = −25→25
8151 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.053H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.164w = 1/[σ2(Fo2) + (0.0823P)2 + 0.2871P] where P = (Fo2 + 2Fc2)/3
S = 1.04(Δ/σ)max < 0.001
2919 reflectionsΔρmax = 0.26 e Å3
181 parametersΔρmin = −0.36 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.095 (8)

Special details

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)

xyzUiso*/Ueq
O10.65861 (11)0.14472 (16)0.26194 (6)0.0409 (3)
O20.24707 (14)0.1457 (2)0.33085 (6)0.0577 (4)
O30.09211 (11)0.10250 (16)0.19163 (6)0.0412 (3)
O40.11784 (12)0.12437 (18)0.05791 (5)0.0459 (3)
H4A0.13860.11220.01900.069*
O1W0.16228 (15)0.0842 (3)−0.07501 (6)0.0581 (4)
H1A0.181 (3)0.166 (4)−0.1024 (17)0.097 (10)*
H1B0.080 (3)0.039 (4)−0.0954 (14)0.079 (8)*
C10.65891 (18)0.1459 (2)0.33241 (8)0.0377 (3)
C20.8053 (2)0.1522 (2)0.37783 (9)0.0491 (4)
H2A0.89550.15480.36020.059*
C30.8131 (2)0.1546 (3)0.44946 (10)0.0577 (5)
H3A0.90960.15750.48050.069*
C40.6771 (3)0.1527 (3)0.47583 (9)0.0593 (5)
H4B0.68370.15500.52420.071*
C50.5341 (2)0.1475 (2)0.43070 (9)0.0497 (4)
H5A0.44450.14640.44870.060*
C60.52170 (18)0.1439 (2)0.35728 (7)0.0367 (3)
C70.36878 (17)0.1408 (2)0.30878 (7)0.0360 (3)
C80.37350 (15)0.13504 (18)0.23329 (7)0.0299 (3)
C90.23858 (15)0.12734 (19)0.17825 (7)0.0316 (3)
C100.25162 (16)0.12938 (19)0.10794 (7)0.0343 (3)
C110.39927 (17)0.1332 (2)0.09150 (7)0.0374 (3)
H11A0.40750.13310.04460.045*
C120.53188 (17)0.1372 (2)0.14382 (8)0.0372 (3)
H12A0.62930.13850.13250.045*
C130.51916 (16)0.13944 (19)0.21397 (7)0.0318 (3)
C140.0097 (2)0.2739 (3)0.19948 (11)0.0578 (5)
H14A−0.09040.24340.20860.087*
H14B−0.00350.34680.15700.087*
H14C0.06810.34570.23810.087*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0304 (5)0.0548 (7)0.0354 (6)−0.0022 (4)0.0027 (4)−0.0018 (4)
O20.0468 (6)0.0962 (10)0.0337 (6)−0.0072 (6)0.0163 (5)−0.0084 (6)
O30.0315 (5)0.0527 (7)0.0412 (6)−0.0061 (4)0.0118 (4)−0.0017 (4)
O40.0377 (6)0.0689 (8)0.0284 (5)−0.0012 (5)0.0010 (4)0.0009 (4)
O1W0.0456 (7)0.0910 (11)0.0357 (6)−0.0150 (7)0.0044 (5)0.0005 (6)
C10.0426 (7)0.0330 (7)0.0337 (7)−0.0023 (5)0.0000 (6)−0.0023 (5)
C20.0439 (8)0.0466 (9)0.0490 (9)−0.0025 (7)−0.0071 (7)−0.0036 (7)
C30.0627 (11)0.0509 (10)0.0459 (9)−0.0027 (8)−0.0187 (8)−0.0028 (7)
C40.0798 (13)0.0582 (11)0.0317 (8)−0.0053 (9)−0.0063 (8)−0.0023 (7)
C50.0643 (10)0.0517 (10)0.0304 (7)−0.0039 (7)0.0042 (7)−0.0028 (6)
C60.0453 (8)0.0339 (7)0.0285 (7)−0.0035 (5)0.0029 (5)−0.0022 (5)
C70.0400 (7)0.0387 (7)0.0296 (7)−0.0042 (5)0.0082 (5)−0.0030 (5)
C80.0315 (6)0.0306 (6)0.0276 (6)−0.0029 (5)0.0062 (5)−0.0006 (5)
C90.0307 (6)0.0333 (7)0.0315 (7)−0.0026 (5)0.0081 (5)−0.0002 (5)
C100.0347 (7)0.0370 (7)0.0298 (6)−0.0018 (5)0.0039 (5)0.0014 (5)
C110.0415 (7)0.0442 (8)0.0286 (7)−0.0004 (6)0.0119 (6)0.0021 (5)
C120.0341 (7)0.0448 (8)0.0355 (7)−0.0009 (6)0.0138 (5)0.0008 (6)
C130.0302 (6)0.0325 (7)0.0324 (7)−0.0016 (5)0.0055 (5)−0.0013 (5)
C140.0417 (8)0.0675 (12)0.0693 (11)0.0063 (8)0.0235 (8)−0.0022 (9)

Geometric parameters (Å, °)

O1—C11.3708 (18)C4—H4B0.9300
O1—C131.3737 (16)C5—C61.409 (2)
O2—C71.2372 (17)C5—H5A0.9300
O3—C91.3801 (16)C6—C71.469 (2)
O3—C141.439 (2)C7—C81.4790 (18)
O4—C101.3576 (17)C8—C131.4116 (18)
O4—H4A0.8200C8—C91.4191 (18)
O1W—H1A0.83 (3)C9—C101.3973 (19)
O1W—H1B0.81 (3)C10—C111.4036 (19)
C1—C61.394 (2)C11—C121.375 (2)
C1—C21.398 (2)C11—H11A0.9300
C2—C31.381 (3)C12—C131.3935 (19)
C2—H2A0.9300C12—H12A0.9300
C3—C41.400 (3)C14—H14A0.9600
C3—H3A0.9300C14—H14B0.9600
C4—C51.371 (3)C14—H14C0.9600
C1—O1—C13119.30 (11)C13—C8—C9117.41 (12)
C9—O3—C14115.13 (12)C13—C8—C7118.99 (12)
C10—O4—H4A109.5C9—C8—C7123.59 (12)
H1A—O1W—H1B104 (3)O3—C9—C10117.56 (12)
O1—C1—C6122.10 (13)O3—C9—C8121.77 (12)
O1—C1—C2115.87 (14)C10—C9—C8120.48 (12)
C6—C1—C2122.02 (14)O4—C10—C9117.45 (12)
C3—C2—C1118.55 (17)O4—C10—C11122.66 (13)
C3—C2—H2A120.7C9—C10—C11119.88 (12)
C1—C2—H2A120.7C12—C11—C10120.79 (12)
C2—C3—C4120.59 (16)C12—C11—H11A119.6
C2—C3—H3A119.7C10—C11—H11A119.6
C4—C3—H3A119.7C11—C12—C13119.46 (12)
C5—C4—C3120.29 (16)C11—C12—H12A120.3
C5—C4—H4B119.9C13—C12—H12A120.3
C3—C4—H4B119.9O1—C13—C12114.70 (12)
C4—C5—C6120.70 (17)O1—C13—C8123.34 (12)
C4—C5—H5A119.6C12—C13—C8121.95 (13)
C6—C5—H5A119.6O3—C14—H14A109.5
C1—C6—C5117.85 (14)O3—C14—H14B109.5
C1—C6—C7121.30 (13)H14A—C14—H14B109.5
C5—C6—C7120.84 (14)O3—C14—H14C109.5
O2—C7—C6121.24 (13)H14A—C14—H14C109.5
O2—C7—C8123.82 (13)H14B—C14—H14C109.5
C6—C7—C8114.92 (12)
C13—O1—C1—C6−0.65 (19)C14—O3—C9—C10−93.42 (16)
C13—O1—C1—C2−179.73 (12)C14—O3—C9—C891.70 (16)
O1—C1—C2—C3179.71 (14)C13—C8—C9—O3173.03 (12)
C6—C1—C2—C30.6 (2)C7—C8—C9—O3−7.70 (19)
C1—C2—C3—C4−0.7 (3)C13—C8—C9—C10−1.70 (18)
C2—C3—C4—C50.3 (3)C7—C8—C9—C10177.57 (12)
C3—C4—C5—C60.1 (3)O3—C9—C10—O45.96 (18)
O1—C1—C6—C5−179.30 (13)C8—C9—C10—O4−179.09 (12)
C2—C1—C6—C5−0.3 (2)O3—C9—C10—C11−172.99 (12)
O1—C1—C6—C7−0.2 (2)C8—C9—C10—C111.96 (19)
C2—C1—C6—C7178.83 (13)O4—C10—C11—C12−179.64 (13)
C4—C5—C6—C1−0.1 (2)C9—C10—C11—C12−0.7 (2)
C4—C5—C6—C7−179.18 (15)C10—C11—C12—C13−0.7 (2)
C1—C6—C7—O2−177.43 (14)C1—O1—C13—C12−179.55 (12)
C5—C6—C7—O21.6 (2)C1—O1—C13—C8−0.03 (18)
C1—C6—C7—C81.57 (19)C11—C12—C13—O1−179.57 (12)
C5—C6—C7—C8−179.36 (13)C11—C12—C13—C80.9 (2)
O2—C7—C8—C13176.82 (14)C9—C8—C13—O1−179.21 (12)
C6—C7—C8—C13−2.15 (17)C7—C8—C13—O11.49 (19)
O2—C7—C8—C9−2.4 (2)C9—C8—C13—C120.28 (19)
C6—C7—C8—C9178.59 (12)C7—C8—C13—C12−179.03 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O4—H4A···O1W0.821.902.7126 (16)174
O1W—H1A···O2i0.83 (3)2.03 (3)2.857 (2)174 (3)
O1W—H1B···O4ii0.81 (3)2.34 (3)2.9540 (19)134 (2)
O1W—H1B···O3ii0.81 (3)2.37 (3)3.1195 (17)155 (2)

Symmetry codes: (i) x, −y+1/2, z−1/2; (ii) −x, −y, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5095).

References

  • Bruker (1997). SMART and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.
  • Chen, G. Y., Zhu, G. Y., Han, C. R., Zhao, J., Song, X. P. & Fong, W. F. (2008). Arkivoc, 13, 249–254.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Zou, J., Jin, D. Z., Chen, W. L., Wang, J., Liu, Q. F., Zhu, X. Z. & Zhao, W. M. (2005). J. Nat. Prod.68, 1514–1518. [PubMed]

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