5-(Adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole (4) was identified as a potential 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) inhibitor and this paper describes the in-depth structural analysis thereof. Compound 4 was synthesized in a 92% yield and its 3D-structure confirmed by single-crystal X-ray diffraction. Hirshfeld surface analysis indicated that H…H, C-H…C, C-H…Cl and especially C-H…N hydrogen bond interactions are the primary contributors to the intermolecular stabilisation in the crystal. In order to explore the properties of 4, free from the influence of the crystal field, density functional theory (DFT) calculations were conducted. Results indicated that the DFT optimized geometry of 4 produced a conformer (4a) that is significantly different from the crystal structure. Further experiments confirmed that the crystal structure is not the absolute minimum conformation. This indicated that the crystal packing forces has significantly influenced the conformation thereof. Frontier molecular orbital energies and net atomic charges were also calculated to elucidate the electronic properties of 4a. These results provided insight into areas of the molecule that may present with the ability to form binding interactions at the 11β-HSD1 active site. Molecular docking experiments revealed important intermolecular interactions between 4a and 11β-HSD1. These results indicate that 4 may be considered for further drug design endeavors.

/pdf/crystal-structure-hirshfeld-surface-analysis-and-dft-studies-14fcb9lhf4.pdf

Crystal structure, Hirshfeld surface analysis and DFT studies of 5-(adamantan-1-yl)-3-[(4-chlorobenzyl)sulfanyl]-4-methyl-4H-1,2,4-triazole, a potential 11β-HSD1 inhibitor.

Three adamantane-1,3,4-thiadiazole hybrid derivatives namely; N-ethyl-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amine I, N-(4-fluorophenyl)-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amine II and (4-bromophenyl)-5-(adamantan-1-yl)-N-1,3,4-thiadiazole-2-amine III, have been synthesized and crystal structures have been determined at low temperature. The structures revealed that the orientation of the amino group is different in non-halogenated structures. Intra- and intermolecular interactions were characterized on the basis of the quantum theory of atoms-in-molecules (QTAIM) approach. Intermolecular interaction energies for different molecular pairs have been obtained using the PIXEL method. Hirshfeld surface analysis and 2D-fingerprint plots revealed that the relative contributions of different non-covalent interactions are comparable in compounds with halogen (Br and F) substitutions. Crystal structures of II and III show isostructural behaviour with 1D supramolecular constructs. In all three structures, the N–H⋯N hydrogen bond was found to be stronger among other noncovalent interactions. The H–H bonding showed a closed shell in nature and played significant roles in the stabilization of these crystal structures.

/pdf/quantitative-assessment-of-the-nature-of-noncovalent-4m8126uzu6.pdf

Quantitative assessment of the nature of noncovalent interactions in N -substituted-5-(adamantan-1-yl)-1,3,4-thiadiazole-2-amines: insights from crystallographic and QTAIM analysis

A detailed experimental and theoretical investigation on the intermolecular interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles is reported. The intermolecular interactions are analyzed and quantified by PIXEL, DFT and quantum theory of atoms in molecules (QTAIM) calculations. The results showed that the absence of strong classical hydrogen bonds and the presence of several weak intermolecular C–H⋯N, C–H⋯halogen, halogen⋯halogen and π stacking interactions play important roles in the stabilization of crystal structures. Four different π stacking dimers (homo parallel, homo slipped parallel, hetero anti-parallel and hetero anti-parallel slipped) are observed and found to be the most stabilized dimeric motifs in all structures. The hetero anti-parallel (−10.6 kcal mol−1) and slipped anti-parallel (−9.1 kcal mol−1) π⋯π interactions have the highest stabilization energies among the other interactions observed in the present study. The substituted halogen atoms (X = F, Cl and Br) are involved in the variant and invariant C–H⋯X, C⋯X and halogen⋯halogen interactions in all three families. The relative contributions of various non-covalent interactions are calculated using Hirshfeld surface analysis and 2D fingerprint plots. Further, detailed UV-vis spectral studies are reported for the title compounds in solution and solid phases. These results are compared with the simulated spectra and good agreement is found between experimental and theoretical spectra.

Quantitative analysis of weak non-covalent interactions in (Z)-3-(4-halophenyl)-2-(pyridin-2/3/4-yl)acrylonitriles

Investigation of potential anti-malarial lead candidate 2-(4-fluorobenzylthio)-5-(5-bromothiophen-2-yl)-1,3,4-oxadiazole: Insights from crystal structure, DFT, QTAIM and hybrid QM/MM binding energy analysis

Gangadharan Ganesh Muthu

Papers

Theoretical investigations of two adamantane derivatives: A combined X-ray, DFT, QTAIM analysis and molecular docking