Experimental study and DFT calculation for the strength of intermolecular interactions in Schiff base with the phenylarsonic acid scaffold

Experimental, Theoretical, and In Silico Studies of Potential CDC7 Kinase Inhibitors

In this work, we present the synthesis, solid-state characterization, and in silico studies of two pyrazole derivatives: 5-(2-methylphenoxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (I) and 5-(4-methylphenoxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (II). The molecular crystal properties, in terms of intermolecular hydrogen bonds and other weak interactions, are analyzed using single crystal X-ray diffraction. The Hirshfeld surfaces computational method is used to quantify the intermolecular interactions, density functional theory for theoretical structural optimization, and its comparison with the experimental structure and in-silico studies using docking and molecular dynamics studies of I and II with CDC7-kinase. In addition, the quantum theory of atoms in molecules (QTAIM) approach is applied to calculate the topological properties of electron density and the Laplacian of electron density of the chemical bonds of both molecules. Compounds I and II crystallize in a monoclinic crystal system, and molecules are connected via C-H···O intermolecular hydrogen bonds. Hirshfeld surfaces analysis revealed that the H···H type intercontact contributes more toward the crystal packing. DFT-optimized structures show a perfect overlay with the experimental structures. The in silico results show that both I (-41.50 kcal/mol) and II (-44.53 kcal/mol) exhibit strong binding free energies as ligands binding to the active sites of the CDC7-kinase. The most significant contributions for ligand and protein binding in both compounds are dominated by van der Waals interactions.

The effect of hydrogen bonding on the π depletion and the π-π stacking interaction

Non-covalent interactions such as hydrogen bonding and π-π stacking are essential types of interactions governing molecular self-assembly. The π-π stacking ability of aromatic rings depends on the electron density of the π orbitals, which is affected by the electron-withdrawing or electron-donating properties of the substituents. We have here studied the effect of hydrogen bonding on the strength of the π-π stacking interactions by calculating the binding energies at the explicitly correlated Møller-Plesset (MP2-F12) perturbation theory level using polarized triple-ζ quality basis sets. The stacking interactions in the presence of hydrogen bonding are found to be stronger than in the absence of the hydrogen bonding suggesting that hydrogen bonds lead to π depletion, which affects the aromatic character of the aromatic rings and increases the strength of the π-π stacking interaction. We have also studied how hydrogen bonding affects the stacking interaction by calculating local orbital locator integrated pi over plane (LOLIPOP) indices. Comparing LOLIPOP indices with the stacking-interaction energies calculated at the MP2-F12 level shows that there is no clear correlation between the stacking-interaction energies and LOLIPOP indices.