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Crystal structure of (5R,6S,E)-5-acetoxy-2-methyl-6-((2aR,3R,5aS,5bS,11aR,12aS)-2a,5a,8,8-tetramethyl-9-oxotetradecahydro-1H,12H-cyclopenta[a]cyclopropa[e]phenanthren-3-yl)hept-2-enoic acid, C32H48O5

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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 5

Abstract

C32H48O5, orthorhombic, P212121 (no. 19), a = 7.1564(10) Å, b = 17.542(3) Å, c = 23.134(4) Å, V = 2904.2(8) Å3, Z = 4, Rgt(F) = 0.0555, wRref(F2) = 0.1343, T = 273(2) K.

CCDC no.: 2342737

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 needle
Size: 0.25 × 0.23 × 0.21 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.08 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θmax, completeness: 27.8°, 98 %
N(hkl)measured, N(hkl)unique, Rint: 30,980, 6722, 0.076
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ (Iobs), 3814
N(param)refined: 345
Programs: Olex2, 1 Bruker, 2 SHELX, 3 Diamond 4
Table 2:

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

Atom x y z Uiso*/Ueq
C1 −0.0502 (5) 0.7529 (2) 0.26246 (16) 0.0563 (10)
C2 −0.1096 (5) 0.8286 (3) 0.23513 (18) 0.0657 (12)
C3 0.0599 (5) 0.8743 (2) 0.22024 (17) 0.0563 (10)
C4 0.1942 (5) 0.8927 (2) 0.26912 (16) 0.0529 (10)
C5 0.2450 (4) 0.8144 (2) 0.29767 (14) 0.0416 (8)
C6 0.3884 (5) 0.8196 (2) 0.34592 (16) 0.0507 (9)
C7 0.4346 (4) 0.7402 (2) 0.36772 (15) 0.0468 (9)
C8 0.2680 (4) 0.70463 (19) 0.39853 (14) 0.0361 (8)
C9 0.0869 (4) 0.70729 (18) 0.36224 (14) 0.0377 (8)
C10 0.0739 (5) 0.76757 (19) 0.31431 (14) 0.0420 (8)
C11 −0.0149 (5) 0.6319 (2) 0.35245 (15) 0.0492 (9)
C12 −0.0113 (5) 0.5729 (2) 0.40214 (14) 0.0448 (8)
C13 0.1240 (4) 0.59194 (17) 0.45083 (13) 0.0341 (7)
C14 0.3066 (4) 0.62489 (19) 0.42353 (13) 0.0363 (7)
C15 0.4403 (5) 0.6259 (2) 0.47544 (15) 0.0508 (9)
C16 0.3853 (5) 0.5566 (2) 0.51185 (16) 0.0528 (10)
C17 0.2032 (4) 0.52399 (19) 0.48706 (14) 0.0379 (8)
C18 0.0292 (5) 0.64987 (19) 0.49128 (15) 0.0502 (9)
C19 −0.0251 (5) 0.7796 (2) 0.37094 (15) 0.0510 (9)
C20 0.0776 (5) 0.4872 (2) 0.53366 (14) 0.0447 (8)
C21 −0.1044 (5) 0.4560 (3) 0.5092 (2) 0.0762 (14)
C22 0.1816 (5) 0.4261 (2) 0.56779 (14) 0.0482 (9)
C23 0.2186 (6) 0.3506 (2) 0.53863 (17) 0.0570 (10)
C24 0.3572 (5) 0.3534 (2) 0.48977 (16) 0.0504 (9)
C25 0.3521 (5) 0.3134 (2) 0.44116 (16) 0.0499 (9)
C26 0.5011 (6) 0.3231 (2) 0.39763 (16) 0.0526 (10)
C27 0.2024 (7) 0.2570 (3) 0.42635 (19) 0.0850 (15)
C28 0.3900 (5) 0.5710 (2) 0.37773 (15) 0.0519 (9)
C29 0.0981 (7) 0.9484 (2) 0.3117 (2) 0.0799 (14)
C30 0.3688 (6) 0.9312 (2) 0.24515 (19) 0.0680 (12)
C31 0.1375 (10) 0.3918 (3) 0.6672 (2) 0.0894 (17)
C32 −0.0049 (11) 0.3718 (3) 0.71167 (18) 0.117 (2)
H2 0.500854 0.844089 0.331679 0.061*
H3 0.539642 0.743012 0.394144 0.056*
H4 0.470682 0.708262 0.335372 0.056*
H5 −0.160267 0.775300 0.371188 0.061*
H6 0.025064 0.817696 0.397044 0.061*
H7 0.022020 0.523525 0.386271 0.054*
H8 −0.136115 0.568620 0.418157 0.054*
H9 0.483265 0.518399 0.510390 0.063*
H10 0.367231 0.571520 0.551826 0.063*
H11 0.569064 0.621968 0.462731 0.061*
H12 0.307216 0.568178 0.345139 0.078*
H13 0.509162 0.590163 0.365425 0.078*
H14 0.405446 0.521111 0.394077 0.078*
H15 0.425615 0.672596 0.497476 0.061*
H16 0.237735 0.483707 0.459724 0.045*
H17 0.263750 0.314896 0.567439 0.068*
H18A −0.073784 0.625898 0.510676 0.075*
H18 0.457192 0.386770 0.494129 0.060*
H19 0.093027 0.283681 0.413378 0.127*
H20 0.246124 0.223904 0.396219 0.127*
H21A −0.164980 0.424996 0.537775 0.114*
H21 0.172262 0.227400 0.459959 0.127*
H22 0.101241 0.330939 0.523856 0.068*
H23 0.300103 0.447191 0.581742 0.058*
H24 −0.118004 0.399571 0.704209 0.175*
H25 −0.029972 0.318115 0.710145 0.175*
H26 0.041531 0.384959 0.749306 0.175*
H27 0.044128 0.527500 0.561079 0.054*
H28 −0.078223 0.425739 0.475554 0.114*
H29A −0.184767 0.497590 0.498733 0.114*
H29 −0.013742 0.925396 0.326541 0.120*
H32 −0.015600 0.692294 0.469045 0.075*
H33 0.117985 0.667545 0.519365 0.075*
H34 0.038207 0.607965 0.318396 0.059*
H35A −0.144521 0.643282 0.343778 0.059*
H35 0.697 (7) 0.380 (3) 0.379 (2) 0.090 (17)*
H36 0.244166 0.737361 0.432058 0.043*
H37 0.338930 0.850184 0.377339 0.061*
H39 0.435111 0.896070 0.220833 0.102*
H40 0.447899 0.946680 0.276543 0.102*
H41 0.333286 0.975143 0.222978 0.102*
H42 0.181568 0.959516 0.343044 0.120*
H43 0.067019 0.994702 0.291814 0.120*
H44 −0.160122 0.724603 0.274435 0.068*
H45 0.016765 0.722460 0.234239 0.068*
H46 −0.187126 0.856950 0.262019 0.079*
H47 −0.182247 0.818998 0.200495 0.079*
H58 0.306453 0.785016 0.267052 0.050*
O1 0.0904 (4) 0.89191 (18) 0.17016 (12) 0.0732 (9)
O2 0.0611 (4) 0.40969 (15) 0.61723 (10) 0.0650 (8)
O3 0.3059 (8) 0.3876 (3) 0.67335 (19) 0.156 (2)
O4 0.6241 (4) 0.3774 (2) 0.40968 (14) 0.0803 (10)
O5 0.5121 (5) 0.28645 (17) 0.35414 (12) 0.0786 (9)

1 Source of material

As a medicinal herb, Pteris wallichiana C. Agardh has been used for the treatment of dysentery and traumatic injury for a long time. 5 Thus, we conducted a phytochemical investigation on this plant for a better development. The whole plant of Pteris wallichiana C. Agardh (47.5 kg) was collected from Changning County, Yunnan Province. The air-dried plant material was respectively extracted by 95 % methanol for twice, 85 % methanol for twice and 70 % methanol for once (seven days each time) at room temperature. The total extract (about 10.3 kg) was obtained by concentration under vacuum. Then the obtained extract was dissolved in warm water and extracted with isovolumic petroleum ether, ethyl acetate and n-butanol, respectively, to provide three fractions. The ethyl acetate fraction (304 g) was subjected to MCI column chromatography, eluting with methanol-water system (volume radio 50–100 %) to obtain four fractions (A–D). After repeated silica gel column chromatography, the title compound (24 mg) was purified and isolated from fraction B. The compound was further recrystallized with methanol to obtain a white needle-like crystal suitable for X-ray diffraction.

2 Experimental details

The carbon-bound hydrogen atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms with d(C–H) = 0.93–0.98 Å, Uiso(H) = 1.5 times Ueq(C) and 1.2 times Ueq(O).

3 Comment

The Pteris Wallichiana C. Agardh is a member of Pteris genus in the family Pteridaceae. It is a ethnomedicine that has the functions of clearing away heat and relieving dysentery, stabilizing shock and stopping bleeding. Thus, it is used for the treatment of dysentery, wind shock in children and traumatic bleeding. The previous studies have shown that this genus has good biological activities. 6 , 7 , 8 , 9 , 10 In order to better develop and utilize the Pteris wallichiana, its chemical constituents were preliminarily studied and the title compound was obtained. The compound has three ketone groups, one hydroxyl group and one double bond. The bond lengths and bond angles derived from the title structure are within the normal ranges. The ketone bonds were determined by the distance of 1.219(4) Å(C3–O3), 1.327(4) Å(C26–O2), 1.216(7) Å(C31–O5). The hydroxyl group was identified by the distance of 1.196(4) Å(C26′–O3′). And the double bond was identified by the distance of 1.326(5) Å (C24′–C25′). In general all bond lengths and angles are in the expected ranges. 11 , 12

Corresponding author: Juan Zou, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, P.R. China, E-mail:

Funding source: National Natural Science Foundation of China

Award Identifier / Grant number: 81660723

Funding source: National Natural Science Foundation of China

Award Identifier / Grant number: 82360689

Funding source: Natural-Scientific Research Program of Department of Education of Guizhou Province, Qianjiaoji

Award Identifier / Grant number: (2023)070

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

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

  3. Research funding: This work was funded by National Natural Science Foundation of China [No. 81660723], the National Natural Science Foundation of China [No. 82360689], the Natural-Scientific Research Program of Department of Education of Guizhou Province, Qianjiaoji [No. (2023)070].

References

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Received: 2024-03-31
Accepted: 2024-06-17
Published Online: 2024-07-23
Published in Print: 2024-10-28

© 2024 the author(s), published by De Gruyter, Berlin/Boston

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

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  55. Retractions
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  57. Retraction of: Crystal structure of aqua(2,2′-bipyridine-k 2 N:N′)(nitrato)-(4-aminobenzoato)cadmium(II) nitrate, [Cd(H2O)(NO3)(C10H8N2)(C7H7NO2)][NO3]
https://doi.org/10.1515/ncrs-2024-0151
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Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Editorial 2024 – New developments and changes of Zeitschrift für Kristallographie – New Crystal Structures
  4. New Crystal Structures
  5. Hydrogen bonding and π⋅⋅⋅halogen interactions in the crystal structure of bis(theophyllinium) hexachloridoplatinate(IV) monohydrate
  6. The crystal structure of 6-amino-2-carboxypyridin-1-ium perchlorate, C6H7ClN2O6
  7. Crystal structure of poly[(μ4-(3-amino-1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ 4 N:O:O':O')(1-methylpyrroldin-2-one-κ1O)dicopper(II)] – 1-methylpyrroldin-2-one (1/3), C40H48Cu2N12O12
  8. The crystal structure of 18-crown-6-k6O6(2,4,5-trinitroimidazol-1-ido-k1O)potassium(I)
  9. Crystal structure of poly[tetraaqua-bis(μ2-5-bromoisophthalato-κ3O,O′:O″)-(μ2-1,5-bis(imidazol-2-methyl)pentane-κ2N:N′)dicadmium(II)] dihydrate
  10. Crystal structure of (5R,6S,E)-5-acetoxy-2-methyl-6-((2aR,3R,5aS,5bS,11aR,12aS)-2a,5a,8,8-tetramethyl-9-oxotetradecahydro-1H,12H-cyclopenta[a]cyclopropa[e]phenanthren-3-yl)hept-2-enoic acid, C32H48O5
  11. The crystal structure of poly[diaqua-bis(μ2 -thiocyanato-κ2N:O)cobalt(II) monohydrate
  12. The crystal structure of 1,3,5-tri(1H-imidazol-1-yl)benzene–2,3,5,6-tetrachlorobenzene-1,4-dicarboxylic acid (1/1)
  13. Crystal structure of dichlorido-bis(1-[(2-ethyl-benzimidazole-1-yl)methyl]-1H–benzotriazole) cadmium(II), C32H32CdN10OCl2
  14. The crystal structure of N′-(tert-butyl)-N′-(3,5-dimethylbenzoyl)-3-methoxy-N,2-dimethylbenzohydrazide, C23H30N2O3
  15. Crystal stucture of 3-benzamido-N-(2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)-2-fluorobenzamide
  16. Crystal structure of bis(μ-benzeneselenolato)-(tetracarbonyl)-{μ-[N-(diphenylphosphanyl)-N-(3-ethynylphenyl)-P,P-diphenylphosphinous amide]} diiron, C48H35Fe2NO4P2Se2
  17. The crystal structure of 2′-(p-tolyl)-4′H-spiro[isochromane-1,1′-naphthalene]-3,4′-dione, C25H18O3
  18. The crystal structure of poly[hexaqua-tetrakis(μ4-pyridine-2,4-dicarboxylate-κ5N: O: O′: O″: O‴)-bi(μ2-pyridine-2,4-dicarboxylate-κ3N: O: O′)-digadolinium(III)tricopper (II)], [Gd2Cu3(C7H3NO4)6(H2O)6] n
  19. Crystal structure of poly[bis(4-(4-(pyridin-4-yl)phenyl)pyridin-1-ium-κ1N)-(μ4-benzene-1,2,4,5-tetracarboxylato-κ5O:O′: O″:O‴:O⁗)-(μ2-2,5-dicarboxyterephthalato-κ2O:O′)dizinc(II)], C52H32N4O16Zn2
  20. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 2-carboxy-6-nitrobenzoate monohydrate, C24H25FN4O10
  21. Crystal structure of dichlorido-(1-((3,5-dimethyl-2,3-dihydro-1H-1,2,3-triazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-k1N)zinc(II), C22H24ZnN12Cl2
  22. The crystal structure of (3-chlorothiophene-2-carboxylato-κ2O, O′)-(2,2′-dipyridyl-κ2N,N′)lead(II), C20H12Cl2N2O4S2Pb
  23. Synthesis and crystal structure of (Z)-4-((1-(3-fluorophenyl)-1H-1,2,3-triazol-4-yl)methylene)-5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one, C19H14FN5O
  24. The crystal structure of the coordination compound catena-poly[(18-crown-6-ether-κ6O6)(4,5-dinitroimidazolato-κ1O)potassium(I)]
  25. Crystal structure of 7-(diethylamino)-3-(trifluoroacetyl)-2H-chromen-2-one, C15H14F3NO3
  26. Crystal structure of dichlorido-1-[(2-ethylimidazole-1-yl)methyl]-1H–benzotriazole κ1N zinc(II), C24H26ZnN10Cl2
  27. Crystal and molecular structure of 5-bromopyridine-2,3-diamine
  28. Crystal structure of catena-poly[bis(μ2-1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine-3-carboxylato-k3-O,O′:O″)hexaqua-dicobalt tetrahydrate], C26H36N4O20Co2
  29. Crystal structure of thiocyanate-κ1N-bis(μ1-2,6-diformyl-4-methylphenol oxime-κ2N,O)-manganese(III) acetonitrile solvate, C21H21MnN6O6S
  30. The crystal structure of pyrrolidin-1-yl pivalate, C9H13NO4
  31. The crystal structure of 2,2′-(2,2-diphenylethene-1,1-diyl)bis(1,4-dimethoxybenzene), C30H28O4
  32. Crystal structure of bis(benzyltrimethylammonium) tetrathiotungstate(VI), {(C6H5CH2)(CH3)3N}2[WS4]
  33. The crystal structure of ethyl (Z)-2-(ethoxymethylene)-3-oxobutanoate, C9H14O4
  34. The crystal structure of (E)-6-bromo-3,5-dimethyl-2-(1-phenylprop-1-en-2-yl)-3Himidazo[4,5b]pyridine, C17H16BrN3
  35. Crystal structure of (3S,3′S,4R,4′S)-3′-(furan-3-yl)-3-hydroxy-4′-methyl-3,5,6′,7′-tetrahydro-1H,3′H-4,5′-spirobi[isobenzofuran]-1,1′(4′H)-dione-methanol (1/1), C21H22O7
  36. Cocrystal structure of progesterone-isophthalic acid, C25H33O4
  37. The crystal structure of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one, C17H12FN3O
  38. Crystal structure of S-(4-carboxybutyl)- l -cysteine
  39. The cocrystal of 2,2′-(hydrazine-1,1-diyl)bis(1H-imidazole-4,5-dicarbonitrile)– methanol (2/3)
  40. Crystal structure of (1′R,2′S,4′R,6′S)-4,6-dihydroxy-1′,8′,8′-trimethyl-3-(3-methylbutanoyl)-4′,8′,6′,1′,7,2′-hexahydro-1H-4′,6′-methanoxanthene-8-carbaldehyde, C23H30O5
  41. Crystal structure of (3,6-di(2-pyridyl)-4-methylphenyl pyridazine-k 2 N,N′)-bis(1-phenyl-pyrazole-κ 2 C,N) iridium(III) hexafluorophosphate, C39H29F6IrN8P
  42. Crystal structure of 1,5-bis[(E)-1-(2-hydroxyphenyl)ethylidene]thiocarbonohydrazide dimethyl sulfoxide monosolvate, C17H18N4O2S·C2H6OS
  43. Crystal structure of (S)-4-(2-(4-(2-acetyl-5-chlorophenyl)-3-methoxy-6-oxopyridazin-1(6H)-yl)-3-phenylpropanamido)benzoic acid monohydrate, C29H26ClN3O7
  44. The crystal structure of 1,3-bis(2,4-dinitro-1H-imidazol-1-yl)propane
  45. Crystal structure of 4-chlorobenzyl (S)-2-(6-methoxynaphthalen-2-yl)propanoate, C21H19ClO3
  46. Crystal structure of 1-(5-(benzo[d][1,3]dioxol-5-yl)-4-benzyl-1-(4-bromophenyl)-4,5-dihydro-1H-1,2,4-triazol-3-yl)ethan-1-one, C24H20BrN3O3
  47. The crystal structure of (Z)-3′-(2-(1-(3,4-dimethyl-phenyl)-3-methyl-5-oxo-1,5-dihydro-4H-pyrazol-4-ylidene)hydrazinyl)-2′-hydroxy-[1,1′-biphenyl]-3-carboxylicacid ─ methanol (1/1), C26H26N4O5
  48. Crystal structure of (S)-1-phenylpropan-1-aminium (S)-(1-phenylpropyl)carbamate C19H26N2O2
  49. Synthesis and crystal structure of methyl 2-((5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl)thio)acetate, C18H16BrN3O2S
  50. The crystal structure of trichlorobis(pyridine-2,6-dithio-κS-carbomethylamido)antimony(III), [SbCl3(C9H11N3S2)2]
  51. Crystal structure of 1,8-dihydroxy-3-{[(triphenylstannyl)oxy]carbonyl} anthracene-9,10-dione, C33H22O6Sn
  52. The crystal structure of (E)-4-(2-(pyridin-4-ylmethylene)hydrazine-1-carbonyl)pyridin-1-ium-2-olate dihydrate, C12H14N4O4
  53. The crystal structure of 6-amino-pyridinium-2-carboxylate, C6H6N2O2
  54. The crystal structure of catena-poly[aqua-nitrato-κ3O,O:O′′-(1,10-phenanthroline-κ2N,N′)sodium(I)], C24H18N6O7Na2
  55. Retractions
  56. Retraction of: Crystal structure of bis[diaquaisonicotinatosamarium(III)]-µ-isonicotinato-[diisonicotinatocopper(II)], CuSm2(C6H4NO2)8(H2O)4
  57. Retraction of: Crystal structure of aqua(2,2′-bipyridine-k 2 N:N′)(nitrato)-(4-aminobenzoato)cadmium(II) nitrate, [Cd(H2O)(NO3)(C10H8N2)(C7H7NO2)][NO3]
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