Insights into the weak Csp3–H···H–Csp3 mediated supramolecular architecture in ethyl 2-(5-bromopentanamido)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate, a probable selective COX-2 lead molecule: An integrated crystallographic and theoretical approach

Al-Ghulikah, Hanan A.; Gopalan, Akilandeswari; Vahisan, Laxmi Priya Sathiya; Khalaf, Mohamed A.; Ghabbour, Hazem A.; El-Emam, Ali A.; Percino, M. Judith; Thamotharan, Subbiah

doi:10.1016/j.molstruc.2019.127019

Cited by 9 publications

(3 citation statements)

References 56 publications

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“…Proton NMR chemical shifts have appeared to loosely correlate with the exchange‐interaction energies for the considered cyclic hydrocarbons . Although, the nature of close C−H⋅⋅⋅H−C contacts is still controversial, it shall be noticed, that more and more suggestions appear in the recent literature which highlight the importance of rather attractive C−H⋅⋅⋅H−C contacts …”

Section: Resultsmentioning

confidence: 99%

Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho‐Xylene Isomers

et al. 2020

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It is shown herein that intuitive and text‐book steric‐clash based interpretation of the higher energy “in‐in” xylene isomer (as arising solely from the repulsive CH⋅⋅⋅HC contact) with respect to the corresponding global‐minimum “out‐out” configuration (where the clashing C−H bonds are tilted out) is misleading. It is demonstrated that the two hydrogen atoms engaged in the CH⋅⋅⋅HC contact in “in‐in” are involved in attractive interaction so they cannot explain the lower stability of this isomer. We have proven, based on the arsenal of modern bonding descriptors (EDDB, HOMA, NICS, FALDI, ETS‐NOCV, DAFH, FAMSEC, IQA), that in order to understand the relative stability of “in‐in” versus “out‐out” xylenes isomers one must consider the changes in the electronic structure encompassing the entire molecules as arising from the cooperative action of hyperconjugation, aromaticity and unintuitive London dispersion plus charge delocalization based intra‐molecular CH⋅⋅⋅HC interactions.

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Section: Resultsmentioning

confidence: 99%

Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho‐Xylene Isomers

et al. 2020

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“…These contacts operated in a non-electrostatic fashion and provide additional stability to various supramolecular topologies observed in these structures. We also described the importance of similar H···H short contacts observed in adamantane and other organic compounds previously, and these contacts were described as H–H bonding interactions. ,,− …”

Section: Results and Discussionmentioning

confidence: 71%

Probing the Effect of Halogen Substituents (Br, Cl, and F) on the Non-covalent Interactions in 1-(Adamantan-1-yl)-3-arylthiourea Derivatives: A Theoretical Study

et al. 2021

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The effect of halogen substituents (X = Br, Cl, and F) on the crystal packing and intra-and intermolecular interactions in four adamantane−thiourea hybrid derivatives is investigated using different theoretical tools. The bromo and chloro derivatives exhibit 3D isostructurality as evident from lattice parameters, molecular conformation, and crystal packing. The density functional theory study suggests that the molecular conformation of the parent (unsubstituted) and fluoro derivatives exhibits a stable low energy anti−syn conformation. In contrast, bromo and chloro derivatives adopt stable and relatively high energy minima on their potential energy surfaces. Hirshfeld surface analysis reveals the effect of halogen substituents on the intermolecular contacts. The halogen atoms mainly reduce the contribution of H•••H contacts toward crystal packing. PIXEL energy analysis indicates the strong dimer formed by N−H•••S hydrogen bonds in all four structures. It also revealed that a vast number of H•••H contacts observed in different dimers of these structures either presented along with other conventional interactions or solely stabilize the dimeric topology. The topological parameters for intermolecular interactions in these structures suggest an intermediate bonding character between shared and closed-shell interactions for N−H•••S hydrogen bonds in the parent and chloro derivatives. In contrast, the N−H•••S hydrogen bond in other structures is of a closed-shell interaction. Among four derivatives, the fluoro derivative is weakly packed in the solid state based on the PIXEL method's lattice energy calculation.

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“…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 ). It is also noted that the concept of H-H bonding has also been debated in the literature ( Poater et al, 2006 ).…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2023

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A single crystal X-ray diffraction analysis was performed on two positional isomers (m-tolyl and p-tolyl) of acrylonitrile derivatives, namely, (Z)-3-(4-(pyridin-2-yl) phenyl)-2-(m-tolyl) acrylonitrile (1) and (Z)-3-(4-(pyridin-2-yl)phenyl)-2-(p-tolyl) acrylonitrile (2). Compound 1 crystallized in the monoclinic P21/n space group with two crystallographically independent molecules. Compound 2 also possesses two crystallographically independent molecules and crystallized in the triclinic P-1 space group. The Hirshfeld surface analysis revealed that, in both isomers, intermolecular H⋅⋅⋅H/C/N contacts contribute significantly to the crystal packing. More than 40% of the contribution arises from intermolecular C–H⋅⋅⋅C(π) contacts. In both compounds, the relative contribution of these contacts is comparable, indicating that the positional isomeric effects are marginal. The structures in which these isomers are arranged in the solid state are very similar, and the lattice energies are also comparable between the isomers. The Coulomb-London-Pauli-PIXEL (CLP-PIXEL) energy analysis identified the energetically significant dimers. The strength of the intra- and intermolecular interactions was evaluated using the quantum theory of atoms in molecules approach. The UV-Vis absorbance in three different solvents (chloroform, ethanol, and ethyl acetate) for isomers 1 and 2 are very similar. This result is in good agreement with the time-dependent density-functional theory (TD-DFT) calculations.

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Insights into the weak Csp3–H···H–Csp3 mediated supramolecular architecture in ethyl 2-(5-bromopentanamido)-4,5,6,7-tetrahydrobenzo[b]thiophene-3-carboxylate, a probable selective COX-2 lead molecule: An integrated crystallographic and theoretical approach

Cited by 9 publications

References 56 publications

Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho‐Xylene Isomers

Origin of Hydrocarbons Stability from a Computational Perspective: A Case Study of Ortho‐Xylene Isomers

Probing the Effect of Halogen Substituents (Br, Cl, and F) on the Non-covalent Interactions in 1-(Adamantan-1-yl)-3-arylthiourea Derivatives: A Theoretical Study

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

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