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

Abstract

Single crystals of two pyridine isomers containing cyano and thiophene moieties {systematic names: (Z)-2-(pyridine-2-yl)-3-(thiophen-2-yl)acrylonitrile, C 12 H 8 N 2 S, I and (Z)-2-(pyridine-3-yl)-3-(thiophen-2yl)acrylonitrile, C 12 H 8 N 2 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 ≈ 4 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 • • •N, C-H • • • π, C-H • • •S, π • • • π and S • • • 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.

Solution and Solid-State Photophysical Properties of Positional Isomeric Acrylonitrile Derivatives with Core Pyridine and Phenyl Moieties: Experimental and DFT Studies

“…The interactions associated with these energies for I – V are shown in Figure 16 , Figure 17 , Figure 18 , Figure 19 and Figure 20 . These values are very similar for reported compounds with acrylonitrile moieties with non-hydrogen-bonding interactions [ 43 , 44 , 46 ]. Also, most of the interaction energy values are within the expected range for these synthons calculated by PIXEL and can be used to identify intermolecular interactions that are perceived as binding [ 83 , 86 , 90 , 91 ].…”

“…The optical properties can also be altered by substituents located in various positions around the molecular structure [ 41 , 43 , 44 ]. Especially, the optical properties of compounds containing a pyridine ring and with α-cyanostilbenes with dimethylamine, diphenylamine, halogen atoms and N -ethylcarbazole substituents have been reported [ 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 ].…”

Weak noncovalent interactions in two positional isomers of acrylonitrile derivatives: inputs from PIXEL energy, Hirshfeld surface and QTAIM analyses

“…The remaining two of them are H⋅⋅⋅H contacts (H-H bonding) formed between H atoms of rings A and B and between vinylic CH and H atom of the ring C ( Figure 3A ). The former H-H bonding and C–H⋅⋅⋅C contacts were observed in closely related structures repored earlier ( Venkatesan et al, 2018 ; Udayakumar et al, 2019c , 2019b , 2020 ). The importance of the non-electrostatic origin of the H-H bonding has been discussed elsewhere ( Matta et al, 2003 ; Al-Ghulikah et al, 2020 ; El-Emam et al, 2020 ).…”

“…This is primarily due to the electronic nature, size, flexibility of the molecular backbone, and position (multiple) of substituents as well as steric demands ( Desiraju et al, 2011 ; Gavezzotti, 2013 ; Brandenburg and Grimme, 2014 ; Tiekink, 2014 ; Beran, 2016 ). There are numerous factors that influence solid-state fluorescence, including crystal packing ( Wang and Li, 2017 ; Wu et al, 2017 ), molecular conformation, and noncovalent interactions ( Butler et al, 2017 ; Udayakumar et al, 2019c , 2019b , 2020 ; Jana et al, 2020 ). Significant positional effects may occur due to the stabilization of polar structures.…”

Quantitative analysis of hydrogen and chalcogen bonds in two pyrimidine-5-carbonitrile derivatives, potential DHFR inhibitors: an integrated crystallographic and theoretical study

“…A similar intramolecular interaction has also been observed in many cyano containing organic compounds reported earlier from our group. [59][60][61] This intramolecular interaction was further examined in both X-ray and optimized structures using QTAIM analysis. In the X-ray geometry of 1, the bond path is established between H and cyano carbon (hence it is a C-H/C interaction) whereas in the corresponding optimized structure, the bond path is shied to cyano N from cyano carbon (hence it is a C-H/N interaction).…”