Crystal Structure of (E)-2-(3,3,3-tri­fluoro­prop-1-en-1-yl)aniline

Kubono, K.; Tani, K.; Omote, M.; Ogawa, F.; Matsumoto, T.

doi:10.1107/S2056989018012756

research communications

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 74| Part 10| October 2018| Pages 1448-1450

https://doi.org/10.1107/S2056989018012756

Open

access

Crystal Structure of (E)-2-(3,3,3-trifluoroprop-1-en-1-yl)aniline

Koji Kubono,^a Keita Tani,^a ^* Masaaki Omote,^b Futa Ogawa ^b and Taisuke Matsumoto ^c

^aDivision of Natural Sciences, Osaka Kyoiku University, Kashiwara, Osaka 582-8582, Japan, ^bFaculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka 573-0101, Japan, and ^cInstitute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
^*Correspondence e-mail: ktani@cc.osaka-kyoiku.ac.jp

Edited by H. Ishida, Okayama University, Japan (Received 13 July 2018; accepted 10 September 2018; online 18 September 2018)

The molecule of the title compound, C₉H₈F₃N, adopts an E configuration with respect to the C=C double bond. The dihedral angle between the benzene ring and the prop-1-enyl group is 25.4 (3)°. In the crystal, molecules are linked via pairs of N—H⋯F hydrogen bonds into inversion dimers with an R₂²(16) ring motif. The dimers are linked by C—H⋯N hydrogen bonds, forming a ribbon structure along the b-axis direction. The ribbons are linked by N—H⋯π and C—H⋯π interactions, generating a three-dimensional network.

Keywords: crystal structure; 3,3,3-trifluoroprop-1-en; aniline; hydrogen bonding.

CCDC reference: 1866671

1. Chemical context

Fluorescein, rhodamine etc. are water-soluble fluorescent reagents. Their derivatives exhibit strong fluorescence in aqueous solution and so can be utilized as ion-probes and in bio-imaging (Aron et al., 2016 ; Li et al., 2016 ). However, complicated procedures are required to obtain them. It is therefore desirable to develop a new fluorescent reagent with a simple structure that can be obtained by a short-step synthetic process. The title compound has a quite simple structure and is a small molecule, consisting of aniline and 3,3,3-trifluoroprop-1-enyl units, which emits strong fluorescence not only in organic solvents but also in an aqueous medium (H₂O/DMSO, 90:10, v/v). Since aniline derivatives with 2,4-bis(3,3,3-trifluoroprop-1-enyl) have been used as fluorogenic substrates for dipepeptidyl peptidase-4 (Ogawa et al., 2017 ), the title compound can be treated as a simple but essential component in emitting fluorescence. Hence, it is important to study the relationship between the fluorescent properties and the molecular structure of the title compound. We report here its molecular and crystal structure.

2. Structural commentary

The molecular structure of the title compound is shown in Fig. 1. The molecule adopts an E configuration with respect to the C=C double bond. The dihedral angle between the benzene ring and the prop-1-enyl group is 25.4 (3)°. The C5—C10—C11—C12 and C9—C10—C11—C12 torsion angles are −158.9 (3) and 24.6 (4)°, respectively. The bond lengths and angles in the title compound are normal and agree with those in other trifluoropropenylaniline compounds (Shimizu et al., 2009 ; Lin et al., 2014 ).

Figure 1
The molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids for non-H atoms are drawn at the 50% probability level.

3. Supramolecular features

In the crystal, two molecules are associated through a pair of intermolecular N—H⋯F hydrogen bonds (Table 1), forming a centrosymmetric dimer with an R₂²(16) ring motif (Fig. 2). The dimers are further linked by C—H⋯N hydrogen bonds (Table 1), forming a ribbon with a C(6) chain motif along the b-axis direction. The ribbons are linked by N—H⋯π and C—H⋯π interactions (Table 1), generating a three-dimensional network.

Table 1
Hydrogen-bond geometry (Å, °)

Cg1 is the centroid of the C5–C10 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N4—H4A⋯F2ⁱ	0.90 (3)	2.46 (4)	3.352 (3)	169 (3)
C12—H12⋯N4ⁱⁱ	0.95	2.56	3.432 (4)	152
N4—H4B⋯Cg1ⁱⁱⁱ	0.88 (3)	2.59 (4)	3.315 (2)	140 (3)
C9—H9⋯Cg1^iv	0.95	2.73	3.480 (3)	136
Symmetry codes: (i) -x+1, -y, -z+1; (ii) x, y-1, z; (iii) $[-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (iv) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Figure 2
A packing diagram of the title compound, viewed along the b axis. The N—H⋯F and C—H⋯N hydrogen bonds and N—H⋯π and C—H⋯π interactions are shown as dashed lines.

4. Database survey

A search of the Cambridge Structural Database (CSD, Version 5.39; May 2018; Groom et al., 2016 ) gave 16 hits for 2-(3,3,3-trifluoroprop-1-en-1-yl)azabenzene derivatives, and gave 18 and 45 hits for (E)-3,3,3-trifluoroprop-1-enyl and 2-aminophenyl-1-enyl fragments, respectively. Of these structures, those that resemble the title compound are 4-[2-(3,3,3-trifluoroprop-1-en-1-yl)phenyl]morpholine (Lin et al., 2014), N-acetyl-N-{2-[(Z)-2-chloro-3,3,3-trifluoroprop-1-enyl]phenyl}acetamide (Niu et al., 2009 ) and (E,E)-1,4-dipiperidino-2,5-bis(3,3,3-trifluoroprop-1-enyl)benzene (Shimizu et al., 2009).

5. Synthesis and crystallization

The title compound was prepared by a modification of a reported procedure (Omote et al., 2013 ). In a glove box purged with argon gas, iodoaniline (1.0 mmol), (2-methylallyl)palladium(II) chloride dimer (0.1mmol), CuF₂ (2.0 mmol) and 2,2′-bipyridyl (2.0 mmol) were placed in a flask. To the flask were added anhydrous DMF (6.0 ml) and (E)-trimethyl-(3,3,3-trifluoroprop-1-enyl)silane (2.0 mmol), and the mixture was stirred at 353 K. After the reaction mixture had been stirred for 4 h, it was poured into ice–water. The mixture was extracted with CH₂Cl₂, and the organic layer was dried over anhydrous MgSO₄. After the solid had been filtered off, the solvent was removed in vacuo, and the residue was purified by silica gel column chromatography to give the product in 68% yield. Colourless single crystals were obtained by recrystallization from an ethyl acetate–hexane (1:10, v/v) solution (m.p. 321–322 K). ¹H NMR (CDCl₃) δ: 3.81 (2H, s), 6.13 (1H, qd, J = 15.9, 6.5 Hz), 6.72 (1H, dd, J = 8.2, 0.9 Hz), 6.80 (1H, dt, J = 7.5, 0.9 Hz), 7.18 (1H, dt, J = 7.8, 1.4 Hz), 7.24 (1H, qd, J = 15.9, 2.1 Hz), 7.29 (1H, dd, J = 7.8, 1.4 Hz). ¹³C NMR (CDCl₃) δ: 116.6 (q, J = 33.4 Hz), 116.8, 119.2, 119.4, 123.6 (q, J = 269.0 Hz), 127.9, 130.9, 133.3 (q, J = 6.8 Hz), 144.8. ¹⁹F NMR (CDCl₃) δ: 12.07 (3F, dd, J = 6.5, 2.2 Hz). MS m/z 187 (M⁺), HRMS calculated for C₉H₈F₃N 187.1617 (M⁺), found 187.0603.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. The amino H atoms were located in a difference Fourier map and refined freely. The C-bound H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and refined using a riding model with U_iso(H) = 1.2U_eq(C). One outlier ( $[\overline{5}]$ 11) was omitted in the last cycle of refinement.

Table 2
Experimental details

Crystal data
Chemical formula	C₉H₈F₃N
M_r	187.16
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	123
a, b, c (Å)	7.3925 (4), 6.2777 (3), 18.6065 (9)
β (°)	96.243 (7)
V (Å³)	858.37 (8)
Z	4
Radiation type	Cu Kα
μ (mm⁻¹)	1.16
Crystal size (mm)	0.40 × 0.26 × 0.08

Data collection
Diffractometer	Rigaku R-AXIS RAPID
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995 )
T_min, T_max	0.543, 0.912
No. of measured, independent and observed [F² > 2.0σ(F²)] reflections	4753, 1566, 1178
R_int	0.049
(sin θ/λ)_max (Å⁻¹)	0.602

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.061, 0.175, 1.03
No. of reflections	1566
No. of parameters	126
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.49, −0.39
Computer programs: RAPID-AUTO (Rigaku, 2006 ), SIR92 (Altomare et al., 1993 ), SHELXL2014/7 (Sheldrick, 2015 ), PLATON (Spek, 2009 ) and CrystalStructure (Rigaku, 2016 ).

Supporting information

CCDC reference: 1866671

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S2056989018012756/is5499sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018012756/is5499Isup2.hkl

checkCIF report

Computing details top

Data collection: RAPID-AUTO (Rigaku, 2006); cell refinement: RAPID-AUTO (Rigaku, 2006); data reduction: RAPID-AUTO (Rigaku, 2006); program(s) used to solve structure: SIR92 (Altomare et al., 1993); program(s) used to refine structure: SHELXL2014/7 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: CrystalStructure (Rigaku, 2016).

(E)-2-(3,3,3-trifluoroprop-1-en-1-yl)aniline top

Crystal data top

C₉H₈F₃N	F(000) = 384.00
M_r = 187.16	D_x = 1.448 Mg m⁻³
Monoclinic, P2₁/c	Cu Kα radiation, λ = 1.54187 Å
a = 7.3925 (4) Å	Cell parameters from 4006 reflections
b = 6.2777 (3) Å	θ = 4.8–68.2°
c = 18.6065 (9) Å	µ = 1.16 mm⁻¹
β = 96.243 (7)°	T = 123 K
V = 858.37 (8) Å³	Platelet, colourless
Z = 4	0.40 × 0.26 × 0.08 mm

Data collection top

Rigaku R-AXIS RAPID diffractometer	1178 reflections with F² > 2.0σ(F²)
Detector resolution: 10.000 pixels mm^-1	R_int = 0.049
ω scans	θ_max = 68.2°, θ_min = 4.8°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −8→8
T_min = 0.543, T_max = 0.912	k = −6→7
4753 measured reflections	l = −22→22
1566 independent reflections

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.061	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.175	H atoms treated by a mixture of independent and constrained refinement
S = 1.03	w = 1/[σ²(F_o²) + (0.1029P)² + 0.1188P] where P = (F_o² + 2F_c²)/3
1566 reflections	(Δ/σ)_max < 0.001
126 parameters	Δρ_max = 0.49 e Å⁻³
0 restraints	Δρ_min = −0.39 e Å⁻³
Primary atom site location: structure-invariant direct methods

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. Refinement was performed using all reflections. The weighted R-factor (wR) and goodness of fit (S) are based on F². R-factor (gt) are based on F. The threshold expression of F² > 2.0 sigma(F²) is used only for calculating R-factor (gt).

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

	x	y	z	U_iso*/U_eq
F1	0.2762 (3)	−0.0078 (3)	0.52691 (8)	0.0597 (7)
F2	0.3860 (2)	−0.3171 (3)	0.51696 (8)	0.0569 (6)
F3	0.0979 (2)	−0.2730 (4)	0.50888 (9)	0.0661 (7)
N4	0.3895 (3)	0.4055 (4)	0.31939 (13)	0.0343 (6)
C5	0.3078 (3)	0.2521 (4)	0.27331 (13)	0.0272 (6)
C6	0.2853 (3)	0.2886 (4)	0.19799 (12)	0.0293 (6)
H6	0.3289	0.4171	0.1791	0.035*
C7	0.2009 (3)	0.1398 (4)	0.15202 (13)	0.0311 (6)
H7	0.1863	0.1670	0.1015	0.037*
C8	0.1362 (4)	−0.0502 (4)	0.17775 (12)	0.0311 (6)
H8	0.0788	−0.1528	0.1453	0.037*
C9	0.1567 (3)	−0.0871 (4)	0.25119 (12)	0.0276 (6)
H9	0.1123	−0.2164	0.2691	0.033*
C10	0.2413 (3)	0.0608 (4)	0.30004 (11)	0.0220 (6)
C11	0.2527 (3)	0.0253 (4)	0.37877 (12)	0.0276 (6)
H11	0.2651	0.1475	0.4090	0.033*
C12	0.2471 (3)	−0.1615 (4)	0.41076 (12)	0.0310 (6)
H12	0.2410	−0.2856	0.3814	0.037*
C13	0.2497 (4)	−0.1887 (4)	0.48945 (13)	0.0346 (7)
H4A	0.448 (4)	0.362 (6)	0.3618 (18)	0.070 (11)*
H4B	0.448 (5)	0.497 (5)	0.2944 (18)	0.067 (11)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
F1	0.1045 (18)	0.0494 (12)	0.0245 (8)	0.0050 (11)	0.0032 (10)	−0.0071 (8)
F2	0.0673 (13)	0.0635 (13)	0.0370 (10)	0.0222 (10)	−0.0073 (9)	0.0154 (8)
F3	0.0571 (12)	0.1073 (17)	0.0329 (9)	−0.0274 (11)	−0.0002 (8)	0.0251 (10)
N4	0.0379 (14)	0.0297 (13)	0.0346 (13)	−0.0050 (11)	0.0003 (11)	−0.0022 (11)
C5	0.0267 (13)	0.0255 (13)	0.0292 (13)	0.0036 (11)	0.0021 (10)	−0.0008 (11)
C6	0.0319 (14)	0.0290 (14)	0.0271 (13)	0.0045 (12)	0.0035 (10)	0.0050 (11)
C7	0.0310 (14)	0.0389 (16)	0.0236 (12)	0.0041 (12)	0.0035 (10)	0.0037 (11)
C8	0.0332 (15)	0.0355 (15)	0.0239 (13)	−0.0023 (12)	0.0000 (11)	−0.0043 (11)
C9	0.0295 (13)	0.0276 (14)	0.0254 (12)	0.0026 (12)	0.0009 (10)	0.0004 (11)
C10	0.0211 (13)	0.0241 (13)	0.0201 (11)	0.0020 (10)	−0.0010 (9)	−0.0007 (10)
C11	0.0295 (15)	0.0293 (14)	0.0232 (12)	0.0010 (11)	−0.0008 (10)	−0.0024 (10)
C12	0.0388 (15)	0.0315 (15)	0.0218 (12)	0.0012 (12)	−0.0008 (11)	0.0002 (11)
C13	0.0400 (16)	0.0373 (16)	0.0254 (13)	0.0004 (13)	−0.0013 (11)	0.0035 (11)

Geometric parameters (Å, º) top

F1—C13	1.336 (3)	C7—H7	0.9500
F2—C13	1.348 (3)	C8—C9	1.378 (3)
F3—C13	1.326 (3)	C8—H8	0.9500
N4—C5	1.383 (3)	C9—C10	1.398 (3)
N4—H4A	0.90 (3)	C9—H9	0.9500
N4—H4B	0.88 (3)	C10—C11	1.475 (3)
C5—C10	1.409 (3)	C11—C12	1.318 (3)
C5—C6	1.412 (3)	C11—H11	0.9500
C6—C7	1.371 (3)	C12—C13	1.472 (3)
C6—H6	0.9500	C12—H12	0.9500
C7—C8	1.389 (4)

C5—N4—H4A	118 (2)	C10—C9—H9	119.1
C5—N4—H4B	109 (2)	C9—C10—C5	119.0 (2)
H4A—N4—H4B	116 (3)	C9—C10—C11	121.2 (2)
N4—C5—C10	121.3 (2)	C5—C10—C11	119.7 (2)
N4—C5—C6	119.9 (2)	C12—C11—C10	125.6 (2)
C10—C5—C6	118.7 (2)	C12—C11—H11	117.2
C7—C6—C5	120.3 (2)	C10—C11—H11	117.2
C7—C6—H6	119.8	C11—C12—C13	123.7 (2)
C5—C6—H6	119.8	C11—C12—H12	118.1
C6—C7—C8	121.4 (2)	C13—C12—H12	118.1
C6—C7—H7	119.3	F3—C13—F1	106.1 (2)
C8—C7—H7	119.3	F3—C13—F2	106.1 (2)
C9—C8—C7	118.7 (2)	F1—C13—F2	104.4 (2)
C9—C8—H8	120.6	F3—C13—C12	113.4 (2)
C7—C8—H8	120.6	F1—C13—C12	113.9 (2)
C8—C9—C10	121.8 (2)	F2—C13—C12	112.1 (2)
C8—C9—H9	119.1

N4—C5—C6—C7	−178.5 (2)	N4—C5—C10—C11	2.2 (4)
C10—C5—C6—C7	−0.3 (4)	C6—C5—C10—C11	−176.1 (2)
C5—C6—C7—C8	−0.3 (4)	C9—C10—C11—C12	24.6 (4)
C6—C7—C8—C9	0.5 (4)	C5—C10—C11—C12	−158.9 (3)
C7—C8—C9—C10	−0.3 (4)	C10—C11—C12—C13	−176.8 (2)
C8—C9—C10—C5	−0.2 (4)	C11—C12—C13—F3	115.4 (3)
C8—C9—C10—C11	176.3 (2)	C11—C12—C13—F1	−6.2 (4)
N4—C5—C10—C9	178.7 (2)	C11—C12—C13—F2	−124.5 (3)
C6—C5—C10—C9	0.5 (3)

Hydrogen-bond geometry (Å, º) top

Cg1 is the centroid of the C5–C10 ring.

D—H···A	D—H	H···A	D···A	D—H···A
N4—H4A···F2ⁱ	0.90 (3)	2.46 (4)	3.352 (3)	169 (3)
C12—H12···N4ⁱⁱ	0.95	2.56	3.432 (4)	152
N4—H4B···Cg1ⁱⁱⁱ	0.88 (3)	2.59 (4)	3.315 (2)	140 (3)
C9—H9···Cg1^iv	0.95	2.73	3.480 (3)	136

Symmetry codes: (i) −x+1, −y, −z+1; (ii) x, y−1, z; (iii) −x+1, y+1/2, −z+1/2; (iv) −x, y−1/2, −z+1/2.

Funding information

Funding for this research was provided by: the Cooperative Research Program of Network Joint Reserarch Center for Materials and Devices (Institute for Materials Chemistry and Engineering, Kyushu University) (No. 20181296).

References

Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343–350. CrossRef Web of Science IUCr Journals Google Scholar
Aron, A. T., Loehr, M. O., Bogena, J. & Chang, C. J. (2016). J. Am. Chem. Soc. 138, 14338–14346. CrossRef Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. Web of Science CSD CrossRef IUCr Journals Google Scholar
Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan. Google Scholar
Li, D., Li, C.-Y., Li, Y.-F., Li, Z. & Xu, F. (2016). Anal. Chim. Acta, 934, 218–225. CrossRef Google Scholar
Lin, Q.-Y., Xu, X.-H. & Qing, F.-L. (2014). J. Org. Chem. 79, 10434–10446. CrossRef Google Scholar
Niu, J.-J., Li, Z.-G. & Xu, J.-W. (2009). Acta Cryst. E65, o1305. CrossRef IUCr Journals Google Scholar
Ogawa, F., Takeda, M., Miyanaga, K., Tani, K., Yamazawa, R., Ito, K., Tarui, A., Sato, A. & Omote, M. (2017). Beilstein J. Org. Chem. 13, 2690–2697. CrossRef Google Scholar
Omote, M., Tanaka, M., Tanaka, M., Ikeda, A., Tarui, A., Sato, K. & Ando, A. (2013). J. Org. Chem. 78, 6196–6201. CrossRef Google Scholar
Rigaku (2006). RAPID-AUTO. Rigaku Corporation, Tokyo, Japan. Google Scholar
Rigaku (2016). CrystalStructure. Rigaku Corporation, Tokyo, Japan. Google Scholar
Sheldrick, G. M. (2015). Acta Cryst. C71, 3–8. Web of Science CrossRef IUCr Journals Google Scholar
Shimizu, M., Takeda, Y., Higashi, M. & Hiyama, T. (2009). Angew. Chem. Int. Ed. 48, 3653–3656. CrossRef Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar