6,7,8-Trimethoxy­coumarin from Cryptocarya bracteolata

The title compound, C₁₂H₁₂O₅, isolated from the bark of Cryptocarya bracteolata, has a planar fused-ring system.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.041
• wR factor = 0.118
• Data-to-parameter ratio = 16.5

checkCIF/PLATON results

No syntax errors found



Alert level C
ABSTM02_ALERT_3_C  The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
            Tmin and Tmax reported:      0.738     0.979
            Tmin(prime) and Tmax expected:      0.962     0.979
            RR(prime) =      0.767
            Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large .............       0.77

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

6,7,8-Trimethoxycoumarin has been isolated from a wide range plants such as, for example, Acmadenia sheilae (Rutaceae) (Campbell, 1996), Artemisia adamsii (Bohlmann et al., 1985), Aralia bipinnata (Hsiao & Chiang, 1995), Baccharis species (Bohlmann et al., 1981), Bupleurum fruiticescens (Gonzalez et al., 1975), Bupleurum salicifolium (Estevez-Braun et al., 1995), Cedrelopsis grevei (Eshiett & Taylor, 1968), Cuscuta reflexa (Anis et al., 1999; Anis et al., 2002), Duranta repens (Iqbal et al., 2003), Euodia latifolia (Goh et al., 1990), Euodia (Rutaceae) (Goh et al., 1989), Euphorbia antiquorum (Sang et al., 2005), Euphorbia quinquecostata (Mbwambo et al., 1996), Fraxinus ornus (Iossifova et al., 1994), Guazuma tomentosa Kunth (Anjaneyulu & Murty, 1981), Pelargonium reniforme (Wagner, & Bladt, 1975), Picnomon acarna (Laskaris et al., 1995), Platypodium elegans (Amaral et al., 2001), Pterocaulon sphacelatum (Semple et al., 1999), Pterocaulon serrulatum (Macleod & Rasmussen, 1998), Ruta angustifolia (Del Castillo et al., 1984), Ruta angustifolia Pers (Borges del Castillo et al., 1987), Ruta oerojasme (Gonzalez et al., 1972), Ruta sp. Tene. 29662 (Gonzalez et al., 1977), Rutoideae: tribe Diosmeae (Campbell et al., 1986), Sapium chihsinianum S. Lee (Qi et al., 2004), Sapium sebiferum (Yang & Kinghorn, 1985; Shi et al., 2006), Tanacetum cilicium (Oksuz, 1990), Tanacetum heterotomum (Goren et al., 1988), Tagetes florida (Rios & Flores, 1976), Xanthoxylum inerme (Fagara boninensis) (Ishi et al., 1972), Xanthoxylum inerme Koidz. (Fagara boninensis Koidz.) (Ishii et al., 1981), Xanthoxylum integrifoliolum (Merr.) Merr. (Fagara integrifoliola Merr.) (Ishii et al., 1982), Zanthoxylum microcarpum, Zanthoxylum procerum (Boulware & Stermitz, 1981), Xanthoxylum nitidum (Roxb.) D. C. (Fagara nitida Roxb.) (Ishikawa et al., 1995), Zanthoxylum ailanthoides (Cheng et al., 2005; Shi et al., 2005), Zanthoxylum lemairie (Adesina et al., 1997), Zanthoxylum rugosum A. St. Hill & Tul (Facundo et al., 2002) and Zanthoxylum utile Huang (Ren et al., 1991). The compound (I) has been evaluated for a variety of biological activities and almost all spectrosopic analyses already have been carried out on it.

The compound has been isolated from Cryptocarya bracteolata; its crystal structure shows a planar conformation for the coumarin (Fig. 1). The compound complements the list of coumarins having methoxy (and/or hydroxy) groups in the 5 to 8 positions of the coumarin fused-ring, i.e., 6-methoxy- (Bauers et al., 2002; Gnanaguru et al., 1985), 7-methoxy- (Bhadbhade et al., 1984; Gnanaguru et al., 1984; Gnanaguru et al., 1985; Ramasubbu, et al., 1981; Ramasubbu et al., 1982), 8-methoxy- (Baures et al., 2002; Gnanaguru et al., 1985), 5,7-dimethoxy- (Ye & Fan, 2007), 7-hydroxy-6-methoxy- (Kimura et al., 1980), 7-hydroxy-5,6-dimethoxy- (Wagner et al., 1974) and 7-hydroxy-6,8-dimethoxy- (Li et al., 2001) coumarins.

Related literature

For the isolation and spectroscopic characterization of 6,7,8-trimethoxycoumarin that has been isolated from other plants, see: Adesina et al. (1997); Amaral et al. (2001); Anis et al. (1999, 2002); Anjaneyulu & Murty (1981); Bohlmann et al. (1981, 1985); Boulware & Stermitz (1981); Borges del Castillo et al. (1987); Campbell (1996); Campbell et al. (1986); Cheng et al. (2005); Del Castillo et al. (1984); Eshiett & Taylor (1968); Estevez-Braun et al. (1995); Facundo et al. (2002); Goh et al. (1989, 1990); Gonzalez et al. (1972, 1975, 1977); Goren et al. (1988); Hsiao & Chiang (1995); Iqbal et al. (2003); Ishi et al. (1972); Ishii et al. (1981, 1982); Ishikawa et al. (1995); Laskaris et al. (1995); Macleod & Rasmussen (1998); Mbwambo et al. (1996); Oksuz (1990); Qi et al. (2004); Ren et al. (1991); Rios & Flores (1976); Sang et al. (2005); Semple et al. (1999); Shi et al. (2005, 2006); Wagner & Bladt (1975); Yang & Kinghorn (1985).

For the crystal structures of coumarins having methoxy (and/or hydroxy) groups in the 5 to 8 positions, see: Bauers et al. (2002); Bhadbhade et al. (1984); Gnanaguru et al. (1984, 1985); Kimura et al. (1980); Li et al. (2001); Ramasubbu et al. (1981, 1982); Wagner et al. (1974).

For related literature, see: Iossifova et al. (1994); Ye & Fan (2007).

S2. Experimental

Cryptocarya bracteolata was collected in Mersing, Johor in 1997. Specimens were deposited at the Forest Research Institute of Malaysia herbarium and the Department of Chemistry, University of Malaya.

The bark of C. bracteolata (2.7 kg) was extracted with n-hexane; the solvent was then removed under vacuum. The plant material was moistened with 10% ammonium hydroxide overnight. It was extracted with dichloromethane (8 L) for 17 h to yield the crude extract (89 g). A portion (30 g) was subjected to column chromatography on silica gel 60 GF₂₅₄ by using a step gradient of dichloromethane and methanol. The separation afforded 15 fractions; the second (100% dichloromethane) gave 5,6,7-trimethoxy-2H-chromen-2-one (24.5 g), whose formulation was established by spectroscopic analysis.

S3. Refinement

The carbon-bound hydrogen atoms were placed at calculated positions (C–H 0.93 to 0.98 Å) and were inlcuded in the refinement in the riding model approximation, with U(H) set to 1.2 to 1.5 U_eq(C).

Computing details

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures

Fig. 1. View of (I); displacement ellipsoids are drawn at the 50% probability level, and hydrogen atoms as spheres of arbitrary radius.

6,7,8-Trimethoxycoumarin

Crystal data

C12H12O5	F(000) = 992
Mr = 236.22	Dx = 1.399 Mg m^−3
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 11077 reflections
a = 13.9688 (6) Å	θ = 3.1–27.4°
b = 8.1164 (4) Å	µ = 0.11 mm^−1
c = 19.790 (1) Å	T = 295 K
V = 2243.7 (2) Å^3	Prism, colourless
Z = 8	0.34 × 0.28 × 0.19 mm

Data collection

Rigaku R-AXIS RAPID IP diffractometer	2561 independent reflections
Radiation source: fine-focus sealed tube	1836 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.044
ω scans	θmax = 27.4°, θmin = 3.1°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −18→18
Tmin = 0.738, Tmax = 0.979	k = −10→10
19734 measured reflections	l = −25→25

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.041	H-atom parameters constrained
wR(F^2) = 0.118	w = 1/[σ^2(Fo^2) + (0.0577P)^2 + 0.3525P] where P = (Fo^2 + 2Fc^2)/3
S = 1.04	(Δ/σ)max = 0.001
2561 reflections	Δρmax = 0.18 e Å^−3
155 parameters	Δρmin = −0.15 e Å^−3
0 restraints	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0102 (13)

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.65727 (10)	0.89131 (17)	0.55051 (7)	0.0721 (4)
O2	0.61944 (7)	0.74494 (13)	0.46074 (5)	0.0488 (3)
O3	0.67995 (7)	0.60631 (14)	0.34306 (6)	0.0526 (3)
O4	0.55894 (8)	0.41023 (14)	0.26964 (6)	0.0555 (3)
O5	0.37230 (8)	0.38596 (15)	0.30093 (6)	0.0603 (3)
C1	0.59401 (13)	0.8219 (2)	0.52022 (8)	0.0522 (4)
C2	0.49443 (13)	0.8134 (2)	0.53901 (8)	0.0550 (4)
H2	0.4745	0.8655	0.5784	0.066*
C3	0.42979 (12)	0.7333 (2)	0.50165 (8)	0.0503 (4)
H3	0.3660	0.7320	0.5151	0.060*
C4	0.45761 (10)	0.64940 (18)	0.44103 (7)	0.0412 (3)
C5	0.55343 (10)	0.65873 (17)	0.42246 (7)	0.0399 (3)
C6	0.58711 (9)	0.58398 (18)	0.36371 (7)	0.0409 (3)
C7	0.52399 (10)	0.49282 (18)	0.32449 (7)	0.0426 (4)
C8	0.42667 (10)	0.48059 (19)	0.34304 (8)	0.0447 (4)
C9	0.39418 (10)	0.55879 (19)	0.40050 (8)	0.0452 (4)
H9	0.3299	0.5514	0.4124	0.054*
C11	0.74647 (13)	0.4929 (3)	0.37015 (11)	0.0789 (6)
H11A	0.8092	0.5169	0.3529	0.118*
H11B	0.7285	0.3831	0.3574	0.118*
H11C	0.7469	0.5018	0.4185	0.118*
C12	0.52936 (13)	0.4738 (3)	0.20538 (8)	0.0633 (5)
H12A	0.5565	0.4078	0.1700	0.095*
H12B	0.5510	0.5855	0.2008	0.095*
H12C	0.4608	0.4706	0.2024	0.095*
C13	0.27263 (12)	0.3741 (2)	0.31493 (11)	0.0676 (5)
H13A	0.2426	0.3051	0.2817	0.101*
H13B	0.2445	0.4820	0.3135	0.101*
H13C	0.2635	0.3274	0.3590	0.101*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0684 (8)	0.0789 (9)	0.0690 (8)	−0.0085 (7)	−0.0197 (7)	−0.0105 (7)
O2	0.0417 (6)	0.0543 (6)	0.0503 (6)	−0.0043 (5)	−0.0045 (5)	0.0004 (5)
O3	0.0335 (5)	0.0614 (7)	0.0628 (7)	−0.0001 (5)	0.0059 (5)	0.0087 (6)
O4	0.0522 (6)	0.0630 (7)	0.0513 (6)	0.0108 (5)	0.0005 (5)	−0.0067 (5)
O5	0.0433 (6)	0.0690 (8)	0.0684 (8)	−0.0092 (5)	−0.0064 (5)	−0.0122 (6)
C1	0.0588 (10)	0.0503 (9)	0.0476 (9)	0.0013 (8)	−0.0091 (8)	0.0028 (7)
C2	0.0639 (10)	0.0571 (9)	0.0440 (8)	0.0041 (8)	0.0015 (8)	−0.0010 (8)
C3	0.0486 (8)	0.0547 (9)	0.0476 (8)	0.0055 (7)	0.0065 (7)	0.0078 (7)
C4	0.0377 (7)	0.0440 (8)	0.0418 (7)	0.0039 (6)	0.0014 (6)	0.0088 (6)
C5	0.0365 (7)	0.0401 (7)	0.0432 (8)	−0.0013 (6)	−0.0045 (6)	0.0079 (6)
C6	0.0328 (7)	0.0434 (8)	0.0465 (8)	0.0026 (6)	0.0011 (6)	0.0093 (6)
C7	0.0378 (7)	0.0453 (8)	0.0446 (8)	0.0051 (6)	−0.0006 (6)	0.0039 (6)
C8	0.0381 (7)	0.0452 (8)	0.0507 (8)	−0.0006 (6)	−0.0057 (6)	0.0033 (7)
C9	0.0325 (7)	0.0497 (8)	0.0536 (9)	0.0011 (6)	0.0012 (6)	0.0079 (7)
C11	0.0417 (9)	0.0966 (15)	0.0984 (14)	0.0217 (10)	0.0040 (10)	0.0124 (13)
C12	0.0645 (11)	0.0784 (12)	0.0471 (9)	−0.0005 (10)	−0.0010 (8)	−0.0051 (9)
C13	0.0424 (9)	0.0710 (12)	0.0894 (13)	−0.0121 (8)	−0.0108 (9)	−0.0008 (10)

Geometric parameters (Å, º)

O1—C1	1.207 (2)	C4—C9	1.403 (2)
O2—C1	1.379 (2)	C5—C6	1.393 (2)
O2—C5	1.3834 (17)	C6—C7	1.388 (2)
O3—C6	1.3718 (17)	C7—C8	1.412 (2)
O3—C11	1.413 (2)	C8—C9	1.379 (2)
O4—C7	1.3661 (18)	C9—H9	0.9300
O4—C12	1.433 (2)	C11—H11A	0.9600
O5—C8	1.3643 (18)	C11—H11B	0.9600
O5—C13	1.423 (2)	C11—H11C	0.9600
C1—C2	1.441 (2)	C12—H12A	0.9600
C2—C3	1.336 (2)	C12—H12B	0.9600
C2—H2	0.9300	C12—H12C	0.9600
C3—C4	1.433 (2)	C13—H13A	0.9600
C3—H3	0.9300	C13—H13B	0.9600
C4—C5	1.3902 (19)	C13—H13C	0.9600
C1—O2—C5	121.66 (12)	O5—C8—C9	125.42 (13)
C6—O3—C11	115.00 (13)	O5—C8—C7	114.64 (14)
C7—O4—C12	115.18 (12)	C9—C8—C7	119.93 (14)
C8—O5—C13	117.63 (13)	C8—C9—C4	120.31 (13)
O1—C1—O2	116.53 (16)	C8—C9—H9	119.8
O1—C1—C2	126.89 (17)	C4—C9—H9	119.8
O2—C1—C2	116.57 (14)	O3—C11—H11A	109.5
C3—C2—C1	122.18 (16)	O3—C11—H11B	109.5
C3—C2—H2	118.9	H11A—C11—H11B	109.5
C1—C2—H2	118.9	O3—C11—H11C	109.5
C2—C3—C4	120.75 (15)	H11A—C11—H11C	109.5
C2—C3—H3	119.6	H11B—C11—H11C	109.5
C4—C3—H3	119.6	O4—C12—H12A	109.5
C5—C4—C9	119.03 (14)	O4—C12—H12B	109.5
C5—C4—C3	117.17 (14)	H12A—C12—H12B	109.5
C9—C4—C3	123.80 (13)	O4—C12—H12C	109.5
O2—C5—C4	121.63 (13)	H12A—C12—H12C	109.5
O2—C5—C6	116.89 (12)	H12B—C12—H12C	109.5
C4—C5—C6	121.47 (13)	O5—C13—H13A	109.5
O3—C6—C7	120.29 (13)	O5—C13—H13B	109.5
O3—C6—C5	120.68 (13)	H13A—C13—H13B	109.5
C7—C6—C5	118.95 (13)	O5—C13—H13C	109.5
O4—C7—C6	118.60 (13)	H13A—C13—H13C	109.5
O4—C7—C8	121.09 (13)	H13B—C13—H13C	109.5
C6—C7—C8	120.25 (13)
C5—O2—C1—O1	178.68 (14)	C4—C5—C6—C7	−2.6 (2)
C5—O2—C1—C2	−2.4 (2)	C12—O4—C7—C6	−110.92 (16)
O1—C1—C2—C3	179.80 (17)	C12—O4—C7—C8	71.85 (19)
O2—C1—C2—C3	1.0 (2)	O3—C6—C7—O4	7.7 (2)
C1—C2—C3—C4	0.9 (3)	C5—C6—C7—O4	−175.38 (13)
C2—C3—C4—C5	−1.5 (2)	O3—C6—C7—C8	−175.06 (13)
C2—C3—C4—C9	177.99 (15)	C5—C6—C7—C8	1.9 (2)
C1—O2—C5—C4	1.9 (2)	C13—O5—C8—C9	3.9 (2)
C1—O2—C5—C6	−179.19 (13)	C13—O5—C8—C7	−177.30 (14)
C9—C4—C5—O2	−179.40 (12)	O4—C7—C8—O5	−2.0 (2)
C3—C4—C5—O2	0.1 (2)	C6—C7—C8—O5	−179.21 (13)
C9—C4—C5—C6	1.7 (2)	O4—C7—C8—C9	176.87 (13)
C3—C4—C5—C6	−178.74 (13)	C6—C7—C8—C9	−0.3 (2)
C11—O3—C6—C7	−95.09 (18)	O5—C8—C9—C4	178.20 (14)
C11—O3—C6—C5	88.04 (18)	C7—C8—C9—C4	−0.6 (2)
O2—C5—C6—O3	−4.60 (19)	C5—C4—C9—C8	−0.1 (2)
C4—C5—C6—O3	174.30 (13)	C3—C4—C9—C8	−179.61 (14)
O2—C5—C6—C7	178.49 (12)