Startseite Naturwissenschaften The crystal structure of a matrine derivative: 41S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3′,2′,1′-ij][1,6]naphthyridin-10-one, C20H34N4O
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The crystal structure of a matrine derivative: 41S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3′,2′,1′-ij][1,6]naphthyridin-10-one, C20H34N4O

  • Xing-An Cheng , Liu Zhan-Mei , Wu Bo , Huang Su-Qing , Xiong Xia-Ling und Jiang Xu-Hong EMAIL logo
Veröffentlicht/Copyright: 9. Februar 2018

Abstract

C20H34N4O, triclinic, P1 (no. 1), a = 7.8545(6) Å, b = 10.8802(9) Å, c = 12.3714(9) Å, α = 73.200(7)°, β = 75.372(6)°, γ = 71.091(7)°, V = 942.65(13) Å3, Z = 2, Rgt(F) = 0.0591, wRref(F2) = 0.1641, T = 293(2) K.

CCDC no.:: 1548785

One of the two crystallographically independent title molecules, which are present in the asymmetric unit of the title crystal structure is shown in the figure1. Tables 1 and 2 contain details on the crystal structure and measurement conditions and a list of the atoms including atomic coordinates and displacement parameters.

Table 1:

Data collection and handling.

Crystal:Block, colorless
Size:0.6 × 0.4 × 0.30 mm
Wavelength:Cu Kα radiation (1.54178 Å)
μ:0.60 mm−1
Diffractometer, scan mode:Multiwire proportional, φ and ω-scans
2θmax, completeness:74.3°, >96%
N(hkl)measured, N(hkl)unique, Rint:6049, 4265, 0.017
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 4193
N(param)refined:453
Programs:OLEX2 [1], SHELX [2]
Table 2:

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

AtomxyzUiso*/Ueq
N10.1915(3)0.4068(2)0.3951(2)0.0226(5)
N1′−0.1552(3)−0.0920(3)0.5661(2)0.0265(6)
N160.2844(4)0.6551(3)0.1389(2)0.0293(6)
N16′−0.1938(3)−0.3665(3)0.8085(2)0.0260(6)
N190.6503(3)0.8697(3)0.1458(2)0.0238(5)
N19′−0.4630(4)−0.6372(3)0.7845(2)0.0280(6)
N220.8348(3)1.0756(2)0.0838(2)0.0225(5)
N22′−0.6559(4)−0.8387(3)0.8490(2)0.0286(6)
O180.3094(3)0.7246(2)−0.05300(18)0.0263(5)
O18′−0.1262(3)−0.4865(2)0.9819(2)0.0320(5)
C20.0853(5)0.3141(3)0.4069(3)0.0310(7)
H2A−0.01280.32240.47240.037*
H2B0.16340.22350.42120.037*
C30.0047(4)0.3401(3)0.3003(3)0.0300(7)
H3A−0.08060.42820.28880.036*
H3B−0.06200.27530.31060.036*
C3′0.0415(6)−0.0248(4)0.6520(3)0.0420(9)
H3′A−0.0516−0.00820.71850.050*
H3′B0.11660.03580.63600.050*
C40.1550(4)0.3307(3)0.1952(3)0.0251(6)
H4A0.22950.23910.20140.030*
H4B0.10090.35720.12690.030*
C4′0.1592(5)−0.1673(4)0.6783(3)0.0357(8)
H4′A0.2029−0.18470.74940.043*
H4′B0.2646−0.17960.61750.043*
C50.2743(4)0.4205(3)0.1853(2)0.0212(6)
H50.38140.39890.12610.025*
C5′0.0513(4)−0.2664(3)0.6892(3)0.0244(6)
H5′0.1384−0.35470.69110.029*
C60.3444(4)0.3961(3)0.2971(2)0.0224(6)
H60.42620.30550.31170.027*
C6′−0.0410(4)−0.2303(3)0.5847(2)0.0241(6)
H6′0.0547−0.23960.51690.029*
C70.4543(4)0.4962(3)0.2855(2)0.0259(6)
H70.56040.48130.22420.031*
C7′−0.1561(5)−0.3278(3)0.5995(3)0.0337(7)
H7′−0.0728−0.41780.60490.040*
C80.5248(4)0.4675(4)0.3984(3)0.0312(7)
H8A0.61290.38060.40950.037*
H8B0.58610.53380.39370.037*
C8′−0.2404(7)−0.2920(5)0.4925(3)0.0515(11)
H8′A−0.1442−0.30640.42690.062*
H8′B−0.3176−0.34960.50220.062*
C9′−0.3525(6)−0.1484(5)0.4705(3)0.0508(11)
H9′A−0.4572−0.13620.53180.061*
H9′B−0.3973−0.12560.39900.061*
C100.2607(4)0.3762(3)0.5017(2)0.0283(6)
H10A0.33860.28550.51450.034*
H10B0.15860.38170.56510.034*
C10′−0.2380(5)−0.0573(4)0.4639(3)0.0396(9)
H10C−0.1420−0.06220.39700.048*
H10D−0.31430.03390.45450.048*
C110.3322(5)0.6425(3)0.2496(3)0.0293(7)
H110.21830.65130.30570.035*
C11′−0.2967(5)−0.3275(3)0.7127(3)0.0302(7)
H11′−0.3693−0.23480.70970.036*
C120.4095(5)0.7567(3)0.2446(3)0.0290(7)
H12A0.31130.83850.24310.035*
H12B0.46080.73780.31320.035*
C12′−0.4312(4)−0.4098(3)0.7371(3)0.0294(7)
H12C−0.5366−0.37690.79210.035*
H12D−0.4731−0.39980.66690.035*
C130.5540(5)0.7756(3)0.1413(3)0.0284(7)
H130.64520.68890.14340.034*
C13′−0.3454(5)−0.5552(3)0.7838(3)0.0311(7)
H13′−0.2305−0.58220.73170.037*
C140.4740(4)0.8080(3)0.0334(2)0.0219(6)
H14A0.40380.90080.01970.026*
H14B0.57390.7978−0.03100.026*
C14′−0.2974(4)−0.5693(3)0.8993(3)0.0232(6)
H14C−0.4091−0.55760.95560.028*
H14D−0.2216−0.65910.92320.028*
C150.3523(4)0.7233(3)0.0364(2)0.0206(6)
C15′−0.1976(4)−0.4707(3)0.8991(2)0.0224(6)
C170.1746(4)0.5678(3)0.1459(3)0.0259(6)
H17A0.14390.58220.07110.031*
H17B0.06140.59000.19920.031*
C17′−0.0879(4)−0.2752(3)0.8003(2)0.0242(6)
H17C−0.0247−0.30560.86520.029*
H17D−0.1699−0.18720.80340.029*
C200.8181(4)0.8640(3)0.0611(3)0.0229(6)
H20A0.78850.9060−0.01500.027*
H20B0.88610.77180.06220.027*
C20′−0.6319(5)−0.6276(3)0.8692(3)0.0316(7)
H20C−0.6974−0.53460.86630.038*
H20D−0.6031−0.66830.94560.038*
C210.9328(4)0.9354(3)0.0883(3)0.0250(6)
H21A0.96250.89280.16420.030*
H21B1.04630.92910.03360.030*
C21′−0.7502(5)−0.6981(3)0.8439(3)0.0312(7)
H21C−0.8631−0.69030.89930.037*
H21D−0.7810−0.65560.76820.037*
C230.6568(4)1.0873(3)0.1595(3)0.0265(7)
H23A0.58851.18060.14930.032*
H23B0.67511.05470.23860.032*
C23′−0.4789(5)−0.8511(3)0.7706(3)0.0318(7)
H23C−0.5000−0.81530.69210.038*
H23D−0.4131−0.94470.77830.038*
C240.5463(4)1.0092(3)0.1358(3)0.0257(6)
H24A0.43231.01550.19010.031*
H24B0.51751.04680.05920.031*
C24′−0.3633(5)−0.7778(3)0.7950(3)0.0315(7)
H24C−0.3358−0.81630.87180.038*
H24D−0.2488−0.78640.74110.038*
C250.9419(5)1.1413(3)0.1172(3)0.0291(7)
H25A0.96151.09890.19430.044*
H25B0.87701.23360.11280.044*
H25C1.05761.13460.06640.044*
C25′−0.7675(6)−0.9021(4)0.8168(3)0.0367(8)
H25D−0.7833−0.86210.73860.055*
H25E−0.8848−0.89040.86600.055*
H25F−0.7077−0.99560.82440.055*

Source of materials

The synthesis of the title compound was carried out using the michael addition reaction. A mixture of sophocarpine (0.31 g, 1.25 mmol), N-methyl piperazine (0.5 mL, 2.5 mmol) were dissolved in 12 mL deionized water, and stirred vigorously at 60°. After 6 h, the crude reaction mixture was collected and concentrated with a rotary evaporator. The concentrated solution was purified by the silica gel column chromatography eluting with ethanol. The product was dissolved in petroleum ether and heated at 80° for 1–2 min, and then 1% active carbon was added into the solution with continued stirring vigorously by a glass rod. After standing for 2 minutes, the solution was filtrated with filter tissue into a 10 mL glass sample bottle. The title compound (systematic name (41S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3′,2′,1′-ij][1,6]naphthyridin-10-one) was crystallized from petroleum ether, whereupon a few colorless, rod-shape crystals suitable for X-ray diffraction analysis were obtained.

Experimental details

Hydrogen atoms were placed in calculated positions and were included in the refinement in the riding model approximation, with Uiso(H) set to 1.2Ueq(C) [1, 2] .

Discussion

As a major quinolizindine alkaloid isolated from Sophora flavescens AIT, matrine has attracted considerable attention due to its broad biological activities, such as anti-inflammatory properties, notable antiviral activities, anti-tumor, anti-nociceptive effects [3], [4], [5], [6], [7]. The matrine is also wildly used as a biological pesticide due to its notable insecticidal activity [8, 9] . Therefore, it is interesting to carry out the structure modification of matrine to evaluate its biological activities [10], [11], [12], [13].

The skeletons of matrine and its derivatives contain a quinolizidinic A-B ring system fused with a quinolizidinone C—D ring system [14]. The stable property of D ring in matrine makes it hard to be modified. Sophocarpine is usually used as the starting material for structure modification of matrine because it contains an a,b-unsaturated carbonyl group that is reactive toward a variety of useful nucleophiles.

In the present study, the title compound was synthesized by introducing N-methyl piperazine group to C13 of sophocarpine and a bond (C13—N19) with length 1.476(4) Å was formed in this compound, which makes its C13 translate into chiral carbon with a configuration of S (cf. the figure). The single bond length of C13—C14 [1.520(4) Å] in D ring of the title compound is longer in comparison with that of the double bond in sophocarpine, 1.3229(18) Å. As a matter of fact, the bond lengths of C12—C13[1.493(4) Å],C11—C12 [1.531(4) Å] and C14—C15[1.516(4) Å] in the title compound do not change significantly compared to that of sophocarpine, being 1.4925(16) Å, 1.529(16) Å and 1.478(16) Å respectively. The bond angle of C12—C13—C14 with a value of 108.2(3)° in D ring of the title compound as well as the other angles are in the expected ranges [15]. All these indicate that the introduction of N-methyl piperazine group to C13 of D ring mainly affects the length of the near bonds, the angle and the configuration of C13. In addition, the mean plane of the N-methyl piperazyl group is nearly coplanar to the plane of group C14—C13—12. The molecules were packed in the crystal structure without any hydrogen bonds and the benzene rings of molecules in the crystal structure show no π–π interaction.

Acknowledgements

This work was sponsored by the National Natural Science Foundation of China (No. 21406274, 201376281). Special Fund of Scientific and Technological Innovation Research for College Students in Guangdong Province, China (Climbing Program of College Students in Guangdong Province, China) (K1178350111). National Training Program of Innovation and Entrepreneurship for College Students (201711347012). Innovative Training Program for College Students in Guangdong (201711347055).

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Received: 2017-10-6
Accepted: 2018-1-17
Published Online: 2018-2-9
Published in Print: 2018-3-28

©2018 Xing-An Cheng et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Artikel in diesem Heft

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  32. Crystal structure of bis(N,N,N-trimethylbutanaminium) poly[heptaselenidotristannate(IV)], C14H36N2Se7Sn3
  33. The crystal structure of N-((3,5-di-tert-butyl-4-hydroxyphenyl)(phenyl)methyl)-4-methylbenzenesulfonamide, C28H35N3S
  34. Crystal structure of 2-(4-chlorophenyl)-2,3-dihydro-1H-perimidine, C17H13Cl1N2
  35. The Crystal structure of 2-iodo-1-(p-tolyl)propan-1-one, C10H11IO
  36. Crystal structure of ethyl 1-(4-bromobenzyl)-3-phenyl-1H-pyrazole-5-carboxylate, C19H17BrN2O2
  37. Crystal structure of ethyl 1-(4-fluorobenzyl)-3-phenyl-1H-pyrazole-5-carboxylate, C19H17FN2O2
  38. Crystal structure of catena-poly[diaqua-(μ2-2,5-dihydroxyterephthalato-κ4O,O′:O′′,O′′′)cadmium(II)], C8H8O8Cd
  39. Crystal structure of tetraaqua-bis[6-(1H-imidazol-1-yl-κN)nicotinato]zinc(II), C18H20N6O8Zn
  40. Crystal structure of dichlorido-bis(N-phenyl-2-(quinolin-8-yloxy)acetamide-κ2N,O) – acetone (2/1), C35.5H31N4O4.5Cl2Cu
  41. Crystal Structure of ethyl (E)-3,4-dimethyl-5-((2-(4-methylbenzoyl)hydrazono)methyl)-1H-pyrrole-2-carboxylate — water — ethanol (1/1/1), C20H29N3O5
  42. Crystal structure of 5-((4-(1H-benzo[d]imidazol-2-yl)-2-methoxyphenoxy)methyl)-2-chlorothiazole - trichloromethane - methanol (1/1/1), C20H19Cl4N3O3S
  43. The crystal structure of a matrine derivative: 41S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3′,2′,1′-ij][1,6]naphthyridin-10-one, C20H34N4O
  44. Crystal structure of cesium beryllophosphate, Be3Cs2P4O14
  45. Crystal Structure of 3-((3-hydroxybenzyl)ammonio)-3-phenylpropanoate, C16H17NO3
  46. Crystal structure of 9,10-dimethoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinolin-7-ium chloride — 4-hydroxy-3-methoxybenzoic acid — water (2/1/5), C48H54N2Cl2O17
  47. The crystal structure of (1R, 2R)-N1,N2-diferrocenyl-1,2-cyclohexanedicarboxamide, C28H30Fe2N2O2
  48. Crystal structure of N-(2-methylphenyl)ethoxycarbothioamide, C10H13NOS
  49. Crystal Structure of ethyl (E)-2,4-dimethyl-5-((2-tosylhydrazono)methyl)-1H-pyrrole-3-carboxylate monohydrate, C17H23N3O5
  50. Crystal structure of Diiodo-(N′-((quinolin-8-yl)methylene)isonicotinohydrazide κ3N,N′,O)cadium(II) – dimethylformamide (1/1), C19H19N5O2CdI2
  51. Crystal structure of dinitrato-(N′-((quinolin-8-yl)methylene)isonicotinohydrazide κ3-N,N′,O)copper(II), C16H12N6O7Cu
  52. Crystal structure of benzoato-κO-bis(1,3,5-triaza-7-phosphaadamantane-κP)silver(I) monohydrate C19H31AgN6O3P2
  53. Crystal structure of (E)-2-(anthracen-9-ylmethylene)hydrazine-1-carbothioamide, C16H13N3S
  54. The crystal structure of 8-chloro-7-ethyl-1,3-dimethyl-1H-purine-2,6(3H,7H)-dione, C9H11ClN4O2
  55. Crystal structure of {5,5′-((propane-1,3-diylbis(azanylylidene))bis(methanylylidene))bis(3-(ethoxycarbonyl)-2,4-dimethylpyrrol-1-ido)-κ4N,N′,N′′,N′′′}zinc(II), C23H30N4O4Cu
  56. Crystal structure of bis(4-dimethylamino-pyridin-1-ium)tetrafluorosuccinate, C18H22F4N4O4
  57. Crystal structure of dimethyl 3,9-dibenzyl-6,12-dicyclohexyl-3,9-diazahexacyclo [6.4.0.02,7.04,11.05,10]-dodecane-1,11-dicarboxylate, C40H50N2O4
  58. Crystal structure of diethyl 3,9-diphenyl-6,12-bis(3-methoxyphenyl)-3,9-diazahexacyclo[6.4.0.02,7.04,11.05,10]dodecane-1,11-dicarboxylate, C42H42N2O6
  59. Crystal structure of bis(acetato-κO)-bis(1-(pyridin-2-yl)ethan-1-one oxime-κ2N,N′)nickel(II), C18H22N4NiO6
  60. Crystal structure of (N-(3-ethoxy-2-oxidobenzylidene)-4-fluorobenzohydrazonato-κ3N,O,O′)-diphenyltin(IV), C28H23FN2O3Sn
  61. Crystal structure of {N-(3-ethoxy-2-oxidobenzylidene)-4-fluorobenzohydrazonato-κ3O,N,O′}dimethyltin(IV), C18H19FN2O3Sn
Heruntergeladen am 19.12.2025 von https://www.degruyterbrill.com/document/doi/10.1515/ncrs-2017-0282/html
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