Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling

Order parameter and connectivity topology analysis of crystalline ceramics for nuclear waste immobilization

We apply bond order and topological methods to the problem of analysing the results of radiation damage cascade simulations in ceramics. Both modified Steinhardt local order and connectivity topology analysis techniques provide results that are both translationally and rotationally invariant and which do not rely on a particular choice of a reference structure. We illustrate the methods with new analyses of molecular dynamics simulations of single cascades in the pyrochlores Gd2Ti2O7 and Gd2Zr2O7 similar to those reported previously (Todorov et al 2006 J. Phys.: Condens. Matter 18 2217). Results from the Steinhardt and topology analyses are consistent, while often providing complementary information, since the Steinhardt parameters are sensitive to changes in angular arrangement even when the overall topological connectivity is fixed. During the highly non-equilibrium conditions at the start of the cascade, both techniques reveal significant localized transient structural changes and variation in the cation connectivity. After a few picoseconds, the connectivity is largely fixed, while the order parameters continue to change. In the zirconate there is a shift to the anion disordered system while in the titanate there is substantial reversion and healing back to the parent pyrochlore structure

Kinetic Monte Carlo modeling of oxide thin film growth.

In spite of the increasing interest in and application of ultrathin film oxides in commercial devices, the understanding of the mechanisms that control the growth of these films at the atomic scale remains limited and scarce. This limited understanding prevents the rational design of novel solutions based on precise control of the structure and properties of ultrathin films. Such a limited understanding stems in no minor part from the fact that most of the available modeling methods are unable to access and robustly sample the nanosecond to second timescales required to simulate both atomic deposition and surface reorganization at ultrathin films. To contribute to this knowledge gap, here we have combined molecular dynamics and adaptive kinetic Monte Carlo simulations to study the deposition and growth of oxide materials over an extended timescale of up to ∼0.5 ms. In our pilot studies, we have examined the growth of binary oxide thin films on oxide substrates. We have investigated three scenarios: (i) the lattice parameter of both the substrate and thin film are identical, (ii) the lattice parameter of the thin film is smaller than the substrate, and (iii) the lattice parameter is greater than the substrate. Our calculations allow for the diffusion of ions between deposition events and the identification of growth mechanisms in oxide thin films. We make a detailed comparison with previous calculations. Our results are in good agreement with the available experimental results and demonstrate important limitations in former calculations, which fail to sample phase space correctly at the temperatures of interest (typically 300-1000 K) with self-evident limitations for the representative modeling of thin films growth. We believe that the present pilot study and proposed combined methodology open up for extended computational support in the understanding and design of ultrathin film growth conditions tailored to specific applications

Adaptive kinetic Monte Carlo simulation of solid oxide fuel cell components

Millisecond length simulations have been performed to directly calculate accurate ionic conductivities in solid oxide fuel cell (SOFC) electrolyte and cathode materials using adaptive kinetic Monte Carlo (aKMC).</p

Simulations of doped CeO2 at finite dopant concentrations

Monte Carlo calculations are reported of calcium- and gadolinium-doped ceria solid solutions, Ce1 − xCaxO2 − x (CDC) and Ce1 − xGdxO2 − x/2 (GDC) as a function of dopant concentration x. Previous work has largely been restricted to the dilute defect limit, made a priori assumptions of the formation of particular clusters, and neglected temperature effects. All these constraints are removed in our study. We examine and compare the formation of Ca and Gd-nanodomains with increasing dopant concentration. The growth of Ca-rich domains in Ce1 − xCaxO2 − x is particularly marked even at low concentrations of calcium.Conductivities of the configurations generated in the Monte Carlo simulations are calculated using molecular dynamics. The Monte Carlo generates the thermodynamically most stable low-energy atomic arrangements and these configurations possess low conductivities relative to those in which the dopants are distributed at random; the nanodomains formed by the dopants reduce oxygen mobility due to the low local concentration of oxygen vacancies and the blocking of pathways for vacancy migration. The calculated conductivity of a Σ5(310) grain boundary of Ce1 − xGdxO2 − x/2 with overall composition x = 0.2 is comparable to that of the bulk material despite pronounced segregation to the interfacial region.Overall our results illustrate the importance of kinetic vs. thermodynamic control in synthesis of these systems.</p