Home Crystal structure of (8R,10R,14R, Z)-2-((3–Fluoropyridin-4-yl) methylene)-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, C36H52FNO3
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Crystal structure of (8R,10R,14R, Z)-2-((3–Fluoropyridin-4-yl) methylene)-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, C36H52FNO3

  • Mei Zhang , Qing-Guo Meng , Gui-Ge Hou , Sheng Jiang , Yong-Sheng Jin and Yue Gao EMAIL logo
Published/Copyright: July 30, 2021

Abstract

C36H52FNO3, orthorhombic, P212121 (no. 19), a = 7.8016(7) Å, b = 13.1609(10) Å, c = 30.536(2) Å, V = 3135.3(4) Å3, Z = 4, R gt (F) = 0.0657, wR ref (F2) = 0.1435, T = 100 K.

CCDC no.: 2087492

The molecular structure is shown in the figure. Displacement ellipsoids are drawn at the 30% probability level. 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: 0.13 × 0.12 × 0.10 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.08 mm−1
Diffractometer, scan mode: SuperNova,
θmax, completeness: 25.0°, >99%
N(hkl)measured, N(hkl)unique, Rint: 14226, 5509, 0.095
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 3824
N(param)refined: 379
Programs: CrysAlisPRO [1], SHELX [2], [3], [4]
Table 2:

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

Atom x y z Uiso*/Ueq
C1 0.2876 (6) 0.7168 (3) 0.60218 (14) 0.0267 (11)
H1A 0.391895 0.711210 0.585065 0.032*
H1B 0.201292 0.674928 0.588127 0.032*
C2 0.2280 (6) 0.8262 (3) 0.60106 (14) 0.0271 (11)
C3 0.1648 (6) 0.8737 (3) 0.64248 (15) 0.0270 (11)
C4 0.1101 (6) 0.8075 (3) 0.68105 (13) 0.0245 (11)
C5 0.1568 (6) 0.6943 (3) 0.67499 (13) 0.0241 (10)
H5 0.063715 0.666078 0.657200 0.029*
C6 0.1523 (7) 0.6339 (4) 0.71757 (15) 0.0344 (12)
H6A 0.247982 0.654206 0.735862 0.041*
H6B 0.047317 0.649423 0.733223 0.041*
C7 0.1616 (7) 0.5208 (4) 0.70934 (15) 0.0367 (13)
H7A 0.061956 0.500185 0.692562 0.044*
H7B 0.157977 0.485487 0.737197 0.044*
C8 0.3249 (6) 0.4888 (3) 0.68446 (14) 0.0275 (11)
C9 0.3439 (6) 0.5559 (3) 0.64300 (14) 0.0237 (10)
H9 0.248135 0.535487 0.624201 0.028*
C10 0.3222 (6) 0.6738 (3) 0.64821 (14) 0.0234 (10)
C11 0.5050 (6) 0.5247 (3) 0.61719 (17) 0.0342 (12)
H11A 0.512165 0.565863 0.590916 0.041*
H11B 0.605323 0.539177 0.634859 0.041*
C12 0.5085 (7) 0.4125 (4) 0.60404 (16) 0.0360 (13)
H12 0.420024 0.400024 0.581915 0.043*
C13 0.4765 (6) 0.3444 (3) 0.64334 (15) 0.0272 (11)
H13 0.572895 0.354512 0.663464 0.033*
C14 0.3121 (6) 0.3757 (3) 0.66842 (14) 0.0262 (11)
C15 0.3062 (8) 0.2928 (4) 0.70371 (16) 0.0412 (14)
H15A 0.381189 0.309854 0.727964 0.049*
H15B 0.190522 0.284310 0.714747 0.049*
C16 0.3676 (6) 0.1958 (4) 0.68072 (15) 0.0355 (13)
H16A 0.271161 0.151548 0.674560 0.043*
H16B 0.447942 0.159411 0.699215 0.043*
C17 0.4566 (6) 0.2288 (3) 0.63713 (14) 0.0248 (11)
H17 0.373820 0.218237 0.613419 0.030*
C18 0.4772 (7) 0.5014 (4) 0.71648 (16) 0.0406 (14)
H18A 0.484252 0.570963 0.725801 0.061*
H18B 0.581699 0.482664 0.701979 0.061*
H18C 0.460133 0.458459 0.741503 0.061*
C19 0.4816 (6) 0.7281 (4) 0.66655 (17) 0.0336 (12)
H19A 0.581300 0.706522 0.650655 0.050*
H19B 0.494925 0.711423 0.696960 0.050*
H19C 0.467863 0.800246 0.663459 0.050*
C20 0.6169 (6) 0.1648 (3) 0.62624 (14) 0.0259 (11)
C21 0.7709 (6) 0.1363 (3) 0.55358 (14) 0.0278 (11)
C22 0.7212 (7) 0.0240 (3) 0.55536 (15) 0.0334 (12)
H22A 0.614124 0.014163 0.539798 0.040*
H22B 0.808645 −0.015991 0.540749 0.040*
C23 0.7014 (7) −0.0131 (3) 0.60216 (17) 0.0370 (13)
H23A 0.664489 −0.083511 0.602121 0.044*
H23B 0.810835 −0.009248 0.617123 0.044*
C24 0.5703 (6) 0.0516 (3) 0.62608 (16) 0.0314 (12)
H24A 0.560877 0.027979 0.656078 0.038*
H24B 0.459356 0.042988 0.612253 0.038*
C25 0.7660 (6) 0.1871 (4) 0.65689 (15) 0.0360 (13)
H25A 0.852674 0.136031 0.653322 0.054*
H25B 0.726081 0.186868 0.686630 0.054*
H25C 0.813223 0.252583 0.650055 0.054*
C26 0.7344 (7) 0.1796 (4) 0.50828 (15) 0.0427 (14)
H26A 0.614838 0.171870 0.501664 0.064*
H26B 0.801332 0.143779 0.486873 0.064*
H26C 0.764126 0.250339 0.507754 0.064*
C27 0.9583 (6) 0.1531 (4) 0.56523 (16) 0.0371 (13)
H27A 0.981809 0.224626 0.566207 0.056*
H27B 1.029718 0.121637 0.543501 0.056*
H27C 0.981740 0.123517 0.593348 0.056*
C28 0.1773 (7) 0.8549 (4) 0.72367 (15) 0.0385 (13)
H28A 0.299030 0.844937 0.725551 0.058*
H28B 0.122654 0.822938 0.748248 0.058*
H28C 0.152381 0.926278 0.723871 0.058*
C29 −0.0879 (6) 0.8160 (4) 0.68132 (15) 0.0298 (11)
H29A −0.120492 0.884406 0.688456 0.045*
H29B −0.134178 0.770291 0.702755 0.045*
H29C −0.131715 0.798728 0.652905 0.045*
C30 0.1515 (6) 0.3583 (4) 0.63932 (18) 0.0409 (13)
H30A 0.138679 0.287031 0.633559 0.061*
H30B 0.165081 0.394166 0.612156 0.061*
H30C 0.051609 0.383047 0.654253 0.061*
C31 0.2241 (6) 0.8849 (4) 0.56523 (16) 0.0308 (12)
H31 0.183236 0.950435 0.569761 0.037*
C32 0.2741 (6) 0.8621 (3) 0.52005 (14) 0.0264 (11)
C33 0.3199 (6) 0.9395 (3) 0.49219 (16) 0.0283 (11)
C34 0.3694 (6) 0.9244 (4) 0.44913 (16) 0.0331 (12)
H34 0.399698 0.980146 0.432114 0.040*
C35 0.3272 (8) 0.7547 (4) 0.45781 (16) 0.0429 (14)
H35 0.328042 0.689437 0.446141 0.051*
C36 0.2773 (7) 0.7658 (4) 0.50100 (16) 0.0366 (12)
H36 0.245824 0.709137 0.517320 0.044*
F1 0.3172 (4) 1.03671 (18) 0.50736 (9) 0.0384 (7)
N1 0.3748 (5) 0.8318 (3) 0.43148 (13) 0.0357 (10)
O1 0.1510 (4) 0.9668 (2) 0.64495 (11) 0.0365 (8)
O2 0.6732 (6) 0.3964 (3) 0.58506 (16) 0.0782 (16)
H2 0.692325 0.335271 0.583501 0.117*
O3 0.6564 (4) 0.1952 (2) 0.58156 (9) 0.0262 (7)

Source of material

The title compound was synthesized by three-step chemical reactions in turn. First, ginsenoside of stems and leaves (GSL) was degraded by 10% sulfuric acid ethanol solution and purified by silica gel column chromatography. After recrystallization in ethyl acetate and CH2Cl2, the pure white crystalline product panaxadiol (PD; systematic name: (3S, 5R,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17 -((R)-2,6,6-trimethyltetra-hydro-2H-pyran-2-yl) hexadecahydro-1H-cyclopenta[a] phen-anthrene-3,12-diol)-was obtained. Second, panaxadiol and PCC were dissolved in 25 ml dichloromethane(methylene chloride) solution and stirred for 4 h at room temperature. The product 3-oxo-panaxadiol was purified by silica gel column chromatography. Finally, in a representative experiment 0.72 mL (25%) of sodium hydroxide aqueous solution was added dropwise to the mixture of 3-oxo-panaxadiol (100 mg; 0.218 mmol) and 3-fluoropyridine-4-formaldehyde (0.022 ml; 0.218 mmol) in 1.4 mL methanol and stirred at room temperature for 2.5 h. The in process-control was monitored by silica gel thin layer chromatography (TLC, 254 nm), the developing solvent is petroleum ether and ethyl acetate. When the reaction was finished, the reaction system was extracted twice with appropriate amount of water and ethyl acetate, and the third time with brine and ethyl acetate. The crude yellow oil was obtained by vacuum distillation of the organic phase and the title compound was purified by silica gel column chromatography. Suitable crystals of the title compound were obtained by recrystallization in ethyl acetate system and dried under vacuo at 65 °C for 5 h.

Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms, with d(C–H) = 0.97 Å (methylene), d(C–H) = 0.98 Å (aromatic), d(C–H) = 0.96 Å (methyl), d(C–H) = 0.93 Å (alkenyl) and d(O–H) = 0.82 Å (–OH). The absolute configuration was derived from the synthesis and the configuration of the educts.

Comment

Ginsenoside are divided into two groups according to their glycosidic structures: dammarane and oleanane. There are two types of dammaranes: protopanaxadiol type [5, 6] and protopanaxatriol type sharing a tetrahydrofuran ring and a dammarane skeleton. Because these ginsenosides and their derivatives have a wide range of biological activities, such as anticancer, enhancing myocardial function [7], anti-inflammatory [8] and analgesic, their synthesis and biological activities have attracted extensive attention. At the same time the conformation of the compound will have a certain influence on the biological activity [9]. Our laboratory has done a lot of research work on panaxadiol derivatives [10, 11] and panaxatriol derivatives [12], and obtained crystal structures [13] with good data. The title compound is a PD derivative. It is possible to modify the structure of ginsenoside which is an important saponin in ginsenoside [14].

Single crystal X-ray structure analysis of the title compound revealed that the substituents are at on C(2), the structure of the title compound is similar to that of panaxadiol. In the crystal structure, the pyridine ring is planar, and the other six membered rings except the ring with the keto group have chair conformation. The bond lengths and angles are all in the expected ranges [12].


Corresponding author: Yue Gao, Department of Lab Teaching, School of Pharmacy, Naval Medical University, Shanghai, 200433, P. R. China, E-mail:

Award Identifier / Grant number: 81473104, 81773563, 81573585

Funding source: Science Foundation

Award Identifier / Grant number: 13ZJZ06

  1. Author contributions: 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). Meanwhile, this work was also supported by National Natural Science Foundation of China (Grant no. 81573585) and other Science Foundation (No. 13ZJZ06).

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

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Received: 2021-06-17
Accepted: 2021-07-19
Published Online: 2021-07-30
Published in Print: 2021-12-20

© 2021 Mei Zhang 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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  37. Crystal structure of (4,7,13,16,21,24-hexaoxa-1,10-diazabicyclo[8.8.8]hexacosane-κ 8 N 2, O 6) potassium cyclopentadienide, [K([2.2.2]crypt)]Cp, C23H41KN2O6
  38. The crystal structure of bis(2-oxidopyridin-1-ium-3-carboxylato-κ2O,O′)-(phenantroline-κ2N,N′)manganese(II) - methanol (1/3), C27H28N4O9Mn
  39. Crystal structure of 4-(dimethylamino)pyridinium dibromido-tris(4-chlorophenyl-κC)stannate(IV), C25H23Br2Cl3N2Sn
  40. Crystal structure of (3E,5E)-1-(4-cyanobenzenesulfonyl)-3,5-bis(3-fluorobenzylidene)piperidin-4-one-dichloromethane (1/1), C27H20Cl2F2N2O3S
  41. Crystal structure of (3E,5E)-3,5-bis(4-fluorobenzylidene)-1-((4-trifluoromethyl)benzenesulfonyl)piperidin-4-one, C26H18F5NO3S
  42. Crystal structure of chlorido-(4-methyl-2-((phenylimino)methyl)phenolato-κ2 N,O)-(pyridine-κ1 N)platinum(II), C19H17ClN2OPt
  43. Crystal structure of (4-methylbenzyl)(triphenyl)phosphonium chloride dihydrate, C26H28ClO2P
  44. The crystal structure of poly[μ2-chlorido-(μ2-1,2-bis(4-pyridyl)ethane-κ2N:N′silver(I)], C12H12AgClN2
  45. Crystal structure of poly[(μ4-benzene-1,2,4,5-tetracarboxylato)-bis(μ2-adipohydrazide)dicadmium], C11H15N4O6Cd
  46. The crystal structure of (E)-N′-(butan-2-ylidene)isonicotinohydrazide 0.5 hydrate C10H13N3O·0.5H2O
  47. The crystal structure of bis(6-phenylpyridine-2-carboxylate-κ2 N,O)-(2,2′-bipyridine-κ2 N,N′)zinc(II) monohydrate, C34H26N4O5Zn
  48. The crystal structure of (1R *,2S *)-1,2-bis(2-fluorophenyl)-3,8-dimethoxyacenaphthene-1,2-diol, C26H20F2O4
  49. Crystal structure of catena-poly[(μ2-1-((2-ethyl-4-methyl-1H-imidazol-1-yl)methyl)-1H-benzotriazole-κ2N:N′)-(nitrato-κ2O,O′)silver (I)], C13H15Ag1N6O3
  50. The crystal structure of [(phenantroline-κ2 N,N′)-bis(6-phenylpyridine-2-carboxylate-κ2 N,O)cobalt(II)]monohydrate, C36H26N4O5Co
  51. Crystal structure of (1E)-N-[(1E)-1-(4-chlorophenyl)ethylidene]-2-[1-(4-chlorophenyl)ethylidene]hydrazine-1-carbohydrazonamide, C 17 H 17 Cl 2 N 5
  52. The crystal structure of (E)-2-((tert-butylimino)methyl)-4-chlorophenol, C11H14ClNO
  53. Crystal structure of all-cis-2,4,6-trihydroxycyclohexane- 1,3,5-triaminium chloride sulfate, C6H18ClN3O7S
  54. Crystal structure of dichlorido-bis(dimethyl sulfoxide-κO)bis(4-methylphenyl-κC 1)tin(IV), C18H26Cl2O2S2Sn
  55. Crystal structure of dichlorido-bis(4-chlorophenyl-κC 1)(2,2′-bipyridyl-κ 2 N,N′)tin(IV), C22H16Cl4N2Sn
  56. Redetermination of the crystal structure of (E)-5-bromo-2-hydroxybenzaldehyde oxime, C 7 H 6 BrNO 2
  57. The crystal structure of (E)-amino(2-(4-methylbenzylidene)hydrazineyl)methaniminium 4-methylbenzoate, C9H13N4 + C8H7O2
  58. Crystal structure of 2-chloro-3-(isopentylamino)naphthalene-1,4-dione, C 15 H 16 ClNO 2
  59. The crystal structure of bis(2-acetyl-5-methoxyphenyl)carbonate 1.5 hydrate, C19H18O7
  60. The crystal structure of poly[(μ 4-4,4′-(azanediylbis(methylene))dibenzoato-κ 4 O:N:O′:Oʺ)zinc(II)], C16H13NO4Zn
  61. The crystal structure of catena-poly[(1,10-phenanthroline-k2N,N′)-(μ3-tetraoxidomoybdato(VI)-k3O:O′:O″)manganese(II)] C12H8N2O4MoMn
  62. Crystal structure of catena-poly[(4-hydroxyl-5-(methoylcarbonyl)thiophene-2-carboxylato-κ1 O)-(μ2-piperazine-1,4-diylbis(pyridin-4-ylmethanone)-κ2 N:N′)silver(I)] monohydrate, C23H23AgN4O8S
  63. Crystal structure of bis(4-bromo-2-(((3-bromopropyl)imino)methyl)phenolato-κ2N,O)-oxido-vanadium(IV), C20H20Br4N2O3V
  64. The crystal structure of (2a′S,2a1′S,3R,5a′S,7′R)-5-(furan-3-yl)-2a′,2a1′-dihydroxy-7′-methyldecahydro-2H-spiro[furan-3,6′-naphtho[1,8-bc]furan]-2,2′(2a′H)-dione, C19H22O7
  65. The crystal structure of 3-bromopicolinic acid, C6H4BrNO2
  66. Crystal structure of 1,1′-(1,4-phenylenebis(methylene))bis(pyridin-1-ium) bis(1,2-dicyanoethene-1,2-dithiolato-κ2 S,S) platinum(II), C26H18N6PtS4
  67. Synthesis and crystal structure of 5-(8-((3-carboxyazetidin-1-ium-1-yl)methyl)-7-hydroxy-4-oxo-4H-chromen-3-yl)-2-hydroxybenzenesulfonate monohydrate, C20H19NO10S
  68. The crystal structure of 3-amino-5-carboxypyridin-1-ium bromide, C6H7BrN2O2
  69. The crystal structure of (2-hydroxy-5-methyl-phenyl)-(1H-pyrazol-4-yl)-methanone hemihydrate, C11H10.5N2O2.5
  70. Crystal structure of tetraaqua-(2-(4-formylphenoxy)acetato-k1O)cadmium(II), C18H22O12Cd
  71. Crystal structure of diethyl 6,12-dimethyl-3,9-di-p-tolyl-3,9-diazapentacyclo[6.4.0.02,7.04,11.05,10]dodecane-1,5-dicarboxylate, C32H38N2O4
  72. Crystal structure of (E)-N′-(1-(3-chloro-4-fluorophenyl)ethylidene)-4-hydroxy – tetrahydrofuran (2/1), C17H16ClFN2O2.5
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