Absolute configuration of micromelin

Hoong-Kun Fun; Ittipon Siridechakorn; Surat Laphookhieo; Suchada Chantrapromma

doi:10.1107/S1600536811022720

. 2011 Jun 18;67(Pt 7):o1706–o1707. doi: 10.1107/S1600536811022720

Absolute configuration of micromelin

Hoong-Kun Fun ^a,^*,^‡, Ittipon Siridechakorn ^b, Surat Laphookhieo ^b, Suchada Chantrapromma ^c,^§

PMCID: PMC3151812 PMID: 21837101

Abstract

The title compound {systematic name: 7-methoxy-6-[(1R,2R,5R)-5-methyl-4-oxo-3,6-dioxabicyclo[3.1.0]hexan-2-yl]-2H-chromen-2-one}, C₁₅H₁₂O₆, is a coumarin, which was isolated from the roots of Micromelum glanduliferum. There are two molecules in the asymmetric unit with slight differences in bond angles. In both molecules, the furan ring adopts a flattened envelope conformation. In the crystal, molecules are linked by weak C—H⋯O interactions into chains along the a axis. Aromatic π–π stacking interactions with centroid–centroid distances in the range 3.6995 (11)–3.8069 (11) Å and C⋯O short contacts [3.030 (2)–3.171 (3) Å] also occur.

Related literature

For bond-length data, see: Allen et al. (1987 ▶). For ring conformations, see: Cremer & Pople (1975 ▶). For background to plants in the Rutaceae family, coumarins and their activities, see: Ito et al. (1997 ▶, 2000 ▶); Kamperdick et al. (1999 ▶); Rahmani et al. (2003 ▶); Tangyuenyongwatthana et al. (1992 ▶); Tantishaiyakul et al. (1986 ▶); Tantivatana et al. (1983 ▶); Thuy et al. (1999 ▶). For the stability of the temperature controller used in the data collection, see Cosier & Glazer, (1986 ▶).

Experimental

Crystal data

C₁₅H₁₂O₆
M _r = 288.25
Monoclinic,
a = 6.7514 (2) Å
b = 23.7537 (8) Å
c = 8.0730 (3) Å
β = 90.000 (1)°
V = 1294.67 (8) Å³
Z = 4
Cu Kα radiation
μ = 0.98 mm⁻¹
T = 100 K
0.56 × 0.22 × 0.19 mm

Data collection

Bruker APEX DUO CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.609, T _max = 0.838
21511 measured reflections
4392 independent reflections
4392 reflections with I > 2σ(I)
R _int = 0.028

Refinement

R[F ² > 2σ(F ²)] = 0.022
wR(F ²) = 0.059
S = 1.06
4392 reflections
384 parameters
1 restraint
H-atom parameters constrained
Δρ_max = 0.13 e Å⁻³
Δρ_min = −0.13 e Å⁻³
Absolute structure: Flack (1983 ▶), 2632 Friedel pairs
Flack parameter: 0.06 (10)

Data collection: APEX2 (Bruker, 2009 ▶); cell refinement: SAINT (Bruker, 2009 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536811022720/hb5904sup1.cif

e-67-o1706-sup1.cif^{(28.3KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536811022720/hb5904Isup2.hkl

e-67-o1706-Isup2.hkl^{(215.2KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536811022720/hb5904Isup3.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
C3B—H3B⋯O4Aⁱ	0.93	2.60	3.450 (2)	152
C5A—H5A⋯O2Aⁱⁱ	0.93	2.60	3.518 (3)	171
C5B—H5B⋯O2Bⁱⁱⁱ	0.93	2.57	3.493 (2)	173
C8A—H8A⋯O5Aⁱⁱⁱ	0.93	2.58	3.440 (3)	155
C8B—H8B⋯O5Bⁱⁱ	0.93	2.42	3.298 (3)	157
C10A—H10A⋯O2B	0.98	2.35	3.186 (2)	142
C10B—H10B⋯O2A^iv	0.98	2.29	3.171 (3)	150
C14B—H14E⋯O4A^v	0.96	2.49	3.423 (3)	163
C15B—H15D⋯O4A^v	0.96	2.46	3.405 (2)	166

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) .

Acknowledgments

SL thanks the Thailand Research Fund (grant No. RSA5280011) for financial support. IS thanks Mae Fah Luang University for an MSc graduate student research grant. SC thanks the Prince of Songkla University for financial support through the Crystal Materials Research Unit (CMRU). The authors also thank Universiti Sains Malaysia for the Research University Grant No. 1001/PFIZIK/811160.

supplementary crystallographic information

Comment

Coumarins are important secondary metabolites which occur commonly in the Rutaceae family. Many of them have been isolated from several genera of Rutaceae especially from Micromelum and Clausena genera (Ito et al., 1997; 2000; Kamperdick et al., 1999; Rahmani et al., 2003; Tangyuenyongwatthana et al., 1992; Tantishaiyakul et al., 1986; Thuy et al., 1999) and some of these compounds show interesting biological activities (Tantishaiyakul et al., 1986; Tantivatana et al., 1983). Although Micromelum glanduliferum is one of Rutaceae plants, however, no phytochemical investigation has been reported. As part of our continuing studies of the phytochemical constituents and bioactive compounds in Thai medicinal plants, we report herein the crystal structure of the title compound which was isolated from the roots of M. glanduliferum which were collected from Nongkai Province in the northeastern part of Thailand.

There are two crystallograpic independent molecules A and B in the asymmetric unit of (I), C₁₅H₁₂O₆, (Fig. 1) with the same conformation but with slight differences in bond angles. In the structure of (I), the furan ring (C10–C13/O3) is in a flattened envelope conformation with the puckering atom O3 of 0.064 (1) Å, and puckering parameter Q = 0.0991 (18) Å and φ = 9.2 (11)° (Cremer & Pople, 1975) for molecule A and the corresponding values are -0.053 (1) Å, 0.0820 (19) Å and φ = 10.1 (15)° for molecule B. The benzene and dihydro-pyran ring system (C1–C9/O1) is planar with the r.m.s. 0.0089 (2) Å for molecule A [0.0149 (2) Å for molecule B]. The methoxy group is almost planarly attached to the benzene ring with the torsion angle C15–O6–C7–C8 = 2.3 (3)° for molecule A and 2.6 (3)° for molecule B. The orientation of the oxirane ring (C10–C13–O5) can be indicated by the dihedral angle between the furan and oxirane rings being 79.46 (15)° for molecule A [79.48 (16)° for molecule B]. The bond distances in (I) are within normal ranges (Allen et al., 1987). The absolute configuration at atoms C10, C11 and C13 or positions 1, 2 and 5 of the micromelin are R,R,R configurations.

In the crystal (Fig. 2), molecules are linked by C—H···O weak interactions into 2D chains along the a axis. π–π interactions were observed with centroid···centroid distances: Cg₁···Cg₃ = 3.7698 (7) Å; Cg₂···Cg₅ = 3.7102 (11) Å; Cg₃···Cg₄ = 3.6995 (11) Å and 3.7666 (11) Å (symmetry code: 1+x, y, z); Cg₁, Cg₂, Cg₃, Cg₄ and Cg₅ are the centroids of C10A–C13A/O3A, C1A–C4A/C9A/O1A, C4A–C9A, C1B–C4B/C9B/O1B and C4B–C9B rings, respectively. C···O [3.030 (2)-3.171 (3) Å] short contacts were also observed.

Experimental

The chemical contents of the roots of M. glanduliferum (5.25 kg) were successively extracted with CH₂Cl₂ over the period of 3 days at room temperature. Removal the solvent under reduced pressure provided CH₂Cl₂ extract which were subjected to quick column chromatography (QCC) over silica gel and eluted with a gradient of n-hexane-EtOAc (100% n-hexane to 100% EtOAc) to provide nine fractions (A-I). Fraction F (6.23 g) was washed with n-hexane and recrystallized from CH₂Cl₂/CH₃OH (1:4 v/v) to give colourless needles of the title compound. Mp 491.0-492.2 K (decompose).