Understanding noble gas incorporation in mantle minerals: an atomistic study.

Ab initio calculations in forsterite (Mg 2 SiO 4 ) are used to gain insight into the formation of point defects and incorporation of noble gases. We calculate the enthalpies of incorporation both at pre-existing vacancies in symmetrically non-equivalent sites, and at interstitial positions. At high pressure, most structural changes affect the MgO 6 units and the enthalpies of point defects increase, with those involving Mg and Si vacancies increasing more than those involving O sites. At 15 GPa Si vacancies and Mg interstitials have become the predominant intrinsic defects. We use these calculated enthalpies to estimate the total uptake of noble gases into the bulk crystal as a function of temperature and pressure both in the presence and absence of other heterovalent trace elements. For He and Ne our calculated solubilities point to atoms occupying mainly interstitial sites in agreement with previous experimental work. In contrast, Ar most likely substitutes for Mg due to its larger size and the deformation it causes within the crystal. Incorporation energies, as well as atomic distances suggest that the incorporation mainly depend on the size mismatch between host and guest atoms. Polarization effects arising from the polarizability of the noble gas atom or the presence of charged defects are minimal and do not contribute significantly to the uptake. Finally, the discrepancies between our results and recent experiments suggest that there are other incorporation mechanisms such as adsorption at internal and external interfaces, voids and grain boundaries which must play a major role in noble gas storage and solubility.

Multilevel quantum mechanical calculations show the role of promoter molecules in the dehydration of methanol to dimethyl ether in H-ZSM-5.

Methyl carboxylate esters promote the formation of dimethyl ether (DME) from the dehydration of methanol in H-ZSM-5 zeolite. We employ a multilevel quantum method to explore the possible associative and dissociative mechanisms in the presence, and absence, of six methyl ester promoters. This hybrid method combines density functional theory, with dispersion corrections (DFT-D3), for the full periodic system, with second-order Møller-Plesset perturbation theory (MP2) for small clusters representing the reaction site, and coupled cluster with single, double, and perturbative triple substitution (CCSD(T)) for the reacting molecules. The calculated adsorption enthalpy of methanol, and reaction enthalpies of the dehydration of methanol to DME within H-ZSM-5, agree with experiment to within chemical accuracy (∼4 kJ mol-1). For the promoters, a reaction pathway via an associative mechanism gives lower overall reaction enthalpies and barriers compared to the reaction with methanol only. Each stage of this mechanism is explored and related to experimental data. We provide evidence that suggests the promoter's adsorption to the Brønsted acid site is the most important factor dictating its efficiency.

Interactive molecular dynamics in virtual reality for modelling materials and catalysts.

Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.

Fast-ion conduction and local environments in BIMEVOX.

The energy landscape of the fast-ion conductor Bi4V2O11 is studied using density functional theory. There are a large number of energy minima, dominated by low-lying thermally accessible configurations in which there are equal numbers of oxygen vacancies in each vanadium-oxygen layer, a range of vanadium coordinations and a large variation in Bi-O and V-O distances. By dividing local minima in the energy landscape into sets of configurations, we then examine diffusion in each different layer using ab initio molecular dynamics. These simulations show that the diffusion mechanism mainly takes place in the 〈110〉 directions in the vanadium layers, involving the cooperative motion of the oxide ions between the O(2) and O(3) sites in these layers, but not O(1) in the Bi-O layers, in agreement with experiment. O(1) vacancies in the Bi-O layers are readily filled by the migration of oxygens from the V-O layers. The calculated ionic conductivity is in reasonable agreement with the experiment. We compare ion conduction in δ-Bi4V2O11 with that in δ-Bi2O3. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.

Cooperative excitations in superionic PbF2.

Links between dynamical Frenkel defects and collective diffusion of fluorides in ß-PbF2 are explored using Born-Oppenheimer molecular dynamics. The calculated self-diffusion coefficient and ionic conductivity are 3.2 × 10-5 cm2 s-1 and 2.4 Ω-1 cm-1 at 1000 K in excellent agreement with pulsed field gradient and conductivity measurements. The calculated ratio of the tracer-diffusion coefficient and the conductivity-diffusion coefficient (the Haven ratio) is slightly less than unity (about 0.85), which in previous work has been interpreted as providing evidence against collective 'multi-ion' diffusion. By contrast, our molecular dynamics simulations show that fluoride diffusion is highly collective. Analysis of different mechanisms shows a preference for direct collinear 'kick-out' chains where a fluoride enters an occupied tetrahedral hole/cavity and pushes the resident fluoride out of its cavity. Jumps into an occupied cavity leave behind a vacancy, thereby forming dynamic Frenkel defects which trigger a chain of migrating fluorides assisted by local relaxations of the lead ions to accommodate these chains. The calculated lifetime of the Frenkel defects and the collective chains is approximately 1 ps in good agreement with that found from neutron diffraction. This article is part of the Theo Murphy meeting issue 'Understanding fast-ion conduction in solid electrolytes'.

Predicted strong spin-phonon interactions in Li-doped diamond.

DFT calculations of the Li substitutional defect in diamond based on the B3LYP functional and a 64-atom supercell indicate that (i) the quartet (Sz = 3/2) state is lower in energy than the doublet (Sz = 1/2) state by 0.07 eV (810 K) for fully relaxed static structures and by 0.09 eV (1045 K) with the inclusion of zero-point vibrations, (ii) the effective charges at the Li and four neighbouring C sites are similar in the two spin states, but there are substantial differences in the corresponding spin distributions, and (iii) there are unprecedented differences in the Raman spectra of the two spin states, in terms of both frequency distributions and intensities, that can most reasonably be attributed to strong spin-phonon coupling, in view of the very similar charge distributions in the two states. These differences are an order of magnitude greater than those reported previously for any bulk transition metal or rare-earth compound. The basis sets and functional used in these calculations predict many of the relevant constants (a0, c11, c44) of diamond mostly to within 1% of the experimental values, most notably the TO(X) Raman frequency and the phonon density of states. Comparisons with the calculated Raman spectra of the quintet (Sz = 2) and singlet (Sz = 0) spin states of the neutral vacancy defect, which have similar spin distributions at the four neighbouring C atoms (Cn) to the vacancy site as those at the corresponding Cn sites in the quartet and singlet states of the Li defect, show that the differences in the two Raman spectra of the latter defect are closely related to those in the former.

Ab initio study of negative electron affinity from light metals on the oxygen-terminated diamond (1 1 1) surface.

Recent computational work has shown that light metals adsorbed onto the oxygenated diamond (1 0 0) surface have the potential to give diamond a temperature-stable negative electron affinity (NEA). Here, we use density functional theory to study three of these metals, lithium, magnesium and aluminium, on the (1 1 1) surface. We show that all three of these metals adsorbed onto the ketone O-terminated diamond surface can possess a large NEA and adsorption energies above that of H-termination at monolayer (ML) or sub-ML coverages. Adsorption onto the ether O-terminated surface gives similarly large NEAs but lower adsorption energies. These results are promising for the development of novel NEA surfaces such as those required for thermionic devices.

Graphene and novel graphitic ZnO and ZnS nanofilms: the energy landscape, non-stoichiometry and water dissociation.

The energy landscapes of ultra-thin nanofilms of ZnO and ZnS are examined in detail using periodic hybrid density functional calculations. We predict new staggered graphitic forms, which are stable only for the thinnest films and are of particular interest as the electronic structure shows a spontaneous symmetry breaking across the film and consequently a marked decrease in band gap with thickness. The relative energies of the various forms, their structural and electronic properties and their variation with film thickness are discussed. Possible kinetic pathways for transitions from the graphitic forms are examined by explicit evaluation of transition state energies. For polar surfaces, such as (0001) würtzite and (111) zinc blende, many different mechanisms operate to remove or reduce the surface dipole depending on the number of layers in the nanofilm. The polar ZnS nanofilms, but not the polar ZnO analogues or any non-polar film, are predicted to spontaneously become non-stoichiometric by loss of zinc atoms from the surface. The behaviour of adsorbed water on the ultra-thin films is also examined. There is no dissociation on any ZnS film. For ZnO, dissociation into OH- and H+ takes place not only on (101̄0) würtzite, but also on (110) zinc blende. This result that does not appear to have been reported previously and deserves future experimental study. While we concentrate on ZnO and ZnS, similar energy landscapes are expected for any oxide or sulphide which adopts the würtzite or zinc blende structure in the bulk.

A theoretical study of substitutional boron-nitrogen clusters in diamond.

Substitutional clusters of multiple light element dopants are a promising route to the elusive shallow donor in diamond. To understand the behaviour of co-dopants, this report presents an extensive first principles study of possible clusters of boron and nitrogen. We use periodic hybrid density functional calculations to predict the geometry, stability and electronic excitation energies of a range of clusters containing up to five N and/or B atoms. Excitation energies from hybrid calculations are compared to those from the empirical marker method, and are in good agreement. When a boron-rich or nitrogen-rich cluster consists of three to five atoms, the minority dopant element-a nitrogen or boron atom respectively-can be in either a central or peripheral position. We find B-rich clusters are most stable when N sits centrally, whereas N-rich clusters are most stable with B in a peripheral position. In the former case, excitation energies mimic those of the single boron acceptor, while the latter produce deep levels in the band-gap. Implications for probable clusters that would arise in high-pressure high-temperature co-doped diamond and their properties are discussed.

Adventures in boron chemistry - the prediction of novel ultra-flexible boron oxide frameworks.

Recent periodic density functional calculations have predicted the existence of ultra-flexible low-energy forms of boron oxides in which rigid boron-oxygen heterocycles are linked by flexible B-O-B bridges. The minima in the energy landscapes of these frameworks are remarkably broad, with widths in excess of those of many hybrid metal-organic frameworks. Enormous changes in cell volume, which can exceed a factor of two, are accompanied by negligible changes in energy. Here we explore the underlying reasons for this behaviour using molecular electronic-structure calculations, periodic density functional theory and template-based geometric simulations. The angular flexibility of the B-O-B bridge depends only upon the geometry of the local B2O5 unit, independent of the configuration of neighbouring bridges. Unique cooperativity between the bending and twisting motions of the bridges leads to considerable anisotropy in framework flexibility. Exceptional flexibility is conferred not only by the intrinsic bending flexibility of the bridges but by topological factors, crucially the relaxation of torsional constraints when B3O3 rings are present. We test these conclusions by showing how the flexibility of the frameworks can be tuned by decoration with isoelectronic rings. The new nanoporous boron oxides presented in this work are predicted to be potential novel guest-host materials because of their flat energy landscapes. Furthermore, such structures can be generated systematically from silicates by the substitution of B2O54- for SiO44-. A borate analogue of ß-cristobalite is shown to be isoenergetic with the known B2O3-I polymorph. We raise the possibility of new families of frameworks and zeolite analogues.

Negative electron affinity from aluminium on the diamond (1 0 0) surface: a theoretical study.

Density functional theory calculations were performed to model the adsorption of up to 1 monolayer (ML) of aluminium on the bare and O-terminated (1 0 0) diamond surface. Large adsorption energies of up to -6.36 eV per atom are observed for the Al-adsorbed O-terminated diamond surface. Most adsorption sites give a negative electron affinity (NEA), with the largest NEAs -1.47 eV on the bare surface (1 ML coverage) and -1.36 eV on the O-terminated surface (0.25 ML coverage). The associated adsorption energies per Al atom for these sites are -4.11 eV and -5.24 eV, respectively. Thus, with suitably controlled coverage, Al on diamond shows promise as a thermally-stable surface for electron emission applications.

Piezoelectric effects in boron nitride nanotubes predicted by the atomistic finite element method and molecular mechanics.

We calculate the tensile and shear moduli of a series of boron nitride nanotubes and their piezoelectric response to applied loads. We compare in detail results from a simple molecular mechanics (MM) potential, the universal force field, with those from the atomistic finite element method (AFEM) using both Euler-Bernoulli and Timoshenko beam formulations. The MM energy minimisations are much more successful than those using the AFEM, and we analyse the failure of the latter approach both qualitatively and quantitatively.

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.

GaP-ZnS solid solutions: Semiconductors for efficient visible light absorption and emission.

GaP-ZnS solid solutions and multilayered structures have a tunable direct band gap in the energy range for absorption and emission of visible light. A direct band gap of around 2.0 eV, the optimum for photocatalysis of water splitting, is readily accessible with these systems.

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.

Improving density functional theory for crystal polymorph energetics.

We show that the quality of density functional theory (DFT) predictions for the relative stabilities of polymorphs of crystalline para-diiodobenzene (PDIB) is dramatically improved through a simple two-body correction using wavefunction-based electronic structure theory. PDIB has two stable polymorphs under ambient conditions, and like Hongo et al. [J. Phys. Chem. Lett., 1, 1789 (2010)] we find that DFT makes wildly variable predictions of the relative stabilities, depending on the approximate functional used. The two-body corrected scheme, using Grimme's spin-scaled variant of second-order Møller-Plesset perturbation theory and any of the tested density functionals, predicts the α-polymorph to be more stable, consistent with experiment, and produces a relative stability that agrees with the benchmark quantum Monte-Carlo results of Hongo et al. within statistical uncertainty.

Solvation of Ti(IV) in aqueous solution under ambient and supercritical conditions.

We examine the structure of the hydrated Ti(IV) complex under both ambient and supercritical conditions using first-principles molecular dynamics. We find that an unanticipated fivefold coordination of Ti(IV) is favoured under ambient conditions, with rapid interconversions between square pyramidal and trigonal bipyramidal structures. At supercritical conditions the Ti coordination increases from five to six, adopting both octahedral and trigonal prismatic geometries. At 1000 K, the magnitude of the increase in the Ti to oxygen coordination number with increasing water density is similar to that of Li-O under comparable conditions. We present a detailed picture of the bonding in the hydrated Ti(IV) complex under both ambient and supercritical conditions.

Predicting crystal structures ab initio: group 14 nitrides and phosphides.

Crystal structures are predicted for a range of group 14 nitrides and phosphides with 1 : 1 stoichiometry, following our method of starting from the known structures for a range of binary compounds and looking for trends in the preferred local bonding environments in the optimised structures. We have previously applied this method to predict the structures of carbon nitride and phosphorus carbide. Here, we use a similar approach to predict the structures of silicon and germanium nitrides and phosphides with 1 : 1 stoichiometry. We find that the local bonding environments in the preferred structures for the nitrides are the same as those for the 3 : 4 stoichiometry. For the phosphides, we have found several possible structures with similar energies. Structures containing hypervalent phosphorus must be considered as these are often low in energy, particularly for GeP; these have not been included in previous work. The greater tendency to form hypervalent phosphorus in GeP than SiP can be rationalised by considering the bond enthalpies for the two compositions.

Ultrathin oxide films and heterojunctions: CaO layers on BaO and SrO.

We examine the form of the islands formed by CaO on BaO and SrO substrates using both periodic density functional theory and atomistic simulation techniques. (100) edges dominate the island morphology and we examine how the CaO adjusts to the substrate in small and medium sized islands and at much larger coverages. There is no direct overlay of CaO ion pairs over OBa or OSr pairs in the top substrate layer. Rather, island bond lengths are all much shorter than those even in bulk CaO, even in the interior of the islands, and more similar to those in CaO clusters and isolated thin films. Corner atoms are associated with particularly short Ca-O bond lengths and the low coordination numbers at such positions. The islands show a marked deviation from planarity which can be broadly rationalized in terms of different preferential bond lengths for Ca and O with substrate O and Ba (Sr), respectively. The marked preferences for particular bond lengths lead to the formation of loops or gaps in non-square islands, areas where islands interact and along the mid-edges of large islands. Exchange with the much larger cations in the substrate is surprisingly facile. Our results indicate the difficulties of preparing sharp, ordered thin oxide films even at low temperatures.

Simplified Monte Carlo simulations of chemical vapour deposition diamond growth.

A simple one-dimensional Monte Carlo model has been developed to simulate the chemical vapour deposition (CVD) of a diamond (100) surface. The model considers adsorption, etching/desorption, lattice incorporation, and surface migration along and across the dimer rows. The top of a step-edge is considered to have an infinite Ehrlich-Schwoebel potential barrier, so that mobile surface species cannot migrate off the edge. The reaction probabilities are taken from experimental or calculated literature values for standard CVD diamond conditions. The criterion used for the critical nucleus needed to form a new layer is considered to be two surface carbon species bonded together, which forms an immobile, unetchable step on the surface. This nucleus can arise from two migrating species meeting, or from direct adsorption of a carbon species next to a migrating species. The analysis includes film growth rate, surface roughness, and the evolving film morphology as a function of varying reaction probabilities. Using standard CVD diamond parameters, the simulations reveal that a smooth film is produced with apparent step-edge growth, with growth rates (∼1 µm h(-1)) consistent with experiment. The ß-scission reaction was incorporated into the model, but was found to have very little effect upon growth rates or film morphology. Renucleation events believed to be due to reactive adsorbates, such as C atoms or CN groups, were modelled by creating random surface defects which form another type of critical nucleus upon which to nucleate a new layer. These were found to increase the growth rate by a factor of ∼10 when the conditions were such that the rate-limiting step for growth was new layer formation. For other conditions these surface defects led to layered 'wedding cake' structures or to rough irregular surfaces resembling those seen experimentally during CVD of nanocrystalline diamond.