Home The crystal structure of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one, C17H12FN3O
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The crystal structure of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one, C17H12FN3O

  • Hang-Cheng Ni EMAIL logo , Min Zhao , Wen-An Li , Zhen-Xiang Liu ORCID logo , Ling-Li Shao and Miao-Miao Chen
Published/Copyright: August 1, 2024
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Zeitschrift für Kristallographie - New Crystal Structures
From the journal Zeitschrift für Kristallographie - New Crystal Structures Volume 239 Issue 5

Abstract

C17H12FN3O, orthorhombic, Pbca (no. 61), a = 14.7608(7) Å, b = 7.2802(4) Å, c = 24.4842(13) Å, V = 2,631.1(2) Å3, Z = 8, R gt (F) = 0.0900, wR ref (F2) = 0.1841, T = 170 K.

CCDC no.: 2356296

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: Colourless needle
Size: 0.16 × 0.05 × 0.03 mm
Wavelength: Ga Kα radiation (1.34139 Å)
μ: 0.55 mm−1
Diffractometer, scan mode: Bruker D8 Venture, φ and ω
θmax, completeness: 60.6°, >99 %
N(hkl)measured, N(hkl)unique, Rint: 35,195, 2,942, 0.101
Criterion for Iobs, N(hkl)gt: 2,184
N(param)refined: 200
Programs: SHELX, 1 , 2 Diamond, 3 Olex2 4
Table 2:

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

Atom x y z Uiso*/Ueq
F1 0.68276 (14) 0.3525 (3) 0.07452 (8) 0.0334 (6)
O1 0.94911 (14) 0.7494 (3) 0.35277 (9) 0.0243 (6)
N1 0.71291 (17) 0.6754 (4) 0.32795 (10) 0.0173 (6)
C1 0.5860 (2) 0.7586 (5) 0.38344 (13) 0.0206 (7)
H1 0.546862 0.727991 0.354016 0.025*
N2 0.83105 (17) 0.7873 (4) 0.41100 (10) 0.0164 (6)
C2 0.5498 (2) 0.8176 (5) 0.43244 (13) 0.0228 (7)
H2 0.486042 0.827756 0.436662 0.027*
N3 0.92398 (18) 0.4840 (4) 0.20256 (11) 0.0231 (6)
H3 0.973187 0.449892 0.184977 0.028*
C3 0.6074 (2) 0.8621 (5) 0.47573 (13) 0.0231 (7)
H3A 0.582123 0.900087 0.509585 0.028*
C4 0.7007 (2) 0.8518 (5) 0.47015 (13) 0.0206 (7)
H4 0.739271 0.883258 0.499778 0.025*
C5 0.7374 (2) 0.7944 (4) 0.42014 (12) 0.0166 (7)
C6 0.6804 (2) 0.7437 (4) 0.37678 (13) 0.0169 (7)
C7 0.8008 (2) 0.6700 (4) 0.32002 (12) 0.0165 (7)
C8 0.8670 (2) 0.7389 (4) 0.36154 (13) 0.0179 (7)
C9 0.8931 (2) 0.8421 (5) 0.45489 (13) 0.0231 (7)
H9A 0.882586 0.971297 0.464237 0.035*
H9B 0.955810 0.826383 0.442633 0.035*
H9C 0.882308 0.765399 0.487128 0.035*
C10 0.8336 (2) 0.5937 (4) 0.26894 (12) 0.0171 (7)
C11 0.9218 (2) 0.5550 (5) 0.25400 (13) 0.0201 (7)
H11 0.973418 0.574955 0.276368 0.024*
C12 0.8367 (2) 0.4739 (4) 0.18233 (13) 0.0191 (7)
C13 0.7774 (2) 0.5389 (4) 0.22290 (12) 0.0175 (7)
C14 0.6838 (2) 0.5369 (5) 0.21243 (13) 0.0197 (7)
H14 0.642080 0.578940 0.239201 0.024*
C15 0.6533 (2) 0.4726 (5) 0.16242 (13) 0.0226 (7)
H15 0.590255 0.469167 0.154598 0.027*
C16 0.7159 (2) 0.4130 (5) 0.12373 (13) 0.0233 (7)
C17 0.8077 (2) 0.4114 (5) 0.13159 (13) 0.0234 (7)
H17 0.848727 0.370414 0.104291 0.028*

1 Source of materials

The 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one was obtained through an economic iron chloride catalyzed oxidative cross-coupling approach. In detail, a Schlenk-tube equipped with a magnetic stir bar was charged with 1-methylquinoxalin-2(1H)-one (0.5 mmol, 80.0 mg) and 6-fluoro-1H-indole (1.0 mmol, 135.1 mg). FeCl3 solution (0.01 mmol/mL in CH3CN, 5 mL) and di-tert-butyl peroxide (DTBP, 1.0 mmol, 184.1 μL) were added. Then, the reaction mixture was stirred at 30 °C for 24 h. After that, the resulting mixture was analyzed by HPLC, and the mixture was filtered to give the pure yellow product 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one (92.8 mg) in a 63 % yield. 1H NMR (400 MHz, DMSO‑d6) δ 11.81 (s, 1H), 8.97–8.82 (m, 2H), 7.89 (d, J = 7.9 Hz, 1H), 7.52 (t, J = 2.8 Hz, 2H), 7.37 (s, 1H), 7.30 (d, J = 9.7 Hz, 1H), 7.07 (t, J = 9.3 Hz, 1H), 3.71 (d, J = 2.0 Hz, 3H). 13C NMR (101 MHz, DMSO‑d6) δ 159.25 (d, J = 236.4 Hz), 153.55, 150.30, 136.40 (d, J = 12.5 Hz), 133.73 (d, J = 2.6 Hz), 132.82, 131.58, 128.43, 128.42, 124.14 (d, J = 9.6 Hz), 123.42, 123.01, 114.43, 111.45, 109.07 (d, J = 23.4 Hz), 98.06 (d, J = 25.7 Hz), 29.08. HRMS (ESI): m/z calcd. for C17H12N3OF[M+H]+: 294.1043. Found: 294.1046.

Preparing of crystals of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one: dissolve the compound (5.0 mg) in ethyl acetate to obtain a pale-yellow transparent solution. Allow the solution to stand at room temperature and let it evaporate naturally. Transparent block crystals will form at the bottom of the vessel, which are the single crystals of the described compound.

2 Experimental details

After absorption correction, the crystal structure was solved using the Olex2 software 1 and the programs SHELXT 2 program and refined with SHELXL 3 and the molecular graphics were drawn by using DIAMOND software. 4 All hydrogens were generated geometrically (C–H bond fixed at 0.96 Å), assigned isotropic thermal parameters, and allowed to ride on their parent carbon atoms before the final cycle of refinement.

3 Comment

Fluorinated compounds, distinguished by their unique physical, chemical, and physiological properties, have been extensively leveraged across a myriad of sectors, notably within the pharmaceuticals, agricultural, materials, and electronics industries. 5 , 6 , 7 The application of fluorinated compounds within the realm of medicinal chemistry has been marked by their unique impact on the bioavailability, metabolic stability, and target specificity of therapeutic agents, thereby significantly advancing the development of novel pharmaceuticals.

Quinoxalinones represent a prominent class of heterocyclic compounds, with a broad spectrum of applications in the fields of medicinal chemistry and the development of advanced functional materials. 8 , 9 , 10 , 11 , 12 Specifically, the subclass of 3-(indol-3-yl)quinoxalin-2-one derivatives, which integrates both a quinoxalinone framework and an indole moiety, has demonstrated remarkable biological activities, such as potent antibacterial effects, inhibition of platelet aggregation, and a suppression of human tumor cell proliferation. 13 , 14 , 15 Traditionally, Brønsted acids have been utilized as catalysts for the cross-coupling of quinoxalinones with indoles, typically under elevated temperature conditions. 16 Additionally, molecular iodine has been recognized for its efficacy in facilitating this reaction. 17 The emergence of electrochemical and photochemical approaches has introduced innovative methodologies into the reaction system. 18 , 19 , 20 , 21

In this study, we present the single-crystal structure of a novel fluorinated derivative of 3-(indol-3-yl)quinoxalin-2-one, which could hold significant implications for its application across the pharmaceutical, agricultural, materials, and electronics industries.

The newly formed C–C single bond in the structure connects two rigid rings, and with the exception of the two hydrogen atoms on the methyl group, almost all atoms lie in the same plane along the a-axis direction. Geometric parameters are all in the expected ranges. The oxygen atom of each molecule forms a zigzag one-dimensional chain structure through hydrogen bonding interactions with the hydrogen H3 a (a = 2 − x, 0.5 + y, 0.5 − z) on the nitrogen of adjacent molecules, denoted as N3–H3⋯O1. Furthermore, the fluorine atom on the molecule simultaneously interacts with the hydrogen H2 b on the benzene carbon C2 and the hydrogen H9c c on the methyl group of two other adjacent quinolone molecules, where (b = 1 − x, −0.5 + y, 0.5 − z, c = 1.5 − x, 1 − y, −0.5 + z), resulting in a three-dimensional supramolecular architecture.

Corresponding author: Hang-Cheng Ni, Pharmaceutical College, Jinhua Polytechnic, Zhejiang, 321017, P.R. China, E-mail:

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

  2. Research funding: This research was supported by Zhejiang Provincial Natural Science Foundation of China under Grant No. LQ20B010005 and the Scientific Research Project of Jinhua Advanced Research Institute (GYY202105).

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

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Received: 2024-05-31
Accepted: 2024-07-11
Published Online: 2024-08-01
Published in Print: 2024-10-28

© 2024 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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  52. The crystal structure of (E)-4-(2-(pyridin-4-ylmethylene)hydrazine-1-carbonyl)pyridin-1-ium-2-olate dihydrate, C12H14N4O4
  53. The crystal structure of 6-amino-pyridinium-2-carboxylate, C6H6N2O2
  54. The crystal structure of catena-poly[aqua-nitrato-κ3O,O:O′′-(1,10-phenanthroline-κ2N,N′)sodium(I)], C24H18N6O7Na2
  55. Retractions
  56. Retraction of: Crystal structure of bis[diaquaisonicotinatosamarium(III)]-µ-isonicotinato-[diisonicotinatocopper(II)], CuSm2(C6H4NO2)8(H2O)4
  57. Retraction of: Crystal structure of aqua(2,2′-bipyridine-k 2 N:N′)(nitrato)-(4-aminobenzoato)cadmium(II) nitrate, [Cd(H2O)(NO3)(C10H8N2)(C7H7NO2)][NO3]
https://doi.org/10.1515/ncrs-2024-0234
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Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Editorial 2024 – New developments and changes of Zeitschrift für Kristallographie – New Crystal Structures
  4. New Crystal Structures
  5. Hydrogen bonding and π⋅⋅⋅halogen interactions in the crystal structure of bis(theophyllinium) hexachloridoplatinate(IV) monohydrate
  6. The crystal structure of 6-amino-2-carboxypyridin-1-ium perchlorate, C6H7ClN2O6
  7. Crystal structure of poly[(μ4-(3-amino-1H-1,2,4-triazol-1-yl)benzene-1,3-dicarboxylato-κ 4 N:O:O':O')(1-methylpyrroldin-2-one-κ1O)dicopper(II)] – 1-methylpyrroldin-2-one (1/3), C40H48Cu2N12O12
  8. The crystal structure of 18-crown-6-k6O6(2,4,5-trinitroimidazol-1-ido-k1O)potassium(I)
  9. Crystal structure of poly[tetraaqua-bis(μ2-5-bromoisophthalato-κ3O,O′:O″)-(μ2-1,5-bis(imidazol-2-methyl)pentane-κ2N:N′)dicadmium(II)] dihydrate
  10. Crystal structure of (5R,6S,E)-5-acetoxy-2-methyl-6-((2aR,3R,5aS,5bS,11aR,12aS)-2a,5a,8,8-tetramethyl-9-oxotetradecahydro-1H,12H-cyclopenta[a]cyclopropa[e]phenanthren-3-yl)hept-2-enoic acid, C32H48O5
  11. The crystal structure of poly[diaqua-bis(μ2 -thiocyanato-κ2N:O)cobalt(II) monohydrate
  12. The crystal structure of 1,3,5-tri(1H-imidazol-1-yl)benzene–2,3,5,6-tetrachlorobenzene-1,4-dicarboxylic acid (1/1)
  13. Crystal structure of dichlorido-bis(1-[(2-ethyl-benzimidazole-1-yl)methyl]-1H–benzotriazole) cadmium(II), C32H32CdN10OCl2
  14. The crystal structure of N′-(tert-butyl)-N′-(3,5-dimethylbenzoyl)-3-methoxy-N,2-dimethylbenzohydrazide, C23H30N2O3
  15. Crystal stucture of 3-benzamido-N-(2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)-2-fluorobenzamide
  16. Crystal structure of bis(μ-benzeneselenolato)-(tetracarbonyl)-{μ-[N-(diphenylphosphanyl)-N-(3-ethynylphenyl)-P,P-diphenylphosphinous amide]} diiron, C48H35Fe2NO4P2Se2
  17. The crystal structure of 2′-(p-tolyl)-4′H-spiro[isochromane-1,1′-naphthalene]-3,4′-dione, C25H18O3
  18. The crystal structure of poly[hexaqua-tetrakis(μ4-pyridine-2,4-dicarboxylate-κ5N: O: O′: O″: O‴)-bi(μ2-pyridine-2,4-dicarboxylate-κ3N: O: O′)-digadolinium(III)tricopper (II)], [Gd2Cu3(C7H3NO4)6(H2O)6] n
  19. Crystal structure of poly[bis(4-(4-(pyridin-4-yl)phenyl)pyridin-1-ium-κ1N)-(μ4-benzene-1,2,4,5-tetracarboxylato-κ5O:O′: O″:O‴:O⁗)-(μ2-2,5-dicarboxyterephthalato-κ2O:O′)dizinc(II)], C52H32N4O16Zn2
  20. The crystal structure of 4-(3-carboxy-1-ethyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)piperazin-1-ium 2-carboxy-6-nitrobenzoate monohydrate, C24H25FN4O10
  21. Crystal structure of dichlorido-(1-((3,5-dimethyl-2,3-dihydro-1H-1,2,3-triazol-1-yl)methyl)-1H-benzo[d][1,2,3]triazole-k1N)zinc(II), C22H24ZnN12Cl2
  22. The crystal structure of (3-chlorothiophene-2-carboxylato-κ2O, O′)-(2,2′-dipyridyl-κ2N,N′)lead(II), C20H12Cl2N2O4S2Pb
  23. Synthesis and crystal structure of (Z)-4-((1-(3-fluorophenyl)-1H-1,2,3-triazol-4-yl)methylene)-5-methyl-2-phenyl-2,4-dihydro-3H-pyrazol-3-one, C19H14FN5O
  24. The crystal structure of the coordination compound catena-poly[(18-crown-6-ether-κ6O6)(4,5-dinitroimidazolato-κ1O)potassium(I)]
  25. Crystal structure of 7-(diethylamino)-3-(trifluoroacetyl)-2H-chromen-2-one, C15H14F3NO3
  26. Crystal structure of dichlorido-1-[(2-ethylimidazole-1-yl)methyl]-1H–benzotriazole κ1N zinc(II), C24H26ZnN10Cl2
  27. Crystal and molecular structure of 5-bromopyridine-2,3-diamine
  28. Crystal structure of catena-poly[bis(μ2-1-(3-carboxyphenyl)-5-methyl-4-oxo-1,4-dihydropyridazine-3-carboxylato-k3-O,O′:O″)hexaqua-dicobalt tetrahydrate], C26H36N4O20Co2
  29. Crystal structure of thiocyanate-κ1N-bis(μ1-2,6-diformyl-4-methylphenol oxime-κ2N,O)-manganese(III) acetonitrile solvate, C21H21MnN6O6S
  30. The crystal structure of pyrrolidin-1-yl pivalate, C9H13NO4
  31. The crystal structure of 2,2′-(2,2-diphenylethene-1,1-diyl)bis(1,4-dimethoxybenzene), C30H28O4
  32. Crystal structure of bis(benzyltrimethylammonium) tetrathiotungstate(VI), {(C6H5CH2)(CH3)3N}2[WS4]
  33. The crystal structure of ethyl (Z)-2-(ethoxymethylene)-3-oxobutanoate, C9H14O4
  34. The crystal structure of (E)-6-bromo-3,5-dimethyl-2-(1-phenylprop-1-en-2-yl)-3Himidazo[4,5b]pyridine, C17H16BrN3
  35. Crystal structure of (3S,3′S,4R,4′S)-3′-(furan-3-yl)-3-hydroxy-4′-methyl-3,5,6′,7′-tetrahydro-1H,3′H-4,5′-spirobi[isobenzofuran]-1,1′(4′H)-dione-methanol (1/1), C21H22O7
  36. Cocrystal structure of progesterone-isophthalic acid, C25H33O4
  37. The crystal structure of 3-(6-fluoro-1H-indol-3-yl)-1-methylquinoxalin-2(1H)-one, C17H12FN3O
  38. Crystal structure of S-(4-carboxybutyl)- l -cysteine
  39. The cocrystal of 2,2′-(hydrazine-1,1-diyl)bis(1H-imidazole-4,5-dicarbonitrile)– methanol (2/3)
  40. Crystal structure of (1′R,2′S,4′R,6′S)-4,6-dihydroxy-1′,8′,8′-trimethyl-3-(3-methylbutanoyl)-4′,8′,6′,1′,7,2′-hexahydro-1H-4′,6′-methanoxanthene-8-carbaldehyde, C23H30O5
  41. Crystal structure of (3,6-di(2-pyridyl)-4-methylphenyl pyridazine-k 2 N,N′)-bis(1-phenyl-pyrazole-κ 2 C,N) iridium(III) hexafluorophosphate, C39H29F6IrN8P
  42. Crystal structure of 1,5-bis[(E)-1-(2-hydroxyphenyl)ethylidene]thiocarbonohydrazide dimethyl sulfoxide monosolvate, C17H18N4O2S·C2H6OS
  43. Crystal structure of (S)-4-(2-(4-(2-acetyl-5-chlorophenyl)-3-methoxy-6-oxopyridazin-1(6H)-yl)-3-phenylpropanamido)benzoic acid monohydrate, C29H26ClN3O7
  44. The crystal structure of 1,3-bis(2,4-dinitro-1H-imidazol-1-yl)propane
  45. Crystal structure of 4-chlorobenzyl (S)-2-(6-methoxynaphthalen-2-yl)propanoate, C21H19ClO3
  46. Crystal structure of 1-(5-(benzo[d][1,3]dioxol-5-yl)-4-benzyl-1-(4-bromophenyl)-4,5-dihydro-1H-1,2,4-triazol-3-yl)ethan-1-one, C24H20BrN3O3
  47. The crystal structure of (Z)-3′-(2-(1-(3,4-dimethyl-phenyl)-3-methyl-5-oxo-1,5-dihydro-4H-pyrazol-4-ylidene)hydrazinyl)-2′-hydroxy-[1,1′-biphenyl]-3-carboxylicacid ─ methanol (1/1), C26H26N4O5
  48. Crystal structure of (S)-1-phenylpropan-1-aminium (S)-(1-phenylpropyl)carbamate C19H26N2O2
  49. Synthesis and crystal structure of methyl 2-((5-bromo-4-(4-cyclopropylnaphthalen-1-yl)-4H-1,2,4-triazol-3-yl)thio)acetate, C18H16BrN3O2S
  50. The crystal structure of trichlorobis(pyridine-2,6-dithio-κS-carbomethylamido)antimony(III), [SbCl3(C9H11N3S2)2]
  51. Crystal structure of 1,8-dihydroxy-3-{[(triphenylstannyl)oxy]carbonyl} anthracene-9,10-dione, C33H22O6Sn
  52. The crystal structure of (E)-4-(2-(pyridin-4-ylmethylene)hydrazine-1-carbonyl)pyridin-1-ium-2-olate dihydrate, C12H14N4O4
  53. The crystal structure of 6-amino-pyridinium-2-carboxylate, C6H6N2O2
  54. The crystal structure of catena-poly[aqua-nitrato-κ3O,O:O′′-(1,10-phenanthroline-κ2N,N′)sodium(I)], C24H18N6O7Na2
  55. Retractions
  56. Retraction of: Crystal structure of bis[diaquaisonicotinatosamarium(III)]-µ-isonicotinato-[diisonicotinatocopper(II)], CuSm2(C6H4NO2)8(H2O)4
  57. Retraction of: Crystal structure of aqua(2,2′-bipyridine-k 2 N:N′)(nitrato)-(4-aminobenzoato)cadmium(II) nitrate, [Cd(H2O)(NO3)(C10H8N2)(C7H7NO2)][NO3]
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