Galina P. Petrova

Support nanostructure boosts oxygen transfer to catalytically active platinum nanoparticles

Interactions of metal particles with oxide supports can radically enhance the performance of supported catalysts. At the microscopic level, the details of such metal-oxide interactions usually remain obscure. This study identifies two types of oxidative metal-oxide interaction on well-defined models of technologically important Pt-ceria catalysts: (1) electron transfer from the Pt nanoparticle to the support, and (2) oxygen transfer from ceria to Pt. The electron transfer is favourable on ceria supports, irrespective of their morphology. Remarkably, the oxygen transfer is shown to require the presence of nanostructured ceria in close contact with Pt and, thus, is inherently a nanoscale effect. Our findings enable us to detail the formation mechanism of the catalytically indispensable Pt-O species on ceria and to elucidate the extraordinary structure-activity dependence of ceria-based catalysts in general.

Catalytic role of vicinal OH in ester aminolysis: proton shuttle versus hydrogen bond stabilization.

This computational study provoked by the process of peptide bond formation in the ribosome investigates the influence of the vicinal OH group in monoacylated diols on the elementary acts of ester aminolysis. Two alternative approaches for this influence on ester ammonolysis were considered: stabilization of the transition states by hydrogen bonds and participation of the vicinal hydroxyl in proton transfer (proton shuttle). The activation due to hydrogen bonds of the vicinal hydroxyl via tetragonal transition states was rather modest; the free energy of activation was reduced by only 5.2 kcal/mol compared to the noncatalyzed reaction. The catalytic activation via the proton shuttle mechanism with participation of the vicinal OH in the proton transfer via hexagonal transition states resulted in considerable reduction of the free energy of activation to 33.5 kcal/mol, i.e., 16.0 kcal/mol lower than in the referent process. Accounting for the influence of the environment on the reaction center by a continuum model (for ε from 5 to 80) resulted in further stabilization of the rate-determining transition state by 4-5 kcal/mol. The overall reduction of the reaction barrier by about 16 kcal/mol as compared to the noncatalyzed process corresponds to about 10(9)-fold acceleration of the reaction, in agreement with the experimental estimate for acceleration of this process in the ribosome.

Interaction of ethene and ethyne with bare and hydrogenated Ir4 clusters. A density functional study

The paper reports a computational study of species that can be formed during ethene hydrogenation on iridium clusters. The simulated concentrations of the complexes (C2Hm)Ir4Hn (m = 2–5, 0 ≤ n ≤ 14 − m) based on calculated Gibbs free energies suggest at low temperature and high hydrogen pressure π-bonded ethene to be the dominant species at the Ir4 cluster covered by hydrides. At higher temperature and lower H2 pressure, this model predicts ethylidyne and, subsequently, di-σ-coordinated ethyne with a minor or zero amount of hydride ligands on the metal cluster. Ethyl, vinyl, and vinylidene species were calculated to be less stable over the range of the hydrogen coverage studied. Ethane desorption from the most stable complex was calculated to be thermodynamically favorable for systems in which at least three hydride ligands will remain on the metal cluster after desorption. Adsorption of one of these organic ligands and/or hydrogen results in an oxidation of the metal moiety; this effect is more pronounced in complexes with ethylidyne, vinyl, and vinylidene. The calculated vibrational spectra of ethylidyne on Ir4Hn clusters agree well with available experimental data for this species on iridium surfaces and supported metal particles. The spectra of the various organic species in the region of C–H stretching modes (3300–2700 cm−1) were calculated to overlap, in particular in the presence of hydride ligands on the metal moiety.

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

We describe automated procedures for the first stages of a systematic computational investigation of reaction mechanisms. They include (i) selection of computational method and basis set based on statistical analysis of structural and energy data relating to experimental values, (ii) determination of all distinct conformations of transition states with large conformational freedom, and (iii) generation of unknown geometry of the transition states, based on pre-defined connectivity of the atoms involved in the reaction. For the conformational search we employed an efficient procedure for exploration of various possible conformations of the transition states and elimination of the equivalent structures in several steps using molecular-mechanical and quantum-mechanical methods. The procedure was applied to the determination of the structures of transition states and intermediates in the ammonolysis of monoformylated 1,2-ethanediol, which were subsequently used for identification of the lowest energy reaction paths. For the same reaction system we also used the approach for generation of the initial structures of transition states with unknown geometry. The reported procedures are implemented in the MolRan program suite.

Determination of the optimal position of adjacent proton-donor centers for the activation or inhibition of peptide bond formation – A computational model study

The study reports a computational analysis of the influence of proton donor group adjacent to the reaction center during ester ammonolysis of an acylated diol as a model reaction for peptide bond formation. This analysis was performed using catalytic maps constructed after a detailed scanning of the available space around the reaction centers in different transition states, a water molecule acting as a typical proton donor. The calculations suggest that an adjacent proton donor center can reduce the activation barrier of the rate determining transition states by up to 7.2 kcal/mol, while no inhibition of the reaction can be achieved by such a group.

Computational elucidation of the reaction mechanism for synthesis of pyrrolidinedione derivatives via Nef-type rearrangement – cyclization reaction

This paper reports a quantum chemical study of all stages of a one-pot synthesis of pyrrolidinedione derivatives from nitromethane and coumarin, which includes Michael addition, migration of an oxygen atom (Nef-type rearrangement), and cyclization to a pyrrolidine ring. The energy barrier of deprotonated nitromethane addition to coumarin is 21.7 kJ mol−1, while the barrier of proton transfer from the methylene to the nitro group in the nitromethyl group is notably higher, 197.8 kJ mol−1. The second stage of the reaction, migration of an oxygen atom within the nitromethyl group, occurs with lowest energy barrier, 142.4 kJ mol−1, when it is assisted by an additional water molecule. The last stage – cyclization, passes with a very low energy barrier of 11.9 kJ mol−1 but the tautomerization of the nitrosohydroxymethyl group to the hydroxy-N-hydroxyiminomethyl, necessary for the process, has an energy barrier of 178.4 kJ mol−1. Analogous calculations for the same process with the ethyl ester of 3-coumarin-carboxylic acid as substrate show that the relative energies of the intermediates and transition states are by at most 10–16 kJ mol−1 more stable than the corresponding structures with coumarin.

Computational Modelling of Nanoporous Materials

Publisher Summary This chapter reviews the contemporary computational approaches based on quantum chemical or hybrid methods, which are used for modeling of nanoporous materials such as zeolites and other molecular sieves. The computational methods for modeling of micro- and mesoporous materials and various processes on them are divided in two groups according to the level at which the interactions in the system are described – molecular mechanical and quantum chemical methods. The combination between them, the so-called hybrid QM/MM methods, is also applied in various cases, but it is usually considered together with the higher level method—quantum chemical. Since the quantum chemical approaches are orders of magnitude more demanding computationally, they are applied for smaller systems or systems with smaller unit cells compared to molecular mechanical methods. The selection of the model depends on the structure of the system and the properties to be investigated, as well as on the computational method. For crystalline microporous materials, three types of models are used—isolated cluster models, hybrid embedded cluster models, and periodic models. The quantum chemical methods are used for description of problems and processes connected with chemical interactions and reactions, redistribution of electron density, simulation of spectral features connected with the electronic structure of the material, its active centers, or guest species. The simplest way for modeling of processes in zeolites and mesoporous materials are isolated cluster models, which have several drawbacks, but in many cases the obtained results are reasonable.