We investigate how the choice of the link atom bond length affects an electronic transition energy calculation with the so-called our own N-layer integrated molecular orbital molecular mechanics (ONIOM) hybrid method. This follows our previous paper [M. Caricato et al., J. Chem. Phys. 131, 134105 (2009)], where we showed that ONIOM is able to accurately approximate electronic transition energie...

ONIOM calculation is carried out to estimate the acidity of five aliphatic alcohols before and after adsorbing on the tip of (8,0) single-walled carbon nanotube. The ONIOM method is performed using a combination of density functional theory and AM1 semiemperical method for alcohols and their corresponding conjugated bases. Deprotonation Gibbs free energies of alcohols are calculated and compare...

Saccharopine reductase from Magnaporthe grisea, an NADPH-containing enzyme in the α-aminoadipate pathway, catalyses the formation of saccharopine, a precursor to L-lysine, from the substrates glutamate and α-aminoadipate-δ-semialdehyde. Its catalytic mechanism has been investigated using quantum mechanics/molecular mechanics (QM/MM) ONIOM-based approaches. In particular, the overall catalytic p...

A QM/MM method that combines ONIOM quantum chemistry and molecular dynamics is developed and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). A two-layer ONIOM calculation is used for the reaction complex, with an inner part treated at a high level for the chemical reaction (bond breaking) and a middle part treated at a lower level for relevant prote...

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 ...

The ring-shift isomerization of sym-octahydrophenanthrene (sym-OHP) to sym-octahydroanthracene (sym-OHA) catalyzed by acidic zeolites (Mordenite (MOR) and Faujasite (FAU)) was investigated by the ONIOM(DFT:UFF) and DFT approaches. A "five-membered ring" mechanism through carbocation rearrangement via 1-2 migration was proved to be kinetically favored over a "six-membered ring" mechanism through...

It has been proved that fullerene derivatives, in which an oligophenylenevinylene (OPV) group is attached to C(60), present an interesting photophysical phenomenon and can be incorporated into photovoltaic cells. In these systems, the OPV acts as electron donor upon excitation, and then fullerene absorbs photoexcited electrons. These new organic semiconductor materials offer the prospect of low...

oniom calculation is carried out to estimate the acidity of five aliphatic alcohols before and after adsorbing on the tip of (8,0) single-walled carbon nanotube. the oniom method is performed using a combination of density functional theory and am1 semiemperical method for alcohols and their corresponding conjugated bases. deprotonation gibbs free energies of alcohols are calculated and compare...

We demonstrate that the ONIOM method can be used to optimize a conical intersection between the ground and first excited-state potential energy surfaces of previtamin D (precalciferol), with excitation localized in a small part of the molecule: the hexatriene chromophore. These calculations were up to 100 times faster with little loss of accuracy compared to a full non-ONIOM Target calculation....