Theoretical Characterization of the Hydrogen Bonding Interaction Sites of Mycolactone C Using the ONIOM Method

<p>In this work, the ONIOM method, recognized for its effectiveness on large molecules, was used to determine the geometric, energetic, and spectroscopic parameters of hydrogen bond interactions of mycolactone C. Mycolactone C; one of the most virulent forms of toxin, found in Africa and Australia. It has eight (08) oxygen heteroatoms which are all hybridized sp² and sp³. Using quantum chemistry methods, at the ONIOM level (B3LYP/6-311+G (d, p): AM1), we have determined the preferential binding sites of the hydrogen bonds in the eight mycolactone C oxygen heteroatoms studied. Analysis of the results revealed that the heteroatom O₅sp² is the most suitable site for creating a strong hydrogen bond based on the geometric, energetic (free enthalpy of complexation), and spectroscopic (vibration frequency shifts) parameters. Identifying this O5sp2 heteroatom is a significant step forward in developing a methodology for eradicating the infection and the destructive effects of this toxin.</p>

Theoretical insight into dihydrogen activation with β-diketiminato ligand supported Group 13 and 14 elements: mechanism and activity difference

On the basis of density functional theory (DFT) calculations within the framework of the ONIOM method, here we report a new bimolecular mechanism for understating dihydrogen activation using the β-diketiminate...

Computational Studies on the Molecule 1-(2-Hydroxyethyl)-5-Fluorouracil in Gas Phase and Aqueous Solution and Prediction of Its Confinement inside Capped Nanotubes

Density functional theory (DFT) calculations were performed on a fluorouracil derivative at the B3LYP/6−31+G(d) level. Furthermore, the ONIOM method was performed to investigate the possibility of its confinement inside capped nanotubes. The results found of the structural parameters of the optimized molecule are in good agreement with experimental data. The analysis of thermodynamic properties leads us to predict that the confinement of the studied molecule inside capped nanotubes SWCNT(12,0), SWCNT(14,0), and SWCNT(16,0) is possible. The large Eg values found suggest a good stability for the studied molecule. The predicted nonlinear optical (NLO) properties of the studied molecule are much greater than those of urea. Thereby, it is a good candidate as second-order NLO material. The calculated ∆Gsol values suggest that the studied molecule is more soluble than the 5-FU molecule. The results of quantum molecular descriptors show that the studied molecule is hard electrophile and strongly reactive.

Towards high-level theoretical studies of large biodiesel molecules: an ONIOM/RRKM/Master-equation approach to the isomerization and dissociation kinetics of methyl decanoate radicals

The isomerization and dissociation reactions of methyl decanoate (MD) radicals were theoretically investigated by using high-level theoretical calculations based on a two-layer ONIOM method, employing the QCISD(T)/CBS method for the high layer and the M06-2X/6-311++G(d,p) method for the low layer.

Binding of ellagic acid and urolithin metabolites to the CK2 protein, based on the ONIOM method and molecular docking calculations

Using three-layer ONIOM and molecular docking calculations to investigate the binding of urolithins to the active site of the CK2 protein.