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Nodosin, or 13-deoxy-5β-hydroxyenmein, C20H26O6, has been established as a pentacyclic 6,7-seco-ent-kaurane diterpenoid with an enmein skeleton. Two independent intermolecular O—H...O hydrogen bonds are present and link each mol­ecule to four neighbours.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100017406/bm1432sup1.cif
Contains datablocks global, I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270100017406/bm1432Isup2.hkl
Contains datablock I

CCDC reference: 160006

Comment top

The diterpenoid nodosin, (I), has been found in Rabdosia plants (Takeda et al., 1982) and possesses antitumour activity against P 388 lymphocytic leukemia innoculated into mice (Nagao et al., 1982). The X-ray structure analysis shows that nodosin is a structural isomer of enmein (Fujita et al., 1976) with the β-hydroxy group attached to C12 (nodosin) rather than C3 (enmein). \sch

From the assumed absolute stereochemistry shown in Fig. 1, the eight chiral centres present are S for C1, C8, C10, C11 and C14, and R for C5, C6 and C12. The ring conformations (see scheme) approximate to chair, screw-boat, boat, C15 envelope and half-chair For A—E, respectively.

Details of two well defined intermolecular hydrogen bonds are shown in Table 2. Here the two hydroxy groups O1 and O6 act as donor atoms and O2 and O4 act as acceptor atoms. Within the molecule, O6 is also close to H1A (2.26 Å), H5 (2.54 Å) and H15B (2.35 Å) and these interactions result in a longer O6—C12 of 1.435 (4) Å compared with 01-C6 of 1.403 (3) Å. As shown in Fig. 2 the two independent hydrogen bonds result in an arrangement such that each molecule is held in the crystal by four intermolecular hydrogen bonds. The hydrogen bonding pattern is two-dimensional as there are no hydrogen bonds linking molecules in the direction of the b axis.

Some geometrical features of the molecule determined by PLATON (Spek, 1998) are shown in Table 1. Here the longest bond, C10—C11 1.58 (4) Å, is located where in-plane bending due to ring strain is most evident. The deviations from ideal sp3 angular values around C10 are shown by C16—C10—C15 101.2 (3)° and C9—C10—C11 117.3 (3)°. Table 1 also shows the endocyclic torsion angles that describe the somewhat planar portions of the fused rings.

Similar structures based on spectroscopic evidence have been reported (Takeda et al., 1986) and the absolute configuration of a related structure, acetyl-bromoacetyl-dihydroenmein (Natsume & Iltaka, 1966) is known. Unfortunately the name, nodosin, has also been applied to a glycosylisoflavone (Ilyas et al., 1994).

Related literature top

For related literature, see: Fujita et al. (1976); Ilyas et al. (1994); Nagao et al. (1982); Natsume & Iltaka (1966); Spek (1998); Takeda et al. (1982, 1986).

Experimental top

Nodosin was extracted from the Chinese medicinal plant Rabdosia serra (Maxim.) Hara (Family: Labiatae). The extracting solvent was aqueous ethanol (70%) and the recrystallizing solvent was acetone.

Refinement top

The hydroxy hydrogen atoms were freely refined and the remaining hydrogen atoms were initially placed in calculated positions and thereafter allowed to ride on their attached atoms with common isotropic temperature factors which converged to 0.029 (2) Å2 (non-methyl H atoms) and 0.051 (5) Å2 (methyl H atoms). Constrained C—H distances were 0.95, 1.00, 0.99 and 0.98 Å for sp2, methine, methylene and methyl groups, respectively.

Computing details top

Data collection: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998); cell refinement: DENZO and COLLECT; data reduction: DENZO and COLLECT; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997).

Figures top
[Figure 1] Fig. 1. The atomic arrangement in the molecule (50% probability displacement ellipsoids).
[Figure 2] Fig. 2. The intermolecular hydrogen bonding viewed normal to the (010) plane. Symmetry operations are shown by superscripted Roman numerals [(i) -1 + x, y, z; (ii) 1 + x, y, z; (iii) 1/2 - x, -y, -1/2 - z; (iv) 1/2 - x, -y, 1/2 + z].
Nodosin top
Crystal data top
C20H26O6Dx = 1.330 Mg m3
Mr = 362.41Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121Cell parameters from 6964 reflections
a = 7.474 (3) Åθ = 1.9–27.5°
b = 15.262 (6) ŵ = 0.10 mm1
c = 15.870 (8) ÅT = 150 K
V = 1810.3 (14) Å3Block, colourless
Z = 40.1 × 0.08 × 0.08 mm
F(000) = 776
Data collection top
Enraf Nonius kappaCCD area detector
diffractometer
2220 independent reflections
Radiation source: Enraf Nonius FR591 rotating anode1534 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.072
Detector resolution: 9.091 pixels mm-1θmax = 27.5°, θmin = 1.9°
ϕ and ω scans to fill Ewald sphereh = 69
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
k = 1819
Tmin = 0.95, Tmax = 0.99l = 2020
6964 measured reflections
Refinement top
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)] = 0.047 w = 1/[σ2(Fo2) + (0.0392P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.103(Δ/σ)max = 0.001
S = 1.02Δρmax = 0.21 e Å3
2220 reflectionsΔρmin = 0.21 e Å3
246 parametersExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.022 (2)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983)
Secondary atom site location: difference Fourier mapAbsolute structure parameter: not reliably determined
Crystal data top
C20H26O6V = 1810.3 (14) Å3
Mr = 362.41Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 7.474 (3) ŵ = 0.10 mm1
b = 15.262 (6) ÅT = 150 K
c = 15.870 (8) Å0.1 × 0.08 × 0.08 mm
Data collection top
Enraf Nonius kappaCCD area detector
diffractometer
2220 independent reflections
Absorption correction: multi-scan
(SORTAV; Blessing, 1995)
1534 reflections with I > 2σ(I)
Tmin = 0.95, Tmax = 0.99Rint = 0.072
6964 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.047H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.103Δρmax = 0.21 e Å3
S = 1.02Δρmin = 0.21 e Å3
2220 reflectionsAbsolute structure: Flack (1983)
246 parametersAbsolute structure parameter: not reliably determined
0 restraints
Special details top

Experimental. Please note cell_measurement_ fields are not relevant to area detector data, the entire data set is used to refine the cell, which is indexed from all observed reflections in a 10 degree phi range.

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) top
xyzUiso*/Ueq
O10.1276 (3)0.02306 (14)0.24840 (15)0.0318 (6)
H10.216 (5)0.050 (2)0.278 (2)0.049 (12)*
O20.3339 (3)0.05284 (14)0.16645 (13)0.0304 (6)
O30.0567 (3)0.16159 (13)0.04022 (13)0.0281 (5)
O40.0819 (3)0.06953 (15)0.14519 (14)0.0376 (6)
O50.1684 (3)0.09942 (15)0.06004 (14)0.0381 (6)
O60.3190 (3)0.08013 (14)0.12022 (14)0.0294 (6)
H60.423 (5)0.070 (2)0.140 (2)0.037 (11)*
C10.0074 (4)0.17544 (19)0.0467 (2)0.0250 (7)
H1A0.14110.17230.04680.029 (2)*
C20.0479 (5)0.26616 (19)0.0727 (2)0.0298 (8)
H2A0.17910.27290.06680.029 (2)*
H2B0.01120.31020.03640.029 (2)*
C30.0067 (5)0.2799 (2)0.1642 (2)0.0322 (8)
H3A0.13670.26910.17000.029 (2)*
H3B0.01680.34150.18030.029 (2)*
C40.0943 (4)0.2193 (2)0.2236 (2)0.0293 (8)
C50.0602 (4)0.12166 (18)0.19773 (18)0.0223 (7)
H50.05890.10330.22040.029 (2)*
C60.2019 (4)0.0596 (2)0.2318 (2)0.0256 (7)
H6A0.25670.08430.28410.029 (2)*
C70.2643 (4)0.0852 (2)0.08756 (19)0.0274 (7)
H7A0.32530.14020.07130.029 (2)*
H7B0.28250.04150.04230.029 (2)*
C80.0649 (4)0.10143 (19)0.10162 (18)0.0217 (7)
C90.0350 (4)0.0818 (2)0.07301 (19)0.0265 (8)
C100.0567 (4)0.0113 (2)0.02202 (19)0.0241 (7)
C110.0379 (4)0.01631 (19)0.07722 (19)0.0223 (7)
H110.04160.03350.09370.029 (2)*
C120.2170 (4)0.0005 (2)0.12226 (19)0.0236 (7)
H120.19070.01350.18260.029 (2)*
C130.3202 (4)0.07723 (19)0.08453 (19)0.0267 (7)
H13A0.27700.13180.11140.029 (2)*
H13B0.44840.07070.09890.029 (2)*
C140.3028 (4)0.0869 (2)0.01186 (19)0.0283 (8)
H140.41480.11100.03740.029 (2)*
C150.2544 (4)0.0032 (2)0.0495 (2)0.0285 (7)
H15A0.26650.00350.11170.029 (2)*
H15B0.32880.05060.02530.029 (2)*
C160.0147 (5)0.0800 (2)0.0440 (2)0.0300 (8)
C170.1414 (4)0.1404 (2)0.0360 (2)0.0305 (8)
C180.1260 (5)0.2261 (2)0.0489 (2)0.0408 (9)
H18A0.01340.25050.06370.029 (2)*
H18B0.22770.26300.04340.029 (2)*
C190.0169 (5)0.2312 (2)0.3125 (2)0.0389 (9)
H19A0.08080.19290.35190.051 (5)*
H19B0.03100.29230.33000.051 (5)*
H19C0.11040.21580.31220.051 (5)*
C200.2939 (5)0.2458 (2)0.2266 (2)0.0344 (9)
H20A0.34680.23890.17050.051 (5)*
H20B0.30410.30700.24450.051 (5)*
H20C0.35730.20820.26670.051 (5)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0284 (14)0.0306 (13)0.0364 (14)0.0046 (11)0.0065 (11)0.0119 (11)
O20.0204 (13)0.0423 (13)0.0284 (12)0.0020 (11)0.0007 (10)0.0082 (11)
O30.0332 (13)0.0307 (12)0.0202 (11)0.0024 (10)0.0011 (11)0.0026 (10)
O40.0456 (16)0.0412 (14)0.0259 (13)0.0028 (12)0.0097 (11)0.0006 (11)
O50.0378 (16)0.0384 (13)0.0382 (15)0.0109 (12)0.0082 (12)0.0029 (11)
O60.0169 (13)0.0279 (13)0.0433 (14)0.0016 (11)0.0044 (11)0.0024 (11)
C10.0274 (18)0.0286 (16)0.0191 (16)0.0018 (14)0.0004 (14)0.0016 (15)
C20.034 (2)0.0253 (17)0.0303 (19)0.0004 (15)0.0051 (16)0.0032 (15)
C30.033 (2)0.0257 (17)0.037 (2)0.0003 (15)0.0000 (16)0.0018 (16)
C40.0278 (19)0.0301 (17)0.0301 (18)0.0040 (15)0.0022 (15)0.0019 (15)
C50.0193 (18)0.0259 (17)0.0216 (16)0.0019 (14)0.0003 (14)0.0026 (13)
C60.0229 (18)0.0269 (17)0.0270 (17)0.0009 (14)0.0024 (14)0.0021 (14)
C70.0222 (18)0.0350 (19)0.0249 (16)0.0001 (15)0.0023 (14)0.0039 (15)
C80.0146 (16)0.0248 (16)0.0256 (17)0.0006 (14)0.0005 (13)0.0020 (14)
C90.0251 (19)0.0294 (19)0.0251 (18)0.0049 (15)0.0022 (14)0.0003 (16)
C100.0218 (17)0.0252 (16)0.0254 (17)0.0036 (14)0.0013 (14)0.0002 (14)
C110.0198 (18)0.0259 (16)0.0212 (16)0.0019 (14)0.0003 (13)0.0012 (14)
C120.0198 (18)0.0250 (16)0.0261 (17)0.0003 (15)0.0001 (13)0.0012 (14)
C130.0207 (18)0.0268 (17)0.0326 (18)0.0002 (15)0.0011 (14)0.0018 (15)
C140.027 (2)0.0257 (18)0.0322 (18)0.0005 (15)0.0046 (15)0.0020 (15)
C150.0265 (17)0.0292 (17)0.0297 (18)0.0017 (15)0.0036 (14)0.0011 (16)
C160.037 (2)0.0335 (19)0.0191 (16)0.0072 (17)0.0004 (15)0.0001 (16)
C170.035 (2)0.0272 (18)0.0293 (19)0.0026 (16)0.0046 (16)0.0005 (16)
C180.050 (3)0.033 (2)0.039 (2)0.0042 (18)0.0048 (18)0.0044 (17)
C190.045 (2)0.040 (2)0.032 (2)0.0072 (19)0.0065 (17)0.0079 (17)
C200.037 (2)0.0340 (19)0.0326 (19)0.0106 (16)0.0038 (16)0.0024 (16)
Geometric parameters (Å, º) top
O1—C61.403 (4)C5—C61.521 (4)
O2—C61.435 (4)C5—C81.557 (4)
O2—C71.443 (4)C7—C81.527 (4)
O3—C91.335 (4)C8—C111.558 (4)
O3—C11.475 (4)C9—C101.510 (4)
O4—C91.212 (4)C10—C161.533 (4)
O5—C161.213 (4)C10—C151.546 (4)
O6—C121.435 (4)C10—C111.583 (4)
C1—C21.503 (4)C11—C121.537 (4)
C1—C81.526 (4)C12—C131.536 (4)
C2—C31.522 (5)C13—C141.542 (4)
C3—C41.521 (4)C14—C171.507 (5)
C4—C191.535 (4)C14—C151.542 (4)
C4—C201.546 (5)C16—C171.492 (5)
C4—C51.566 (4)C17—C181.329 (4)
C6—O2—C7110.8 (2)O4—C9—O3118.3 (3)
C9—O3—C1117.1 (2)O4—C9—C10121.9 (3)
O3—C1—C2107.4 (2)O3—C9—C10119.7 (3)
O3—C1—C8108.2 (2)C9—C10—C16111.6 (3)
C2—C1—C8115.3 (3)C9—C10—C15109.9 (3)
C1—C2—C3108.4 (3)C16—C10—C15101.2 (3)
C4—C3—C2112.0 (3)C9—C10—C11117.3 (3)
C3—C4—C19108.1 (3)C16—C10—C11103.8 (2)
C3—C4—C20109.8 (3)C15—C10—C11111.7 (2)
C19—C4—C20107.7 (3)C12—C11—C8116.4 (2)
C3—C4—C5109.6 (3)C12—C11—C10112.2 (2)
C19—C4—C5106.9 (3)C8—C11—C10109.3 (2)
C20—C4—C5114.4 (3)O6—C12—C13112.3 (2)
C6—C5—C8102.1 (2)O6—C12—C11108.6 (2)
C6—C5—C4112.7 (3)C13—C12—C11112.2 (3)
C8—C5—C4116.2 (2)C12—C13—C14114.7 (3)
O1—C6—O2110.1 (2)C17—C14—C15101.4 (3)
O1—C6—C5110.6 (3)C17—C14—C13111.8 (3)
O2—C6—C5105.5 (2)C15—C14—C13108.6 (3)
O2—C7—C8106.3 (2)C14—C15—C10100.8 (3)
C1—C8—C7112.5 (3)O5—C16—C17127.4 (3)
C1—C8—C5113.9 (2)O5—C16—C10126.8 (3)
C7—C8—C5101.4 (2)C17—C16—C10105.7 (3)
C1—C8—C11107.5 (2)C18—C17—C16121.8 (3)
C7—C8—C11108.0 (3)C18—C17—C14130.0 (3)
C5—C8—C11113.4 (2)C16—C17—C14108.2 (3)
C9—O3—C1—C2174.3 (3)O4—C9—C10—C11154.2 (3)
C9—O3—C1—C849.2 (3)O3—C9—C10—C1129.7 (4)
O3—C1—C2—C3176.5 (2)C1—C8—C11—C1286.0 (3)
C8—C1—C2—C355.8 (4)C7—C8—C11—C12152.4 (3)
C1—C2—C3—C465.1 (3)C5—C8—C11—C1240.9 (4)
C2—C3—C4—C19174.3 (3)C1—C8—C11—C1042.5 (3)
C2—C3—C4—C2068.5 (3)C7—C8—C11—C1079.1 (3)
C2—C3—C4—C558.1 (4)C5—C8—C11—C10169.3 (2)
C3—C4—C5—C6159.8 (3)C9—C10—C11—C12135.2 (3)
C19—C4—C5—C683.3 (3)C16—C10—C11—C12101.2 (3)
C20—C4—C5—C635.9 (4)C15—C10—C11—C127.1 (4)
C3—C4—C5—C842.5 (4)C9—C10—C11—C84.4 (4)
C19—C4—C5—C8159.4 (3)C16—C10—C11—C8128.0 (3)
C20—C4—C5—C881.4 (4)C15—C10—C11—C8123.7 (3)
C7—O2—C6—O1103.5 (3)C8—C11—C12—O646.8 (3)
C7—O2—C6—C515.7 (3)C10—C11—C12—O680.2 (3)
C8—C5—C6—O186.3 (3)C8—C11—C12—C13171.5 (2)
C4—C5—C6—O1148.3 (3)C10—C11—C12—C1344.4 (3)
C8—C5—C6—O232.7 (3)O6—C12—C13—C1486.2 (3)
C4—C5—C6—O292.7 (3)C11—C12—C13—C1436.4 (4)
C6—O2—C7—C88.5 (3)C12—C13—C14—C1787.3 (3)
O3—C1—C8—C747.2 (3)C12—C13—C14—C1523.7 (4)
C2—C1—C8—C773.1 (3)C17—C14—C15—C1044.5 (3)
O3—C1—C8—C5161.8 (2)C13—C14—C15—C1073.3 (3)
C2—C1—C8—C541.5 (4)C9—C10—C15—C14163.4 (2)
O3—C1—C8—C1171.6 (3)C16—C10—C15—C1445.3 (3)
C2—C1—C8—C11168.1 (3)C11—C10—C15—C1464.6 (3)
O2—C7—C8—C1150.2 (2)C9—C10—C16—O537.8 (4)
O2—C7—C8—C528.1 (3)C15—C10—C16—O5154.6 (3)
O2—C7—C8—C1191.3 (3)C11—C10—C16—O589.5 (4)
C6—C5—C8—C1157.6 (3)C9—C10—C16—C17145.8 (3)
C4—C5—C8—C134.5 (4)C15—C10—C16—C1729.0 (3)
C6—C5—C8—C736.5 (3)C11—C10—C16—C1786.9 (3)
C4—C5—C8—C786.5 (3)O5—C16—C17—C182.1 (5)
C6—C5—C8—C1179.0 (3)C10—C16—C17—C18178.5 (3)
C4—C5—C8—C11157.9 (3)O5—C16—C17—C14177.6 (3)
C1—O3—C9—O4177.9 (3)C10—C16—C17—C141.2 (3)
C1—O3—C9—C101.7 (4)C15—C14—C17—C18153.2 (4)
O4—C9—C10—C1634.6 (4)C13—C14—C17—C1891.3 (4)
O3—C9—C10—C16149.3 (3)C15—C14—C17—C1627.1 (3)
O4—C9—C10—C1576.8 (4)C13—C14—C17—C1688.4 (3)
O3—C9—C10—C1599.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O4i0.91 (3)1.96 (4)2.841 (3)162 (3)
O6—H6···O2ii0.85 (4)1.88 (4)2.728 (3)171 (3)
Symmetry codes: (i) x+1/2, y, z1/2; (ii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC20H26O6
Mr362.41
Crystal system, space groupOrthorhombic, P212121
Temperature (K)150
a, b, c (Å)7.474 (3), 15.262 (6), 15.870 (8)
V3)1810.3 (14)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.1 × 0.08 × 0.08
Data collection
DiffractometerEnraf Nonius kappaCCD area detector
diffractometer
Absorption correctionMulti-scan
(SORTAV; Blessing, 1995)
Tmin, Tmax0.95, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
6964, 2220, 1534
Rint0.072
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.047, 0.103, 1.02
No. of reflections2220
No. of parameters246
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.21, 0.21
Absolute structureFlack (1983)
Absolute structure parameternot reliably determined

Computer programs: DENZO (Otwinowski & Minor, 1997) and COLLECT (Hooft, 1998), DENZO and COLLECT, SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997).

Selected geometric parameters (Å, º) top
O1—C61.403 (4)C1—C21.503 (4)
O5—C161.213 (4)C10—C111.583 (4)
O6—C121.435 (4)
C7—C8—C5101.4 (2)O5—C16—C10126.8 (3)
C16—C10—C15101.2 (3)C17—C16—C10105.7 (3)
C9—C10—C11117.3 (3)C18—C17—C16121.8 (3)
C12—C11—C8116.4 (2)C18—C17—C14130.0 (3)
O5—C16—C17127.4 (3)C16—C17—C14108.2 (3)
C1—O3—C9—C101.7 (4)C9—C10—C11—C84.4 (4)
C15—C10—C11—C127.1 (4)C10—C16—C17—C141.2 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1···O4i.91 (3)1.96 (4)2.841 (3)162 (3)
O6—H6···O2ii.85 (4)1.88 (4)2.728 (3)171 (3)
Symmetry codes: (i) x+1/2, y, z1/2; (ii) x1, y, z.
 

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