A quantitative study of weak noncovalent interactions in two pyridine isomers containing nitrile and thiophene moieties: a combined X-ray and theoretical investigation

  • Mani Udayakumar
  • Margarita Cerón
  • Paulina Ceballos
  • Perumal Venkatesan
  • M Judith Percino
  • Subbiah ThamotharanEmail author
Regular Article


Single crystals of two pyridine isomers containing cyano and thiophene moieties {systematic names: (Z)-2-(pyridine-2-yl)-3-(thiophen-2-yl)acrylonitrile, \(\hbox {C}_{{12}}\hbox {H}_{{8}}\hbox {N}_{{2}}\hbox {S}\), I and (Z)-2-(pyridine-3-yl)-3-(thiophen-2-yl)acrylonitrile, \(\hbox {C}_{{12}}\hbox {H}_{{8}}\hbox {N}_{{2}}\hbox {S}\), II} were obtained from ethanol-cyclohexane mixture. The thiophene ring was found to be disordered over two orientations (syn and anti) in II. The potential energy surface scan of thiophene ring rotation suggests that the syn conformer is more stable by \(\approx 4 \,\hbox {kcal mol}^{-1}\) than that of the anti-conformer. The optimized structures obtained using the DFT method (M06-2X/cc-pVTZ level of theory) show a high degree of similarity with the experimental structures. A detailed experimental and theoretical analysis on the intra- and intermolecular interactions observed in these structures is reported. The molecules arranged in the crystalline state are completely different in I and II. Intermolecular interactions are qualitatively analyzed using Hirshfeld surface and its associated 2D fingerprint plots. The intermolecular interaction energies of different molecular pairs are calculated using the PIXEL method. Several weak non-covalent interactions such as C–H \(\cdot \cdot \cdot \hbox {N}\), C–H \(\cdot \cdot \cdot \uppi \), C–H \(\cdot \cdot \cdot \hbox {S}\), \(\uppi \cdot \cdot \cdot \uppi \) and \(\hbox {S}\cdot \cdot \cdot \hbox {N}\) contacts play a vital role in the stabilization of crystal structures. These interactions are further explored by the topological analysis of the electron density based on the quantum theory of the atoms-in-molecules approach.

Graphic abstract

Crystal structures of two pyridine isomers of acrylonitrile derivatives are reported. Structures are stabilized by several weak non-covalent interactions such as C–H \(\cdot \cdot \cdot \hbox {N}\), C–H \(\cdot \cdot \cdot \uppi \), C–H \(\cdot \cdot \cdot \hbox {S}\), \(\uppi \cdot \cdot \cdot \uppi \) and \(\hbox {S}\cdot \cdot \cdot \hbox {N}\) contacts in the solid state. Evaluation of these weak non-covalent interactions has been performed by means of the quantum theory of atoms-in-molecules approach (QTAIM).


Pyridine nitrile thiophene PIXEL QTAIM MESP 



The authors would like to thank Laboratorio Nacional de Supercoìmputo del Sureste (LNS-BUAP) for the calculus service and the 100184100-VIEP2019 (VIEP-BUAP) and SA/103.5/15/12684 (PRODEP-SEP) projects, as well as Dr. Maxime A. Siegler (Johns Hopkins University) for the assistance with data collection. ST thanks the DST-SERB (SB/YS/LS-19/2014) for financial assistance.

Supplementary material

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Supplementary material 1 (pdf 2269 KB)
12039_2019_1636_MOESM2_ESM.pdf (1.1 mb)
Supplementary material 2 (pdf 1082 KB)


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Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.Biomolecular Crystallography Laboratory, Department of Bioinformatics, School of Chemical and BiotechnologySASTRA Deemed UniversityThanjavurIndia
  2. 2.Unidad de Polímeros y Electrónica Orgánica, Instituto de CienciasBenemérita Universidad Autónoma de PueblaSan Pedro ZacachimalpaMexico

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