2,3,4,5,6-Penta­fluoro-trans-cinnamic acid

Navarrete, A.; Somanathan, R.; Aguirre, G.

doi:10.1107/S1600536813024513

organic compounds

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ISSN: 2056-9890

Volume 69| Part 10| October 2013| Page o1519

doi:10.1107/S1600536813024513

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2,3,4,5,6-Pentafluoro-trans-cinnamic acid

Angélica Navarrete,^a Ratnasamy Somanathan ^a and Gerardo Aguirre ^a ^*

^aCentro de Graduados e Investigación del Instituto Tecnológico de Tijuana, Apdo. Postal 1166, 22500, Tijuana, B.C., Mexico
^*Correspondence e-mail: gaguirre777@gmail.com

(Received 17 July 2013; accepted 2 September 2013; online 7 September 2013)

The title compound, C₉H₃F₅O₂, crystallizes as O—H⋯O hydrogen-bonded carboxylic acid dimers that, together with C—H⋯F interactions and O⋯F [2.8065 (13) and 2.9628 (13) Å] and F⋯F [2.6665 (11), 2.7049 (12) and 2.7314 (12) Å] contacts, form a sheet-like structure. The sheets are stacked via short π–π interactions [centroid–centroid distance = 4.3198 (11) Å]. An intramolecular C—H⋯F interaction is also observed.

Related literature

For related structures, see: Goud et al. (1995 ); Quan & Sun, (2013 ). For the biological activity of N-alkenyl amides, see: Brettle & Mosedale (1988 ). For fluorinated N-alkenyl amides, see: Aguirre et al. (1998 ).

Experimental

Crystal data

C₉H₃F₅O₂
M_r = 238.11
Triclinic, $[P \overline 1]$
a = 4.3198 (9) Å
b = 7.4921 (17) Å
c = 13.225 (3) Å
α = 93.612 (12)°
β = 93.912 (12)°
γ = 103.769 (12)°
V = 413.37 (15) Å³
Z = 2
Mo Kα radiation
μ = 0.21 mm⁻¹
T = 100 K
0.35 × 0.30 × 0.09 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2008 ) T_min = 0.931, T_max = 0.982
11089 measured reflections
2405 independent reflections
2000 reflections with I > 2σ(I)
R_int = 0.026

Refinement

R[F² > 2σ(F²)] = 0.031
wR(F²) = 0.104
S = 0.70
2405 reflections
145 parameters
H-atom parameters constrained
Δρ_max = 0.50 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O2—H2A⋯O1ⁱ	0.84	1.81	2.6485 (13)	179
C7—H7⋯F4ⁱⁱ	0.95	2.47	3.4074 (14)	169
C8—H8⋯F5	0.95	2.22	2.8434 (14)	123
Symmetry codes: (i) -x+1, -y+3, -z+1; (ii) x+1, y+1, z.

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT; 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

Crystal structure: contains datablock I. DOI: 10.1107/S1600536813024513/gg2124sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536813024513/gg2124Isup2.hkl

Supporting information file. DOI: 10.1107/S1600536813024513/gg2124Isup3.cml

checkCIF report

Comment top

N-Alkenyl amides are a rapidly emerging class of naturally occurring substances, widely distributed in higher plants, marine and microorganisms, and they exhibit an array of biological properties, including antibiotic, protein kinase inhibition an antitumor activity (Brettle & Mosedale, 1988). In particular we are interested in the synthesis of fluorinated N-alkenyl amides from commercially available fluorocinnamic acids and aldehydes (Aguirre et al., 1998). In our synthesis of pentafluorinated enamide, we used 2,3,4,5,6-Pentafluoro-trans-cinnamic acid as the starting material, which is commercially available and herein we report the crystal structure (Fig. 1).

In the crystal structure adjacent networks are linked together via intermolecular hydrogen bond interactions (Table 1). The molecules form typical carboxylic acid dimers (Fig. 2) and stack via π–π interactions.

Related literature top

For related structures, see: Goud et al. (1995); Quan & Sun, (2013). For the biological activity of N-alkenyl amides, see: Brettle & Mosedale (1988). For fluorinated N-alkenyl amides, see: Aguirre et al. (1998).

Experimental top

2,3,4,5,6 Pentafluorocinnamic acid obtained from the Aldrich Chemical Company, was dissolved in chloroform. Slow evaporation at room temperature produces plates. One of which was cut provide the experimental sample. Melting point 154–156 °C.

¹H NMR (CDCl₃): δ 10.5 (s, 1H), 7.7 (d, J=16 Hz, 1H), 6.8 (d, J=16 Hz, 1H) p.p.m.; ¹³C NMR (CDCl₃): δ 171.0 (s), 145.6 (d, J_C—F=253 Hz), 142.1 (d, J_C—F=253 Hz), 137.8 (d, J_C—F=252 Hz), 130.6 (s), 125.3 (t, J_C—F=5.8 Hz), 109.6 (d, J_C—F=17 Hz) p.p.m.; ¹⁹F NMR (CDCl₃): δ – 140.2 (dd, J=18,4 Hz), -151.3 (tt, J=20. 3 Hz), -162.4 (t,d, J=20,6 Hz) p.p.m.. EMIE m/e: [M]⁺ 238.

Computing details top

Data collection: APEX2 (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); 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).

Figures top

	Fig. 1. The molecular structure of the title compound with the atom numbering scheme, displacement ellipsoids are drawn at 30% probability level. H atoms are present as small spheres of arbitrary radius.
	Fig. 2. A packing diagram of (I). Intermolecular hydrogen bonds are shown as dashed lines.

(E)-3-(2,3,4,5,6-Pentafluorophenyl)prop-2-enoic acid top

Crystal data top

C₉H₃F₅O₂	Z = 2
M_r = 238.11	F(000) = 236
Triclinic, P1	D_x = 1.913 Mg m⁻³
Hall symbol: -P 1	Mo Kα radiation, λ = 0.71073 Å
a = 4.3198 (9) Å	Cell parameters from 5831 reflections
b = 7.4921 (17) Å	θ = 3.1–30.6°
c = 13.225 (3) Å	µ = 0.21 mm⁻¹
α = 93.612 (12)°	T = 100 K
β = 93.912 (12)°	Needle, colorless
γ = 103.769 (12)°	0.35 × 0.30 × 0.09 mm
V = 413.37 (15) Å³

Data collection top

Bruker APEXII CCD diffractometer	2405 independent reflections
Radiation source: fine-focus sealed tube	2000 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
ϕ and ω scans	θ_max = 30.0°, θ_min = 1.6°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −6→6
T_min = 0.931, T_max = 0.982	k = −10→10
11089 measured reflections	l = −18→18

Refinement top

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)] = 0.031	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.104	H-atom parameters constrained
S = 0.70	w = 1/[σ²(F_o²) + (0.091P)² + 0.3271P] where P = (F_o² + 2F_c²)/3
2405 reflections	(Δ/σ)_max = 0.001
145 parameters	Δρ_max = 0.50 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Crystal data top

C₉H₃F₅O₂	γ = 103.769 (12)°
M_r = 238.11	V = 413.37 (15) Å³
Triclinic, P1	Z = 2
a = 4.3198 (9) Å	Mo Kα radiation
b = 7.4921 (17) Å	µ = 0.21 mm⁻¹
c = 13.225 (3) Å	T = 100 K
α = 93.612 (12)°	0.35 × 0.30 × 0.09 mm
β = 93.912 (12)°

Data collection top

Bruker APEXII CCD diffractometer	2405 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2008)	2000 reflections with I > 2σ(I)
T_min = 0.931, T_max = 0.982	R_int = 0.026
11089 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.031	0 restraints
wR(F²) = 0.104	H-atom parameters constrained
S = 0.70	Δρ_max = 0.50 e Å⁻³
2405 reflections	Δρ_min = −0.23 e Å⁻³
145 parameters

Special details top

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.

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

	x	y	z	U_iso*/U_eq
C1	0.6800 (2)	0.93946 (14)	0.75051 (8)	0.0134 (2)
C2	0.9181 (2)	0.96009 (14)	0.83065 (8)	0.0144 (2)
C3	0.9520 (2)	0.81768 (15)	0.88834 (8)	0.0157 (2)
C4	0.7427 (3)	0.64649 (14)	0.86844 (8)	0.0163 (2)
C5	0.5033 (2)	0.62006 (14)	0.79029 (8)	0.0159 (2)
C6	0.4761 (2)	0.76388 (14)	0.73261 (8)	0.0142 (2)
C7	0.6612 (2)	1.09717 (14)	0.69294 (8)	0.0144 (2)
H7	0.8193	1.2081	0.7125	0.017*
C8	0.4473 (3)	1.10410 (14)	0.61580 (8)	0.0154 (2)
H8	0.2826	0.9980	0.5926	0.018*
C9	0.4709 (2)	1.27831 (14)	0.56750 (8)	0.0147 (2)
F1	1.12678 (16)	1.12300 (9)	0.85325 (5)	0.01929 (16)
F2	1.18772 (16)	0.84479 (10)	0.96299 (5)	0.02165 (17)
F3	0.76994 (18)	0.50721 (10)	0.92323 (5)	0.02419 (18)
F4	0.29659 (17)	0.45665 (9)	0.77171 (6)	0.02230 (17)
F5	0.23906 (16)	0.72905 (9)	0.65828 (5)	0.01916 (16)
O1	0.6780 (2)	1.41951 (11)	0.59342 (6)	0.01988 (18)
O2	0.2455 (2)	1.26544 (11)	0.49321 (6)	0.01934 (18)
H2A	0.2724	1.3661	0.4664	0.029*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0131 (4)	0.0122 (4)	0.0147 (4)	0.0025 (3)	0.0006 (3)	0.0021 (3)
C2	0.0135 (4)	0.0125 (4)	0.0157 (4)	0.0004 (3)	0.0002 (3)	0.0007 (4)
C3	0.0139 (4)	0.0190 (5)	0.0137 (4)	0.0040 (4)	−0.0018 (3)	0.0017 (4)
C4	0.0180 (5)	0.0144 (5)	0.0179 (5)	0.0052 (4)	0.0011 (4)	0.0067 (4)
C5	0.0155 (5)	0.0105 (4)	0.0204 (5)	0.0008 (4)	0.0005 (4)	0.0026 (4)
C6	0.0131 (4)	0.0136 (4)	0.0152 (4)	0.0022 (3)	−0.0016 (3)	0.0023 (3)
C7	0.0151 (4)	0.0109 (4)	0.0167 (4)	0.0019 (3)	0.0012 (4)	0.0028 (3)
C8	0.0168 (4)	0.0113 (4)	0.0175 (5)	0.0022 (3)	0.0006 (4)	0.0032 (3)
C9	0.0161 (4)	0.0129 (4)	0.0157 (4)	0.0043 (4)	0.0012 (3)	0.0023 (3)
F1	0.0182 (3)	0.0145 (3)	0.0207 (3)	−0.0033 (2)	−0.0033 (2)	0.0010 (2)
F2	0.0195 (3)	0.0258 (4)	0.0182 (3)	0.0046 (3)	−0.0065 (3)	0.0033 (3)
F3	0.0281 (4)	0.0184 (3)	0.0267 (4)	0.0059 (3)	−0.0029 (3)	0.0122 (3)
F4	0.0220 (3)	0.0117 (3)	0.0294 (4)	−0.0028 (2)	−0.0029 (3)	0.0058 (3)
F5	0.0165 (3)	0.0153 (3)	0.0223 (3)	−0.0008 (2)	−0.0077 (2)	0.0037 (2)
O1	0.0215 (4)	0.0132 (4)	0.0223 (4)	0.0002 (3)	−0.0048 (3)	0.0050 (3)
O2	0.0205 (4)	0.0137 (4)	0.0220 (4)	0.0017 (3)	−0.0059 (3)	0.0056 (3)

Geometric parameters (Å, º) top

C1—C2	1.4000 (14)	C5—C6	1.3814 (14)
C1—C6	1.3941 (14)	C6—F5	1.3363 (12)
C1—C7	1.4606 (14)	C7—C8	1.3408 (15)
C2—F1	1.3360 (12)	C7—H7	0.9500
C2—C3	1.3797 (15)	C8—C9	1.4740 (15)
C3—F2	1.3388 (12)	C8—H8	0.9500
C3—C4	1.3800 (15)	C9—O1	1.2244 (13)
C4—F3	1.3304 (12)	C9—O2	1.3172 (13)
C4—C5	1.3814 (15)	O2—H2A	0.8400
C5—F4	1.3298 (12)

C6—C1—C2	115.35 (9)	C4—C5—C6	120.03 (10)
C6—C1—C7	125.16 (9)	F5—C6—C5	116.98 (9)
C2—C1—C7	119.49 (9)	F5—C6—C1	120.37 (9)
F1—C2—C3	117.27 (9)	C5—C6—C1	122.65 (9)
F1—C2—C1	119.82 (9)	C8—C7—C1	127.75 (10)
C3—C2—C1	122.91 (10)	C8—C7—H7	116.1
F2—C3—C4	120.01 (10)	C1—C7—H7	116.1
F2—C3—C2	120.26 (10)	C7—C8—C9	119.20 (10)
C4—C3—C2	119.73 (10)	C7—C8—H8	120.4
F3—C4—C3	120.83 (10)	C9—C8—H8	120.4
F3—C4—C5	119.85 (10)	O1—C9—O2	123.66 (10)
C3—C4—C5	119.32 (9)	O1—C9—C8	123.65 (10)
F4—C5—C4	119.82 (9)	O2—C9—C8	112.69 (9)
F4—C5—C6	120.15 (9)	C9—O2—H2A	109.5

C6—C1—C2—F1	179.53 (9)	C3—C4—C5—C6	0.34 (16)
C7—C1—C2—F1	−0.46 (15)	F4—C5—C6—F5	−0.89 (15)
C6—C1—C2—C3	0.18 (16)	C4—C5—C6—F5	−179.94 (9)
C7—C1—C2—C3	−179.81 (10)	F4—C5—C6—C1	178.10 (9)
F1—C2—C3—F2	−0.48 (15)	C4—C5—C6—C1	−0.94 (17)
C1—C2—C3—F2	178.88 (9)	C2—C1—C6—F5	179.63 (9)
F1—C2—C3—C4	179.89 (9)	C7—C1—C6—F5	−0.38 (16)
C1—C2—C3—C4	−0.74 (17)	C2—C1—C6—C5	0.67 (16)
F2—C3—C4—F3	0.59 (16)	C7—C1—C6—C5	−179.34 (10)
C2—C3—C4—F3	−179.78 (9)	C6—C1—C7—C8	1.45 (18)
F2—C3—C4—C5	−179.16 (9)	C2—C1—C7—C8	−178.56 (10)
C2—C3—C4—C5	0.47 (16)	C1—C7—C8—C9	−179.90 (10)
F3—C4—C5—F4	1.54 (16)	C7—C8—C9—O1	0.40 (17)
C3—C4—C5—F4	−178.71 (9)	C7—C8—C9—O2	−179.81 (9)
F3—C4—C5—C6	−179.41 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···O1ⁱ	0.84	1.81	2.6485 (13)	179
C7—H7···F4ⁱⁱ	0.95	2.47	3.4074 (14)	169
C8—H8···F5	0.95	2.22	2.8434 (14)	123

Symmetry codes: (i) −x+1, −y+3, −z+1; (ii) x+1, y+1, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2A···O1ⁱ	0.84	1.81	2.6485 (13)	179
C7—H7···F4ⁱⁱ	0.95	2.47	3.4074 (14)	169
C8—H8···F5	0.95	2.22	2.8434 (14)	123

Symmetry codes: (i) −x+1, −y+3, −z+1; (ii) x+1, y+1, z.

Acknowledgements

We gratefully acknowledge support for this project from the Dirección General de Educación Superior Tecnológica (DGEST) 2536.09-P.

References

Aguirre, G., Somanathan, R. & Hellberg, L. H. (1998). J. Fluorine Chem. 90, 5–8. Web of Science CrossRef CAS Google Scholar
Brettle, R. & Mosedale, A. J. (1988). J. Chem. Soc. Perkin Trans. 1, pp. 2185–2195. CrossRef Web of Science Google Scholar
Bruker (2008). APEX2, SADABS and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Goud, B. S., Reddy, P. K., Panneerselvam, K. & Desiraju, G. R. (1995). Acta Cryst. C51, 683–685. CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
Quan, J. & Sun, H.-S. (2013). Acta Cryst. E69, o30. CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar