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.

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.

Diffusion in gadolinium doped ceria thin films: a combined Monte Carlo and molecular dynamics study.

The mobility of oxygen ions at surfaces and interfaces in solid oxide fuel materials is controversial. Experiments are complex and conflicting results for grain boundary and surface O2- diffusion have been obtained. Thus, it is not clear what the necessary conditions are to optimise O2- diffusion during the manufacturing process. To aid the interpretation of experimental results, combined Monte Carlo and molecular dynamics simulations were applied to model thin films of CeO2 on binary oxide substrates. The objective of this work is to determine the effects of both tensile lattice strain and segregation on the calculated diffusion coefficients. The distribution of Gd3+ and O2- ions has been interpreted as evidence for the formation of a space charge layer at both the interface and surface. The space charge layer impacts the calculated diffusion coefficients at the thin film surface. Moderate tensile strain in the CeO2 thin film has little influence on the segregation of Gd3+ ions.

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 Gd(2)Ti(2)O(7) and Gd(2)Zr(2)O(7) 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.

Guest-adaptable and water-stable peptide-based porous materials by imidazolate side chain control.

The peptide-based porous 3D framework, ZnCar, has been synthesized from Zn(2+) and the natural dipeptide carnosine (ß-alanyl-L-histidine). Unlike previous extended peptide networks, the imidazole side chain of the histidine residue is deprotonated to afford Zn-imidazolate chains, with bonding similar to the zeolitic imidazolate framework (ZIF) family of porous materials. ZnCar exhibits permanent microporosity with a surface area of 448 m(2) g(-1) , and its pores are 1D channels with 5 Šopenings and a characteristic chiral shape. This compound is chemically stable in organic solvents and water. Single-crystal X-ray diffraction (XRD) showed that the ZnCar framework adapts to MeOH and H2 O guests because of the torsional flexibility of the main His-ß-Ala chain, while retaining the rigidity conferred by the Zn-imidazolate chains. The conformation adopted by carnosine is driven by the H bonds formed both to other dipeptides and to the guests, permitting the observed structural transformations.

Monte Carlo simulation and free energies of mixed oxide nanoparticles.

A Monte Carlo Exchange technique is used to study the thermodynamic properties of MgO-MnO nanoparticles ranging in size from 1728 to 21,952 ions. The solubility of Mg(2+) is much greater in MnO than the reverse, reflecting the difference in size between the two cations. The solubility, for a given temperature, diminishes with nanoparticle size. As the Mn concentration is progressively increased the Mn(2+) ions occupy the corners, edges and then surface sites of the nanoparticle before entering subsurface layers. We do not observe any pronounced ordering of the cations within the body of the nanoparticles themselves. The enthalpies of forming ternary nanoparticles from particles of MgO and MnO of the same size vary with the size of the nanoparticle and become more positive for a given concentration as the particle size increases. Free energies of mixing of the two end-member nanoparticles have been determined using the semigrand ensemble. The consolute temperature (the temperature above which there is complete miscibility) increases non-linearly with the size of the nanoparticle by approximately 70% over the size range considered.

Non-hexagonal ice at hexagonal surfaces: the role of lattice mismatch.

It has long been known that ice nucleation usually proceeds heterogeneously on the surface of a foreign body. However, little is known at the microscopic level about which properties of a material determine its effectiveness at nucleating ice. This work focuses on the long standing, conceptually simple, view on the role of a good crystallographic match between bulk ice and the underlying substrate. We use grand canonical Monte Carlo to generate the first overlayer of water at the surface and find that the traditional view of heterogeneous nucleation does not adequately account for the array of structures that water may form at the surface. We find that, in order to describe the structures formed, a good match between the substrate and the nearest neighbour oxygen-oxygen distance is a better descriptor than a good match to the bulk ice lattice constant.

Monte Carlo simulation of segregation in ceramic thin films.

A Monte Carlo exchange technique is used to study segregation in thin ceramic films with application to MgO/MnO. The approach is not restricted to the dilute limit. Surface concentrations as a function of temperature and film composition are determined directly from the simulations. For all compositions studied (Mn(chi)Mg(1-chi)O, 0 < or = chi < or = 1) the (001) surface is Mn(2+) rich; the occupancy of sites by Mn(2+) decreases rapidly with depth. The ratio of the number of Mn(2+) to Mg(2+) ions at the surface decreases as a function of temperature. The calculated enthalpies of segregation of Mn(2+) for the thin film are strongly dependent on the total Mn(2+) concentration at small Mn(2+) concentrations, with the enthalpy of segregation varying by a factor of two with surface coverage.

Simulating surface diffusion and surface growth in ceramics.

We examine the movement of ion pairs on the surfaces of simple oxides. Using temperature-accelerated dynamics the elementary processes involved are identified and the activation energies of these used as input to kinetic Monte Carlo simulations. Results are presented for the motion of BaO and SrO ion pairs on the (100) surfaces of BaO and SrO, respectively, and the formation of island pairs on these surfaces is studied. The simulations reveal the importance of exchange mechanisms in surface diffusion and growth of oxides. The importance of such reactions has been recognised previously for metallic surfaces but not for ionic systems, where it has been assumed that ionic surface diffusion is surface diffusion via the hopping motion of ion pairs from one surface site to another. Exchange mechanisms can dominate transport processes both on terraces and steps for both homoepitaxial and heteroepitaxial growth. We suggest the unavoidable mixing when an exchange mechanism operates must be considered when attempting to grow sharp interfaces in oxide nanostructures.