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Acta Crystallogr Sect E Struct Rep Online. 2008 August 1; 64(Pt 8): o1538.
Published online 2008 July 19. doi:  10.1107/S1600536808021752
PMCID: PMC2962163

Arctigenin: a lignan from Arctium lappa

Abstract

The title compound {systematic name: (3R-trans)-4-[(3,4-dimethoxy­phen­yl)meth­yl]-3-[(4-hydr­oxy-3-methoxy­phen­yl)meth­yl]-4,5-dihydrofuran-2(3H)-one}, C21H24O6, has a dibenz­yl­butyrolactone skeleton. The two aromatic rings are inclined at a dihedral angle of 68.75 (7)° with respect to each other. The lactone ring adopts an envelope conformation. A series of O—H(...)O and C—H(...)O hydrogen bonds contribute to the stabilization of the crystal packing. The absolute configuration was assigned on the basis of the published literature.

Related literature

For related literature, see: Awale et al. (2006 [triangle]). For a similar structure, see: Bruno-Colmenárez et al. (2007 [triangle]).

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Object name is e-64-o1538-scheme1.jpg

Experimental

Crystal data

  • C21H24O6
  • M r = 372.40
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-64-o1538-efi1.jpg
  • a = 9.4845 (19) Å
  • b = 10.065 (2) Å
  • c = 19.915 (4) Å
  • V = 1901.2 (7) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.10 mm−1
  • T = 113 (2) K
  • 0.14 × 0.12 × 0.10 mm

Data collection

  • Rigaku Saturn CCD area-detector diffractometer
  • Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2005 [triangle]) T min = 0.987, T max = 0.991
  • 13910 measured reflections
  • 2581 independent reflections
  • 2449 reflections with I > 2σ(I)
  • R int = 0.037

Refinement

  • R[F 2 > 2σ(F 2)] = 0.032
  • wR(F 2) = 0.079
  • S = 1.06
  • 2581 reflections
  • 251 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.15 e Å−3

Data collection: CrystalClear (Rigaku/MSC, 2005 [triangle]); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2005 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808021752/bt2739sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808021752/bt2739Isup2.hkl

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

supplementary crystallographic information

Comment

Arctigenin has been identified as an antitumor agent with the ability to eliminate the tolerance of cancer cells to nutrient strarvation (Awale et al., 2006).

The title compound has a dibenzylbutyrolactone skeleton (Fig. 1). The two aromatic rings have a dihedral angle of 68.75 (7)°. The lactone ring adopts an envelope conformation. A series of O—H···O and C—H···O hydrogen bonds contribute to the stabilization of the crystal packing (Table 1).

Experimental

Arctigenin was isolated from Chinese medicine Arctium lappa. Crystal blocks were obtained by natural evaporation of a methanolic solution.

Refinement

In the absence of anomalous scatterers Friedel pairs were merged. The absolute configuration was set according to the literature (Awale et al., 2006). The O-bound H atom was located in a difference map and freely refined. All other H atoms were positioned geometrically and refined as riding atoms, with U(H) = 1.2 Ueq(CH and CH2) and C—H ranging from 0.95–1.0Å or U(H) = 1.5 Ueq(CH3) and Cmethyl—H =0.99 Å. The methyl groups were allowed to rotate but not to tip.

Figures

Fig. 1.
The molecular structure of (I) with the atom-numbering scheme and 50% probability displacement ellipsoids.

Crystal data

C21H24O6F000 = 792
Mr = 372.40Dx = 1.301 Mg m3
Orthorhombic, P212121Mo Kα radiation λ = 0.71073 Å
Hall symbol: P 2ac 2abCell parameters from 5995 reflections
a = 9.4845 (19) Åθ = 2.3–27.9º
b = 10.065 (2) ŵ = 0.10 mm1
c = 19.915 (4) ÅT = 113 (2) K
V = 1901.2 (7) Å3Block, colourless
Z = 40.14 × 0.12 × 0.10 mm

Data collection

Rigaku Saturn CCD area-detector diffractometer2581 independent reflections
Radiation source: rotating anode2449 reflections with I > 2σ(I)
Monochromator: confocalRint = 0.037
Detector resolution: 7.31 pixels mm-1θmax = 27.8º
T = 113(2) Kθmin = 2.1º
ω scansh = −12→12
Absorption correction: multi-scan(CrystalClear; Rigaku/MSC, 2005)k = −11→13
Tmin = 0.987, Tmax = 0.991l = −26→16
13910 measured reflections

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.032  w = 1/[σ2(Fo2) + (0.0475P)2 + 0.1518P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.079(Δ/σ)max = 0.001
S = 1.06Δρmax = 0.20 e Å3
2581 reflectionsΔρmin = −0.15 e Å3
251 parametersExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.032 (3)
Secondary atom site location: difference Fourier map

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 (Å2)

xyzUiso*/Ueq
O10.07380 (13)0.28900 (13)0.73971 (6)0.0287 (3)
O20.23820 (12)0.17843 (12)0.82576 (5)0.0228 (3)
O30.38552 (14)0.79457 (13)0.92594 (6)0.0329 (3)
O40.34335 (15)0.69713 (14)1.02429 (6)0.0362 (3)
O50.96166 (13)0.15373 (12)0.87738 (6)0.0226 (3)
H51.036 (2)0.195 (2)0.8592 (10)0.034*
O61.04322 (12)0.40766 (12)0.88872 (6)0.0241 (3)
C10.44649 (17)0.48348 (17)0.79244 (7)0.0196 (3)
C20.35798 (18)0.53926 (18)0.74441 (8)0.0230 (3)
H20.38270.62190.72460.028*
C30.23339 (18)0.47622 (18)0.72471 (8)0.0247 (4)
H30.17470.51590.69170.030*
C40.19554 (17)0.35649 (18)0.75310 (8)0.0226 (3)
C50.28519 (17)0.29699 (17)0.80056 (7)0.0196 (3)
C60.40879 (17)0.35955 (17)0.81937 (7)0.0192 (3)
H60.46930.31800.85110.023*
C7−0.0319 (2)0.3594 (2)0.70329 (11)0.0412 (5)
H7A−0.00030.37300.65690.062*
H7B−0.04850.44580.72460.062*
H7C−0.11960.30790.70330.062*
C80.32263 (19)0.11735 (19)0.87673 (9)0.0276 (4)
H8A0.33050.17740.91530.041*
H8B0.41680.09880.85880.041*
H8C0.27840.03400.89100.041*
C90.57710 (16)0.55340 (17)0.81719 (7)0.0209 (3)
H9A0.61650.60680.77990.025*
H9B0.64820.48550.82940.025*
C100.55425 (17)0.64553 (16)0.87818 (8)0.0213 (3)
H100.64790.68270.89160.026*
C110.4557 (2)0.76166 (18)0.86314 (9)0.0287 (4)
H11A0.51000.83890.84640.034*
H11B0.38560.73610.82860.034*
C120.39834 (18)0.69247 (18)0.96988 (8)0.0257 (4)
C130.48662 (16)0.58224 (16)0.94058 (8)0.0192 (3)
H130.42290.50860.92590.023*
C140.58852 (17)0.52865 (17)0.99399 (7)0.0211 (3)
H14A0.64350.60351.01290.025*
H14B0.53340.48841.03100.025*
C150.68864 (17)0.42650 (16)0.96613 (8)0.0194 (3)
C160.65324 (16)0.29296 (17)0.96147 (7)0.0205 (3)
H160.56510.26330.97850.025*
C170.74541 (16)0.20166 (17)0.93208 (7)0.0206 (3)
H170.72010.11050.92950.025*
C180.87370 (16)0.24419 (16)0.90675 (7)0.0188 (3)
C190.91196 (16)0.37751 (17)0.91323 (7)0.0187 (3)
C200.82073 (16)0.46753 (17)0.94260 (7)0.0192 (3)
H200.84790.55800.94690.023*
C211.08409 (19)0.54337 (18)0.89079 (10)0.0329 (4)
H21A1.09050.57260.93760.049*
H21B1.01390.59730.86710.049*
H21C1.17610.55380.86910.049*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0263 (6)0.0277 (7)0.0322 (6)−0.0037 (6)−0.0070 (5)0.0021 (5)
O20.0269 (6)0.0178 (6)0.0237 (5)0.0014 (5)0.0016 (5)0.0025 (4)
O30.0430 (7)0.0206 (6)0.0353 (7)0.0115 (6)0.0054 (6)0.0006 (5)
O40.0416 (7)0.0322 (8)0.0349 (7)0.0107 (7)0.0139 (6)−0.0030 (6)
O50.0210 (5)0.0180 (6)0.0288 (6)0.0004 (5)0.0004 (5)−0.0031 (5)
O60.0187 (5)0.0194 (6)0.0342 (6)−0.0017 (5)0.0050 (5)−0.0041 (5)
C10.0205 (7)0.0212 (8)0.0171 (7)0.0035 (7)0.0033 (6)0.0004 (6)
C20.0258 (8)0.0209 (8)0.0222 (8)0.0017 (7)0.0033 (6)0.0036 (6)
C30.0247 (8)0.0270 (9)0.0222 (8)0.0030 (7)−0.0030 (6)0.0041 (7)
C40.0225 (7)0.0241 (9)0.0214 (7)0.0008 (7)−0.0002 (6)−0.0028 (6)
C50.0250 (8)0.0159 (7)0.0179 (7)0.0034 (7)0.0053 (6)0.0007 (6)
C60.0218 (7)0.0200 (8)0.0158 (7)0.0060 (7)0.0023 (6)−0.0002 (6)
C70.0310 (10)0.0340 (11)0.0584 (12)−0.0034 (10)−0.0192 (9)0.0041 (10)
C80.0271 (8)0.0259 (9)0.0297 (9)0.0047 (8)0.0052 (7)0.0108 (7)
C90.0193 (7)0.0229 (8)0.0206 (7)0.0009 (7)0.0030 (6)0.0030 (6)
C100.0223 (7)0.0177 (8)0.0237 (7)−0.0003 (7)0.0015 (6)0.0014 (6)
C110.0358 (9)0.0193 (8)0.0308 (9)0.0049 (8)0.0032 (7)0.0029 (7)
C120.0250 (8)0.0215 (8)0.0307 (8)0.0035 (7)0.0022 (7)−0.0025 (7)
C130.0187 (7)0.0162 (8)0.0227 (8)0.0006 (6)0.0017 (6)−0.0015 (6)
C140.0213 (7)0.0222 (8)0.0198 (7)0.0007 (7)0.0028 (6)0.0000 (6)
C150.0208 (7)0.0223 (8)0.0149 (7)0.0024 (7)−0.0018 (6)0.0008 (6)
C160.0192 (7)0.0220 (8)0.0204 (7)−0.0012 (7)0.0001 (6)0.0027 (6)
C170.0218 (7)0.0182 (8)0.0218 (7)−0.0020 (7)−0.0035 (6)0.0019 (6)
C180.0193 (7)0.0182 (8)0.0190 (7)0.0037 (6)−0.0036 (6)−0.0017 (6)
C190.0163 (7)0.0217 (8)0.0183 (7)−0.0010 (6)−0.0018 (6)0.0009 (6)
C200.0204 (7)0.0186 (8)0.0188 (7)−0.0003 (7)−0.0023 (6)−0.0009 (6)
C210.0260 (9)0.0208 (9)0.0519 (11)−0.0064 (8)0.0114 (8)−0.0055 (8)

Geometric parameters (Å, °)

O1—C41.366 (2)C9—C101.543 (2)
O1—C71.426 (2)C9—H9A0.9900
O2—C51.369 (2)C9—H9B0.9900
O2—C81.432 (2)C10—C111.526 (2)
O3—C121.355 (2)C10—C131.537 (2)
O3—C111.455 (2)C10—H101.0000
O4—C121.203 (2)C11—H11A0.9900
O5—C181.3665 (19)C11—H11B0.9900
O5—H50.90 (2)C12—C131.507 (2)
O6—C191.3712 (19)C13—C141.535 (2)
O6—C211.421 (2)C13—H131.0000
C1—C21.391 (2)C14—C151.506 (2)
C1—C61.404 (2)C14—H14A0.9900
C1—C91.508 (2)C14—H14B0.9900
C2—C31.398 (2)C15—C161.389 (2)
C2—H20.9500C15—C201.400 (2)
C3—C41.379 (2)C16—C171.397 (2)
C3—H30.9500C16—H160.9500
C4—C51.405 (2)C17—C181.385 (2)
C5—C61.383 (2)C17—H170.9500
C6—H60.9500C18—C191.396 (2)
C7—H7A0.9800C19—C201.383 (2)
C7—H7B0.9800C20—H200.9500
C7—H7C0.9800C21—H21A0.9800
C8—H8A0.9800C21—H21B0.9800
C8—H8B0.9800C21—H21C0.9800
C8—H8C0.9800
C4—O1—C7116.50 (15)C9—C10—H10108.1
C5—O2—C8116.88 (13)O3—C11—C10106.62 (13)
C12—O3—C11109.96 (13)O3—C11—H11A110.4
C18—O5—H5109.9 (15)C10—C11—H11A110.4
C19—O6—C21116.75 (13)O3—C11—H11B110.4
C2—C1—C6117.88 (16)C10—C11—H11B110.4
C2—C1—C9122.16 (15)H11A—C11—H11B108.6
C6—C1—C9119.94 (14)O4—C12—O3120.85 (17)
C1—C2—C3121.34 (16)O4—C12—C13128.17 (17)
C1—C2—H2119.3O3—C12—C13110.98 (13)
C3—C2—H2119.3C12—C13—C14109.88 (13)
C4—C3—C2120.12 (15)C12—C13—C10103.87 (13)
C4—C3—H3119.9C14—C13—C10116.31 (13)
C2—C3—H3119.9C12—C13—H13108.8
O1—C4—C3125.08 (15)C14—C13—H13108.8
O1—C4—C5115.51 (16)C10—C13—H13108.8
C3—C4—C5119.40 (16)C15—C14—C13112.45 (12)
O2—C5—C6125.01 (14)C15—C14—H14A109.1
O2—C5—C4114.90 (15)C13—C14—H14A109.1
C6—C5—C4120.07 (15)C15—C14—H14B109.1
C5—C6—C1121.14 (15)C13—C14—H14B109.1
C5—C6—H6119.4H14A—C14—H14B107.8
C1—C6—H6119.4C16—C15—C20118.66 (15)
O1—C7—H7A109.5C16—C15—C14122.23 (15)
O1—C7—H7B109.5C20—C15—C14119.10 (15)
H7A—C7—H7B109.5C15—C16—C17120.90 (15)
O1—C7—H7C109.5C15—C16—H16119.6
H7A—C7—H7C109.5C17—C16—H16119.6
H7B—C7—H7C109.5C18—C17—C16119.94 (15)
O2—C8—H8A109.5C18—C17—H17120.0
O2—C8—H8B109.5C16—C17—H17120.0
H8A—C8—H8B109.5O5—C18—C17119.10 (15)
O2—C8—H8C109.5O5—C18—C19121.42 (15)
H8A—C8—H8C109.5C17—C18—C19119.46 (15)
H8B—C8—H8C109.5O6—C19—C20125.01 (15)
C1—C9—C10114.99 (13)O6—C19—C18114.57 (14)
C1—C9—H9A108.5C20—C19—C18120.42 (15)
C10—C9—H9A108.5C19—C20—C15120.55 (15)
C1—C9—H9B108.5C19—C20—H20119.7
C10—C9—H9B108.5C15—C20—H20119.7
H9A—C9—H9B107.5O6—C21—H21A109.5
C11—C10—C13102.73 (13)O6—C21—H21B109.5
C11—C10—C9113.07 (13)H21A—C21—H21B109.5
C13—C10—C9116.48 (13)O6—C21—H21C109.5
C11—C10—H10108.1H21A—C21—H21C109.5
C13—C10—H10108.1H21B—C21—H21C109.5
C6—C1—C2—C31.7 (2)O3—C12—C13—C14137.62 (14)
C9—C1—C2—C3−176.52 (14)O4—C12—C13—C10−167.32 (18)
C1—C2—C3—C40.2 (2)O3—C12—C13—C1012.54 (18)
C7—O1—C4—C3−11.9 (2)C11—C10—C13—C12−21.56 (16)
C7—O1—C4—C5167.03 (16)C9—C10—C13—C12−145.71 (14)
C2—C3—C4—O1177.18 (15)C11—C10—C13—C14−142.41 (14)
C2—C3—C4—C5−1.7 (2)C9—C10—C13—C1493.44 (17)
C8—O2—C5—C61.7 (2)C12—C13—C14—C15−174.92 (14)
C8—O2—C5—C4−176.99 (13)C10—C13—C14—C15−57.32 (19)
O1—C4—C5—O21.0 (2)C13—C14—C15—C16−85.45 (19)
C3—C4—C5—O2179.99 (14)C13—C14—C15—C2093.00 (17)
O1—C4—C5—C6−177.79 (13)C20—C15—C16—C17−1.9 (2)
C3—C4—C5—C61.2 (2)C14—C15—C16—C17176.52 (14)
O2—C5—C6—C1−177.86 (14)C15—C16—C17—C18−0.4 (2)
C4—C5—C6—C10.8 (2)C16—C17—C18—O5−179.14 (13)
C2—C1—C6—C5−2.2 (2)C16—C17—C18—C192.5 (2)
C9—C1—C6—C5176.05 (13)C21—O6—C19—C20−3.5 (2)
C2—C1—C9—C1089.17 (18)C21—O6—C19—C18176.67 (15)
C6—C1—C9—C10−89.02 (18)O5—C18—C19—O6−0.7 (2)
C1—C9—C10—C11−63.25 (19)C17—C18—C19—O6177.63 (13)
C1—C9—C10—C1355.42 (19)O5—C18—C19—C20179.43 (14)
C12—O3—C11—C10−17.30 (19)C17—C18—C19—C20−2.2 (2)
C13—C10—C11—O323.87 (17)O6—C19—C20—C15−179.96 (14)
C9—C10—C11—O3150.24 (14)C18—C19—C20—C15−0.1 (2)
C11—O3—C12—O4−177.32 (17)C16—C15—C20—C192.2 (2)
C11—O3—C12—C132.8 (2)C14—C15—C20—C19−176.31 (14)
O4—C12—C13—C14−42.2 (2)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O5—H5···O2i0.90 (2)2.04 (2)2.8280 (17)146 (2)
O5—H5···O60.90 (2)2.22 (2)2.6799 (18)111.7 (17)
O5—H5···O1i0.90 (2)2.58 (2)3.2406 (18)130.8 (16)
C3—H3···O5ii0.952.343.278 (2)168
C14—H14A···O4iii0.992.863.687 (2)142
C14—H14B···O5iv0.992.423.373 (2)162
C20—H20···O4iii0.952.533.446 (2)162

Symmetry codes: (i) x+1, y, z; (ii) −x+1, y+1/2, −z+3/2; (iii) x+1/2, −y+3/2, −z+2; (iv) x−1/2, −y+1/2, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT2739).

References

  • Awale, S., Lu, J., Kalaumi, S. K., Kurashima, Y., Tezuka, Y., Kadaota, S. & Esumi, H. (2006). Cancer Res.66, 1751–1757. [PubMed]
  • Bruno-Colmenárez, J., Usubillaga, A., Khouri, N. & Díaz de Delgado, G. (2007). Acta Cryst. E63, o2046–o2047.
  • Rigaku/MSC (2005). CrystalClear and CrystalStructure Rigaku Corporation, Tokyo, Japan.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography