Molecular dynamics simulation of an activated transfer reaction in zeolites

The activated transfer of a light particle between two heavier species in the micropores of silicalite and ZK4 zeolites has been studied through molecular dynamics (MD) simulations. A three-body potential controls the exchange of the light particle between the heavier ones; an effective barrier of a few kBT separates the two stable regions corresponding to symmetric "reactant" and "product" species. Harmonic forces always retain the reactants at favorable distances so that in principle only the energetic requirement must be fulfilled for the transfer to occur. The rate constant for the process (obtained from a correlation analysis of equilibrium MD trajectories) decreases by more than one order of magnitude when the barrier height is increased from 2kBT to 5kBT following an Arrhenius-type behavior. The transfer rates are always lower in ZK4. When the reaction is studied in a liquid solvent the calculated rate constants are closer to those obtained in silicalite. Since with this model the diffusive approach of the reactants is almost irrelevant on the reactive dynamics, only the different ability of each environment to transfer the appropriate energy amount to the reactants and then promote the barrier passage could be invoked to explain the observed behavior. We found that structural, rather than energetic, effects are mainly involved on this point. The lower efficiency of ZK4 seems to arise from the frequent trapping of the reactive complex in the narrow ZK4 windows in which the transfer is forbidden and from the weaker interaction of the reactive complex with the host framework compared to silicalite

Diffusion and vibrational relaxation of a diatomic molecule in the pore network of a pure silica zeolite: a molecular dynamics study

The vibrational relaxation and the diffusion of diatomic molecules in the zeolite silicalite have been studied through molecular dynamics simulations in the microcanonical statistical ensemble. The adopted model accounts for the vibrations of the framework and sorbed atoms using a harmonic potential for the silicalite and a Morse potential for the diatomic molecule. The results show that the framework favors the relaxation of diatomics oscillating at frequencies near to its characteristic vibrational frequencies, leading in such cases to lower relaxation times and to an increasing in the energy exchanged per collision. The diffusion of a two-site oscillating molecule representing ethane has been also investigated; the diffusion coefficient and the heat of adsorption agree very well with the experimental data. Arrhenius parameters for the diffusion have been calculated, and some insights into the diffusion mechanism have been obtained from log–log plots and by inspection of the distribution of the ethane molecules in the silicalite channels. Therefore the simplified model adopted seems to adequately describe the diffusive motion and the guest–host energy exchanges, and it could be useful in order to study simple bimolecular reactions in zeolites

"Two-step" model of molecular diffusion in silicalite

The influence of the particle "memory" on long-range diffusion in the channel network of silicalite is taken into account by considering pairs of subsequent steps between the channel intersections. It is shown that in this case the correlation rule between the principal elements of the diffusion tensor has to be modified by including an additional term, which takes account of the deviation of molecular propagation from complete randomness. The obtained relations are discussed in terms of molecular dynamics simulations of ethane in silicalite

Two- and <i>N</i>-step correlated models for the analysis of molecular dynamics trajectories of linear molecules in silicalite

Recent molecular dynamics data on the diffusion of linear diatomic and triatomic molecules in the zeolite silicalite are analyzed in terms of a new correlated model [F. Jousse, S. M. Auerbach, and D. P. Vercauteren, J. Chem. Phys. 112, 1531 (2000)] capable to account for both first- and higher-order correlation effects. This "N-step" model reproduces very well our calculated mean square displacements and diffusion coefficients of the molecules considered. The improvements with respect to the results obtained with our previous "two-step" model [P. Demontis, J. Kärger, G. B. Suffritti, and A. Tilocca, Phys. Chem. Chem. Phys. 2, 1455 (2000)] are remarkable for all molecules except chlorine, showing that only in this case the effect of (negative) correlations spanning more than two jumps between channel intersections (~20 Å) can be neglected. The basic trajectory analysis in terms of single- and two-step models, besides being an useful reference, provides all the input data needed for the application of the N-step model. Indeed, in its silicalite formulation, the N-step model is strongly linked to the two-step one because it calculates the probability of a sequence of jumps in the same channel by means of the correlations between any two consecutive jumps. Finally, the possibility to obtain qualitative insight into the diffusive mechanism through various kind of correlation coefficients is discussed

Application of the two-step model to the diffusion of linear diatomic and triatomic molecules in silicalite

Molecular dynamics simulations of the diffusion of diatomic oscillators representing the halogen molecules and of linear flexible triatomic species modelling CO2 and CS2 have been carried out in the zeolite silicalite. The main purpose was to compare the performance of the random walk model to that of its "two-step" extension in representing molecular migration inside such an interconnected 3-D pore network. The two-step model always gives a better estimate of the elements of the diffusion tensor, and also provides some interesting insight into the features of the molecular motion of the studied species. The analysis of the two-step event probabilities is also applied to assess the extent of diffusive memory in each case

A Classical molecular dynamics study of recombination reactions in a microporous solid

Classical molecular dynamics calculations have been applied to the study of the recombination reaction of photodissociated radical species. Within a simplified reaction scheme it has been possible to get qualitative information about the influence of the environment. A comparison has been made between reactions in a liquid solvent and in a complex structured environment, such as a microporous silicate. Marked differences in the recombination yield and in the energy relaxation mechanism have been observed

The antioxidant properties of Ce-containing bioactive glass nanoparticles explained by Molecular Dynamics simulations

Molecular dynamics simulations of two glass nanoparticles with composition 25Na2O\ub725CaO 50SiO2 mol% (Ce-K NP) and 46.1SiO2\ub724.4Na2O\ub726.9CaO\ub7 2.6P2O5 mol.% (Ce-BG NP) doped with 3.6 mol% of CeO2 have been carried out in order to explain the enhanced antioxidant properties of the former glass with respect to the latter. The present models show that the different catalase mimetic activity of the two NPs is related to the Ce3+/Ce4+ ratio exposed at their surface. In fact, this ratio is about 3.5 and 13 in the bulk and at the surface of the Ce-BG NP, and 1.0 and 2.1 in the bulk and at the surface of the Ce-K NPs, respectively. Since both oxidation states are necessary for the catalysis of the dismutation reaction of hydrogen peroxides, NPs with a very high Ce3+/Ce4+ ratio possess poorer antioxidant properties. Moreover, our simulations reveal that the already low silicate connectivity found in the bulk glasses examined here is further reduced on the nanoparticle surface, whereas the Na+/Ca2+ ratio rapidly increases. Sodium, calcium and cerium sites in proximity of the surface are found to be under-coordinated, prone to quickly react with water present in physiological environments, thus accelerating the glass biodegradatio

Electric-field-dependent empirical potentials for molecules and crystals: a first application to flexible water molecule adsorbed in zeolites

A general method to include electric-field-dependent terms in empirical potential functions representing interatomic interactions is proposed. It is applied to derive an intramolecular potential model for the water molecule able to reproduce the effects of an electric field on its geometry and dynamics: to enlarge the HOH angle, to increase slightly the OH bond lengths, to red-shift the stretching vibrational frequencies, and to blue-shift slightly the bending mode frequency. These effects have been detected experimentally for water adsorbed in zeolites and have been confirmed by quantum mechanical calculations. The electric-field-dependent intramolecular potential model for water has been combined with a newly refined intermolecular potential for bulk water and with new potentials representing cation–water and aluminosilicate–water interactions in order to simulate, by classical molecular dynamics (MD) technique, the behavior of water adsorbed in zeolites. The performances of the model have been checked by a MD simulation of liquid water at room temperature, by the structural and vibrational properties of the water dimer, and by test MD calculations on a hydrated natural zeolite (natrolite). The results are encouraging, and the simulations will be extended to study the behavior of water adsorbed in other zeolites, including diffusion and some aspects of ion exchange processes

Cystic echinococcosis in cattle dairy farms: spatial distribution and epidemiological dynamics

A study monitoring cystic echinococcosis (CE) in adult dairy cattle from intensive livestock farms located in the municipality of Arborea (Sardinia, Italy) was carried out between 2012 and 2015. A retrospective study of veterinary reporting forms of post-mortem inspections in 10 different Italian slaughterhouses was also performed. In addition, data on viability and molecular characterisation of hydatid cysts removed from parasitised organs in cattle was carried out. A geographical information system (GIS) with data layers of the study area and the geo-referenced points of 160 cattle farms was constructed. CE was found in 21.9% (35/160) of the surveyed farms. The retrospective study revealed that 0.05% (13/23,656) of adult slaughtered animals (over one year of age) from Arborea had tested positive to CE. The results stratified per year showed the following CE prevalences: 0.09% (5/5673) in 2012; 0.02% (1/5682) in 2013; 0.08% (5/6261) in 2014; and 0.03% (2/6040) in 2015 (χ2 with 3 degrees of freedom=3.81; P=0.282). The E. granulosus sensu stricto (formerly called G1 or sheep strain) was detected in all cysts subjected to molecular analysis. The GIS analysis showed that CE is fairly resilient in the Arborea territory where most of cattle farms are located, while a small cluster of cases was found located in the southeastern part of Arborea, close to districts where sheep farms are situated. The present survey reports the presence of CE in Sardinian dairy cattle intensive farms and suggests that the parasitic pressure of CE in the island continues to be very strong