Home The crystal structure of 13-(pyrazole-1-yl-4-carbonitrile)-matrine, C19H25N5O
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The crystal structure of 13-(pyrazole-1-yl-4-carbonitrile)-matrine, C19H25N5O

  • Jun-Jie Li , Fang-Yun Dong , Qi-Wen Zou , Yin Feng , Yu-Tao Yang , Kai-Xuan Su , Yong-Fu Huang , Xu-Hong Jiang EMAIL logo and Xing-An Cheng ORCID logo EMAIL logo
Published/Copyright: July 14, 2021

Abstract

C19H25N5O, monoclinic, P21 (no. 4), a = 16.0600(2) Å, b = 5.3992(1) Å, c = 19.8514(2) Å, β = 94.260(1)°, V = 1716.58(4) Å3, Z = 4, R gt (F) = 0.0350, wRref(F2) = 0.0908, T = 100.00(10) K.

CCDC no.: 2084341

The asymmetric unit of 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: White needle
Size: 0.40 × 0.05 × 0.05 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 0.67 mm−1
Diffractometer, scan mode: XtaLAB AFC12 (RINC), ω
θmax, completeness: 74.4°, >99%
N(hkl)measured, N(hkl)unique, Rint: 19,482, 6659, 0.035
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 6104
N(param)refined: 451
Programs: CrysAlisPRO [1], Olex2 [2], SHELX [3], [4]
Table 2:

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

Atom x y z Uiso*/Ueq
O1 0.61389 (12) 0.9919 (4) 0.35567 (9) 0.0391 (5)
N1 0.31671 (12) 0.4352 (4) 0.34687 (9) 0.0234 (4)
N2 0.51615 (12) 0.7128 (4) 0.31649 (9) 0.0246 (4)
N3 0.55200 (11) 0.9264 (3) 0.11484 (9) 0.0208 (4)
N4 0.55026 (12) 1.1484 (4) 0.08205 (9) 0.0245 (4)
N5 0.66689 (15) 0.6244 (5) −0.08007 (10) 0.0356 (5)
C1 0.28799 (15) 0.3801 (5) 0.41368 (11) 0.0266 (5)
H1A 0.270856 0.208030 0.414943 0.032*
H1B 0.239600 0.481695 0.420793 0.032*
C2 0.35452 (16) 0.4269 (5) 0.47039 (11) 0.0287 (5)
H2A 0.401376 0.316388 0.465753 0.034*
H2B 0.332035 0.393528 0.513492 0.034*
C3 0.38406 (16) 0.6953 (5) 0.46834 (12) 0.0308 (5)
H3A 0.430722 0.718835 0.501631 0.037*
H3B 0.339245 0.804291 0.479830 0.037*
C4 0.41087 (15) 0.7630 (5) 0.39827 (11) 0.0267 (5)
H4 0.418567 0.942963 0.397370 0.032*
C5 0.34218 (14) 0.6977 (4) 0.34262 (11) 0.0231 (5)
H5 0.293288 0.800629 0.349550 0.028*
C6 0.37111 (14) 0.7575 (4) 0.27228 (11) 0.0224 (5)
H6 0.381337 0.936189 0.270310 0.027*
C7 0.30177 (14) 0.6943 (5) 0.21765 (11) 0.0254 (5)
H7A 0.254798 0.804905 0.221680 0.031*
H7B 0.322265 0.718606 0.173380 0.031*
C8 0.27309 (14) 0.4274 (5) 0.22442 (11) 0.0273 (5)
H8A 0.225660 0.395923 0.192408 0.033*
H8B 0.317782 0.315809 0.214201 0.033*
C9 0.24869 (14) 0.3798 (5) 0.29557 (11) 0.0264 (5)
H9A 0.200626 0.480975 0.303902 0.032*
H9B 0.232634 0.207489 0.299556 0.032*
C10 0.45480 (13) 0.6235 (4) 0.26312 (10) 0.0214 (4)
H10 0.445903 0.446846 0.271348 0.026*
C11 0.48917 (14) 0.6463 (4) 0.19419 (10) 0.0217 (4)
H11A 0.535635 0.532891 0.191442 0.026*
H11B 0.446196 0.600625 0.159492 0.026*
C12 0.51823 (14) 0.9082 (4) 0.18167 (10) 0.0219 (4)
H12 0.470491 1.020770 0.182956 0.026*
C13 0.58493 (14) 0.9838 (4) 0.23694 (11) 0.0229 (5)
H13A 0.638289 0.919942 0.224887 0.027*
H13B 0.588852 1.163081 0.237277 0.027*
C14 0.57123 (14) 0.8979 (5) 0.30799 (11) 0.0255 (5)
C15 0.49437 (15) 0.6444 (5) 0.38408 (11) 0.0281 (5)
H15A 0.537633 0.700455 0.417294 0.034*
H15B 0.490225 0.465712 0.387461 0.034*
C16 0.58419 (14) 1.1032 (5) 0.02445 (11) 0.0252 (5)
H16 0.591020 1.221134 −0.008828 0.030*
C17 0.60850 (14) 0.8539 (4) 0.02014 (11) 0.0239 (5)
C18 0.58693 (14) 0.7471 (4) 0.07974 (11) 0.0244 (5)
H18 0.595073 0.582984 0.092864 0.029*
C19 0.64161 (15) 0.7293 (5) −0.03540 (12) 0.0273 (5)
O1A 0.69289 (10) 0.5096 (3) 0.20975 (8) 0.0280 (4)
N1A 0.94177 (12) −0.0844 (4) 0.11555 (9) 0.0234 (4)
N2A 0.78851 (11) 0.2006 (4) 0.21440 (9) 0.0224 (4)
N3A 0.86964 (11) 0.3998 (4) 0.41541 (9) 0.0223 (4)
N4A 0.86554(13) 0.6260 (4) 0.44492 (9) 0.0263 (4)
N5A 0.95268 (13) 0.1140 (4) 0.63331 (10) 0.0328 (5)
C1A 0.92850 (15) −0.1423 (5) 0.04309 (12) 0.0278 (5)
HP 0.938446 −0.317529 0.036489 0.033*
HQ 0.968730 −0.051015 0.018718 0.033*
C2A 0.84134 (16) −0.0789 (5) 0.01399 (11) 0.0290 (5)
HU 0.800995 −0.181424 0.035023 0.035*
HV 0.836663 −0.112748 −0.034127 0.035*
C3A 0.82232 (15) 0.1936 (5) 0.02607 (11) 0.0279 (5)
HB 0.764585 0.227930 0.011161 0.034*
HC 0.857603 0.296117 −0.000082 0.034*
C4A 0.83760 (15) 0.2571 (4) 0.10097 (11) 0.0250 (5)
HI 0.833769 0.437432 0.105371 0.030*
C5A 0.92565 (14) 0.1789 (4) 0.12866 (11) 0.0223 (5)
HR 0.966176 0.277232 0.105556 0.027*
C6A 0.93890 (14) 0.2331 (5) 0.20508 (11) 0.0238 (5)
HD 0.932588 0.411970 0.211435 0.029*
C7A 1.02816 (14) 0.1625 (5) 0.23071 (12) 0.0264 (5)
HJ 1.067477 0.270893 0.210430 0.032*
HK 1.034998 0.184448 0.279304 0.032*
C8A 1.04677 (14) −0.1054 (5) 0.21319 (12) 0.0284 (5)
HW 1.104972 −0.142122 0.225791 0.034*
HX 1.012704 −0.215452 0.238291 0.034*
C9A 1.02830 (15) −0.1479 (5) 0.13786 (12) 0.0278 (5)
HS 1.065961 −0.047989 0.113183 0.033*
HT 1.038351 −0.320466 0.127531 0.033*
C10A 0.86944 (14) 0.1016 (4) 0.24192 (11) 0.0218 (4)
HA 0.870944 −0.074517 0.230181 0.026*
C11A 0.87720 (14) 0.1204 (4) 0.31866 (11) 0.0223 (4)
HN 0.839572 0.002709 0.337407 0.027*
HO 0.933726 0.078677 0.335445 0.027*
C12A 0.85639 (14) 0.3799 (4) 0.34144 (11) 0.0223 (5)
H 0.893394 0.497714 0.320869 0.027*
C13A 0.76625 (14) 0.4393 (4) 0.31696 (11) 0.0238 (5)
HE 0.728969 0.339940 0.342165 0.029*
HF 0.755077 0.612159 0.326069 0.029*
C14A 0.74803 (13) 0.3898 (4) 0.24193 (11) 0.0229 (4)
C15A 0.77126 (14) 0.1425 (5) 0.14267 (11) 0.0240 (5)
HL 0.716689 0.206129 0.127136 0.029*
HM 0.770641 −0.035699 0.136517 0.029*
C16A 0.88540 (15) 0.5855 (4) 0.51023 (12) 0.0266 (5)
HG 0.887428 0.707272 0.543434 0.032*
C17A 0.90290 (14) 0.3340 (4) 0.52224 (11) 0.0239 (5)
C18A 0.89178 (14) 0.2217 (4) 0.45980 (11) 0.0242 (5)
HH 0.898427 0.054348 0.450456 0.029*
C19A 0.92993 (14) 0.2143 (5) 0.58413 (12) 0.0261 (5)

Source of material

1H-pyrazole-4-carbonitrile (0.1380 g, 1.482 mmol), sophocarpine (0.2000 g, 0.8117 mmol), cesium fluoride (0.1200 g, 0.37 mmol) were dissolved in 1,4-dioxane (8 mL). The resulting mixture reacted at 120 °C for 2.5 h. After stirring, the crude mixture was concentrated under reduced pressure and purified using flash chromatography on silica gel with acetonitrile and ethanol as eluent to give the desired product as white solid. A crystal suitable for diffraction was obtained by slow evaporation from its ethanol solution at room temperature.

Experimental details

Hydrogen atoms were placed in calculated positions and were refined in the riding model approximation, with Uiso(H) set to 1.2Ueq.

Comment

Matrine, a major alkaloid isolated from Traditional Chinese Medicine (TCM) Sophora flavescens, has attracted a growing interest due to its broad bioactivities, including pesticide activity, anti-tumor and anti-fibrotic [5], [6], [7]. So it is of great value to promote bioactivities through structure modification. Many matrine derivatives were synthesized in previous studies and showed better pesticidal activities than matrine [8], [9]. However, strict synthesis procedures and purification are needed to obtain the final product.

In our previous study, a series of matrine derivatives were synthesized by introducing nitro-containing heterocyclic into the C-12 position of the matrine skeleton using a one-pot Michael addition [10], [11], [12]. In this study, 1H-pyrazole-4-carbonitrile was introduced into the C-12 position of the sophocarpine, and a bond (C12–N3, 1.473(3) Å) was formed, which transforms C-12 to a chiral carbon center. The asymmetric unit contains two molecules, and they are connected to neighboring ones by C–H⋯N, and C–H⋯O hydrogen bonds. The length of the C-11–C-12 bond is longer (1.531(3) and 1.517(3) Å for each molecule in asymmetric unit) compared to the counterpart of sophocarpine (1.3229(18) Å) [13], indicating that the C-11–C-12 bond is saturated. All bond lengths and angles of this structure are in the expected ranges and in good agreement with a similar structure [14, 15]. These results indicate that 1H-pyrazole-4-carbonitrile was introduced into the matrine skeleton, and that introduction mainly affects nearby bonds.


Corresponding authors: Xing-An Cheng, Institute of Natural Product Chemistry, College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China; and Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China, E-mail: ; and Xu-Hong Jiang, Institute of Natural Product Chemistry, College of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong 510225, China, E-mail:

Funding source: the National Natural Science Foundation of China 10.13039/501100001809

Award Identifier / Grant number: 21406274

Funding source: Characteristic innovation projects in Colleges and Universities in Guangdong Province

Award Identifier / Grant number: 2018KTSCX093

Funding source: Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests

Award Identifier / Grant number: 2020KSYS005

Funding source: Innovative Training Program for College Students in Guangdong

Award Identifier / Grant number: 202011347075

Funding source: the Natural Science Foundation of Guangdong Province 10.13039/501100003453

Award Identifier / Grant number: 2017A030313140

Funding source: Guangdong Special Commissioners of Science and Technology

Award Identifier / Grant number: KA1810303

Funding source: Guangdong Quality Engineering Project and Teaching Team Project

Award Identifier / Grant number: KA190573931

Award Identifier / Grant number: KA190574204

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

  2. Research funding: This study was funded by National Natural Science Foundation of China (21406274), Characteristic innovation projects in Colleges and Universities in Guangdong Province (2018KTSCX093), Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests (2020KSYS005), Innovative Training Program for College Students in Guangdong (202011347075), the Natural Science Foundation of Guangdong Province (2017A030313140), Guangdong Special Commissioners of Science and Technology (KA1810303), Guangdong Quality Engineering Project and Teaching Team Project (KA190573931, KA190574204).

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

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Received: 2021-05-20
Accepted: 2021-06-28
Published Online: 2021-07-14
Published in Print: 2021-09-27

© 2021 Jun-Jie Li 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. The crystal structure of bis[4-bromo-2-(1H-pyrazol-3-yl) phenolato-κ2N,O] copper(II), C18H12Br2CuN4O2
  38. The crystal structure of poly[(μ 3-imidazolato-κ 3 N:N:N′)(tetrahydrofuran- κ 1 O)lithium(I)], C7H11LiN2O
  39. Crystal structure of N′,N′′′-((1E,1′E)-(propane-2,2-diylbis(1H-pyrrole-5,2diyl))bis(methaneylylidene))di(nicotinohydrazide) pentahydrate, C25H24N8O2·5H2O
  40. Crystal structure of 3-(2-ethoxy-2-oxoethyl)-1-ethyl-1H-imidazol-3-ium hexafluoridophos-phate(V), C9H15F6N2O2P
  41. Crystal structure of (1,10-phenanthroline-κ2N,N′)-bis(3-thiophenecarboxylato-κ2O,O′)copper(II), C22H14N2O4S2Cu
  42. The crystal structure of 2-amino-3-carboxypyridin-1-ium iodide hemihydrate, C6H8IN2O2.5
  43. Crystal structure of (E)-7-methoxy-2-((6-methoxypyridin-2-yl)methylene)-tetralone, C18H17NO3
  44. The crystal structure of [μ-hydroxido-bis[(5,5′-dimethyl-2,2′-bipyridine-κ2N,N′)-tricarbonylrhenium(I)] bromide hemihydrate, C30H26N4O9Re2Br
  45. The crystal structure of 2,5-bis(3,5-dimethylphenyl)thiazolo[5,4-d]thiazole, C20H18N2S2
  46. The crystal structure of 5-benzoyl-1-[(E)-(4-fluorobenzylidene)amino]-4-phenylpyrimidin-2(1H)-one, C24H16FN3O2
  47. Crystal structure of monocarbonyl(N-nitroso-N-oxido-phenylamine-κ 2 O,O′)(tricyclohexylphosphine-κP)rhodium(I), C25H39N2O3PRh
  48. Crystal structure of poly[bis[μ3-1,3,5-tris[(1H-imidazol-1-yl)methyl]benzene-κ3N:N′:N″]nickel(II)] hexafluorosilicate, C36H36N12NiSiF6
  49. The crystal structure of 13-(pyrazole-1-yl-4-carbonitrile)-matrine, C19H25N5O
  50. Crystal structure of 3,5-bis((E)-4-methoxy-2-(trifluoromethyl)benzylidene)-1-methylpiperidin-4-one, C24H21F6NO3
  51. The crystal structure of N,N′-(Disulfanediyldi-2,1-phenylene)di(6′-methylpyridine)-2-carboxamide, C26H22N4O2S2
  52. Crystal structure of (E)-7-fluoro-2-(4-methoxy-2-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C19H14F4O2
  53. Crystal structure of ethyl 1-(4-fluorophenyl)-4-phenyl-1H-pyrrole-3-carboxylate, C19H16FNO2
  54. The crystal structure of cis-diaqua-bis (N-butyl-N-(pyridin-2-yl)pyridin-2-amine-κ2N,N′)cobalt(II)] dichloride trihydrate, C28H44Cl2N6O5Co
  55. Crystal structure of (E)-7-methoxy-2-((6-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C18H17NO3
  56. Crystal structure of (E)-2-((3-fluoropyridin-4-yl)methylene)-7-methoxy-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  57. The crystal structure of 6-bromohexanoic acid, C6H11BrO2
  58. The crystal structure of 4-chloro-thiophenol, C6H5ClS
  59. The crystal structure of 4-bromobenzyl chloride, C7H6BrCl
  60. The crystal structure of di-tert-butyl dicarbonate, C10H18O5
  61. The crystal structure of (2-(4-chlorophenyl)-5-methyl-1,3-dioxan-5-yl)methanol, C12H15ClO3
  62. The crystal structure of the co-crystal: 2-hydroxybenzoic acid – N′-(butan-2-ylidene)pyridine-4-carbohydrazide, C10H13N3O·C7H6O3
  63. Crystal structure and anti-inflammatory activity of (E)-7-fluoro-2-((5-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  64. Crystal structure of (E)-7-fluoro-2-((6-methoxypyridin-3-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  65. Crystal structure of 1,1′-(butane-1,4-diyl)bis(3-propyl-1H-imidazol-3-ium) bis(hexafluoridophosphate), C32H56F24N8P4
  66. The crystal structure of dichlorido-bis(3-methyl-3-imidazolium-1-ylpropionato-κ2)-cadmium(II), C14H20CdCl2N4O4
  67. Crystal structure of 1-(2-cyanobenzyl)-3-cyano-4-phenyl-4-(2-cyanobenzyl)-1,4-dihydropyridine monohydrate, C56H42N8O
  68. The crystal structure of 3-(carboxymethyl)-1-ethenyl-1H-imidazol-3-ium chloride, C7H9N2O2Cl
  69. The crystal structure of adamantylmethoxydiphenylsilane, C23H28OSi
  70. Redetermination of the crystal structure of (2E,4Z,13E,15Z)-3,5,14,16-tetramethyl-2,6,13,17-tetraazatricyclo[16.4.0.07,12]docosa-1(22),2,4,7,9,11,13,15,18,20-decaene, C22H24N4
  71. Crystal structure of (E)-7-hydroxy-2-((6-methoxypyridin-2-yl)methylene)-3,4-dihydronaphthalen-1(2H)-one, C17H15NO3
  72. Crystal structure of catena-poly[diaqua-bis(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2 N:N′)cobalt(II)] dinitrate, C18H28N10O8Co
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