5-Fluoro-3-(1H-indol-3-ylmeth­yl)-1H-indole

Guo, G.

doi:10.1107/S2414314623005904

organic compounds

IUCrDATA

ISSN: 2414-3146

Volume 8| Part 8| August 2023| x230590

https://doi.org/10.1107/S2414314623005904

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5-Fluoro-3-(1H-indol-3-ylmethyl)-1H-indole

Guozhe Guo ^a ^*

^aCollege of Chemistry and Chemical Engineering, Longdong University, Qingyang, Gansu, 745000, People's Republic of China
^*Correspondence e-mail: guoguozhe2008@126.com

Edited by D.-J. Xu, Zhejiang University (Yuquan Campus), China (Received 11 January 2023; accepted 5 July 2023; online 4 August 2023)

The title compound, C₁₇H₁₃FN₂, was synthesized as a potential ligand for the construction of metal–organic frameworks. The two indole motifs present two potential coordination modes. It crystallizes in the orthorhombic system with space group P2₁2₁2₁. The dihedral angle between the fused ring systems is 68.77 (10)°. Weak F⋯H interactions are observed in the crystal.

Keywords: crystal structure.

CCDC reference: 2233347

Structure description

The diarylmethane motif is ubiquitous in natural products, bioactive molecule and medicine (Sakurai et al., 2020 ). The title compound belongs to the diarylmethane family (Safe et al., 2008 ), which shows antioxidant, anti-inflammatory and anticancer bioactivities, and can be found in broccoli.

In the present work, we synthesized the title compound as a potential ligand for the construction of metal–organic frameworks. This ligand is expected to be a good candidate for the construction of coordination polymers with diverse structures. The molecular structure is shown in Fig. 1. The title compound crystallizes in the orthorhombic system, space group P2₁2₁2₁. The dihedral angle between the fused ring systems is 68.77 (10)°. Fig. 2 shows the weak F⋯H and other interactions observed in the crystal Numerical details are given in Table 1.

Table 1
Intermolecular interactions (Å)

Atom1	Atom2	Symm. op. 2	Length	Length − vdW
F1	H16	− $[{1\over 2}]$ + x, − $[{1\over 2}]$ − y, −z	2.48	−0.19
C1	H4	1 − x, − $[{1\over 2}]$ + y, $[{1\over 2}]$ − z	2.88	−0.02
C4	H1	−x, $[{1\over 2}]$ + y, $[{1\over 2}]$ − z	2.55	−0.35
C5	H1	−x, $[{1\over 2}]$ + y, $[{1\over 2}]$ − z	2.58	−0.32
C11	H7	1 + x, y, z	2.82	−0.08
C12	H2	− $[{1\over 2}]$ + x, $[{1\over 2}]$ − y, −z	2.80	−0.10
C16	H2	− $[{1\over 2}]$ + x, $[{1\over 2}]$ − y, −z	2.81	−0.09
C17	H2	− $[{1\over 2}]$ + x, $[{1\over 2}]$ − y, −z	2.64	−0.26

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

Figure 2
The crystal packing of the title compound. Weak interactions between the molecules are shown as dashed lines.

Synthesis and crystallization

To a dried reaction tube (10 ml) with a magnetic stirring bar were added NHPI (N-hydroxyphthalimide ester) ester (0.2 mmol), indole (0.4 mmol) and Ru(bpy)₂(PF₆)₂ (3 mol %) successively. Air was then withdrawn and the tube was backfilled with argon three times. Subsequently, degassed DCM (2 ml) was injected into the tube by syringe. Then, the resulting reaction mixture was irradiated at room temperature under blue LEDs (6 W) for 12 h. The reaction progress was monitored by TLC. After the reaction was completed, the reaction mixture was concentrated under reduced pressure, and the residue was purified by column chromatography to afford the title compound. Single crystals of C₁₇H₁₃FN₂ were obtained by evaporation after one week. Yield: 47 wt%.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2..

Table 2
Experimental details

Crystal data
Chemical formula	C₁₇H₁₃FN₂
M_r	264.29
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	296
a, b, c (Å)	6.0723 (3), 7.8662 (3), 26.2693 (11)
V (Å³)	1254.78 (9)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.09
Crystal size (mm)	0.12 × 0.1 × 0.1

Data collection
Diffractometer	Bruker APEXII CCD
Absorption correction	Multi-scan (SADABS; Krause et al., 2015 )
T_min, T_max	0.691, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections	12005, 2866, 2528
R_int	0.063
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.125, 1.06
No. of reflections	2866
No. of parameters	181
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.53, −0.30
Absolute structure	Flack x determined using 921 quotients [(I⁺)−(I⁻)]/[(I⁺)+(I⁻)] (Parsons et al., 2013 )
Absolute structure parameter	−0.1 (7)
Computer programs: APEX2 and SAINT (Bruker, 2019 ), SHELXT2018/2 (Sheldrick, 2015a ), SHELXL2018/3 (Sheldrick, 2015b ) and OLEX2 (Dolomanov et al., 2009 ).

Structural data

CCDC reference: 2233347

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2414314623005904/xu4049sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2414314623005904/xu4049Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2414314623005904/xu4049Isup3.cml

checkCIF report

Computing details top

Data collection: Bruker APEXII CCD; cell refinement: SAINT V8.40A (Bruker, 2019); data reduction: SAINT V8.40A (Bruker, 2019); program(s) used to solve structure: SHELXT2018/2 (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: Olex2 1.3 (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 1.3 (Dolomanov et al., 2009).

5-Fluoro-3-(1H-indol-3-ylmethyl)-1H-indole top

Crystal data top

C₁₇H₁₃FN₂	D_x = 1.399 Mg m⁻³
M_r = 264.29	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P2₁2₁2₁	Cell parameters from 4629 reflections
a = 6.0723 (3) Å	θ = 2.7–27.4°
b = 7.8662 (3) Å	µ = 0.09 mm⁻¹
c = 26.2693 (11) Å	T = 296 K
V = 1254.78 (9) Å³	Block, colourless
Z = 4	0.12 × 0.1 × 0.1 mm
F(000) = 552

Data collection top

Bruker APEXII CCD diffractometer	2528 reflections with I > 2σ(I)
φ and ω scans	R_int = 0.063
Absorption correction: multi-scan (SADABS; Krause et al., 2015)	θ_max = 27.5°, θ_min = 2.7°
T_min = 0.691, T_max = 0.746	h = −7→7
12005 measured reflections	k = −9→10
2866 independent reflections	l = −34→29

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F² > 2σ(F²)] = 0.047	w = 1/[σ²(F_o²) + (0.051P)² + 0.4902P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.125	(Δ/σ)_max < 0.001
S = 1.06	Δρ_max = 0.53 e Å⁻³
2866 reflections	Δρ_min = −0.30 e Å⁻³
181 parameters	Absolute structure: Flack x determined using 921 quotients [(I⁺)-(I^-)]/[(I⁺)+(I^-)] (Parsons et al., 2013)
0 restraints	Absolute structure parameter: −0.1 (7)
Primary atom site location: dual

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. The H atoms were included in calculated positions and treated as riding atoms: C–H = 0.93- 0.98 Å, with U_iso(H) = 1.2Ueq (C), U_iso(H) = 1.2Ueq (N).

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

	x	y	z	U_iso*/U_eq
F1	0.0864 (4)	−0.1701 (2)	0.06215 (8)	0.0567 (6)
N1	−0.0566 (4)	0.2923 (3)	0.23358 (10)	0.0325 (6)
H1	−0.163457	0.235536	0.246712	0.039*
N2	0.7008 (4)	0.3284 (3)	0.05286 (9)	0.0366 (6)
H2	0.829218	0.336765	0.039262	0.044*
C6	0.1230 (5)	0.3505 (3)	0.25954 (11)	0.0268 (6)
C5	0.2620 (5)	0.4322 (3)	0.22362 (10)	0.0240 (6)
C8	0.1535 (5)	0.4238 (3)	0.17516 (10)	0.0255 (6)
C14	0.2106 (5)	0.1028 (3)	0.08297 (10)	0.0289 (6)
H14	0.081609	0.123845	0.100979	0.035*
C13	0.3747 (5)	0.2253 (3)	0.07888 (10)	0.0264 (6)
C10	0.3965 (5)	0.3978 (3)	0.09673 (10)	0.0264 (6)
C9	0.2277 (5)	0.4995 (3)	0.12576 (11)	0.0285 (6)
H9A	0.288541	0.611254	0.132574	0.034*
H9B	0.099716	0.514911	0.104165	0.034*
C4	0.4575 (5)	0.5076 (4)	0.24071 (11)	0.0293 (6)
H4	0.552343	0.561101	0.217991	0.035*
C12	0.5690 (5)	0.1875 (4)	0.05142 (10)	0.0316 (6)
C17	0.6017 (6)	0.0300 (4)	0.02794 (11)	0.0394 (8)
H17	0.730172	0.006624	0.009970	0.047*
C7	−0.0405 (5)	0.3383 (4)	0.18325 (11)	0.0312 (6)
H7	−0.145343	0.315036	0.158400	0.037*
C3	0.5069 (6)	0.5007 (4)	0.29232 (12)	0.0371 (7)
H3	0.636564	0.549724	0.304113	0.045*
C11	0.5953 (5)	0.4543 (4)	0.07946 (11)	0.0334 (7)
H11	0.651263	0.562800	0.084954	0.040*
C15	0.2462 (6)	−0.0498 (4)	0.05952 (11)	0.0345 (7)
C1	0.1734 (6)	0.3440 (4)	0.31123 (11)	0.0344 (7)
H1A	0.081012	0.289653	0.334300	0.041*
C16	0.4374 (7)	−0.0887 (4)	0.03240 (12)	0.0419 (8)
H16	0.453295	−0.195077	0.017363	0.050*
C2	0.3651 (6)	0.4213 (4)	0.32682 (12)	0.0374 (7)
H2A	0.401270	0.420605	0.361224	0.045*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.0776 (17)	0.0382 (10)	0.0542 (13)	−0.0067 (11)	−0.0121 (12)	−0.0048 (9)
N1	0.0292 (14)	0.0317 (12)	0.0366 (13)	−0.0075 (10)	0.0077 (11)	0.0018 (11)
N2	0.0284 (13)	0.0539 (16)	0.0276 (12)	0.0014 (12)	0.0064 (11)	0.0075 (11)
C6	0.0278 (15)	0.0242 (12)	0.0285 (13)	−0.0002 (11)	0.0056 (12)	−0.0006 (11)
C5	0.0270 (14)	0.0189 (11)	0.0262 (13)	0.0034 (10)	0.0038 (11)	−0.0006 (10)
C8	0.0283 (14)	0.0229 (12)	0.0253 (13)	0.0017 (11)	0.0028 (11)	−0.0011 (10)
C14	0.0341 (16)	0.0307 (14)	0.0220 (13)	0.0051 (12)	−0.0021 (12)	0.0010 (10)
C13	0.0307 (15)	0.0314 (13)	0.0171 (11)	0.0064 (11)	−0.0015 (11)	0.0028 (10)
C10	0.0286 (15)	0.0310 (13)	0.0196 (12)	0.0003 (11)	−0.0006 (11)	0.0040 (10)
C9	0.0337 (15)	0.0263 (12)	0.0256 (13)	0.0023 (12)	−0.0015 (12)	0.0007 (11)
C4	0.0296 (15)	0.0283 (13)	0.0299 (14)	−0.0019 (12)	0.0038 (12)	−0.0016 (11)
C12	0.0325 (16)	0.0433 (16)	0.0191 (12)	0.0083 (13)	0.0004 (12)	0.0052 (11)
C17	0.0423 (19)	0.0527 (19)	0.0233 (14)	0.0218 (16)	0.0028 (14)	0.0028 (13)
C7	0.0293 (15)	0.0312 (14)	0.0329 (15)	−0.0005 (12)	−0.0013 (12)	−0.0012 (12)
C3	0.0363 (18)	0.0389 (16)	0.0361 (16)	−0.0004 (14)	−0.0076 (14)	−0.0065 (13)
C11	0.0344 (17)	0.0390 (16)	0.0268 (14)	−0.0031 (13)	−0.0008 (13)	0.0070 (12)
C15	0.0465 (19)	0.0304 (14)	0.0265 (14)	0.0038 (13)	−0.0086 (14)	0.0013 (11)
C1	0.0425 (18)	0.0313 (14)	0.0294 (15)	0.0008 (13)	0.0117 (13)	0.0009 (12)
C16	0.063 (2)	0.0365 (16)	0.0256 (14)	0.0183 (16)	−0.0052 (16)	−0.0024 (12)
C2	0.0442 (19)	0.0417 (16)	0.0262 (14)	0.0063 (15)	−0.0012 (14)	−0.0030 (13)

Geometric parameters (Å, º) top

F1—C15	1.357 (4)	C10—C9	1.507 (4)
N1—H1	0.8600	C10—C11	1.364 (4)
N1—C6	1.365 (4)	C9—H9A	0.9700
N1—C7	1.374 (4)	C9—H9B	0.9700
N2—H2	0.8600	C4—H4	0.9300
N2—C12	1.368 (4)	C4—C3	1.390 (4)
N2—C11	1.371 (4)	C12—C17	1.398 (4)
C6—C5	1.420 (4)	C17—H17	0.9300
C6—C1	1.393 (4)	C17—C16	1.372 (5)
C5—C8	1.435 (4)	C7—H7	0.9300
C5—C4	1.401 (4)	C3—H3	0.9300
C8—C9	1.497 (4)	C3—C2	1.398 (5)
C8—C7	1.373 (4)	C11—H11	0.9300
C14—H14	0.9300	C15—C16	1.396 (5)
C14—C13	1.391 (4)	C1—H1A	0.9300
C14—C15	1.366 (4)	C1—C2	1.375 (5)
C13—C10	1.442 (4)	C16—H16	0.9300
C13—C12	1.415 (4)	C2—H2A	0.9300

C6—N1—H1	125.2	C5—C4—H4	120.7
C6—N1—C7	109.6 (2)	C3—C4—C5	118.6 (3)
C7—N1—H1	125.2	C3—C4—H4	120.7
C12—N2—H2	125.5	N2—C12—C13	107.7 (3)
C12—N2—C11	109.0 (3)	N2—C12—C17	130.3 (3)
C11—N2—H2	125.5	C17—C12—C13	122.0 (3)
N1—C6—C5	107.1 (2)	C12—C17—H17	121.2
N1—C6—C1	130.6 (3)	C16—C17—C12	117.5 (3)
C1—C6—C5	122.3 (3)	C16—C17—H17	121.2
C6—C5—C8	107.2 (2)	N1—C7—H7	125.1
C4—C5—C6	118.8 (2)	C8—C7—N1	109.8 (3)
C4—C5—C8	133.9 (3)	C8—C7—H7	125.1
C5—C8—C9	127.7 (3)	C4—C3—H3	119.4
C7—C8—C5	106.2 (2)	C4—C3—C2	121.2 (3)
C7—C8—C9	126.0 (3)	C2—C3—H3	119.4
C13—C14—H14	121.3	N2—C11—H11	124.8
C15—C14—H14	121.3	C10—C11—N2	110.4 (3)
C15—C14—C13	117.4 (3)	C10—C11—H11	124.8
C14—C13—C10	133.9 (3)	F1—C15—C14	118.4 (3)
C14—C13—C12	119.4 (3)	F1—C15—C16	117.9 (3)
C12—C13—C10	106.7 (3)	C14—C15—C16	123.7 (3)
C13—C10—C9	127.0 (3)	C6—C1—H1A	121.3
C11—C10—C13	106.2 (3)	C2—C1—C6	117.4 (3)
C11—C10—C9	126.7 (3)	C2—C1—H1A	121.3
C8—C9—C10	115.6 (2)	C17—C16—C15	119.9 (3)
C8—C9—H9A	108.4	C17—C16—H16	120.0
C8—C9—H9B	108.4	C15—C16—H16	120.0
C10—C9—H9A	108.4	C3—C2—H2A	119.1
C10—C9—H9B	108.4	C1—C2—C3	121.7 (3)
H9A—C9—H9B	107.4	C1—C2—H2A	119.1

F1—C15—C16—C17	178.8 (3)	C13—C10—C11—N2	−1.1 (3)
N1—C6—C5—C8	1.5 (3)	C13—C12—C17—C16	0.0 (4)
N1—C6—C5—C4	178.5 (2)	C10—C13—C12—N2	0.3 (3)
N1—C6—C1—C2	−177.1 (3)	C10—C13—C12—C17	−179.0 (3)
N2—C12—C17—C16	−179.2 (3)	C9—C8—C7—N1	−177.8 (3)
C6—N1—C7—C8	1.6 (3)	C9—C10—C11—N2	−177.5 (3)
C6—C5—C8—C9	176.6 (3)	C4—C5—C8—C9	0.2 (5)
C6—C5—C8—C7	−0.5 (3)	C4—C5—C8—C7	−176.9 (3)
C6—C5—C4—C3	−0.6 (4)	C4—C3—C2—C1	1.2 (5)
C6—C1—C2—C3	−1.2 (5)	C12—N2—C11—C10	1.3 (3)
C5—C6—C1—C2	0.2 (4)	C12—C13—C10—C9	176.9 (3)
C5—C8—C9—C10	81.7 (4)	C12—C13—C10—C11	0.4 (3)
C5—C8—C7—N1	−0.6 (3)	C12—C17—C16—C15	0.1 (4)
C5—C4—C3—C2	−0.3 (5)	C7—N1—C6—C5	−1.9 (3)
C8—C5—C4—C3	175.5 (3)	C7—N1—C6—C1	175.8 (3)
C14—C13—C10—C9	−2.1 (5)	C7—C8—C9—C10	−101.7 (3)
C14—C13—C10—C11	−178.6 (3)	C11—N2—C12—C13	−1.0 (3)
C14—C13—C12—N2	179.5 (2)	C11—N2—C12—C17	178.3 (3)
C14—C13—C12—C17	0.2 (4)	C11—C10—C9—C8	−126.1 (3)
C14—C15—C16—C17	−0.4 (5)	C15—C14—C13—C10	178.5 (3)
C13—C14—C15—F1	−178.7 (2)	C15—C14—C13—C12	−0.4 (4)
C13—C14—C15—C16	0.6 (4)	C1—C6—C5—C8	−176.4 (3)
C13—C10—C9—C8	58.2 (4)	C1—C6—C5—C4	0.6 (4)

Intermolecular interactions (Å) top

Atom1	Atom2	Symm. op. 2	Length	Length - vdW
F1	H16	-1/2 + x, -1/2 - y, -z	2.48	-0.19
C1	H4	1 - x, -1/2 + y, 1/2 - z	2.88	-0.02
C4	H1	-x, 1/2 + y, 1/2 - z	2.55	-0.35
C5	H1	-x, 1/2 + y, 1/2 - z	2.58	-0.32
C11	H7	1 + x, y, z	2.82	-0.08
C12	H2	-1/2 + x, 1/2 - y, -z	2.80	-0.10
C16	H2	-1/2 + x, 1/2 - y, -z	2.81	-0.09
C17	H2	-1/2 + x, 1/2 - y, -z	2.64	-0.26

Funding information

We thank the Doctoral Funding Project of Longdong University (XYBYZK2224) for financially supporting this work. We also thank the Youth Foundation of Gansu Province (21JR7RM196) for financial support.

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