Fundamental Structural and Electronic Understanding of Palladium Catalysts on Nitride and Oxide Supports.

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.

Computational Study of the Solid-State Incorporation of Sn(II) Acetate into Zeolite ß.

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 ß 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-ß 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 ß framework, acetic acid forms via a facile hydrogen transfer from the ß 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 CO2 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 O2- and H2O-mediated mechanisms. The kinetic barrier for oxidation via H2 release is 3.26 eV, while the H2O-mediated dehydrogenation process has a minimum barrier of 1.38 eV, which indicates the possible role of residual H2O in the experimental observations of SSI synthesis. However, we find that dehydrogenation is facilitated more significantly by the presence of dioxygen (O2), introduced in the compressed air gas feed, via a two-step process oxidation process that forms H2O2 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 ß occurs during SSI and demonstrate the possible mechanism of top-down synthetic procedures for metal insertion into zeolites.

Evaluating the Role of Anharmonic Vibrations in Zeolite ß Materials.

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-ß), aluminosilicate BEA (H-ß), dealuminated BEA (deAl-ß), and Sn-BEA (Sn-ß). 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-ß, deAl-ß) 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.

Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces.

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.

Investigation of the Pd(1-x)Znxalloy phase diagram usingab initiomodelling approaches.

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.

Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems.

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'.

Multiscale QM/MM modelling of catalytic systems with ChemShell.

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

Methanol synthesis from CO2 and H2 using supported Pd alloy catalysts.

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/Al2O3 and Pd/TiO2 catalysts. Catalyst characterisation shows that the 1 : 1 ß-PdZn alloy is present in all Zn containing post-reaction samples, including PdZn/Ga2O3, with the Pd2Ga alloy formed for the Pd/Ga2O3 sample. The heat of mixing was calculated for a variety of alloy compositions with high values determined for both PdZn and Pd2Ga alloys, at ca. -0.6 eV per atom and ca. -0.8 eV per atom, respectively. However, ZnO is more readily reduced than Ga2O3, providing a possible explanation for the preferential formation of the PdZn alloy, rather than PdGa, when in the presence of Ga2O3.

Dehydrogenation and dehydration of formic acid over orthorhombic molybdenum carbide.

The dehydrogenation and dehydration of formic acid is investigated on the ß-Mo2C (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 CO2 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 CO2 is observed with a selectivity of about 100 %, in line with the experimental reports.

A structure determination protocol based on combined analysis of 3D-ED data, powder XRD data, solid-state NMR data and DFT-D calculations reveals the structure of a new polymorph of l-tyrosine.

We report the crystal structure of a new polymorph of l-tyrosine (denoted the ß 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 13C NMR chemical shifts calculated for the crystal structure using DFT-D methodology are in good agreement with the experimental high-resolution solid-state 13C NMR spectrum. Based on DFT-D calculations using the PBE0-MBD method, the ß 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 ß polymorphs.

A computational study of direct CO2 hydrogenation to methanol on Pd surfaces.

The reaction mechanism of direct CO2 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 CO2, forming a partially charged CO2δ-, 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 CO2δ- on the Pd (111) surface is attributed to negative charge accumulating on the surface Pd atoms that interact directly with the CO2δ- adsorbate. Detailed consideration for sequential hydrogenation of the CO2 shows that HCOOH hydrogenation to H2COOH 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.

Heterogeneous Trimetallic Nanoparticles as Catalysts.

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.

Solid-State Structural Properties of Alloxazine Determined from Powder XRD Data in Conjunction with DFT-D Calculations and Solid-State NMR Spectroscopy: Unraveling the Tautomeric Identity and Pathways for Tautomeric Interconversion.

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 15N NMR data support the presence of the alloxazine tautomer, based on comparison between isotropic chemical shifts in the experimental 15N 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.

A quantitative multiscale perspective on primary olefin formation from methanol.

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.

QM/MM study of the reactivity of zeolite bound methoxy and carbene groups.

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 C2+ 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.

A computational study of the properties of low- and high-index Pd, Cu and Zn surfaces.

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.

A combined periodic DFT and QM/MM approach to understand the radical mechanism of the catalytic production of methanol from glycerol.

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 C3 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 C2 and C3 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.

QM/MM study of the stability of dimethyl ether in zeolites H-ZSM-5 and H-Y.

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.

Tuning the transition barrier of H2 dissociation in the hydrogenation of CO2 to formic acid on Ti-doped Sn2O4 clusters.

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.

Methanol loading dependent methoxylation in zeolite H-ZSM-5.

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(CH3), ν s(C-H) and ν as(C-H), respectively.