Hybrid QM:QM (quantum mechanics:quantum mechanics) and QM:MM (quantum mechanics:molecular mechanics) methods are widely used to calculate the electronic structure of large systems where a full quantum mechanical treatment at a desired high level of theory is computationally prohibitive. The ONIOM (our own N-layer integrated molecular orbital molecular mechanics) approximation is one of the more...

The geometries of various tautomers and isomers of 2-methylamino-2-imidazoline, 2-methylamino-2oxazoline, 2-methylamino-2-thiazoline, 2-phenylamino-2-imidazoline, 2-phenylamino-2-oxazoline, and 2-phenylamino-2-thiazoline have been studied using the Becke3LYP/6–31+G(d,p) DFT, ONIOM(Becke3LYP/6–31+G(d,p):HF/3–21G∗) and ONIOM(Becke3LYP/6–31+G(d,p):AM1) methods. The optimized geometries indicate th...

The energy storage and the molecular rearrangements due to the primary photochemical event in rhodopsin are investigated by using quantum mechanics/molecular mechanics hybrid methods in conjunction with high-resolution structural data of bovine visual rhodopsin. The analysis of the reactant and product molecular structures reveals the energy storage mechanism as determined by the detailed molec...

proton transfer (pt) and methyl group transfer (mgt) occurring in small biomimetic systems, formamide-formamidic acid (fa-fi), and n-formyl-n-methylformamide-(e)-methyl n-formylformimidate (nmfa-nmfi) are investigated in the gas phase and in single-walled carbon nanotubes by using the density functional theory and the oniom approach. it is shown that pt reaction is disfavoured in single-walled ...

In this article, we theoretically analyze the Diels-Alder cycloaddition between cyclopentadiene and C60 for which experimental results on energy barriers and reaction energies are known. The comparison of the results obtained with the two-layered ONIOM approach using different partitions for the high- and low-level layers with those obtained employing the B3LYP/6-31G(d) method for the entire sy...

Glycogen synthase kinase 3β (GSK3β) is a serine/threonine kinase that requires two cofactor Mg(2+) ions for catalysis in regulating many important cellular signals. Experimentally, Li(+) is a competitive inhibitor of GSK3β relative to Mg(2+), while this mechanism is not experienced with other group I metal ions. Herein, we use native Mg(2)(2+)-Mg(1)(2+) GSK3β and its Mg(2)(2+)-M(1)(+) (M = Li, ...

We have studied the convergence properties of embedded and constrained cluster models of proton transfer in zeolites. We applied density functional theory to describe clusters and ONIOM to perform the embedding. We focused on converging the reaction energy and barrier of the O(1) to O(4) jump in H-Y zeolite as well as vibrational and structural aspects of this jump. We found that using successi...

Metal-based anticancer drugs containing Pt (II) (e.g., cisplatin) are among the most effective drugs used in chemotherapy. These agents interfere with DNA’s functions and inhibit its ability to divide, thus destroying cancer cells. However, studies have shown that these types of drugs show limitations because of their lack of specificity in destroying cells. Thus, it is of interest to investiga...

The role of water molecules is increasingly gaining interest in drug design, and several studies have highlighted their paramount contributions to the specificity and the affinity of ligand binding. In this study, we employ the two-layer ONIOM-based quantum mechanics/molecular mechanics (QM/MM) calculations, molecular dynamics (MD) simulations, and molecular docking studies to investigate the e...

The study of the photophysical properties of dendritic-like phosphinothiolate gold(I) complexes has been carried out. The studied complexes are two series of analogous compounds bearing 4 or 8 metal centers: the tetranuclear [Au(4)(S-C(6)H(4)-X)(4){DAB-G0-(PPh(2))(4)}] (X = F (3), MeO (4), Me (5) and NO(2) (6)) and the octanuclear [Au(8)(S-C(6)H(4)-X)(8){DAB-G1-(PPh(2))(8)}] (X = F (9), MeO (10...