Atomic charges of cerbinal

The mol­ecule of the title compound, methyl 1-formyl-6-oxa-6H-indene-4-carboxyl­ate, C₁₁H₈O₄, is planar. There are weak C-H...O intramolecular interactions and an intermolecular hydrogen bond in the structure, and these influence the crystal packing.

S1. Comment

Plants of the Cerbera species are distributed widely in the coastal areas of Southeast Asia and countries surrounding the Indian Ocean. Several research groups have previously isolated various groups of compounds from Cerbera odollam and Cerbera manghas, such as cardenolide glycosides, lignans and normonoterpenoids (Abe et al., 1977, 1988a,b, 1989; Mahran et al., 1972; Malathy & Krishnamoorthy, 1978; Li et al., 1981; Rao et al., 1973, 1974; Yamauchi, 1987). Previously, cerbinal, a yellow compound having an iridoid skeleton, was reported to be isolated from the bark of Cerbera manghas (Abe et al., 1977) and was identified by spectroscopic methods but there is no information about its bioactivity. Recently, our group isolated cerbinal from the bark of Cerbera odollam. Preliminary testing against mycobacterium tuberculosis and breast-cancer cells exhibited moderate bioactivity.

The NMR spectrum and a resonance-theory prediction for the title compound, (I), suggested that the planarity of the molecule would allow electron delocalization from the ring O atom towards the five-membered ring. The planarity of the molecule was confirmed by the present structure determination. The electron delocalization was also confirmed by a theoretical calculation of the charge distributions using a PC version of MOPAC97, with an AM1 set of parameters. Full optimization of the ground-state gas-phase structure gives the results presented in Fig. 1. The dipole is directed from C4 towards, but slightly below, C5. This molecule might be useful as a simple model for stereoselectivity studies and as a starting material in other syntheses.

The title compound (Fig. 2) has a planar aromatic structure, with a highly conjugated π system. The bond lengths and angles show normal values (Table 1) (Allen et al., 1987); C1—C2 and C3—C4 show double-bond character. The fused five-membered and pyran rings are planar, with the C2 atom deviating by a maximum of 0.007 (3) Å. The mean plane through the fused five-membered ring forms a dihedral angle of 0.08 (16)° with the mean plane of the pyran ring. The carbomethoxyl and formyl groups are coplanar with their attached rings [C4—C10—O4—C11 = 179.1 (3)° and C7—C8—C9—O1 = 179.5 (3)°]. Two weak intramolecular C—H···O interactions form O4—C10—C4—C3—H3A and O2—C10—C4—C5—C6—H6A closed rings. The O atoms of the carbomethoxyl group are involved in these weak intramolecular interactions; C3—H3A···O4 [H3A···O4 = 2.3284 Å and C3—H3A···O4 = 103°] and C6—H6A···O2 [H6A···O2 = 2.5699 Å and C6—H6A···O2 = 109°], whereas the O atom of formyl group is involved in an intermolecular hydrogen bond (Table 2). In additon, two intermolecular π–π interactions between the centroids of five- and six-membered ring, i.e. Cg1 and Cg2, respectively, were also observed; Cg1···Cg2ⁱⁱ = 3.571 Å and Cg1···Cg2ⁱⁱⁱ = 3.575 Å [symmetry codes: (ii) -1 - x, 1/2 + y, 3/2 - z; (iii) -x, 1/2 + y, 3/2 - z]. These π–π interactions are analogous to charge-transfer interactions in complexes. The intermolecular C—H···O interactions interconnect the molecules into infinite molecular ribbons along the c axis and these ribbons are stacked along the a axis (Fig. 3). All these interactions, as well as van der Waals interactions, stabilize the molecular and acentric packing structure in the crystal.

Related literature

For related literature, see: Abe et al. (1977, 1988a, 1988b, 1989); Allen et al. (1987); Li et al. (1981); Mahran et al. (1972); Malathy & Krishnamoorthy (1978); Rao (1973); Rao et al. (1974); Yamauchi et al. (1987).

S2. Experimental

The air-dried bark of Cerbera odollam (1.50 kg) was ground and extracted by soaking in hexane (25 l) for 5 d at room temperature. The mixture was filtered and concentrated under reduced pressure to give the crude extracts. Upon concentration under reduced pressure, the hexane extract yielded precipitates which were filtered out and recrystallized from CHCl₃ to yield yellow needle-shaped crystals of compound (I) (m.p. 449–451 K).

S3. Refinement

H atoms were refined as riding with C—H distances of 0.93 and 0.96 Å.

Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 1990).

Figures

	Fig. 1. The MOPAC97-calculated charge distribution on the title compound. The direction of the calculated dipole moment (1.91 D) is indicated by the arrow.
	Fig. 2. The structure of the title compound showing 50% probability displacement ellipsoids and the atom-numbering scheme.
	Fig. 3. Packing diagram of the title compound viewed down the a axis. The hydrogen bonds are represented by dashed lines.

Methyl 1-formyl-6-oxa-6H-indene-4-carboxylate

Crystal data

C11H8O4	Dx = 1.479 Mg m^−3
Mr = 204.17	Melting point: 449-451 K K
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
a = 6.8622 (2) Å	Cell parameters from 3144 reflections
b = 10.8244 (1) Å	θ = 2.5–28.3°
c = 12.3446 (3) Å	µ = 0.11 mm^−1
V = 916.95 (4) Å^3	T = 293 K
Z = 4	Needle, yellow
F(000) = 424	0.46 × 0.16 × 0.14 mm

Data collection

Siemens SMART CCD area-detector diffractometer	900 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.083
Graphite monochromator	θmax = 28.3°, θmin = 2.5°
Detector resolution: 8.33 pixels mm^-1	h = −9→8
ω scans	k = −13→14
6418 measured reflections	l = −16→11
1323 independent reflections

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)] = 0.056	H-atom parameters constrained
wR(F^2) = 0.145	w = 1/[σ^2(Fo^2) + (0.0799P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 1.01	(Δ/σ)max = 0.036
1323 reflections	Δρmax = 0.35 e Å^−3
138 parameters	Δρmin = −0.45 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: 0.015 (5)

Special details

Experimental. Crystal decay was monitored by SAINT (Siemens, 1996) and was found to be negligible.

The data collection covered over a hemisphere of reciprocal space by a combination of three sets of exposures; each set had a different ϕ angle (0.88 and 180°) for the crystal and each exposure of 30 s covered 0.3° in ω. The crystal-to-detector distance was 4.023 cm and the detector swing angle was -35°. Coverage of the unit set is 99.5% complete.

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. The structure was solved by direct methods and refined by full-matrix least-squares techniques. After checking their presence in the difference map, all H-atoms were geometrically fixed and allowed to ride on their attached atoms with U_iso = 1.2U_eq for the attached atoms and U_iso = 1.5U_eq for methyl H-atoms. The methyl H-atoms were refined as rigid rotators.

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	0.1363 (5)	0.3189 (2)	0.16333 (19)	0.0618 (7)
O2	0.1100 (5)	0.12325 (19)	0.72795 (17)	0.0553 (7)
O3	0.1279 (4)	0.47706 (16)	0.49857 (15)	0.0410 (6)
O4	0.1314 (4)	0.3151 (2)	0.79461 (16)	0.0433 (6)
C1	0.1279 (5)	0.2860 (3)	0.4065 (2)	0.0287 (6)
C2	0.1313 (6)	0.4101 (3)	0.4055 (2)	0.0366 (7)
H2A	0.1361	0.4513	0.3394	0.044*
C3	0.1239 (6)	0.4169 (3)	0.5954 (2)	0.0356 (7)
H3A	0.1218	0.4641	0.6583	0.043*
C4	0.1229 (5)	0.2919 (2)	0.6052 (2)	0.0276 (6)
C5	0.1243 (5)	0.2191 (2)	0.5093 (2)	0.0275 (6)
C6	0.1225 (5)	0.0940 (3)	0.4859 (2)	0.0360 (7)
H6A	0.1193	0.0301	0.5362	0.043*
C7	0.1263 (6)	0.0807 (3)	0.3717 (2)	0.0398 (7)
H7A	0.1266	0.0054	0.3354	0.048*
C8	0.1296 (5)	0.1955 (3)	0.3213 (2)	0.0337 (7)
C9	0.1345 (6)	0.2176 (3)	0.2059 (3)	0.0445 (8)
H9A	0.1365	0.1489	0.1606	0.053*
C10	0.1214 (5)	0.2336 (3)	0.7136 (2)	0.0339 (6)
C11	0.1271 (7)	0.2634 (3)	0.9036 (2)	0.0490 (9)
H11A	0.1352	0.3291	0.9557	0.074*
H11B	0.2355	0.2084	0.9130	0.074*
H11C	0.0076	0.2188	0.9139	0.074*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0816 (18)	0.0745 (16)	0.0293 (12)	0.004 (2)	0.0014 (14)	0.0078 (12)
O2	0.0955 (19)	0.0390 (12)	0.0316 (12)	−0.0035 (16)	−0.0027 (17)	0.0100 (10)
O3	0.0637 (14)	0.0296 (9)	0.0298 (11)	−0.0017 (12)	−0.0017 (14)	0.0028 (9)
O4	0.0647 (13)	0.0451 (11)	0.0201 (10)	−0.0038 (15)	−0.0014 (12)	0.0009 (9)
C1	0.0267 (13)	0.0351 (13)	0.0242 (13)	−0.0013 (18)	−0.0014 (14)	0.0001 (12)
C2	0.0476 (16)	0.0380 (15)	0.0242 (14)	0.000 (2)	0.0031 (17)	0.0060 (12)
C3	0.0500 (16)	0.0321 (14)	0.0246 (14)	−0.004 (2)	−0.0007 (18)	−0.0012 (12)
C4	0.0288 (13)	0.0312 (13)	0.0227 (13)	−0.0011 (16)	−0.0002 (15)	0.0012 (11)
C5	0.0235 (12)	0.0333 (13)	0.0256 (13)	0.0040 (17)	0.0010 (15)	0.0000 (13)
C6	0.0415 (15)	0.0311 (13)	0.0354 (16)	−0.0019 (17)	−0.0005 (19)	−0.0024 (13)
C7	0.0441 (16)	0.0403 (16)	0.0349 (16)	0.0051 (19)	−0.0014 (19)	−0.0118 (13)
C8	0.0327 (14)	0.0436 (16)	0.0248 (13)	−0.0013 (19)	0.0015 (15)	−0.0036 (12)
C9	0.0468 (18)	0.0605 (19)	0.0261 (15)	−0.001 (2)	0.0032 (18)	−0.0062 (16)
C10	0.0360 (15)	0.0414 (16)	0.0243 (13)	−0.0023 (18)	−0.0012 (18)	0.0037 (12)
C11	0.064 (2)	0.063 (2)	0.0195 (14)	−0.004 (2)	−0.0014 (18)	0.0049 (13)

Geometric parameters (Å, º)

O1—C9	1.217 (4)	C4—C5	1.423 (4)
O2—C10	1.210 (3)	C4—C10	1.479 (4)
O3—C2	1.359 (3)	C5—C6	1.384 (4)
O3—C3	1.361 (3)	C6—C7	1.417 (4)
O4—C10	1.336 (4)	C6—H6A	0.9300
O4—C11	1.457 (4)	C7—C8	1.390 (4)
C1—C2	1.344 (4)	C7—H7A	0.9300
C1—C8	1.438 (4)	C8—C9	1.445 (4)
C1—C5	1.461 (4)	C9—H9A	0.9300
C2—H2A	0.9300	C11—H11A	0.9600
C3—C4	1.359 (4)	C11—H11B	0.9600
C3—H3A	0.9300	C11—H11C	0.9600
C2—O3—C3	119.2 (2)	C7—C6—H6A	126.1
C10—O4—C11	115.9 (2)	C8—C7—C6	110.8 (3)
C2—C1—C8	132.4 (3)	C8—C7—H7A	124.6
C2—C1—C5	120.3 (3)	C6—C7—H7A	124.6
C8—C1—C5	107.3 (2)	C7—C8—C1	106.3 (2)
C1—C2—O3	121.6 (2)	C7—C8—C9	126.1 (3)
C1—C2—H2A	119.2	C1—C8—C9	127.6 (3)
O3—C2—H2A	119.2	O1—C9—C8	125.1 (3)
C4—C3—O3	123.7 (3)	O1—C9—H9A	117.5
C4—C3—H3A	118.1	C8—C9—H9A	117.5
O3—C3—H3A	118.1	O2—C10—O4	123.1 (3)
C3—C4—C5	118.5 (2)	O2—C10—C4	123.7 (3)
C3—C4—C10	120.4 (2)	O4—C10—C4	113.2 (2)
C5—C4—C10	121.1 (2)	O4—C11—H11A	109.5
C6—C5—C4	135.6 (3)	O4—C11—H11B	109.5
C6—C5—C1	107.7 (3)	H11A—C11—H11B	109.5
C4—C5—C1	116.7 (2)	O4—C11—H11C	109.5
C5—C6—C7	107.8 (3)	H11A—C11—H11C	109.5
C5—C6—H6A	126.1	H11B—C11—H11C	109.5

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C11—H11A···O1^i	0.96	2.57	3.262 (3)	130

Symmetry code: (i) x, y, z+1.