organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

3,6,8-Trihy­dr­oxy-3,4,5,7-tetra­methyl-3,4-di­hydro­isocoumarin

aSchool of Basic Science, Guangzhou Medical College, Guangzhou 510182, People's Republic of China, and bGuangdong Institute for Drug Control, Guangzhou 510180, People's Republic of China
*Correspondence e-mail: yywentao@yahoo.com.cn

(Received 26 May 2011; accepted 6 June 2011; online 18 June 2011)

In the title compound, C13H16O5, one of the three hy­droxy groups is involved in intra­molecular O—H⋯O hydrogen bonds. The other two hy­droxy groups contribute to the three-dimensional hydrogen-bonding network, which consolidates the crystal packing.

Related literature

For related structures, see: Wang et al. (2003[Wang, J.-F., Fang, M.-J., Zhao, Y.-F., Huang, Y.-J., Su, W.-J. & Ng, S. W. (2003). Acta Cryst. E59, o1208-o1209.]); Krohn et al. (1997[Krohn, K., Bahramsari, R., Floorke, U., Ludewig, K., Kliche-Spory, C., Michel, A., Aust, H. J., Draeger, S., Schulz, B. & Antus, S. (1997). Phytochemistry, 45, 313-320.]).

[Scheme 1]

Experimental

Crystal data
  • C13H16O5

  • Mr = 252.26

  • Orthorhombic, P 21 21 21

  • a = 7.4731 (3) Å

  • b = 9.9742 (7) Å

  • c = 16.4066 (12) Å

  • V = 1222.92 (13) Å3

  • Z = 4

  • Cu Kα radiation

  • μ = 0.88 mm−1

  • T = 150 K

  • 0.40 × 0.20 × 0.20 mm

Data collection
  • Oxford Diffraction Xcalibur diffractometer with Onyx (Nova) detector

  • Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.]) Tmin = 0.719, Tmax = 0.843

  • 11941 measured reflections

  • 2199 independent reflections

  • 2165 reflections with I > 2σ(I)

  • Rint = 0.029

Refinement
  • R[F2 > 2σ(F2)] = 0.025

  • wR(F2) = 0.069

  • S = 1.07

  • 2199 reflections

  • 171 parameters

  • H-atom parameters constrained

  • Δρmax = 0.22 e Å−3

  • Δρmin = −0.14 e Å−3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), 883 Friedel pairs

  • Flack parameter: 0.13 (15)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O4—H4⋯O5 0.84 1.87 2.6040 (13) 145
O2—H2⋯O5i 0.84 1.95 2.7851 (13) 172
O3—H3⋯O2ii 0.84 2.15 2.8942 (14) 148
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]; (ii) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: CrysAlis PRO (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: 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.]); software used to prepare material for publication: OLEX2.

Supporting information


Comment top

The title compound, C13H16O5 (I), also known as sclerotinin A, was isolated from culture filtrate of the endophytic fungus phomposis sp from mangrove trees from the coast of the South China Sea. Herewith we present the structure of sclerotinin A.

The crystal structure of the title compound is shown in Fig. 1. The titel compound crystalizes in orthorhombic cell setting P2(1)2(1)2(1) space group, containing four formula units in the unit cell. As can be found,

In (I), all non-H atoms, except C1, C2, C4 and O2, are coplanar with the mean deviation of 0.039 (2) Å. The C2/C3/C5/C6/C7/O1 heterocycle exhibits an envelope configuration with C2 out of the plane formed by the other five atoms 0.308 (2) Å. All the bond lengths and angles are comparable with those found in similar compounds reported previously (Wang et al., 2003; Krohn et al., 1997).

In the crystal structure, intermolecular O—H···O hydrogen bonds (Table 1) generate three-dimensional network, which consolidate the crystal packing.

Related literature top

For related structures, see: Wang et al. (2003); Krohn et al. (1997).

Experimental top

A strain of the fungus phomposis sp was isolated from the mangrove tree, Zhanjiang, and was stored at the Department of Applied Chemistry, Zhongshan University, Guangzhou, China. Starter cultures (from Professor Shining Zhou) were maintained on cornmeal seawater agar. Plugs of agar supporting mycelial growth were cut and transferred aseptically to a 500 ml Erlenmeyer flask containing 300 ml of liquid medium (glucose 1%, peptone 0.2%, yeast extract 0.1%, NaCl 0.25%, pH 7.0). The flask was incubated at 303 K on a rotary shaker for 3 days. The mycelium was aseptically incubated at 303 K for 5 weeks. The cultures (130 L) were filtered through cheesecloth. The filtrate was concentrated to 3 L below 328 K and extracted several times by shaking with twofold volume of the ethyl acetate. The combined extracts were concentrated and chromatographed on silica gel using a gradient elution from petroleum to ethyl acetate, obtaining compound sclerotinin A from the 30% ethyl acetate/petroleum ether fraction. Crystals of the title compound suitable for single-crystal X-ray diffraction analysis were obtained by recrystallization from methanol.

Refinement top

All the H atoms were geometrically positioned (C—H 0.98 A°, O—H 0.84 A°), and were refined as riding, with Uiso(H) = 1.2-1.5 Ueq(C, O).

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2006); cell refinement: CrysAlis PRO (Oxford Diffraction, 2006); data reduction: CrysAlis PRO (Oxford Diffraction, 2006); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I) with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.
3,6,8-Trihydroxy-3,4,5,7-tetramethyl-3,4-dihydroisocoumarin top
Crystal data top
C13H16O5F(000) = 536
Mr = 252.26Dx = 1.370 Mg m3
Orthorhombic, P212121Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2abCell parameters from 1678 reflections
a = 7.4731 (3) Åθ = 5.2–68.2°
b = 9.9742 (7) ŵ = 0.88 mm1
c = 16.4066 (12) ÅT = 150 K
V = 1222.92 (13) Å3Block, colourless
Z = 40.40 × 0.20 × 0.20 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer with Onyx (Nova) detector
2199 independent reflections
Radiation source: Nova (Cu) X-ray Source2165 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.029
Detector resolution: 8.2417 pixels mm-1θmax = 68.2°, θmin = 5.2°
ω scansh = 78
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
k = 1111
Tmin = 0.719, Tmax = 0.843l = 1918
11941 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.025 w = 1/[σ2(Fo2) + (0.0427P)2 + 0.1914P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.069(Δ/σ)max < 0.001
S = 1.07Δρmax = 0.22 e Å3
2199 reflectionsΔρmin = 0.14 e Å3
171 parametersExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0039 (7)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 883 Friedel pairs
Secondary atom site location: difference Fourier mapAbsolute structure parameter: 0.13 (15)
Crystal data top
C13H16O5V = 1222.92 (13) Å3
Mr = 252.26Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 7.4731 (3) ŵ = 0.88 mm1
b = 9.9742 (7) ÅT = 150 K
c = 16.4066 (12) Å0.40 × 0.20 × 0.20 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer with Onyx (Nova) detector
2199 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
2165 reflections with I > 2σ(I)
Tmin = 0.719, Tmax = 0.843Rint = 0.029
11941 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.069Δρmax = 0.22 e Å3
S = 1.07Δρmin = 0.14 e Å3
2199 reflectionsAbsolute structure: Flack (1983), 883 Friedel pairs
171 parametersAbsolute structure parameter: 0.13 (15)
0 restraints
Special details top

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) top
xyzUiso*/Ueq
O10.50038 (12)0.41865 (9)0.52036 (5)0.0280 (2)
O20.26458 (13)0.35748 (9)0.43613 (5)0.0295 (2)
H20.26190.28020.45640.044*
O50.77901 (13)0.38899 (10)0.48436 (6)0.0319 (2)
C80.74508 (17)0.54758 (12)0.34132 (7)0.0242 (3)
O30.53133 (15)0.79291 (11)0.20856 (6)0.0397 (3)
H30.62320.79960.17930.060*
O40.90385 (13)0.48275 (9)0.34758 (6)0.0319 (2)
H40.90370.43460.38960.048*
C90.72242 (18)0.63290 (12)0.27480 (7)0.0273 (3)
C60.60748 (17)0.53081 (12)0.39893 (7)0.0228 (3)
C120.42314 (18)0.69223 (13)0.32709 (8)0.0280 (3)
C70.63436 (17)0.44348 (12)0.46828 (7)0.0244 (3)
C110.56276 (19)0.70428 (13)0.26991 (8)0.0284 (3)
C50.44607 (16)0.60298 (12)0.39092 (7)0.0231 (3)
C30.30879 (17)0.58956 (12)0.45805 (7)0.0253 (3)
H3A0.18760.60200.43330.030*
C40.3370 (2)0.70133 (14)0.52100 (9)0.0355 (3)
H4C0.44850.68500.55090.053*
H4B0.23640.70240.55930.053*
H4A0.34430.78800.49300.053*
C100.8647 (2)0.64783 (16)0.21033 (8)0.0379 (3)
H10A0.81580.62150.15730.057*
H10B0.96680.59030.22380.057*
H10C0.90410.74150.20800.057*
C20.31545 (17)0.44997 (13)0.49601 (7)0.0257 (3)
C10.20825 (19)0.43331 (14)0.57328 (8)0.0333 (3)
H1C0.25440.49430.61510.050*
H1B0.21840.34060.59250.050*
H1A0.08230.45420.56240.050*
C130.2588 (2)0.77862 (17)0.31733 (10)0.0434 (4)
H13B0.15460.73150.33960.065*
H13A0.23900.79720.25940.065*
H13C0.27590.86330.34660.065*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0301 (5)0.0298 (5)0.0240 (4)0.0021 (4)0.0010 (4)0.0057 (3)
O20.0414 (5)0.0225 (4)0.0245 (4)0.0063 (4)0.0003 (4)0.0013 (3)
O50.0311 (5)0.0304 (5)0.0341 (5)0.0052 (4)0.0028 (4)0.0079 (4)
C80.0268 (6)0.0197 (5)0.0262 (6)0.0001 (5)0.0028 (5)0.0033 (5)
O30.0429 (6)0.0429 (5)0.0332 (5)0.0073 (5)0.0039 (4)0.0184 (4)
O40.0303 (5)0.0333 (5)0.0322 (5)0.0061 (4)0.0016 (4)0.0053 (4)
C90.0333 (7)0.0245 (6)0.0240 (6)0.0027 (5)0.0005 (5)0.0006 (5)
C60.0287 (6)0.0180 (5)0.0218 (6)0.0013 (5)0.0018 (4)0.0017 (4)
C120.0319 (7)0.0245 (6)0.0278 (6)0.0014 (5)0.0017 (5)0.0031 (5)
C70.0299 (6)0.0195 (5)0.0239 (6)0.0007 (5)0.0021 (5)0.0017 (5)
C110.0364 (7)0.0235 (6)0.0253 (6)0.0007 (5)0.0022 (5)0.0042 (5)
C50.0259 (6)0.0193 (5)0.0240 (5)0.0013 (5)0.0020 (5)0.0015 (5)
C30.0271 (6)0.0229 (6)0.0259 (6)0.0018 (5)0.0001 (5)0.0017 (5)
C40.0423 (7)0.0277 (6)0.0364 (7)0.0009 (6)0.0059 (6)0.0067 (5)
C100.0398 (8)0.0414 (7)0.0326 (7)0.0026 (6)0.0068 (6)0.0077 (6)
C20.0281 (6)0.0263 (6)0.0226 (6)0.0004 (5)0.0016 (5)0.0002 (5)
C10.0375 (7)0.0366 (7)0.0259 (6)0.0019 (6)0.0041 (5)0.0035 (5)
C130.0406 (8)0.0431 (8)0.0464 (8)0.0119 (7)0.0008 (7)0.0166 (6)
Geometric parameters (Å, º) top
O1—C71.3395 (15)C5—C31.5111 (17)
O1—C21.4721 (16)C3—C21.5260 (17)
O2—C21.4003 (15)C3—C41.5343 (18)
O2—H20.8400C3—H3A1.0000
O5—C71.2384 (16)C4—H4C0.9800
C8—O41.3552 (16)C4—H4B0.9800
C8—C91.3942 (17)C4—H4A0.9800
C8—C61.4067 (18)C10—H10A0.9800
O3—C111.3601 (15)C10—H10B0.9800
O3—H30.8400C10—H10C0.9800
O4—H40.8400C2—C11.5088 (17)
C9—C111.3917 (19)C1—H1C0.9800
C9—C101.5073 (18)C1—H1B0.9800
C6—C51.4108 (18)C1—H1A0.9800
C6—C71.4469 (16)C13—H13B0.9800
C12—C51.3851 (17)C13—H13A0.9800
C12—C111.4082 (19)C13—H13C0.9800
C12—C131.509 (2)
C7—O1—C2119.30 (9)C3—C4—H4C109.5
C2—O2—H2109.5C3—C4—H4B109.5
O4—C8—C9117.19 (11)H4C—C4—H4B109.5
O4—C8—C6122.16 (11)C3—C4—H4A109.5
C9—C8—C6120.65 (11)H4C—C4—H4A109.5
C11—O3—H3109.5H4B—C4—H4A109.5
C8—O4—H4109.5C9—C10—H10A109.5
C11—C9—C8117.48 (12)C9—C10—H10B109.5
C11—C9—C10120.93 (11)H10A—C10—H10B109.5
C8—C9—C10121.59 (12)C9—C10—H10C109.5
C8—C6—C5120.11 (11)H10A—C10—H10C109.5
C8—C6—C7119.90 (11)H10B—C10—H10C109.5
C5—C6—C7119.94 (11)O2—C2—O1107.79 (10)
C5—C12—C11117.83 (12)O2—C2—C1111.88 (10)
C5—C12—C13123.22 (12)O1—C2—C1104.30 (10)
C11—C12—C13118.93 (12)O2—C2—C3107.81 (9)
O5—C7—O1115.81 (10)O1—C2—C3109.57 (10)
O5—C7—C6123.57 (11)C1—C2—C3115.22 (11)
O1—C7—C6120.61 (11)C2—C1—H1C109.5
O3—C11—C9121.54 (12)C2—C1—H1B109.5
O3—C11—C12114.87 (12)H1C—C1—H1B109.5
C9—C11—C12123.58 (11)C2—C1—H1A109.5
C12—C5—C6120.27 (11)H1C—C1—H1A109.5
C12—C5—C3121.60 (11)H1B—C1—H1A109.5
C6—C5—C3117.86 (10)C12—C13—H13B109.5
C5—C3—C2110.86 (10)C12—C13—H13A109.5
C5—C3—C4109.44 (10)H13B—C13—H13A109.5
C2—C3—C4112.57 (11)C12—C13—H13C109.5
C5—C3—H3A107.9H13B—C13—H13C109.5
C2—C3—H3A107.9H13A—C13—H13C109.5
C4—C3—H3A107.9
O4—C8—C9—C11177.25 (11)C11—C12—C5—C62.13 (18)
C6—C8—C9—C112.70 (17)C13—C12—C5—C6176.37 (13)
O4—C8—C9—C102.78 (17)C11—C12—C5—C3176.12 (11)
C6—C8—C9—C10177.27 (11)C13—C12—C5—C32.4 (2)
O4—C8—C6—C5178.45 (10)C8—C6—C5—C121.01 (17)
C9—C8—C6—C51.50 (17)C7—C6—C5—C12176.51 (11)
O4—C8—C6—C70.92 (17)C8—C6—C5—C3175.22 (10)
C9—C8—C6—C7179.03 (11)C7—C6—C5—C32.31 (16)
C2—O1—C7—O5164.73 (11)C12—C5—C3—C2153.52 (11)
C2—O1—C7—C616.22 (16)C6—C5—C3—C232.36 (14)
C8—C6—C7—O56.00 (18)C12—C5—C3—C481.73 (14)
C5—C6—C7—O5171.53 (11)C6—C5—C3—C492.39 (13)
C8—C6—C7—O1175.02 (10)C7—O1—C2—O270.86 (13)
C5—C6—C7—O17.45 (17)C7—O1—C2—C1170.08 (10)
C8—C9—C11—O3177.94 (11)C7—O1—C2—C346.21 (14)
C10—C9—C11—O32.09 (19)C5—C3—C2—O264.88 (12)
C8—C9—C11—C121.55 (19)C4—C3—C2—O2172.15 (11)
C10—C9—C11—C12178.42 (12)C5—C3—C2—O152.17 (12)
C5—C12—C11—O3179.62 (11)C4—C3—C2—O170.79 (13)
C13—C12—C11—O31.81 (19)C5—C3—C2—C1169.38 (11)
C5—C12—C11—C90.9 (2)C4—C3—C2—C146.42 (15)
C13—C12—C11—C9177.71 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···O50.841.872.6040 (13)145
O2—H2···O5i0.841.952.7851 (13)172
O3—H3···O2ii0.842.152.8942 (14)148
Symmetry codes: (i) x1/2, y+1/2, z+1; (ii) x+1, y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC13H16O5
Mr252.26
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)7.4731 (3), 9.9742 (7), 16.4066 (12)
V3)1222.92 (13)
Z4
Radiation typeCu Kα
µ (mm1)0.88
Crystal size (mm)0.40 × 0.20 × 0.20
Data collection
DiffractometerOxford Diffraction Xcalibur
diffractometer with Onyx (Nova) detector
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2006)
Tmin, Tmax0.719, 0.843
No. of measured, independent and
observed [I > 2σ(I)] reflections
11941, 2199, 2165
Rint0.029
(sin θ/λ)max1)0.602
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.025, 0.069, 1.07
No. of reflections2199
No. of parameters171
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.22, 0.14
Absolute structureFlack (1983), 883 Friedel pairs
Absolute structure parameter0.13 (15)

Computer programs: CrysAlis PRO (Oxford Diffraction, 2006), SHELXTL (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O4—H4···O50.841.872.6040 (13)145
O2—H2···O5i0.841.952.7851 (13)172
O3—H3···O2ii0.842.152.8942 (14)148
Symmetry codes: (i) x1/2, y+1/2, z+1; (ii) x+1, y+1/2, z+1/2.
 

Acknowledgements

This work was supported by the Guangzhou Science and Technology Projects Fund (grant No. 2010Y1-C371), the Guangzhou Municipal Bureau of Education Projects Fund (grant No. 10 A168) and the doctoral startup fund of Guangzhou Medical College (grant No. 2008 C25).

References

First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationFlack, H. D. (1983). Acta Cryst. A39, 876–881.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationKrohn, K., Bahramsari, R., Floorke, U., Ludewig, K., Kliche-Spory, C., Michel, A., Aust, H. J., Draeger, S., Schulz, B. & Antus, S. (1997). Phytochemistry, 45, 313–320.  CrossRef CAS PubMed Web of Science Google Scholar
First citationOxford Diffraction (2006). CrysAlis PRO. Oxford Diffraction Ltd, Abingdon, England.  Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWang, J.-F., Fang, M.-J., Zhao, Y.-F., Huang, Y.-J., Su, W.-J. & Ng, S. W. (2003). Acta Cryst. E59, o1208–o1209.  Web of Science CSD CrossRef IUCr Journals Google Scholar

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