Home The crystal structure of 5-benzoyl-1-[(E)-(4-fluorobenzylidene)amino]-4-phenylpyrimidin-2(1H)-one, C24H16FN3O2
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The crystal structure of 5-benzoyl-1-[(E)-(4-fluorobenzylidene)amino]-4-phenylpyrimidin-2(1H)-one, C24H16FN3O2

  • Zeliha Atioğlu ORCID logo EMAIL logo , Halis Karataş and Zülbiye Kökbudak
Published/Copyright: June 24, 2021
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 236 Issue 5

Abstract

C24H16FN3O2, monoclinic, P21 (no. 4), a = 6.0024(5) Å, b = 19.474(2) Å, c = 8.3531(8) Å, β = 91.750(9)°, V = 975.95(16) Å3, Z = 2, R gt (F) = 0.0409, wR ref (F 2) = 0.0832, T = 294(2) K.

CCDC no.: 2065479

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 (see Figure 1).

Figure 1: The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
Figure 1:

The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.

Table 1:

Data collection and handling.

Crystal: Colourless prism
Size: 0.30 × 0.28 × 0.22 mm
Wavelength: Mo Kα radiation (0.71073 Å)
μ: 0.10 mm−1
Diffractometer, scan mode: Xcalibur, ω
θ max, completeness: 25.0°, 99%
N(hkl)measured, N(hkl)unique, R int: 3430, 2195, 0.029
Criterion for I obs, N(hkl)gt: I obs > 2 σ(I obs), 1680
N(param)refined: 271
Programs: CrysAlisPRO [1], SHELX [2], [3], WinGX/ORTEP [4], PLATON [5], structure refinement [6]
Table 2:

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

Atom x y z U iso*/U eq
F1 −0.4207 (4) 0.28738 (16) 0.1087 (3) 0.0791 (9)
O1 0.6332 (4) 0.34582 (17) 0.7251 (3) 0.0543 (9)
O2 1.2532 (4) 0.55868 (17) 0.4500 (4) 0.0591 (9)
N1 0.8934 (5) 0.42981 (19) 0.7518 (4) 0.0410 (9)
N2 0.6280 (5) 0.43114 (17) 0.5354 (4) 0.0374 (9)
N3 0.4484 (5) 0.40886 (18) 0.4361 (4) 0.0419 (9)
C1 0.3085 (6) 0.3668 (2) 0.4894 (5) 0.0432 (11)
H1 0.324181 0.349847 0.593261 0.052*
C2 0.1208 (6) 0.3451 (2) 0.3843 (5) 0.0383 (10)
C3 0.0859 (7) 0.3726 (2) 0.2318 (5) 0.0473 (12)
H3 0.186226 0.404403 0.192823 0.057*
C4 −0.0956 (7) 0.3531 (3) 0.1380 (5) 0.0544 (13)
H4 −0.120613 0.371454 0.036286 0.065*
C5 −0.2381 (7) 0.3057 (3) 0.1993 (5) 0.0518 (13)
C6 −0.2093 (6) 0.2766 (3) 0.3458 (5) 0.0508 (13)
H6 −0.309460 0.244095 0.382256 0.061*
C7 −0.0266 (6) 0.2965 (2) 0.4396 (5) 0.0451 (11)
H7 −0.002663 0.277079 0.540383 0.054*
C8 0.7159 (6) 0.3977 (3) 0.6754 (5) 0.0410 (11)
C9 0.9907 (6) 0.4836 (2) 0.6921 (5) 0.0374 (10)
C10 1.1779 (6) 0.5125 (2) 0.7918 (5) 0.0412 (11)
C11 1.2220 (7) 0.5821 (3) 0.7999 (5) 0.0552 (13)
H11 1.132344 0.612730 0.741724 0.066*
C12 1.3981 (8) 0.6065 (3) 0.8937 (6) 0.0686 (16)
H12 1.426222 0.653441 0.898224 0.082*
C13 1.5313 (7) 0.5623 (3) 0.9797 (6) 0.0654 (15)
H13 1.652549 0.578989 1.039870 0.078*
C14 1.4860 (7) 0.4932 (3) 0.9774 (6) 0.0594 (14)
H14 1.573843 0.463213 1.038699 0.071*
C15 1.3099 (6) 0.4681 (3) 0.8842 (5) 0.0493 (12)
H15 1.279576 0.421298 0.883255 0.059*
C16 0.7334 (6) 0.4853 (2) 0.4729 (5) 0.0374 (10)
H16 0.676756 0.504300 0.377982 0.045*
C17 0.9192 (6) 0.5135 (2) 0.5426 (4) 0.0351 (10)
C18 1.0509 (6) 0.5639 (2) 0.4506 (5) 0.0398 (10)
C19 0.9352 (6) 0.6188 (2) 0.3553 (5) 0.0372 (10)
C20 1.0452 (7) 0.6474 (3) 0.2296 (5) 0.0544 (13)
H20 1.185055 0.630978 0.203635 0.065*
C21 0.9491 (9) 0.7003 (3) 0.1416 (6) 0.0667 (15)
H21 1.023022 0.719103 0.055728 0.080*
C22 0.7424 (8) 0.7251 (3) 0.1819 (6) 0.0597 (14)
H22 0.678019 0.761289 0.124294 0.072*
C23 0.6341 (7) 0.6969 (2) 0.3049 (6) 0.0529 (13)
H23 0.494585 0.713686 0.330536 0.064*
C24 0.7271 (6) 0.6434 (2) 0.3939 (5) 0.0423 (11)
H24 0.650722 0.624309 0.478349 0.051*

Source of material

The title Schiff base was synthesized according to the following procedure. About 1.0 mmol of aminopyrimidine derivative {1-amino-5-benzoyl-4-phenylpyrimidin-2(1H)-one} was dissolved in 30 mL of ethyl alcohol, and put to a solution of 4-fluorobenzaldehyde (1.2 mmol). A catalytic amount of p-toluene sulfonic acid was used as catalyst. The reaction mixture was refluxed for 6 h and then stirred for 24 h at 25 °C. Ethyl alcohol was aspirated, and diethyl ether was put over product. The solid obtained, was filtered after stirred in the cold for 24 h. The final product was purified two times by crystallization in ethyl alcohol. Yield: 70%; m.p.: 175–177 °C; color: white. H NMR IR: υ = 3030.0 (aromatic C–H), 1674.1, 1652.9 (C=O), 1622.0 and 1595.0 (C=N and C=C), 780.2–680.1 cm−1 (pyrimidine ring). 1 H NMR (400 MHz, DMSO) δ 9.25 (s, 1H), 8.69 (s, 1H), 8.00 (dd, J = 8.1, 5.4 Hz, 2H), 7.82 (d, J = 7.3 Hz, 2H), 7.60–7.29 (m, 10H). 13 C NMR (100 MHz, DMSO) δ 192.01, 171.20, 166.05, 163.96, 151.53, 149.23, 137.26, 133.88, 132.07, 131.97, 131.14, 130.18, 129.14, 129.06, 128.69, 116.94, 116.72, 116.06. Anal. Calcd. For C24H16FN3O2 (397.401 g/mol). C, 72.54; H, 4.06; N, 10.57. Found: C, 72.35; H, 3.85; N, 10.35.

Experimental details

All H atoms were positioned at geometrically idealized positions and were refined using a riding-model approximation, with U iso(H) = 1.2U eq(C). The Flack parameter (0.1(10) from 328 selected quotients) was calculated using Parsons’ method [6].

Comment

Pyrimidine derivatives are important classes of heterocyclic molecules that indicate a broad spectrum of biological activities such as antibacterial, anticancer, antioxidant and analgesic activities [7], [8], [9]. Therefore, the synthesis of pyrimidine-based molecules has achieved great significance in recent years. Schiff bases, also called imines, are obtained by a condensation reaction between a primary amine and aldehyde or ketone under mild condition. They find use as catalysts, intermediates in organic synthesis, pigments and dyes, polymer stabilizers [10]. Schiff bases also exhibit a wide range of biological activities [11], [12].

All atoms in the pyrimidine ring (N1/N2/C8/C9/C16/C17) are almost coplanar, the largest deviation from the mean plane was calculated to be 0.049(5) Å for C8. The orientations of the substituents with respect to the pyrimidine ring are defined by the dihedral angles of 10.9(2), 32.5(2) and 62.2(2)° for a fluro phenyl ring A(C2–C7), and two phenyl rings B(C10–C15), C(C19–C24), respectively. The other angles between the ring planes are 43.5(2)° for A/B, 60.0(2)° for A/C and 73.4 (2)° for B/C. All bond distances and angles are in good agreement with those in related structures [13–15].

The molecular conformation is affected by a weak intramolecular C1–H1···O1 contact. In the crystal structure, molecules are linked by weak intermolecular C22–H22 ··· F1 (−x, y+1/2, −z) and two C–H ··· π interactions [C7–H7···Cg4 (−x+1, y−1/2, −z+1) and C13–H13···Cg4 (x+1, y, z+1); where Cg4 is the centroid of the C19–C24 phenyl ring], forming a three dimensional network.

Corresponding author: Zeliha Atioğlu, Avionics Department, School of Applied Sciences, Cappadocia University, 50420, Mustafapaşa, Ürgüp, Nevşehir, Turkey, E-mail:

Acknowledgment

I would like to thank Assoc. Professor Dr. Muhittin Aygün (Dokuz Eylül University, Ízmir) for aid with the data collection of the title compound.

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

  2. Research funding: The research did not receive funding support.

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

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Received: 2021-05-31
Accepted: 2021-06-14
Published Online: 2021-06-24
Published in Print: 2021-09-27

© 2021 Zeliha Atioğlu 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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  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
https://doi.org/10.1515/ncrs-2021-0216
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of [aqua-(4-iodopyridine-2,6-dicarboxylato-κ3 O,N,O′)-(1,10-phenanothroline-κ2 N,N′)copper(II)] dihydrate, C19H16O7N3CuI
  4. The crystal structure of tetrakis(1-isopropyl-1H-imidazolium) octamolybdate, C24H44Mo8N8O26
  5. Crystal structure of catena-poly[bis(µ2-3,5-bis(1-imidazolyl)pyridine-κ2 N:N′)-(µ2-3-nitrophthalato-k3 O,O′:O″)cadmium(II)] dihydrate, C30H25N11O8Cd
  6. The crystal structure of diaqua-bis(2-(3-(1H-pyrazol-4-yl)-1H-1,2,4-triazol-5-yl)pyridine-κ2 N:N′)-bis(3,5-dicarboxybenzoato-κ1 O)cobalt(II), C38H30CoN12O14
  7. Crystal structure of the nickel(II) complex aqua-(2,6-di(pyrazin-2-yl)-4,4′-bipyridine-κ3 N,N′,N′′)-(phthalato-κ2 O,O′)nickel(II) tetrahydrate, C26H26N6O9Ni
  8. The crystal structure of 1-[5-(2-fluorophenyl)-1-(pyridine-3-sulfonyl)-1H-pyrrol-3-yl]-N-methylmethanaminium 3-carboxyprop-2-enoate, C21H20FN3O6S
  9. The crystal structure of 1,2-bis(4-pyridyl)ethane - 4,4-dihydroxydiphenylmethane (1/1), C25H21N2O2
  10. Crystal structure of bis(2-((E)-5-chloro-2-hydroxybenzylidene)hydrazineyl)methaniminium trifluoroacetate dihydrate, C34H36Cl4N10O12
  11. Crystal structure of 1-cyclopropyl-7-ethoxy-6,8-difluoro-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid, C15H13F2NO4
  12. Crystal structure of methyl 3-(1H-naphtho[1,8-de][1,3,2]diazaborinin-2(3H)-yl)benzoate, C18H15BN2O2
  13. Crystal structure of (E)-N′-(2-chloro-6-hydroxybenzylidene)-2-hydroxybenzohydrazide, C14H11ClN2O3
  14. Crystal structure of Al-rich fluorophlogopite, K1.0(Mg2.8Al0.2)(Si2.8Al1.2)O10F2
  15. The crystal structure of 4,5-diiodo-1,3-dimesityl-1H-1,2,3-triazol-3-ium hexafluoridoantimonate(V), C20H22F6I2N3Sb
  16. Crystal structure of tris(3-iodopyridin-1-ium) catena-poly[(hexachlorido-κ1 Cl)-(μ2-trichlorido-κ2 Cl:Cl)diantimony(III)], C15H15Cl9I3N3Sb2
  17. Crystal structure of methyl 2-(1H-naphtho[1,8-de][1.3.2]diazaborinin-2(3H-yl)benzoate C18H15BN2O2
  18. The crystal structure of 1,8-bis(4-methoxybenzoyl)naphthalene-2,7-diyl dibenzoate, C40H28O8
  19. Crystal structure of 2-bromo-1,3,6,8-tetramethylBOPHY (BOPHY = bis(difluoroboron)-1,2-bis((1H-pyrrol-2-yl)methylene)hydrazine), C14H15B2BrF4N4
  20. The crystal structure of (E)-3-chloro-2-(2-(2-fluorobenzylidene)hydrazinyl)pyridine, C12H9ClFN3
  21. Crystal structure of bis(µ2- 4-iodopyridine-2,6-dicarboxylato-κ3O:N:O′)-bis(4-iodopyridine-2,6-dicarboxylato-κ3O:N:O′)-bis(µ2-1-(4-pyridyl)piperazine-κ2N:N′)-hexa-aqua-tetra-copper(II), C46H46Cu4I4N10O22
  22. Crystal structure of poly[diaqua-(μ2-2,5-dihydroxyterephthalato-κ2O:O′)(μ2-bis(4-pyridylformyl)piperazine-κ2N:N′)cadmium(II)] dihydrate, C24H28CdN4O12
  23. Crystal structure of poly[aqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)-(μ3-2,3,5,6-tetrafluoroterephthalato-κ3O:O′:O′′)cadmium(II)], C17H14N4O5F4Cd
  24. Crystal structure of 6-(quinolin-8-yl)benzo[a]phenanthridin-5(6H)-one, C26H16N2O
  25. The crystal structure of aqua-bis(6-chloropicolinato-κ2N,O)copper(II), C12H8Cl2N2O5Cu
  26. Crystal structure of catena-poly[diaqua-bis(μ2-4,4′-bipyridyl-κ2N:N′) disilver(I)] 4-oxidopyridine-3-sulfonate trihydrate, C25H29Ag2N5O9S
  27. The crystal structure of 4-(3-bromophenyl)pyrimidin-2-amine, C10H8BrN3
  28. Crystal structure of 6-oxo-4-phenyl-1-propyl-1,6-dihydropyridine-3-carbonitrile, C15H14N2O
  29. Crystal structure of 4-(2,2-difluoroethyl)-2,4-dimethyl-6-(trifluoromethyl)isoquinoline-1,3(2H,4H)-dione, C14H12F5NO2
  30. Crystal structure of dibromido-(1-methyl-1H-imidazole-κ1N)-(3-(3-methyl-1H-imidazol-3-ium-1-yl)propanoato-κ1O)zinc(II), C11H16Br2N4O2Zn
  31. The crystal structure of 1,1′-(((2 (dimethylamino)ethyl)azanediyl)bis(methylene)) bis(naphthalen-2-olato-κ4 N,N′,O,O′)-(pyridine-2,6-dicarboxylato-N,O,O′)- titanium(IV) ─ dichloromethane (2/1), C33H29N3O6Ti
  32. The layered crystal structure of bis(theophyllinium) hexachloridostannate (IV), C14H18N8O8SnCl6
  33. The crystal structre of 3-(1-ethenyl-1H-imidazol-3-ium-3-yl)propane-1-sulfonate, C8H12N2O3S
  34. Synthesis and crystal structure of di-tert-butyl 1″-acetyl-2,2″,9′-trioxo-4a′,9a′-dihydro-1′H,3′H,9′H-dispiro[indoline-3,2′-xanthene-4′,3″-indoline]-1,3′-dicarboxylate, C39H38N2O9
  35. The crystal structure of 4-chloro-2-(quinolin-8-yl)isoindoline-1,3-dione, C17H9ClN2O2
  36. The crystal structure of 1-fluoro-4-(p-tolylethynyl)benzene, C15H11F
  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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