Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807046363/fl2161sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807046363/fl2161Isup2.hkl |
CCDC reference: 663837
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C) = 0.004 Å
- R factor = 0.041
- wR factor = 0.108
- Data-to-parameter ratio = 8.1
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT230_ALERT_2_B Hirshfeld Test Diff for O8 - C23 .. 10.77 su PLAT412_ALERT_2_B Short Intra XH3 .. XHn H9 .. H18C .. 1.79 Ang.
Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given ....... ? PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ? PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.98 Ratio PLAT220_ALERT_2_C Large Non-Solvent O Ueq(max)/Ueq(min) ... 2.57 Ratio PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.35 Ratio PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for O8 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C31
Alert level G REFLT03_ALERT_4_G 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. From the CIF: _diffrn_reflns_theta_max 25.10 From the CIF: _reflns_number_total 2711 Count of symmetry unique reflns 2718 Completeness (_total/calc) 99.74% 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 PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C7 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C8 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C9 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C10 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C13 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C14 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C15 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C17 = . S
0 ALERT level A = In general: serious problem 2 ALERT level B = Potentially serious problem 8 ALERT level C = Check and explain 12 ALERT level G = General alerts; check 13 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 6 ALERT type 2 Indicator that the structure model may be wrong or deficient 1 ALERT type 3 Indicator that the structure quality may be low 2 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
The plant stem bark was collected from the martime plains near Conakry, Republic of Guinea (west Africa) in November 2005. Air-dried and powdered raw material (495 g) were extracted by 5L methanol using a Soxhlet extrator. The MeOH extract was dried under reduced pressure to yield a crude extract (51 g). The crude extract was suspended in 300 ml water and partitioned with 400 ml trichloromethane three times to yield CHCl3 fraction (5 g). This part was separated by conventional chromatography on silica gel, eluting with mixtures of hexane and acetone (increasing polarity). The purified powder (32 mg) of the title compound was obtained from the hexane:acetone = 4:1 fractions. Transparent rod shaped crystals of the title compound were suitable for X-ray diffraction after recrystallization from a solution of 5% CHCl3 in MeOH by slow evaporation at room temperature.
Since the most electron-rich atom is oxygen it was not possible to determine the absolute configuration. Therefore, Friedel reflections were merged before final refinement because of the absence of significant anomalous scattering effects. All H atoms were geometrically fixed and allowed to ride on the corresponding non-H atom with C—H = 0.96 Å, O—H = 0.83 Å, and Uiso(H) = 1.5Ueq(C) of the attached C atom for methyl H atoms and 1.2Ueq(C) for other H atoms.
African mahogany Khaya senegalensis is a large evergreen tree growing mainly in the sub-Saharan savannah forests from Senegal to Uganda (Adesida et al., 1971). The plant is one of the most popular medicinal meliaceous plants used in African traditional remedies. It is used as a bitter tonic, folk and popular medicine against malaria, fever, mucous diarrhea, and venereal diseases as well as an anthelmintic and a taeniacide remedy (Olayinka et al., 1992; Iwu, 1993). Our earlier study showed that its stem bark extract displayed anti-proliferative, anti-inflammatory and pro-apoptotic effects on HT-29, HCT-15, HCA-7 cells (Androulakis et al., 2006). In the course of our chemical investigation of the plant bark, the title compound, was isolated as a major product from the CHCl3 extract. This D-seco limonoid was originally isolated from the seeds of Khaya nyasica in Tanzania (Adesida et al., 1971) and was also found to be present in the fresh seeds of Khaya senegalensis (Govindachari & Kumari, 1998) in India and in the stem bark of khaya ivorensis in the Democratic Republic of Congo (Abdelgaleil et al., 2005). It was reported that this tetranortriterpenoid displayed moderate antifungal and antibacterial activities (Abdelgaleil et al., 2005). Also, the title compound showed growth inhibitory activities against different cell lines in our preliminary anti-cancer bioassay (Zhang et al., 2007). Although its structure was tentatively identified, no spectral data were presented in previous publications. Considering its biological importanc, we have undertaken the X-ray crystal analysis of this limonoid in order to firmly establish its structure and relative stereochemistry.
The title compound (Fig.1) contains four six-membered rings A—D, one three-membered ring E (C14/C15/O5), and one furan ring F linked to atom C17 of ring D through a C—C bond in an equatorial position, known as a D-seco type limonoid. The ring junctions A/B, B/C and C/D are all trans, while D/E is cis. The six-membered rings A—D adopt chair, chair, twist boat and half-chair conformations, while rings E and F are fairly planar moieties. The bond lengths and angles are with normal ranges (Allen et al., 1987), fairly close to their expected values and the data are comparable with the corresponding values in those of two similar D-seco limonoids: gedunin (Toscano et al., 1996) and 7-oxogedunin (Waratchareeyakul et al., 2004). The strong classical intra-molecular hydrogen bond, O3—H3···O1 and inter-molecular hydrogen-bonding interactions O4—H4···O3 (Table 1) connect the molecules together to form a network.
Geometry: Allen et al. (1987); Background: Androulakis et al. (2006); Iwu (1993); Olayinka et al. (1992). Isolation, NMR and MS data, and biological activity of the title compound: Abdelgaleil et al. (2005); Adesida et al. (1971); Govindachari & Kumari (1998); Zhang et al. (2007). Similar D-seco limonoids (gedunin and 7-oxogedunin): Toscano et al. (1996); Waratchareeyakul et al. (2004).
Data collection: CrystalClear (Rigaku/MSC, 2006); cell refinement: CrystalClear (Rigaku/MSC, 2006); data reduction: CrystalClear (Rigaku/MSC, 2006); program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL (Bruker, 2000); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: PLATON (Spek,2003).
Fig. 1. view of the title compound, showing 50% probability displacement and the atom-numbering scheme |
C28H38O8 | Dx = 1.239 Mg m−3 |
Mr = 502.58 | Melting point: _audit_update_record _audit_creation_method 'SHELXL-97' _chemical_name_systematic K |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.7107 Å |
a = 10.907 (2) Å | Cell parameters from 12261 reflections |
b = 14.200 (3) Å | θ = 1.9–25.7° |
c = 17.391 (4) Å | µ = 0.09 mm−1 |
V = 2693.5 (9) Å3 | T = 298 K |
Z = 4 | Rod, colourless |
F(000) = 1080 | 0.48 × 0.46 × 0.29 mm |
Rigaku Mercury CCD (2x2 bin mode) diffractometer | 2711 independent reflections |
Radiation source: Sealed Tube | 2485 reflections with I > 2σ(I) |
Graphite Monochromator monochromator | Rint = 0.030 |
Detector resolution: 14.6199 pixels mm-1 | θmax = 25.1°, θmin = 2.2° |
ω scans | h = −12→13 |
Absorption correction: multi-scan (REQAB; Rigaku/MSC, 2006) | k = −16→16 |
Tmin = 0.958, Tmax = 0.974 | l = −20→20 |
23488 measured reflections |
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)] = 0.041 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.07 | w = 1/[s2(Fo2) + (0.063P)2 + 0.4442P] |
2711 reflections | (Δ/σ)max < 0.001 |
333 parameters | Δρmax = 0.15 e Å−3 |
0 restraints | Δρmin = −0.18 e Å−3 |
C28H38O8 | V = 2693.5 (9) Å3 |
Mr = 502.58 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 10.907 (2) Å | µ = 0.09 mm−1 |
b = 14.200 (3) Å | T = 298 K |
c = 17.391 (4) Å | 0.48 × 0.46 × 0.29 mm |
Rigaku Mercury CCD (2x2 bin mode) diffractometer | 2711 independent reflections |
Absorption correction: multi-scan (REQAB; Rigaku/MSC, 2006) | 2485 reflections with I > 2σ(I) |
Tmin = 0.958, Tmax = 0.974 | Rint = 0.030 |
23488 measured reflections |
R[F2 > 2σ(F2)] = 0.041 | 0 restraints |
wR(F2) = 0.109 | H-atom parameters constrained |
S = 1.07 | Δρmax = 0.15 e Å−3 |
2711 reflections | Δρmin = −0.18 e Å−3 |
333 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 F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > σ(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ 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 | ||
O1 | −0.24761 (17) | 0.03344 (13) | 0.00185 (10) | 0.0417 (4) | |
O2 | −0.4201 (3) | −0.0522 (2) | 0.00453 (17) | 0.0943 (10) | |
O3 | −0.2722 (3) | 0.22356 (16) | −0.04014 (13) | 0.0752 (8) | |
H3 | −0.2628 | 0.1805 | −0.0084 | 0.090* | |
O4 | 0.1384 (2) | 0.09520 (13) | 0.03037 (11) | 0.0482 (5) | |
H4 | 0.1596 | 0.1513 | 0.0307 | 0.058* | |
O5 | 0.27970 (17) | −0.15088 (15) | 0.01582 (12) | 0.0533 (5) | |
O6 | 0.25238 (19) | −0.16923 (15) | 0.17687 (12) | 0.0583 (5) | |
O7 | 0.3671 (2) | −0.0430 (2) | 0.18949 (16) | 0.0853 (8) | |
O8 | −0.0200 (3) | −0.3910 (3) | 0.2456 (2) | 0.1073 (11) | |
C1 | −0.2334 (2) | 0.0143 (2) | −0.08101 (13) | 0.0390 (6) | |
H1 | −0.2682 | −0.0462 | −0.0926 | 0.047* | |
C2 | −0.3041 (3) | 0.0904 (2) | −0.12480 (17) | 0.0533 (7) | |
H2A | −0.3063 | 0.0739 | −0.1783 | 0.064* | |
H2B | −0.3871 | 0.0916 | −0.1064 | 0.064* | |
C3 | −0.2496 (3) | 0.1879 (2) | −0.11678 (17) | 0.0593 (8) | |
H3A | −0.2930 | 0.2281 | −0.1518 | 0.071* | |
C4 | −0.1123 (3) | 0.1934 (2) | −0.13845 (16) | 0.0535 (7) | |
C5 | −0.0427 (3) | 0.11459 (17) | −0.09381 (15) | 0.0402 (6) | |
H5 | −0.0529 | 0.1310 | −0.0407 | 0.048* | |
C6 | 0.0963 (3) | 0.11405 (18) | −0.10582 (16) | 0.0441 (6) | |
H6A | 0.1147 | 0.0883 | −0.1555 | 0.053* | |
H6B | 0.1266 | 0.1775 | −0.1044 | 0.053* | |
C7 | 0.1605 (2) | 0.05603 (18) | −0.04411 (15) | 0.0409 (6) | |
H7 | 0.2471 | 0.0569 | −0.0539 | 0.049* | |
C8 | 0.1167 (2) | −0.04691 (16) | −0.04239 (13) | 0.0327 (5) | |
C9 | −0.0258 (2) | −0.04659 (15) | −0.03695 (13) | 0.0305 (5) | |
H9 | −0.0433 | −0.0148 | 0.0105 | 0.037* | |
C10 | −0.0948 (2) | 0.01254 (16) | −0.09987 (13) | 0.0327 (5) | |
C11 | −0.0774 (2) | −0.14678 (17) | −0.02572 (16) | 0.0401 (6) | |
H11A | −0.1611 | −0.1420 | −0.0091 | 0.048* | |
H11B | −0.0772 | −0.1785 | −0.0745 | 0.048* | |
C12 | −0.0064 (3) | −0.20695 (17) | 0.03248 (16) | 0.0446 (6) | |
H12A | −0.0642 | −0.2399 | 0.0643 | 0.053* | |
H12B | 0.0404 | −0.2532 | 0.0050 | 0.053* | |
C13 | 0.0805 (2) | −0.15048 (17) | 0.08430 (13) | 0.0346 (5) | |
C14 | 0.1681 (2) | −0.09790 (16) | 0.03037 (14) | 0.0346 (5) | |
C15 | 0.2863 (3) | −0.0707 (2) | 0.06512 (18) | 0.0507 (7) | |
H15 | 0.3256 | −0.0155 | 0.0449 | 0.061* | |
C16 | 0.3058 (3) | −0.0916 (3) | 0.14789 (19) | 0.0581 (8) | |
C17 | 0.1596 (2) | −0.21977 (19) | 0.13252 (16) | 0.0449 (6) | |
H17 | 0.2003 | −0.2623 | 0.0980 | 0.054* | |
C18 | 0.0126 (3) | −0.0847 (2) | 0.14002 (15) | 0.0453 (6) | |
H18A | 0.0710 | −0.0529 | 0.1721 | 0.068* | |
H18B | −0.0421 | −0.1210 | 0.1715 | 0.068* | |
H18C | −0.0336 | −0.0392 | 0.1113 | 0.068* | |
C19 | −0.0872 (3) | −0.03207 (19) | −0.18109 (14) | 0.0437 (6) | |
H19A | −0.0809 | −0.0993 | −0.1765 | 0.066* | |
H19B | −0.0163 | −0.0082 | −0.2074 | 0.066* | |
H19C | −0.1596 | −0.0164 | −0.2097 | 0.066* | |
C20 | 0.0914 (3) | −0.2766 (2) | 0.19140 (18) | 0.0543 (7) | |
C21 | 0.0267 (4) | −0.3566 (3) | 0.1786 (2) | 0.0758 (10) | |
H21 | 0.0153 | −0.3851 | 0.1290 | 0.091* | |
C22 | 0.0852 (4) | −0.2612 (3) | 0.2719 (2) | 0.0794 (11) | |
H22 | 0.1235 | −0.2106 | 0.2996 | 0.095* | |
C23 | 0.0167 (5) | −0.3296 (3) | 0.3024 (3) | 0.0912 (14) | |
H23 | −0.0040 | −0.3351 | 0.3558 | 0.109* | |
C28 | −0.1018 (4) | 0.1874 (3) | −0.22687 (18) | 0.0718 (10) | |
H28A | −0.1493 | 0.1350 | −0.2452 | 0.108* | |
H28B | −0.0175 | 0.1788 | −0.2410 | 0.108* | |
H28C | −0.1322 | 0.2445 | −0.2494 | 0.108* | |
C29 | −0.0636 (4) | 0.2901 (2) | −0.1140 (3) | 0.0825 (12) | |
H29A | −0.1159 | 0.3385 | −0.1342 | 0.124* | |
H29B | 0.0180 | 0.2984 | −0.1336 | 0.124* | |
H29C | −0.0623 | 0.2940 | −0.0589 | 0.124* | |
C30 | 0.1665 (3) | −0.0979 (2) | −0.11413 (16) | 0.0493 (7) | |
H30A | 0.1459 | −0.0624 | −0.1593 | 0.074* | |
H30B | 0.1307 | −0.1595 | −0.1175 | 0.074* | |
H30C | 0.2540 | −0.1035 | −0.1103 | 0.074* | |
C31 | −0.3440 (3) | −0.0070 (2) | 0.03741 (18) | 0.0533 (7) | |
C32 | −0.3406 (3) | 0.0131 (3) | 0.12206 (19) | 0.0743 (11) | |
H32A | −0.4218 | 0.0076 | 0.1429 | 0.112* | |
H32B | −0.3104 | 0.0757 | 0.1304 | 0.112* | |
H32C | −0.2875 | −0.0314 | 0.1470 | 0.112* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0403 (9) | 0.0501 (10) | 0.0347 (8) | 0.0061 (8) | 0.0047 (8) | 0.0034 (8) |
O2 | 0.0707 (16) | 0.131 (3) | 0.0810 (18) | −0.0390 (18) | 0.0204 (15) | −0.0125 (18) |
O3 | 0.114 (2) | 0.0517 (12) | 0.0600 (13) | 0.0383 (14) | 0.0212 (14) | 0.0016 (11) |
O4 | 0.0665 (12) | 0.0353 (9) | 0.0427 (10) | −0.0147 (9) | −0.0038 (9) | −0.0048 (8) |
O5 | 0.0383 (10) | 0.0660 (13) | 0.0555 (11) | 0.0188 (9) | 0.0077 (9) | 0.0045 (10) |
O6 | 0.0500 (11) | 0.0700 (13) | 0.0549 (11) | −0.0003 (10) | −0.0148 (10) | 0.0165 (11) |
O7 | 0.0725 (16) | 0.108 (2) | 0.0753 (16) | −0.0286 (16) | −0.0363 (14) | 0.0087 (16) |
O8 | 0.104 (2) | 0.095 (2) | 0.123 (3) | 0.0002 (19) | 0.026 (2) | 0.061 (2) |
C1 | 0.0392 (14) | 0.0467 (14) | 0.0312 (12) | 0.0056 (11) | −0.0009 (10) | 0.0004 (10) |
C2 | 0.0527 (16) | 0.0635 (18) | 0.0438 (15) | 0.0192 (15) | −0.0016 (13) | 0.0097 (14) |
C3 | 0.080 (2) | 0.0537 (16) | 0.0441 (15) | 0.0302 (16) | 0.0029 (15) | 0.0086 (13) |
C4 | 0.078 (2) | 0.0381 (14) | 0.0449 (15) | 0.0115 (14) | 0.0049 (15) | 0.0105 (12) |
C5 | 0.0540 (15) | 0.0334 (12) | 0.0330 (12) | 0.0024 (11) | 0.0043 (12) | 0.0007 (10) |
C6 | 0.0564 (16) | 0.0353 (13) | 0.0405 (14) | −0.0098 (12) | 0.0065 (12) | 0.0044 (11) |
C7 | 0.0410 (13) | 0.0412 (13) | 0.0404 (13) | −0.0087 (11) | 0.0057 (11) | 0.0012 (11) |
C8 | 0.0337 (11) | 0.0320 (11) | 0.0325 (11) | −0.0017 (10) | 0.0035 (10) | −0.0029 (10) |
C9 | 0.0353 (11) | 0.0276 (11) | 0.0286 (11) | −0.0011 (9) | −0.0006 (9) | −0.0025 (9) |
C10 | 0.0373 (12) | 0.0324 (12) | 0.0285 (11) | 0.0010 (10) | 0.0009 (10) | 0.0001 (9) |
C11 | 0.0430 (13) | 0.0310 (11) | 0.0464 (14) | −0.0070 (10) | −0.0102 (11) | 0.0009 (11) |
C12 | 0.0486 (14) | 0.0288 (12) | 0.0563 (15) | −0.0069 (11) | −0.0076 (13) | 0.0050 (11) |
C13 | 0.0360 (12) | 0.0314 (11) | 0.0364 (12) | 0.0026 (10) | 0.0007 (10) | 0.0019 (10) |
C14 | 0.0307 (11) | 0.0331 (11) | 0.0400 (13) | 0.0042 (10) | 0.0025 (10) | −0.0043 (10) |
C15 | 0.0364 (13) | 0.0583 (17) | 0.0575 (17) | −0.0052 (13) | −0.0058 (12) | 0.0104 (15) |
C16 | 0.0426 (15) | 0.071 (2) | 0.0601 (18) | −0.0019 (15) | −0.0149 (14) | 0.0086 (16) |
C17 | 0.0429 (13) | 0.0433 (13) | 0.0486 (15) | 0.0090 (12) | −0.0014 (12) | 0.0045 (12) |
C18 | 0.0501 (15) | 0.0463 (14) | 0.0395 (13) | 0.0143 (13) | 0.0052 (12) | 0.0036 (11) |
C19 | 0.0525 (15) | 0.0477 (14) | 0.0310 (12) | 0.0035 (12) | −0.0020 (12) | −0.0058 (11) |
C20 | 0.0543 (16) | 0.0491 (16) | 0.0596 (18) | 0.0119 (13) | 0.0040 (14) | 0.0208 (14) |
C21 | 0.089 (3) | 0.062 (2) | 0.076 (2) | −0.0034 (19) | 0.007 (2) | 0.0257 (19) |
C22 | 0.100 (3) | 0.079 (2) | 0.059 (2) | 0.013 (2) | 0.010 (2) | 0.0194 (19) |
C23 | 0.112 (3) | 0.091 (3) | 0.070 (2) | 0.023 (3) | 0.031 (3) | 0.039 (2) |
C28 | 0.098 (3) | 0.068 (2) | 0.0496 (17) | 0.017 (2) | 0.0084 (18) | 0.0247 (16) |
C29 | 0.115 (3) | 0.0352 (15) | 0.097 (3) | 0.0076 (19) | 0.006 (3) | 0.0101 (17) |
C30 | 0.0500 (16) | 0.0561 (16) | 0.0418 (14) | 0.0093 (14) | 0.0078 (12) | −0.0101 (13) |
C31 | 0.0432 (15) | 0.0650 (18) | 0.0519 (16) | 0.0034 (14) | 0.0122 (14) | 0.0070 (15) |
C32 | 0.066 (2) | 0.107 (3) | 0.0494 (17) | 0.013 (2) | 0.0184 (16) | 0.0155 (19) |
O1—C31 | 1.348 (3) | C11—C12 | 1.534 (4) |
O1—C1 | 1.475 (3) | C11—H11A | 0.9600 |
O2—C31 | 1.195 (4) | C11—H11B | 0.9600 |
O3—C3 | 1.447 (4) | C12—C13 | 1.534 (4) |
O3—H3 | 0.8299 | C12—H12A | 0.9600 |
O4—C7 | 1.430 (3) | C12—H12B | 0.9600 |
O4—H4 | 0.8299 | C13—C14 | 1.534 (3) |
O5—C15 | 1.427 (4) | C13—C18 | 1.536 (3) |
O5—C14 | 1.453 (3) | C13—C17 | 1.554 (3) |
O6—C16 | 1.345 (4) | C14—C15 | 1.475 (4) |
O6—C17 | 1.461 (3) | C15—C16 | 1.485 (4) |
O7—C16 | 1.203 (4) | C15—H15 | 0.9600 |
O8—C21 | 1.363 (5) | C17—C20 | 1.501 (4) |
O8—C23 | 1.376 (6) | C17—H17 | 0.9600 |
C1—C2 | 1.530 (4) | C18—H18A | 0.9599 |
C1—C10 | 1.547 (3) | C18—H18B | 0.9599 |
C1—H1 | 0.9600 | C18—H18C | 0.9599 |
C2—C3 | 1.513 (5) | C19—H19A | 0.9599 |
C2—H2A | 0.9600 | C19—H19B | 0.9599 |
C2—H2B | 0.9600 | C19—H19C | 0.9599 |
C3—C4 | 1.546 (5) | C20—C21 | 1.356 (5) |
C3—H3A | 0.9600 | C20—C22 | 1.419 (5) |
C4—C29 | 1.533 (5) | C21—H21 | 0.9600 |
C4—C28 | 1.544 (4) | C22—C23 | 1.335 (6) |
C4—C5 | 1.560 (4) | C22—H22 | 0.9600 |
C5—C6 | 1.530 (4) | C23—H23 | 0.9600 |
C5—C10 | 1.560 (3) | C28—H28A | 0.9599 |
C5—H5 | 0.9600 | C28—H28B | 0.9599 |
C6—C7 | 1.523 (4) | C28—H28C | 0.9599 |
C6—H6A | 0.9600 | C29—H29A | 0.9599 |
C6—H6B | 0.9600 | C29—H29B | 0.9599 |
C7—C8 | 1.538 (3) | C29—H29C | 0.9599 |
C7—H7 | 0.9600 | C30—H30A | 0.9599 |
C8—C30 | 1.541 (3) | C30—H30B | 0.9599 |
C8—C9 | 1.558 (3) | C30—H30C | 0.9599 |
C8—C14 | 1.562 (3) | C31—C32 | 1.500 (5) |
C9—C11 | 1.542 (3) | C32—H32A | 0.9599 |
C9—C10 | 1.571 (3) | C32—H32B | 0.9599 |
C9—H9 | 0.9600 | C32—H32C | 0.9599 |
C10—C19 | 1.550 (3) | ||
C31—O1—C1 | 116.9 (2) | C14—C13—C12 | 106.3 (2) |
C3—O3—H3 | 109.5 | C14—C13—C18 | 113.0 (2) |
C7—O4—H4 | 109.5 | C12—C13—C18 | 113.0 (2) |
C15—O5—C14 | 61.59 (16) | C14—C13—C17 | 107.0 (2) |
C16—O6—C17 | 120.3 (2) | C12—C13—C17 | 109.2 (2) |
C21—O8—C23 | 106.2 (3) | C18—C13—C17 | 108.2 (2) |
O1—C1—C2 | 107.6 (2) | O5—C14—C15 | 58.35 (18) |
O1—C1—C10 | 108.2 (2) | O5—C14—C13 | 112.13 (19) |
C2—C1—C10 | 113.5 (2) | C15—C14—C13 | 114.9 (2) |
O1—C1—H1 | 109.1 | O5—C14—C8 | 113.55 (19) |
C2—C1—H1 | 109.1 | C15—C14—C8 | 121.6 (2) |
C10—C1—H1 | 109.1 | C13—C14—C8 | 119.83 (19) |
C3—C2—C1 | 113.7 (2) | O5—C15—C14 | 60.06 (16) |
C3—C2—H2A | 108.8 | O5—C15—C16 | 115.5 (3) |
C1—C2—H2A | 108.8 | C14—C15—C16 | 118.0 (3) |
C3—C2—H2B | 108.8 | O5—C15—H15 | 117.0 |
C1—C2—H2B | 108.8 | C14—C15—H15 | 117.0 |
H2A—C2—H2B | 107.7 | C16—C15—H15 | 117.0 |
O3—C3—C2 | 109.8 (3) | O7—C16—O6 | 119.0 (3) |
O3—C3—C4 | 111.8 (3) | O7—C16—C15 | 123.2 (3) |
C2—C3—C4 | 113.9 (2) | O6—C16—C15 | 117.7 (3) |
O3—C3—H3A | 107.0 | O6—C17—C20 | 104.3 (2) |
C2—C3—H3A | 107.0 | O6—C17—C13 | 111.0 (2) |
C4—C3—H3A | 107.0 | C20—C17—C13 | 115.7 (2) |
C29—C4—C28 | 107.5 (3) | O6—C17—H17 | 108.5 |
C29—C4—C3 | 108.3 (3) | C20—C17—H17 | 108.5 |
C28—C4—C3 | 108.2 (3) | C13—C17—H17 | 108.5 |
C29—C4—C5 | 109.6 (3) | C13—C18—H18A | 109.5 |
C28—C4—C5 | 114.8 (3) | C13—C18—H18B | 109.5 |
C3—C4—C5 | 108.3 (2) | H18A—C18—H18B | 109.5 |
C6—C5—C4 | 114.7 (2) | C13—C18—H18C | 109.5 |
C6—C5—C10 | 110.3 (2) | H18A—C18—H18C | 109.5 |
C4—C5—C10 | 117.1 (2) | H18B—C18—H18C | 109.5 |
C6—C5—H5 | 104.4 | C10—C19—H19A | 109.5 |
C4—C5—H5 | 104.4 | C10—C19—H19B | 109.5 |
C10—C5—H5 | 104.4 | H19A—C19—H19B | 109.5 |
C7—C6—C5 | 111.2 (2) | C10—C19—H19C | 109.5 |
C7—C6—H6A | 109.4 | H19A—C19—H19C | 109.5 |
C5—C6—H6A | 109.4 | H19B—C19—H19C | 109.5 |
C7—C6—H6B | 109.4 | C21—C20—C22 | 105.5 (3) |
C5—C6—H6B | 109.4 | C21—C20—C17 | 126.6 (3) |
H6A—C6—H6B | 108.0 | C22—C20—C17 | 127.8 (3) |
O4—C7—C6 | 110.5 (2) | C20—C21—O8 | 110.7 (4) |
O4—C7—C8 | 107.44 (19) | C20—C21—H21 | 124.7 |
C6—C7—C8 | 112.6 (2) | O8—C21—H21 | 124.7 |
O4—C7—H7 | 108.7 | C23—C22—C20 | 107.8 (4) |
C6—C7—H7 | 108.7 | C23—C22—H22 | 126.1 |
C8—C7—H7 | 108.7 | C20—C22—H22 | 126.1 |
C7—C8—C30 | 108.7 (2) | C22—C23—O8 | 109.8 (4) |
C7—C8—C9 | 108.0 (2) | C22—C23—H23 | 125.1 |
C30—C8—C9 | 113.7 (2) | O8—C23—H23 | 125.1 |
C7—C8—C14 | 110.2 (2) | C4—C28—H28A | 109.5 |
C30—C8—C14 | 108.2 (2) | C4—C28—H28B | 109.5 |
C9—C8—C14 | 108.09 (19) | H28A—C28—H28B | 109.5 |
C11—C9—C8 | 111.68 (19) | C4—C28—H28C | 109.5 |
C11—C9—C10 | 113.97 (19) | H28A—C28—H28C | 109.5 |
C8—C9—C10 | 115.93 (19) | H28B—C28—H28C | 109.5 |
C11—C9—H9 | 104.6 | C4—C29—H29A | 109.5 |
C8—C9—H9 | 104.6 | C4—C29—H29B | 109.5 |
C10—C9—H9 | 104.6 | H29A—C29—H29B | 109.5 |
C1—C10—C19 | 104.6 (2) | C4—C29—H29C | 109.5 |
C1—C10—C5 | 109.1 (2) | H29A—C29—H29C | 109.5 |
C19—C10—C5 | 114.9 (2) | H29B—C29—H29C | 109.5 |
C1—C10—C9 | 109.20 (19) | C8—C30—H30A | 109.5 |
C19—C10—C9 | 113.00 (19) | C8—C30—H30B | 109.5 |
C5—C10—C9 | 105.96 (19) | H30A—C30—H30B | 109.5 |
C12—C11—C9 | 114.4 (2) | C8—C30—H30C | 109.5 |
C12—C11—H11A | 108.7 | H30A—C30—H30C | 109.5 |
C9—C11—H11A | 108.7 | H30B—C30—H30C | 109.5 |
C12—C11—H11B | 108.7 | O2—C31—O1 | 123.4 (3) |
C9—C11—H11B | 108.7 | O2—C31—C32 | 126.1 (3) |
H11A—C11—H11B | 107.6 | O1—C31—C32 | 110.5 (3) |
C13—C12—C11 | 114.10 (19) | C31—C32—H32A | 109.5 |
C13—C12—H12A | 108.7 | C31—C32—H32B | 109.5 |
C11—C12—H12A | 108.7 | H32A—C32—H32B | 109.5 |
C13—C12—H12B | 108.7 | C31—C32—H32C | 109.5 |
C11—C12—H12B | 108.7 | H32A—C32—H32C | 109.5 |
H12A—C12—H12B | 107.6 | H32B—C32—H32C | 109.5 |
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O1 | 0.83 | 2.10 | 2.810 (2) | 143 |
O4—H4···O3i | 0.83 | 1.93 | 2.758 (2) | 171 |
Symmetry code: (i) x+1/2, −y+1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C28H38O8 |
Mr | 502.58 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 298 |
a, b, c (Å) | 10.907 (2), 14.200 (3), 17.391 (4) |
V (Å3) | 2693.5 (9) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.48 × 0.46 × 0.29 |
Data collection | |
Diffractometer | Rigaku Mercury CCD (2x2 bin mode) |
Absorption correction | Multi-scan (REQAB; Rigaku/MSC, 2006) |
Tmin, Tmax | 0.958, 0.974 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 23488, 2711, 2485 |
Rint | 0.030 |
(sin θ/λ)max (Å−1) | 0.597 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.109, 1.07 |
No. of reflections | 2711 |
No. of parameters | 333 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.15, −0.18 |
Computer programs: CrystalClear (Rigaku/MSC, 2006), SHELXTL (Bruker, 2000), PLATON (Spek,2003).
D—H···A | D—H | H···A | D···A | D—H···A |
O3—H3···O1 | 0.83 | 2.10 | 2.810 (2) | 143 |
O4—H4···O3i | 0.83 | 1.93 | 2.758 (2) | 171 |
Symmetry code: (i) x+1/2, −y+1/2, −z. |
African mahogany Khaya senegalensis is a large evergreen tree growing mainly in the sub-Saharan savannah forests from Senegal to Uganda (Adesida et al., 1971). The plant is one of the most popular medicinal meliaceous plants used in African traditional remedies. It is used as a bitter tonic, folk and popular medicine against malaria, fever, mucous diarrhea, and venereal diseases as well as an anthelmintic and a taeniacide remedy (Olayinka et al., 1992; Iwu, 1993). Our earlier study showed that its stem bark extract displayed anti-proliferative, anti-inflammatory and pro-apoptotic effects on HT-29, HCT-15, HCA-7 cells (Androulakis et al., 2006). In the course of our chemical investigation of the plant bark, the title compound, was isolated as a major product from the CHCl3 extract. This D-seco limonoid was originally isolated from the seeds of Khaya nyasica in Tanzania (Adesida et al., 1971) and was also found to be present in the fresh seeds of Khaya senegalensis (Govindachari & Kumari, 1998) in India and in the stem bark of khaya ivorensis in the Democratic Republic of Congo (Abdelgaleil et al., 2005). It was reported that this tetranortriterpenoid displayed moderate antifungal and antibacterial activities (Abdelgaleil et al., 2005). Also, the title compound showed growth inhibitory activities against different cell lines in our preliminary anti-cancer bioassay (Zhang et al., 2007). Although its structure was tentatively identified, no spectral data were presented in previous publications. Considering its biological importanc, we have undertaken the X-ray crystal analysis of this limonoid in order to firmly establish its structure and relative stereochemistry.
The title compound (Fig.1) contains four six-membered rings A—D, one three-membered ring E (C14/C15/O5), and one furan ring F linked to atom C17 of ring D through a C—C bond in an equatorial position, known as a D-seco type limonoid. The ring junctions A/B, B/C and C/D are all trans, while D/E is cis. The six-membered rings A—D adopt chair, chair, twist boat and half-chair conformations, while rings E and F are fairly planar moieties. The bond lengths and angles are with normal ranges (Allen et al., 1987), fairly close to their expected values and the data are comparable with the corresponding values in those of two similar D-seco limonoids: gedunin (Toscano et al., 1996) and 7-oxogedunin (Waratchareeyakul et al., 2004). The strong classical intra-molecular hydrogen bond, O3—H3···O1 and inter-molecular hydrogen-bonding interactions O4—H4···O3 (Table 1) connect the molecules together to form a network.