Literature DB >> 21754539

Absolute configuration of fibaruretin B.

Hoong-Kun Fun, Abdul Wahab Salae, Ibrahim Abdul Razak, Melati Khairuddean, Suchada Chantrapromma.   

Abstract

The title furan-oditerpenoid, known as fibaruretin B (systematic name: 2β,3α-dihy-droxy-2,3,7,8α-tetra-hydro-penianthic acid lactone), C(20)H(24)O(7), was isolated from the roots of Arcangelisia flava. The absolute configurations at positions 2, 3, 4, 4a, 7, 9, 10a and 10b of fibaruretin B are S, R, S, R, S, S, S and S, respectively. In the crystal structure, the mol-ecules are linked into infinite chains along the c axis by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions.

Entities:  

Year:  2011        PMID: 21754539      PMCID: PMC3089215          DOI: 10.1107/S1600536811014887

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


Related literature

For ring conformations, see: Cremer & Pople (1975 ▶). For bond-length data, see: Allen et al. (1987 ▶). For background to and activities of furan­oditerpenoids, see: Ito & Furukawa (1969 ▶); Keawpradub et al. (2005 ▶); Moody et al. (2006 ▶); Nguyen-Pouplin et al. (2007 ▶); Su et al. (2008 ▶). For a related structure, see: Bakhari et al. (1998 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶).

Experimental

Crystal data

C20H24O7 M = 376.39 Monoclinic, a = 7.0942 (2) Å b = 11.7149 (4) Å c = 10.1921 (3) Å β = 90.805 (1)° V = 846.96 (5) Å3 Z = 2 Cu Kα radiation μ = 0.93 mm−1 T = 100 K 0.43 × 0.12 × 0.08 mm

Data collection

Bruker APEX DUO CCD area-detector diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T min = 0.692, T max = 0.926 11247 measured reflections 2645 independent reflections 2641 reflections with I > 2σ(I) R int = 0.018

Refinement

R[F 2 > 2σ(F 2)] = 0.025 wR(F 2) = 0.066 S = 1.09 2645 reflections 254 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.19 e Å−3 Δρmin = −0.15 e Å−3 Absolute structure: Flack (1983 ▶), with 1098 Friedel pairs Flack parameter: 0.03 (12) 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 and PLATON (Spek, 2009 ▶). Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536811014887/is2703sup1.cif Structure factors: contains datablocks I. DOI: 10.1107/S1600536811014887/is2703Isup2.hkl Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H24O7F(000) = 400
Mr = 376.39Dx = 1.476 Mg m3
Monoclinic, P21Melting point = 539–540 K
Hall symbol: P 2ybCu Kα radiation, λ = 1.54178 Å
a = 7.0942 (2) ÅCell parameters from 2645 reflections
b = 11.7149 (4) Åθ = 4.3–66.5°
c = 10.1921 (3) ŵ = 0.93 mm1
β = 90.805 (1)°T = 100 K
V = 846.96 (5) Å3Needle, colourless
Z = 20.43 × 0.12 × 0.08 mm
Bruker APEX DUO CCD area-detector diffractometer2645 independent reflections
Radiation source: sealed tube2641 reflections with I > 2σ(I)
graphiteRint = 0.018
φ and ω scansθmax = 66.5°, θmin = 4.3°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −8→8
Tmin = 0.692, Tmax = 0.926k = −11→13
11247 measured reflectionsl = −11→12
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.066w = 1/[σ2(Fo2) + (0.0393P)2 + 0.1838P] where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max = 0.001
2645 reflectionsΔρmax = 0.19 e Å3
254 parametersΔρmin = −0.15 e Å3
1 restraintAbsolute structure: Flack (1983), with 1098 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.03 (12)
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
O10.09153 (14)1.02466 (10)0.68755 (10)0.0211 (2)
O20.32424 (17)1.15137 (10)0.70124 (12)0.0296 (3)
O30.27902 (16)0.75672 (11)0.80552 (11)0.0252 (3)
H1O30.255 (4)0.732 (2)0.883 (3)0.061 (8)*
O40.55436 (14)0.96856 (12)0.80516 (10)0.0239 (3)
H1O40.527 (3)0.965 (2)0.888 (3)0.046 (6)*
O50.31561 (13)0.83615 (10)0.09804 (9)0.0178 (2)
O60.53283 (13)0.96975 (11)0.09604 (9)0.0206 (2)
O7−0.09239 (17)0.58024 (10)−0.04095 (11)0.0275 (3)
C10.08225 (19)0.83863 (15)0.58193 (13)0.0188 (3)
H1A−0.01530.86800.52350.023*
H1B0.05420.75890.59810.023*
C20.07216 (19)0.90202 (14)0.70997 (14)0.0185 (3)
H2A−0.04590.88510.75470.022*
C30.2412 (2)0.87467 (14)0.79792 (13)0.0181 (3)
H3A0.22070.90520.88610.022*
C40.39121 (19)0.94530 (14)0.72888 (14)0.0170 (3)
C50.45100 (19)0.89413 (13)0.59309 (13)0.0147 (3)
C60.56241 (19)0.98757 (13)0.51939 (14)0.0162 (3)
H6A0.49271.05860.52470.019*
H6B0.68210.99890.56470.019*
C70.60174 (18)0.96286 (14)0.37404 (14)0.0163 (3)
H7A0.61051.03470.32720.020*
H7B0.72250.92460.36760.020*
C80.44977 (18)0.88869 (13)0.30780 (13)0.0145 (3)
H8A0.49010.80960.32180.017*
C90.25169 (18)0.89794 (14)0.37078 (13)0.0151 (3)
C100.27476 (18)0.84594 (14)0.51044 (13)0.0147 (3)
H10A0.30780.76600.49400.018*
C110.1130 (2)0.82256 (15)0.28832 (13)0.0200 (3)
H11A0.05320.76840.34650.024*
H11B0.01490.87120.25160.024*
C120.20406 (19)0.75715 (14)0.17735 (13)0.0158 (3)
H12A0.28550.69690.21320.019*
C130.0605 (2)0.70654 (14)0.08547 (14)0.0169 (3)
C14−0.1096 (2)0.75809 (15)0.03551 (14)0.0214 (3)
H14A−0.15190.83180.05170.026*
C15−0.1952 (2)0.67891 (16)−0.03912 (14)0.0245 (4)
H15A−0.30910.6896−0.08370.029*
C160.0642 (2)0.60018 (15)0.03548 (15)0.0226 (3)
H16A0.16000.54750.05080.027*
C170.43951 (19)0.90427 (14)0.16102 (14)0.0161 (3)
C180.2742 (2)1.05332 (15)0.70502 (14)0.0196 (3)
C190.5852 (2)0.79280 (14)0.61724 (14)0.0185 (3)
H19A0.68600.81600.67510.028*
H19B0.63630.76810.53530.028*
H19C0.51700.73110.65640.028*
C200.17620 (19)1.02044 (14)0.36919 (14)0.0185 (3)
H20A0.05091.02150.40360.028*
H20B0.17361.04850.28070.028*
H20C0.25671.06810.42230.028*
U11U22U33U12U13U23
O10.0209 (5)0.0249 (7)0.0177 (5)0.0024 (4)0.0029 (4)−0.0014 (5)
O20.0385 (6)0.0192 (7)0.0313 (6)−0.0040 (5)0.0147 (5)−0.0054 (5)
O30.0353 (6)0.0215 (6)0.0189 (6)−0.0015 (5)0.0068 (5)0.0065 (5)
O40.0183 (5)0.0407 (7)0.0125 (5)−0.0077 (5)−0.0016 (4)−0.0034 (5)
O50.0203 (5)0.0222 (6)0.0109 (4)−0.0035 (4)0.0008 (4)−0.0001 (4)
O60.0215 (5)0.0262 (6)0.0143 (5)−0.0042 (5)0.0021 (4)0.0028 (4)
O70.0346 (6)0.0253 (7)0.0225 (6)−0.0079 (5)−0.0056 (4)−0.0038 (5)
C10.0175 (7)0.0248 (9)0.0141 (6)−0.0075 (6)0.0010 (5)−0.0010 (6)
C20.0169 (7)0.0244 (9)0.0145 (7)−0.0046 (6)0.0041 (5)0.0001 (6)
C30.0209 (7)0.0223 (9)0.0112 (7)−0.0035 (6)0.0025 (5)−0.0010 (6)
C40.0162 (6)0.0217 (9)0.0131 (6)−0.0044 (6)−0.0011 (5)−0.0020 (6)
C50.0147 (6)0.0171 (8)0.0124 (6)−0.0016 (6)0.0005 (5)−0.0007 (6)
C60.0148 (6)0.0187 (8)0.0152 (7)−0.0021 (6)−0.0003 (5)−0.0005 (6)
C70.0140 (6)0.0205 (8)0.0144 (7)−0.0022 (6)0.0016 (5)0.0005 (6)
C80.0143 (6)0.0155 (8)0.0138 (7)0.0006 (5)0.0007 (5)0.0001 (6)
C90.0142 (6)0.0189 (8)0.0122 (6)−0.0022 (6)0.0012 (5)−0.0010 (6)
C100.0153 (6)0.0158 (8)0.0130 (7)−0.0029 (5)0.0010 (5)−0.0015 (5)
C110.0159 (6)0.0296 (9)0.0144 (7)−0.0044 (6)0.0011 (5)−0.0045 (6)
C120.0170 (6)0.0171 (8)0.0132 (6)−0.0010 (6)0.0001 (5)0.0029 (6)
C130.0197 (7)0.0185 (8)0.0124 (6)−0.0032 (6)0.0022 (5)0.0012 (6)
C140.0226 (7)0.0249 (9)0.0167 (7)−0.0005 (6)−0.0008 (5)0.0000 (6)
C150.0248 (7)0.0310 (10)0.0177 (7)−0.0055 (7)−0.0041 (6)0.0004 (6)
C160.0280 (8)0.0209 (9)0.0190 (7)−0.0036 (6)−0.0008 (6)−0.0012 (6)
C170.0146 (6)0.0178 (8)0.0158 (7)0.0040 (6)0.0010 (5)−0.0013 (6)
C180.0254 (7)0.0210 (9)0.0125 (6)−0.0025 (6)0.0070 (5)−0.0040 (6)
C190.0166 (6)0.0218 (9)0.0172 (6)0.0012 (6)0.0005 (5)0.0035 (6)
C200.0171 (6)0.0232 (9)0.0152 (7)0.0032 (6)−0.0005 (5)0.0016 (6)
O1—C181.3482 (19)C7—C81.5338 (19)
O1—C21.462 (2)C7—H7A0.9700
O2—C181.203 (2)C7—H7B0.9700
O3—C31.409 (2)C8—C171.5078 (19)
O3—H1O30.86 (3)C8—C91.5568 (17)
O4—C41.4117 (16)C8—H8A0.9800
O4—H1O40.87 (3)C9—C201.532 (2)
O5—C171.3437 (18)C9—C101.5548 (19)
O5—C121.4677 (17)C9—C111.5593 (19)
O6—C171.2156 (19)C10—H10A0.9800
O7—C151.367 (2)C11—C121.518 (2)
O7—C161.3677 (18)C11—H11A0.9700
C1—C21.504 (2)C11—H11B0.9700
C1—C101.5593 (18)C12—C131.4962 (19)
C1—H1A0.9700C12—H12A0.9800
C1—H1B0.9700C13—C161.347 (2)
C2—C31.521 (2)C13—C141.436 (2)
C2—H2A0.9800C14—C151.340 (2)
C3—C41.528 (2)C14—H14A0.9300
C3—H3A0.9800C15—H15A0.9300
C4—C181.531 (2)C16—H16A0.9300
C4—C51.5720 (18)C19—H19A0.9600
C5—C191.539 (2)C19—H19B0.9600
C5—C61.550 (2)C19—H19C0.9600
C5—C101.6006 (18)C20—H20A0.9600
C6—C71.5388 (19)C20—H20B0.9600
C6—H6A0.9700C20—H20C0.9600
C6—H6B0.9700
C18—O1—C2108.45 (12)C20—C9—C8112.23 (12)
C3—O3—H1O3109.8 (19)C10—C9—C8105.44 (11)
C4—O4—H1O4109.2 (15)C20—C9—C11107.87 (11)
C17—O5—C12117.74 (10)C10—C9—C11109.21 (12)
C15—O7—C16106.07 (12)C8—C9—C11107.75 (11)
C2—C1—C10115.53 (12)C9—C10—C1111.57 (11)
C2—C1—H1A108.4C9—C10—C5114.52 (11)
C10—C1—H1A108.4C1—C10—C5117.14 (11)
C2—C1—H1B108.4C9—C10—H10A103.9
C10—C1—H1B108.4C1—C10—H10A103.9
H1A—C1—H1B107.5C5—C10—H10A103.9
O1—C2—C1110.12 (12)C12—C11—C9114.55 (11)
O1—C2—C3102.95 (12)C12—C11—H11A108.6
C1—C2—C3111.13 (12)C9—C11—H11A108.6
O1—C2—H2A110.8C12—C11—H11B108.6
C1—C2—H2A110.8C9—C11—H11B108.6
C3—C2—H2A110.8H11A—C11—H11B107.6
O3—C3—C2112.76 (13)O5—C12—C13105.82 (10)
O3—C3—C4115.02 (13)O5—C12—C11109.30 (12)
C2—C3—C499.38 (11)C13—C12—C11111.92 (11)
O3—C3—H3A109.7O5—C12—H12A109.9
C2—C3—H3A109.7C13—C12—H12A109.9
C4—C3—H3A109.7C11—C12—H12A109.9
O4—C4—C3114.97 (12)C16—C13—C14105.98 (13)
O4—C4—C18111.49 (13)C16—C13—C12125.95 (15)
C3—C4—C1898.12 (11)C14—C13—C12128.05 (15)
O4—C4—C5109.22 (11)C15—C14—C13106.37 (16)
C3—C4—C5113.41 (12)C15—C14—H14A126.8
C18—C4—C5109.13 (12)C13—C14—H14A126.8
C19—C5—C6107.67 (11)C14—C15—O7110.84 (14)
C19—C5—C4109.10 (11)C14—C15—H15A124.6
C6—C5—C4107.64 (12)O7—C15—H15A124.6
C19—C5—C10106.79 (12)C13—C16—O7110.72 (14)
C6—C5—C10113.19 (11)C13—C16—H16A124.6
C4—C5—C10112.30 (10)O7—C16—H16A124.6
C7—C6—C5115.73 (12)O6—C17—O5118.17 (13)
C7—C6—H6A108.3O6—C17—C8126.71 (13)
C5—C6—H6A108.3O5—C17—C8115.10 (12)
C7—C6—H6B108.3O2—C18—O1121.13 (15)
C5—C6—H6B108.3O2—C18—C4129.41 (14)
H6A—C6—H6B107.4O1—C18—C4109.46 (13)
C8—C7—C6113.24 (11)C5—C19—H19A109.5
C8—C7—H7A108.9C5—C19—H19B109.5
C6—C7—H7A108.9H19A—C19—H19B109.5
C8—C7—H7B108.9C5—C19—H19C109.5
C6—C7—H7B108.9H19A—C19—H19C109.5
H7A—C7—H7B107.7H19B—C19—H19C109.5
C17—C8—C7113.08 (12)C9—C20—H20A109.5
C17—C8—C9111.68 (11)C9—C20—H20B109.5
C7—C8—C9114.33 (11)H20A—C20—H20B109.5
C17—C8—H8A105.6C9—C20—H20C109.5
C7—C8—H8A105.6H20A—C20—H20C109.5
C9—C8—H8A105.6H20B—C20—H20C109.5
C20—C9—C10114.15 (11)
C18—O1—C2—C1−94.59 (13)C2—C1—C10—C9−121.36 (14)
C18—O1—C2—C323.98 (14)C2—C1—C10—C513.4 (2)
C10—C1—C2—O164.85 (17)C19—C5—C10—C9−116.27 (13)
C10—C1—C2—C3−48.58 (18)C6—C5—C10—C92.04 (17)
O1—C2—C3—O3−164.81 (11)C4—C5—C10—C9124.18 (13)
C1—C2—C3—O3−46.95 (16)C19—C5—C10—C1110.25 (14)
O1—C2—C3—C4−42.52 (13)C6—C5—C10—C1−131.43 (13)
C1—C2—C3—C475.34 (15)C4—C5—C10—C1−9.29 (18)
O3—C3—C4—O4−77.80 (16)C20—C9—C11—C12124.47 (13)
C2—C3—C4—O4161.55 (13)C10—C9—C11—C12−110.95 (14)
O3—C3—C4—C18163.86 (12)C8—C9—C11—C123.10 (18)
C2—C3—C4—C1843.21 (13)C17—O5—C12—C13171.56 (12)
O3—C3—C4—C548.87 (17)C17—O5—C12—C1150.87 (15)
C2—C3—C4—C5−71.78 (15)C9—C11—C12—O5−51.14 (16)
O4—C4—C5—C1952.16 (16)C9—C11—C12—C13−168.04 (13)
C3—C4—C5—C19−77.48 (15)O5—C12—C13—C16105.01 (16)
C18—C4—C5—C19174.28 (12)C11—C12—C13—C16−136.03 (16)
O4—C4—C5—C6−64.40 (15)O5—C12—C13—C14−76.91 (17)
C3—C4—C5—C6165.96 (12)C11—C12—C13—C1442.1 (2)
C18—C4—C5—C657.71 (14)C16—C13—C14—C150.54 (17)
O4—C4—C5—C10170.36 (13)C12—C13—C14—C15−177.84 (14)
C3—C4—C5—C1040.72 (17)C13—C14—C15—O7−0.09 (18)
C18—C4—C5—C10−67.53 (15)C16—O7—C15—C14−0.40 (17)
C19—C5—C6—C773.55 (14)C14—C13—C16—O7−0.81 (17)
C4—C5—C6—C7−168.95 (12)C12—C13—C16—O7177.62 (13)
C10—C5—C6—C7−44.25 (16)C15—O7—C16—C130.76 (16)
C5—C6—C7—C829.86 (17)C12—O5—C17—O6179.82 (13)
C6—C7—C8—C17155.77 (13)C12—O5—C17—C80.97 (18)
C6—C7—C8—C926.47 (18)C7—C8—C17—O6−2.4 (2)
C17—C8—C9—C20−71.31 (15)C9—C8—C17—O6128.28 (16)
C7—C8—C9—C2058.69 (15)C7—C8—C17—O5176.37 (12)
C17—C8—C9—C10163.84 (13)C9—C8—C17—O5−52.99 (17)
C7—C8—C9—C10−66.16 (16)C2—O1—C18—O2−174.62 (13)
C17—C8—C9—C1147.30 (17)C2—O1—C18—C45.10 (14)
C7—C8—C9—C11177.30 (12)O4—C4—C18—O227.2 (2)
C20—C9—C10—C161.69 (15)C3—C4—C18—O2148.19 (15)
C8—C9—C10—C1−174.68 (12)C5—C4—C18—O2−93.50 (18)
C11—C9—C10—C1−59.14 (16)O4—C4—C18—O1−152.46 (11)
C20—C9—C10—C5−74.33 (14)C3—C4—C18—O1−31.50 (13)
C8—C9—C10—C549.30 (16)C5—C4—C18—O186.81 (13)
C11—C9—C10—C5164.85 (12)
D—H···AD—HH···AD···AD—H···A
O3—H1O3···O5i0.86 (3)2.54 (3)3.1305 (15)127 (2)
O4—H1O4···O6i0.87 (3)2.12 (3)2.9708 (14)165 (2)
C3—H3A···O5i0.982.393.1295 (16)131
C6—H6A···O20.972.433.1718 (19)133
C8—H8A···O2ii0.982.293.2113 (19)157
C19—H19C···O30.962.312.9489 (18)124
C20—H20B···O7iii0.962.533.4613 (18)164
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
O3—H1O3⋯O5i0.86 (3)2.54 (3)3.1305 (15)127 (2)
O4—H1O4⋯O6i0.87 (3)2.12 (3)2.9708 (14)165 (2)
C3—H3A⋯O5i0.982.393.1295 (16)131
C6—H6A⋯O20.972.433.1718 (19)133
C8—H8A⋯O2ii0.982.293.2113 (19)157
C19—H19C⋯O30.962.312.9489 (18)124
C20—H20B⋯O7iii0.962.533.4613 (18)164

Symmetry codes: (i) ; (ii) ; (iii) .

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