research communications
E)-2-cyano-3-(thiophen-2-yl)acrylate: two conformers forming a discrete disorder
of ethyl (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
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.
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 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 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.
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 forming (010) sheets. In the [010] direction, only weak dipolar interactions or act between neighboring sheets to consolidate the three-dimensional array of the 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.
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.
6. Refinement
Crystal data, data collection and structure . 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 Ueq value of the parent atom.
details are summarized in Table 2Supporting information
CCDC reference: 1563845
https://doi.org/10.1107/S2056989017010799/ff2150sup1.cif
contains datablock I. DOI: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
Data collection: CrysAlis PRO (Agilent, 2014); cell
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).C10H9NO2S | F(000) = 432 |
Mr = 207.24 | Dx = 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 |
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 | Rint = 0.068 |
ω scans | θmax = 26.4°, θmin = 3.1° |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2014) | h = −16→16 |
Tmin = 0.760, Tmax = 1.000 | k = −8→8 |
9896 measured reflections | l = −14→14 |
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(Fo2) + (0.053P)2 + 0.7374P] where P = (Fo2 + 2Fc2)/3 |
S = 1.14 | (Δ/σ)max < 0.001 |
1171 reflections | Δρmax = 0.35 e Å−3 |
96 parameters | Δρmin = −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) |
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. |
x | y | z | Uiso*/Ueq | 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 |
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) |
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) |
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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