Home Physical Sciences The crystal structure of (3S,8R,10R,14R)-17-((2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4,4,8,10,14-pentamethyl-12-oxohexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H52O5
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The crystal structure of (3S,8R,10R,14R)-17-((2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4,4,8,10,14-pentamethyl-12-oxohexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H52O5

  • Li Liu ORCID logo , Hui-yun Wang , Xia Zhou , Sheng-Nan Zhang , Xiao-Qian Chen , Feng-Lan Zhao and Qing-Guo Meng EMAIL logo
Published/Copyright: September 26, 2020

Abstract

C32H52O5, monoclinic, P21 (no. 4), a = 11.816(2) Å, b = 7.4064(15) Å, c = 17.101(3) Å, β = 97.01(3)°, V = 1485.5(5) Å3, Z = 2, Rgt(F) = 0.0543, wRref(F2) = 0.1501, T = 293(2) K.

CCDC no.: 2016696

The molecular structure is shown in the figure. Table 1 contains crystallographic data and Table 2 contains the list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Colourless block
Size:0.40 × 0.30 × 0.23 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.07 mm−1
Diffractometer, scan mode:Bruker SMART, φ and ω
θmax, completeness:27.5°, >99%
N(hkl)measured, N(hkl)unique, Rint:35271, 6062, 0.030
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 5664
N(param)refined:344
Programs:Bruker [1], Olex2 [2], SHELX [3], [4]
Table 2:

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2).

AtomxyzUiso*/Ueq
O10.44583(16)0.4324(3)0.86271(10)0.0521(5)
O20.2157(6)0.1904(4)0.38416(18)0.170(3)
O30.11104(19)0.5070(3)0.14260(11)0.0594(5)
O40.30274(16)0.3679(5)0.07513(13)0.0710(6)
H40.3103360.4560810.1042980.107*
O50.5566(2)0.1878(5)0.85784(14)0.0835(8)
C10.2901(3)0.3063(3)0.66386(14)0.0500(6)
H1A0.2258030.2262210.6502040.060*
H1B0.3539690.2594580.6394550.060*
C20.3213(3)0.3058(4)0.75344(15)0.0551(6)
H2A0.2556430.3426960.7785280.066*
H2B0.3421960.1845470.7710710.066*
C30.4194(2)0.4327(4)0.77729(13)0.0452(5)
H30.4862890.3890370.7543010.054*
C40.3969(2)0.6295(4)0.75138(13)0.0420(5)
C50.35894(17)0.6254(3)0.66065(12)0.0346(4)
H50.4251240.5772940.6381540.042*
C60.3400(2)0.8135(3)0.62347(13)0.0436(5)
H6A0.2676300.8615600.6353100.052*
H6B0.3999060.8943870.6458530.052*
C70.3401(2)0.8036(3)0.53420(13)0.0438(5)
H7A0.4149940.7656720.5229580.053*
H7B0.3260380.9233090.5121350.053*
C80.25020(16)0.6727(3)0.49352(12)0.0324(4)
C90.25915(17)0.4885(3)0.53869(12)0.0340(4)
H90.3346410.4416660.5312060.041*
C100.25941(17)0.4958(3)0.63020(12)0.0351(4)
C110.1747(3)0.3494(4)0.49748(15)0.0591(7)
H11A0.1868670.2332580.5233250.071*
H11B0.0972740.3875180.5020910.071*
C120.1901(4)0.3304(4)0.41130(16)0.0724(10)
C130.1789(2)0.5028(3)0.36621(13)0.0403(5)
H130.1045190.5551660.3728810.048*
C140.27240(17)0.6324(3)0.40627(12)0.0370(4)
C150.2595(3)0.7905(4)0.34770(15)0.0566(7)
H15A0.3282850.8630290.3521270.068*
H15B0.1957970.8669290.3570090.068*
C160.2378(3)0.7002(5)0.26586(15)0.0568(7)
H16A0.3080590.6940970.2419940.068*
H16B0.1824890.7693040.2314850.068*
C170.1919(2)0.5080(4)0.27799(13)0.0444(5)
H170.2513550.4214080.2683220.053*
C180.1332(2)0.7646(4)0.49385(14)0.0475(6)
H18A0.1283780.8165960.5447500.071*
H18B0.0738320.6765890.4824700.071*
H18C0.1246090.8577180.4545460.071*
C190.1424(2)0.5484(5)0.65466(15)0.0519(6)
H19A0.1353500.6774900.6549340.078*
H19B0.1360420.5022670.7064150.078*
H19C0.0828530.4980310.6178520.078*
C200.0833(2)0.4627(5)0.22126(14)0.0579(8)
C21−0.0195(3)0.5748(9)0.2359(2)0.0973(17)
H21A0.0017140.6998250.2401300.146*
H21B−0.0464230.5361190.2838920.146*
H21C−0.0788780.5592780.1927970.146*
C220.0568(3)0.2594(6)0.21771(18)0.0796(12)
H22A0.0852250.2005030.2668610.096*
H22B−0.0245410.2380950.2066170.096*
C230.1187(3)0.1929(6)0.15105(18)0.0678(8)
H23A0.1986390.1702920.1686500.081*
H23B0.0841050.0838240.1276080.081*
C240.1038(2)0.3498(5)0.09433(13)0.0529(7)
H240.0270670.3436210.0653710.063*
C250.1900(2)0.3650(6)0.03479(14)0.0604(8)
C260.1830(4)0.1974(9)−0.0166(3)0.1028(18)
H26A0.2371420.206728−0.0539850.154*
H26B0.1075590.186644−0.0441730.154*
H26C0.2000590.0926990.0158110.154*
C270.1691(3)0.5357(9)−0.0134(2)0.0927(15)
H27A0.1733770.6382880.0211010.139*
H27B0.0947600.530539−0.0431340.139*
H27C0.2257880.546477−0.0488470.139*
C280.5107(3)0.7311(5)0.76732(17)0.0655(9)
H28A0.5636140.6831330.7343110.098*
H28B0.5411380.7165510.8216140.098*
H28C0.4984910.8570070.7559910.098*
C290.3107(3)0.7221(4)0.79902(15)0.0556(7)
H29A0.2860970.8339330.7741050.083*
H29B0.3462570.7456230.8515520.083*
H29C0.2460660.6445400.8010890.083*
C300.5184(2)0.3066(5)0.89477(15)0.0553(7)
C310.5431(3)0.3327(6)0.98201(16)0.0712(10)
H31A0.5887910.4390430.9927520.107*
H31B0.5835270.2296081.0050800.107*
H31C0.4726780.3462851.0041400.107*
C320.3910(2)0.5503(7)0.40207(17)0.0714(11)
H32A0.3938250.4310050.4241980.107*
H32B0.4478880.6244940.4313110.107*
H32C0.4054290.5440780.3480930.107*

Source of material

A solution of 20(S),24(S)-epoxy-dammar-3,12,25-triol in dichloromethane was cooled to 270 K. A dichloromethane solution with m-CPBA was added slowly. After stirring for 1 h, isopropanol was added and stirred for another 1 h. The organic solvent was washed successively with saturated sodium bicarbonate solution, water and brine, and dried over sodium sulfate. The organic solvent was evaporated in vacuum, yielding a white solid. Acetic anhydride was added to a solution of the aforementioned intermediate in pyridine and was stirred for 11 h at room temperature. After evaporation under reduced pressure, the residue was dissolved with ethyl acetate and washed successively by water and brine, and dried over anhydrous sodium sulfate. The ethyl acetate was condensed in vacuo to yield a white solid. The objective compound was obtained from oxidation of the acetylated intermediate by 2,3-dicyano-5,6-dichlorobenzoquinone (DDQ) in dichloromethane at room temperature for about 1 h, which was purified by silica-gel column chromatography. Suitable crystals were obtained by slow evaporation in ethyl acetate.

Experimental details

All H atoms were included in calculated positions and refined as riding atoms, with O—H = 0.82 or 0.85 Å and Uiso(H) = 1.2Ueq(O), H atoms on C atoms were placed in geometrically idealized positions and constrained to ride on their parent C atoms, with C—H = 0.96 Å, Uiso (H) = 1.5Ueq(C) for methyl H atoms, and with C—H = 0.98 Å and 0.97 Å for methine and methylene H atoms, and both with Uiso (H) = 1.2Ueq.

The absolute configuration was derived from the synthesis and the configuration of the educts.

Comment

20(S)-ocotillol-type saponin sharing a tetrahydrofuran ring and a dammarane skeleton, are a class of rare ginsenosides [5], which was achieved by base degradation from leaves and stems of Panax quinquefolius and they play a key role in neuroprotection [6], antibacterial [7] and antitumor activities [8]. It has been reported to possess good potential for myocardial ischemia and myocardial injury [9], [10]. It is also a potent approach to modify the structures of natural products and preparing a variety of derivatives for the search of new compounds. It is worth noting that our previous studies showed that similar compounds have corresponding stereoselective bioactivities [11], [12], [13], [14]. Because of its potential medicinal value, synthesis and biological activity of 20(S)-ocotillol-type saponin and its derivatives have attracted much attention.

As shown in the figure, the bond angles of C30—O1—C3, O3—C20—C21 and O5—C30—O1 are 117.5(2)°, 107.7(3)° and 123.9(2)° respectively. The bond distance of O2—C12 is 1.190(5) Å. There are some intermolecular O—H⋯O hydrogen bonds. The bond lengths and angles are all in the expected ranges [15].

Acknowledgements

X-ray data were collected at Institute of Medical Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, Peoples Republic of China. This work was supported by the National Natural Science Foundation of China (No. 81473104, 81773563) and Science and Technology Innovation Development Plan of Yantai (No. 2020XDRH105).

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Received: 2020-07-22
Accepted: 2020-08-13
Published Online: 2020-09-26
Published in Print: 2020-10-27

©2020 Li Liu et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  42. Crystal structure of poly[triaqua-bis(μ3-3,3′-((5-carboxylato-1,3-phenylene)bis(oxy))dibenzoato)-tris(1,10-phenanthroline)cobalt(II)], C78H46N6O20Co3
  43. The crystal structure of 2,4-dihydroxybenzoic acid–nicotinamide–methanol (1/1/1), C15H18N2O6
  44. The crystal structure of aqua{N,N,N′,N′-tetrakis[(1H-benzimidazol-κN3) methyl]cyclohexane-1,2-diamine}lead(II) diacetate–methanol (1/2), C44H54N10O7Pb
  45. Crystal structure of (2-amino-5-bromo-3-iodophenyl)(3-(4-chlorophenyl)oxiran-2-yl)methanone, C15H10BrClINO2
  46. Synthesis and crystal structure of 3-octyl-5,5-diphenylimidazolidine-2,4-dione, C23H28N2O2
  47. Synthesis and crystal structure of 2-azido-N-(4-nitrophenyl)acetamide, C8H7N5O3
  48. Crystal structure of tert-butyl (1S,2R,5R)-2-(hydroxymethyl)-4-(4-methoxyphenyl)-6-oxa-3-azabicyclo[3.1.0]hexane-3-carboxylate, C17H23NO5
  49. Crystal structure of 4-[(4-methoxy-2-nitrophenyl)carbamoyl]butanoic acid, C12H14N2O6
  50. Crystal structure of 3-ethyl-1-[(E)-[(2E)-3-phenylprop-2-en-1-ylidene]amino]thiourea, C12H15N3S
  51. Crystal structure of 4,4′-bipyridin-1,1′-dium poly[bis(μ4-benzene-1,3,5-triyltris(hydrogen phosphonato-κ4O:O′:O′′:O′′′))zinc(II)], C11H11NO9P3Zn
  52. Crystal structure of (μ2-1,1′-bis(diphenylphosphino)butane-κ2P,P′)-bis[(Z)-N-(3-fluorophenyl)-O-methylthiocarbamato-κS]-di-gold(I), C44H42Au2F2N2O2P2S2
  53. Crystal structure of (μ2-1,1′-bis(diphenylphosphino)hexane-κ2P,P′)-bis[(Z)-N-(3-fluorophenyl)-O-methylthiocarbamato-κS]digold(I), C46H46Au2F2N2O2P2S2
  54. Crystal structure of tetrakis (N-(2-hydroxyethyl)-N-isopropylcarbamodithioato-κS,S′)-(μ2(2-(pyridin-4-yl)vinyl)pyridine-κN,N′)dicadmium(II), C36H58Cd2N6O4S8
  55. Crystal structure of 4-(2-(benzo[b]thiophen-2-yl)-3,3,4,4,5,5-hexafluorocyclopent-1-en-1-yl)-1,5-dimethyl-1H-pyrrole-2-carbonitrile, C20H12F6N2S
  56. Crystal structure of bis(octahydrocyclopenta[c]pyrrolium)pentachlorobismuthate(III), (C7NH14)2BiCl5
  57. The crystal structure of diaqua-tris(nitrato-κ2O,O′)-bis(4,4,5,5-tetramethyl-2-(p-pyridyl)imidazoline-1-oxyl 3-oxide-κN)samarium(III), C24H36N9O15Sm
  58. Synthesis and crystal structure of methyl 2-(2-((tert-butoxycarbonyl)amino)phenyl)-2-(4-oxo-4H-chromen-3-yl)acetate, C23H23NO6
  59. Crystal structure of O-hexyl benzoylcarbamothioate, C14H19NO2S
  60. Crystal structure of chlorido-(O-methyl phenylcarbamothioamide-κS)-bis(triphenylphosphane-κP)silver(I), C44H39AgClNOP2S
  61. Crystal structure of chlorido-(O-ethyl phenylcarbamothioamide-κS)-bis(triphenylphosphane-κP)-silver(I), C45H41AgClNOP2S
  62. Crystal structure of 4-[(2-methoxyphenyl)carbamoyl]butanoic acid, C12H15NO4
  63. Crystal structure of ethyl 4-methyl-2-oxo-5-phenyl-1,3,4-oxadiazinane-3-carboxylate, C13H16N2O4
  64. Crystal structure of catena-poly[diaqua(μ2-2-(hydroxymethyl)-1H-imidazole-4,5-dicarboxylato)cadmium(II)], C6H8CdN2O7
  65. Crystal structure of (1S)-N-(chloromethyl)-1-((4S,6aR,8aS, 8bR,9aR)-4-methoxy-6a,8a-dimethyl-1,3,4, 5,6,6a,6b,7,8,8a,9a,10,10a,10b-tetradecahydro-8bH-naphtho[2′,1′:4,5] indeno[1,2-b]oxiren-8b-yl)-N-methylethan-1-amine, C24H46ClNO5
  66. Crystal structure of 4-[(3,5-dichlorophenyl)carbamoyl]butanoic acid, C11H11Cl2NO3
  67. Crystal structure of (2Z)-2-amino-3-[(E)-[(2,4-dihydroxyphenyl)methylidene]-amino]but-2-enedinitrile, C11H8N4O2
  68. Crystal structure of 3-methyl-1-[(E)-(4-phenylbutan-2-ylidene)amino]thiourea, C12H17N3S
  69. Crystal structure of carbonyl{hydridotris[3-phenyl-5-methylpyrazol-1-yl]borato-κ3N,N′N′′}copper(I), C31H28BCuN6O
  70. Crystal structure of ethane-1,2-diylbis(diphenylphosphine oxide) – dihydrogenperoxide (1/2), C26H28O6P2
  71. Crystal structure of 2-(pyridin-2-ylamino)pyridinium chloride dibenzyldichlorostannane, [C10H10N3]Cl, C14H14Cl2Sn
  72. Crystal structure of 4-[(3-methoxyphenyl)carbamoyl]butanoic acid, C12H15NO4
  73. Crystal structure of dichlorido-bis(tri-4-tolylphosphane oxide-κO)-di(4-chlorophenyl-κC)tin(IV), C54H50Cl4O2P2Sn
  74. Crystal structure of dichloridodimethylbis(tri-4-tolylphosphane oxide-κO)-tin(IV), C44H48Cl2O2P2Sn
  75. Crystal structure of chlorido(2-methylquinolin-8-olato-κ2N,O)-bis(4-tolyl-κC)tin(IV), C24H22ClNOSn
  76. Crystal structure of (E)-dichloro(1-chloro-3-methoxyprop-1-en-2-yl)(4-methoxyphenyl)-λ4-tellane, C11H13Cl3O2Te
  77. Crystal structure of bis{N-methyl-N′-[3-(4-methoxyphenyl)-1-methylpropane-1-ylidene]carbamohydrazonothioato}zinc(II), C26H36N6O2S2Zn
  78. Crystal structure of (2-carboxy-4-(3-carboxy-5-carboxylatophenoxy)benzoato-κ2O,O′)bis(1,10-phenantroline-κ2N,N′)cobalt(II), C40H24N4O9Co
  79. The crystal structure of (3S,8R,10R,14R)-17-((2S,5S)-5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)-4,4,8,10,14-pentamethyl-12-oxohexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H52O5
  80. Crystal structure of (μ2-1,1′-bis(diphenylphosphino)ferrocene-κ2P,P′)-bis[(Z)N-(3-fluorophenyl)-O-methylthiocarbamato-S]digold(I) chloroform solvate, C50H42Au2F2FeN2O2P2S2, CHCl3
  81. Crystal structure of poly[bis(μ2-1,4-di(1H-imidazol-1-yl)benzene-κ2N:N′)-(μ2-tetraoxidomolybdato(VI)-κ2O:O′)cobalt(II)], C24H20N8O4MoCo
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