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The natural compound 5,10-di­hydroxy-2,2-di­methylpyrano­[3,2-b]­xanthen-6(2H)-one (6-deoxy­jacareubin), C18H14O5, was isolated from leaves of Vismia latifolia (Guttiferae family). The compound has four six-membered rings. The mol­ecule has two planar benzeno­id and one planar pyran­oid ring, plus a pyran­oid ring in a distorted chair conformation. The crystal is stabilized by one intra- and one intermolecular hydrogen bond.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270101009246/da1189sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270101009246/da1189Isup2.hkl
Contains datablock I

CCDC reference: 173384

Comment top

The title compound is a natural xanthone. Xanthones are heterocyclic ring systems that have many pharmacological applications (Santos et al., 2000a). It was isolated from Vismia Latifolia Choisy (Syn. Hypericum latifolium Aubl.). This species belongs to the Guttiferae family, subfamily Hypericoideae and tribe Vismieae and it is a tree commonly known in the Bahia state (Brazil) as pau-de-sangue. This plant is widely used in traditional medicine as a tonic and febrifugal agent (Corrêa, 1978). Previous works have reported the presence of several xanthones, terpenoids, benzophenones, flavonoids and anthranoids from Vismia species (Santos et al., 2000b; Santos et al., 1999; Nagem & De Oliveira, 1997; Peres & Nagem, 1997; Nagem & Alves, 1995; Nagem & Ferreira, 1993; Delle Monache et al., 1983).

As part of a chemotaxonomic study of the Guttiferae (Vismia genus), we have determined the structure of the compound know as 6-deoxyjacareubin, (I). We have identified (I) by spectroscopic methods (UV, EI—MS, H-1 and C-13 NMR) and the gamma-pyrone was confirmed by the X-ray data. This compound was first isolated from Calophyllum Inophyllum by Jackson et al. (1969). It is described as antifungal agent against Postia placenta (ReyesChilpa et al., 1997) and Cladosporium cucumerinum (Rocha et al., 1994). For this reason, we have also tested its biological activity in fungus (Cândida albicans, Aspergillus fumigatus, Aspergillus ochraceus (allutaceus) and Penicillium citrinum) and bacteria (Escherichia coli and Streptococcus muttans). Our tests, however, did not show biological inhibition on these organisms. \sch

Figure 1 is an ORTEP-3 (Farrugia, 1997) view of the title compound. As expected, the molecule is almost flat. All atoms in the A, B and C rings lie within 0.149 (1) Å of the least-squares plane through the three-ring system. The A, B and C rings are also individually almost planar, including the oxygen atoms O1, O2 and O3 linked to them. The largest deviations from the individual least-squares planes are 0.006 (2), 0.037 (1) and 0.009 (1) Å for rings A, B and C, respectively. The least-squares planes of the A and B rings form an angle of 3.64 (8)°, and those of the B and C rings form an angle of 3.69 (8)°. The planes of the A and C rings form an angle of 7.31 (9)°. The planes of the A and C ring systems intersect on a line which is approximately through the middle of the B ring. A folding point along an imaginary line drawn between O5 and C6 defines an angle of 6.55 (6)° (least-squares planes of rings A and C calculated by including O5 and C6). Ring D is in a deformed chair conformation. The weighted average absolute torsion angle (Domenicano et al., 1975) in the D ring is 27 (8)°. The main bond lengths and bond angles appear in Table 1. The mean value of the intramolecular C—C bond distances within the A and C benzenoid rings is 1.39 (1) Å, which agrees well with the normal aromatic value. In the same way, the mean bond angles in rings A and C are [120 (2)°]. The average value of the two C—O5 bond lengths in the pyranoid ring (B ring) is 1.373 (2) Å. The observed geometry of the pyranoid ring (ring B) agrees well with similar pyranxanthones geometries (Ho et al., 1987; Vijayalakshmi et al., 1987; Ferguson et al., 1985; Söderholm et al., 1976).

The molecule exhibits a moderated intramolecular hydrogen bond, O3—H3'···O2, with an O···O distance of 2.561 (2) Å (Table 2). The intermolecular hydrogen bond between hydroxyl group O1—H1' and adjacent carboxyl oxygen O2 at x + 1, y, z [O···O distance is 2.778 (2) Å] stabilizes the structure and gives rise to a chain parallel to the [100] direction. The separation between the least-squares planes through the molecules at x,y,z and -x,-y,-z is 3.67 (2) Å.

Experimental top

Dried and ground leaves (1502 g) were extracted (at room temperature) with n-hexane (32.85 g) and EtOH (200.0 g) in succession. The ethanol extract was stirred with water for 24 h and filtered. The soluble portion was extracted with CHCl3, EtOAc and n-butanol in succession. The solid obtained by evaporation (under vacuum) of the fraction soluble in CHCl3 (30.0 g) was chromatographed on silica gel (Merck) (352 g) CC and eluted with CH2Cl2, EtOAc and EtOH. The ninety fractions obtained yielded nine groups (D1—D9). D3 (frs 4–6, 658.0 mg) was washed with petrol-ether giving an insoluble portion that was washed with methanol yielding 6-deoxyjacareubina (101.0 mg) as a yellow solid. The powder mass obtained was crystallized from methanol by slow evaporation at room temperature.

Refinement top

The hydrogen atoms of the phenyl and methyl groups were stereochemically positioned and were refined with fixed individual displacement parameters [Uiso(H) = 1.2Ueq(C) or 1.5Ueq(Cmethoxyl)] using a riding model with aromatic C—H = 0.93 Å and methyl C—H = 0.98 Å. The hydroxyl H atoms were located by difference Fourier synthesis and were set isotropic.

Computing details top

Data collection: Collect (Nonius, 1997-2000); cell refinement: HKL SCALEPACK (Otwinowski & Minor, 1997); data reduction: HKL DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS86 (Sheldrick, 1986); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX publication routines (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. ORTEP-3 view of the compound 6-deroxyjacareubin, showing the atoms and rings labeling and 50% probability ellipsoids.
[Figure 2] Fig. 2. View of the chain of hydrogen bonds parallel to [100]. Symmetry codes from top to bottom are 1 + x, y, z; x, y, z; 1 - x, y, z.
1,5-dihydroxy-2,,2,-dimethylpyrano-5,,6,:2,3-xanthone top
Crystal data top
C18H14O5Z = 2
Mr = 310.29F(000) = 324
Triclinic, P1Dx = 1.424 Mg m3
Hall symbol: -P 1Melting point: 503-505 K K
a = 7.4450 (2) ÅMo Kα radiation, λ = 0.71070 Å
b = 9.5200 (3) ÅCell parameters from 3315 reflections
c = 10.9390 (3) Åθ = 1.0–27.5°
α = 105.051 (2)°µ = 0.11 mm1
β = 103.154 (2)°T = 293 K
γ = 93.083 (2)°Prism, yellow
V = 723.80 (4) Å30.24 × 0.17 × 0.12 mm
Data collection top
Nonius KappaCCD
diffractometer
2674 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.014
Horizonally mounted graphite crystal monochromatorθmax = 27.5°, θmin = 2.0°
Detector resolution: 9 pixels mm-1h = 09
ϕ scans and ω scans winth κ offsetsk = 1212
6210 measured reflectionsl = 1413
3319 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.150H atoms treated by a mixture of independent and constrained refinement
S = 1.02 w = 1/[σ2(Fo2) + (0.0624P)2 + 0.4P]
where P = (Fo2 + 2Fc2)/3
3319 reflections(Δ/σ)max = 0.003
218 parametersΔρmax = 0.41 e Å3
0 restraintsΔρmin = 0.49 e Å3
Crystal data top
C18H14O5γ = 93.083 (2)°
Mr = 310.29V = 723.80 (4) Å3
Triclinic, P1Z = 2
a = 7.4450 (2) ÅMo Kα radiation
b = 9.5200 (3) ŵ = 0.11 mm1
c = 10.9390 (3) ÅT = 293 K
α = 105.051 (2)°0.24 × 0.17 × 0.12 mm
β = 103.154 (2)°
Data collection top
Nonius KappaCCD
diffractometer
2674 reflections with I > 2σ(I)
6210 measured reflectionsRint = 0.014
3319 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.150H atoms treated by a mixture of independent and constrained refinement
S = 1.02Δρmax = 0.41 e Å3
3319 reflectionsΔρmin = 0.49 e Å3
218 parameters
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
O10.20011 (17)0.51755 (16)0.19870 (14)0.0491 (4)
H1'0.269 (5)0.439 (3)0.146 (3)0.095 (10)*
O20.49153 (16)0.32309 (15)0.04343 (14)0.0524 (4)
O30.41897 (18)0.08552 (18)0.14370 (17)0.0621 (5)
H3'0.481 (5)0.162 (4)0.079 (3)0.108 (11)*
O40.20030 (17)0.14926 (13)0.27926 (12)0.0418 (3)
O50.05941 (15)0.29604 (12)0.04833 (11)0.0351 (3)
C10.0187 (2)0.52917 (18)0.19702 (16)0.0351 (4)
C20.0936 (2)0.65696 (19)0.27140 (17)0.0394 (4)
H20.04330.73160.32140.047*
C30.2806 (2)0.67601 (19)0.27285 (17)0.0409 (4)
H30.35360.76310.32340.049*
C40.3585 (2)0.56726 (19)0.20019 (17)0.0392 (4)
H40.48380.58030.20190.047*
C50.2478 (2)0.43641 (18)0.12333 (16)0.0336 (3)
C60.3222 (2)0.31847 (19)0.04209 (17)0.0363 (4)
C70.1897 (2)0.19686 (18)0.04208 (16)0.0341 (3)
C80.2418 (2)0.0822 (2)0.13413 (18)0.0395 (4)
C90.1133 (2)0.03402 (19)0.21636 (17)0.0380 (4)
C100.1599 (3)0.1591 (2)0.30798 (19)0.0478 (5)
H100.28330.17390.30420.057*
C110.0236 (3)0.2516 (2)0.39687 (19)0.0485 (5)
H110.05180.33470.45240.058*
C120.1758 (3)0.22398 (19)0.40898 (17)0.0428 (4)
C130.3071 (3)0.3651 (2)0.4532 (2)0.0537 (5)
H13A0.30670.41670.54100.081*
H13B0.26740.42520.39630.081*
H13C0.43050.34270.45020.081*
C140.2330 (3)0.1254 (2)0.4971 (2)0.0547 (5)
H14A0.23220.17580.58520.082*
H14B0.35580.10090.49450.082*
H14C0.14730.03740.46720.082*
C150.0706 (2)0.03511 (18)0.20446 (16)0.0346 (4)
C160.1272 (2)0.07304 (17)0.11465 (16)0.0339 (3)
H160.24940.06830.10750.041*
C170.0034 (2)0.18804 (17)0.03607 (15)0.0312 (3)
C180.0604 (2)0.41890 (17)0.12208 (15)0.0316 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0284 (6)0.0482 (8)0.0594 (8)0.0008 (5)0.0134 (6)0.0058 (6)
O20.0242 (6)0.0544 (8)0.0643 (9)0.0020 (5)0.0104 (6)0.0061 (7)
O30.0270 (6)0.0644 (9)0.0758 (10)0.0003 (6)0.0175 (7)0.0165 (8)
O40.0373 (6)0.0388 (6)0.0401 (7)0.0070 (5)0.0074 (5)0.0008 (5)
O50.0257 (5)0.0341 (6)0.0397 (6)0.0007 (4)0.0083 (4)0.0007 (5)
C10.0283 (7)0.0380 (8)0.0362 (8)0.0031 (6)0.0066 (6)0.0070 (7)
C20.0371 (9)0.0370 (9)0.0381 (9)0.0048 (7)0.0063 (7)0.0029 (7)
C30.0354 (8)0.0365 (8)0.0415 (9)0.0028 (7)0.0016 (7)0.0031 (7)
C40.0290 (8)0.0406 (9)0.0416 (9)0.0028 (7)0.0043 (7)0.0061 (7)
C50.0266 (7)0.0362 (8)0.0340 (8)0.0001 (6)0.0041 (6)0.0065 (6)
C60.0244 (7)0.0407 (9)0.0397 (9)0.0008 (6)0.0068 (6)0.0059 (7)
C70.0243 (7)0.0366 (8)0.0370 (8)0.0011 (6)0.0060 (6)0.0048 (7)
C80.0259 (8)0.0444 (9)0.0435 (9)0.0036 (7)0.0093 (7)0.0039 (7)
C90.0311 (8)0.0390 (9)0.0387 (9)0.0032 (7)0.0073 (7)0.0032 (7)
C100.0408 (9)0.0472 (10)0.0485 (10)0.0077 (8)0.0121 (8)0.0001 (8)
C110.0520 (11)0.0427 (10)0.0433 (10)0.0063 (8)0.0116 (8)0.0005 (8)
C120.0450 (10)0.0395 (9)0.0358 (9)0.0020 (7)0.0051 (7)0.0024 (7)
C130.0599 (12)0.0429 (10)0.0450 (10)0.0104 (9)0.0021 (9)0.0021 (8)
C140.0554 (12)0.0548 (12)0.0506 (11)0.0007 (9)0.0055 (9)0.0169 (9)
C150.0305 (8)0.0337 (8)0.0348 (8)0.0010 (6)0.0034 (6)0.0066 (6)
C160.0249 (7)0.0355 (8)0.0382 (8)0.0004 (6)0.0063 (6)0.0069 (7)
C170.0267 (7)0.0324 (8)0.0333 (8)0.0038 (6)0.0072 (6)0.0071 (6)
C180.0277 (7)0.0319 (8)0.0311 (7)0.0001 (6)0.0038 (6)0.0057 (6)
Geometric parameters (Å, º) top
O1—C11.354 (2)C5—C181.392 (2)
O1—H1'0.87 (3)C5—C61.460 (2)
O2—C61.255 (2)C6—C71.439 (2)
O3—C81.346 (2)C7—C171.402 (2)
O3—H3'0.89 (3)C7—C81.418 (2)
O4—C151.360 (2)C8—C91.388 (2)
O4—C121.470 (2)C9—C151.404 (2)
O5—C171.373 (2)C9—C101.458 (2)
O5—C181.373 (2)C10—C111.327 (3)
C1—C21.381 (2)C11—C121.504 (3)
C1—C181.400 (2)C12—C131.517 (2)
C2—C31.390 (2)C12—C141.522 (3)
C3—C41.374 (2)C15—C161.383 (2)
C4—C51.403 (2)C16—C171.378 (2)
C1—O1—H1'116 (2)C8—C9—C15117.7 (2)
C8—O3—H3'105 (2)C8—C9—C10124.0 (2)
C15—O4—C12116.8 (1)C15—C9—C10118.1 (2)
C17—O5—C18119.0 (1)C11—C10—C9119.0 (2)
O1—C1—C2118.5 (2)C10—C11—C12120.9 (2)
O1—C1—C18123.3 (2)O4—C12—C11109.3 (1)
C2—C1—C18118.2 (2)O4—C12—C13104.5 (2)
C1—C2—C3121.2 (2)C11—C12—C13112.2 (2)
C4—C3—C2120.5 (2)O4—C12—C14107.4 (2)
C3—C4—C5119.6 (2)C11—C12—C14111.8 (2)
C18—C5—C4119.4 (2)C13—C12—C14111.3 (2)
C18—C5—C6118.7 (1)O4—C15—C16117.0 (1)
C4—C5—C6121.9 (1)O4—C15—C9120.0 (2)
O2—C6—C7121.5 (2)C16—C15—C9122.9 (2)
O2—C6—C5122.3 (2)C17—C16—C15117.8 (1)
C7—C6—C5116.2 (1)O5—C17—C16116.1 (1)
C17—C7—C8117.6 (1)O5—C17—C7121.3 (1)
C17—C7—C6121.0 (2)C16—C17—C7122.6 (2)
C8—C7—C6121.5 (1)O5—C18—C5123.6 (1)
O3—C8—C9118.8 (2)O5—C18—C1115.4 (1)
O3—C8—C7119.8 (2)C5—C18—C1121.1 (1)
C9—C8—C7121.4 (2)
O1—C1—C2—C3179.4 (2)C10—C11—C12—C13148.1 (2)
C18—C1—C2—C30.4 (3)C10—C11—C12—C1486.1 (2)
C1—C2—C3—C40.2 (3)C12—O4—C15—C16152.2 (2)
C2—C3—C4—C50.4 (3)C12—O4—C15—C930.6 (2)
C3—C4—C5—C180.1 (3)C8—C9—C15—O4177.5 (2)
C3—C4—C5—C6178.7 (2)C10—C9—C15—O41.4 (3)
C18—C5—C6—O2176.1 (2)C8—C9—C15—C160.5 (3)
C4—C5—C6—O25.1 (3)C10—C9—C15—C16175.7 (2)
C18—C5—C6—C75.0 (2)O4—C15—C16—C17178.7 (1)
C4—C5—C6—C7173.8 (2)C9—C15—C16—C171.5 (3)
O2—C6—C7—C17175.5 (2)C18—O5—C17—C16175.1 (1)
C5—C6—C7—C175.6 (2)C18—O5—C17—C74.1 (2)
O2—C6—C7—C84.8 (3)C15—C16—C17—O5177.6 (1)
C5—C6—C7—C8174.2 (2)C15—C16—C17—C71.5 (3)
C17—C7—C8—O3180.0 (2)C8—C7—C17—O5178.6 (2)
C6—C7—C8—O30.2 (3)C6—C7—C17—O51.2 (3)
C17—C7—C8—C90.6 (3)C8—C7—C17—C160.5 (3)
C6—C7—C8—C9179.2 (2)C6—C7—C17—C16179.7 (2)
O3—C8—C9—C15180.0 (2)C17—O5—C18—C54.7 (2)
C7—C8—C9—C150.7 (3)C17—O5—C18—C1174.7 (2)
O3—C8—C9—C104.1 (3)C4—C5—C18—O5178.8 (2)
C7—C8—C9—C10176.5 (2)C6—C5—C18—O50.1 (2)
C8—C9—C10—C11168.9 (2)C4—C5—C18—C10.5 (3)
C15—C9—C10—C1115.2 (3)C6—C5—C18—C1179.3 (2)
C9—C10—C11—C123.6 (3)O1—C1—C18—O50.3 (2)
C15—O4—C12—C1145.8 (2)C2—C1—C18—O5178.7 (1)
C15—O4—C12—C13166.1 (2)O1—C1—C18—C5179.7 (2)
C15—O4—C12—C1475.6 (2)C2—C1—C18—C50.7 (3)
C10—C11—C12—O432.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O2i0.87 (3)1.97 (3)2.778 (2)154 (3)
O1—H1···O50.87 (3)2.38 (4)2.733 (2)105 (3)
O3—H3···O20.89 (3)1.74 (3)2.561 (2)152 (4)
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC18H14O5
Mr310.29
Crystal system, space groupTriclinic, P1
Temperature (K)293
a, b, c (Å)7.4450 (2), 9.5200 (3), 10.9390 (3)
α, β, γ (°)105.051 (2), 103.154 (2), 93.083 (2)
V3)723.80 (4)
Z2
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.24 × 0.17 × 0.12
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
6210, 3319, 2674
Rint0.014
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.051, 0.150, 1.02
No. of reflections3319
No. of parameters218
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.41, 0.49

Computer programs: Collect (Nonius, 1997-2000), HKL SCALEPACK (Otwinowski & Minor, 1997), HKL DENZO and SCALEPACK (Otwinowski & Minor, 1997), SHELXS86 (Sheldrick, 1986), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX publication routines (Farrugia, 1999).

Selected geometric parameters (Å, º) top
O1—C11.354 (2)C10—C111.327 (3)
O3—C81.346 (2)C11—C121.504 (3)
O4—C151.360 (2)C12—C131.517 (2)
O4—C121.470 (2)C12—C141.522 (3)
C9—C101.458 (2)
O4—C12—C11109.3 (1)O4—C12—C14107.4 (2)
O4—C12—C13104.5 (2)C11—C12—C14111.8 (2)
C11—C12—C13112.2 (2)C13—C12—C14111.3 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1'···O2i0.87 (3)1.97 (3)2.778 (2)154 (3)
O3—H3'···O20.89 (3)1.74 (3)2.561 (2)152 (4)
Symmetry code: (i) x+1, y, z.
 

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