Home The crystal structure of (8R,10R,12R,14R)- 12-hydroxy-16-(5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)- 4,4,8,10,14-pentamethyltetradecahydro-3H- cyclopenta[a]phenanthrene-3,6(2H)-dione, C30H48O5
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The crystal structure of (8R,10R,12R,14R)- 12-hydroxy-16-(5-(2-hydroxypropan-2-yl)-2-methyltetrahydrofuran-2-yl)- 4,4,8,10,14-pentamethyltetradecahydro-3H- cyclopenta[a]phenanthrene-3,6(2H)-dione, C30H48O5

  • Xiao-Hui Wang ORCID logo , Hui-yun Wang , Sheng-Nan Zhang , Jia Song , Lun-Hai Liang , Feng-Lan Zhao and Qing-Guo Meng EMAIL logo
Published/Copyright: November 2, 2020

Abstract

C30H48O5, orthorhombic, P212121 (no. 19), a = 11.6608(10) Å, b = 14.8098(15) Å, c = 15.9975(16) Å, V = 2762.7(5) Å3, Z = 4, Rgt(F) = 0.0586, wRref (F2) = 0.1580, T = 293(2) K.

CCDC no.: 2024015

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:0.42 × 0.40 × 0.31 mm
Wavelength:Cu Kα radiation (1.54178 Å)
μ:0.62 mm−1
Diffractometer, scan mode:Bruker SMART, φ and ω
θmax, completeness:66.0°, >99 %
N(hkl)measured, N(hkl)unique, Rint:6065, 4116, 0.044
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2044
N(param)refined:326
Programs:Bruker [1], Olex2 [2], SHELX [3], [4]
Table 2:

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

AtomxyzUiso*/Ueq
O10.1841 (4)0.9592 (3)0.8869 (4)0.1043 (18)
O20.5365 (3)0.7560 (3)0.9715 (3)0.0883 (14)
O30.1132 (4)0.3882 (3)0.8648 (3)0.0867 (14)
H30.1239190.3369610.8824480.130*
O40.2026 (3)0.2327 (3)0.9135 (2)0.0606 (11)
O50.2499 (5)0.2876 (4)0.7412 (3)0.1093 (18)
H50.2159140.3230600.7717580.164*
C10.1760 (4)0.7306 (4)0.8353 (4)0.0612 (16)
H1A0.1493910.6912320.7909090.073*
H1B0.1196830.7285960.8798750.073*
C20.1827 (5)0.8273 (4)0.8017 (4)0.0735 (19)
H2A0.2293360.8280440.7515110.088*
H2B0.1062830.8476060.7868130.088*
C30.2334 (6)0.8911 (5)0.8653 (5)0.073 (2)
C40.3497 (5)0.8645 (4)0.9033 (4)0.0678 (18)
C50.3370 (4)0.7649 (4)0.9326 (3)0.0588 (16)
H5A0.2772540.7675470.9756020.071*
C60.4398 (5)0.7264 (4)0.9778 (4)0.0683 (18)
C70.4121 (5)0.6436 (4)1.0295 (4)0.0692 (18)
H7A0.3556080.6592301.0715910.083*
H7B0.4807920.6232171.0578990.083*
C80.3649 (4)0.5665 (4)0.9742 (4)0.0566 (15)
C90.2643 (4)0.6054 (4)0.9197 (4)0.0531 (14)
H90.2054770.6233450.9601920.064*
C100.2912 (4)0.6937 (4)0.8690 (4)0.0563 (15)
C110.2074 (5)0.5309 (4)0.8667 (4)0.0668 (18)
H11A0.1427740.5563110.8366870.080*
H11B0.2620640.5088080.8258710.080*
C120.1660 (5)0.4522 (4)0.9200 (4)0.0643 (17)
H120.1074540.4747090.9587710.077*
C130.2649 (5)0.4139 (4)0.9710 (4)0.0554 (15)
H130.3254960.3973540.9314530.066*
C140.3144 (4)0.4891 (4)1.0283 (4)0.0581 (15)
C150.3987 (5)0.4336 (4)1.0819 (4)0.0697 (18)
H15A0.4670970.4183661.0503720.084*
H15B0.4208650.4665191.1317910.084*
C160.3298 (5)0.3485 (4)1.1042 (4)0.0697 (18)
H16A0.2870020.3577601.1555220.084*
H16B0.3806020.2973181.1116860.084*
C170.2462 (5)0.3317 (4)1.0293 (4)0.0599 (16)
H170.1672190.3331361.0502110.072*
C180.2692 (4)0.2387 (4)0.9909 (4)0.0600 (16)
C190.3941 (4)0.2216 (4)0.9624 (4)0.0687 (18)
H19A0.4405960.2750480.9713430.082*
H19B0.4274100.1719210.9935870.082*
C200.3887 (5)0.1990 (6)0.8709 (4)0.090 (2)
H20A0.4368680.1473650.8582790.108*
H20B0.4136970.2498490.8373130.108*
C210.2633 (5)0.1774 (4)0.8541 (4)0.0641 (17)
H210.2491750.1136630.8669030.077*
C220.2229 (5)0.1972 (5)0.7650 (5)0.075 (2)
C230.0948 (5)0.1821 (5)0.7571 (4)0.092 (2)
H23A0.0547990.2245320.7918730.138*
H23B0.0764220.1217440.7745560.138*
H23C0.0720000.1903330.6999850.138*
C240.2860 (6)0.1355 (6)0.7043 (5)0.123 (3)
H24A0.2628860.1492840.6481570.184*
H24B0.2678320.0737230.7166910.184*
H24C0.3671930.1446430.7098330.184*
C250.4414 (5)0.8819 (5)0.8350 (4)0.085 (2)
H25A0.4184200.8530360.7839420.127*
H25B0.5137390.8577760.8529080.127*
H25C0.4487470.9457030.8258340.127*
C260.3763 (7)0.9243 (5)0.9793 (5)0.095 (2)
H26A0.3833650.9859670.9616680.142*
H26B0.4468380.9049551.0045370.142*
H26C0.3151840.9192781.0193010.142*
C270.4677 (4)0.5325 (4)0.9207 (4)0.0695 (19)
H27A0.5092780.5834190.8990570.104*
H27B0.4396190.4966700.8750680.104*
H27C0.5177430.4966290.9548190.104*
C280.3729 (5)0.6778 (5)0.7935 (4)0.0700 (18)
H28A0.3645490.6168860.7739580.105*
H28B0.4507250.6877680.8107190.105*
H28C0.3537510.7189820.7493070.105*
C290.2219 (5)0.5249 (4)1.0910 (4)0.0734 (19)
H29A0.2591690.5490411.1396060.110*
H29B0.1723700.4761981.1071640.110*
H29C0.1775170.5714421.0645680.110*
C300.2271 (6)0.1636 (4)1.0489 (4)0.082 (2)
H30A0.1487280.1748781.0640950.122*
H30B0.2736750.1622981.0983380.122*
H30C0.2323980.1066211.0206150.122*

Source of material

A solution of 20(S)-protopanaxatriol in dichloromethane was cooled to 270 K. A dichloromethane solution with m-chloroperoxybenzoic acid (m-CPBA) was added slowly. After stirring for 1 h, isopropanol was added and stirred for another 1 h. The organic phase was washed successively with saturated sodium bicarbonate solution, water and brine, and dried over sodium sulfate. The organic phase was evaporated in vacuum, yielding a white solid. The mixture of the intermediate above in dichloromethane was treated with pyridinium chlorochromate at room temperature for 6 h to obtain the title compound, which was purified by silica-gel column chromatography (petroleum ether: ethyl acetate = 1:2, v/v). Suitable crystal was obtained by slow evaporation in ethyl acetate.

Experimental details

All hydrogen 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.

Comment

Ginsenosides can be classifed as ocotillol-type, oleanolic acid type, protopanaxadiol (PPD) type, protopanaxatriol (PPT) type [5], [6], [7]. The ocotillol-type triterpenes are a rare kind of ginsenosides characterized by a tetrahydrofuran ring on the side chain [8], [9], [10], [11]. It has been reported that ocotillol-type triterpenes have antibacterial, antioxidative, anti-inflammatory, neuroprotective and cardioprotective properties [12], [13], [14], [15], [16]. It is worth noting that the stereo-configuration of the C-24 position may influence their stereoselectivity in pharmacological action and pharmacokinetics [17]. For example, the 24R-epimer exerted the cardioprotective effects, whilst the 24S-epimer had no effect and the bioavailability of the 24R-epimer was about 14 times that of the 24S-epimer. Moreover, our previous studies also showed that similar compounds have corresponding stereoselective bioactivities [18]. Therefore, the structural modification of ocotillol-type triterpenes may be of great value for obtaining novel derivatives for pharmacological screening and structure-activity relationship studies.

The asymmetric unit of the title compound consists of one molecule composed of tetrahydrofuran ring and a dammarane skeleton. The tetrahydrofuran ring adopts an envelope conformation with C18 forming the flap. The C20–C19–C18–C30 torsion angle is 110.7(7)°, suggesting the C18 with S form. The C19–C20–C21–H21 and C19–C20–C21–C22 torsion angles are −86.1(6) and 150.9(6)°, suggesting the C21 is in the R configuration. Two carbon-oxygen double bonds exist in the compound, the C–O double bond distance (C3–O1) is 1.209(9) Å, the C–O bond distance (C6–O2) is 1.216(7) Å. The intramolecular O3–H3…O4 and O5–H5…O3 hydrogen bonds are present. The corresponding O3…O4 and H3…O4 distances are 2.646(6) and 1.8600 Å, respectively, and O3–H3…O4 is 159.200°. The corresponding O5…O3 and H5…O3 distances are 2.945(8) and 2.1400 Å, respectively, and O5–H5…O3 is 167.000°. The bond lengths and angles are all in the expected ranges [19], [20].


Corresponding author: Qing-Guo Meng, School of Pharmacy, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Yantai University, Yantai, P. R. China, e-mail:

Award Identifier / Grant number: 81473104, 81773563

Funding source: Science and Technology Innovation Development Plan of Yantai

Award Identifier / Grant number: 2020XDRH105

Acknowledgments

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.

  1. Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: 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).

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.

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Received: 2020-08-24
Accepted: 2020-10-12
Published Online: 2020-11-02
Published in Print: 2021-01-26

© 2020 Xiao-Hui Wang 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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  39. Synthesis and crystal structure of 2-azido-N-phenylacetamide, C8H8N4O
  40. Crystal structure of chlorido{hydridotris[3-phenyl-5-methylpyrazol-1-yl-κN3]borato}copper(II), C30H28BClCuN6
  41. Crystal structure of benzanthrone – a redetermination for correct molecular geometry and localization of hydrogen atoms
  42. Crystal structure of 4-bromobenzaldehyde – complete redetermination at 200 K, C7H5BrO
  43. Crystal structure and spectroscopic properties of chlorido{hydridotris[3-,5-dimethylpyrazol-1-yl-κN3]borato}(3-,5-dimethylpyrazol-1-yl-κN)copper(II), C20H30BClCuN8
  44. The crystal structure of 4-((2-hydroxynaphthalen-1-yl)(pyrrolidin-1-yl)methyl)benzonitrile, C22H20N2O
  45. Crystal structure of 4-ethyl-3-phenylisoquinolin-1(2H)-one, C17H15NO
  46. Crystal structure of (tricyclohexylphosphane-κP)-[(Z)-N-(3-fluorophenyl)-O-methylthiocarbamato-k1S]gold(I), C26H40AuFNOPS
  47. Crystal structure of (3S,8R,10R,12R,14R)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl) hexadecahydro-1H-cyclopenta[a]phenanthren-3-yl acetate, C32H54O4
  48. The crystal structure of 2-[(S)-1-(naphthalen-1-yl)ethyl]-2,3,7,7a- tetrahydro-3a,6-epoxyisoindol-1(6H)-one, C19H20NO2
  49. Crystal structure of {hydridotris[3-(t-butyl)-5-isopropylpyrazol-1-yl-κN3]borato}thallium(I), C30H52BN6Tl
  50. Synthesis and crystal structure of 1-octyl-3-phenylquinoxalin-2(1H)-one, C22H26N2O
  51. The crystal structure of 2,6-difluorophenol, C6H4F2O
  52. 4-(9H-Fluoren-9-yl)-4-methylmorpholin-4-ium bromide, C18H20BrNO
  53. The crystal structure of 2,4-dimethylimidazole monohydrate, C5H10N2O
  54. The crystal structure of 1,2-dimethylimidazole, C5H8N2
  55. The crystal structure of 3-ammonio-4-aminobenzoate, C7H8N2O2 – a second polymorph
  56. The crystal structure of 4-hydroxy-2,5-bis(1-methyl-1H-imidazol-3-ium-2-ylthio)-3,6-dioxocyclohexa-1,4-dienolate chloride monohydrate, C14H15N4O5S2Cl
  57. The crystal structure of butyrylferrocene, C14H16FeO
  58. The crystal structure of bi-1,1′-cyclopentane-1,1′-diol, C10H18O2
  59. The crystal structure of 2-iso-propylimidazole, C6H10N2
  60. The crystal structure of aqua-tris (1,3-diphenylpropane-1,3-dionato-κ2O,O′)-lanthanum(III), C45H35LaO7
  61. Crystal structure of (3E,5E)-3,5-bis-4-methoxy-3-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
  62. The crystal structure of 3,5-dichloro-6-diazo-2,4-dinitrocyclohexa-2,4-dien-1-one, C6Cl2N4O5
  63. Crystal structure of carbonyl(2-methylquinolin-8-olato-κ2N,O)(triphenylarsine-κAs)rhodium(I), C29H23AsNO2Rh
  64. Crystal structure of (1aS,1a1S,2S)-4a-butoxy-1a,1a1,2,4a,5,6-hexahydro-1H-cyclobuta[de]naphthalen-2-yl-4-nitrobenzoate, C22H25NO5
  65. Crystal structure of carbonyl(2-oxopyridin-1(2H)-olato-k2O,O′)(triphenylarsine-κAs)rhodium(I), C24H19AsNO3Rh
  66. Crystal structure of catena-poly[triqua-bis(μ2-4-carboxy-2-(1H-tetrazol-1-yl)-1H-imidazole-5-carboxylato-k3N,O:O′)barium(II)] tetrahydrate, C14H14BaN12O15
  67. Crystal structure of (E)-3′,6′-bis(ethylamino)-2-((quinoxalin-2-ylmethylene)amino)spiro[isoindoline-1,9′-xanthen]-3-one, C35H32N6O2
  68. Crystal structure of diaqua-bis(μ2-5-chloro-salicylato-κ3O,O′:O′)-bis(5-chloro-salicylato-κ2O,O′)-bis(1,10-phenanthroline-κ2N,N′) dilead(II) – water (1/2), C52H36C14N4O14Pb2·2(H2O)
  69. Crystal structure of (E)-2-(4-ethoxycarbonyl-3,5-dimethyl-2-(pyrrole-2-ylmethyleneamino)-3′,6′-dihydroxylspiro[isoindoline-1,9′-xanthen]-3-one-methanol (1/1), C31H29N3O7
  70. The crystal structure of 5H-dibenzo[b,e]azepine-6,11-dione, C14H9NO2
  71. Crystal structure of (E)-2-(4-fluoro-2-(trifluoromethyl)benzylidene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  72. The crystal structure of N-(2-methoxy-4,5-bis[phenylselanyl]phenyl)picolinamide, C25H20N2O2Se2
  73. The crystal structure of (E)-2-(5-bromo-2-hydroxybenzylidene)-N-phenylhydrazine-1- carboxamide monohydrate, C14H14BrN3O3
  74. Crystal structure of fac-tricarbonyl-(nitrato-k1O)-bis(pyridine-κN)-rhenium, C13H10O6N3Re
  75. Crystal structure of (E)-2-(((1H-pyrrol-2-yl)methylene)amino)-3′,6′-dihydroxyspiro[isoindoline-1,9′-xanthen]-3-one — methanol (1/2), C27H25N3O6
  76. The crystal structure of 4-amino-N′-(4-aminobenzoyl)benzohydrazide monohydrate, C14H16N4O3
  77. Crystal structure of bis(amino(carbamothioylamino)methaniminium) 5-hydroxyisophthalate monohydrate, C12H20N8O6S2
  78. The crystal structure of 2-(chloromethyl)pyridine, C6H6ClN
  79. The crystal structure of 1-bromo-4-iodo-benzene, C6H4BrI
  80. The crystal structure of 2,6-dimethyl-4-nitro-phenol, C8H9NO3
  81. The crystal structure of 3-chloropropionic acid, C3H5ClO2
  82. The crystal structure of 2-(2-methoxyphenyl)acetic acid, C9H10O3
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