We have explored mechanically embedded three-layer QM/QM/MM ONIOM models for computational studies of binding in Al-substituted zeolites. In all the models considered, the high-level-theory layer consists of the adsorbate molecule and of the framework atoms within the first two coordination spheres of the Al atom and is treated at the M06-2X/6-311G(2df,p) level. For simplicity, flexibility and ...

Linear–dendrite copolymers containing hyper branched poly(citric acid) and linear poly(ethylene glycol) blocks PCA–PEG–PCA are promising nonmaterial to use  in nanomedicine. To investigate their potential application in biological systems (especially for drug carries) ONIOM2 calculations were applied to study the nature of particular interactions between drug and the polymeric nanoparticle...

In many applications of multilevel/multiscale methods, an active zone must be modeled by a high-level electronic structure method, while a larger environmental zone can be safely modeled by a lower-level electronic structure method, molecular mechanics, or an analytic potential energy function. In some cases though, the active zone must be redefined as a function of simulation time. Examples in...

Quantum chemical calculations of the structures and thermodynamics of homolytic dissociation of the central P-P and N-N bonds in tetrakis(disyl)diphosphine and tetrakis(di-tert-butylsilyl)hydrazine have been performed. The theory predicted negative standard enthalpies for homolytic bond dissociation in both cases, -71.0 and -108.4 kJ mol(-1) for the diphosphine and hydrazine, respectively, usin...

For large reactive systems, the calculation of energies can be simplified by treating the active part with a high-level quantum mechanical ~QM! ~ab initio or density functional! approach and the environment with a less sophisticated semiempirical ~SE! approach, as an improvement over the widely used hybrid quantum mechanical/molecular mechanical ~QM/MM! methods. An example is the interaction be...

Zinc proteases are ubiquitous and the zinc ion plays a central function in the catalytic mechanism of these enzymes. A novel class of mechanism-based inhibitors takes advantage of the zinc ion chemistry in carboxypeptidase A (CPA) to promote covalent attachment of an inhibitor to the carboxylate of Glu-270, resulting in irreversible inhibition of the enzyme. The effect of the active site zinc i...

Spin trapping of hydroperoxyl radical (HOO.) by the amide-linked conjugate of 5-carbamoyl-5-methyl-1-pyrroline N-oxide (AMPO) to β-cyclodextrin (β-CD) was studied computationally using a two-layered ONIOM method. From a conformational perspective, the "internal" conformation of 5R-β-CD-AMPO is more favored than the "external" conformation in which the nitrone is located outside of the cavity of...

The adsorption of methanol, formaldehyde and formic acid on the Si(100)-2]1 surface have been investigated by means of Ðrst-principles density functional cluster model calculations and ab initio ONIOM calculations. The dissociative adsorption of methanol on the Si(100) surface takes place readily, giving rise to and 3 SiÈH surface species. The reaction, occurring barrierlessly via a stable chem...

Hybrid energy methods such as QM/MM and ONIOM, that combine different levels of theory into one calculation, have been very successful in describing large systems. Geometry optimization methods can take advantage of the partitioning of these calculations into a region treated at a quantum mechanical (QM) level of theory and the larger, remaining region treated by an inexpensive method such as m...