Startseite The crystal structure of methyl 5-(trifluoromethyl)-1H-pyrrole-2-carboxylate, C7H6F3NO2
Artikel Open Access

The crystal structure of methyl 5-(trifluoromethyl)-1H-pyrrole-2-carboxylate, C7H6F3NO2

  • De-Zheng Yang , Ting Gao , Chun-Shen Zhao ORCID logo EMAIL logo und Hui-Fang Chai EMAIL logo
Veröffentlicht/Copyright: 1. Februar 2021

Abstract

C7H6F3NO2, monoclinic, P21/c (no. 14), a = 11.3688(4) Å, b = 10.6836(3) Å, c = 14.4518(5) Å, β = 112.5320(10)°, V = 1621.32(9) Å3, Z = 8, Rgt(F) = 0.0554, wRref(F2) = 0.1647, T = 170 K.

CCDC no.: 2050628

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:0.15 × 0.08 × 0.05 mm
Wavelength:Mo Kα radiation (0.71073 Å)
μ:0.16 mm−1
Diffractometer, scan mode:D8 VENTURE, φ and ω
θmax, completeness:26.4°, 99%
N(hkl)measured, N(hkl)unique, Rint:11412, 3274, 0.032
Criterion for Iobs, N(hkl)gt:Iobs > 2 σ(Iobs), 2312
N(param)refined:237
Programs:Bruker [1], SHELX [2], [, 3]
Table 2:

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

AtomxyzUiso*/Ueq
C10.0337 (3)0.3464 (3)0.1344 (2)0.0448 (7)
C20.1335 (2)0.2582 (2)0.19820 (18)0.0349 (6)
C30.1279 (2)0.1307 (2)0.2081 (2)0.0403 (6)
H30.0558010.0787570.1763750.048*
C40.2487 (2)0.0921 (2)0.2736 (2)0.0393 (6)
H40.2741260.0086690.2946750.047*
C50.3237 (2)0.1972 (2)0.30199 (17)0.0305 (5)
C60.4564 (2)0.2143 (2)0.36847 (18)0.0318 (5)
C70.6436 (2)0.1151 (3)0.4773 (2)0.0438 (7)
H7A0.6962430.1386190.4399430.066*
H7B0.6716800.0337200.5095460.066*
H7C0.6522310.1784380.5285250.066*
C80.7811 (2)0.5299 (3)0.5109 (2)0.0430 (7)
C90.6746 (2)0.6193 (2)0.45203 (19)0.0354 (6)
C100.6724 (3)0.7477 (3)0.4509 (2)0.0410 (6)
H100.7408180.8019570.4870980.049*
C110.5499 (2)0.7835 (2)0.3859 (2)0.0399 (6)
H110.5196400.8667660.3699110.048*
C120.4815 (2)0.6757 (2)0.34952 (19)0.0341 (6)
C130.3515 (2)0.6542 (2)0.27872 (19)0.0341 (6)
C140.1508 (2)0.7447 (3)0.1907 (2)0.0498 (8)
H14A0.1473440.7100440.1269110.075*
H14B0.1085600.8264920.1789190.075*
H14C0.1075470.6878550.2205420.075*
F10.01233 (19)0.43870 (18)0.18574 (17)0.0737 (6)
F20.0653 (2)0.3989 (2)0.06466 (17)0.0848 (7)
F3−0.07533 (17)0.28633 (19)0.08960 (18)0.0856 (8)
F40.7548 (2)0.4700 (2)0.57893 (15)0.0800 (7)
F50.8013 (2)0.44724 (18)0.45315 (15)0.0691 (6)
F60.88561 (19)0.5951 (2)0.5545 (2)0.0969 (9)
N10.25247 (18)0.29785 (18)0.25546 (15)0.0328 (5)
H10.2792100.3758620.2615210.039*
N20.55882 (19)0.57552 (19)0.39021 (16)0.0349 (5)
H20.5373230.4962290.3784070.042*
O10.51099 (17)0.31426 (16)0.38549 (14)0.0463 (5)
O20.51183 (16)0.10685 (15)0.40926 (13)0.0388 (5)
O30.31022 (17)0.55360 (16)0.24295 (14)0.0423 (5)
O40.28230 (16)0.75919 (17)0.25813 (15)0.0433 (5)

Source of material

All chemicals, reagents and solvents are of analytical grade and are commercially available. Methyl 1H-pyrrole-2-carboxylate (15 g, 119.87 mmol) and sodium trifluoromethanesulfinate (56.12 g, 359.62 mmol) were dissolved in dichloromethane (150 mL) and water (60 mL) (DCM:H2O = 5:2), and slowly tert-butyl hydroperoxide (57.65 mL, 599.37 mmol) was added dropwise at 0 °C. The mixture was warmed to room temperature and reacted for 12 h. Subsequently, the reaction mixture was poured into water and extracted with dichloromethane. The organic phase was then dehydrated with anhydrous sodium sulfate and concentrated at reduced pressure to afford a yellow liquid. The crude mixture was purified by silica gel column chromatography, eluted with ethyl acetate and petroleum ether (ethyl acetate: petroleum ether = 10: 3) to give a white solid (13.73 g, yield 59.32%). 1H NMR (400 MHz, CDCl3) δ 9.62 (s, 1H), 6.39 (d, 1H), 6.65 (d, 1H), 3.95 (s, 3H). Crystals were grown in petroleum ether at room temperature.

Experimental details

All hydrogen atoms were placed in geometrically calculated positions. The Uiso values of the hydrogen atoms of methyl groups were set to 1.5 Ueq(Cmethyl) and the Uiso values of all other hydrogen atoms were set to 1.2 Ueq.

Comment

Fluorine-containing compounds play an extremely important role in many fields such as agriculture, medicine, and materials. In recent years, trifluoromethyl (CF3) groups have gradually received widespread attention. The reason is that the presence of trifluoromethyl can significantly improve the physical, chemical and biological properties of the parent molecule, such as lipophilicity, solubility, and metabolic stability [4], [5], [6]. According to reports, 20% of medicines and 30% of pesticides contain at least one fluorine atom [7], [8], [9], [10], among which trifluoromethyl-containing compounds account for a large proportion [11]. For example, fluvoxamine and fluoxetine can be used to treat depression[12], [, 13], sitagliptin can be used to treat diabetes [14], mefloquine can be used to treat malaria [15]. However, almost all organic molecules containing trifluoromethyl groups are artificially synthesized, which makes it important to develop new, efficient and feasible trifluoromethylation methods.

The structure of the title compound was elucidated by spectroscopic method and X-ray diffraction. There are two crystallographically independent molecules in the asymmetric unit (see the Figure). All bond lengths and angles in the crystal structure are within the normal range [16]. The crystal structure shows that the molecules are stabilized by intermolecular N1–H…O3 (distance = 2.832 Å) and N1–H…O3 (distance = 2.839 Å) hydrogen bonds, forming dimers (see the Figure). The intermolecular packing is stabilized by van der Waals forces. In addition to the afore-described interactions, it is worth noting that the crystal packing is further stabilized by one weak π-π stacking interaction. The distance of two Pyrrole rings of two molecules was found to be 3.691 Å.


Corresponding authors: Chun-Shen Zhao, Guizhou Engineering Laboratory for Synthetic Drugs, Guiyang, 550025, P. R. China; School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, P. R. China; and Key Laboratory of Guizhou for Fermentation Engineering and Biomedicine, Guiyang, 550025, P. R. China, E-mail: ; and Hui-Fang Chai, School of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, P. R. China, E-mail:

Funding source: Guizhou University

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

  2. Research funding: Guizhou University of Traditional Chinese Medicine 2018 annual academic new seedling cultivation and innovation exploration special project cultivation project plan. Qiankehe platform talent (2018)5766–14).

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

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Received: 2020-12-16
Accepted: 2021-01-18
Published Online: 2021-02-01
Published in Print: 2021-05-26

© 2021 De-Zheng Yang et al., published by De Gruyter, Berlin/Boston

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

Artikel in diesem Heft

  1. Frontmatter
  2. New Crystal Structures
  3. The crystal structure of bis(μ2-5-chloro-2-oxido-N-(1-oxidoethylidene)benzohydrazonato-κ5N,O,O′:N′,O′′)hexkis(pyridine-κ1N)trinickel(II) - pyridine (1/1), C63H57Cl2N13Ni3O6
  4. Crystal structure of [(μ2-succinato κ3O,O′:O′′)-bis-(5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclotetradecane)]dinickel(II)] diperchlorate, dihydrate C36H82Cl2N8Ni2O15
  5. Crystal structure of catena-poly[aquabis(3-nitrobenzoato-κ2O:O′)-(μ2-pyrazine-N: N′)cadmium(II)], C18H14N4O9Cd
  6. Crystal structure of 4-(2,2-difluoroethyl)-2,4,6-trimethylisoquinoline-1,3(2H,4H)-dione, C14H15F2NO2
  7. The crystal structure of thioxanthen-9-one-10,10-dioxide, C13H8O3S – a second polymorph
  8. Crystal structure of (E)-2-((2-methoxy-3-pyridyl)methylene)-7-fluoro-3,4-dihydronaphthalen-1(2H)-one, C17H14FNO2
  9. The crystal structure of diaquahydrogen 2,5-dimethylbenzenesulphonate, C8H14O5S
  10. The crystal structure of N-(4-(cyclohexylimino)pent-2-en-2-yl)cyclohexanamine, C17H30N2
  11. The twinned crystal structure of 1,3-phenylenedimethanaminium dibromide, C8H14Br2N2
  12. Crystal structure of 2,4,7,9-tetranitro-10H-benzofuro[3,2-b]indole – dimethyl sulfoxide (1/1), C16H11N5O10S
  13. Crystal structure of 2,6-bis(2-(pyridin-3-yl)ethyl)pyrrolo[3,4-f]isoindole-1,3,5,7(2H,6H)-tetraone, C24H18N4O4
  14. The crystal structure of 3,4-dichlorobenzoic acid chloride, C7H3Cl3O
  15. Crystal structure of 1,1′-(1,4-phenylenebis(methylene))bis(pyridin-1-ium) bis(1,2-dicyanoethene-1,2-dithiolato-k2S:S)zinc(II), C26H18N6ZnS4
  16. Crystal structure of tetrakis(μ-naphthalene-1-carboxylato-κ2O,O′)bis(methanol)copper(II), C46H36Cu2O10
  17. Crystal structure of 9-methyl-3-methylene-1,2,3,9-tetrahydro-4H-carbazol-4-one, C14H13NO
  18. Crystal structure of bis(amino(carbamothioylamino)methaniminium) 3-nitrophthalate monohydrate, C12H19N9O7S2
  19. Crystal structure of 3,3′-(1,2-phenylene-bis(methylene))bis(1-ethyl-1H-imidazol-3-ium) bis(hexafluorophosphate), C18H24F12N4P2
  20. The crystal structure of 5-hydroxy-6,8-dimethoxy-2-methyl-4H-benzo[g]chromen-4-one– rubrofusarin B, C16H14O5
  21. The crystal structure of bis(ethanol-kO)- bis(6-aminopicolinato-k2N,O)manganese(II), C16H22O6N4Mn
  22. The crystal structure of 3,3′-((carbonylbis(azanediyl))bis(ethane-2,1-diyl)) bis(1-methyl-1H-benzo[d]imidazol-3-ium) tetrafluoroborate monohydrate, C21H28N6O3B2F8
  23. Crystal structure of dimethanol-dichlorido-bis( μ2-2-(((1,5-dimethyl-3-oxo-2- phenyl-2,3-dihydro-1H-pyrazol-4-yl)imino)methyl)phenolato- κ4O:O,O′,N)dinickel (II), C20H24ClNiN3O4
  24. The crystal structure of methyl 5-(trifluoromethyl)-1H-pyrrole-2-carboxylate, C7H6F3NO2
  25. Crystal structure of (OC‐6‐13)‐aqua‐tris (3‐bromopyridine‐κ1N)‐bis(trifluoroacetato‐κ1O)cadmium(II) C19H14Br3CdF6N3O5
  26. Crystal structure of methyl (E)-3-(4-(2-ethoxy-2-oxoethoxy)phenyl) acrylate, C14H16O5
  27. Crystal structure of methyl 4-acetoxy-3,5-dimethoxybenzoate, C12H14O6
  28. The crystal structure of 2-(1H-benzimidazol-2-yl)-3-bromo-5-chlorophenol, C13H8BrClN2O
  29. The crystal structure of bis(μ2-5-chloro-N-(2-methyl-1-oxidopropylidene)-2-oxidobenzohydrazonate-κ5N,O,O′:N′,O′′)pentakis(pyridine-κ1N)tricopper(II), C47H45Cl2N9Cu3O6
  30. Synthesis and crystal structure of catena-poly[aqua-bis(nitrato-κ2O:O′)- (μ2-((1 H-imidazol-1-yl)methyl)benzene-κ2 N,N′)-H2O-κ2O]cadmium(II), C14H16N6O7Cd
  31. The crystal structure of pentakis(carbonyl)-{μ-[2,3-bis(sulfanyl)propan-1-olato]}-(triphenylphosphane)diiron (FeFe)C26H21Fe2O6PS2
  32. Crystal structure of ethyl-2-(3-benzoylthioureido)propanoate, C13H16N2O3S
  33. Crystal structure of 2-methoxy-4b,5,14,15-tetrahydro-6H-isoquinolino[2′,1′:1,6] pyrazino[2,3-b]quinoxaline, C19H18N4O
  34. Crystal structure of 2,2′-[ethane-1,2-diylbis(azanylylidenemethylylidene)]bis(6-chlorophenol), C16H14Cl2N2O2
  35. The crystal structure of (Z)-3-((2-(2-(2-aminophenoxy)ethoxy)phenyl)amino)-1-phenylbut-2-en-1-one, C24H24N2O3
  36. The crystal structure of 10-(3,5-di(pyridin-4-yl)phenyl)-10H-phenoxazine dihydrate, C28H23N3O3
  37. Crystal structure of poly[dipoly[aqua-di(µ2-pyrazin-2-olato-κ2N:N′) zinc(II)], C8H8N4O3Zn
  38. Crystal structure of poly[tetra(μ2-cyanido-κ2N:O)-bis(N,N-dimethylformamide-κO)-manganese(II)-platinum(II)], C10H14MnN6O2Pt
  39. The crystal structure of aqua-chlorido-6,6′-((ethane-1,2-diylbis(azaneylylidene))bis(methaneylylidene))bis(2,4-dichlorophenolato-κ4N,N′,O,O′)manganese(III), C16H12Cl5MnN2O3
  40. Crystal structure of [di(µ2-cyanido)-dicyanido-bis(dimethyl sulfoxide-κO)- bis(2,2′-(ethane-1,2-diylbis(azanylylidenemethanylylidene))diphenolato-κ4,N,N′,O,O′)- dimanganese(III)-platinum(II)], C40H40Mn2N8O6PtS2
  41. The crystal structure of (azido)-κ1N-6,6′-((cyclohexane-1,2-diylbis(azanylylidene)) bis(methanylylidene))bis(3-bromophenolato-κ4N,N,O,O)-(methanol)-manganese(III)–methanol(1/1), C22H26Br2MnN5O4
  42. Crystal structure of 7-chloro-N-(4-iodobenzyl)-1,2,3,4-tetrahydroacridin-9-amine, C20H18ClIN2
  43. Crystal structure of catena-poly[(1,4,8,11-tetraazacyclotetradecane-κ4N,N,N,N′′′)-bis(μ2-thiocyanato-κ2N:S)-bis(thiocyanato-κS)-nickel(II)palladium(II)], C14H24N8NiPdS4
  44. Crystal structure of 3-chloro-4-(4-ethylpiperazin-1-yl)aniline monohydrate, C12H20ClN3O
  45. Crystal structure of the 2D coordination polymer poly[diaqua-bis(μ2-3- methoxyisonicotinato-κ2N:O)cobalt(II)] — dimethylformamide (1/1), C20H30CoN4O10
  46. Crystal structure of 4-[(5-chloro-2-hydroxybenzylidene)amino]-3-propyl-1H-1,2,4-triazole-5(4H)-thione, C12H13ClN4OS
  47. Crystal structure of N-(5-(2-(benzyl(1-(4-methoxyphenyl)propan-2-yl)amino)-1-hydroxyethyl)-2-(benzyloxy)phenyl)formamide, C33H36N2O4
  48. Crystal structure of 3-(methoxycarbonyl)-7-oxabicyclo[2.2.1]heptane-2-carboxylic acid, C9H12O5
  49. The crystal structure of 1-((dimethylamino)(3-nitrophenyl)methyl)naphthalen-2-ol, C19H18N2O3
  50. Crystal structure of catena-poly[di(μ2-cyanido-κ2C:N)-dicyanido-tetrakis(dimethyl sulfoxide-κO)-manganese(II)-platinum(II)], C12H24MnN4O4PtS4
  51. Crystal structure of 4-amino-N-(2-pyrimidinyl)benzenesulfonamide–1,4-dioxane (1/1), C14H18N4O4S
  52. Crystal structure of bis{1-[(benzotriazol-1-yl)methyl]-1H-1,3-(2-methyl-imidazol)}di-chloridomercury(II), [Hg(C11H11N5)2Cl2], C22H22N10Cl2Hg
  53. Crystal structure of 2, 3-bis((4-methylbenzoyl)oxy) succinic acid–N, N-dimethylformamide (1/1), C23H25NO9
  54. Crystal structure of catena-poly[bis(4-(4-carboxyphenoxy)benzoato-κ1O)-μ2-(1,4-bis(1-imidazolyl)benzene-κ2N:N′)cobalt(II)], C40H28N4O10Co
  55. Crystal structure of 1H-imidazol-3-ium poly[aqua-(μ4-glutarato-κ6O,O′:O′:O′′,O′′′:O′′′)-(nitrato-κ2O,O′)strontium(II)], C8H13N3O8Sr
  56. Crystal structure of (R)-6-(benzo[b]thiophen-5-yl)-2-methyl-2,6-dihydrobenzo [5,6] silino[4,3,2-cd]indole, C23H17NSSi
  57. Crystal structure of catena-poly[bis(μ2-thiocyanato-κ2N:S)-(2-(5-methyl-1H-pyrazol-3-yl)pyridine-κ2N,N′)cadmium(II)]–dioxane (1/1), C15H17CdN5O2S2
  58. Crystal structure of poly[aqua-(μ2-1,4-bis(2′-carboxylatophenoxy)benzene-κ2O:O′)-(μ2-4,4′-bipyridione-κ2N:N′)cadmium(II)] monhydrate, C30H22CdN2O7⋅H2O
  59. Crystal structure of catena-poly[tetraaqua-(μ2-4,4′-bipyridine-k2N:N′)-bis(μ2-4′-methyl-[1,1′-biphenyl]-3,5-dicarboxylato-k4O,O′:O″,O′″)dicadmium(II)] dihydrate, C20H20NO7Cd
  60. Crystal structure of 1‐tert‐butyl‐3‐(2,6‐diisopropyl‐4‐phenoxyphenyl)‐2-methylisothiourea, C24H34N2OS
  61. Crystal structure of catena-poly[triaqua-(μ2-1,3-di(1H-imidazol-1-yl)propane-κ2N:N′)-(4,4′-(1H-1,2,4-triazole-3,5-diyl)dibenzoato-κ1O)cobalt(II)] — N,N′-dimethylformamide (1/1), C28H34N8O8Co
  62. Crystal structure of tetraaqua-bis(1,4-di(1H-imidazol-1-yl)benzene-κ1N)manganese(II) 2,3-dihydroxyterephthalate, C32H32MnN8O10
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