Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807041906/wn2198sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807041906/wn2198Isup2.hkl |
CCDC reference: 273264
Key indicators
- Single-crystal X-ray study
- T = 297 K
- Mean (C-C) = 0.002 Å
- R factor = 0.048
- wR factor = 0.141
- Data-to-parameter ratio = 13.0
checkCIF/PLATON results
No syntax errors found
Alert level B PLAT420_ALERT_2_B D-H Without Acceptor O5 - H5A ... ?
Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.99 Ratio PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C14 PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.01 PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 4
Alert level G PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 1
0 ALERT level A = In general: serious problem 1 ALERT level B = Potentially serious problem 5 ALERT level C = Check and explain 1 ALERT level G = General alerts; check 1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 4 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 1 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
Air-dried roots of Cratoxylum formosum ssp. pruniflorum (5.30 kg) were ground and extracted with CH2Cl2 (2x20 l for 2x5 days) at room temperature. The residue obtained after evaporation of the solvent was subjected to quick column chromatography (QCC) on silica gel, using hexane as first eluent and then increasing polarity with EtOAc and acetone, to afford 8 fractions (F1–F8). Fraction F3 was separated by CC with 10% acetone–hexane to give the title compound. Yellow needle-shaped single crystals suitable for X-ray diffraction analysis were obtained by slow evaporation of the solvents from a CHCl3/CH3OH (7:3 v/v) solution after several days (M.p. 452–453 K).
H atoms of the methanol molecule and the H atoms attached to O5 and O7 were located in a difference map. The remaining H atoms were placed in calculated positions with O—H distance of 0.82 Å and C—H distances in the range 0.93–0.97 Å. The Uiso(H) values were constrained to be 1.5Ueq(carrier atom) for hydroxyl and methyl H atoms and 1.2Ueq(carrier atom) for the remaining H atoms. Owing to a large fraction of weak data at higher angles, the 2θ maximum was limited to 50°. A rotating group model was used for the methyl groups.
Some species of plants in the genus Cratoxylum have been used for the treatment of diuretic, stomachic, and tonic effects (Kitanov et al., 1988), as well as for diarrhea and flatulence (Aderson, 1986). In our ongoing research of bioactive compounds from medicinal plants, the title compound, gerontoxanthone I, was isolated from a dichloromethane extract of the roots of Cratoxylum formosum ssp. pruniflorum, collected from Nhongkai Province in the northeasthern part of Thailand. As the title compound showed strong antibacterial and cytotoxic activities (Boonnak, Karalai, et al., 2006), its X-ray crystal structure was determined in order to gain more information for further SAR (Structure and Activity Relationship) analysis. In our previous studies, we have reported the crystal structures of xanthone and anthraquinone compounds from the roots and barks of this plant (Boonnak et al., 2005; Boonnak, Chantrapromma & Fun, 2006; Boonnak, Karalai et al., 2006; Chantrapromma et al., 2005; 2006; Fun et al., 2006). We report here the crystal structure of the methanol solvate of gerontoxanthone I.
In the title compound (Fig. 1), the xanthone skeleton (rings A, B and C) is essentially planar, the maximum deviation from planarity being 0.043 (2) Å for atom C3. The O2—H2A···O1 and O4—H4A···O3 hydrogen bonds generate S(5) and S(6) ring motifs, respectively (Bernstein et al., 1995) and help to stabilize the planarity of the structure. There are also weak intramolecular C—H···O interactions; C18—H18B···O6 and C19—H19A···O4 generate S(6) and S(5) ring motifs respectively (Table 1).
The orientation of the 3-methylbut-2-enyl [C19–C23] side chain with respect to the benzene ring C is indicated by the torsion angle of C13—C12—C19—C20 = -93.25 (17)°, [90.6 (2)° in the monohydrate compound (Boonnak, Chantrapromma & Fun, 2006)], indicating a (-)-synclinal conformation (Fig. 1). The 1,1-dimethylprop-2-enyl [C14–C18] substituent is attached to the benzene ring at C10 with the torsion angle C9—C10—C14—C15 of -137.06 (17)° [-52.6 (3)° in Boonnak, Chantrapromma & Fun, 2006], indicating a (-)-anticlinal conformation. Bond distances and angles in the title compound are in normal ranges (Allen et al., 1987) and comparable to those reported in the gerontoxanthone I monohydrate (Boonnak, Chantrapromma & Fun, 2006) and other closely related structures (Boonnak et al., 2005; Boonnak, Karalai et al., 2006; Chantrapromma et al., 2005; 2006; Fun et al., 2006). The methanol solvent molecule is also involved in hydrogen bonds (Table 1).
In the crystal packing (Fig. 2), the gerontoxanthone I molecules are linked together into chains along the a axis by the intermolecular O2—H1O2···O4 hydrogen bond (symmetry code: -1 + x, y, z) and weak C19—H19A···O2 interaction (symmetry code: 1 + x, y, z) (Table 1) and are further linked to the methanol molecules by O1—H1O1···O7 (symmetry code: -1 + x, y, -1 + z) and O7—H1O7···O3 (symmetry code: 1 - x, 1 - y, 1 - z) hydrogen bonds (Table 1). This packing is different from the three dimensional crystal packing of the monohydrate compound (Boonnak, Chantrapromma & Fun, 2006). The crystal structure is stabilized by intra- and intermolecular O—H···O hydrogen bonds, weak C—H···O intra- and intramolecular interactions (Table 1). In addition, the molecular packing is further stabilized by a C—H···π interaction between one of the methyl groups of the 3-methylbut-2-enyl side chain and the centroid of the C1–C6 benzene ring (Cg1) (Table 1).
For related literature on hydrogen-bond motifs, see: Bernstein et al. (1995). For related literature on values of bond lengths, see: Allen et al. (1987). For related structures, see, for example: Boonnak et al. (2005); Boonnak, Chantrapromma & Fun (2006); Boonnak, Karalai et al. (2006); Chantrapromma et al. (2005, 2006); Fun et al. (2006). For related literature on bioactivities of xanthones, see, for example: Aderson (1986); Boonnak, Karalai et al. (2006); Kitanov et al. (1988).
Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXTL (Sheldrick, 1997); program(s) used to refine structure: SHELXTL (Sheldrick, 1997); molecular graphics: SHELXTL (Sheldrick, 1997); software used to prepare material for publication: SHELXTL (Sheldrick, 1997) and PLATON (Spek, 2003).
C23H24O6·CH4O | F(000) = 912 |
Mr = 428.46 | Dx = 1.302 Mg m−3 |
Monoclinic, P21/c | Melting point = 452–453 K |
Hall symbol: -P 2ybc | Mo Kα radiation, λ = 0.71073 Å |
a = 10.0411 (8) Å | Cell parameters from 3834 reflections |
b = 20.1500 (16) Å | θ = 2.3–25.0° |
c = 12.1807 (7) Å | µ = 0.10 mm−1 |
β = 117.534 (5)° | T = 297 K |
V = 2185.4 (3) Å3 | Needle, yellow |
Z = 4 | 0.55 × 0.29 × 0.19 mm |
Siemens SMART CCD area-detector diffractometer | 3834 independent reflections |
Radiation source: fine-focus sealed tube | 3429 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
Detector resolution: 8.33 pixels mm-1 | θmax = 25.0°, θmin = 2.3° |
ω scans | h = −11→11 |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | k = −23→23 |
Tmin = 0.950, Tmax = 0.982 | l = −7→14 |
11274 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)] = 0.048 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.141 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0853P)2 + 0.4621P] where P = (Fo2 + 2Fc2)/3 |
3834 reflections | (Δ/σ)max < 0.001 |
296 parameters | Δρmax = 0.19 e Å−3 |
1 restraint | Δρmin = −0.36 e Å−3 |
C23H24O6·CH4O | V = 2185.4 (3) Å3 |
Mr = 428.46 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 10.0411 (8) Å | µ = 0.10 mm−1 |
b = 20.1500 (16) Å | T = 297 K |
c = 12.1807 (7) Å | 0.55 × 0.29 × 0.19 mm |
β = 117.534 (5)° |
Siemens SMART CCD area-detector diffractometer | 3834 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 3429 reflections with I > 2σ(I) |
Tmin = 0.950, Tmax = 0.982 | Rint = 0.018 |
11274 measured reflections |
R[F2 > 2σ(F2)] = 0.048 | 1 restraint |
wR(F2) = 0.141 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | Δρmax = 0.19 e Å−3 |
3834 reflections | Δρmin = −0.36 e Å−3 |
296 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 | ||
O1 | −0.16926 (13) | 0.49056 (7) | 0.21463 (12) | 0.0639 (4) | |
H1O1 | −0.222 (3) | 0.5096 (14) | 0.146 (3) | 0.096* | |
O2 | 0.02703 (12) | 0.42552 (7) | 0.42133 (11) | 0.0636 (4) | |
H1O2 | −0.0623 | 0.4333 | 0.3972 | 0.095* | |
O3 | 0.48730 (12) | 0.48078 (7) | 0.25536 (11) | 0.0570 (3) | |
O4 | 0.73927 (12) | 0.42967 (6) | 0.40403 (11) | 0.0536 (3) | |
H1O4 | 0.6776 | 0.4502 | 0.3439 | 0.080* | |
O5 | 0.77233 (13) | 0.30854 (7) | 0.74175 (13) | 0.0638 (4) | |
H5A | 0.727 (3) | 0.3031 (13) | 0.789 (3) | 0.100 (8)* | |
O6 | 0.30754 (11) | 0.40989 (5) | 0.47182 (9) | 0.0449 (3) | |
O7 | 0.6422 (2) | 0.53884 (12) | 0.99678 (17) | 0.0999 (6) | |
H1O7 | 0.595 (5) | 0.525 (2) | 0.9244 (17) | 0.176 (18)* | |
C1 | 0.17612 (17) | 0.50642 (8) | 0.18518 (14) | 0.0453 (4) | |
H1B | 0.2105 | 0.5248 | 0.1329 | 0.054* | |
C2 | 0.02873 (17) | 0.51419 (8) | 0.15877 (14) | 0.0472 (4) | |
H2A | −0.0361 | 0.5380 | 0.0889 | 0.057* | |
C3 | −0.02461 (16) | 0.48670 (8) | 0.23586 (14) | 0.0459 (4) | |
C4 | 0.07148 (16) | 0.45290 (8) | 0.34219 (14) | 0.0434 (3) | |
C5 | 0.22065 (15) | 0.44518 (7) | 0.36748 (13) | 0.0387 (3) | |
C6 | 0.27565 (16) | 0.47090 (7) | 0.29057 (13) | 0.0395 (3) | |
C7 | 0.43129 (16) | 0.45928 (7) | 0.32226 (13) | 0.0408 (3) | |
C8 | 0.51977 (15) | 0.42168 (7) | 0.43328 (13) | 0.0385 (3) | |
C9 | 0.45495 (15) | 0.39753 (7) | 0.50637 (13) | 0.0381 (3) | |
C10 | 0.53244 (16) | 0.35998 (7) | 0.61333 (14) | 0.0419 (3) | |
C11 | 0.68362 (16) | 0.34693 (7) | 0.64363 (14) | 0.0437 (4) | |
C12 | 0.75637 (15) | 0.37038 (7) | 0.57675 (14) | 0.0407 (3) | |
C13 | 0.67322 (15) | 0.40703 (7) | 0.47158 (13) | 0.0397 (3) | |
C14 | 0.46210 (18) | 0.32904 (9) | 0.69122 (16) | 0.0530 (4) | |
C15 | 0.5654 (2) | 0.33895 (13) | 0.82710 (18) | 0.0704 (6) | |
H15A | 0.6029 | 0.3816 | 0.8514 | 0.084* | |
C16 | 0.6087 (3) | 0.29370 (19) | 0.9158 (3) | 0.1141 (12) | |
H16A | 0.5746 | 0.2502 | 0.8967 | 0.137* | |
H16B | 0.6733 | 0.3054 | 0.9972 | 0.137* | |
C17 | 0.4329 (4) | 0.25566 (12) | 0.6555 (3) | 0.1012 (9) | |
H17A | 0.3985 | 0.2339 | 0.7078 | 0.152* | |
H17B | 0.5242 | 0.2352 | 0.6656 | 0.152* | |
H17C | 0.3577 | 0.2519 | 0.5706 | 0.152* | |
C18 | 0.3143 (2) | 0.36078 (13) | 0.67513 (19) | 0.0753 (6) | |
H18A | 0.2879 | 0.3426 | 0.7353 | 0.113* | |
H18B | 0.2357 | 0.3516 | 0.5934 | 0.113* | |
H18C | 0.3273 | 0.4079 | 0.6866 | 0.113* | |
C19 | 0.92107 (15) | 0.35478 (7) | 0.62011 (14) | 0.0430 (4) | |
H19A | 0.9650 | 0.3897 | 0.5924 | 0.052* | |
H19B | 0.9730 | 0.3543 | 0.7099 | 0.052* | |
C20 | 0.94472 (16) | 0.28944 (8) | 0.57296 (15) | 0.0456 (4) | |
H20A | 0.9067 | 0.2860 | 0.4876 | 0.055* | |
C21 | 1.01301 (18) | 0.23594 (8) | 0.63764 (17) | 0.0533 (4) | |
C22 | 1.0272 (3) | 0.17404 (10) | 0.5744 (2) | 0.0791 (6) | |
H22A | 0.9881 | 0.1823 | 0.4873 | 0.119* | |
H22B | 0.9715 | 0.1387 | 0.5869 | 0.119* | |
H22C | 1.1310 | 0.1616 | 0.6087 | 0.119* | |
C23 | 1.0826 (3) | 0.23100 (11) | 0.7756 (2) | 0.0756 (6) | |
H23A | 1.0799 | 0.2737 | 0.8096 | 0.113* | |
H23B | 1.1850 | 0.2166 | 0.8077 | 0.113* | |
H23C | 1.0277 | 0.1995 | 0.7981 | 0.113* | |
C24 | 0.6202 (7) | 0.6016 (2) | 0.9882 (4) | 0.186 (2) | |
H24A | 0.6362 | 0.6187 | 0.9217 | 0.223* | |
H24B | 0.6890 | 0.6224 | 1.0644 | 0.223* | |
H24C | 0.5190 | 0.6107 | 0.9722 | 0.223* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0327 (6) | 0.0978 (10) | 0.0607 (7) | 0.0177 (6) | 0.0213 (5) | 0.0222 (7) |
O2 | 0.0348 (6) | 0.0987 (10) | 0.0647 (8) | 0.0163 (6) | 0.0292 (6) | 0.0302 (7) |
O3 | 0.0383 (6) | 0.0864 (9) | 0.0505 (6) | 0.0073 (5) | 0.0240 (5) | 0.0220 (6) |
O4 | 0.0333 (5) | 0.0794 (8) | 0.0545 (7) | 0.0092 (5) | 0.0256 (5) | 0.0206 (6) |
O5 | 0.0421 (6) | 0.0850 (9) | 0.0676 (8) | 0.0232 (6) | 0.0282 (6) | 0.0380 (7) |
O6 | 0.0290 (5) | 0.0620 (6) | 0.0457 (6) | 0.0085 (4) | 0.0189 (5) | 0.0151 (5) |
O7 | 0.0808 (11) | 0.1318 (17) | 0.0661 (10) | 0.0343 (11) | 0.0160 (9) | 0.0218 (10) |
C1 | 0.0373 (8) | 0.0569 (9) | 0.0414 (8) | 0.0024 (6) | 0.0178 (6) | 0.0067 (7) |
C2 | 0.0375 (8) | 0.0566 (9) | 0.0416 (8) | 0.0087 (6) | 0.0133 (6) | 0.0075 (7) |
C3 | 0.0311 (7) | 0.0554 (9) | 0.0480 (8) | 0.0067 (6) | 0.0155 (6) | 0.0009 (7) |
C4 | 0.0327 (7) | 0.0547 (9) | 0.0456 (8) | 0.0049 (6) | 0.0204 (6) | 0.0047 (6) |
C5 | 0.0310 (7) | 0.0444 (7) | 0.0389 (7) | 0.0032 (5) | 0.0147 (6) | 0.0023 (6) |
C6 | 0.0323 (7) | 0.0448 (7) | 0.0401 (7) | 0.0011 (6) | 0.0156 (6) | 0.0012 (6) |
C7 | 0.0334 (7) | 0.0508 (8) | 0.0398 (7) | −0.0001 (6) | 0.0183 (6) | 0.0025 (6) |
C8 | 0.0304 (7) | 0.0445 (7) | 0.0412 (8) | 0.0006 (5) | 0.0170 (6) | 0.0015 (6) |
C9 | 0.0271 (7) | 0.0451 (8) | 0.0427 (7) | 0.0015 (5) | 0.0166 (6) | 0.0017 (6) |
C10 | 0.0336 (7) | 0.0479 (8) | 0.0460 (8) | 0.0021 (6) | 0.0199 (6) | 0.0076 (6) |
C11 | 0.0353 (7) | 0.0481 (8) | 0.0469 (8) | 0.0064 (6) | 0.0184 (6) | 0.0095 (6) |
C12 | 0.0307 (7) | 0.0447 (8) | 0.0466 (8) | 0.0029 (6) | 0.0177 (6) | 0.0024 (6) |
C13 | 0.0311 (7) | 0.0470 (8) | 0.0442 (8) | −0.0004 (6) | 0.0203 (6) | 0.0012 (6) |
C14 | 0.0413 (8) | 0.0624 (10) | 0.0590 (10) | 0.0025 (7) | 0.0262 (7) | 0.0196 (8) |
C15 | 0.0429 (9) | 0.1156 (16) | 0.0581 (10) | 0.0101 (10) | 0.0279 (8) | 0.0288 (11) |
C16 | 0.0689 (14) | 0.195 (3) | 0.0909 (17) | 0.0497 (17) | 0.0475 (13) | 0.078 (2) |
C17 | 0.125 (2) | 0.0777 (15) | 0.129 (2) | −0.0289 (14) | 0.083 (2) | 0.0060 (14) |
C18 | 0.0423 (9) | 0.1250 (18) | 0.0686 (12) | 0.0133 (10) | 0.0340 (9) | 0.0399 (12) |
C19 | 0.0299 (7) | 0.0508 (8) | 0.0478 (8) | 0.0040 (6) | 0.0176 (6) | 0.0065 (6) |
C20 | 0.0319 (7) | 0.0571 (9) | 0.0484 (8) | 0.0031 (6) | 0.0191 (6) | 0.0033 (7) |
C21 | 0.0432 (8) | 0.0526 (9) | 0.0642 (10) | 0.0049 (7) | 0.0251 (8) | 0.0062 (8) |
C22 | 0.0806 (14) | 0.0597 (11) | 0.0947 (15) | 0.0130 (10) | 0.0385 (12) | −0.0020 (11) |
C23 | 0.0811 (14) | 0.0732 (13) | 0.0703 (12) | 0.0236 (11) | 0.0330 (11) | 0.0244 (10) |
C24 | 0.280 (6) | 0.137 (3) | 0.115 (3) | 0.066 (4) | 0.070 (4) | −0.008 (3) |
O1—C3 | 1.3547 (18) | C12—C19 | 1.5183 (19) |
O1—H1O1 | 0.85 (3) | C14—C15 | 1.506 (3) |
O2—C4 | 1.3529 (19) | C14—C17 | 1.531 (3) |
O2—H1O2 | 0.8200 | C14—C18 | 1.543 (2) |
O3—C7 | 1.2617 (18) | C15—C16 | 1.324 (3) |
O4—C13 | 1.3526 (17) | C15—H15A | 0.9300 |
O4—H1O4 | 0.8200 | C16—H16A | 0.9300 |
O5—C11 | 1.3550 (18) | C16—H16B | 0.9300 |
O5—H5A | 0.89 (3) | C17—H17A | 0.9600 |
O6—C9 | 1.3616 (17) | C17—H17B | 0.9600 |
O6—C5 | 1.3627 (17) | C17—H17C | 0.9600 |
O7—C24 | 1.279 (5) | C18—H18A | 0.9600 |
O7—H1O7 | 0.831 (10) | C18—H18B | 0.9600 |
C1—C2 | 1.370 (2) | C18—H18C | 0.9600 |
C1—C6 | 1.405 (2) | C19—C20 | 1.499 (2) |
C1—H1B | 0.9300 | C19—H19A | 0.9700 |
C2—C3 | 1.393 (2) | C19—H19B | 0.9700 |
C2—H2A | 0.9300 | C20—C21 | 1.324 (2) |
C3—C4 | 1.385 (2) | C20—H20A | 0.9300 |
C4—C5 | 1.391 (2) | C21—C23 | 1.496 (3) |
C5—C6 | 1.389 (2) | C21—C22 | 1.507 (3) |
C6—C7 | 1.445 (2) | C22—H22A | 0.9600 |
C7—C8 | 1.443 (2) | C22—H22B | 0.9600 |
C8—C9 | 1.410 (2) | C22—H22C | 0.9600 |
C8—C13 | 1.4193 (19) | C23—H23A | 0.9600 |
C9—C10 | 1.392 (2) | C23—H23B | 0.9600 |
C10—C11 | 1.411 (2) | C23—H23C | 0.9600 |
C10—C14 | 1.551 (2) | C24—H24A | 0.9600 |
C11—C12 | 1.404 (2) | C24—H24B | 0.9600 |
C12—C13 | 1.376 (2) | C24—H24C | 0.9600 |
C3—O1—H1O1 | 109.7 (18) | C18—C14—C10 | 116.03 (13) |
C4—O2—H1O2 | 109.5 | C16—C15—C14 | 127.2 (3) |
C13—O4—H1O4 | 109.5 | C16—C15—H15A | 116.4 |
C11—O5—H5A | 108.6 (17) | C14—C15—H15A | 116.4 |
C9—O6—C5 | 121.30 (11) | C15—C16—H16A | 120.0 |
C24—O7—H1O7 | 104 (3) | C15—C16—H16B | 120.0 |
C2—C1—C6 | 120.51 (14) | H16A—C16—H16B | 120.0 |
C2—C1—H1B | 119.7 | C14—C17—H17A | 109.5 |
C6—C1—H1B | 119.7 | C14—C17—H17B | 109.5 |
C1—C2—C3 | 120.42 (14) | H17A—C17—H17B | 109.5 |
C1—C2—H2A | 119.8 | C14—C17—H17C | 109.5 |
C3—C2—H2A | 119.8 | H17A—C17—H17C | 109.5 |
O1—C3—C4 | 115.40 (14) | H17B—C17—H17C | 109.5 |
O1—C3—C2 | 124.11 (14) | C14—C18—H18A | 109.5 |
C4—C3—C2 | 120.49 (14) | C14—C18—H18B | 109.5 |
O2—C4—C3 | 123.39 (13) | H18A—C18—H18B | 109.5 |
O2—C4—C5 | 118.20 (13) | C14—C18—H18C | 109.5 |
C3—C4—C5 | 118.39 (14) | H18A—C18—H18C | 109.5 |
O6—C5—C6 | 122.75 (12) | H18B—C18—H18C | 109.5 |
O6—C5—C4 | 115.11 (12) | C20—C19—C12 | 112.88 (12) |
C6—C5—C4 | 122.13 (13) | C20—C19—H19A | 109.0 |
C5—C6—C1 | 118.02 (13) | C12—C19—H19A | 109.0 |
C5—C6—C7 | 118.51 (13) | C20—C19—H19B | 109.0 |
C1—C6—C7 | 123.47 (13) | C12—C19—H19B | 109.0 |
O3—C7—C8 | 121.37 (13) | H19A—C19—H19B | 107.8 |
O3—C7—C6 | 121.45 (13) | C21—C20—C19 | 128.13 (15) |
C8—C7—C6 | 117.18 (12) | C21—C20—H20A | 115.9 |
C9—C8—C13 | 117.94 (13) | C19—C20—H20A | 115.9 |
C9—C8—C7 | 120.60 (13) | C20—C21—C23 | 124.55 (17) |
C13—C8—C7 | 121.46 (13) | C20—C21—C22 | 121.00 (17) |
O6—C9—C10 | 116.49 (12) | C23—C21—C22 | 114.45 (16) |
O6—C9—C8 | 119.66 (12) | C21—C22—H22A | 109.5 |
C10—C9—C8 | 123.84 (13) | C21—C22—H22B | 109.5 |
C9—C10—C11 | 114.48 (13) | H22A—C22—H22B | 109.5 |
C9—C10—C14 | 125.11 (13) | C21—C22—H22C | 109.5 |
C11—C10—C14 | 120.26 (13) | H22A—C22—H22C | 109.5 |
O5—C11—C12 | 113.44 (13) | H22B—C22—H22C | 109.5 |
O5—C11—C10 | 121.74 (13) | C21—C23—H23A | 109.5 |
C12—C11—C10 | 124.81 (13) | C21—C23—H23B | 109.5 |
C13—C12—C11 | 117.79 (12) | H23A—C23—H23B | 109.5 |
C13—C12—C19 | 121.96 (13) | C21—C23—H23C | 109.5 |
C11—C12—C19 | 120.25 (13) | H23A—C23—H23C | 109.5 |
O4—C13—C12 | 119.35 (12) | H23B—C23—H23C | 109.5 |
O4—C13—C8 | 119.54 (13) | O7—C24—H24A | 109.5 |
C12—C13—C8 | 121.11 (13) | O7—C24—H24B | 109.5 |
C15—C14—C17 | 112.63 (19) | H24A—C24—H24B | 109.5 |
C15—C14—C18 | 102.58 (16) | O7—C24—H24C | 109.5 |
C17—C14—C18 | 108.52 (18) | H24A—C24—H24C | 109.5 |
C15—C14—C10 | 110.00 (14) | H24B—C24—H24C | 109.5 |
C17—C14—C10 | 107.19 (16) | ||
C6—C1—C2—C3 | −0.3 (2) | C8—C9—C10—C11 | −0.6 (2) |
C1—C2—C3—O1 | −178.16 (15) | O6—C9—C10—C14 | 2.9 (2) |
C1—C2—C3—C4 | 2.0 (2) | C8—C9—C10—C14 | −176.02 (14) |
O1—C3—C4—O2 | −0.4 (2) | C9—C10—C11—O5 | −176.97 (14) |
C2—C3—C4—O2 | 179.48 (15) | C14—C10—C11—O5 | −1.3 (2) |
O1—C3—C4—C5 | 177.91 (14) | C9—C10—C11—C12 | 1.9 (2) |
C2—C3—C4—C5 | −2.2 (2) | C14—C10—C11—C12 | 177.57 (15) |
C9—O6—C5—C6 | −0.3 (2) | O5—C11—C12—C13 | 176.72 (14) |
C9—O6—C5—C4 | 178.79 (13) | C10—C11—C12—C13 | −2.2 (2) |
O2—C4—C5—O6 | 0.1 (2) | O5—C11—C12—C19 | −2.8 (2) |
C3—C4—C5—O6 | −178.31 (13) | C10—C11—C12—C19 | 178.28 (14) |
O2—C4—C5—C6 | 179.21 (14) | C11—C12—C13—O4 | −179.14 (13) |
C3—C4—C5—C6 | 0.8 (2) | C19—C12—C13—O4 | 0.4 (2) |
O6—C5—C6—C1 | 179.88 (13) | C11—C12—C13—C8 | 1.2 (2) |
C4—C5—C6—C1 | 0.8 (2) | C19—C12—C13—C8 | −179.33 (13) |
O6—C5—C6—C7 | 0.5 (2) | C9—C8—C13—O4 | −179.69 (13) |
C4—C5—C6—C7 | −178.59 (13) | C7—C8—C13—O4 | 1.2 (2) |
C2—C1—C6—C5 | −1.1 (2) | C9—C8—C13—C12 | 0.0 (2) |
C2—C1—C6—C7 | 178.30 (14) | C7—C8—C13—C12 | −179.13 (14) |
C5—C6—C7—O3 | 179.25 (14) | C9—C10—C14—C15 | −137.06 (17) |
C1—C6—C7—O3 | −0.1 (2) | C11—C10—C14—C15 | 47.7 (2) |
C5—C6—C7—C8 | −0.4 (2) | C9—C10—C14—C17 | 100.2 (2) |
C1—C6—C7—C8 | −179.77 (14) | C11—C10—C14—C17 | −75.0 (2) |
O3—C7—C8—C9 | −179.44 (14) | C9—C10—C14—C18 | −21.2 (3) |
C6—C7—C8—C9 | 0.2 (2) | C11—C10—C14—C18 | 163.56 (17) |
O3—C7—C8—C13 | −0.3 (2) | C17—C14—C15—C16 | −12.2 (3) |
C6—C7—C8—C13 | 179.32 (13) | C18—C14—C15—C16 | 104.3 (2) |
C5—O6—C9—C10 | −178.87 (13) | C10—C14—C15—C16 | −131.7 (2) |
C5—O6—C9—C8 | 0.1 (2) | C13—C12—C19—C20 | −93.25 (17) |
C13—C8—C9—O6 | −179.22 (12) | C11—C12—C19—C20 | 86.25 (17) |
C7—C8—C9—O6 | −0.1 (2) | C12—C19—C20—C21 | −115.91 (17) |
C13—C8—C9—C10 | −0.3 (2) | C19—C20—C21—C23 | −0.3 (3) |
C7—C8—C9—C10 | 178.84 (14) | C19—C20—C21—C22 | −179.77 (16) |
O6—C9—C10—C11 | 178.37 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O1···O7i | 0.85 (3) | 1.79 (3) | 2.632 (2) | 170 (3) |
O2—H1O2···O1 | 0.82 | 2.29 | 2.7117 (19) | 113 |
O2—H1O2···O4ii | 0.82 | 2.03 | 2.7995 (19) | 155 |
O4—H1O4···O3 | 0.82 | 1.81 | 2.5505 (18) | 149 |
O7—H1O7···O3 | 0.83 (2) | 1.95 (2) | 2.755 (2) | 161 (4) |
C18—H18B···O6 | 0.96 | 2.25 | 2.638 (2) | 103 |
C19—H19A···O2iii | 0.97 | 2.54 | 3.378 (2) | 145 |
C19—H19A···O4 | 0.97 | 2.50 | 2.8451 (19) | 101 |
C22—H22B···Cg1iv | 0.96 | 3.10 | 3.705 (2) | 123 |
Symmetry codes: (i) x−1, y, z−1; (ii) x−1, y, z; (iii) x+1, y, z; (iv) x+1, −y−1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C23H24O6·CH4O |
Mr | 428.46 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 297 |
a, b, c (Å) | 10.0411 (8), 20.1500 (16), 12.1807 (7) |
β (°) | 117.534 (5) |
V (Å3) | 2185.4 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.55 × 0.29 × 0.19 |
Data collection | |
Diffractometer | Siemens SMART CCD area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.950, 0.982 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 11274, 3834, 3429 |
Rint | 0.018 |
(sin θ/λ)max (Å−1) | 0.595 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.048, 0.141, 1.05 |
No. of reflections | 3834 |
No. of parameters | 296 |
No. of restraints | 1 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.19, −0.36 |
Computer programs: SMART (Siemens, 1996), SAINT (Siemens, 1996), SHELXTL (Sheldrick, 1997) and PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H1O1···O7i | 0.85 (3) | 1.79 (3) | 2.632 (2) | 170 (3) |
O2—H1O2···O1 | 0.82 | 2.2852 | 2.7117 (19) | 113 |
O2—H1O2···O4ii | 0.82 | 2.0336 | 2.7995 (19) | 155 |
O4—H1O4···O3 | 0.82 | 1.8135 | 2.5505 (18) | 149 |
O7—H1O7···O3 | 0.83 (2) | 1.954 (19) | 2.755 (2) | 161 (4) |
C18—H18B···O6 | 0.96 | 2.2540 | 2.638 (2) | 103 |
C19—H19A···O2iii | 0.97 | 2.5399 | 3.378 (2) | 145 |
C19—H19A···O4 | 0.97 | 2.4985 | 2.8451 (19) | 101 |
C22—H22B···Cg1iv | 0.96 | 3.0967 | 3.705 (2) | 123 |
Symmetry codes: (i) x−1, y, z−1; (ii) x−1, y, z; (iii) x+1, y, z; (iv) x+1, −y−1/2, z−1/2. |
Some species of plants in the genus Cratoxylum have been used for the treatment of diuretic, stomachic, and tonic effects (Kitanov et al., 1988), as well as for diarrhea and flatulence (Aderson, 1986). In our ongoing research of bioactive compounds from medicinal plants, the title compound, gerontoxanthone I, was isolated from a dichloromethane extract of the roots of Cratoxylum formosum ssp. pruniflorum, collected from Nhongkai Province in the northeasthern part of Thailand. As the title compound showed strong antibacterial and cytotoxic activities (Boonnak, Karalai, et al., 2006), its X-ray crystal structure was determined in order to gain more information for further SAR (Structure and Activity Relationship) analysis. In our previous studies, we have reported the crystal structures of xanthone and anthraquinone compounds from the roots and barks of this plant (Boonnak et al., 2005; Boonnak, Chantrapromma & Fun, 2006; Boonnak, Karalai et al., 2006; Chantrapromma et al., 2005; 2006; Fun et al., 2006). We report here the crystal structure of the methanol solvate of gerontoxanthone I.
In the title compound (Fig. 1), the xanthone skeleton (rings A, B and C) is essentially planar, the maximum deviation from planarity being 0.043 (2) Å for atom C3. The O2—H2A···O1 and O4—H4A···O3 hydrogen bonds generate S(5) and S(6) ring motifs, respectively (Bernstein et al., 1995) and help to stabilize the planarity of the structure. There are also weak intramolecular C—H···O interactions; C18—H18B···O6 and C19—H19A···O4 generate S(6) and S(5) ring motifs respectively (Table 1).
The orientation of the 3-methylbut-2-enyl [C19–C23] side chain with respect to the benzene ring C is indicated by the torsion angle of C13—C12—C19—C20 = -93.25 (17)°, [90.6 (2)° in the monohydrate compound (Boonnak, Chantrapromma & Fun, 2006)], indicating a (-)-synclinal conformation (Fig. 1). The 1,1-dimethylprop-2-enyl [C14–C18] substituent is attached to the benzene ring at C10 with the torsion angle C9—C10—C14—C15 of -137.06 (17)° [-52.6 (3)° in Boonnak, Chantrapromma & Fun, 2006], indicating a (-)-anticlinal conformation. Bond distances and angles in the title compound are in normal ranges (Allen et al., 1987) and comparable to those reported in the gerontoxanthone I monohydrate (Boonnak, Chantrapromma & Fun, 2006) and other closely related structures (Boonnak et al., 2005; Boonnak, Karalai et al., 2006; Chantrapromma et al., 2005; 2006; Fun et al., 2006). The methanol solvent molecule is also involved in hydrogen bonds (Table 1).
In the crystal packing (Fig. 2), the gerontoxanthone I molecules are linked together into chains along the a axis by the intermolecular O2—H1O2···O4 hydrogen bond (symmetry code: -1 + x, y, z) and weak C19—H19A···O2 interaction (symmetry code: 1 + x, y, z) (Table 1) and are further linked to the methanol molecules by O1—H1O1···O7 (symmetry code: -1 + x, y, -1 + z) and O7—H1O7···O3 (symmetry code: 1 - x, 1 - y, 1 - z) hydrogen bonds (Table 1). This packing is different from the three dimensional crystal packing of the monohydrate compound (Boonnak, Chantrapromma & Fun, 2006). The crystal structure is stabilized by intra- and intermolecular O—H···O hydrogen bonds, weak C—H···O intra- and intramolecular interactions (Table 1). In addition, the molecular packing is further stabilized by a C—H···π interaction between one of the methyl groups of the 3-methylbut-2-enyl side chain and the centroid of the C1–C6 benzene ring (Cg1) (Table 1).