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.

Structure prediction of crystals, surfaces and nanoparticles.

We review the current techniques used in the prediction of crystal structures and their surfaces and of the structures of nanoparticles. The main classes of search algorithm and energy function are summarized, and we discuss the growing role of methods based on machine learning. We illustrate the current status of the field with examples taken from metallic, inorganic and organic systems. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.

What is the best or most relevant global minimum for nanoclusters? Predicting, comparing and recycling cluster structures with WASP@N.

To address the question posed in the title, we have created, and now report details of, an open-access database of cluster structures with a web-assisted interface and toolkit as part of the WASP@N project. The database establishes a map of connectivities within each structure, the information about which is coded and kept as individual labels, called hashkeys, for the nanoclusters. These hashkeys are the basis for structure comparison within the database, and for establishing a map of connectivities between similar structures (topologies). The database is successfully used as a key element in a data-mining study of (MX)12 clusters of three binary compounds (LiI, SrO and GaAs) of which the database has no prior knowledge. The structures are assessed on the energy landscapes determined by the corresponding bulk interatomic potentials. Global optimisation, using a Lamarckian genetic algorithm, is used to search for low lying minima on the same energy landscape to confirm that the data-mined structures form a representative sample of the landscapes, with only very few structures missing from the close energy neighbourhood of the respective global minima.

Thermodynamically accessible titanium clusters TiN, N = 2-32.

We have performed a genetic algorithm search on the tight-binding interatomic potential energy surface (PES) for small TiN (N = 2-32) clusters. The low energy candidate clusters were further refined using density functional theory (DFT) calculations with the PBEsol exchange-correlation functional and evaluated with the PBEsol0 hybrid functional. The resulting clusters were analysed in terms of their structural features, growth mechanism and surface area. The results suggest a growth mechanism that is based on forming coordination centres by interpenetrating icosahedra, icositetrahedra and Frank-Kasper polyhedra. We identify centres of coordination, which act as centres of bulk nucleation in medium sized clusters and determine the morphological features of the cluster.

Band alignment of rutile and anatase TiO2.

The most widely used oxide for photocatalytic applications owing to its low cost and high activity is TiO2. The discovery of the photolysis of water on the surface of TiO2 in 1972 launched four decades of intensive research into the underlying chemical and physical processes involved. Despite much collected evidence, a thoroughly convincing explanation of why mixed-phase samples of anatase and rutile outperform the individual polymorphs has remained elusive. One long-standing controversy is the energetic alignment of the band edges of the rutile and anatase polymorphs of TiO2 (ref. ). We demonstrate, through a combination of state-of-the-art materials simulation techniques and X-ray photoemission experiments, that a type-II, staggered, band alignment of ~ 0.4 eV exists between anatase and rutile with anatase possessing the higher electron affinity, or work function. Our results help to explain the robust separation of photoexcited charge carriers between the two phases and highlight a route to improved photocatalysts.

Nucleation of zeolitic imidazolate frameworks: from molecules to nanoparticles.

We have studied the clusters involved in the initial stages of nucleation of Zeolitic Imidazolate Frameworks, employing a wide range of computational techniques. In the pre-nucleating solution, the prevalent cluster is the ZnIm4 cluster (formed by a zinc cation, Zn2+, and four imidazolate anions, Im-), although clusters such as ZnIm3, Zn2Im7, Zn2Im7, Zn3Im9, Zn3Im10, or Zn4Im12 have energies that are not much higher, so they would also be present in solution at appreciable quantities. All these species, except ZnIm3, have a tetrahedrally coordinated Zn2+ cation. Small ZnxImy clusters are less stable than the ZnIm4 cluster. The first cluster that is found to be more stable than ZnIm4 is the Zn41Im88 cluster, which is a disordered cluster with glassy structure. Bulk-like clusters do not begin to be more stable than glassy clusters until much larger sizes, since the larger cluster we have studied (Zn144Im288) is still less stable than the glassy Zn41Im88 cluster, suggesting that Ostwald's rule (the less stable polymorph crystallizes first) could be fulfilled, not for kinetic, but for thermodynamic reasons. Our results suggest that the first clusters formed in the nucleation process would be glassy clusters, which then undergo transformation to any of the various crystal structures possible, depending on the kinetic routes provided by the synthesis conditions. Our study helps elucidate the way in which the various species present in solution interact, leading to nucleation and crystal growth.

From ergodicity to extended phase diagrams.

Structure prediction of stable and metastable phases is put on equal footing for the first time, with a solid thermodynamical background. How to estimate the lifetime of metastable phases is demonstrated by recent groundbreaking work of Jansen, Pentin, and Schön. At the heart lies the exploration of the Gibbs free-energy landscapes and the extended phase diagrams for complex systems.

The Interplay of Interstitial and Substitutional Copper in Zinc Oxide.

Cu impurities are reported to have significant effects on the electrical and optical properties of bulk ZnO. In this work, we study the defect properties of Cu in ZnO using hybrid quantum mechanical/molecular mechanical (QM/MM)-embedded cluster calculations based on a multi-region approach that allows us to model defects at the true dilute limit, with polarization effects described in an accurate and consistent manner. We compute the electronic structure, energetics, and geometries of Cu impurities, including substitutional and interstitial configurations, and analyze their effects on the electronic structure. Under ambient conditions, CuZn is the dominant defect in the d9 state and remains electronically passive. We find that, however, as we approach typical vacuum conditions, the interstitial Cu defect becomes significant and can act as an electron trap.

Evolutionary structure prediction and electronic properties of indium oxide nanoclusters.

Indium sesquioxide is widely used as a transparent conducting oxide in modern optoelectronic devices; the rising cost of indium has generated interest in the nanoscale properties of In(2)O(3), and questions arise as to the nature of its physicochemical properties below the bulk regime. We report the stable and metastable stoichiometric clusters of (In(2)O(3))(n), where n = 1-10, as predicted from an evolutionary search within the classical interatomic potential and quantum density functional energy landscapes. In contrast to the paradigm set by ZnO, which favours high symmetry bubble-like structures, the In(2)O(3) nanoclusters are found to tend towards dense, low symmetry structures approaching the bulk system at remarkably small molecular masses. Electronic characterisation is performed at the hybrid density functional and many-body GW levels to obtain accurate predictions of the spectroscopic properties, with mean values of the ionisation potentials and electron affinities calculated as 7.7 and 1.7 eV, respectively.

Exploration of multiple energy landscapes for zirconia nanoclusters.

We have predicted the stable and low-energy metastable structures for (ZrO(2))(n) clusters, where n = 1 to 12, employing Density Functional Theory (DFT) at the PBEsol0 level. A process of data mining and the application of an evolutionary algorithm to three different energy landscapes, as defined by interatomic potentials, for each cluster size, was used to generated the plausible structures for refinement using DFT at the PBEsol level. The structures for zirconia were found to be similar to that predicted for titania except that the order, with respect to the binding energies, of the configurations for the two compounds were different for the larger sized clusters. The energies of the local minima configurations and their respective HOMO and LUMO are discussed, as well as the insights gained from employing more than one set of interatomic potentials in the initial global optimisations.

On the problem of cluster structure diversity and the value of data mining.

Data mining, involving cross examination of cluster structure pools collected for ZnO, GaN, LiF and AgI, has been applied to predict plausible cluster structures of related binary materials. We consider the energy landscapes of (MX)(12) clusters for materials that possess tetrahedral bulk phases, wurtzite or sphalerite, including LiF, BeO, BN, AlN, SiC, CuF, ZnO, GaN, GeC and AgI. The energy is evaluated using the hybrid PBEsol0 density functional for structures optimised at the PBEsol level. We report a novel encapsulated iodide structure for AgI and a series of new CuF structures, where significant differences are found between the results for the two functionals.

Modelling nano-clusters and nucleation.

We review the growing role of computational techniques in modelling the structures and properties of nano-particulate oxides and sulphides. We describe the main methods employed, including those based on both electronic structure and interatomic potential approaches. Particular attention is paid to the techniques used in searching for global minima in the energy landscape defined by the nano-particle cluster. We summarise applications to the widely studied ZnO and ZnS systems, to silica nanochemistry and to group IV oxides including TiO(2). We also consider the special case of silica cluster chemistry in solution and its importance in understanding the hydrothermal synthesis of microporous materials. The work summarised, together with related experimental studies, demonstrates a rich and varied nano-cluster chemistry for these materials.

Crystal structure prediction from first principles.

The prediction of structure at the atomic level is one of the most fundamental challenges in condensed matter science. Here we survey the current status of the field and consider recent developments in methodology, paying particular attention to approaches for surveying energy landscapes. We illustrate the current state of the art in this field with topical applications to inorganic, especially microporous solids, and to molecular crystals; we also look at applications to nanoparticulate structures. Finally, we consider future directions and challenges in the field.

Are octahedral clusters missing on the carbon energy landscape?

We report a new class of carbon nanostructures at a lower sub-nano end of the size scale with a surprising stability, as compared to the well-known carbon fullerenes. The octahedral carbon clusters contain tetragonal rings, which, in spite of a common belief, prove to be an energy efficient means of plying graphene sheets to make three-dimensional spheroid shapes, similar to fullerenes. The two families of structures are shown to be competitive at small sizes (∼20 atoms) at room temperature, and for higher temperatures, at both small and large sizes (>200 atoms). Our calculations demonstrate that both vibrational and electronic spectra of these cluster families are similar, which thus might cloud their experimental identification. However, there is a sufficiently strong shift in vibrational frequencies below 160 and in the range of 600-800 cm-1, which should help to identify different types of carbon clusters experimentally. We propose octahedral clusters and other structures containing tetragonal rings as viable structural elements and building units in inorganic chemistry and materials science of carbon along with fullerenes.

Structure and Properties of Nanosilicates with Olivine (Mg2SiO4) N and Pyroxene (MgSiO3) N Compositions.

Magnesium-rich silicates are ubiquitous both terrestrially and astronomically, where they are often present as small particles. Nanosized Mg-rich silicate particles are likely to be particularly important for understanding the formation, processing, and properties of cosmic dust grains. Although astronomical observations and laboratory studies have revealed much about such silicate dust, our knowledge of this hugely important class of nanosolids largely rests on top-down comparisons with the properties of bulk silicates. Herein, we provide a foundational bottom-up study of the structure and properties of Mg-rich nanosilicates based on carefully procured atomistic models. Specifically, we employ state-of-the-art global optimization methods to search for the most stable structures of silicate nanoclusters with olivine (Mg2SiO4) N and pyroxene (MgSiO3) N compositions with N = 1-10. To ensure the reliability of our searches, we develop a new interatomic potential that has been especially tuned for nanosilicates. Subsequently, we refine these searches and calculate a range of physicochemical properties of the most stable nanoclusters using accurate density functional theory based electronic structure calculations. We report a detailed analysis of structural and energy properties, charge distributions, and infrared vibrational spectra, where in all cases we compare our finding for nanosilicates with those of the corresponding bulk silicate crystals. For most properties considered, we find large differences with respect to the bulk limit, underlining the limitations of a top-down approach for describing these species. Overall, our work provides a new platform for an accurate and detailed understanding of nanoscale silicates.