Home Physical Sciences Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S
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Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S

  • Yingchun Fang , Changlei Song ORCID logo EMAIL logo , Yu-e Duan , Xiaoxue Xie and Qingbo Du
Published/Copyright: February 24, 2025
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 240 Issue 3

Abstract

C20H7Cl2F8N5O3S, monoclinic, P21/n (no. 14), a = 7.78993(14) Å, b = 11.8299(2) Å, c = 25.8640(5) Å, β = 93.1491(17)°, V = 2379.87(7) Å3, Z = 4, Rgt(F) = 0.0540, wRref(F2) = 0.1306, T = 100 K.

CCDC no.: 2422832

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: Clear light colourless block
Size: 0.12 × 0.10 × 0.10 mm
Wavelength: Cu Kα radiation (1.54184 Å)
μ: 4.20 mm−1
Diffractometer, scan mode: Rigaku, Synergy, HyPix, φ and ω scans
θmax, completeness: 71.1°, 100 %
N(hkl)measured, N(hkl)unique, Rint: 11582, 4508, 0.030
Criterion for Iobs, N(hkl)gt: Iobs > 2 σ(Iobs), 4,223
N(param)refined: 390
Programs: Rigaku, 1 Olex2, 2 SHELX 3 , 4
Table 2:

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

x y z Uiso*/Ueq
Cl1 0.69034 (13) 0.63675 (8) 0.73260 (4) 0.0499 (3)
Cl2 0.24050 (11) 0.37725 (8) 0.62286 (3) 0.0443 (2)
S1 0.04661 (8) 0.64347 (5) 0.80877 (2) 0.02156 (17)
F4 0.3240 (3) 0.77674 (18) 0.82028 (9) 0.0490 (6)
F5 0.2931 (3) 0.66252 (19) 0.88237 (8) 0.0462 (5)
F6 0.1264 (3) 0.8039 (2) 0.87404 (12) 0.0710 (9)
F7 0.3911 (3) 1.04613 (16) 0.63247 (7) 0.0373 (4)
F8 0.1436 (3) 0.80823 (16) 0.50333 (8) 0.0482 (6)
O1 −0.0107 (3) 0.56185 (17) 0.84797 (8) 0.0297 (5)
O2 0.1018 (3) 0.81029 (19) 0.73317 (8) 0.0372 (6)
O3 0.3245 (3) 0.73556 (18) 0.59696 (8) 0.0351 (5)
N1 0.3704 (3) 0.50706 (19) 0.71503 (9) 0.0243 (5)
N2 0.3853 (3) 0.42874 (19) 0.75328 (9) 0.0268 (5)
N3 0.2520 (4) 0.3464 (2) 0.87025 (10) 0.0400 (7)
N4 0.2365 (3) 0.6745 (2) 0.68766 (9) 0.0279 (5)
H4 0.2681 (3) 0.6580 (2) 0.65640 (9) 0.0334 (7)*
N5 0.1874 (3) 0.8514 (2) 0.65244 (9) 0.0291 (6)
H5 0.1453 (3) 0.9200 (2) 0.65527 (9) 0.0349 (7)*
C2 0.6821 (4) 0.5164 (3) 0.58868 (13) 0.0355 (8)
C3 0.5320 (4) 0.4549 (3) 0.58467 (12) 0.0332 (7)
H3 0.4988 (4) 0.4163 (3) 0.55351 (12) 0.0399 (8)*
C4 0.4301 (4) 0.4503 (2) 0.62700 (11) 0.0260 (6)
C5 0.4800 (4) 0.5059 (2) 0.67268 (11) 0.0236 (6)
C6 0.6333 (4) 0.5660 (2) 0.67617 (12) 0.0303 (7)
C7 0.7354 (4) 0.5717 (3) 0.63410 (15) 0.0387 (8)
H7 0.8403 (4) 0.6128 (3) 0.63629 (15) 0.0464 (10)*
C8 0.2802 (4) 0.4667 (2) 0.78822 (11) 0.0248 (6)
C9 0.2632 (4) 0.4010 (2) 0.83436 (11) 0.0291 (7)
C10 0.2590 (4) 0.5924 (2) 0.72492 (11) 0.0247 (6)
C11 0.1975 (4) 0.5695 (2) 0.77282 (11) 0.0232 (6)
C12 0.2102 (4) 0.7278 (2) 0.84775 (13) 0.0295 (7)
C13 0.1693 (4) 0.7797 (2) 0.69484 (12) 0.0282 (6)
C14 0.2634 (4) 0.8275 (2) 0.60674 (11) 0.0274 (6)
C15 0.2676 (4) 0.9231 (2) 0.56947 (11) 0.0256 (6)
C16 0.2114 (5) 0.9091 (3) 0.51785 (12) 0.0317 (7)
C17 0.2169 (5) 0.9941 (3) 0.48153 (12) 0.0356 (8)
H17 0.1745 (5) 0.9823 (3) 0.44682 (12) 0.0427 (9)*
C18 0.2861 (5) 1.0974 (3) 0.49707 (12) 0.0359 (8)
H18 0.2937 (5) 1.1565 (3) 0.47242 (12) 0.0431 (9)*
C19 0.3441 (5) 1.1159 (3) 0.54774 (13) 0.0350 (7)
H19 0.3914 (5) 1.1869 (3) 0.55818 (13) 0.0420 (9)*
C20 0.3320 (4) 1.0292 (3) 0.58280 (11) 0.0283 (6)
F1 0.9688 (12) 0.5866 (11) 0.5652 (4) 0.060 (3)a
F2 0.8555 (18) 0.4413 (8) 0.5299 (5) 0.063 (3)a
F3 0.754 (4) 0.603 (2) 0.5115 (11) 0.045 (4)a
C1 0.820 (3) 0.5394 (17) 0.5507 (8) 0.047 (3)a
F1A 0.7452 (6) 0.4406 (3) 0.50546 (15) 0.0542 (13)
F2A 0.9496 (5) 0.5117 (6) 0.55385 (17) 0.0751 (17)
F3A 0.7586 (17) 0.6199 (8) 0.5166 (4) 0.0453 (18)
C1A 0.7835 (9) 0.5205 (6) 0.5401 (3) 0.0383 (14)

  1. aOccupancy: 0.289 (8).

1 Source of materials

2,6-Difluorobenzoyl isocyanate (0.1 mol, 18.3 g) was added to a three-neck flask and heated to 40 °C. Drop 5-amino-1-(2,6-dichloro-4-(trifluoromethyl)phenyl-4-((trifluoromethyl)sulfinyl)-1h–pyrazole-3-carbonitrile (0.1 mol, 43.7 g) of dichloroethane (100 g) solution with stirring at 40–45 °C. The suspension was stirred at 80 °C for 2 h and slowly cooled to 0 °C. Then the mixture was filtered and dried at 70–80 °C to get white powder. The white powder was dissolved in a mixed solution (ethyl acetate: n-heptane = 2:1, v/v) and then slowly volatilized at room temperature to obtain the single crystal.

2 Experimental details

Absorption corrections were used by using multi-scan program. 1 The structure was solved with SHELX. 3 , 4 Hydrogen atoms were placed in their geometrically idealized positions. Hydrogen atoms were constrained to ride on their parent atoms.

3 Comment

Urea-based organic compounds are pivotal in the realm of drug discovery and development, owing to their distinct chemical architectures and broad spectrum of biological activities. Recent studies have shown that the classic drug phenobarbital, which contains a urea structure, has great potential to replace conventional benzodiazepine in the treatment of alcohol withdrawal syndrome (AWS). 5 Glimepiride containing sulfonylurea structure is the third generation of long-acting anti-diabetic drugs, the main mechanism of its hypoglycemic effect is to stimulate the secretion of insulin by islet bet which is very important in the treatment of diabetes. 6 Levastinib, a versatile anticancer drug containing urea structure, is often used in clinical studies in combination with other medicines and has shown excellent results. 7 In this paper, a new compound was synthesized by referring to the phenylpyrazole structure of the analgesic celecoxib and the structure of the drug urea described above. 8

The title molecule in the crystal structure is a flexible molecule and each title molecule contains two phenyl rings, one pyrazole ring and one urea group. Intermolecular and intramolecular connectivity are achieved through hydrogen bonds. First hydrogen bond is N4–H4⃛O3, the distance of N4–H4 bond is 0.88 Å, the distance of H4⃛O3 bond is 1.86 Å, the angle of N4–H4⃛O3 is 138°, its an intramolecular hydrogen bond. 9 Second hydrogen bond is N5–H5⃛F7, the distance of N5–H5 bond is 0.88 Å, the distance of H5⃛F7 bond is 2.52 Å, the angle of N5–H5⃛F7 is 104°, its an intramolecular hydrogen bond. 10 Third hydrogen bond is N4–H5⃛O1, the distance of N4–H5 bond is 0.95 Å, the distance of H5⃛O1 bond is 1.98 Å, the angle of N4–H5⃛O1 is 168°.

In addition, there are two intermolecular C–F⋯π interactions and one intramolecular C–O⋯π interaction among the aromatic rings from neighboring molecules. The first C–F⋯π interaction is C12–F4⃛Cg i (C2–C7; symmetry code i: 1 − x, 1/2 + y, 3/2 − z), the shortest distance between F and center of Cg i is 3.118(3) Å. 11 The second C–F⋯π interaction is C12–F6⃛Cg i , the shortest distance between F and center of Cg i is 3.346(3) Å. The first C–O⋯π interaction is C14–O3⃛Cg ii (C2–C7; symmetry code i: x, y, z), the shortest distance between F and center of Cg ii is 3.414(3) Å. 12 All geometric parameters are in the expected ranges. 13

Corresponding author: Changlei Song, North Anhui Health Vocational College, Suzhou, 234000, Anhui, P.R. China, E-mail:

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

  2. Research funding: None declared.

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

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Received: 2025-01-07
Accepted: 2025-02-11
Published Online: 2025-02-24
Published in Print: 2025-06-26

© 2025 the author(s), published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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  2. New Crystal Structures
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  4. Crystal structure of catena-poly[(μ3-4,4′-oxydibenzoato- κ5 O,O′: O″,O‴:O‴)-bis(2,4,6-tri(3-pyridine)-1,3,5-triazine-κ1 N)cadmium(II)], C50H32CdN12O5
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  19. Synthesis and crystal structure of 6-methoxy-7-[(4-methoxyphenyl)methoxy]-2H-1-benzopyran-2-one, C18H16O5
  20. Synthesis and crystal structure of ethyl 4-((4-trifluoromethylbenzyl)amino)benzo, C17H16F3NO2
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https://doi.org/10.1515/ncrs-2025-0016
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Articles in the same Issue

  1. Frontmatter
  2. New Crystal Structures
  3. Crystal structure of 5,5′-bis(2,4,6-trinitrophenyl)-2,2′-bi(1,3,4-oxadiazole), C16H4N10O14
  4. Crystal structure of catena-poly[(μ3-4,4′-oxydibenzoato- κ5 O,O′: O″,O‴:O‴)-bis(2,4,6-tri(3-pyridine)-1,3,5-triazine-κ1 N)cadmium(II)], C50H32CdN12O5
  5. The crystal structure of 1,4-diazepane-1,4-diium potassium trinitrate, C5H14KN5O9
  6. The crystal structure of benzyl 2,2,5,5-tetramethylthiazolidine-4-carboxylate, C15H21NO2S
  7. Crystal structure of 2-hydroxyethyl-triphenylphosphonium tetracyanidoborate, C24H20BN4OP
  8. The crystal structure of 1-methyl-3-(N-methylnitrous amide–N-methylene) imidazolidine-2,4,5-trione
  9. Crystal structure of N-((3-cyano-1-(2,6-dichloro-4-(trifluoromethyl)phenyl)-4-(2,2,2-trifluoroacetyl)-1H-pyrazol-5-yl)carbamoyl)-2,6-difluorobenzamide, C20H7Cl2F8N5O3S
  10. Crystal structure of 5-(2,2-difluoropropyl)-5-methylbenzo[4,5]imidazo[2,1-a] isoquinolin-6(5H)-one, C20H18F2N2O
  11. The crystal structure of N′,N″-[1,2-bis(4-chlorophenyl)ethane-1,2-diylidene]bis(furan-2- carbohydrazide), C24H16Cl2N4O4
  12. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromoantimony(III), [C25H21BrP]+[SbBr4]−
  13. Crystal structure of [(4-bromobenzyl)triphenylphosphonium] tetrabromidoindium(III), [C25H21BrP]+[InBr4]−
  14. The crystal structure of 4-carboxy-2-oxobutan-1-aminium chloride, C5H10ClNO3
  15. Crystal structure of (4-(4-chlorophenyl)-1H-pyrrole-3-carbonyl)ferrocene, C21H16ClFeNO
  16. The crystal structure of dichlorido(η6-p-cymene)(triphenylarsine)ruthenium(II), C28H29AsCl2Ru
  17. Crystal structure of (Z)-2-hydroxy-N′-(1-(o-tolyl)ethylidene)benzohydrazide, C16H16N2O2
  18. The crystal structure of 10-(1-bromoethyl)-14-(bromomethyl)dibenzo[a, c]acridine, C24H17NBr2
  19. Synthesis and crystal structure of 6-methoxy-7-[(4-methoxyphenyl)methoxy]-2H-1-benzopyran-2-one, C18H16O5
  20. Synthesis and crystal structure of ethyl 4-((4-trifluoromethylbenzyl)amino)benzo, C17H16F3NO2
  21. The crystal structure of (Z)-2-(tert-butyl)-6-(7-(tert-butyl)-5-methylbenzo[d][1,3]oxathiol-2-ylidene)-4-methylcyclohexa-2,4-dien-1-one, C23H28O2S
  22. The crystal structure of (R)-2-aminobutanamide hydrochloride, C4H11ClN2O
  23. Crystal structure of bromido[hydridotris(3-tert-butyl-5-isopropylpyrazolyl)borato-κ3 N,N′,N″]copper(II), C30H52BBrCuN6
  24. Crystal structure of chlorido{hydridotris[3-mesityl-5-methyl-1H-pyrazol-1-yl-κN3]borato}-copper(II) dichloromethane monosolvate
  25. Crystal structure of 4-[3,5-bis(propan-2-yl)-1H-pyrazol-4-yl]pyridine, C14H19N3
  26. Crystal structure of ((4-(4-bromophenyl)-1H-pyrrol-3-yl)methyl)ferrocene, C21H16BrFeNO
  27. Crystal structure of [(4-chlorobenzyl)triphenylphosphonium] dichloridocopper(I), {[C25H21ClP]+[CuCl2]−}n
  28. The crystal structure of {Cu(2,9-diisopropyl-4,7-diphenyl-1,10-phenanthroline)[4,5-bis(diphenylphosphino)-9,9-dimethylxanthene]}+ PF6−·1.5(EtOAC)
  29. Crystal structure of 3,5-bis(t-butyl)-1H-pyrazol-4-amine, C11H21N3
  30. Crystal structure of [(2,4-dichlorobenzyl)triphenylphosphonium] trichloridocopper(II), [C25H20Cl2P]+[CuCl3]−
  31. The crystal structure of dipotassium sulfide, K2S
  32. Crystal structure of (4-(4-methoxyphenyl)-1H-pyrrole-3-carbonyl)ferrocene, C22H19FeNO2
  33. Crystal structure of (E)-6-(4-methylpiperazin-1-yl)-2-(4-(trifluoromethyl)benzylidene)-3, 4-dihydronaphthalen-1(2H)-one, C23H23F3N2O
  34. Crystal structure of (E)-6-morpholino-2-(4-(trifluoromethyl)benzylidene)-3,4-dihydronaphthalen-1(2H)-one, C22H20F3NO2
  35. Crystal structure of Ce9Ir37Ge25
  36. The crystal structure of ethyl 6-(2-nitrophenyl)imidazo[2,1-b]thiazole-3-carboxylate, C14H11N3O4S
  37. Crystal structure of (4-(4-isopropylphenyl)-1H-pyrrol-3-yl)(ferrocenyl)methanone, C24H23FeNO
  38. Crystal structure of bis(methylammonium) tetrathiotungstate(VI), (CH3NH3)2[WS4]
  39. Crystal structure of 6,11-dihydro-12H-benzo[e]indeno[1,2-b]oxepin-12-one, C17H12O2
  40. Crystal structure of 3-[(4-phenylpiperidin-1-yl)methyl]-5-(thiophen-2-yl)-2,3-dihydro-1,3,4- oxadiazole-2-thione, C18H19N3OS2
  41. Crystal structure of N-isopropyl-1,8-naphthalimide C15H13NO2
  42. TiNiSi-type EuPdBi
  43. Crystal structure of 1-(p-tolylphenyl)-4-(2-thienoyl)-3-methyl-1H-pyrazol-5-ol, C16H14N2O2S
  44. The crystal structure of 3-(3-carboxypropyl)-2-nitro-1H-pyrrole 1-oxide, C7H9N3O5
  45. The crystal structure of tetraaqua-bis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k2O:N)-tetrakis(2-(2-methyl-5-nitro-1H-imidazol-1-yl)acetato-k1N)trizinc(II) hexahydrate C36H52N18O32Zn3
  46. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 4-hydroxy-3,5-dimethoxybenzoate monohydrate, C25H30FN3O9
  47. Crystal structure of bis(DL-1-carboxy-2-(1H-indol-3-yl)ethan-1-aminium) oxalate — acetic acid (1/2)
  48. Crystal structure of methyl (E)-4-((4-methylphenyl)sulfonamido)but-2-enoate, C12H15NO4S
  49. The crystal structure of actarit, C10H11NO3
  50. The crystal structure of bicyclol, C19H18O9
  51. The crystal structure of topiroxostat, C13H8N6
  52. Crystal structure of 2,2-dichloro-N-methyl-N-(4-p-tolylthiazol-2-yl)acetamide, C13H12Cl2N2OS
  53. Crystal structure of 4-(trifluoromethyl)-7-coumarinyl trifluoromethanesulfonate C11H4F6O5S
  54. Crystal structure of (1,4,7,10,13,16-hexaoxacyclooctadecane-κ6O6)-((Z)-N,N′-bis(2-(dimethylamino)phenyl)carbamimidato-κ1N)potassium(I)
  55. Crystal structure of (Z)-2-(5-((4-(dimethylamino)naphthalen-1-yl)methylene)-4-oxo-2-thioxothiazolidin-3-yl)acetic acid, C18H16N2O3S2
  56. Crystal structure of (4-fluorobenzyl)triphenylphosphonium bromide, C25H21BrFP
  57. The crystal structure of dichlorido-[6-(pyridin-2-yl)phenanthridine-κ2N, N′]zinc(II)-chloroform (1/1), C19H13N2ZnCl5
  58. Crystal structure of (E)-(3-(2,4-dichlorophenyl)acryloyl)ferrocene, C19H14Cl2FeO
  59. The crystal structure of (E)-7-chloro-1-cyclopropyl-6-fluoro-3-((2-hydroxybenzylidene)amino)quinolin-4(1H)-one, C19H14ClFN2O2
  60. Crystal structure of 2-bromo-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13BrFNO4S2
  61. Crystal structure of 2-chloro-11-(((fluoromethyl)sulfonyl)methyl)-6-methyl-6,11-dihydrodibenzo[c,f][1,2]thiazepine 5,5-dioxide, C16H13ClFNO4S2
  62. Crystal structure of 5-(2,2-difluoropropyl)-5-methyl-6-oxo-5,6-dihydrobenzo[4,5]imidazo[2,1-a]isoquinoline-3-carbonitrile, C20H15F2N3O
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