Crystal structure of ethyl (E)-2-cyano-3-(thio­phen-2-yl)acrylate: two conformers forming a discrete disorder

Castro Agudelo, B.; Cárdenas, J.C.; Macías, M.A.; Ochoa-Puentes, C.; Sierra, C.A.

doi:10.1107/S2056989017010799

research communications

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 73| Part 9| September 2017| Pages 1287-1289

https://doi.org/10.1107/S2056989017010799

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Crystal structure of ethyl (E)-2-cyano-3-(thiophen-2-yl)acrylate: two conformers forming a discrete disorder

Brian Castro Agudelo,^a Juan C. Cárdenas,^a Mario A. Macías,^b ^* Cristian Ochoa-Puentes ^a and Cesar A. Sierra ^a ^*

^aDepartamento de Química, Universidad Nacional de Colombia, Bogotá D.C., Colombia, and ^bDepartamento de Química, Universidad de los Andes, Carrera 1 No 18A-12, Bogotá D.C., Colombia
^*Correspondence e-mail: ma.maciasl@uniandes.edu.co, casierraa@unal.edu.co

Edited by K. Fejfarova, Institute of Biotechnology CAS, Czech Republic (Received 15 June 2017; accepted 21 July 2017; online 4 August 2017)

In the title compound, C₁₀H₉NO₂S, all the non-H atoms, except for the ethyl fragment, lie nearly in the same plane. Despite the molecular planarity, the ethyl fragment presents more than one conformation, giving rise to a discrete disorder, which was modelled with two different crystallographic sites for the ethoxy O and ethoxy α-C atoms, with occupancy values of 0.5. In the crystal, the three-dimensional array is mainly directed by C—H⋯(O,N) interactions, giving rise to inversion dimers with R₂²(10) and R₂²(14) motifs and infinite chains running along the [100] direction.

Keywords: crystal structure; thiophene-based cyanoacrylate derivatives; molecular disorder.

CCDC reference: 1563845

1. Chemical context

Cyanoacrylate derivatives are organic compounds with a very important industrial interest due to their use as monomers in the production of adhesives and polymer materials (Gololobov & Krylova, 1995 ). Furthermore, these compounds have been described as promissory intermediates for heterocycle synthesis (Gololobov et al., 1995) and as nitrile-activated precursors in bioreduction reactions (Winkler et al., 2014 ). Still, their most outstanding application is related to their very attractive absorption properties in the UV–Vis region. This capability has been widely described in the literature where cyanoacrylates were employed as precursors for the synthesis of dye-sensitized photovoltaic materials (Chen et al., 2013 ; Zietz et al., 2014 ; Lee et al., 2009 ) and sensors (Zhang et al., 2010 ). Considering that the absorption properties are related to the molecular structure of cyanoacrylate compounds (Ma et al., 2014 ), it is therefore very useful to know their crystal structures in detail in order to have a better understanding of the link between the structures and properties of these derivatives. In this contribution, we present the crystal structure of a thiophene-based cyanoacrylate derivative with promising applications in the synthesis of ligands for metal sensing.

2. Structural commentary

Fig. 1 shows the molecule of the title compound. The near planarity of the molecule (r.m.s. deviation of 0.006 Å) means that nearly all atoms lie in the same plane perpendicular to [010] except for the ethyl ester fragment (O2/C2/O1/C1/C1A), which presents a discrete disorder due to the existence of two conformations of the ethyl moiety that overlay in the same crystallographic site. This disorder was modelled using two sites for the O1, C1 and C1A atoms with occupancy values of 0.5. The split fragment is observed as a reflection of two ethyl moieties in the two opposite sides of the mirror plane that contains the molecule. These atoms lie, respectively, 0.21 (2), 0.340 (7) and −1.010 (10) Å out of this plane. The planarity allows the formation of a weak intramolecular C5—H5⋯O2 close contact (Fig. 1 and Table 1), which generates an S(6) motif. This molecule is similar to (E)-ethyl-2-cyano-3-(furan-2-yl)acrylate (Kalkhambkar et al., 2012 ), differing in the five-membered ring, which is a furanyl in this compound, and presenting a distorted planarity compared with the title compound [dihedral angles of 177.5–179.0° in the two molecules of the asymmetric unit compared with the value of 180.0° in the C6-C5-C3-C2 fragment of the title compound]. Also, no molecular disorder was reported in the furanyl molecule.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C5—H5⋯O2	0.93	2.42	2.799 (3)	104
C7—H7⋯O2ⁱ	0.93	2.55	3.363 (3)	147
C5—H5⋯O2ⁱ	0.93	2.57	3.425 (3)	153
C9—H9⋯N2ⁱⁱ	0.93	2.60	3.520 (4)	172
Symmetry codes: (i) -x+1, -y+1, -z; (ii) -x, -y+1, -z.

Figure 1
The molecular structure of the title compound, showing anisotropic displacement ellipsoids drawn at the 50% probability level. The intramolecular C—H⋯O hydrogen bond is shown as a dashed line (see Table 1

) and the discrete disorder in the ethyl moiety is also observed.

3. Supramolecular features

In the crystal, the packing is directed by C5—H5⋯O2ⁱ and C7—H7⋯O2ⁱ [symmetry code: (i) −x + 1, −y + 1, −z] (see Table 1 and Fig. 2) interactions, which connect pairs of inversion-related molecules, forming slabs of infinite chains running along [100] with R₂²(10) and R₂²(14) motifs, respectively (see Fig. 2). These slabs are further linked by weak C9—H9⋯N2ⁱⁱ [symmetry code: (ii) −x, −y + 1, −z] interactions along the a-axis direction (Table 1). Neighboring chains interact along [001] direction by van der Waals forces, forming (010) sheets. In the [010] direction, only weak dipolar interactions or van der Waals forces act between neighboring sheets to consolidate the three-dimensional array of the crystal structure. Despite the molecular similarity with (E)-ethyl-2-cyano-3-(furan-2-yl)acrylate (Kalkhambkar et al., 2012), the inversion-related molecules in Kalkhambkar's structure, joined by similar intermolecular hydrogen bonds, are further connected by different sorts of C—H⋯O and C—H⋯N weaker interactions involving the furanyl ring.

Figure 2
The crystal structure of the title compound, showing the C—H⋯(O, N) hydrogen-bonding interactions (dotted lines) along the [100] direction.

4. Database survey

A search of the Cambridge Structural Database (CSD Version 5.37 with two updates, Groom et al., 2016 ) for the complete molecule given the option for any substituent in the five-membered ring and/or allowing a saturated chain longer than the ethyl fragment gave three hits, all of them forming parts of molecules bigger than the title compound, giving different supramolecular interactions due not only to the loss of planarity, as in the case of the ethyl-3-(3-chloro-4-cyano-5-{[4-(dimethylamino)phenyl]diazenyl}-2-thienyl)-2-cyanoacrylate (Xu et al., 2016 ), but also due to an increase in the saturated chains as in the case of octyl-2-cyano-3-(4,6-dibromo-7,7-dimethyl-7H-thieno[3′,4′:4,5]silolo[2,3-b]thiophen-2-yl)acrylate (Liu et al., 2016 ) and ethyl-2-cyano-3-(3,3′′′-dihexyl-2,2′:5′,2′′:5′′,2′′′-quaterthiophen-5-yl)acrylate (Miyazaki et al., 2011 ). A search considering any heteroatom in the place of S1 gave six hits. Among them, the more similar compounds correspond to ethyl-(2E)-2-cyano-3-(1-methyl-1H-pyrrol-2-yl)prop-2-enoate (Asiri et al., 2011 ), (E)-ethyl-2-cyano-3-(1H-pyrrol-2-yl)acrylate (Yuvaraj et al., 2011 ) and (E)-ethyl-2-cyano-3-(furan-2-yl)acrylate (Kalkhambkar et al., 2012), the last one being the most similar compound since its molecular conformation is also planar, with the ethyl fragment out of the plane and a furanyl forming the five-membered ring.

5. Synthesis and crystallization

All reagents and solvents were purchased from commercial sources and used as received. In a two-necked round-bottom flask equipped with a condenser, thiophene-2-carboxaldehyde (740 mg, 6.6 mmol), cyanoacetic acid ethyl ester (753 mg, 6.6 mmol) and piperidine (6,8 µL, 1% mol) were stirred in ethanol for three h. A yellowish brown solid was obtained and recrystallized from ethanol solution (see Fig. 3). The product was filtered out and then dried under vacuum. The yellowish brown solid was dissolved in methanol and yellow crystals were grown through slow evaporation of the solvent at room temperature with 80% yield. Melting point: 366–367 K, reported: 365–367 K (Jia et al. 2015 ). ¹H NMR: (DMSO-d⁶, 400 MHz, d, ppm): 1,41 (t, 2H), 4,38 (q, 3H), 7.25 (dd, 1H), 7,81 (d, 1H), 7,85 (d, 1H), 8.36 (s, 1H). ¹³C NMR (DMSO-d⁶, 100 MHz, d, ppm): 14.19, 62.54, 99.3, 115.6, 128.6, 135.1, 136.1, 137.1, 146.6, 162.8.

Figure 3
Schematic representation of the synthetic pathway of ethyl (E)-2-cyano-3-(thiophen-2-yl)acrylate.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2. H atoms were placed in calculated positions (C—H: 0.93–0.97 Å) and included as riding contributions with isotropic displacement parameters set at 1.2–1.5 times the U_eq value of the parent atom.

Table 2
Experimental details

Crystal data
Chemical formula	C₁₀H₉NO₂S
M_r	207.24
Crystal system, space group	Monoclinic, C2/m
Temperature (K)	298
a, b, c (Å)	13.637 (2), 6.8965 (16), 11.817 (3)
β (°)	109.28 (2)
V (Å³)	1049.0 (4)
Z	4
Radiation type	Mo Kα
μ (mm⁻¹)	0.28
Crystal size (mm)	0.19 × 0.12 × 0.07

Data collection
Diffractometer	Agilent SuperNova, Dual, Cu at zero, Atlas
Absorption correction	Multi-scan (CrysAlis PRO; Agilent, 2014 )
T_min, T_max	0.760, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections	9896, 1171, 1049
R_int	0.068
(sin θ/λ)_max (Å⁻¹)	0.625

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.047, 0.126, 1.14
No. of reflections	1171
No. of parameters	96
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.24
Computer programs: CrysAlis PRO (Agilent, 2014), SUPERFLIP (Palatinus & Chapuis, 2007 ), SHELXL2014 (Sheldrick, 2015 ) and Mercury (Macrae et al., 2008 ).

Supporting information

CCDC reference: 1563845

Crystal structure: contains datablock I. DOI: https://doi.org/10.1107/S2056989017010799/ff2150sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989017010799/ff2150Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989017010799/ff2150Isup3.cml

checkCIF report

Computing details top

Data collection: CrysAlis PRO (Agilent, 2014); cell refinement: CrysAlis PRO (Agilent, 2014); data reduction: CrysAlis PRO (Agilent, 2014); program(s) used to solve structure: SUPERFLIP (Palatinus & Chapuis, 2007); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).

Ethyl (E)-2-cyano-3-(thiophen-2-yl)acrylate top

Crystal data top

C₁₀H₉NO₂S	F(000) = 432
M_r = 207.24	D_x = 1.312 Mg m⁻³
Monoclinic, C2/m	Mo Kα radiation, λ = 0.71073 Å
a = 13.637 (2) Å	Cell parameters from 2818 reflections
b = 6.8965 (16) Å	θ = 4.5–26.3°
c = 11.817 (3) Å	µ = 0.28 mm⁻¹
β = 109.28 (2)°	T = 298 K
V = 1049.0 (4) Å³	Parallelepiped, yellow
Z = 4	0.19 × 0.12 × 0.07 mm

Data collection top

Agilent SuperNova, Dual, Cu at zero, Atlas diffractometer	1171 independent reflections
Radiation source: SuperNova (Mo) X-ray Source	1049 reflections with I > 2σ(I)
Detector resolution: 5.3072 pixels mm^-1	R_int = 0.068
ω scans	θ_max = 26.4°, θ_min = 3.1°
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014)	h = −16→16
T_min = 0.760, T_max = 1.000	k = −8→8
9896 measured reflections	l = −14→14

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.047	H-atom parameters constrained
wR(F²) = 0.126	w = 1/[σ²(F_o²) + (0.053P)² + 0.7374P] where P = (F_o² + 2F_c²)/3
S = 1.14	(Δ/σ)_max < 0.001
1171 reflections	Δρ_max = 0.35 e Å⁻³
96 parameters	Δρ_min = −0.24 e Å⁻³
0 restraints	Extinction correction: SHELXL2016 (Sheldrick, 2016), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: iterative	Extinction coefficient: 0.007 (2)

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.

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
S1	0.11266 (5)	0.500000	−0.02961 (7)	0.0560 (3)
N2	0.2293 (2)	0.500000	0.2653 (2)	0.0733 (9)
O2	0.53999 (15)	0.500000	0.1743 (2)	0.0732 (7)
C2	0.4730 (2)	0.500000	0.2195 (3)	0.0568 (7)
C3	0.36045 (19)	0.500000	0.1505 (2)	0.0480 (6)
C4	0.2879 (2)	0.500000	0.2153 (3)	0.0531 (7)
C7	0.2120 (2)	0.500000	−0.1795 (3)	0.0555 (7)
H7	0.264802	0.500000	−0.213002	0.067*
C6	0.22929 (19)	0.500000	−0.0583 (2)	0.0470 (6)
C5	0.33082 (19)	0.500000	0.0298 (2)	0.0468 (6)
H5	0.385193	0.500000	−0.001307	0.056*
C8	0.1056 (2)	0.500000	−0.2475 (3)	0.0630 (8)
H8	0.080614	0.500000	−0.330873	0.076*
C9	0.0436 (2)	0.500000	−0.1786 (3)	0.0616 (8)
H9	−0.028547	0.500000	−0.209250	0.074*
O1	0.48964 (18)	0.531 (3)	0.3371 (2)	0.064 (3)	0.5
C1	0.5976 (3)	0.5493 (10)	0.4143 (4)	0.073 (3)	0.5
H1A	0.600898	0.615277	0.487917	0.088*	0.5
H1B	0.636145	0.625544	0.374142	0.088*	0.5
C1A	0.6446 (5)	0.3535 (15)	0.4422 (6)	0.127 (3)	0.5
H1AA	0.641144	0.288738	0.369077	0.191*	0.5
H1AB	0.607205	0.279578	0.483442	0.191*	0.5
H1AC	0.715902	0.365498	0.492230	0.191*	0.5

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
S1	0.0331 (4)	0.0805 (6)	0.0559 (5)	0.000	0.0168 (3)	0.000
N2	0.0468 (14)	0.122 (3)	0.0570 (16)	0.000	0.0246 (12)	0.000
O2	0.0353 (10)	0.130 (2)	0.0567 (13)	0.000	0.0184 (9)	0.000
C2	0.0379 (14)	0.082 (2)	0.0506 (16)	0.000	0.0144 (12)	0.000
C3	0.0353 (13)	0.0627 (16)	0.0477 (15)	0.000	0.0161 (11)	0.000
C4	0.0373 (13)	0.0740 (19)	0.0472 (15)	0.000	0.0127 (12)	0.000
C7	0.0428 (14)	0.0724 (19)	0.0527 (16)	0.000	0.0179 (12)	0.000
C6	0.0334 (12)	0.0580 (15)	0.0512 (15)	0.000	0.0161 (11)	0.000
C5	0.0332 (12)	0.0559 (15)	0.0530 (15)	0.000	0.0167 (11)	0.000
C8	0.0491 (16)	0.088 (2)	0.0462 (16)	0.000	0.0074 (12)	0.000
C9	0.0368 (14)	0.079 (2)	0.0622 (18)	0.000	0.0069 (13)	0.000
O1	0.0410 (11)	0.103 (10)	0.0458 (12)	−0.003 (2)	0.0122 (9)	−0.008 (2)
C1	0.046 (2)	0.112 (9)	0.055 (2)	−0.005 (2)	0.0070 (17)	−0.019 (3)
C1A	0.093 (5)	0.188 (9)	0.077 (4)	0.053 (5)	−0.004 (3)	−0.019 (5)

Geometric parameters (Å, º) top

S1—C9	1.700 (3)	C5—H5	0.9300
S1—C6	1.732 (3)	C8—C9	1.354 (5)
N2—C4	1.139 (4)	C8—H8	0.9300
O2—C2	1.200 (3)	C9—H9	0.9300
C2—O1	1.350 (5)	O1—C1	1.459 (5)
C2—C3	1.482 (4)	C1—C1A	1.485 (11)
C3—C5	1.347 (4)	C1—H1A	0.9700
C3—C4	1.437 (4)	C1—H1B	0.9700
C7—C6	1.372 (4)	C1A—H1AA	0.9600
C7—C8	1.407 (4)	C1A—H1AB	0.9600
C7—H7	0.9300	C1A—H1AC	0.9600
C6—C5	1.431 (4)

C9—S1—C6	91.57 (14)	C9—C8—H8	123.6
O2—C2—O1	124.3 (3)	C7—C8—H8	123.6
O2—C2—C3	123.9 (3)	C8—C9—S1	112.4 (2)
O1—C2—C3	111.0 (2)	C8—C9—H9	123.8
C5—C3—C4	123.0 (2)	S1—C9—H9	123.8
C5—C3—C2	118.5 (2)	C2—O1—C1	116.7 (3)
C4—C3—C2	118.5 (2)	O1—C1—C1A	109.5 (8)
N2—C4—C3	179.1 (3)	O1—C1—H1A	109.8
C6—C7—C8	112.7 (3)	C1A—C1—H1A	109.8
C6—C7—H7	123.6	O1—C1—H1B	109.8
C8—C7—H7	123.6	C1A—C1—H1B	109.8
C7—C6—C5	123.4 (2)	H1A—C1—H1B	108.2
C7—C6—S1	110.6 (2)	C1—C1A—H1AA	109.5
C5—C6—S1	126.0 (2)	C1—C1A—H1AB	109.5
C3—C5—C6	130.5 (3)	H1AA—C1A—H1AB	109.5
C3—C5—H5	114.7	C1—C1A—H1AC	109.5
C6—C5—H5	114.7	H1AA—C1A—H1AC	109.5
C9—C8—C7	112.8 (3)	H1AB—C1A—H1AC	109.5

O2—C2—C3—C5	0.000 (1)	C2—C3—C5—C6	180.000 (1)
O1—C2—C3—C5	170.1 (8)	C7—C6—C5—C3	180.000 (1)
O2—C2—C3—C4	180.000 (1)	S1—C6—C5—C3	0.000 (1)
O1—C2—C3—C4	−9.9 (8)	C6—C7—C8—C9	0.000 (1)
C8—C7—C6—C5	180.000 (1)	C7—C8—C9—S1	0.000 (1)
C8—C7—C6—S1	0.000 (1)	C6—S1—C9—C8	0.000 (1)
C9—S1—C6—C7	0.000 (1)	O2—C2—O1—C1	−5.6 (17)
C9—S1—C6—C5	180.0	C3—C2—O1—C1	−175.6 (9)
C4—C3—C5—C6	0.000 (1)	C2—O1—C1—C1A	−79.5 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C5—H5···O2	0.93	2.42	2.799 (3)	104
C7—H7···O2ⁱ	0.93	2.55	3.363 (3)	147
C5—H5···O2ⁱ	0.93	2.57	3.425 (3)	153
C9—H9···N2ⁱⁱ	0.93	2.60	3.520 (4)	172

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

Acknowledgements

The authors are grateful for financial support from the Universidad de los Andes. MAM thanks Professor Leopoldo Suescun from UdelaR (Montevideo, Uruguay) for useful and important discussions.

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