Guada Barea

Theoretical modeling of the heme group with a hybrid QM/MM method

The quality of the results obtained in calculations with the hybrid QM/MM method IMOMM on systems where the heme group is partitioned in QM and MM regions is evaluated through the performance of calculations on the 4‐coordinate [Fe(P)] (P = porphyrin), the 5‐coordinate [Fe(P)(1−(Me)Im)] (Im = imidazole) and the 6‐coordinate [Fe(P)(1−(Me)Im)(O2)] systems. The results are compared with those obtained from much more expensive pure quantum mechanics calculations on model systems. Three different properties are analyzed—namely, the optimized geometries, the binding energies of the axial ligands to the heme group, and the energy cost of the biochemically relevant out‐of‐plane displacement of the iron atom. Agreement is especially good in the case of optimized geometries and energy cost of out‐of‐plane displacements, with larger discrepancies in the case of binding energies.

Theoretical study of the reaction mechanism of the uncatalyzed epoxidation of alkenes by iodosylbenzene

The origin of the barrier for the uncatalyzed epoxidation of alkenes by iodosylbenzene is examined from a computational point of view. The reaction of a monomeric unit with ethylene presents a very low barrier, in disagreement with experimental data indicating the requirement of a catalyst. The polymeric structure of iodosylbenzene was then analyzed and the importance of the presence of a terminal hydration water in its linear structure confirmed. The reaction of a model dimer with ethylene is shown to have a high barrier, in good agreement with experiment. Implications of this result with respect to the nature of the catalytic mechanism are briefly discussed.

Basis set influence on the ab initio description of the dihydrogen complex [Os(PH3)2Cl(CO)H(H2)]1

Abstract Systematic RHF calculations on the [Os(PH3)2Cl(CO)H(H2)] complex with eleven different basis sets are presented. Among the basis sets considered there are examples of valence double-ζ quality and of valence triple-ζ quality, as well as examples containing diffuse and polarization functions and examples without them. The comparison of the optimized geometries and the total energies leads to the definition of a hierarchy of basis set qualities for the computation of the structure and reactivity of transition metal complexes.

Theoretical assessment on the viability of possible intermediates in the reaction mechanism of catalase and peroxidase models

IMOMM (Becke3LYP:MM3) calculations are performed on different proposed intermediates in the reaction pathway of biomimetic models of catalase and peroxidase enzymes. These calculations allow the identification of their ground state, structural features and relative energies. The relative energies are shown to depend heavily on the nature of the substrates involved in the reaction, and they are analyzed in detail for the case of the oxidation of alcohol to aldehyde by hydrogen peroxide. All the considered intermediates are found to be within a reasonable energy span.