organic compounds
N-Cyclohexyl-2-(5-fluoro-1H-indol-3-yl)-2-oxoacetamide
aSchool of Pharmacy, Tianjin Medical University, Tianjin 300070, People's Republic of China, bMedical College of Chinese People's Armed Police Forces, Tianjin 300162, People's Republic of China, and cTianjin Key Laboratory for Biomarkers of Occupational, and Environmental Hazards, Tianjin 300162, People's Republic of China
*Correspondence e-mail: tjch2010@yahoo.cn
In title compound, C16H17FN2O2, the cyclohexane ring adopts a chair conformation.. The crystal packing is stabilized by weak π–π stacking interactions [centroid–centroid distance = 3.503 (5) Å] and intermolecular C—H⋯O, N—H⋯O and N—H⋯F hydrogen-bond interactions.
Related literature
For the biological activity of the title compound and its derivatives, see: Souli et al. (2008); Chai et al. (2006); Radwan et al. (2007); Karthikeyan et al. (2009). For the preparation, see: Bacher et al. (2001). For bond-length and angle data for similar structures, see: Liu et al. (2011); Sonar et al. (2006).
Experimental
Crystal data
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Refinement
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Data collection: CrystalClear (Rigaku, 2005); cell CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.
Supporting information
10.1107/S1600536811024299/hg5056sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811024299/hg5056Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811024299/hg5056Isup3.cml
The target compound was synthesized by two steps. Oxalyl chloride was added dropwise to 5-fluorine indole in dry ether. 5-fluorine indole-3-yl-glyoxyl chloride which was the crude product, cyclohexane, two drops of triethylamine were in dry dichloromethane. The reaction mixture was washed with water and dried over Na2SO4 and concentrated in vacuo (Bacher et al., 2001). The residue was resolved in a methanol solution. Slow evaporation over two week at room temperature gave light-white crystals suitable for X-ray analysis.
All C H atoms were found on difference maps, with C—H = 0.95–1.00 Å and H atoms bonded N were refined freely with N—H = 0.90 and 0.94 Å and included in the final cycles of
using a riding model, with Uiso(H) = 1.2Ueq(C) for aryl and methylene H atoms.Data collection: CrystalClear (Rigaku, 2005); cell
CrystalClear (Rigaku, 2005); data reduction: CrystalClear (Rigaku, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).Fig. 1. View of the title compound, with displacement ellipsoids drawn at the 40% probability level. |
C16H17FN2O2 | F(000) = 608 |
Mr = 288.32 | Dx = 1.393 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 5346 reflections |
a = 11.5065 (15) Å | θ = 1.7–29.1° |
b = 9.7666 (12) Å | µ = 0.10 mm−1 |
c = 12.3139 (16) Å | T = 113 K |
β = 96.639 (5)° | Prism, colorless |
V = 1374.5 (3) Å3 | 0.20 × 0.16 × 0.12 mm |
Z = 4 |
Rigaku Saturn CCD area-detector diffractometer | 3717 independent reflections |
Radiation source: rotating anode | 3007 reflections with I > 2σ(I) |
Multilayer monochromator | Rint = 0.035 |
Detector resolution: 14.63 pixels mm-1 | θmax = 29.2°, θmin = 2.7° |
ω and ϕ scans | h = −15→15 |
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | k = −12→13 |
Tmin = 0.980, Tmax = 0.988 | l = −16→16 |
18432 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.037 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0605P)2] where P = (Fo2 + 2Fc2)/3 |
3717 reflections | (Δ/σ)max = 0.001 |
198 parameters | Δρmax = 0.27 e Å−3 |
0 restraints | Δρmin = −0.28 e Å−3 |
C16H17FN2O2 | V = 1374.5 (3) Å3 |
Mr = 288.32 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 11.5065 (15) Å | µ = 0.10 mm−1 |
b = 9.7666 (12) Å | T = 113 K |
c = 12.3139 (16) Å | 0.20 × 0.16 × 0.12 mm |
β = 96.639 (5)° |
Rigaku Saturn CCD area-detector diffractometer | 3717 independent reflections |
Absorption correction: multi-scan (CrystalClear; Rigaku, 2005) | 3007 reflections with I > 2σ(I) |
Tmin = 0.980, Tmax = 0.988 | Rint = 0.035 |
18432 measured reflections |
R[F2 > 2σ(F2)] = 0.037 | 0 restraints |
wR(F2) = 0.098 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.27 e Å−3 |
3717 reflections | Δρmin = −0.28 e Å−3 |
198 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes. |
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
F1 | −0.25500 (5) | 1.05586 (6) | 0.22558 (5) | 0.02199 (16) | |
O1 | 0.03563 (6) | 0.68310 (7) | 0.38752 (6) | 0.01933 (17) | |
O2 | 0.10442 (6) | 0.59789 (7) | 0.66261 (6) | 0.01922 (17) | |
N1 | −0.11616 (7) | 0.93484 (9) | 0.65153 (7) | 0.01534 (18) | |
N2 | 0.18874 (7) | 0.53328 (8) | 0.51269 (7) | 0.01509 (18) | |
C1 | −0.16319 (8) | 0.97805 (10) | 0.54839 (8) | 0.0138 (2) | |
C2 | −0.24187 (9) | 1.08328 (10) | 0.51989 (8) | 0.0164 (2) | |
H2A | −0.2737 | 1.1364 | 0.5739 | 0.020* | |
C3 | −0.27217 (8) | 1.10769 (10) | 0.40949 (8) | 0.0167 (2) | |
H3 | −0.3255 | 1.1788 | 0.3859 | 0.020* | |
C4 | −0.22354 (9) | 1.02687 (10) | 0.33359 (8) | 0.0156 (2) | |
C5 | −0.14663 (8) | 0.92118 (9) | 0.35915 (8) | 0.0140 (2) | |
H5 | −0.1162 | 0.8682 | 0.3042 | 0.017* | |
C6 | −0.11544 (8) | 0.89560 (9) | 0.47050 (8) | 0.01231 (19) | |
C7 | −0.03768 (8) | 0.79970 (10) | 0.53188 (7) | 0.01268 (19) | |
C8 | −0.04120 (8) | 0.83109 (9) | 0.64156 (8) | 0.0141 (2) | |
H8 | 0.0030 | 0.7858 | 0.7009 | 0.017* | |
C9 | 0.03360 (8) | 0.69899 (10) | 0.48630 (7) | 0.01308 (19) | |
C10 | 0.11288 (8) | 0.60472 (9) | 0.56399 (8) | 0.0135 (2) | |
C11 | 0.26943 (8) | 0.43341 (10) | 0.56915 (8) | 0.0150 (2) | |
H11 | 0.2231 | 0.3700 | 0.6112 | 0.018* | |
C12 | 0.36197 (9) | 0.50230 (11) | 0.64966 (9) | 0.0204 (2) | |
H12A | 0.3235 | 0.5562 | 0.7034 | 0.024* | |
H12B | 0.4092 | 0.5657 | 0.6099 | 0.024* | |
C13 | 0.44143 (10) | 0.39422 (12) | 0.70913 (9) | 0.0249 (3) | |
H13A | 0.5025 | 0.4399 | 0.7597 | 0.030* | |
H13B | 0.3948 | 0.3352 | 0.7530 | 0.030* | |
C14 | 0.49948 (9) | 0.30599 (11) | 0.62842 (9) | 0.0229 (2) | |
H14A | 0.5538 | 0.3632 | 0.5912 | 0.028* | |
H14B | 0.5457 | 0.2328 | 0.6688 | 0.028* | |
C15 | 0.40945 (9) | 0.24164 (10) | 0.54345 (9) | 0.0205 (2) | |
H15A | 0.3630 | 0.1735 | 0.5795 | 0.025* | |
H15B | 0.4503 | 0.1930 | 0.4884 | 0.025* | |
C16 | 0.32700 (8) | 0.34877 (10) | 0.48594 (8) | 0.0168 (2) | |
H16A | 0.3716 | 0.4100 | 0.4418 | 0.020* | |
H16B | 0.2659 | 0.3024 | 0.4358 | 0.020* | |
H1 | −0.1231 (12) | 0.9799 (14) | 0.7178 (12) | 0.043 (4)* | |
H2 | 0.1848 (11) | 0.5448 (12) | 0.4395 (11) | 0.027 (3)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
F1 | 0.0241 (3) | 0.0273 (3) | 0.0137 (3) | 0.0058 (3) | −0.0016 (2) | 0.0056 (2) |
O1 | 0.0251 (4) | 0.0224 (4) | 0.0100 (3) | 0.0067 (3) | 0.0000 (3) | −0.0008 (3) |
O2 | 0.0269 (4) | 0.0197 (4) | 0.0110 (3) | 0.0042 (3) | 0.0019 (3) | 0.0041 (3) |
N1 | 0.0181 (4) | 0.0177 (4) | 0.0103 (4) | −0.0015 (3) | 0.0018 (3) | −0.0032 (3) |
N2 | 0.0171 (4) | 0.0157 (4) | 0.0121 (4) | 0.0022 (3) | −0.0002 (3) | 0.0017 (3) |
C1 | 0.0145 (4) | 0.0148 (5) | 0.0118 (4) | −0.0030 (4) | 0.0008 (3) | −0.0013 (3) |
C2 | 0.0154 (5) | 0.0157 (5) | 0.0187 (5) | −0.0010 (4) | 0.0035 (4) | −0.0036 (4) |
C3 | 0.0141 (5) | 0.0144 (5) | 0.0214 (5) | 0.0009 (4) | 0.0011 (4) | 0.0006 (4) |
C4 | 0.0160 (5) | 0.0179 (5) | 0.0123 (5) | −0.0020 (4) | −0.0013 (3) | 0.0023 (4) |
C5 | 0.0153 (5) | 0.0148 (5) | 0.0119 (5) | −0.0015 (4) | 0.0013 (3) | −0.0011 (3) |
C6 | 0.0129 (4) | 0.0124 (4) | 0.0116 (4) | −0.0022 (4) | 0.0014 (3) | −0.0004 (3) |
C7 | 0.0143 (4) | 0.0132 (4) | 0.0102 (4) | −0.0028 (4) | 0.0002 (3) | 0.0004 (3) |
C8 | 0.0154 (4) | 0.0150 (5) | 0.0116 (5) | −0.0027 (4) | 0.0006 (3) | −0.0001 (3) |
C9 | 0.0149 (4) | 0.0136 (4) | 0.0102 (4) | −0.0024 (4) | −0.0006 (3) | 0.0005 (3) |
C10 | 0.0162 (5) | 0.0116 (4) | 0.0122 (4) | −0.0025 (4) | 0.0000 (3) | 0.0007 (3) |
C11 | 0.0148 (5) | 0.0143 (5) | 0.0154 (5) | 0.0006 (4) | −0.0010 (4) | 0.0022 (4) |
C12 | 0.0193 (5) | 0.0202 (5) | 0.0200 (5) | 0.0004 (4) | −0.0041 (4) | −0.0017 (4) |
C13 | 0.0211 (5) | 0.0283 (6) | 0.0230 (6) | 0.0024 (5) | −0.0071 (4) | 0.0016 (4) |
C14 | 0.0163 (5) | 0.0217 (5) | 0.0295 (6) | 0.0023 (4) | −0.0027 (4) | 0.0053 (4) |
C15 | 0.0173 (5) | 0.0164 (5) | 0.0277 (6) | 0.0010 (4) | 0.0020 (4) | 0.0012 (4) |
C16 | 0.0154 (5) | 0.0162 (5) | 0.0185 (5) | −0.0009 (4) | 0.0007 (4) | 0.0003 (4) |
F1—C4 | 1.3671 (11) | C7—C9 | 1.4358 (14) |
O1—C9 | 1.2291 (11) | C8—H8 | 0.9500 |
O2—C10 | 1.2313 (12) | C9—C10 | 1.5470 (13) |
N1—C8 | 1.3454 (13) | C11—C12 | 1.5249 (14) |
N1—C1 | 1.3874 (12) | C11—C16 | 1.5261 (14) |
N1—H1 | 0.939 (14) | C11—H11 | 1.0000 |
N2—C10 | 1.3324 (13) | C12—C13 | 1.5270 (14) |
N2—C11 | 1.4655 (12) | C12—H12A | 0.9900 |
N2—H2 | 0.905 (13) | C12—H12B | 0.9900 |
C1—C2 | 1.3877 (14) | C13—C14 | 1.5265 (16) |
C1—C6 | 1.4113 (13) | C13—H13A | 0.9900 |
C2—C3 | 1.3846 (14) | C13—H13B | 0.9900 |
C2—H2A | 0.9500 | C14—C15 | 1.5206 (14) |
C3—C4 | 1.3895 (14) | C14—H14A | 0.9900 |
C3—H3 | 0.9500 | C14—H14B | 0.9900 |
C4—C5 | 1.3723 (14) | C15—C16 | 1.5300 (13) |
C5—C6 | 1.3992 (13) | C15—H15A | 0.9900 |
C5—H5 | 0.9500 | C15—H15B | 0.9900 |
C6—C7 | 1.4466 (13) | C16—H16A | 0.9900 |
C7—C8 | 1.3901 (13) | C16—H16B | 0.9900 |
C8—N1—C1 | 109.38 (8) | N2—C11—C12 | 111.79 (8) |
C8—N1—H1 | 123.5 (9) | N2—C11—C16 | 110.02 (8) |
C1—N1—H1 | 126.2 (9) | C12—C11—C16 | 110.54 (8) |
C10—N2—C11 | 122.51 (8) | N2—C11—H11 | 108.1 |
C10—N2—H2 | 116.5 (8) | C12—C11—H11 | 108.1 |
C11—N2—H2 | 120.8 (8) | C16—C11—H11 | 108.1 |
N1—C1—C2 | 129.11 (9) | C11—C12—C13 | 109.95 (8) |
N1—C1—C6 | 107.90 (9) | C11—C12—H12A | 109.7 |
C2—C1—C6 | 122.99 (9) | C13—C12—H12A | 109.7 |
C3—C2—C1 | 117.30 (9) | C11—C12—H12B | 109.7 |
C3—C2—H2A | 121.3 | C13—C12—H12B | 109.7 |
C1—C2—H2A | 121.3 | H12A—C12—H12B | 108.2 |
C2—C3—C4 | 119.17 (9) | C14—C13—C12 | 111.15 (9) |
C2—C3—H3 | 120.4 | C14—C13—H13A | 109.4 |
C4—C3—H3 | 120.4 | C12—C13—H13A | 109.4 |
F1—C4—C5 | 118.04 (9) | C14—C13—H13B | 109.4 |
F1—C4—C3 | 117.05 (9) | C12—C13—H13B | 109.4 |
C5—C4—C3 | 124.91 (9) | H13A—C13—H13B | 108.0 |
C4—C5—C6 | 116.40 (9) | C15—C14—C13 | 111.51 (8) |
C4—C5—H5 | 121.8 | C15—C14—H14A | 109.3 |
C6—C5—H5 | 121.8 | C13—C14—H14A | 109.3 |
C5—C6—C1 | 119.23 (9) | C15—C14—H14B | 109.3 |
C5—C6—C7 | 134.48 (9) | C13—C14—H14B | 109.3 |
C1—C6—C7 | 106.27 (8) | H14A—C14—H14B | 108.0 |
C8—C7—C9 | 127.81 (9) | C14—C15—C16 | 111.87 (8) |
C8—C7—C6 | 106.20 (8) | C14—C15—H15A | 109.2 |
C9—C7—C6 | 125.88 (8) | C16—C15—H15A | 109.2 |
N1—C8—C7 | 110.23 (8) | C14—C15—H15B | 109.2 |
N1—C8—H8 | 124.9 | C16—C15—H15B | 109.2 |
C7—C8—H8 | 124.9 | H15A—C15—H15B | 107.9 |
O1—C9—C7 | 123.40 (9) | C11—C16—C15 | 110.71 (8) |
O1—C9—C10 | 117.35 (8) | C11—C16—H16A | 109.5 |
C7—C9—C10 | 119.25 (8) | C15—C16—H16A | 109.5 |
O2—C10—N2 | 124.75 (9) | C11—C16—H16B | 109.5 |
O2—C10—C9 | 122.28 (8) | C15—C16—H16B | 109.5 |
N2—C10—C9 | 112.97 (8) | H16A—C16—H16B | 108.1 |
C8—N1—C1—C2 | −178.59 (10) | C6—C7—C8—N1 | 1.51 (10) |
C8—N1—C1—C6 | 0.56 (11) | C8—C7—C9—O1 | −175.91 (9) |
N1—C1—C2—C3 | 178.08 (9) | C6—C7—C9—O1 | −0.28 (16) |
C6—C1—C2—C3 | −0.96 (14) | C8—C7—C9—C10 | 3.92 (15) |
C1—C2—C3—C4 | 0.18 (14) | C6—C7—C9—C10 | 179.56 (8) |
C2—C3—C4—F1 | −179.24 (8) | C11—N2—C10—O2 | 2.07 (15) |
C2—C3—C4—C5 | 0.59 (15) | C11—N2—C10—C9 | −177.56 (8) |
F1—C4—C5—C6 | 179.28 (8) | O1—C9—C10—O2 | −168.77 (9) |
C3—C4—C5—C6 | −0.55 (15) | C7—C9—C10—O2 | 11.39 (14) |
C4—C5—C6—C1 | −0.23 (13) | O1—C9—C10—N2 | 10.87 (12) |
C4—C5—C6—C7 | −178.32 (10) | C7—C9—C10—N2 | −168.98 (9) |
N1—C1—C6—C5 | −178.22 (8) | C10—N2—C11—C12 | −68.08 (12) |
C2—C1—C6—C5 | 1.00 (14) | C10—N2—C11—C16 | 168.70 (8) |
N1—C1—C6—C7 | 0.37 (10) | N2—C11—C12—C13 | 178.16 (8) |
C2—C1—C6—C7 | 179.58 (9) | C16—C11—C12—C13 | −58.92 (11) |
C5—C6—C7—C8 | 177.15 (10) | C11—C12—C13—C14 | 57.56 (12) |
C1—C6—C7—C8 | −1.12 (10) | C12—C13—C14—C15 | −54.88 (12) |
C5—C6—C7—C9 | 0.74 (17) | C13—C14—C15—C16 | 53.30 (12) |
C1—C6—C7—C9 | −177.53 (9) | N2—C11—C16—C15 | −178.68 (8) |
C1—N1—C8—C7 | −1.32 (11) | C12—C11—C16—C15 | 57.37 (11) |
C9—C7—C8—N1 | 177.83 (9) | C14—C15—C16—C11 | −54.54 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···F1i | 0.905 (13) | 2.275 (13) | 3.1234 (11) | 156.1 (11) |
N1—H1···O2ii | 0.939 (14) | 1.863 (14) | 2.7786 (11) | 164.5 (13) |
C8—H8···O1iii | 0.95 | 2.31 | 3.0586 (12) | 136 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, y+1/2, −z+3/2; (iii) x, −y+3/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C16H17FN2O2 |
Mr | 288.32 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 113 |
a, b, c (Å) | 11.5065 (15), 9.7666 (12), 12.3139 (16) |
β (°) | 96.639 (5) |
V (Å3) | 1374.5 (3) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.20 × 0.16 × 0.12 |
Data collection | |
Diffractometer | Rigaku Saturn CCD area-detector diffractometer |
Absorption correction | Multi-scan (CrystalClear; Rigaku, 2005) |
Tmin, Tmax | 0.980, 0.988 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 18432, 3717, 3007 |
Rint | 0.035 |
(sin θ/λ)max (Å−1) | 0.687 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.037, 0.098, 1.04 |
No. of reflections | 3717 |
No. of parameters | 198 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.27, −0.28 |
Computer programs: CrystalClear (Rigaku, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
D—H···A | D—H | H···A | D···A | D—H···A |
N2—H2···F1i | 0.905 (13) | 2.275 (13) | 3.1234 (11) | 156.1 (11) |
N1—H1···O2ii | 0.939 (14) | 1.863 (14) | 2.7786 (11) | 164.5 (13) |
C8—H8···O1iii | 0.95 | 2.31 | 3.0586 (12) | 135.8 |
Symmetry codes: (i) −x, y−1/2, −z+1/2; (ii) −x, y+1/2, −z+3/2; (iii) x, −y+3/2, z+1/2. |
Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 30873363), the Program of the Science Foundation of Tianjin (08JCYBJC070000) and the Major Program of the Science Foundation of Tianjin (09ZCKFSH01700).
References
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Indole and their derivatives are well known as substances with biologically activity such as anti-cancer (Souli et al., 2008), anti-virus(Chai et al., 2006), anti-tubercular (Karthikeyan et al., 2009), and anti-inflammatory (Radwan et al., 2007). In recent years, our recent study is paying attention to synthesize different kinds of indole derivatives with improved bioactivities. In this paper, we reported the crystal structure of title compound.
In title compound, C16H17FN2O2, bond lengths and angles are normal and in good agreement with those reported previously (Liu et al., 2011; Sonar, et al., 2006). The cyclohexane ring (C11—C16) adopts a chair conformation. π—π interactions are indicated by the short distance (Cg1···Cg2 distance of 3.503 (5) Å, symmetry code: -x,1 - y,-z) between the centroids of the pyrrole ring (N1/C1/C6—C8) (Cg1) and benzene ring C1—C6 (Cg2) (Table 1). There are weaker C—H···O N—H···F and N—H···O intermolecular interactions, which stabilized the structure (Table 1)