Home Crystal structure of (E)-4-(6-(4-(2-(pyridin-4-yl)vinyl)phenoxy)pyrimidin-4-yl)morpholine, C21H20N4O2
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Crystal structure of (E)-4-(6-(4-(2-(pyridin-4-yl)vinyl)phenoxy)pyrimidin-4-yl)morpholine, C21H20N4O2

  • Su-Fen Bai , Jia-Xuan Liu , Shan-Shan Li , Chun-Yu Tian and Xiao-Jin La EMAIL logo
Published/Copyright: May 5, 2022

Abstract

C21H20N4O2, triclinic, P 1 (no. 2), a = 5.874(3) Å, b = 16.526(7) Å, c = 20.147(8) Å, α = 67.140(5)°, β = 83.287(6)°, γ = 86.910(6)°, V = 1789.7(14) Å3, Z = 4, Rgt(F) = 0.0614, wRref(F2) = 0.1675, T = 296 K.

CCDC no.: 2143917

The asymmetric unit of the title crystal 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: 0.18 × 0.16 × 0.14 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.09 mm−1
Diffractometer, scan mode: Bruker APEX-II, φ and ω
θmax, completeness: 25.2°, 98%
N(hkl)measured, N(hkl)unique, Rint: 9263, 6352, 0.050
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 2989
N(param)refined: 487
Programs: Bruker [1], SHELX [2, 3]
Table 2:

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

Atom x y z Uiso*/Ueq
O1 0.5299 (4) 0.62884 (16) 0.30751 (11) 0.0577 (7)
O2 1.0063 (4) 0.64440 (17) −0.05117 (11) 0.0653 (7)
O3 0.0291 (4) 0.85345 (16) 0.41130 (11) 0.0560 (7)
O4 0.4165 (4) 0.79593 (18) 0.07116 (12) 0.0639 (7)
N1 0.5381 (6) 0.6460 (2) 0.83867 (15) 0.0627 (9)
N2 0.8961 (5) 0.56661 (18) 0.31338 (13) 0.0500 (7)
N3 1.0908 (4) 0.55214 (18) 0.20679 (14) 0.0469 (7)
N4 0.9242 (4) 0.59575 (18) 0.10022 (13) 0.0475 (7)
N5 0.0921 (8) 0.9195 (2) 0.92154 (17) 0.0829 (11)
N6 0.3983 (5) 0.90779 (18) 0.36990 (14) 0.0493 (7)
N7 0.5769 (5) 0.90094 (19) 0.25852 (14) 0.0499 (7)
N8 0.3838 (4) 0.85246 (17) 0.18781 (13) 0.0444 (7)
C1 0.7242 (7) 0.6753 (2) 0.79246 (19) 0.0614 (10)
H1 0.845922 0.693583 0.808712 0.074*
C2 0.7491 (6) 0.6803 (2) 0.72236 (17) 0.0529 (9)
H2 0.883826 0.702357 0.692853 0.063*
C3 0.5771 (6) 0.6532 (2) 0.69539 (16) 0.0429 (8)
C4 0.3817 (6) 0.6221 (2) 0.74314 (17) 0.0526 (9)
H4 0.258953 0.602480 0.728277 0.063*
C5 0.3690 (6) 0.6201 (2) 0.81203 (18) 0.0607 (10)
H5 0.234769 0.599600 0.842341 0.073*
C6 0.6064 (6) 0.6565 (2) 0.62072 (16) 0.0486 (9)
H6 0.740367 0.681911 0.592455 0.058*
C7 0.4625 (6) 0.6273 (2) 0.58992 (16) 0.0478 (9)
H7 0.329677 0.601653 0.618782 0.057*
C8 0.4853 (6) 0.6302 (2) 0.51631 (16) 0.0439 (8)
C9 0.3167 (6) 0.5944 (2) 0.49335 (17) 0.0541 (10)
H9 0.186883 0.570678 0.524956 0.065*
C10 0.3368 (6) 0.5931 (2) 0.42456 (17) 0.0549 (10)
H10 0.222363 0.567991 0.410732 0.066*
C11 0.5238 (6) 0.6284 (2) 0.37732 (16) 0.0466 (9)
C12 0.6907 (6) 0.6679 (2) 0.39679 (17) 0.0547 (10)
H12 0.816655 0.693599 0.364019 0.066*
C13 0.6691 (6) 0.6691 (2) 0.46550 (17) 0.0545 (10)
H13 0.780851 0.696784 0.478084 0.065*
C14 0.7183 (6) 0.6018 (2) 0.27506 (16) 0.0447 (8)
C15 0.7092 (5) 0.6116 (2) 0.20517 (15) 0.0434 (8)
H15 0.579583 0.634376 0.181411 0.052*
C16 0.9034 (5) 0.5860 (2) 0.17059 (16) 0.0405 (8)
C17 1.0709 (6) 0.5442 (2) 0.27502 (17) 0.0493 (9)
H17 1.197056 0.519446 0.300015 0.059*
C18 0.7348 (5) 0.6230 (2) 0.05496 (15) 0.0528 (10)
H18A 0.619510 0.653879 0.074943 0.063*
H18B 0.664353 0.571627 0.054180 0.063*
C19 0.8224 (6) 0.6818 (3) −0.02057 (17) 0.0600 (10)
H19A 0.697878 0.695368 −0.050990 0.072*
H19B 0.872330 0.736505 −0.020025 0.072*
C20 1.1932 (6) 0.6233 (3) −0.00672 (17) 0.0635 (11)
H20A 1.247410 0.676542 −0.004640 0.076*
H20B 1.318893 0.597930 −0.028235 0.076*
C21 1.1200 (6) 0.5599 (2) 0.06813 (17) 0.0545 (10)
H21A 1.077780 0.504715 0.066611 0.065*
H21B 1.246191 0.548514 0.097682 0.065*
C22 −0.0776 (8) 0.9434 (3) 0.8785 (2) 0.0799 (13)
H22 −0.204368 0.972142 0.891800 0.096*
C23 −0.0767 (7) 0.9285 (2) 0.81633 (18) 0.0634 (11)
H23 −0.199303 0.947950 0.788544 0.076*
C24 0.1047 (6) 0.8846 (2) 0.79436 (17) 0.0496 (9)
C25 0.2794 (7) 0.8582 (2) 0.83933 (18) 0.0644 (11)
H25 0.406764 0.828357 0.827838 0.077*
C26 0.2642 (8) 0.8760 (3) 0.9004 (2) 0.0762 (12)
H26 0.383350 0.856288 0.929661 0.091*
C27 0.1235 (6) 0.8684 (2) 0.72777 (17) 0.0562 (10)
H27 0.249662 0.835502 0.719988 0.067*
C28 −0.0204 (6) 0.8956 (2) 0.67702 (17) 0.0514 (9)
H28 −0.149375 0.926434 0.686060 0.062*
C29 −0.0008 (6) 0.8830 (2) 0.60926 (16) 0.0443 (8)
C30 −0.1779 (6) 0.9112 (2) 0.56425 (17) 0.0509 (9)
H30 −0.308912 0.936674 0.578915 0.061*
C31 −0.1624 (6) 0.9021 (2) 0.49902 (17) 0.0516 (9)
H31 −0.281980 0.921612 0.469955 0.062*
C32 0.0286 (6) 0.8644 (2) 0.47657 (16) 0.0454 (9)
C33 0.2054 (6) 0.8333 (2) 0.52050 (17) 0.0528 (9)
H33 0.333924 0.806485 0.505977 0.063*
C34 0.1878 (6) 0.8427 (2) 0.58560 (17) 0.0512 (9)
H34 0.305996 0.821501 0.615011 0.061*
C35 0.2167 (6) 0.8697 (2) 0.36136 (16) 0.0428 (8)
C36 0.1984 (6) 0.8480 (2) 0.30351 (16) 0.0467 (9)
H36 0.066137 0.822365 0.299623 0.056*
C37 0.3830 (5) 0.8654 (2) 0.25067 (16) 0.0417 (8)
C38 0.5680 (6) 0.9195 (2) 0.31673 (18) 0.0550 (10)
H38 0.699830 0.944670 0.321572 0.066*
C39 0.2086 (6) 0.7952 (2) 0.18246 (16) 0.0534 (9)
H39A 0.060153 0.808887 0.202404 0.064*
H39B 0.245130 0.734340 0.210680 0.064*
C40 0.1974 (6) 0.8072 (3) 0.10508 (17) 0.0602 (10)
H40A 0.091910 0.764916 0.103507 0.072*
H40B 0.138941 0.865535 0.078556 0.072*
C41 0.5633 (6) 0.8630 (3) 0.06904 (17) 0.0621 (11)
H41A 0.495182 0.920083 0.043990 0.075*
H41B 0.709438 0.859647 0.042244 0.075*
C42 0.6018 (6) 0.8537 (2) 0.14389 (16) 0.0514 (9)
H42A 0.686069 0.799735 0.166924 0.062*
H42B 0.693383 0.902329 0.141000 0.062*

Source of material

A mixture of (E)-4-(2-(pyridin-4-yl)vinyl)phenol (197 mg, 1 mmol) and 4,6-dichloropyrimidine (205 mg, 1 mmol) was suspended in DMF (5 ml), then copper powder (6.4 mg, 0.1 mmol) and cesium carbonate (815 mg, 2.5 mmol) were added. The reaction mixture was held at 110 °C under nitrogen for 6 h and then diluted with ethyl acetate (30 ml). The organic layer was washed with brine, dried over anhydrous Na2SO4, filtered and concentrated. The residue was purified by chromatography (petroleum ether: ethyl acetate = 6:1, v/v) on silica gel to give (E)-4-chloro-6-(4-(2-(pyridin-4-yl)vinyl)phenoxy)pyrimidine as a yellow solid. A mixture of (E)-4-chloro-6-(4-(2-(pyridin-4-yl)vinyl)phenoxy)pyrimidine (307 mg, 1 mmol) and morpholine (87 mg, 1 mmol) in DMF (5 ml) was heated in a microwave reactor at 130 °C and 100 W for 30 min. The reaction mixture was diluted with ethyl acetate (30 ml). The organic layer was washed with brine, dried over anhydrous Na2SO4, filtered and concentrated. The residue was purified by chromatography (petroleum ether: ethyl acetate = 10:1, v/v) on silica gel to give the title compound as a white solid [4].

Experimental details

All hydrogen atoms were placed in the calculated positions and constrained to ride on their parent atoms.

Comment

Nitrogen containing heterocycles especially pyrimidines form an important class of heterocyclic compounds [5, 6]. Heterocycles containing pyrimidine ring exist as the basic structures of many natural botanicals and bioactive compounds, and are widely found in herbal medicines with therapeutic effects on diabetes [7], [8], [9].

There are two crystallographically independent molecules in the asymmetric unit (see the figure). The bond lengths and angles are in the expected ranges [10].


Corresponding author: Xiao-Jin La, College of Traditional Chinese Medicine, North China University of Science and Technology, 063210 Caofeidian District, Tangshan, P. R. China, E-mail:

Funding source: Science and Technology Partnership Program, Ministry of Science and Technology of China

Award Identifier / Grant number: KY201904005

Funding source: Tangshan Science and Technology Innovation Team Training Program to Ji-an Li

Award Identifier / Grant number: 19130205C

Funding source: Science and Technology Planning Project of Hebei Province, China

Award Identifier / Grant number: 14397705D

  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 Hebei Key Laboratory of Integrated Traditional Chinese and Western Medicine for Diabetes and Its Complications, College of Traditional Chinese Medicine, North China University of Science and Technology, 21 Bohai Road, Tangshan 063210, China. This work was supported by Science and Technology Partnership Program, Ministry of Science and Technology of China (KY201904005), Tangshan Science and Technology Innovation Team Training Program (19130205C) to Ji-an Li, Science and Technology Planning Project of Hebei Province, China (No. 14397705D).

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

References

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Received: 2022-01-23
Accepted: 2022-03-07
Published Online: 2022-05-05
Published in Print: 2022-08-26

© 2022 Su-Fen Bai 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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  63. Crystal structure of 1,2-bis(2,4-dinitro-1H-imidazol-1-yl)ethane – dimethylformamide (1/1), C11H13N9O9
  64. Crystal structure of (Z)-3-((tert-butylamino) methylene)-2-(2-hydroxynaphthalen-1-yl) chroman-4-one, C24H23NO3
  65. Synthesis and crystal structure of (E)-1-(4-(((E)-3-(tert-butyl)-2-hydroxybenzylidene)amino)phenyl)ethan-1-one O-ethyl oxime, C21H26N2O2
  66. Crystal structure of the double salt bis(5-amino-1,2,4-triazol-4-ium-3-yl)methane hydrogen oxalate hemioxalate, C8H11N8O6
  67. Hydrothermal synthesis and crystal structure of catena-poly[diaqua-bis(μ2-4-[(4-pyridinylmethyl)amino]benzoato-κ2N:O)cobalt(II)]–1,2bi(4-pyridyl)ethene–water (1/1/1), C50H50N8O8Co
  68. Crystal structure of 3-(3-bromophenyl)-1′,3′-dimethyl-2′H,3H,4H-spiro[furo[3, 2-c]chromene-2,5′-pyrimidine]-2′,4,4′,6′(1′H,3′H) tetraone, C22H15BrN2O6
  69. The crystal structure of poly[aqua-(μ2-4,4′- bis(imidazolyl)biphenyl-κ2N:N′)-(μ2-3-nitrobenzene-1,2-dicarboxylato-κ2O:O′)]copper (II) hydrate, C26H21N5O8Cu
  70. The crystal structure of bis(4-(6-carboxy-8-ethyl-3-fluoro-5-oxo-5,8-dihydro-1,8-naphthyridin-2- yl)piperazin-1-ium) adipate tetrahydrate, C36H52F2N8O14
  71. Synthesis and crystal structure of poly[aqua(μ4-(1R,2S,4R)-4-hydroxy-1-((7-hydroxy-3-(4-hydroxy-3-sulfonatophenyl)-4-oxo-4H-chromen-8-yl)methyl)pyrrolidin-1-ium-2-carboxylate-κ4O:O′:O″:O‴)sodium(I)] monohydrate, C21H22NNaO12S
  72. Crystal structure of chlorido-(η6-toluene)(2,2′-bipyridine-κ2N,N′)ruthenium(II) hexafluorophosphate, C17H16ClN2RuPF6
  73. The crystal structure of (R)-6-hydroxy-8-methoxy-3-methylisochroman-1-one, C11H12O4
  74. Crystal structure of catena-poly[(5,5,7,12,12,14-hexamethyl -1,4,8,11-tetraazacyclotetradecane- κ4N,N′,Nʺ,N‴)nickel(II)-(μ2-perchlorato-κ2O:O′)] 3,5-dicarboxybenzoate – methanol (1/2), C27H49ClN4NiO12
  75. The crystal structure of 4-(chloromethyl)benzonitrile, C8H6ClN
  76. The crystal structure of dimethylammonium 8-[(7,9-dioxo-6,10-dioxaspiro[4.5]decan-8-ylidene)methyl]-9-oxo-6,10-dioxaspiro[4.5]dec-7-en-7-olate, C19H25NO8
  77. Crystal structure of (2R,3S,4S,5R,6S)-2-(acetoxymethyl)-6-((1-acetyl-5-bromo-4-chloro-1H-indol-3-yl)oxy)tetrahydro-2H-pyran-3,4,5-triyl triacetate hemihydrate C24H25BrClNO11
  78. The crystal structure of the co-crystal tetrakis[2-(tris(4-methoxyphenyl)stannyl)ethyl]silane – tetrahydrofuran – toluene – tetrahydrofurane (1/1/1), C103H116O13SiSn4
  79. Crystal structure of methyl 3-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)propanoate, C16H13NO4
  80. Crystal structure of ethyl (Z)-3-amino-2-cyano-3-(2-oxo-2H-chromen-3-yl)acrylate, C15H12N2O4
  81. Crystal structure of methyl 2-(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)acetate, C15H11NO4
  82. Crystal structure of catena-poly[diaqua-bis(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)cobalt(II)] tetrafluoroterephthalate, C26H28N8O6F4Co
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