A combined experimental and DFT study of a novel unsymmetrical azine 2-(4-methoxybenzylidene)-1-(1-(4-isobutylphenyl) ethylidene) hydrazine

New bis hydrazone: Synthesis, X-ray crystal structure, DFT computations, conformational study and in silico study of the inhibition activity of SARS-CoV-2

The aim of this work was to synthesize new bis hydrazone derived from benzil in good yield, namely: (1Z,2Z)-1,2-bis (3-Chlorophenyl Hydrazino) Benzil, encoded by 3-Cl BHB. The benzil (or 1,2-diphenyl ethanedione) reacts with 3-Cl phenyl hydrazine by reflux method using ethanol as solvent to obtain the target compound. The obtained product is depicted by UV-Vis, IR spectroscopy and XRD-crystals analysis. All various contacts intra and intermolecular found in 3-Cl BHB were determined by the X-ray diffraction technique performed on single crystals. On the other hand, the optimized geometric structure of 3-Cl BHB was computed by the DFT/B3LYP method with 6-31 G (d, p) level. So, the bond lengths and angles, frontier molecular orbitals (FMO), surface electrostatic potential of the molecule (MEP), global reactivity descriptors, Mulliken atomic charges, computed vibrational analysis and electronic absorption spectrum were determined to get a good understanding of the electronic properties and the active sites of 3-Cl BHB, then to compare them with experimental data. Additionally, a conformational study was carried out using the same method (DFT). The structure-activity relationships established through molecular docking studies showed that 3-Cl BHB structure strongly binds to the receptors M^pro (-8.90 Kcal/mol) and RdRp (-8.60 Kcal/mol) which confirm its inhibition activity against COVID-19.

An automated framework for NMR chemical shift calculations of small organic molecules

When using nuclear magnetic resonance (NMR) to assist in chemical identification in complex samples, researchers commonly rely on databases for chemical shift spectra. However, authentic standards are typically depended upon to build libraries experimentally. Considering complex biological samples, such as blood and soil, the entirety of NMR spectra required for all possible compounds would be infeasible to ascertain due to limitations of available standards and experimental processing time. As an alternative, we introduce the in silico Chemical Library Engine (ISiCLE) NMR chemical shift module to accurately and automatically calculate NMR chemical shifts of small organic molecules through use of quantum chemical calculations. ISiCLE performs density functional theory (DFT)-based calculations for predicting chemical properties—specifically NMR chemical shifts in this manuscript—via the open source, high-performance computational chemistry software, NWChem. ISiCLE calculates the NMR chemical shifts of sets of molecules using any available combination of DFT method, solvent, and NMR-active nuclei, using both user-selected reference compounds and/or linear regression methods. Calculated NMR chemical shifts are provided to the user for each molecule, along with comparisons with respect to a number of metrics commonly used in the literature. Here, we demonstrate ISiCLE using a set of 312 molecules, ranging in size up to 90 carbon atoms. For each, calculation of NMR chemical shifts have been performed with 8 different levels of DFT theory, and with solvation effects using the implicit solvent Conductor-like Screening Model. The DFT method dependence of the calculated chemical shifts have been systematically investigated through benchmarking and subsequently compared to experimental data available in the literature. Furthermore, ISiCLE has been applied to a set of 80 methylcyclohexane conformers, combined via Boltzmann weighting and compared to experimental values. We demonstrate that our protocol shows promise in the automation of chemical shift calculations and, ultimately, the expansion of chemical shift libraries.

Crystal structures and Hirshfeld surface analysis of four 1,4-bis(methoxyphenyl)-2,3-diazabuta-1,3-dienes: comparisons of the intermolecular interactions in related compounds

The crystal structures of four azines, namely 1-3-bis(4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 1, 1,3-bis(2,3-dimethoxyphenyl)-2,3-diaza-1,4-butadiene, 2, 1,3-bis(2-hydroxy-3-methoxyphenyl)-2,3-diaza-1,4-butadiene, 3, and 1,3-bis(2-hydroxy-4-methoxyphenyl)-2,3-diaza-1,4-butadiene, 4, are reported. Molecules of 3 and 4, and both independent molecules of 2, Mol A and Mol B, possess inversion centers. The central C=N–N=C units in each molecule is planar with an (E,E) conformation. The intermolecular interactions found in the four compounds are C–H···O, C–H–N, C–H---π and π---π interactions. However, there is no consistent set of intermolecular interactions for the four compounds. Compound, 1, has a two-dimensional undulating sheet structure, generated from C–H···O and C–H···N intermolecular hydrogen bonds. The only recognized intermolecular interaction in 2 is a C–H···O hydrogen bond, which results in a zig-zag chain of alternating molecules, Mol A and Mol B. While 3 forms a puckered sheet of molecules, solely via C–H···π interactions, its isomeric compound, 4, has a more elaborate three-dimensional structure generated from a combination of C–H···O hydrogen bonds, C–H···π and π···π interactions.

The findings in this study, based on both PLATON and Hirshfeld approaches, for the four representative compounds match well the reported structural findings in the literature of related compounds, which are based solely on geometric parameters.

Crystal structures and Hirshfeld surface analyses of halogen substituted azine derivatives, 1,4-bis(halophenyl)-2,3-diazabuta-1,3-dienes

The crystal structures and Hirshfeld surface analyses are reported, from data collected at 100 K, of six 1,4-bis(X,Y-phenyl)-2,3-diazabuta-1,3-dienes (1–6), namely (1: X, Y=H, 4-Cl; 2: X, Y=3,4-Cl2; 3: X, Y=2,4-Cl2; 4: X, Y=H, 2-Br, H; 5: X, Y=H, 3-Br; 6: X, Y=H, 4-Br. The six halogen derivatives crystallise in the monoclinic group P21/c. In each case, the asymmetric unit is one half of the molecule, with the molecules lying across inversion centres, midway between the N–N bonds, with the central C–C=N–N=C–C fragments having all transoid conformations. Each of the six molecules deviates a little from overall planarity. The π···π stacking interactions are the most important intermolecular interactions in each of the six compounds. In the cases of 3 and 4, the π···π stacks are augmented by additional C–X···π (X=Cl or Br) interactions, while in 4, the π···π stacks are linked by weak Br···Br interactions, and in 3, weak Cl···Cl contacts are considered to be also involved in cementing the supra molecular arrangements. The short separations of the layers within the stacks and the extent of the overlaps of the π systems point to significant strengths of the π···π interactions. Comparisons with published structures of related chloro and fluoro compounds indicated similar results: related iodo derivatives, IC6H4CH=N–N=CHC6H4I do not possess as strong π···π interactions. The Hirshfeld analysis indicated further intermolecular contacts which fell outside the normal PLATON cutoff values.