Exploring the length scales, timescales and chemistry of challenging materials (Part 2).

This themed issue explores the different length and timescales that determine the physics and chemistry of a variety of key of materials, explored from the perspective of a wide range of disciplines, including physics, chemistry materials science, Earth science and biochemistry. The topics discussed include catalysis, chemistry under extreme conditions, energy materials, amorphous and liquid structure, hybrid organic materials and biological materials. The issue is in two parts, with this second set of contributions exploring hybrid organic materials, catalysis low-dimensional and graphitic materials, biological materials and naturally occurring, super-hard material as well as dynamic high pressure and new developments in imaging techniques pressure. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

Probing the dynamics and structure of confined benzene in MCM-41 based catalysts.

A combination of Molecular Dynamics (MD) simulations and Quasielastic Neutron Scattering (QENS) experiments has been used to investigate the dynamics and structure of benzene in MCM-41 based catalysts. QENS experiments of benzene as both an unconfined liquid and confined in the catalyst Pt/MCM-41 find that the mobility of benzene decreases upon confinement as shown by the decreased diffusion coefficients. Complementary MD simulations on benzene in MCM-41 show agreement with the QENS experiments when using a novel fully flexible model of MCM-41. Structural information from the MD simulations show that benzene in MCM-41 has a significantly different structure from that of the bulk liquid; with benzene molecules closer together and no prefered orientation.

Computational QM/MM investigation of the adsorption of MTH active species in H-Y and H-ZSM-5.

The transformation of methanol-to-hydrocarbons (MTH) has significant potential as a route to synthesise low-cost fuels; however, the initial stages of the zeolite catalysed MTH process are not well understood. Here, we use hybrid quantum- and molecular-mechanical (QM/MM) embedded-cluster simulations to develop our understanding of the interaction between methanol and the zeolite catalysts H-ZSM-5, and for comparison, the larger pore H-Y. Energies and structures, calculated using hybrid-level density functional theory (hybrid-DFT) and higher-level correlated methods, are compared with previous experimental and computational results. We show that hydrogen-bonds between methanol adsorbates, formed through polarizable O-H bonds, substantially influence the adsorption energetics, structural parameters and vibrational frequencies. Our observations are extended by considering polar solvent molecules in the environment, with the presence of both water or methanol around the adsorption site leading to barrier-less transfer of the zeolite proton to an adsorbed methanol, which will significantly influence the reactivity of the adsorbed methanol.

Ab initio investigation of O2 adsorption on Ca-doped LaMnO3 cathodes in solid oxide fuel cells.

We present a Hubbard-corrected density functional theory (DFT+U) study of the adsorption and reduction reactions of oxygen on the pure and 25% Ca-doped LaMnO3 (LCM25) {100} and {110} surfaces. The effect of oxygen vacancies on the adsorption characteristics and energetics has also been investigated. Our results show that the O2 adsorption/reduction process occurs through the formation of superoxide and peroxide intermediates, with the Mn sites found to be generally more active than the La sites. The LCM25{110} surface is found to be more efficient for O2 reduction than the LCM25{100} surface due to its stronger adsorption of O2, with the superoxide and peroxide intermediates shown to be energetically more favorable at the Mn sites than at the Ca sites. Moreover, oxygen vacancy defect sites on both the {100} and {110} surfaces are shown to be more efficient for O2 reduction, as reflected in the higher adsorption energies calculated on the defective surfaces compared to the perfect surfaces. We show from Löwdin population analysis that the O2 adsorption on the pure and 25% Ca-doped LaMnO3 surfaces is characterized by charge transfer from the interacting surface species into the adsorbed oxygen πg orbital, which results in weakening of the O-O bonds and its subsequent reduction. The elongated O-O bonds were confirmed via vibrational frequency analysis.

Comparing ammonia diffusion in NH3-SCR zeolite catalysts: a quasielastic neutron scattering and molecular dynamics simulation study.

The diffusion of ammonia in the small pore zeolite and potential commercial NH3-SCR catalyst levynite (LEV) was measured and compared with its mobility in the chabazite (CHA) topology (more established in NOx abatement catalysis), using quasielastic neutron scattering (QENS) and molecular dynamics (MD) simulations at 273, 323 and 373 K. The QENS experiments suggest that mobility in LEV is dominated by jump diffusion through the 8-ring windows between cages (as previously observed in CHA) which takes place at very similar rates in the two zeolites, yielding similar experimental self-diffusion coefficients (Ds). After confirming that the same characteristic motions are observed between the MD simulations and the QENS experiments on the picosecond scale, the simulations suggest that on the nanoscale, the diffusivity is higher by a factor of ∼2 in the CHA framework than in LEV. This difference between zeolites is primarily explained by the CHA cages having six 8-ring windows in the building unit, compared to only three such windows in the LEV cage building unit, thereby doubling the geometric opportunities to perform jump diffusion between cages (as characterised by the QENS experiments) leading to the corresponding increase in the MD calculated Ds. The techniques illustrate the importance of probing both pico- and nanoscale dynamics when studying intracrystalline diffusion in both NH3-SCR catalyst design, and in porous materials generally, where notable consistencies and differences may be found on either scale.

Modelling metal centres, acid sites and reaction mechanisms in microporous catalysts.

We discuss the role of QM/MM (embedded cluster) computational techniques in catalytic science, in particular their application to microporous catalysis. We describe the methodologies employed and illustrate their utility by briefly summarising work on metal centres in zeolites. We then report a detailed investigation into the behaviour of methanol at acidic sites in zeolites H-ZSM-5 and H-Y in the context of the methanol-to-hydrocarbons/olefins process. Studying key initial steps of the reaction (the adsorption and subsequent methoxylation), we probe the effect of framework topology and Brønsted acid site location on the energetics of these initial processes. We find that although methoxylation is endothermic with respect to the adsorbed system (by 17-56 kJ mol(-1) depending on the location), there are intriguing correlations between the adsorption/reaction energies and the geometries of the adsorbed species, of particular significance being the coordination of methyl hydrogens. These observations emphasise the importance of adsorbate coordination with the framework in zeolite catalysed conversions, and how this may vary with framework topology and site location, particularly suited to investigation by QM/MM techniques.

Towards microfluidic reactors for in situ synchrotron infrared studies.

Anodically bonded etched silicon microfluidic devices that allow infrared spectroscopic measurement of solutions are reported. These extend spatially well-resolved in situ infrared measurement to higher temperatures and pressures than previously reported, making them useful for effectively time-resolved measurement of realistic catalytic processes. A data processing technique necessary for the mitigation of interference fringes caused by multiple reflections of the probe beam is also described.

Correction: Evidence for a surface gold hydride on a nanostructured gold catalyst.

Correction for 'Evidence for a surface gold hydride on a nanostructured gold catalyst' by I. P. Silverwood et al., Chem. Commun., 2016, 52, 533-536.

Evidence for a surface gold hydride on a nanostructured gold catalyst.

Inelastic neutron scattering shows formation of a surface Au-H species, of key importance for the study of catalytic mechanisms. Previous assignment of this feature in the infrared as a purely Ce(3+) transition is shown to be erroneous on reducing the catalyst using hydrogen and deuterium.

Recent developments in the structural science of materials.

This Editorial surveys the current status and recent developments in the structural science of materials as exemplified by the articles recently published in IUCrJ.

Bio-inspired CO2 conversion by iron sulfide catalysts under sustainable conditions.

The mineral greigite presents similar surface structures to the active sites found in many modern-day enzymes. We show that particles of greigite can reduce CO2 under ambient conditions into chemicals such as methanol, formic, acetic and pyruvic acid. Our results also lend support to the Origin of Life theory on alkaline hydrothermal vents.

Oxidative methane activation over yttrium stabilised zirconia.

The methane C-H bond is extremely stable, requiring significant energy input in reforming processes. We present a novel mechanism for energetically favourable methane C-H bond breaking over yttrium stabilised zirconia in the presence of oxygen, based on results of Density Functional Theory (DFT) and HSE06 hybrid functional calculations. We argue that this mechanism will be relevant to C-H activation over many metal oxide catalyst materials.

Determination of the nitrogen vacancy as a shallow compensating center in GaN doped with divalent metals.

We report accurate energetics of defects introduced in GaN on doping with divalent metals, focusing on the technologically important case of Mg doping, using a model that takes into consideration both the effect of hole localization and dipolar polarization of the host material, and includes a well-defined reference level. Defect formation and ionization energies show that divalent dopants are counterbalanced in GaN by nitrogen vacancies and not by holes, which explains both the difficulty in achieving p-type conductivity in GaN and the associated major spectroscopic features, including the ubiquitous 3.46 eV photoluminescence line, a characteristic of all lightly divalent-metal-doped GaN materials that has also been shown to occur in pure GaN samples. Our results give a comprehensive explanation for the observed behavior of GaN doped with low concentrations of divalent metals in good agreement with relevant experiment.

Molecular dynamics simulations of longer n-alkanes in silicalite: state-of-the-art models achieving close agreement with experiment.

The diffusion of longer n-alkanes (n-C8-n-C16) in silicalite was studied using molecular dynamics (MD) simulations at a temperature range of 300-400 K, with loadings appropriate for direct comparison with previously carried out quasielastic neutron scattering (QENS) studies. The calculated diffusion coefficients were in close agreement with experimental values, significantly closer than those calculated using more primitive framework and hydrocarbon models, and in the case of the longer alkanes, closer agreement than those calculated by MD studies using the same model, but not using experimental loadings. The calculated activation energies of diffusion agreed with experiment to within 1.5 kJ mol(-1) for shorter alkanes of the range, but with a larger difference for tetra and hexadecane, due to factors which cannot be reproduced using periodic boundary conditions. Channel switching between the straight and sinusoidal channel system was found for octane at higher temperatures, where more than one octane molecule was located in the channel, which was attributed to the molecular size of octane, and the repulsion caused by the presence of the extra octane molecules in the channel system, allowing the potential barrier of channel switching at the junctions to be breached.

The reactivity of CO2 and H2 at trapped electron sites at an oxide surface.

We investigate the reactivity to H2 of a chemisorbed CO2 species at electron traps on oxide surfaces, taking the single electron F(+) oxygen vacancy of the MgO(100) terrace as a model system. We find that multiple hydrogen addition steps form three interacting catalytic cycles, leading to the evolution of formaldehyde, methanol or methane. Our results have general implications for the reactivity of CO2 on metal oxides.

Double bubbles: a new structural motif for enhanced electron-hole separation in solids.

Electron-hole separation for novel composite systems comprised of secondary building units formed from different compounds is investigated with the aim of finding suitable materials for photocatalysis. Pure and mixed SOD and LTA superlattices of (ZnO)12 and (GaN)12, single-shell bubbles are constructed as well as core@shell single component frameworks composed of larger (ZnO)48 and (GaN)48 bubbles with each containing one smaller bubble. Enthalpies of formation for all systems are comparable with fullerenes. Hole and electron separation is achieved most efficiently by the edge sharing framework composed of (GaN)12@(ZnO)48 double bubbles, with the hole localised on the nitrogen within the smaller bubbles and the excited electron on zinc within the larger cages.

Segregation effects on the properties of (AuAg)147.

AuAg nanoclusters are promising supported co-catalysts for photocatalytic hydrogen reduction. However, beyond the quantum regime (N > 100) little is known about how the electronic properties of these nanoparticles are affected by chemical ordering. We investigate the effects of chemical ordering on the properties of 147-atom cuboctahedral AuAg nanoclusters, using empirical potentials coupled with an atomic-swap basin-hopping search to optimise the elemental distribution, with the lowest energy arrangements then reminimised using Density Functional Theory (DFT). Force-field calculations show Au atoms preferentially occupy sub-surface positions in the bimetallic structures, which results in the formation of a pseudo-onion structure for Ag-rich compositions. At the DFT-level, however, an Ag core surrounded by an Au shell (Ag@Au) is energetically favoured, as electron density can be drawn more readily when Au atoms are positioned on the nanocluster surface, thus resulting in a partial negative charge. Core@shell configurations are analogous to structures that can be chemically synthesised, and further detailed electronic analysis is discussed in the context of nanocluster applications to co-catalysed photocatalysis.

The reactivity of CO2 on the MgO(100) surface.

We investigate the adsorption of CO2 over an MgO(001) terrace, as calculated using an embedded cluster method. We find adsorbed geometries for CO2 on the perfect surface with energies which differ appreciably from previous studies, and observe that it is polarization of the surface rather than the inclusion of electron correlation which leads to this discrepancy. Our results suggest that both monodentate and tridentate carbonate formation on the MgO(001) surface are favourable processes, with the monodentate structure being of lower energy. Adsorption of CO2 is found to be favourable at both F(0) and F(+) terrace sites, but not at F(2+). We also find that chemisorption at oxygen vacancy sites with a single localized electron (F(+)) could provide a route for the conversion of CO2 to other products, and that this system may be a useful model for other, more effective catalysts.

One-dimensional embedded cluster approach to modeling CdS nanowires.

We present an embedded cluster model to treat one-dimensional nanostructures, using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach. A segment of the nanowire (circa 50 atoms) is treated at a QM level of theory, using density functional theory (DFT) with a hybrid exchange-correlation functional. This segment is then embedded in a further length of wire, treated at an MM level of theory. The interaction between the QM and MM regions is provided by an embedding potential located at the interface. Point charges are placed beyond the ends of the wire segment in order to reproduce the Madelung potential of the infinite system. We test our model on the ideal system of a CdS linear chain, benchmarking our results against calculations performed on a periodic system using a plane-wave DFT approach, with electron exchange and correlation treated at the same level of approximation in both methods. We perform our tests on pure CdS and, importantly, the system containing a single In or Cu impurity. We find excellent agreement in the determined electronic structure using the two approaches, validating our embedded cluster model. As the hybrid QM/MM model avoids spurious interactions between charged defects, it will be of benefit to the analysis of the role of defects in nanowire materials, which is currently a major challenge using a plane-wave DFT approach. Other advantages of the hybrid QM/MM approach over plane-wave DFT include the ability to calculate ionization energies with an absolute reference and access to high levels of theory for the QM region which are not incorporated in most plane-wave codes. Our results concur with available experimental data.