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

Abstract

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 ▶); Krohn et al. (1997 ▶).

Experimental

Crystal data

• C₁₃H₁₆O₅

• M _r = 252.26

• Orthorhombic,

• a = 7.4731 (3) Å

• b = 9.9742 (7) Å

• c = 16.4066 (12) Å

• V = 1222.92 (13) ų

• 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 ▶) T _min = 0.719, T _max = 0.843

• 11941 measured reflections

• 2199 independent reflections

• 2165 reflections with I > 2σ(I)

• R _int = 0.029

Refinement

• R[F ² > 2σ(F ²)] = 0.025

• wR(F ²) = 0.069

• S = 1.07

• 2199 reflections

• 171 parameters

• H-atom parameters constrained

• Δρ_max = 0.22 e Å⁻³

• Δρ_min = −0.14 e Å⁻³

• Absolute structure: Flack (1983 ▶), 883 Friedel pairs

• Flack parameter: 0.13 (15)

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

Supplementary Material

Supplementary material file. DOI: 10.1107/S1600536811021751/cv5104Isup3.cml

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	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) ; (ii) .

supplementary crystallographic information

Comment

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.

Experimental

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

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

Figures

Fig. 1.

The molecular structure of (I) with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level.

Crystal data

C13H16O5	F(000) = 536
Mr = 252.26	Dx = 1.370 Mg m−3
Orthorhombic, P212121	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1678 reflections
a = 7.4731 (3) Å	θ = 5.2–68.2°
b = 9.9742 (7) Å	µ = 0.88 mm−1
c = 16.4066 (12) Å	T = 150 K
V = 1222.92 (13) Å3	Block, colourless
Z = 4	0.40 × 0.20 × 0.20 mm

Data collection

Oxford Diffraction Xcalibur diffractometer with Onyx (Nova) detector	2199 independent reflections
Radiation source: Nova (Cu) X-ray Source	2165 reflections with I > 2σ(I)
mirror	Rint = 0.029
Detector resolution: 8.2417 pixels mm-1	θmax = 68.2°, θmin = 5.2°
ω scans	h = −7→8
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2006)	k = −11→11
Tmin = 0.719, Tmax = 0.843	l = −19→18
11941 measured reflections

Refinement

Refinement on F2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-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 = 1.07	Δρmax = 0.22 e Å−3
2199 reflections	Δρmin = −0.14 e Å−3
171 parameters	Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraints	Extinction coefficient: 0.0039 (7)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 883 Friedel pairs
Secondary atom site location: difference Fourier map	Flack parameter: 0.13 (15)

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.50038 (12)	0.41865 (9)	0.52036 (5)	0.0280 (2)
O2	0.26458 (13)	0.35748 (9)	0.43613 (5)	0.0295 (2)
H2	0.2619	0.2802	0.4564	0.044*
O5	0.77901 (13)	0.38899 (10)	0.48436 (6)	0.0319 (2)
C8	0.74508 (17)	0.54758 (12)	0.34132 (7)	0.0242 (3)
O3	0.53133 (15)	0.79291 (11)	0.20856 (6)	0.0397 (3)
H3	0.6232	0.7996	0.1793	0.060*
O4	0.90385 (13)	0.48275 (9)	0.34758 (6)	0.0319 (2)
H4	0.9037	0.4346	0.3896	0.048*
C9	0.72242 (18)	0.63290 (12)	0.27480 (7)	0.0273 (3)
C6	0.60748 (17)	0.53081 (12)	0.39893 (7)	0.0228 (3)
C12	0.42314 (18)	0.69223 (13)	0.32709 (8)	0.0280 (3)
C7	0.63436 (17)	0.44348 (12)	0.46828 (7)	0.0244 (3)
C11	0.56276 (19)	0.70428 (13)	0.26991 (8)	0.0284 (3)
C5	0.44607 (16)	0.60298 (12)	0.39092 (7)	0.0231 (3)
C3	0.30879 (17)	0.58956 (12)	0.45805 (7)	0.0253 (3)
H3A	0.1876	0.6020	0.4333	0.030*
C4	0.3370 (2)	0.70133 (14)	0.52100 (9)	0.0355 (3)
H4C	0.4485	0.6850	0.5509	0.053*
H4B	0.2364	0.7024	0.5593	0.053*
H4A	0.3443	0.7880	0.4930	0.053*
C10	0.8647 (2)	0.64783 (16)	0.21033 (8)	0.0379 (3)
H10A	0.8158	0.6215	0.1573	0.057*
H10B	0.9668	0.5903	0.2238	0.057*
H10C	0.9041	0.7415	0.2080	0.057*
C2	0.31545 (17)	0.44997 (13)	0.49601 (7)	0.0257 (3)
C1	0.20825 (19)	0.43331 (14)	0.57328 (8)	0.0333 (3)
H1C	0.2544	0.4943	0.6151	0.050*
H1B	0.2184	0.3406	0.5925	0.050*
H1A	0.0823	0.4542	0.5624	0.050*
C13	0.2588 (2)	0.77862 (17)	0.31733 (10)	0.0434 (4)
H13B	0.1546	0.7315	0.3396	0.065*
H13A	0.2390	0.7972	0.2594	0.065*
H13C	0.2759	0.8633	0.3466	0.065*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0301 (5)	0.0298 (5)	0.0240 (4)	0.0021 (4)	−0.0010 (4)	0.0057 (3)
O2	0.0414 (5)	0.0225 (4)	0.0245 (4)	−0.0063 (4)	−0.0003 (4)	0.0013 (3)
O5	0.0311 (5)	0.0304 (5)	0.0341 (5)	0.0052 (4)	−0.0028 (4)	0.0079 (4)
C8	0.0268 (6)	0.0197 (5)	0.0262 (6)	0.0001 (5)	−0.0028 (5)	−0.0033 (5)
O3	0.0429 (6)	0.0429 (5)	0.0332 (5)	0.0073 (5)	0.0039 (4)	0.0184 (4)
O4	0.0303 (5)	0.0333 (5)	0.0322 (5)	0.0061 (4)	0.0016 (4)	0.0053 (4)
C9	0.0333 (7)	0.0245 (6)	0.0240 (6)	−0.0027 (5)	0.0005 (5)	−0.0006 (5)
C6	0.0287 (6)	0.0180 (5)	0.0218 (6)	−0.0013 (5)	−0.0018 (4)	−0.0017 (4)
C12	0.0319 (7)	0.0245 (6)	0.0278 (6)	0.0014 (5)	−0.0017 (5)	0.0031 (5)
C7	0.0299 (6)	0.0195 (5)	0.0239 (6)	−0.0007 (5)	−0.0021 (5)	−0.0017 (5)
C11	0.0364 (7)	0.0235 (6)	0.0253 (6)	−0.0007 (5)	−0.0022 (5)	0.0042 (5)
C5	0.0259 (6)	0.0193 (5)	0.0240 (5)	−0.0013 (5)	−0.0020 (5)	−0.0015 (5)
C3	0.0271 (6)	0.0229 (6)	0.0259 (6)	0.0018 (5)	−0.0001 (5)	0.0017 (5)
C4	0.0423 (7)	0.0277 (6)	0.0364 (7)	0.0009 (6)	0.0059 (6)	−0.0067 (5)
C10	0.0398 (8)	0.0414 (7)	0.0326 (7)	0.0026 (6)	0.0068 (6)	0.0077 (6)
C2	0.0281 (6)	0.0263 (6)	0.0226 (6)	−0.0004 (5)	−0.0016 (5)	−0.0002 (5)
C1	0.0375 (7)	0.0366 (7)	0.0259 (6)	−0.0019 (6)	0.0041 (5)	0.0035 (5)
C13	0.0406 (8)	0.0431 (8)	0.0464 (8)	0.0119 (7)	0.0008 (7)	0.0166 (6)

Geometric parameters (Å, °)

O1—C7	1.3395 (15)	C5—C3	1.5111 (17)
O1—C2	1.4721 (16)	C3—C2	1.5260 (17)
O2—C2	1.4003 (15)	C3—C4	1.5343 (18)
O2—H2	0.8400	C3—H3A	1.0000
O5—C7	1.2384 (16)	C4—H4C	0.9800
C8—O4	1.3552 (16)	C4—H4B	0.9800
C8—C9	1.3942 (17)	C4—H4A	0.9800
C8—C6	1.4067 (18)	C10—H10A	0.9800
O3—C11	1.3601 (15)	C10—H10B	0.9800
O3—H3	0.8400	C10—H10C	0.9800
O4—H4	0.8400	C2—C1	1.5088 (17)
C9—C11	1.3917 (19)	C1—H1C	0.9800
C9—C10	1.5073 (18)	C1—H1B	0.9800
C6—C5	1.4108 (18)	C1—H1A	0.9800
C6—C7	1.4469 (16)	C13—H13B	0.9800
C12—C5	1.3851 (17)	C13—H13A	0.9800
C12—C11	1.4082 (19)	C13—H13C	0.9800
C12—C13	1.509 (2)
C7—O1—C2	119.30 (9)	C3—C4—H4C	109.5
C2—O2—H2	109.5	C3—C4—H4B	109.5
O4—C8—C9	117.19 (11)	H4C—C4—H4B	109.5
O4—C8—C6	122.16 (11)	C3—C4—H4A	109.5
C9—C8—C6	120.65 (11)	H4C—C4—H4A	109.5
C11—O3—H3	109.5	H4B—C4—H4A	109.5
C8—O4—H4	109.5	C9—C10—H10A	109.5
C11—C9—C8	117.48 (12)	C9—C10—H10B	109.5
C11—C9—C10	120.93 (11)	H10A—C10—H10B	109.5
C8—C9—C10	121.59 (12)	C9—C10—H10C	109.5
C8—C6—C5	120.11 (11)	H10A—C10—H10C	109.5
C8—C6—C7	119.90 (11)	H10B—C10—H10C	109.5
C5—C6—C7	119.94 (11)	O2—C2—O1	107.79 (10)
C5—C12—C11	117.83 (12)	O2—C2—C1	111.88 (10)
C5—C12—C13	123.22 (12)	O1—C2—C1	104.30 (10)
C11—C12—C13	118.93 (12)	O2—C2—C3	107.81 (9)
O5—C7—O1	115.81 (10)	O1—C2—C3	109.57 (10)
O5—C7—C6	123.57 (11)	C1—C2—C3	115.22 (11)
O1—C7—C6	120.61 (11)	C2—C1—H1C	109.5
O3—C11—C9	121.54 (12)	C2—C1—H1B	109.5
O3—C11—C12	114.87 (12)	H1C—C1—H1B	109.5
C9—C11—C12	123.58 (11)	C2—C1—H1A	109.5
C12—C5—C6	120.27 (11)	H1C—C1—H1A	109.5
C12—C5—C3	121.60 (11)	H1B—C1—H1A	109.5
C6—C5—C3	117.86 (10)	C12—C13—H13B	109.5
C5—C3—C2	110.86 (10)	C12—C13—H13A	109.5
C5—C3—C4	109.44 (10)	H13B—C13—H13A	109.5
C2—C3—C4	112.57 (11)	C12—C13—H13C	109.5
C5—C3—H3A	107.9	H13B—C13—H13C	109.5
C2—C3—H3A	107.9	H13A—C13—H13C	109.5
C4—C3—H3A	107.9
O4—C8—C9—C11	−177.25 (11)	C11—C12—C5—C6	2.13 (18)
C6—C8—C9—C11	2.70 (17)	C13—C12—C5—C6	−176.37 (13)
O4—C8—C9—C10	2.78 (17)	C11—C12—C5—C3	176.12 (11)
C6—C8—C9—C10	−177.27 (11)	C13—C12—C5—C3	−2.4 (2)
O4—C8—C6—C5	178.45 (10)	C8—C6—C5—C12	−1.01 (17)
C9—C8—C6—C5	−1.50 (17)	C7—C6—C5—C12	176.51 (11)
O4—C8—C6—C7	0.92 (17)	C8—C6—C5—C3	−175.22 (10)
C9—C8—C6—C7	−179.03 (11)	C7—C6—C5—C3	2.31 (16)
C2—O1—C7—O5	−164.73 (11)	C12—C5—C3—C2	153.52 (11)
C2—O1—C7—C6	16.22 (16)	C6—C5—C3—C2	−32.36 (14)
C8—C6—C7—O5	6.00 (18)	C12—C5—C3—C4	−81.73 (14)
C5—C6—C7—O5	−171.53 (11)	C6—C5—C3—C4	92.39 (13)
C8—C6—C7—O1	−175.02 (10)	C7—O1—C2—O2	70.86 (13)
C5—C6—C7—O1	7.45 (17)	C7—O1—C2—C1	−170.08 (10)
C8—C9—C11—O3	177.94 (11)	C7—O1—C2—C3	−46.21 (14)
C10—C9—C11—O3	−2.09 (19)	C5—C3—C2—O2	−64.88 (12)
C8—C9—C11—C12	−1.55 (19)	C4—C3—C2—O2	172.15 (11)
C10—C9—C11—C12	178.42 (12)	C5—C3—C2—O1	52.17 (12)
C5—C12—C11—O3	179.62 (11)	C4—C3—C2—O1	−70.79 (13)
C13—C12—C11—O3	−1.81 (19)	C5—C3—C2—C1	169.38 (11)
C5—C12—C11—C9	−0.9 (2)	C4—C3—C2—C1	46.42 (15)
C13—C12—C11—C9	177.71 (13)

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	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−1/2, −y+1/2, −z+1; (ii) −x+1, y+1/2, −z+1/2.