Synthesis, characterization, crystal structure and supramolecularity of ethyl (E)-2-cyano-3-(3-methylthiophen-2-yl)acrylate and a new polymorph of ethyl (E)-2-cyano-3-(thiophen-2-yl)acrylate

The synthesis, characterization and crystal structure of the title compounds are reported and the crystal supramolecularity is discussed.


Chemical context
Cyanoacrylate derivatives are of industrial interest being subunits used to build many adhesives and polymeric materials (Faggi et al., 2019). They are also considered important intermediate precursors for the synthesis of different heterocyclic derivatives, see for example Qian et al. (2018), and as nitrile-activated species in bioreduction reactions (Brenna et al., 2013(Brenna et al., , 2015Kong et al., 2016) among others. In addition, they show important practical properties, such as in organic dye-sensitized solar cells (DSSCs) (He et al., 2017;Zhou et al., 2015). Within these voltaic cells, cyanoacrylic acid is one of the most commonly employed acceptors. Thiophene and its derivatives, known to exhibit high charge mobility, serve asbridges (donor--acceptor structure) to provide conjugation and enhance light absorbance (Liu et al., 2012).
An understanding of the structure of thiophene-based acrylate subunits is necessary to benefit from their properties in photovoltaic cells. In a continuation of our work on the X-ray structural characterization of thiophene-containing derivatives (Ibrahim et al., 2019;Al-Refai et al., 2014, we report here the synthesis, characterization and crystal structures of two thiophene-based acrylate derivatives, namely, ethyl (E)-2-cyano-3-(3-methylthiophen-2-yl)acrylate (1) and ethyl (E)-2-cyano-3-(3-methylthiophen-2-yl)acrylate (2). Derivative 2 is a polymorph of a reported structure (Castro Agudelo et al., 2017), but with no disorder of the ethoxy group. The crystal supramolecularity of both compounds is also discussed.

Supramolecular features
In the crystal of 1, the A and B molecules each form layers parallel to the ac plane, Fig. 2a. The layers built up from chains of B molecules are connected via C-HÁ Á ÁO hydrogen bonds along the a axis. These chains are further connected through C-HÁ Á ÁO interactions with stacks of molecules A along the c axis. In the b-axis direction, interlayered interactions through van der Waals forces and/or weak dipolar interactions generate a three-dimensional network. In the crystal of 2, inversion dimers are assembled along the c axis through C-HÁ Á ÁO interactions, Fig. 2b. Adjacent dimers (along the c axis) are further connected through C-HÁ Á ÁN interactions, leading to infinite chains propagating along the c-axis direction. The resulting chains interact via van der Waals forces to form sheets parallel to the ac plane (Fig. 2b). The sheets are connected through van der Waals forces and/or weak dipolar interactions, thus consolidating the three-dimensional framework structure. Compounds 1, 2 and the polymorph of 2 (Castro Agudelo et al., 2017) show no apparent degree ofstacking.
molecules are further connected by van der Waals forces into sheets. (3,3 000 -dihexyl-2,2 0 :5 0 ,2 00 :5 00 ,2 000 -quaterthiophen-5-yl)acrylate (AVUFON;Miyazaki et al., 2011). In all derivatives AVUFON, UMUYAE and QUSKAS, the non-H thiophenebased acrylate fragment is almost planar except for the methyl group (or the longer alkyl chain in QUSKAS) being slightly out of the plane. The crystal lattices of AVUFON, UMUYAE and QUSKAS are stabilized by C-HÁ Á ÁO/S, C-HÁ Á ÁO/N and C-HÁ Á ÁN/S intermolecular interactions, respectively. A further search of the CSD for other five-membered rings instead of thiophene provided six hits. Of them, the following three are very similar to the title compounds: Kalkhambkar et al., 2012). In both AYUGEH and EVIZEP, all the non-H atoms are nearly in the same plane, while in ZAQKIN the furan-based cyanoacrylate moiety lies in the same plane except for the methyl groups, which are slightly out of plane. As far as crystal packing is concerned, the molecules in EVIZEP and ZAQKIN are linked into dimers via N-HÁ Á ÁO and C-HÁ Á ÁO hydrogen bonds, respectively, while in AYUGEH the molecules are linked into tapes via both C-HÁ Á ÁO and C-HÁ Á ÁN interactions. The tapes are further interconnected by C-HÁ Á Á interactions into a three-dimensional structure.

Synthesis and crystallization
All reagents and solvent were purchased from Aldrich and used without further purifications. The title compounds were synthesized as outlined in Fig. 3.
In a 250 ml round-bottom flask connected with a condenser, a mixture of the corresponding thiophene-2-carboxaldehyde (1 mmol), ethylcyanoacetate (1.1 mmol) and ammonium acetate (8 mmol) in absolute ethanol was refluxed for 6 h. The reaction was monitored using thin layer chromatography (TLC plates coated with silica gel). After completion, the reaction mixture was cooled to room temperature, and the obtained yellowish-brown precipitate was filtered off, washed with cooled water, dried and recrystallized from ethanol solution to give the final products as pale-yellow crystals (90% yield for both 1 and 2).

Refinement
Detailed crystal data and structure refinement for the title compounds are listed in Table 3. In 1, C-bound hydrogen atoms were included in calculated positions (0.95-0.99 Å ) and refined using a riding model with U iso (H) = 1.2U eq (C) or 1.5U eq (C-methyl). Methyl groups were allowed to rotate to fit best the electron density. All hydrogen atoms in 2 were located in difference-Fourier maps and refined isotropically.  Miyazaki, E., Okanishi, T., Suzuki, Y., Ishine, N., Mori, H., Takimiya  where P = (F o 2 + 2F c 2 )/3 (Δ/σ) max = 0.001 Δρ max = 0.37 e Å −3 Δρ min = −0.49 e Å −3 Special details 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 (Å 2 )
x y z U iso */U eq O1 0.50743 (12)   0.0252 (7) 0.0285 ( Special details 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.