Startseite Crystal structure of (5R,8R,9R,10R,12R, 13R,14R,17S)-2-(E-3-fluorobenzylidene)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl) hexadecahydro-3H-cyclopenta[a]phenanthren-3-one, C37H53FO3
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Crystal structure of (5R,8R,9R,10R,12R, 13R,14R,17S)-2-(E-3-fluorobenzylidene)-12-hydroxy-4,4,8,10,14-pentamethyl-17-((R)-2,6,6-trimethyltetrahydro-2H-pyran-2-yl) hexadecahydro-3H-cyclopenta[a]phenanthren-3-one, C37H53FO3

  • Kuo Cheng ORCID logo , Ya-Bin Song EMAIL logo , Qing-Guo Meng , Bao-Gang Wang , Yun Hou ORCID logo , Wen-Shui Wang und Sheng Jiang
Veröffentlicht/Copyright: 15. Januar 2024

Abstract

C37H53FO3, orthorhombic, P212121 (no. 19), a = 7.4716(8) Å, b = 15.0009(15) Å, c = 28.065(5) Å, V = 3145.5(7) Å3, Z = 4, R gt (F) = 0.0643, wR ref (F2) = 0.1464, T = 293 K.

CCDC no.: 2283345

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: 0.15 × 0.13 × 0.12 mm
Wavelength:

μ:
Mo Kα radiation (0.71073 Å)

0.08 mm−1
Diffractometer, scan mode:

θmax, completeness:
SuperNova,

25.5°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 10139, 5655, 0.057
Criterion for Iobs, N(hkl)gt: Iobs > 2σ(Iobs), 4379
N(param)refined: 379
Programs: CrysAlisPRO [1], SHELX [2, 3]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.6411 (6) 0.0540 (3) 0.25259 (16) 0.0250 (10)
C2 0.5605 (6) −0.0356 (3) 0.24405 (16) 0.0246 (10)
C3 0.3790 (6) −0.0434 (3) 0.21838 (17) 0.0274 (11)
C4 0.3220 (5) 0.0443 (3) 0.19277 (16) 0.0222 (10)
H4 0.256298 0.078136 0.216962 0.027*
C5 0.4772 (5) 0.1065 (3) 0.17742 (16) 0.0197 (10)
C6 0.5760 (6) 0.1325 (3) 0.22391 (17) 0.0283 (11)
H6A 0.677847 0.169683 0.215817 0.034*
H6B 0.495993 0.167770 0.243537 0.034*
C7 0.1863 (6) 0.0282 (3) 0.15306 (17) 0.0267 (11)
H7A 0.244156 −0.003253 0.127091 0.032*
H7B 0.090440 −0.009221 0.165024 0.032*
C8 0.1078 (5) 0.1146 (2) 0.13440 (16) 0.0207 (10)
H8A 0.038396 0.142394 0.159554 0.025*
H8B 0.026801 0.101110 0.108379 0.025*
C9 0.2489 (5) 0.1810 (2) 0.11684 (15) 0.0166 (9)
C10 0.3940 (5) 0.1937 (3) 0.15613 (16) 0.0186 (9)
H10 0.330666 0.221638 0.182805 0.022*
C11 0.1636 (5) 0.2755 (3) 0.10745 (15) 0.0181 (9)
C12 0.3077 (5) 0.3404 (2) 0.08845 (15) 0.0166 (9)
H12 0.361478 0.312149 0.060422 0.020*
C13 0.4573 (5) 0.3530 (3) 0.12480 (16) 0.0221 (10)
H13 0.409607 0.384209 0.152726 0.027*
C14 0.5332 (6) 0.2627 (3) 0.14047 (16) 0.0222 (10)
H14A 0.601597 0.237894 0.114257 0.027*
H14B 0.615396 0.272611 0.166686 0.027*
C15 0.0239 (5) 0.2811 (3) 0.06694 (16) 0.0226 (10)
H15A 0.059275 0.244497 0.040070 0.027*
H15B −0.092950 0.261901 0.077960 0.027*
C16 0.0214 (6) 0.3796 (3) 0.05330 (17) 0.0240 (10)
H16A −0.078830 0.409407 0.068463 0.029*
H16B 0.009225 0.386020 0.019062 0.029*
C17 0.2014 (5) 0.4217 (2) 0.07037 (16) 0.0186 (9)
H17 0.174667 0.459274 0.098014 0.022*
C18 0.2874 (5) 0.4814 (3) 0.03234 (16) 0.0206 (10)
C19 0.1547 (6) 0.5498 (3) 0.01323 (17) 0.0231 (10)
H19A 0.071774 0.520280 −0.008175 0.028*
H19B 0.086120 0.573913 0.039603 0.028*
C20 0.2452 (6) 0.6262 (3) −0.01321 (18) 0.0298 (11)
H20A 0.304118 0.603528 −0.041517 0.036*
H20B 0.155940 0.669366 −0.023118 0.036*
C21 0.3815 (6) 0.6711 (3) 0.01873 (18) 0.0309 (11)
H21A 0.319665 0.700109 0.044862 0.037*
H21B 0.443573 0.716795 0.000679 0.037*
C22 0.5180 (6) 0.6062 (3) 0.03884 (19) 0.0323 (12)
C23 0.6146 (8) 0.6442 (3) 0.0817 (2) 0.0564 (17)
H23A 0.529313 0.657967 0.106225 0.085*
H23B 0.676983 0.697505 0.072639 0.085*
H23C 0.698840 0.601177 0.093503 0.085*
C24 0.3296 (6) 0.1431 (3) 0.07029 (16) 0.0243 (10)
H24A 0.343066 0.079721 0.073180 0.036*
H24B 0.444465 0.169828 0.064707 0.036*
H24C 0.251319 0.156366 0.044107 0.036*
C25 0.6128 (6) 0.0601 (3) 0.14458 (17) 0.0281 (11)
H25A 0.693058 0.103594 0.131454 0.042*
H25B 0.550274 0.030527 0.119208 0.042*
H25C 0.679782 0.017046 0.162561 0.042*
C26 0.3873 (7) −0.1254 (3) 0.18501 (19) 0.0366 (13)
H26A 0.465577 −0.112776 0.158722 0.055*
H26B 0.269586 −0.138391 0.173220 0.055*
H26C 0.432035 −0.175815 0.202369 0.055*
C27 0.6551 (6) 0.5790 (3) 0.0012 (2) 0.0503 (16)
H27A 0.720333 0.527817 0.012198 0.075*
H27B 0.736597 0.627377 −0.004220 0.075*
H27C 0.594464 0.564600 −0.027936 0.075*
C28 0.0703 (5) 0.3142 (3) 0.15232 (15) 0.0197 (10)
H28A 0.156058 0.319918 0.177599 0.030*
H28B −0.024115 0.274842 0.162142 0.030*
H28C 0.021163 0.371697 0.144972 0.030*
C29 0.2456 (7) −0.0632 (3) 0.2587 (2) 0.0415 (14)
H29A 0.271794 −0.120487 0.272305 0.062*
H29B 0.126071 −0.063334 0.246192 0.062*
H29C 0.255695 −0.018190 0.282894 0.062*
C30 0.7624 (6) 0.0587 (3) 0.28762 (16) 0.0243 (10)
H30 0.782540 0.006029 0.304246 0.029*
C31 0.8686 (6) 0.1364 (3) 0.30341 (16) 0.0223 (10)
C32 0.8743 (6) 0.1573 (3) 0.35243 (16) 0.0271 (10)
H32 0.809143 0.124435 0.374530 0.033*
C33 0.9780 (6) 0.2271 (3) 0.36631 (17) 0.0310 (11)
C34 1.0831 (6) 0.2757 (3) 0.33611 (18) 0.0309 (11)
H34 1.154299 0.321914 0.347458 0.037*
C35 1.0807 (6) 0.2543 (3) 0.28823 (18) 0.0345 (12)
H35 1.151275 0.285739 0.266717 0.041*
C36 0.9725 (6) 0.1858 (3) 0.27274 (17) 0.0277 (11)
H36 0.969566 0.172529 0.240384 0.033*
C37 0.3677 (6) 0.4253 (3) −0.00826 (16) 0.0315 (11)
H37A 0.389003 0.462763 −0.035422 0.047*
H37B 0.285598 0.378782 −0.016783 0.047*
H37C 0.478640 0.399502 0.002094 0.047*
F1 0.9792 (4) 0.24862 (19) 0.41389 (10) 0.0484 (8)
O1 0.4259 (4) 0.52890 (18) 0.05861 (11) 0.0257 (7)
O2 0.6064 (4) 0.40139 (19) 0.10659 (12) 0.0311 (8)
H2 0.573599 0.451070 0.098096 0.047*
O3 0.6373 (4) −0.10299 (18) 0.25643 (12) 0.0340 (8)

1 Source of material

Total saponins from ginseng stems and leaves were added to an ethanol solution of 18 % sulfuric acid and heated to reflux for 4 h. The reaction solution was cooled to room temperature, appropriate amount of sodium carbonate was added to neutralize sulfuric acid, the reaction solution was adjusted to pH 7. The residue was extracted with ethyl acetate, washed with saturated brine, dried with anhydrous sodium sulfate, filtered, concentrated under reduced pressure to obtain the crude product, and the crude product was recrystallized with ethyl acetate to obtain the pure product of 20(R)-panaxadiol. 20(R)-panaxadiol and PCC (pyridinium chlorochromate) were dissolved in 25 mL of dichloromethane, and the reaction mixture was stirred at room temperature for 4 h. The intermediate 20(R)-3-oxopanaxadiol was purified by silica gel column chromatography. Methanol (1.4 mL), 20(R)-3-oxopanaxadiol (100 mg, 0.22 mmol), and 2-fluorobenzaldehyde (0.023 mL, 0.22 mmol) were added to a round-bottomed flask, to which 0.72 mL (25 %) aqueous sodium hydroxide was added dropwise, and the flask was stirred for 4 h at room temperature. The reaction was monitored by thin layer chromatography (TLC, 254 nm). At the end of the reaction, appropriate amount of water was added, the reaction mixture was transferred to a partition funnel and extracted with ethyl acetate (twice), the organic phases were combined and washed with saturated sodium chloride solution, dried with anhydrous sodium sulfate, filtered, concentrated under reduced pressure and the crude product was purified by silica gel column chromatography. Recrystallization with ethyl acetate solution gave crystals of the target compound.

2 Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms [3].

3 Comment

Ginseng saponins include protopanoxadiol-type saponin, panaxatriol-type saponin and oleanane-type saponin, sharing a tetrahydrofuran ring and a dammarane skeleton [4]. In recent years, our laboratory has carried out research on the synthesis and single crystal X-ray diffraction of protopanoxadiol derivatives [5], [6], [7] and protopanaxatriol derivatives [8, 9], and the title compound is a 20(R)-panaxadiol derivative. Ginsenosides are important saponins among ginsenosides and their structures can be modified [10].

The ORTEP diagram is presented in the Figure. The title compound contains one drug molecule in the asymmetric unit (cf. the figure). Bond lengths and angles are all in the expected ranges. The title compound has a dammarane type as the parent structure [11], with a benzene ring structure attached to C(1). An α,β-unsaturated ketone group is formed between the benzene ring and the parent nucleus through the Claisen–Schmidt reaction effect. The angle of twist of C(30) = C(1)–C(2) = O(3) is −22.608°. The bond length of C(2)–O(3) is 1.2137 Å. The bond length of C(33)–F(1) is 1.374(5) Å. There is a fluorine substitution on the benzene ring. The benzene ring is non-coplanar with the saturated cyclic ketone and the dihedral angle between them is 54.048°. This twisted configuration may increase the likelihood of interactions with bioactive molecules or the purposes of creating more potent biological activity [12, 13]. The bond length of C(18)–O(1) is 1.4564 Å. The bond length of C(22)–O(1) is 1.4585 Å. There is a pyran ring substitution at the C(17) position and the oxygen atom on the ring acts as a hydrogen bond acceptor to form an intramolecular hydrogen bond. The bond length of C(13)–O(2) is 1.4251 Å. The pyran ring is connected to the five-membered ring via C(17)–C(18), the bond length of C(17)–C(18) is 1.374 Å. It is assumed that the dihedral angles between the five-membered ring and the pyran ring and the six-membered ring where the hydroxyl group is located are small, 3.031 Å and 0.604 Å, respectively, probably due to hydrogen bonding. The compound has a total of 8 chiral carbons, which are: 5R,8R,9R, 10R,12R,13R,14R,17S.


Corresponding author: Ya-Bin Song, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, 100071 Beijing, P.R. China, E-mail:

Acknowledgments

This work was supported by Science and Technology Innovation Development Plan of Yantai (No. 2020XDRH105) and the National Natural Science Foundation of China (No. 81473104).

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

  2. Competing interests: The authors declare no conflicts of interest regarding this article.

  3. Research funding: Science and Technology Innovation Development Plan of Yantai (No. 2020XDRH105) and the National Natural Science Foundation of China (No. 81473104).

References

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Received: 2023-10-30
Accepted: 2023-12-28
Published Online: 2024-01-15
Published in Print: 2024-04-25

© 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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  32. The crystal structure of 6-(benzofuran-2-yl)-2-oxo-4,5-diphenyl-3,4-dihydro-2H-pyran-3-carbonitrile, C26H17NO3
  33. Crystal structure of N-(4-bromobenzyl)-3-(difluoromethyl)-1-methyl-N-(pyridin-2-yl)-1H-pyrazole-4-carboxamide, C18H15BrF2N4O
  34. The crystal structure of the host-guest complex: N-{5-[2-(2,6-dimethylphenoxy)acetamido]-4-hydroxy-1,6-diphenylhexan-2-yl}-3-methyl-2-(2-oxo-1,3-diazinan-1-yl)butanamide-diethyl ether (2/1)
  35. The crystal structure of (Z)-4-amino-N-(1-(4-hydroxyphenyl)propylidene)benzohydrazide, C16H17N3O2
  36. The crystal structure of diethyl 1,4-dihydro-2,6-dimethyl-4-(3-cyanophenyl)-3,5-pyridinedicarboxylate, C20H22N2O4
  37. Crystal structure of 3-(5-((4-(difluoromethoxy)phenyl) sulfonyl)-3,4,5,6-tetrahydropyrrolo[3,4-c]pyrrol-2(1H)-yl) oxetane-3-carboxamide, C17H19F2N3O5S
  38. Crystal structure of 2-((2,6-dichloro-4-(3,5-dimethylisoxazol-4-yl)phenyl)amino)-N-(2-(4-methylpiperazin-1-yl)ethyl)benzamide hydrate, C25H37Cl2N5O6
  39. Crystal structure of 3-(benzo[d]thiazol-2-yl)-5-bromo-2-hydroxybenzaldehyde, C14H8BrNO2S
  40. Crystal structure of 3-(difluoromethyl)-1-methyl-N-(pyridin-2-yl)-1H-pyrazole-4-carboxamide, C11H10F2N4O
  41. Crystal structure of 3-(2-ethoxy-2-oxoethyl)-1-isopropyl-1H-imidazol-3-ium hexafluoridophosphate(V), C20H34F12N4P2
  42. Crystal structure of ethyl 5,6-dichloro-2-methyl-2,3-dihydro-1 H-benzo[d]imidazole-2-carboxylate, C11H12Cl2N2O2
  43. The crystal of structure of (OC-6-22)-pentakis(acetonitrile)bromidoruthenium(II)bromide monohydrate, C10H15Br2N5Ru
  44. Crystal structure of (2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-(((4aS,5R,6S)-1-oxo-5-vinyl-4,4a,5,6-tetrahydro-1H,3H-pyrano[3,4-c]pyran-6-yl)oxy)tetrahydro-2H-pyran-3-yl 2,3-dihydroxybenzoate hydrate, C23H26O12·H2O
  45. The crystal structure of (E)-4-amino-N′-(1-(4-fluorophenyl)propylidene)benzohydrazide, C16H16FN3O
  46. The crystal structure of 2′-(9H-carbazol-9-yl)-[1,1′-binaphthalen]-2-amine, C32H22N2
  47. Crystal structure of poly[μ3-diiodido-[μ2-di(1H-pyrazol-1-yl)methane-κ2N,N′)]dicopper(I)], C7H8Cu2I2N4
  48. Crystal structure of 3-amino-N′-hydroxy-1H-pyrazole-4-carboximidamide, C4H7N5O
  49. The crystal structure of 1,3-diacetyltetrahydroimidazo[4,5-d]imidazole-2,5(1H,3H)-dione, C8H10O4N4
  50. Crystal structure of catena-poly[aqua-(μ2-1,4-diazabicyclo[2.2.2]octane-k2N: N′)-bis(sorbato-κ1O)-copper(II), C18H28CuN2O5
  51. Crystal structure of catena-poly[triaqua-(μ2 -1-(4-carboxylatophenyl)-4-oxo-1,4-dihydropyridazine-3-carboxylato-κ3O,O′:O′′)manganese(II)], C12H12N2O8Mn
  52. The crystal structure of [hexaaquamagnesium(II)] 4-[(pyridine-4-carbonyl)-amino]-phthalate trihydrate, C14H26N2O14Mg
  53. Crystal structure of 1-(p-tolylphenyl)-4-(2-furoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O3
  54. The crystal structure of bis(1,4,7,10,13-pentaoxacyclopentadecane)-potassium(I) dichloridocopper(I), C20H40Cl2CuKO10
  55. The crystal structure of tris(tetra-n-butylammonium) hexanitrato-κ2O,O′-lanthanium(III) C48H108N9O18La
Heruntergeladen am 2.10.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2023-0470/html
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