Home Crystal structure of (3E,5E)-3,5-bis-4-methoxy-3-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
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Crystal structure of (3E,5E)-3,5-bis-4-methoxy-3-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3

  • Xiao-Fan Zhang ORCID logo , Hui-yun Wang , Jia Song , Lun-Hai Liang , Yang-Rong Xu , Feng-Lan Zhao and Qing-Guo Meng EMAIL logo
Published/Copyright: November 12, 2020

Abstract

C24H21F6NO3, monoclinic, P21/c (no. 14), a = 16.6493(9) Å, b = 15.3005(8) Å, c = 8.8554(5) Å, β = 99.746(6)°, V = 2223.3(2) Å3, Z = 4, Rgt(F) = 0.0444, wRref(F2) = 0.1094, T = 100 K.

CCDC no.: 2027111

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:Yellow block
Size:0.13 × 0.12 × 0.09 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.13 mm−1
Diffractometer, scan mode:SuperNova
θmax, completeness:25.5°, >99 %
N(hkl)measured, N(hkl)unique, Rint:9749, 4139, 0.027
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 3344
N(param)refined:310
Programs:CrysAlisPRO [1], SHELX [2], [3]
Table 2:

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

AtomxyzUiso*/Ueq
C10.34239 (10)0.51961 (12)1.0154 (2)0.0209 (4)
H1A0.3588000.4743160.9502400.025*
H1B0.3547620.4995791.1206830.025*
C20.38918 (10)0.60199 (12)0.9979 (2)0.0198 (4)
C30.35617 (11)0.66182 (12)0.8690 (2)0.0213 (4)
C40.27457 (10)0.64132 (12)0.7777 (2)0.0192 (4)
C50.23427 (10)0.55702 (12)0.8111 (2)0.0212 (4)
H5A0.1756450.5626910.7823570.025*
H5B0.2521420.5103110.7505050.025*
C60.45786 (10)0.62848 (12)1.0886 (2)0.0211 (4)
H60.4764390.6828921.0628650.025*
C70.50871 (10)0.58754 (12)1.2203 (2)0.0192 (4)
C80.55976 (11)0.64270 (12)1.3201 (2)0.0234 (4)
H80.5580540.7025821.3017950.028*
C90.61256 (11)0.61061 (13)1.4450 (2)0.0244 (4)
C100.61713 (10)0.52027 (12)1.4723 (2)0.0215 (4)
C110.56644 (10)0.46473 (12)1.3759 (2)0.0217 (4)
H110.5681680.4048601.3942030.026*
C120.51311 (10)0.49823 (12)1.2520 (2)0.0211 (4)
H120.4793960.4601261.1884720.025*
C130.24251 (10)0.70065 (12)0.6724 (2)0.0203 (4)
H130.2724100.7519100.6711750.024*
C140.16736 (10)0.69634 (12)0.5593 (2)0.0189 (4)
C150.13748 (10)0.61818 (12)0.4899 (2)0.0190 (4)
H150.1639080.5660040.5207580.023*
C160.06948 (10)0.61682 (11)0.3762 (2)0.0194 (4)
C170.02792 (10)0.69454 (12)0.3303 (2)0.0209 (4)
C180.05735 (11)0.77299 (12)0.3972 (2)0.0247 (4)
H180.0303950.8250760.3677750.030*
C190.12680 (11)0.77333 (12)0.5077 (2)0.0229 (4)
H190.1470870.8264070.5489000.028*
C200.20988 (11)0.45674 (13)1.0058 (2)0.0297 (5)
H20A0.2259460.4082960.9488140.045*
H20B0.1524300.4666950.9764150.045*
H20C0.2219570.4438891.1133850.045*
C210.66475 (14)0.67136 (14)1.5514 (3)0.0385 (5)
C220.67636 (11)0.40334 (13)1.6317 (2)0.0271 (4)
H22A0.6241350.3843051.6512510.041*
H22B0.7166700.3939671.7214480.041*
H22C0.6906940.3706731.5476420.041*
C230.04149 (12)0.53290 (12)0.2988 (2)0.0269 (4)
C24−0.08211 (13)0.76389 (14)0.1662 (3)0.0378 (5)
H24A−0.1021700.7921750.2491850.057*
H24B−0.1270540.7492260.0872950.057*
H24C−0.0457610.8025820.1253980.057*
F10.65144 (9)0.66507 (8)1.69672 (14)0.0517 (4)
F20.74447 (8)0.65660 (10)1.55706 (18)0.0601 (4)
F30.65177 (9)0.75566 (8)1.51230 (16)0.0562 (4)
F40.03826 (7)0.53547 (8)0.14683 (13)0.0370 (3)
F5−0.03341 (7)0.50918 (8)0.32096 (14)0.0401 (3)
F60.09103 (8)0.46619 (7)0.34974 (15)0.0435 (4)
N10.25459 (8)0.53509 (10)0.97355 (17)0.0211 (3)
O10.39569 (8)0.72479 (9)0.83720 (16)0.0313 (3)
O20.67275 (8)0.49435 (9)1.59430 (15)0.0277 (3)
O3−0.03947 (8)0.68600 (8)0.22099 (16)0.0289 (3)

Source of material

N-methyl-4-piperidone (0.3 mL, 3.0 mmol) and 3-(trifluoromethyl)-4-methoxybenzaldehyde (1.08 g, 5.0 mmol) were dissolved in 10 mL acetic acid. Then dry hydrogen chloride gas was flowed continuously into the solution for 45 min. After gas insertion, the reaction system was stirred at room temperature for seven days. The response endpoint was detected by thin layer chromatography (TLC). When the reaction was stopped, the precipitate was filtered from the reaction system, then it was dissolved in distilled water and adjusted to a neutral pH with saturated aqueous Na2CO3 solution. The precipitate was filtered from the system and dissolved with dichloromethane. The organic phase was washed successively with deionized water and brine, dried over anhydrous sodium sulfate and condensed under vacuum. The crude product was purified by silica-gel column chromatography (petroleum ether: ethyl acetate = 10:1, v/v). Crystals were obtained under ambient conditions via solvent evaporation in the mixed solvents of dichloromethane and methanol (1:1, v/v) and drying under vacuo at 333 K for 3 h.

Experimental details

The H atoms were placed in idealized positions and treated as riding on their parent atoms, with d(C–H) = 0.96 Å (methyl), Uiso(H) = 1.5Ueq(C), and d(C–H) = 0.97 Å (methylene), Uiso(H) = 1.2Ueq(C), and d(C–H) = 0.93 Å (aromatic), Uiso(H) = 1.2Ueq(C).

Comment

During inflammatory neurodegenerative diseases in central nervous system (CNS), the resident microglia become activated and polarized to a pro-inflammatory M1 phenotype [4], which can produce pro-inflammatory cytokines such as tumor necrosis factor-a (TNF-α), interleukin-1b (IL-1b), and interleukin-6 (IL-6) [5], [6], [7]. These pro-inflammatory cytokines disrupt blood-brain barrier (BBB) by activating the nuclear factor kappa B (NF-κB) signaling pathway [8]. In addition, activated microglia can produce reactive oxygen species (ROS), which may indirectly induce neuroinflammation by activating NF-κB [9]. Therefore, developing an NF-κB inhibitor with anti-neuroinflammatory activity and low toxicity may be a therapeutic option for the treatment of inflammatory CNS neurodegenerative diseases [10].

Curcumin has anti-inflammatory, anti-tumor, anti-oxidation and other activities. But its clinical application is limited because of its low stability, poor bioavailability and false positive. Structural modification based on curcumin was carried out and different curcumin analogues have been reported. Therein, (3E, 5E)-3,5-bis(arylene)-4-piperidones (BAPs) was a very distinguished class because they could inhibit tumor growth by anti-inflammatory and inhibiting NF-κB dependent signaling pathways [11]. Some symmetric and dissymmetric BAPs had been designed and synthesized as anti-tumor and anti-inflammatory agents [12], [13], [14], [15], [16], [17], [18]. However, BAPs have rarely been developed as anti-neuroinflammatory drugs. In our recent study, a series of new BAPs were designed and synthesized through Claisen–Schmidt condensation reactions.

Single-crystal structure analysis reveals that the title compound contains one drug molecule in the asymmetric unit (cf. the figure). Bond lengths and angles are all in the expected ranges [20]. The arylidene moieties on both sides of central piperidone adopt the E stereochemistry [19]. The dihedral angles between the two-fluorobenzylidenes and the central piperidone ring are 36.05(2)° and 26.86(3)°, respectively. In the title compound, the peripheric heteroatoms (such as F, N, O, S) can act as hydrogen bonding acceptors for bioactive molecules with the aim of creating more potent antitumor activities and anti-inflammatory activity [21].


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:

Funding source: Science and Technology Innovation Development Plan of Yantai

Award Identifier / Grant number: 2020XDRH105

Award Identifier / Grant number: 81473104

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

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

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Received: 2020-09-25
Accepted: 2020-10-21
Published Online: 2020-11-12
Published in Print: 2021-01-26

© 2020 Xiao-Fan 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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  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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