Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536803001119/lh6023sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536803001119/lh6023Isup2.hkl |
CCDC reference: 204705
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.005 Å
- R factor = 0.066
- wR factor = 0.181
- Data-to-parameter ratio = 12.1
checkCIF results
No syntax errors found ADDSYM reports no extra symmetry
Alert Level C:
REFLT_03 From the CIF: _diffrn_reflns_theta_max 29.44 From the CIF: _reflns_number_total 1651 TEST2: Reflns within _diffrn_reflns_theta_max Count of symmetry unique reflns 1822 Completeness (_total/calc) 90.61% Alert C: < 95% complete General Notes
REFLT_03 From the CIF: _diffrn_reflns_theta_max 29.44 From the CIF: _reflns_number_total 1651 From the CIF: _diffrn_reflns_limit_ max hkl 26. 5. 13. From the CIF: _diffrn_reflns_limit_ min hkl -29. -7. -15. TEST1: Expected hkl limits for theta max Calculated maximum hkl 31. 7. 15. Calculated minimum hkl -31. -7. -15. ALERT: Expected hkl max differ from CIF values REFLT_03 From the CIF: _diffrn_reflns_theta_max 29.44 From the CIF: _reflns_number_total 1651 Count of symmetry unique reflns 1822 Completeness (_total/calc) 90.61% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 0 Fraction of Friedel pairs measured 0.000 Are heavy atom types Z>Si present no Please check that the estimate of the number of Friedel pairs is correct. If it is not, please give the correct count in the _publ_section_exptl_refinement section of the submitted CIF.
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
1 Alert Level C = Please check
Fresh plant (14 g) was gound and was extracted with methanol 3 times in a row. The combined extract was concentrated to a semi-solid mass. Then it was purified by removing fatty material and carotenoids by extracting it with methanol and petroleum ether alternatively. The extract was then subjected to column chromatography with silica gel (60–80 mesh) as stationary phase and n-hexane with an increasing amount of ethyl acetate as mobile phase. Online thin-layer chromatography was performed for each fraction, Phyllanthin was identified by the blue–green colour it gave when sprayed with 10% methanolic sulfuric acid and heated at 358 K for 5 min and compared with a reference. Standard phyllanthin was recrystallized from n-hexane.
The H atoms were positioned geometrically and were treated as riding on their parent C atom, with aromatic C—H distance of 0.93 Å, methoxy C—H distance 0.96 Å and methylene C—H distance of 0.97 Å. Due to the lack of anomalous scatterers the absolute configuration was not determined from the X-ray diffraction data and Friedels pairs were merged. The absolute configuration of (I) is unknown.
Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 1990); software used to prepare material for publication: SHELXL97 and PARST (Nardelli, 1995).
Fig. 1. The molecular structure of (I), showing 30% probability displacement ellipsoids. | |
Fig. 2. Packing of the molecule viewed down the b axis. |
C24H34O6 | F(000) = 452 |
Mr = 418.51 | Dx = 1.166 Mg m−3 |
Monoclinic, C2 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: C 2y | Cell parameters from 2451 reflections |
a = 22.6091 (7) Å | θ = 2.9–25.1° |
b = 5.3506 (2) Å | µ = 0.08 mm−1 |
c = 11.0871 (4) Å | T = 293 K |
β = 117.328 (1)° | Block, colourless |
V = 1191.54 (7) Å3 | 0.20 × 0.20 × 0.20 mm |
Z = 2 |
Siemens SMART CCD diffractometer | 1138 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.072 |
Graphite monochromator | θmax = 29.4°, θmin = 2.1° |
ω scans | h = −29→26 |
4350 measured reflections | k = −7→5 |
1651 independent reflections | l = −15→13 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.066 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.181 | H-atom parameters constrained |
S = 1.02 | w = 1/[σ2(Fo2) + (0.1P)2] where P = (Fo2 + 2Fc2)/3 |
1651 reflections | (Δ/σ)max < 0.001 |
136 parameters | Δρmax = 0.22 e Å−3 |
1 restraint | Δρmin = −0.24 e Å−3 |
C24H34O6 | V = 1191.54 (7) Å3 |
Mr = 418.51 | Z = 2 |
Monoclinic, C2 | Mo Kα radiation |
a = 22.6091 (7) Å | µ = 0.08 mm−1 |
b = 5.3506 (2) Å | T = 293 K |
c = 11.0871 (4) Å | 0.20 × 0.20 × 0.20 mm |
β = 117.328 (1)° |
Siemens SMART CCD diffractometer | 1138 reflections with I > 2σ(I) |
4350 measured reflections | Rint = 0.072 |
1651 independent reflections |
R[F2 > 2σ(F2)] = 0.066 | 1 restraint |
wR(F2) = 0.181 | H-atom parameters constrained |
S = 1.02 | Δρmax = 0.22 e Å−3 |
1651 reflections | Δρmin = −0.24 e Å−3 |
136 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.18603 (14) | 0.2388 (5) | 0.1763 (3) | 0.0525 (7) | |
H1 | 0.1671 | 0.1193 | 0.1083 | 0.063* | |
C2 | 0.25446 (14) | 0.2525 (6) | 0.2500 (3) | 0.0504 (6) | |
C3 | 0.28296 (14) | 0.4318 (7) | 0.3520 (3) | 0.0551 (7) | |
C4 | 0.24336 (15) | 0.5915 (7) | 0.3788 (3) | 0.0591 (8) | |
H4 | 0.2623 | 0.7113 | 0.4466 | 0.071* | |
C5 | 0.17412 (16) | 0.5739 (7) | 0.3037 (4) | 0.0655 (8) | |
H5 | 0.1473 | 0.6818 | 0.3229 | 0.079* | |
C6 | 0.14496 (13) | 0.3996 (6) | 0.2019 (3) | 0.0541 (7) | |
C7 | 0.27271 (18) | −0.0825 (7) | 0.1282 (3) | 0.0688 (9) | |
H7A | 0.3089 | −0.1735 | 0.1263 | 0.103* | |
H7B | 0.2471 | −0.0031 | 0.0420 | 0.103* | |
H7C | 0.2448 | −0.1955 | 0.1464 | 0.103* | |
C8 | 0.3824 (2) | 0.6355 (12) | 0.5097 (4) | 0.1026 (16) | |
H8A | 0.4299 | 0.6195 | 0.5491 | 0.154* | |
H8B | 0.3690 | 0.6311 | 0.5802 | 0.154* | |
H8C | 0.3690 | 0.7914 | 0.4618 | 0.154* | |
C9 | 0.06954 (14) | 0.3821 (6) | 0.1186 (4) | 0.0660 (9) | |
H9A | 0.0501 | 0.3564 | 0.1795 | 0.079* | |
H9B | 0.0586 | 0.2381 | 0.0590 | 0.079* | |
C10 | 0.03874 (11) | 0.6173 (5) | 0.0326 (3) | 0.0516 (7) | |
H10 | 0.0546 | 0.7616 | 0.0937 | 0.062* | |
C11 | 0.06378 (15) | 0.6467 (7) | −0.0710 (4) | 0.0624 (8) | |
H11A | 0.1121 | 0.6417 | −0.0261 | 0.075* | |
H11B | 0.0476 | 0.5094 | −0.1352 | 0.075* | |
C12 | 0.0643 (2) | 0.9193 (13) | −0.2370 (5) | 0.1028 (15) | |
H12A | 0.0472 | 1.0765 | −0.2810 | 0.154* | |
H12B | 0.0490 | 0.7878 | −0.3033 | 0.154* | |
H12C | 0.1121 | 0.9237 | −0.1928 | 0.154* | |
O1 | 0.29828 (10) | 0.1008 (5) | 0.2311 (2) | 0.0712 (7) | |
O2 | 0.35194 (10) | 0.4356 (6) | 0.4181 (2) | 0.0763 (8) | |
O3 | 0.04179 (12) | 0.8754 (6) | −0.1407 (3) | 0.0810 (9) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0560 (14) | 0.0371 (14) | 0.0662 (16) | −0.0013 (13) | 0.0297 (13) | 0.0009 (13) |
C2 | 0.0535 (13) | 0.0422 (15) | 0.0615 (15) | 0.0006 (13) | 0.0317 (12) | 0.0010 (14) |
C3 | 0.0521 (13) | 0.0593 (19) | 0.0529 (15) | 0.0028 (14) | 0.0233 (12) | 0.0037 (15) |
C4 | 0.0660 (16) | 0.055 (2) | 0.0613 (16) | −0.0020 (16) | 0.0339 (14) | −0.0087 (15) |
C5 | 0.0692 (17) | 0.0523 (19) | 0.092 (2) | 0.0097 (16) | 0.0517 (16) | 0.0024 (18) |
C6 | 0.0531 (13) | 0.0373 (15) | 0.0766 (18) | 0.0012 (12) | 0.0339 (13) | 0.0080 (15) |
C7 | 0.081 (2) | 0.056 (2) | 0.078 (2) | 0.0134 (19) | 0.0444 (17) | −0.0054 (18) |
C8 | 0.076 (2) | 0.110 (4) | 0.087 (3) | −0.012 (3) | 0.007 (2) | −0.030 (3) |
C9 | 0.0513 (13) | 0.0439 (17) | 0.106 (2) | 0.0041 (13) | 0.0392 (15) | 0.0181 (18) |
C10 | 0.0422 (12) | 0.0343 (14) | 0.0834 (19) | −0.0005 (11) | 0.0332 (13) | 0.0014 (14) |
C11 | 0.0510 (14) | 0.0497 (17) | 0.096 (2) | 0.0040 (13) | 0.0420 (16) | 0.0040 (17) |
C12 | 0.101 (3) | 0.117 (4) | 0.112 (3) | 0.017 (3) | 0.067 (3) | 0.030 (3) |
O1 | 0.0602 (11) | 0.0603 (15) | 0.0955 (16) | 0.0065 (12) | 0.0378 (11) | −0.0185 (13) |
O2 | 0.0548 (11) | 0.0847 (19) | 0.0769 (14) | 0.0012 (12) | 0.0195 (10) | −0.0198 (14) |
O3 | 0.0768 (15) | 0.0726 (19) | 0.1139 (19) | 0.0186 (14) | 0.0611 (14) | 0.0284 (16) |
C1—C2 | 1.381 (4) | C8—H8A | 0.9600 |
C1—C6 | 1.387 (4) | C8—H8B | 0.9600 |
C1—H1 | 0.9300 | C8—H8C | 0.9600 |
C2—O1 | 1.369 (4) | C9—C10 | 1.539 (4) |
C2—C3 | 1.395 (4) | C9—H9A | 0.9700 |
C3—C4 | 1.365 (4) | C9—H9B | 0.9700 |
C3—O2 | 1.386 (3) | C10—C11 | 1.504 (4) |
C4—C5 | 1.399 (4) | C10—C10i | 1.558 (5) |
C4—H4 | 0.9300 | C10—H10 | 0.9800 |
C5—C6 | 1.377 (4) | C11—O3 | 1.411 (5) |
C5—H5 | 0.9300 | C11—H11A | 0.9700 |
C6—C9 | 1.524 (4) | C11—H11B | 0.9700 |
C7—O1 | 1.411 (4) | C12—O3 | 1.397 (5) |
C7—H7A | 0.9600 | C12—H12A | 0.9600 |
C7—H7B | 0.9600 | C12—H12B | 0.9600 |
C7—H7C | 0.9600 | C12—H12C | 0.9600 |
C8—O2 | 1.417 (6) | ||
C2—C1—C6 | 121.3 (3) | H8B—C8—H8C | 109.5 |
C2—C1—H1 | 119.3 | C6—C9—C10 | 112.8 (2) |
C6—C1—H1 | 119.3 | C6—C9—H9A | 109.0 |
O1—C2—C1 | 124.8 (3) | C10—C9—H9A | 109.0 |
O1—C2—C3 | 115.7 (2) | C6—C9—H9B | 109.0 |
C1—C2—C3 | 119.4 (2) | C10—C9—H9B | 109.0 |
C4—C3—O2 | 124.5 (3) | H9A—C9—H9B | 107.8 |
C4—C3—C2 | 120.1 (2) | C11—C10—C9 | 109.7 (2) |
O2—C3—C2 | 115.3 (3) | C11—C10—C10i | 112.5 (3) |
C3—C4—C5 | 119.7 (3) | C9—C10—C10i | 112.34 (17) |
C3—C4—H4 | 120.2 | C11—C10—H10 | 107.4 |
C5—C4—H4 | 120.2 | C9—C10—H10 | 107.4 |
C6—C5—C4 | 121.1 (3) | C10i—C10—H10 | 107.4 |
C6—C5—H5 | 119.4 | O3—C11—C10 | 110.3 (3) |
C4—C5—H5 | 119.4 | O3—C11—H11A | 109.6 |
C5—C6—C1 | 118.3 (2) | C10—C11—H11A | 109.6 |
C5—C6—C9 | 121.3 (3) | O3—C11—H11B | 109.6 |
C1—C6—C9 | 120.4 (3) | C10—C11—H11B | 109.6 |
O1—C7—H7A | 109.5 | H11A—C11—H11B | 108.1 |
O1—C7—H7B | 109.5 | O3—C12—H12A | 109.5 |
H7A—C7—H7B | 109.5 | O3—C12—H12B | 109.5 |
O1—C7—H7C | 109.5 | H12A—C12—H12B | 109.5 |
H7A—C7—H7C | 109.5 | O3—C12—H12C | 109.5 |
H7B—C7—H7C | 109.5 | H12A—C12—H12C | 109.5 |
O2—C8—H8A | 109.5 | H12B—C12—H12C | 109.5 |
O2—C8—H8B | 109.5 | C2—O1—C7 | 118.6 (2) |
H8A—C8—H8B | 109.5 | C3—O2—C8 | 116.7 (3) |
O2—C8—H8C | 109.5 | C12—O3—C11 | 113.8 (4) |
H8A—C8—H8C | 109.5 | ||
C6—C1—C2—O1 | 179.9 (3) | C2—C1—C6—C9 | 179.6 (3) |
C6—C1—C2—C3 | −0.1 (4) | C5—C6—C9—C10 | 64.7 (4) |
O1—C2—C3—C4 | −179.8 (3) | C1—C6—C9—C10 | −115.3 (3) |
C1—C2—C3—C4 | 0.2 (4) | C6—C9—C10—C11 | 63.8 (3) |
O1—C2—C3—O2 | 1.5 (4) | C6—C9—C10—C10i | −170.3 (3) |
C1—C2—C3—O2 | −178.5 (3) | C9—C10—C11—O3 | −173.6 (2) |
O2—C3—C4—C5 | 178.7 (3) | C10i—C10—C11—O3 | 60.6 (3) |
C2—C3—C4—C5 | 0.2 (5) | C1—C2—O1—C7 | 0.8 (5) |
C3—C4—C5—C6 | −0.7 (5) | C3—C2—O1—C7 | −179.2 (3) |
C4—C5—C6—C1 | 0.8 (5) | C4—C3—O2—C8 | −6.6 (5) |
C4—C5—C6—C9 | −179.2 (3) | C2—C3—O2—C8 | 172.1 (3) |
C2—C1—C6—C5 | −0.4 (4) | C10—C11—O3—C12 | 178.7 (3) |
Symmetry code: (i) −x, y, −z. |
Experimental details
Crystal data | |
Chemical formula | C24H34O6 |
Mr | 418.51 |
Crystal system, space group | Monoclinic, C2 |
Temperature (K) | 293 |
a, b, c (Å) | 22.6091 (7), 5.3506 (2), 11.0871 (4) |
β (°) | 117.328 (1) |
V (Å3) | 1191.54 (7) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.20 × 0.20 × 0.20 |
Data collection | |
Diffractometer | Siemens SMART CCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4350, 1651, 1138 |
Rint | 0.072 |
(sin θ/λ)max (Å−1) | 0.692 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.066, 0.181, 1.02 |
No. of reflections | 1651 |
No. of parameters | 136 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.22, −0.24 |
Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 1990), SHELXL97 and PARST (Nardelli, 1995).
C1—C2 | 1.381 (4) | C6—C9 | 1.524 (4) |
C1—C6 | 1.387 (4) | C7—O1 | 1.411 (4) |
C2—O1 | 1.369 (4) | C8—O2 | 1.417 (6) |
C2—C3 | 1.395 (4) | C9—C10 | 1.539 (4) |
C3—C4 | 1.365 (4) | C10—C11 | 1.504 (4) |
C3—O2 | 1.386 (3) | C10—C10i | 1.558 (5) |
C4—C5 | 1.399 (4) | C11—O3 | 1.411 (5) |
C5—C6 | 1.377 (4) | C12—O3 | 1.397 (5) |
O1—C2—C1 | 124.8 (3) | C4—C3—O2 | 124.5 (3) |
O1—C2—C3 | 115.7 (2) | O2—C3—C2 | 115.3 (3) |
C5—C6—C9—C10 | 64.7 (4) | C3—C2—O1—C7 | −179.2 (3) |
C1—C6—C9—C10 | −115.3 (3) | C4—C3—O2—C8 | −6.6 (5) |
C10i—C10—C11—O3 | 60.6 (3) | C2—C3—O2—C8 | 172.1 (3) |
C1—C2—O1—C7 | 0.8 (5) | C10—C11—O3—C12 | 178.7 (3) |
Symmetry code: (i) −x, y, −z. |
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Phyllanthus amarus is a predominant plant species in South India, especially Tamilnadu. The plant has been used traditionally in the treatment of jaundice, gastropathy, diarrhoea, dysentry, scabies, ulcers and wounds. Phyllanthus amarus has shown profound antiviral activity against hepatitis B virus, as reported by Thyagarajan et al. (1982), Venkateswaran et al. (1987), Mehrotra et al. (1991), Lee et al. (1996) and Ott et al. (1997). Phyllanthus amarus consists of various constituents like lignans, terpenes, alkaloids, flavanoids, phenols and tannins. Lignans form the major component of the plant. Phyllanthin and hypophyllanthin are the two major constituents belonging to the group of lignans which have been extensively investigated by Krishnamurthi & Seshadri (1946), Ramachandra Row et al. (1966), Anjaneyulu et al. (1973) and Houghton et al. (1996).
The present study deals with the molecular structure of phyllanthin, (I), from the South Indian variety of Phyllanthus amarus. The molecular structure of (I) and the atom-numbering scheme are shown in Fig. 1. The bond distance C10—C10i of 1.558 (5) Å [symmetry code: (i) −x, y, −z] confirms the C—C single-bond character. All the C—C and C—O bond lengths are comparable to the reported mean values of Cphenyl—Cphenyl = 1.380 Å, Cphenyl—O = 1.362 Å and C—C = 1.530 Å (Allen et al., 1987).
The exocyclic angles around atoms C2 and C3 show considerable asymmetry, with O1—C2—C1 [124.8 (3)°] being wider than O1—C2—C3 [115.7 (2)°] and C4—C3—O2 [124.5 (3)°] being wider than O2—C3—C2 [115.3 (3)°]. This may be due to the substitution of methoxy group and the steric repulsion between the phenyl ring and the methyl group. A similar effect has also been reported in related structures (Lerbscher et al., 1977; Hough, 1976).
The torsion angles through the bonds C2—O1 and C11—O3 [C1—C2—O1—C7 = 0.8 (5)°, C3—C2—O1—C7 = −179.2 (3)° and C10—C11—O3—C12 = 178.7 (3)°] cofirms the energetically favorable trans conformation. The torsion angles C4—C3—O2—C8 [−6.6 (5)°] and C2—C3—O2—C8 [172.1 (3)°] indicate that the methoxy group deviates slightly from planarity. The values of the torsion angles C5—C6—C9—C10 and C1—-C6—C9–C10 [64.7 (4) and −115.3 (3)°, respectively] show the +synclinal and -anticlinal conformation around these atoms. The phenyl ring is planar and the methoxy groups are coplanar with the phenyl ring, with a maximum deviation of 0.21 Å for atom C8.
The structure is stabilized by a C—H···O intramolecular hydrogen bond (C10—H10···O3i), where the C···Oi distance is 2.943 (4) Å, H···O is 2.54 Å and the C—H···O3i angle is 105° [symmetry code: (i) −x, y, −z]. Symmetry-related molecules are linked by intermolecular C—H···π contacts, so that H7 is 2.80 Å from the centroid of the phenyl ring with an angle of 157° for C7—H7···centroid of C1ii/C2ii/C3ii/C4ii/C5ii/C6ii [symmetry code: (ii) x, −1 + y, z] (Selvanayagam et al., 2002).