Literature DB >> 21754362

Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

Hoong-Kun Fun, Suchada Chantrapromma, Abdul Wahab Salae, Ibrahim Abdul Razak, Chatchanok Karalai.   

Abstract

The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts.

Entities:  

Year:  2011        PMID: 21754362      PMCID: PMC3089143          DOI: 10.1107/S1600536811011457

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the previous determination of the title structure, see: Eugster et al. (1993 ▶). For ring conformations, see: Cremer & Pople (1975 ▶). For bond-length data, see: Allen et al. (1987 ▶). For background to Verbenaceae plants and the bioactivity of diterpenoids, see: Bunluepuech & Tewtrakul (2009 ▶); Edwards et al. (1962 ▶); Kabouche et al. (2007 ▶); Suresh et al. (2011 ▶); Slamenová et al. (2004 ▶); Tezuka et al. (1998 ▶). For a related structure, see: Razak et al. (2010 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995) ▶. For the stability of the temperature controller used in the data collection, see Cosier & Glazer, (1986 ▶).

Experimental

Crystal data

C20H28O3 M = 316.42 Monoclinic, a = 10.2247 (2) Å b = 7.6353 (1) Å c = 10.7292 (2) Å β = 97.992 (1)° V = 829.48 (2) Å3 Z = 2 Cu Kα radiation μ = 0.66 mm−1 T = 100 K 0.52 × 0.31 × 0.15 mm

Data collection

Bruker APEX DUO CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.726, T max = 0.909 5901 measured reflections 2390 independent reflections 2375 reflections with I > 2σ(I) R int = 0.021

Refinement

R[F 2 > 2σ(F 2)] = 0.036 wR(F 2) = 0.098 S = 1.06 2390 reflections 217 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.35 e Å−3 Δρmin = −0.20 e Å−3 Absolute structure: Flack (1983 ▶) 699 Friedel pairs Flack parameter: 0.11 (19) Data collection: APEX2 (Bruker, 2009) ▶; cell refinement: SAINT (Bruker, 2009) ▶; data reduction: SAINT ▶; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL (Sheldrick, 2008 ▶) and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811011457/hb5812sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811011457/hb5812Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H28O3F(000) = 344
Mr = 316.42Dx = 1.267 Mg m3
Monoclinic, P21Melting point = 451–453 K
Hall symbol: P 2ybCu Kα radiation, λ = 1.54178 Å
a = 10.2247 (2) ÅCell parameters from 2390 reflections
b = 7.6353 (1) Åθ = 5.6–72.1°
c = 10.7292 (2) ŵ = 0.66 mm1
β = 97.992 (1)°T = 100 K
V = 829.48 (2) Å3Block, yellow
Z = 20.52 × 0.31 × 0.15 mm
Bruker APEX Duo CCD diffractometer2390 independent reflections
Radiation source: sealed tube2375 reflections with I > 2σ(I)
graphiteRint = 0.021
φ and ω scansθmax = 72.1°, θmin = 5.6°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −12→12
Tmin = 0.726, Tmax = 0.909k = −9→6
5901 measured reflectionsl = −13→12
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.098w = 1/[σ2(Fo2) + (0.0639P)2 + 0.2006P] where P = (Fo2 + 2Fc2)/3
S = 1.06(Δ/σ)max = 0.001
2390 reflectionsΔρmax = 0.35 e Å3
217 parametersΔρmin = −0.20 e Å3
1 restraintAbsolute structure: Flack (1983) 699 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.11 (19)
Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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.
xyzUiso*/Ueq
O10.64538 (13)−0.0889 (2)0.48735 (12)0.0254 (3)
O20.54777 (12)−0.05136 (18)0.25211 (12)0.0219 (3)
H1O20.567 (3)−0.139 (5)0.304 (3)0.055 (9)*
O30.59784 (11)0.55637 (18)0.31995 (11)0.0202 (3)
C10.91254 (18)0.0149 (3)0.61639 (17)0.0244 (4)
H1A0.8633−0.09320.60030.029*
H1B0.95130.04380.54140.029*
C21.02342 (19)−0.0129 (3)0.72689 (19)0.0293 (4)
H2A0.9853−0.05290.79970.035*
H2B1.0828−0.10330.70480.035*
C31.10107 (17)0.1532 (3)0.76032 (17)0.0258 (5)
H3A1.14960.18240.69160.031*
H3B1.16520.13100.83410.031*
C41.01699 (15)0.3115 (3)0.78684 (15)0.0194 (4)
C50.90137 (15)0.3285 (3)0.67650 (14)0.0181 (4)
H5A0.94420.35200.60200.022*
C60.80962 (18)0.4855 (3)0.68588 (18)0.0264 (4)
H6A0.74580.45770.74190.032*
H6B0.86070.58590.71990.032*
C70.73866 (16)0.5283 (3)0.55608 (16)0.0194 (4)
H7A0.66230.60040.56460.023*
H7B0.79720.59590.51080.023*
C80.69435 (15)0.3689 (2)0.48092 (15)0.0155 (4)
C90.72317 (14)0.2047 (2)0.52206 (14)0.0153 (4)
C100.81709 (15)0.1624 (2)0.64288 (14)0.0153 (3)
C110.65384 (15)0.0604 (3)0.44783 (15)0.0174 (4)
C120.58810 (16)0.0954 (3)0.31623 (15)0.0175 (4)
C130.57151 (15)0.2572 (3)0.26820 (15)0.0165 (4)
C140.61740 (15)0.4041 (3)0.35330 (15)0.0156 (3)
C150.51364 (15)0.3012 (3)0.13372 (14)0.0184 (4)
H15A0.50370.42870.12800.022*
C160.61027 (18)0.2461 (3)0.04345 (16)0.0260 (4)
H16A0.69360.30340.06710.039*
H16B0.57500.2790−0.04090.039*
H16C0.62260.12150.04770.039*
C170.37759 (17)0.2199 (3)0.09225 (18)0.0262 (4)
H17A0.31870.25180.15080.039*
H17B0.38560.09470.09000.039*
H17C0.34310.26210.00990.039*
C181.10451 (18)0.4757 (3)0.78830 (19)0.0294 (5)
H18A1.18330.45920.84720.044*
H18B1.05700.57550.81290.044*
H18C1.12790.49480.70580.044*
C190.97379 (18)0.2988 (3)0.91827 (15)0.0266 (4)
H19A1.04930.31380.98130.040*
H19B0.93500.18600.92810.040*
H19C0.91010.38860.92740.040*
C200.73179 (17)0.1029 (3)0.74287 (16)0.0265 (4)
H20A0.67300.01150.70870.040*
H20B0.68130.20030.76660.040*
H20C0.78800.05980.81550.040*
U11U22U33U12U13U23
O10.0347 (7)0.0149 (7)0.0236 (6)−0.0044 (6)−0.0064 (5)0.0030 (5)
O20.0283 (6)0.0142 (8)0.0208 (6)−0.0021 (5)−0.0050 (5)−0.0011 (5)
O30.0217 (6)0.0152 (7)0.0221 (6)−0.0003 (5)−0.0024 (4)0.0026 (5)
C10.0284 (8)0.0194 (11)0.0228 (8)0.0053 (8)−0.0062 (7)−0.0049 (7)
C20.0307 (9)0.0224 (11)0.0313 (10)0.0092 (9)−0.0082 (7)−0.0048 (9)
C30.0194 (8)0.0331 (13)0.0227 (8)0.0065 (8)−0.0046 (6)−0.0044 (8)
C40.0183 (7)0.0220 (11)0.0169 (7)−0.0007 (8)−0.0006 (6)−0.0001 (7)
C50.0189 (7)0.0198 (10)0.0152 (7)−0.0025 (7)0.0009 (6)0.0001 (7)
C60.0310 (9)0.0199 (10)0.0258 (9)0.0003 (8)−0.0055 (7)−0.0054 (8)
C70.0224 (7)0.0148 (10)0.0207 (8)−0.0005 (7)0.0016 (6)−0.0011 (7)
C80.0143 (7)0.0157 (10)0.0163 (7)−0.0009 (6)0.0020 (6)−0.0002 (6)
C90.0147 (6)0.0167 (10)0.0145 (7)−0.0008 (6)0.0020 (5)−0.0005 (6)
C100.0172 (7)0.0158 (9)0.0124 (7)−0.0013 (7)0.0005 (6)0.0006 (6)
C110.0177 (7)0.0158 (10)0.0182 (7)0.0007 (7)0.0015 (6)0.0008 (7)
C120.0176 (7)0.0167 (11)0.0178 (8)−0.0011 (7)0.0016 (6)−0.0020 (7)
C130.0141 (7)0.0179 (10)0.0170 (8)0.0000 (6)0.0004 (6)−0.0003 (7)
C140.0132 (6)0.0157 (9)0.0181 (7)0.0007 (6)0.0029 (6)−0.0001 (7)
C150.0220 (7)0.0160 (10)0.0161 (7)0.0003 (7)−0.0016 (6)0.0009 (7)
C160.0301 (9)0.0294 (12)0.0181 (8)0.0049 (8)0.0020 (6)0.0026 (7)
C170.0224 (8)0.0256 (11)0.0277 (8)0.0000 (8)−0.0065 (6)−0.0001 (8)
C180.0268 (9)0.0307 (12)0.0281 (9)−0.0091 (9)−0.0056 (7)0.0027 (9)
C190.0277 (8)0.0341 (12)0.0167 (8)−0.0016 (8)−0.0013 (6)−0.0050 (8)
C200.0225 (8)0.0388 (13)0.0181 (8)−0.0087 (8)0.0020 (6)0.0034 (8)
O1—C111.224 (2)C8—C141.506 (2)
O2—C121.349 (2)C9—C111.481 (2)
O2—H1O20.88 (4)C9—C101.536 (2)
O3—C141.225 (2)C10—C201.542 (2)
C1—C21.537 (2)C11—C121.501 (2)
C1—C101.542 (2)C12—C131.341 (3)
C1—H1A0.9700C13—C141.481 (3)
C1—H1B0.9700C13—C151.519 (2)
C2—C31.513 (3)C15—C171.532 (2)
C2—H2A0.9700C15—C161.535 (2)
C2—H2B0.9700C15—H15A0.9800
C3—C41.533 (3)C16—H16A0.9600
C3—H3A0.9700C16—H16B0.9600
C3—H3B0.9700C16—H16C0.9600
C4—C191.538 (2)C17—H17A0.9600
C4—C181.539 (3)C17—H17B0.9600
C4—C51.558 (2)C17—H17C0.9600
C5—C61.534 (3)C18—H18A0.9600
C5—C101.548 (3)C18—H18B0.9600
C5—H5A0.9800C18—H18C0.9600
C6—C71.514 (2)C19—H19A0.9600
C6—H6A0.9700C19—H19B0.9600
C6—H6B0.9700C19—H19C0.9600
C7—C81.495 (2)C20—H20A0.9600
C7—H7A0.9700C20—H20B0.9600
C7—H7B0.9700C20—H20C0.9600
C8—C91.348 (3)
C12—O2—H1O2107 (2)C9—C10—C5106.69 (14)
C2—C1—C10112.12 (15)C20—C10—C5115.45 (14)
C2—C1—H1A109.2C1—C10—C5107.17 (13)
C10—C1—H1A109.2O1—C11—C9123.94 (15)
C2—C1—H1B109.2O1—C11—C12116.59 (16)
C10—C1—H1B109.2C9—C11—C12119.46 (16)
H1A—C1—H1B107.9C13—C12—O2123.80 (15)
C3—C2—C1111.93 (18)C13—C12—C11122.80 (16)
C3—C2—H2A109.2O2—C12—C11113.40 (16)
C1—C2—H2A109.2C12—C13—C14116.67 (14)
C3—C2—H2B109.2C12—C13—C15125.48 (17)
C1—C2—H2B109.2C14—C13—C15117.82 (16)
H2A—C2—H2B107.9O3—C14—C13120.92 (15)
C2—C3—C4114.57 (15)O3—C14—C8118.62 (15)
C2—C3—H3A108.6C13—C14—C8120.41 (16)
C4—C3—H3A108.6C13—C15—C17113.86 (15)
C2—C3—H3B108.6C13—C15—C16109.82 (14)
C4—C3—H3B108.6C17—C15—C16110.11 (15)
H3A—C3—H3B107.6C13—C15—H15A107.6
C3—C4—C19111.12 (16)C17—C15—H15A107.6
C3—C4—C18107.69 (15)C16—C15—H15A107.6
C19—C4—C18106.43 (16)C15—C16—H16A109.5
C3—C4—C5108.09 (14)C15—C16—H16B109.5
C19—C4—C5114.68 (13)H16A—C16—H16B109.5
C18—C4—C5108.58 (15)C15—C16—H16C109.5
C6—C5—C10109.26 (13)H16A—C16—H16C109.5
C6—C5—C4114.94 (15)H16B—C16—H16C109.5
C10—C5—C4116.62 (16)C15—C17—H17A109.5
C6—C5—H5A104.9C15—C17—H17B109.5
C10—C5—H5A104.9H17A—C17—H17B109.5
C4—C5—H5A104.9C15—C17—H17C109.5
C7—C6—C5109.12 (15)H17A—C17—H17C109.5
C7—C6—H6A109.9H17B—C17—H17C109.5
C5—C6—H6A109.9C4—C18—H18A109.5
C7—C6—H6B109.9C4—C18—H18B109.5
C5—C6—H6B109.9H18A—C18—H18B109.5
H6A—C6—H6B108.3C4—C18—H18C109.5
C8—C7—C6113.02 (17)H18A—C18—H18C109.5
C8—C7—H7A109.0H18B—C18—H18C109.5
C6—C7—H7A109.0C4—C19—H19A109.5
C8—C7—H7B109.0C4—C19—H19B109.5
C6—C7—H7B109.0H19A—C19—H19B109.5
H7A—C7—H7B107.8C4—C19—H19C109.5
C9—C8—C7122.99 (14)H19A—C19—H19C109.5
C9—C8—C14121.79 (15)H19B—C19—H19C109.5
C7—C8—C14115.20 (15)C10—C20—H20A109.5
C8—C9—C11116.69 (14)C10—C20—H20B109.5
C8—C9—C10123.65 (15)H20A—C20—H20B109.5
C11—C9—C10119.60 (16)C10—C20—H20C109.5
C9—C10—C20107.53 (12)H20A—C20—H20C109.5
C9—C10—C1109.58 (13)H20B—C20—H20C109.5
C20—C10—C1110.27 (16)
C10—C1—C2—C3−56.7 (2)C4—C5—C10—C9−172.64 (13)
C1—C2—C3—C454.2 (2)C6—C5—C10—C20−64.48 (19)
C2—C3—C4—C1976.8 (2)C4—C5—C10—C2067.96 (19)
C2—C3—C4—C18−167.00 (15)C6—C5—C10—C1172.24 (13)
C2—C3—C4—C5−49.9 (2)C4—C5—C10—C1−55.33 (17)
C3—C4—C5—C6−177.96 (16)C8—C9—C11—O1−162.38 (16)
C19—C4—C5—C657.5 (2)C10—C9—C11—O114.7 (2)
C18—C4—C5—C6−61.40 (19)C8—C9—C11—C1217.2 (2)
C3—C4—C5—C1052.25 (18)C10—C9—C11—C12−165.74 (13)
C19—C4—C5—C10−72.3 (2)O1—C11—C12—C13169.20 (16)
C18—C4—C5—C10168.81 (14)C9—C11—C12—C13−10.4 (2)
C10—C5—C6—C7−68.58 (19)O1—C11—C12—O2−10.7 (2)
C4—C5—C6—C7158.12 (15)C9—C11—C12—O2169.71 (14)
C5—C6—C7—C840.90 (19)O2—C12—C13—C14177.82 (14)
C6—C7—C8—C9−4.3 (2)C11—C12—C13—C14−2.1 (2)
C6—C7—C8—C14177.17 (14)O2—C12—C13—C15−4.1 (2)
C7—C8—C9—C11169.78 (13)C11—C12—C13—C15176.03 (14)
C14—C8—C9—C11−11.8 (2)C12—C13—C14—O3−174.92 (15)
C7—C8—C9—C10−7.2 (2)C15—C13—C14—O36.8 (2)
C14—C8—C9—C10171.21 (13)C12—C13—C14—C87.7 (2)
C8—C9—C10—C20105.79 (19)C15—C13—C14—C8−170.58 (13)
C11—C9—C10—C20−71.10 (19)C9—C8—C14—O3−177.84 (15)
C8—C9—C10—C1−134.34 (17)C7—C8—C14—O30.68 (19)
C11—C9—C10—C148.77 (19)C9—C8—C14—C13−0.4 (2)
C8—C9—C10—C5−18.63 (19)C7—C8—C14—C13178.12 (13)
C11—C9—C10—C5164.48 (13)C12—C13—C15—C1754.2 (2)
C2—C1—C10—C9170.62 (16)C14—C13—C15—C17−127.68 (17)
C2—C1—C10—C20−71.2 (2)C12—C13—C15—C16−69.8 (2)
C2—C1—C10—C555.2 (2)C14—C13—C15—C16108.33 (18)
C6—C5—C10—C954.93 (16)
D—H···AD—HH···AD···AD—H···A
O2—H1O2···O10.88 (4)2.05 (3)2.5977 (18)119 (3)
O2—H1O2···O3i0.88 (4)2.35 (4)3.1079 (19)145 (3)
C1—H1A···O10.972.382.993 (2)120
C7—H7A···O1ii0.972.513.131 (3)122
C17—H17B···O20.962.493.071 (2)119
C20—H20A···O10.962.473.125 (2)125
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O2—H1O2⋯O10.88 (4)2.05 (3)2.5977 (18)119 (3)
O2—H1O2⋯O3i0.88 (4)2.35 (4)3.1079 (19)145 (3)
C1—H1A⋯O10.972.382.993 (2)120
C7—H7A⋯O1ii0.972.513.131 (3)122
C17—H17B⋯O20.962.493.071 (2)119
C20—H20A⋯O10.962.473.125 (2)125

Symmetry codes: (i) ; (ii) .

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Authors:  Shicheng Xu; Xinhua Ma; Ruifang Ke; Shihao Deng; Xinzhou Yang; Ping Song
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2017-09-05

2.  Crystal structure of 6,7-de-hydro-royleanone isolated from Taxodium distichum (L.) Rich.

Authors:  Li Chen; Xinhua Ma; ShiHao Deng; XinZhou Yang; Ping Song
Journal:  Acta Crystallogr E Crystallogr Commun       Date:  2018-01-01
  2 in total

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