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Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Modifying traditional Co/TiO 2 -based Fischer-Tropsch (FT) catalysts with Mn promoters induces a selectivity shift from long-chain paraffins toward commercially desirable alcohols and olefins. In this work, we use in situ gas cell scanning transmission electron microscopy (STEM) with energy-dispersive X-ray spectroscopy (EDS) elemental mapping, and near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) to demonstrate how the elemental dispersion and chemical structure of the as-calcined materials evolve during the H 2 activation heat treatment required for industrial CoMn/TiO 2 FT catalysts. We find that Mn additions reduce both the mean Co particle diameter and the size distribution but that the Mn remains dispersed on the support after the activation step. Density functional theory calculations show that the slower surface diffusion of Mn is likely due to the lower number of energetically accessible sites for the Mn on the titania support and that favorable Co-Mn interactions likely cause greater dispersion and slower sintering of Co in the Mn-promoted catalyst. These mechanistic insights into how the introduction of Mn tunes the Co nanoparticle size can be applied to inform the design of future-supported nanoparticle catalysts for FT and other heterogeneous catalytic processes., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

The nature of the support can fundamentally affect the function of a heterogeneous catalyst. For the novel type of isolated metal atom catalysts, sometimes referred to as single-atom catalysts, systematic correlations are still rare. Here, we report a general finding that Pd on nitride supports (non-metal and metal nitride) features a higher oxidation state compared to that on oxide supports (non-metal and metal oxide). Through thorough oxidation state investigations by X-ray absorption spectroscopy (XAS), X-ray photoelectron spectroscopy (XPS), CO-DRIFTS, and density functional theory (DFT) coupled with Bader charge analysis, it is found that Pd atoms prefer to interact with surface hydroxyl group to form a Pd(OH) x species on oxide supports, while on nitride supports, Pd atoms incorporate into the surface structure in the form of Pd-N bonds. Moreover, a correlation was built between the formal oxidation state and computational Bader charge, based on the periodic trend in electronegativity., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Sn-doped zeolites are potent Lewis acid catalysts for important reactions in the context of green and sustainable chemistry; however, their synthesis can have long reaction times and harsh chemical requirements, presenting an obstacle to scale-up and industrial application. To incorporate Sn into the β zeolite framework, solid-state incorporation (SSI) has recently been demonstrated as a fast and solvent-free synthetic method, with no impairment to the high activity and selectivity associated with Sn-β for its catalytic applications. Here, we report an ab initio computational study that combines periodic density functional theory with high-level embedded-cluster quantum/molecular mechanical (QM/MM) to elucidate the mechanistic steps in the synthetic process. Initially, once the Sn(II) acetate precursor coordinates to the β framework, acetic acid forms via a facile hydrogen transfer from the β framework onto the monodentate acetate ligand, with low kinetic barriers for subsequent dissociation of the ligand from the framework-bound Sn. Ketonization of the dissociated acetic acid can occur over the Lewis acidic Sn(II) site to produce CO 2 and acetone with a low kinetic barrier (1.03 eV) compared to a gas-phase process (3.84 eV), helping to explain product distributions in good accordance with experimental analysis. Furthermore, we consider the oxidation of the Sn(II) species to form the Sn(IV) active site in the material by O 2 - and H 2 O-mediated mechanisms. The kinetic barrier for oxidation via H 2 release is 3.26 eV, while the H 2 O-mediated dehydrogenation process has a minimum barrier of 1.38 eV, which indicates the possible role of residual H 2 O in the experimental observations of SSI synthesis. However, we find that dehydrogenation is facilitated more significantly by the presence of dioxygen (O 2 ), introduced in the compressed air gas feed, via a two-step process oxidation process that forms H 2 O 2 as an intermediate and has greatly reduced kinetic barriers of 0.25 and 0.26 eV. The results provide insight into how Sn insertion into β occurs during SSI and demonstrate the possible mechanism of top-down synthetic procedures for metal insertion into zeolites., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

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.

The characterization of zeolitic materials is often facilitated by spectroscopic analysis of vibrations, which informs about the bonding character of the substrate and any adsorbents. Computational simulations aid the interpretation of the spectra but often ignore anharmonic effects that can affect the spectral characteristics significantly. Here, the impact of anharmonicity is demonstrated with a combination of dynamical and static simulations applied to the structures formed during the synthesis of Sn-BEA via solid-state incorporation (SSI): the initial siliceous BEA (Si-β), aluminosilicate BEA (H-β), dealuminated BEA (deAl-β), and Sn-BEA (Sn-β). Heteroatom and defect-containing BEA are shown to have strong anharmonic vibrational contributions, with atomic and elemental resolution highlighting particularly the prevalence for H atoms (H-β, deAl-β) as well as localization to heteroatoms at defect sites. We simulate the vibrational spectra of BEA accounting for anharmonic contributions and observe an improved agreement with experimental data compared to harmonic methods, particularly at wavenumbers below 1500 cm -1 . The results demonstrate the importance of incorporating anharmonic effects in simulations of vibrational spectra, with consequences toward future characterization and application of zeolitic materials., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Polycrystalline boron-doped diamond (BDD) is widely used as a working electrode material in electrochemistry, and its properties, such as its stability, make it an appealing support material for nanostructures in electrocatalytic applications. Recent experiments have shown that electrodeposition can lead to the creation of stable small nanoclusters and even single gold adatoms on the BDD surfaces. We investigate the adsorption energy and kinetic stability of single gold atoms adsorbed onto an atomistic model of BDD surfaces by using density functional theory. The surface model is constructed using hybrid quantum mechanics/molecular mechanics embedding techniques and is based on an oxygen-terminated diamond (110) surface. We use the hybrid quantum mechanics/molecular mechanics method to assess the ability of different density functional approximations to predict the adsorption structure, energy, and barrier for diffusion on pristine and defective surfaces. We find that surface defects (vacancies and surface dopants) strongly anchor adatoms on vacancy sites. We further investigated the thermal stability of gold adatoms, which reveals high barriers associated with lateral diffusion away from the vacancy site. The result provides an explanation for the high stability of experimentally imaged single gold adatoms on BDD and a starting point to investigate the early stages of nucleation during metal surface deposition., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Vibrational spectroscopy is one of the most well-established and important techniques for characterizing chemical systems. To aid the interpretation of experimental infrared and Raman spectra, we report on recent theoretical developments in the ChemShell computational chemistry environment for modelling vibrational signatures. The hybrid quantum mechanical and molecular mechanical approach is employed, using density functional theory for the electronic structure calculations and classical forcefields for the environment. Computational vibrational intensities at chemical active sites are reported using electrostatic and fully polarizable embedding environments to achieve more realistic vibrational signatures for materials and molecular systems, including solvated molecules, proteins, zeolites and metal oxide surfaces, providing useful insight into the effect of the chemical environment on the signatures obtained from experiment. This work has been enabled by the efficient task-farming parallelism implemented in ChemShell for high-performance computing platforms.  This article is part of a discussion meeting issue 'Supercomputing simulations of advanced materials'.

The identification of the stable phases in alloy materials is challenging because composition affects the structural stability of different intermediate phases. Computational simulation, via multiscale modelling approaches, can significantly accelerate the exploration of phase space and help to identify stable phases. Here, we apply such new approaches to understand the complex phase diagram of binary alloys of PdZn, with the relative stability of structural polymorphs considered through application of density functional theory coupled with cluster expansion (CE). The experimental phase diagram has several competing crystal structures, and we focus on three different closed-packed phases that are commonly observed for PdZn, namely the face-centred cubic (FCC), body-centred tetragonal (BCT) and hexagonal close packed (HCP), to identify their respective stability ranges. Our multiscale approach confirms a narrow range of stability for the BCT mixed alloy, within the Zn concentration range from 43.75% to 50%, which aligns with experimental observations. We subsequently use CE to show that the phases are competitive across all concentrations, but with the FCC alloy phase favoured for Zn concentrations below 43.75%, and that the HCP structure favoured for Zn-rich concentrations. Our methodology and results provide a platform for future investigations of PdZn and other close-packed alloy systems with multiscale modelling techniques., (Creative Commons Attribution license.)

The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.

A number of Pd based materials have been synthesised and evaluated as catalysts for the conversion of carbon dioxide and hydrogen to methanol, a useful platform chemical and hydrogen storage molecule. Monometallic Pd catalysts show poor methanol selectivity, but this is improved through the formation of Pd alloys, with both PdZn and PdGa alloys showing greatly enhanced methanol productivity compared with monometallic Pd/Al 2 O 3 and Pd/TiO 2 catalysts. Catalyst characterisation shows that the 1 : 1 β-PdZn alloy is present in all Zn containing post-reaction samples, including PdZn/Ga 2 O 3 , with the Pd 2 Ga alloy formed for the Pd/Ga 2 O 3 sample. The heat of mixing was calculated for a variety of alloy compositions with high values determined for both PdZn and Pd 2 Ga alloys, at ca. -0.6 eV per atom and ca. -0.8 eV per atom, respectively. However, ZnO is more readily reduced than Ga 2 O 3 , providing a possible explanation for the preferential formation of the PdZn alloy, rather than PdGa, when in the presence of Ga 2 O 3 .

The reaction mechanism of direct CO 2 hydrogenation to methanol is investigated in detail on Pd (111), (100) and (110) surfaces using density functional theory (DFT), supporting investigations into emergent Pd-based catalysts. Hydrogen adsorption and surface mobility are firstly considered, with high-coordination surface sites having the largest adsorption energy and being connected by diffusion channels with low energy barriers. Surface chemisorption of CO 2 , forming a partially charged CO 2 δ - , is weakly endothermic on a Pd (111) whilst slightly exothermic on Pd (100) and (110), with adsorption enthalpies of 0.09, -0.09 and -0.19 eV, respectively; the low stability of CO 2 δ - on the Pd (111) surface is attributed to negative charge accumulating on the surface Pd atoms that interact directly with the CO 2 δ - adsorbate. Detailed consideration for sequential hydrogenation of the CO 2 shows that HCOOH hydrogenation to H 2 COOH would be the rate determining step in the conversion to methanol, for all surfaces, with activation barriers of 1.41, 1.51, and 0.84 eV on Pd (111), (100) and (110) facets, respectively. The Pd (110) surface exhibits overall lower activation energies than the most studied Pd (111) and (100) surfaces, and therefore should be considered in more detail in future Pd catalytic studies.

We report the crystal structure of a new polymorph of l-tyrosine (denoted the β polymorph), prepared by crystallization from the gas phase following vacuum sublimation. Structure determination was carried out by combined analysis of three-dimensional electron diffraction (3D-ED) data and powder X-ray diffraction (XRD) data. Specifically, 3D-ED data were required for reliable unit cell determination and space group assignment, with structure solution carried out independently from both 3D-ED data and powder XRD data, using the direct-space strategy for structure solution implemented using a genetic algorithm. Structure refinement was carried out both from powder XRD data, using the Rietveld profile refinement technique, and from 3D-ED data. The final refined structure was validated both by periodic DFT-D calculations, which confirm that the structure corresponds to an energy minimum on the energy landscape, and by the fact that the values of isotropic 13 C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state 13 C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the β polymorph is meta-stable with respect to the previously reported crystal structure of l-tyrosine (now denoted the α polymorph). Crystal structure prediction calculations using the AIRSS approach suggest that there are three other plausible crystalline polymorphs of l-tyrosine, with higher energy than the α and β polymorphs., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The development and application of trimetallic nanoparticles continues to accelerate rapidly as a result of advances in materials design, synthetic control, and reaction characterization. Following the technological successes of multicomponent materials in automotive exhausts and photovoltaics, synergistic effects are now accessible through the careful preparation of multielement particles, presenting exciting opportunities in the field of catalysis. In this review, we explore the methods currently used in the design, synthesis, analysis, and application of trimetallic nanoparticles across both the experimental and computational realms and provide a critical perspective on the emergent field of trimetallic nanocatalysts. Trimetallic nanoparticles are typically supported on high-surface-area metal oxides for catalytic applications, synthesized via preparative conditions that are comparable to those applied for mono- and bimetallic nanoparticles. However, controlled elemental segregation and subsequent characterization remain challenging because of the heterogeneous nature of the systems. The multielement composition exhibits beneficial synergy for important oxidation, dehydrogenation, and hydrogenation reactions; in some cases, this is realized through higher selectivity, while activity improvements are also observed. However, challenges related to identifying and harnessing influential characteristics for maximum productivity remain. Computation provides support for the experimental endeavors, for example in electrocatalysis, and a clear need is identified for the marriage of simulation, with respect to both combinatorial element screening and optimal reaction design, to experiment in order to maximize productivity from this nascent field. Clear challenges remain with respect to identifying, making, and applying trimetallic catalysts efficiently, but the foundations are now visible, and the outlook is strong for this exciting chemical field.

The dehydrogenation and dehydration of formic acid is investigated on the β -Mo 2 C (100) catalyst surface using time independent density functional theory. The energetics of the two mechanisms are calculated, and the thermochemistry and kinetics are discussed using the transition state theory. Subsequently, microkinetic modelling of the system is conducted, considering the batch reactor model. The potential energy landscape of the reaction shows a thermodynamically favourable cleavage of H-COOH to form CO; however, the kinetics show that the dehydrogenation mechanism is faster and CO 2 is continuously formed. The effect of HCOOH adsorption on the surface is also analysed, in a temperature-programmed desorption, with the conversion proceeding at under 350 K and desorption of CO 2 is observed with a selectivity of about 100 %, in line with the experimental reports., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Authors.)

We report the solid-state structural properties of alloxazine, a tricyclic ring system found in many biologically important molecules, with structure determination carried out directly from powder X-ray diffraction (XRD) data. As the crystal structures containing the alloxazine and isoalloxazine tautomers both give a high-quality fit to the powder XRD data in Rietveld refinement, other techniques are required to establish the tautomeric form in the solid state. In particular, high-resolution solid-state 15 N NMR data support the presence of the alloxazine tautomer, based on comparison between isotropic chemical shifts in the experimental 15 N NMR spectrum and the corresponding values calculated for the crystal structures containing the alloxazine and isoalloxazine tautomers. Furthermore, periodic DFT-D calculations at the PBE0-MBD level indicate that the crystal structure containing the alloxazine tautomer has significantly lower energy. We also report computational investigations of the interconversion between the tautomeric forms in the crystal structure via proton transfer along two intermolecular N-H···N hydrogen bonds; DFT-D calculations at the PBE0-MBD level indicate that the tautomeric interconversion is associated with a lower energy transition state for a mechanism involving concerted (rather than sequential) proton transfer along the two hydrogen bonds. However, based on the relative energies of the crystal structures containing the alloxazine and isoalloxazine tautomers, it is estimated that under conditions of thermal equilibrium at ambient temperature, more than 99.9% of the molecules in the crystal structure will exist as the alloxazine tautomer., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

The formation of the first C-C bond and primary olefins from methanol over zeolite and zeotype catalysts has been studied for over 40 years. Over 20 mechanisms have been proposed for the formation of the first C-C bond. In this quantitative multiscale perspective, we decouple the adsorption, desorption, mobility, and surface reactions of early species through a combination of vacuum and sub-vacuum studies using temporal analysis of products (TAP) reactor systems, and through studies with atmospheric fixed bed reactors. These results are supplemented with density functional theory calculations and data-driven physical models, using partial differential equations, that describe the temporal and spatial evolution of species. We consider the effects of steam, early degradation species, and product masking due to the inherent autocatalytic nature of the process, which all complicate the observation of the primary olefin(s). Although quantitative spectroscopic determination of the lifetimes, surface mobility, and reactivity of adspecies is still lacking in the literature, we observe that reaction barriers are competitive with adsorption enthalpies and/or activation energies of desorption, while facile diffusion occurs in the porous structures of the zeolite/zeotype catalysts. Understanding the various processes allows for quantitative evaluation of their competing energetics, which leads to molecular insights as to what governs the catalytic activity during the conversion of methanol to primary olefins over zeolite/zeotype catalysts.

The conversion of methanol-to-hydrocarbons (MTH) is known to occur via an autocatalytic process in zeolites, where framework-bound methoxy species play a pivotal role, especially during catalyst induction. Recent NMR and FT-IR experimental studies suggest that methoxylated zeolites are able to produce hydrocarbons by a mechanism involving carbene migration and association. In order to understand these observations, we have performed QM/MM computational investigations on a range of reaction mechanisms for the reaction of zeolite bound methoxy and carbene groups, which are proposed to initiate hydrocarbon formation in the MTH process. Our simulations demonstrate that it is kinetically unfavourable for methyl species to form on the framework away from the zeolite acid site, and both kinetically and thermodynamically unfavourable for methyl groups to migrate through the framework and aggregate around an acid site. Formation of carbene moieties was considered as an alternative pathway to the formation of C-C bonds; however, the reaction energy for conversion of a methyl to a carbene is unfavourable. Metadynamics simulations help confirm further that methyl species at the framework acid sites would be more reactive towards formed C 2+ species, rather than inter-framework migration, and that the role of carbenes in the formation of the first C-C bond will be via a concerted type of mechanism rather than stepwise.

We report a detailed Density Functional Theory (DFT) based investigation of the structure and stability of bulk and surface structures for the Group 10-12 elements Pd, Cu and Zn, considering the effect of the choice of exchange-correlation density functional and computation parameters. For the initial bulk structures, the lattice parameter and cohesive energy are calculated, which are then augmented by calculation of surface energies and work functions for the lower-index surfaces. Of the 22 density functionals considered, we highlight the mBEEF density functional as providing the best overall agreement with experimental data. The optimal density functional choice is applied to the study of higher index surfaces for the three metals, and Wulff constructions performed for nanoparticles with a radius of 11 nm, commensurate with nanoparticle sizes commonly employed in catalytic chemistry. For Pd and Cu, the low-index (111) facet is dominant in the constructed nanoparticles, covering ∼50% of the surface, with (100) facets covering a further 10 to 25%; however, non-negligible coverage from higher index (332), (332) and (210) facets is also observed for Pd, and (322), (221) and (210) surfaces are observed for Cu. In contrast, only the (0001) and (10-10) facets are observed for Zn. Overall, our results highlight the need for careful validation of computational settings before performing extensive density functional theory investigations of surface properties and nanoparticle structures of metals.

The production of methanol from glycerol over a basic oxide, such as MgO, using high reaction temperatures (320 °C) is a promising new approach to improving atom efficiency in the production of biofuels. The mechanism of this reaction involves the homolytic cleavage of the C 3 feedstock, or its dehydration product hydroxyacetone, to produce a hydroxymethyl radical species which can then abstract an H atom from other species. Obtaining a detailed reaction mechanism for this type of chemistry is difficult due to the large number of products present when the system is operated at high conversions. In this contribution we show how DFT based modelling studies can provide new insights into likely reaction pathways, in particular the source of H atoms for the final step of converting hydroxymethyl radicals to methanol. We show that water is unlikely to be important in this stage of the process, C-H bonds of C 2 and C 3 species can give an energetically favourable pathway and that the disproportionation of hydroxymethyl radicals to methanol and formaldehyde produces a very favourable route. Experimental analysis of reaction products confirms the presence of formaldehyde. The calculations presented in this work also provide new insight into the role of the catalyst surface in the reaction showing that the base sites of the MgO(100) are able to deprotonate hydroxymethyl radicals but not methanol itself. In carrying out the calculations we also show how periodic DFT and QM/MM approaches can be used together to obtain a rounded picture of molecular adsorption to surfaces and homolytic bond cleavage which are both central to the reactions studied.

The methanol-to-hydrocarbons (MTH) process transforms C1 carbon sources to higher hydrocarbons, but details of the mechanism that leads to the formation of the first carbon-carbon bond remain unclear. Here, we present a computational investigation of how a crucial intermediate, dimethyl ether (DME), interacts with different zeolite catalysts (H-ZSM-5, H-Y) to gain insight into the initial stages in the MTH process. We use QM/MM computational simulations to model the conversion of methanol to DME in H-ZSM-5, which is a well characterised and important reaction intermediate. We analyse and compare the stability of DME on several acid sites in H-ZSM-5 and H-Y, and show that the more acidic and open "intersection sites" in the H-ZSM-5 framework are able to bond strongest with DME, with complete deprotonation of the acid site occurring. The conversion of methanol to DME in H-ZSM-5 is calculated as requiring a higher activation energy than framework methoxylation, which indicates that a stepwise (indirect) mechanism, through a methoxy intermediate, is the most likely route to DME formation during the initiation of the MTH process.

A density functional theory study has been performed to investigate cation-doped Sn2O4 clusters for selective catalytic reduction of CO2. We study the influence of Si and Ti dopants on the height of the H2 dissociation barrier for the doped systems, and then the subsequent mechanism for the conversion of CO2 into formic acid (FA) via a hydride pinning pathway. The lowest barrier height for H2 dissociation is observed across the 'Ti-O' bond of the Ti-doped Sn2O4 cluster, with a negatively charged hydride (Ti-H) formed during the heterolytic H2 dissociation, bringing selectivity towards the desired FA product. The formation of a formate intermediate is identified as the rate-determining step (RDS) for the whole pathway, but the barrier height is substantially reduced for the Ti-doped system when compared to the same steps on the undoped Sn2O4 cluster. The free energy of formate formation in the RDS is calculated to be negative, which reveals that the hydride transfer would occur spontaneously. Overall, our results show that the small-sized Ti-doped Sn2O4 clusters exhibit better catalytic activity than undoped clusters in the important process of reducing CO2 to FA when proceeding via the hydride pinning pathway.

The methanol-to-hydrocarbon process is known to proceed autocatalytically in H-ZSM-5 after an induction period where framework methoxy species are formed. In this work, we provide mechanistic insight into the framework methylation within H-ZSM-5 at high methanol loadings and varying acid site densities by means of first-principles molecular dynamics simulations. The molecular dynamics simulations show that stable methanol clusters form in the zeolite pores, and these clusters commonly deprotonate the active site; however, the cluster size is dependent on the temperature and acid site density. Enhanced sampling molecular dynamics simulations give evidence that the barrier for methanol conversion is significantly affected by the neighborhood of an additional acid site, suggesting that cooperative effects influence methanol clustering and reactivity. The insights obtained are important steps in optimizing the catalyst and engineering the induction period of the methanol-to-hydrocarbon process., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

We evaluate the effect of the number of methanol molecules per acidic site of H-ZSM-5 on the methoxylation reaction at room temperature by applying operando diffuse reflectance infrared Fourier transformed spectroscopy (DRIFTS) and mass spectrometry (MS), which capture the methoxylation reaction by simultaneously probing surface adsorbed species and reaction products, respectively. To this end, the methanol loading in H-ZSM-5 (Si/Al ≈ 25) pores is systematically varied between 32, 16, 8 and 4 molecules per unit cell, which corresponds to 8, 4, 2 and 1 molecules per Brønsted acidic site, respectively. The operando DRIFTS/MS data show that the room temperature methoxylation depends on the methanol loading: the higher the methanol loading, the faster the methoxylation. Accordingly, the reaction is more than an order of magnitude faster with 8 methanol molecules per Brønsted acidic site than that with 2 molecules, as evident from the evolution of the methyl rock band of the methoxy species and of water as a function of time. Significantly, no methoxylation is observed with ≤1 molecule per Brønsted acidic site. However, hydrogen bonded methanol occurs across all loadings studied, but the structure of hydrogen bonded methanol also depends on the loading. Methanol loading of ≤1 molecule per acidic site leads to the formation of hydrogen bonded methanol with no proton transfer ( i.e. neutral geometry), while loading ≥2 molecules per acidic site results in a hydrogen bonded methanol with a net positive charge on the adduct (protonated geometry). The infrared vibrational frequencies of methoxy and hydrogen bonded methanol are corroborated by Density Functional Theory (DFT) calculations. Both the experiments and calculations reflect the methoxy bands at around 940, 1180, 2868-2876 and 2980-2973 cm -1 which correspond to ν (C-O), ρ (CH 3 ), ν s (C-H) and ν as (C-H), respectively., (This journal is © The Royal Society of Chemistry 2020.)

In this review, we discuss selected examples from recent literature on the role of the support on directing the nanostructures of Au-based monometallic and bimetallic nanoparticles. The role of support is then discussed in relation to the catalytic properties of Au-based monometallic and bimetallic nanoparticles using different gas phase and liquid phase reactions. The reactions discussed include CO oxidation, aerobic oxidation of monohydric and polyhydric alcohols, selective hydrogenation of alkynes, hydrogenation of nitroaromatics, CO 2 hydrogenation, C-C coupling, and methane oxidation. Only studies where the role of support has been explicitly studied in detail have been selected for discussion. However, the role of support is also examined using examples of reactions involving unsupported metal nanoparticles (i.e., colloidal nanoparticles). It is clear that the support functionality can play a crucial role in tuning the catalytic activity that is observed and that advanced theory and characterization add greatly to our understanding of these fascinating catalysts.

A new polymorph of l-tryptophan was prepared through crystallization from the gas phase, with structure determination carried out directly from powder XRD data augmented by periodic DFT-D calculations. The new polymorph (denoted β) and the previously reported polymorph (denoted α) are both based on alternating hydrophilic and hydrophobic layers, but with substantially different hydrogen-bonding arrangements. The β polymorph exhibits the energetically favourable l2-l2 hydrogen-bonding arrangement, which is unprecedented for amino acids with aromatic side chains. The specific molecular conformations adopted in the β polymorph facilitate this hydrogen-bonding scheme while avoiding steric conflict of the side chains., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language. The redeveloped package is capable of performing QM/MM calculations on systems of significantly increased size, which we illustrate with benchmarks on zirconium dioxide nanoparticles of over 160000 atoms.

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.

The 2018 Faraday Discussion on "Designing Nanoparticle Systems for Catalysis" brought together leading scientists to discuss the current state-of-the-art in the fields of computational chemistry, characterization techniques, and nanomaterial synthesis, and to debate the challenges and opportunities going forward for rational catalyst design. The meeting was a vivid discussion of how the communities accummulate knowledge and on how innovativeness can be combined to have a stronger scientific impact. In the following, we provide an overview of the meeting structure, including plenaries, papers, discussion points and breakout sessions, and we hope to show, to the wider scientific community, that there is great value in continued international discussion and scientific collaboration in these fields.

We present a study of the transitional pathways between high-symmetry structural motifs for AgAu nanoparticles, with a specific focus on controlling the energetic barriers through chemical design. We show that the barriers can be altered by careful control of the elemental composition and chemical arrangement, with core@shell and vertex-decorated arrangements being specifically influential on the barrier heights. We also highlight the complexity of the potential and free energy landscapes for systems where there are low-symmetry geometric motifs that are energetically competitive to the high-symmetry arrangements. In particular, we highlight that some core@shell arrangements preferentially transition through multistep restructuring of low-symmetry truncated octahedra and rosette-icosahedra, instead of via the more straightforward square-diamond transformations, due to lower energy barriers and competitive energetic minima. Our results have promising implications for the continuing efforts in bespoke nanoparticle design for catalytic and plasmonic applications.

We have investigated the energetic properties of Mn-doped MgO bulk and (100) surfaces using a QM/MM embedding computational method, calculating the formation energy for doped systems, as well as for surface defects, and the subsequent effect on chemical reactivity. Low-concentration Mn doping is endothermic for isovalent species in the bulk but exothermic for higher oxidation states under p-type conditions, and compensated by electrons going to the Fermi level rather than cation vacancies. The highest occupied dopant Mn 3d states are positioned in the MgO band gap, about 4.2 eV below the vacuum level. Surface Mn-doping is more favourable than subsurface doping, and marginally exothermic on a (100) surface at high O 2 pressures. For both types of isovalent Mn-doped (100) surfaces, the formation energy for catalytically important oxygen defects is less than for pristine MgO, with F 0 and F 2+ -centres favoured in n- and p-type conditions, respectively. In addition, F + -centres are stabilised by favourable exchange coupling between the Mn 3d states and the vacancy-localised electrons, as verified through calculation of the vertical ionisation potential. The adsorption of CO 2 on to the pristine and defective (100) surface is used as a probe of chemical reactivity, with isovalent subsurface Mn dopants mildly affecting reactivity, whereas isovalent surface-positioned Mn strongly alters the chemical interactions between the substrate and adsorbate. The differing chemical reactivity, when compared to pristine MgO, justifies further detailed investigations for more varied oxidation states and dopant species.

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.

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.

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.

We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

Photocatalytic hydrogen evolution may provide one of the solutions to the shift to a sustainable energy society, but the quantum efficiency of the process still needs to be improved. Precise control of the composition and structure of the metal nanoparticle cocatalysts is essential, and we show that fine-tuning the Au-Pd nanoparticle structure modifies the electronic properties of the cocatalyst significantly. Specifically, Pd(shell)-Au(core) nanoparticles immobilized on TiO2 exhibit extremely high quantum efficiencies for H2 production using a wide range of alcohols, implying that chemical byproducts from the biorefinery industry can be used as feedstocks. In addition, the excellent recyclability of our photocatalyst material indicates a high potential in industrial applications. We demonstrate that this particular elemental segregation provides optimal positioning of the unoccupied d-orbital states, which results in an enhanced utilization of the photoexcited electrons in redox reactions. We consider that the enhanced activity observed on TiO2 is generic in nature and can be transferred to other narrow band gap semiconductor supports for visible light photocatalysis.

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.

The structural preferences of nanoparticles are important for understanding their chemical properties and potential applications, and remain widely debated. Based on recent experimental observations, we present calculations on the stability of high-symmetry AuN and PdN clusters of various structural motifs, performing a systematic search of faceting preferences using mathematical constructs, a semi-empirical potential with two different parameter sets, and a quasi-Newtonian minimisation technique. We have studied the preferred ratios of (100) and (111) faces for two experimentally observed nanostructures: (a) FCC crystals, comparing octahedra with 8 (111) faces to cuboctahedra where the vertices have been systematically removed (for N < 1500); and (b) Marks-decahedra, with differing "stellation" depths (for N < 6000). For PdN and AuN we see preference towards minimisation of (100) surfaces using the parameter sets of both Cleri and Rosato [Cleri and Rosato, Phys. Rev. B: Condens. Matter Mater. Phys., 1993, 48, 22] and Baletto et al. [Baletto et al., J. Chem. Phys., 2002, 116, 3856]. Fully stellated Marks-decahedra are found to be unfavourable at large sizes, with truncated facets identified which are similar to recent experimental observations. We find however that these stellations are deeper in PdN particles than AuN. Truncated-octahedra are found to prefer much reduced (100) surfaces and increased (111) surface areas.

A method for the preparation of smooth deposits of Pt on Au nanorods is described, involving sequential deposition steps with selective blocking of surface sites that reduces Pt-on-Pt deposition. The Au-Pt nanorods prepared by this method have higher long-term stability than those prepared by standard Pt deposition. Electrochemical data show that the resulting structure has more extended regions of Pt surface and enhanced activity toward the carbon monoxide oxidation and oxygen reduction reactions.

This study focuses on the deposition and growth mode of rhodium (Rh) on gold (Au) seed nanorods (NRs). Using a combination of scanning transmission electron microscopy imaging, energy-dispersive X-ray spectroscopy, and UV-visible absorption spectroscopy, we show that Rh deposition results in an uneven overlayer morphology on the Au NR seeds, with a tendency for Rh deposition to occur preferentially on the Au NR ends. The results suggest that complex and kinetically driven metal-metal interactions take place in this system.

A genetic algorithm (GA) coupled with density functional theory (DFT) calculations is used to perform global optimisations for all compositions of 8-atom Au-Ag bimetallic clusters. The performance of this novel GA-DFT approach for bimetallic nanoparticles is tested for structures reported in the literature. New global minimum structures for various compositions are predicted and the 2D-3D transition is located. Results are explained with the aid of an analysis of the electronic density of states. The chemical ordering of the predicted lowest energy isomers are explained via a detailed analysis of the charge separation and mixing energies of the bimetallic clusters. Finally, dielectric properties are computed and the composition and dimensionality dependence of the electronic polarizability and dipole moment is discussed, enabling predictions to be made for future electric beam deflection experiments., (This journal is © The Royal Society of Chemistry 2012)

Whilst technological advancements have allowed imaging at atomic resolution using scanning transmission electron microscopy (STEM), identification of nanocluster structures has proven difficult due to their low thermal stability, and often resultant low-symmetry. In this work, we look at a novel solution to this problem using a genetic algorithm (GA). GAs are search methods for the minimization of statistical problems based on natural evolution. We develop a STEM model first described by Curley et al. (2007) and, using high-symmetry cluster structures as test subjects, look at the effectiveness and efficiency of the GA at optimizing orientation parameters for a cluster when compared to a model solution. We find for a 309-atom icosahedron that a random minimizing search would prove more efficient than a GA; however, for a 309-atom decahedron the GA becomes more effective and efficient than a random search. We predict that as we continue to lower symmetry of our test cases, we will find the GA becomes even more efficient at optimizing this otherwise computationally expensive problem., (Copyright © 2011 Wiley Periodicals, Inc.)