Hirshfeld surface analysis, interaction energy calculations and in silico anti-SARS-CoV-2 potentials of metal (II) 3,4-dimethoxybenzoate with nicotinamide complexes

In this study, types of the intermolecular interactions, the intermolecular interaction energies, void analysis of diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)zinc(II) dihydrate (Complex 1), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)nickel(II) dihydrate (Complex 2), diaquabis(3,4-dimethoxybenzoate)bis(nicotinamide)cobalt(II) dihydrate (Complex 3), whose crystal structures were characterized before, were investigated with the help of the CrystalExplorer program (Version 21.5). It has been determined that H…H, H…O/O…H, H…C/C…H, H…N/N…H, C…C, C…O/O…C, O…O, and C…N/N…C interactions are intermolecular interactions that contribute to the Hirshfeld surface of the complexes. According to the results of the interaction energy analysis calculated with the help of B3LYP/6-31G(d,p), B3LYP/6-31G(d), B3LYP/3-21G, HF/6-31G(d,p), HF/6-31G(d), HF/3-21G, DFT/6-31G(d,p), DFT/6-31G(d), DFT/3-21G, MP2/6-31G(d,p), MP2/6-31G(d), MP2/3-21G basis sets, the major amount of the total energy is contributed by electrostatic and polarization energies. The interactions between Complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 were investigated by Molecular docking studies. It was determined that complexes 1-3 and the main protease enzyme and the spike protein of Omicron variant of the SARS-CoV-2 interact via attractive charges, hydrogen bonding, electrostatic contacts, and hydrophobic interactions. According to the obtained results, further in vivo/in vitro studies are recommended for complex 3. The results determined as a result of interaction energy analysis and molecular docking studies show that the hydrogen bonds formed by the hydrogen bond donor/acceptor groups in the structure of the complexes are an important factor in both the stability of the crystal package and inhibition of important enzymes of SARS CoV-2.