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Embedded Cluster Modelling for Realistic Solid-State Systems

Lead Research Organisation: CARDIFF UNIVERSITY
Department Name: Chemistry

Abstract

The advent of modern highly-parallelised computing (HPC) infrastructure, coupled with development of scalable software packages, has led to unprecedented growth in the application of materials chemistry modelling - it is now unthinkable to perform high-impact research without including simulations to either understand observations or predict novelty. Within the materials chemistry modelling community, the most widely-used technique is periodic density functional theory (DFT). Such an approach is highly efficient for systems with high-symmetry (i.e. few atoms in the unit cell); however, a major challenge exists when expanding the model to tackle problems such as surface reactivity on close-packed ionic materials. The typical workaround is to create a repeating surface model (i.e. a surface supercell), which is big enough in the surface norm and across the vacuum region to ensure the removal of spurious "image" interactions, and has several layers of "inactive" sub-surface atoms included to ensure chemical validity. Whilst pragmatic, this approach is throttling the impact of computational simulation on applied catalytic chemistry, because the increased model size results in computational overheads that limit computational accuracy to the lower levels of DFT. Therefore, new approaches need to be realised that enable higher accuracy, realistic simulation for solid-state systems.

In this work, my aim is to extend the embedded-cluster hybrid quantum-/molecular-mechanics (QM/MM) approach in order to challenge the working norm and offer a viable option instead of periodic-DFT. The embedded-cluster approach removes periodic boundary conditions, and QM/MM can allow the reduction of the electronic space of interest to just the atoms around an active site, thus reducing computational cost without compromising chemical accuracy. To achieve this goal, significant development work is needed to make this technique accessible for solid-state modelling of surface reactions, including streamlining of the setup procedures (cluster design, forcefield parameterisation). Additionally, I propose extensions of QM/MM to accurately model magnetic materials: accurate embedding environments, which apply appropriate potentials to QM atoms at the QM/MM boundary, will be realised through development of novel pseudopotentials and wavefunction embedding approaches. The development outcomes will be validated by investigations of industrially-relevant green catalytic processes for H2 synthesis, which use metal oxides, with our highest-level benchmark being quantum chemical simulations of catalysis on cation-doped iron oxide polymorphs. These investigations will be followed with extension into previously inaccessible fields of materials simulation, such as elucidating reactivity of Mn- and Fe- containing perovskites for the oxygen evolution reaction, and simulating defect properties and reactivity for contemporary 2D magnetic materials. Accurate, high-level DFT and post-Hartree Fock approaches will be realised for extended systems through the Fellowship outcomes, and their application will allow unprecedented insight into chemical properties of emergent materials, as well as opening up a range of further exciting scientific areas beyond the solid-state.

Planned Impact

New simulation techniques and improvement to catalyst design for energy-related catalysis are expected to have impact in a range of important areas spanning society and the national economy through to training and inspiring future leaders. Key areas of impact for this Fellowship are:

I) Society and environment, whereby new processes to simulate and improve catalysts can impact the synthesis and application of sustainable fuels, improving the long-term well-being of the population through prosperity and improvements in environmental sectors such as energy, water and manufacturing. Simulation approaches and mechanistic understanding can be disseminated to industrial partners (Johnson Matthey) and the general public, through stakeholder presentations and outreach events, to ensure broader understanding of the challenges faced. Through interaction with learned societies (Royal Society, Royal Society of Chemistry), the Fellowship outcomes can contribute to the development of UK industrial policy, so as to complement the scientific project outcomes.

II) Economic impact can be realised through the targeted creation of catalysis-based R&D, and subsequent creation of new catalytic processes to address the challenges of synthesising sustainable fuel carriers. Catalysis is integral to the global economy and chemical industry, and the applied objectives of this Fellowship will address global challenges in catalysis that have a major influence on economic prosperity across many sectors. New catalytic processes are key for enabling productivity; the development of new methodologies and software tools will also provide critical support for innovative catalyst design. The Fellow will engage with with industry (Johnson Matthey) to maximise technology transfer and economic impact, and intellectual property (IP) can be expected to be realised.

III) People must be developed so the UK society can be world-leading in the forthcoming data revolution, with leaders for new academic fields nurtured. High-quality training of participant, collaborating and all interested researchers will construct the foundations for their futures in the data economy. The multidisciplinary nature of this Fellowship, spanning computer science, chemistry, physics and materials science, ensures high levels of collaboration and knowledge transfer both within academia and into industry. The international co-operation outlined for software development is an ideal training ground for development of leadership qualities, whilst organisation of meetings, conferences, workshops and outreach activities will develop individuals' personal management skills.

IV) Outreach and engagement will raise the profile of the research and the broader scientific field, with public engagement promoting the benefits of materials chemistry research to the whole of society. Academic colleagues and industrial groups will be impacted through publications in peer-reviewed journals, presentation at national and international conferences, and invited lectures. Engagement with stakeholders will deliver impactful knowledge and understanding, through individual secondments between project partners and cross-networking workshops. The public will be informed of the scientific impact through general science activities, such as national science festivals (RS Summer Festival), through demonstrations at local schools, museums and scientific outreach events (Pint of Science), and through hosting of Summer students within the project team (Nuffield, CUROP, CCP5). Online resources will be used to publicise Fellowship outcomes to a broad international audience.

Publications

10 25 50

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Bauer S (2024) Roadmap on data-centric materials science in Modelling and Simulation in Materials Science and Engineering

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Beynon OT (2023) Evaluating the Role of Anharmonic Vibrations in Zeolite ß Materials. in The journal of physical chemistry. C, Nanomaterials and interfaces

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Beynon OT (2023) Computational Study of the Solid-State Incorporation of Sn(II) Acetate into Zeolite ß. in The journal of physical chemistry. C, Nanomaterials and interfaces

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Bramley G (2023) The application of QM/MM simulations in heterogeneous catalysis in Physical Chemistry Chemical Physics

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Chaudhuri S (2023) Stability of Single Gold Atoms on Defective and Doped Diamond Surfaces. in The journal of physical chemistry. C, Nanomaterials and interfaces

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Crawley JWM (2022) Heterogeneous Trimetallic Nanoparticles as Catalysts. in Chemical reviews

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Guan J (2023) Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems. in Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

 
Description The award is beginning to shape a landscape for new atomistic multiscale modelling, with the realisation of a software platform that allows communicated of large data objects between software packages "in process", which is a manner not previously feasible. We are now using this functionality to develop new software paradigms that depend on integrated communication between multiple existing packages.
Exploitation Route The outlined new software packages are a transferable library that can be implemented in any software package for the purpose of sharing large data objects in memory, in a manner that is non-native for monolithic software in the computational chemistry field; and a package that allows therefore the integration of multiple packages to perform hierarchical embedded modelling in an approach not previously considered.
Sectors Chemicals

Energy

Other

 
Description Appointment to EPSRC Physical Sciences Advisory Group for redefining "Frontier Challenges"
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description "Controlling selectivity of catalysts through the interaction of cobalt with promoters: a computational modelling investigation"
Amount £118,483 (GBP)
Funding ID 2730879 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2026
 
Description "Tuning Zeolite Catalysts using Organic Additives: Molecular Modelling Studies", EPSRC iCASE PhD Studentship
Amount £118,513 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2026
 
Description Implementation of scalable numeric atomic-orbital-based QM-in-QM embedding in FHI-aims
Amount £131,930 (GBP)
Funding ID ARCHER2-eCSE11-14 
Organisation ARCHER 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2024 
End 04/2025
 
Description Improvements in periodic representation of solvated systems with FHI-aims
Amount £75,647 (GBP)
Funding ID ARCHER2-eCSE08-3 
Organisation ARCHER 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2023 
End 10/2023
 
Description International Centre-to-Centre Collaboration: New catalysts for acetylene processes enabling a sustainable future
Amount £1,276,092 (GBP)
Funding ID EP/Z531285/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2024 
End 11/2028
 
Title CCDC 2111430: Experimental Crystal Structure Determination 
Description Related Article: Christopher J. H. Smalley, Andrew J. Logsdail, Colan E. Hughes, Dinu Iuga, Mark T. Young, Kenneth D. M. Harris|2021|Cryst.Growth Des.|22|524|doi:10.1021/acs.cgd.1c01114 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Support publication: 10.1021/acs.cgd.1c01114 
URL http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc28w3ny&sid=DataCite
 
Title CCDC 2114085: Experimental Crystal Structure Determination 
Description Related Article: Christopher J. H. Smalley, Harriet E. Hoskyns, Colan E. Hughes, Duncan N. Johnstone, Tom Willhammar, Mark T. Young, Christopher J. Pickard, Andrew J. Logsdail, Paul A. Midgley, Kenneth D. M. Harris|2022|Chemical Science|13|5277|doi:10.1039/D1SC06467C 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Supports publication: 10.1039/D1SC06467C 
URL http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/ccdc.csd.cc28yw9f&sid=DataCite
 
Title Data files for "Direct Monitoring of the Potassium Charge Carrier in Prussian Blue Cathodes using Potassium K-edge X-ray Absorption Spectroscopy" 
Description Raw X ray absorption spectra from operando potassium K-edge data used in publication available.ascii file contains raw output files of potassium K-edge CV experiments. Within each file is a time and descriptor stamp 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact Support publication: 10.1039/D3TA02631K 
URL https://repository.lboro.ac.uk/articles/dataset/Data_files_for_Direct_Monitoring_of_the_Potassium_Ch...
 
Title Data for: A Computational Study of the Properties of Pd, Cu and Zn Surfaces 
Description The dataset presented is associated with a computational investigation of the surface properties of Pd, Cu, and Zn metals, in order to gain insight for heterogeneous catalytic applications. We use density functional theory computational simulations to obtain materials properties that are subsequently analysed. The dataset herein contains: a) parameterisation of numerical settings for computation b) the absolute energy used to determine relative energy differences. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Supports publication: 10.1039/D1CP01602D 
URL https://research-data.cardiff.ac.uk/articles/dataset/Data_for_A_Computational_Study_of_the_Propertie...
 
Title Data for: QM/MM study of the reactivity of zeolite bound methoxy and carbene groups 
Description This data object contains raw energies from which the the interaction energy of methoxy and carbene groups with a H-ZSM-5 zeolite framework have been calculated. The models from which the data has been obtained include molecular moieties as well as zeolite framework species, with and without framework bonded moieties. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Supports publication: 10.1039/D1CP02535J 
URL https://research-data.cardiff.ac.uk/articles/dataset/Data_for_QM_MM_study_of_the_reactivity_of_zeoli...
 
Title Dehydrogenation and Dehydration of Formic Acid over Orthorhombic Molybdenum Carbide - Data 
Description The dataset presented is associated with a computational investigation of how formic acid, a bio-mass model compound, interacts with the surface of molybdenum carbide, in order to gain insight for biomass conversion processes. We use density functional theory computational simulations to model energetic processes, and transition state theory coupled with microkinetic modelling to simulate reaction rates. The dataset herein contains: a) the absolute energy used to determine relative energy changes; b) the kinetic data used to determine reaction rates. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Supports publication: 10.1016/j.cattod.2021.04.011 
URL https://research.cardiff.ac.uk/converis/portal/detail/Dataset/129383674?auxfun=&lang=en_GB
 
Title Hydrodeoxygenation of Guaiacol Over Orthorhombic Molybdenum Carbide: A DFT and Microkinetic Study - data 
Description The dataset presented is associated with a computational investigation of how guaiacol, a bio-mass model compound, undergoes hydrodeoxygenation on the surface of molybdenum carbide, in order to gain insight for biomass conversion processes. We use density functional theory computational simulations to model energetic processes, and transition state theory coupled with microkinetic modelling to simulate reaction rates. The dataset herein contains: a) the absolute energy used to determine relative energy changes b) the kinetic data used to determine reaction rates 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Supports publication: 10.1039/D1CY01273H 
URL https://research-data.cardiff.ac.uk/articles/dataset/Hydrodeoxygenation_of_Guaiacol_Over_Orthorhombi...
 
Title SI_data.zip from Computational infrared and Raman spectra by hybrid QM/MM techniques: a study on molecular and catalytic material systems 
Description Data archive containing raw vibrational mode data 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Supports publication: 10.1098/rsta.2022.0234 
URL https://rs.figshare.com/articles/dataset/SI_data_zip_from_Computational_infrared_and_Raman_spectra_b...
 
Title Supplementary information files for Tracking the solid-state incorporation of Sn into the framework of dealuminated zeolite beta, and consequences for catalyst design 
Description Supplementary files for article Tracking the solid-state incorporation of Sn into the framework of dealuminated zeolite beta, and consequences for catalyst design Sn-Beta has emerged as a state-of-the-art catalyst for a range of sustainable chemical transformations. Conventionally prepared by bottom-up hydrothermal synthesis methods, recent research has demonstrated the efficiency of several top-down methods of preparation. One attractive top-down approach is Solid-State Incorporation, where a dealuminated Beta zeolite is physically mixed with a solid Sn precursor, in particular Sn(ii) acetate, prior to heat treatment at 550 °C. This procedure is fast and benign, and metal incorporation requires no solvents and hence produces no aqueous Sn-containing waste streams. Although the performances of these catalysts have been well explored in recent years, the mechanism of heteroatom incorporation remains unknown, and hence, opportunities to improve the synthetic procedure via a molecular approach remain. Herein, we use a range of in situ spectroscopic techniques, alongside kinetic and computational methods, to elucidate the mechanisms that occur during preparation of the catalyst, and then improve the efficacy of the synthetic protocol. Specifically, we find that successful incorporation of Sn into the lattice occurs in several distinct steps, including (i) preliminary coordination of the metal ion to the vacant lattice sites of the zeolite during physical grinding; (ii) partial incorporation of the metal ion into the zeolite framework upon selective decomposition of the acetate ligands, which occurs upon heating the physical mixture in an inert gas flow from room temperature to 550 °C; and (iii) full isomorphous substitution of Sn into the lattice alongside its simultaneous oxidation to Lewis acidic Sn(iv), when the physically mixed material is exposed to air during a short (<1 h) isotherm period. Long isotherm steps are shown to be unnecessary, and fully oxidised Sn(iv) precursors are shown to be unsuitable for successful incorporation into the lattice. We also find that the formation of extra-framework Sn oxides is primarily dependent on the quantity of Sn present in the initial physical mixture. Based on these findings, we demonstrate a faster synthetic protocol for the preparation of Sn-Beta materials via Solid-State Incorporation, and benchmark their catalytic performance for the Meerwein-Ponndorf-Verley transfer hydrogenation reaction and the isomerisation of glucose to fructose. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Supports publication: 10.1039/D2TA03837D 
URL https://repository.lboro.ac.uk/articles/dataset/Supplementary_information_files_for_Tracking_the_sol...
 
Description Collaboration with development team for the FHI-aims software package 
Organisation Duke University
Country United States 
Sector Academic/University 
PI Contribution In the current project, we have worked with the core FHI-aims development team to expand software capabilities. The core focus has been contributing an infrastructure to transfer large data objects in/out of the quantum mechanical calculation workflow without requiring to write the data to static memory. The functionality has been realised, and now we are looking to apply this functionality to challenges in embedded-cluster modelling. We are also working to extend the capabilities in ab initio simulations of materials with new approximations to accelerate calculations. Our contributions have been recognised with invitation to the Board for the company that opens the software licence for FHI-aims (MS1P), which is a not-for-profit company based in Germany.
Collaborator Contribution Our collaborators have provided their support in time and expertise, without which the project would have been far less productive. The collaborators supported the organisation of a UK meeting for the software users, and provided tutorials to the participants. Secondments have been completed in 2024, and are on-going in to 2025.
Impact Publications: 10.21105/joss.05186, 10.1088/1361-651X/ad4d0d
Start Year 2020
 
Description Collaboration with the development team for ChemShell 
Organisation Daresbury Laboratory
Country United Kingdom 
Sector Private 
PI Contribution In the current project, we are working to streamline the protocols for setting up condensed-phase multiscale atomistic modelling, particular QM/MM. Our group are working on new functions that can be applied to facilitate this calculation setup through intelligent automation. We have completed secondments to work with the ChemShell development, group and engage in regular meetings to discuss progres.
Collaborator Contribution The project partner has provided time and knowledge to aid software development, as well as hosting of the software and testing infrastructure.
Impact Publications: 10.1039/D3CP00648D Tutorials: Distributed with software package.
Start Year 2020
 
Title Atomic Simulation Interface (ASI) 
Description The Atomic Simulation Interface (ASI) is a native C-style API for density functional theory (DFT) codes. ASI provides an efficient way to import and export large arrays that describe electronic structure (e.g. Hamiltonian, overlap, and density matrices) from DFT codes that are typically monolithic. The ASI API is designed to be implemented and used with minimal performance penalty, avoiding, where possible, unnecessary data copying. It provides direct access to the internal data structures of a code, and reuses existing data distribution over MPI nodes. The ASI API also defines a set of functions that support classical, AIMD (ab initio molecular dynamics), and hybrid QM/MM simulations: exporting potential energy, forces, atomic charges, and electrostatic potential at user defined points, as well as importing nuclear coordinates and arbitrary external electrostatic potentials. The ASI API is implemented in the DFTB+ (Hourahine et al., 2020) and FHI-aims (Blum et al., 2009) codes. A Python wrapper for easy access to ASI functions is also freely available (asi4py). We hope that the ASI API will be widely adopted and used for development of universal and interoperable DFT codes without sacrificing efficiency for portability. 
Type Of Technology Software 
Year Produced 2023 
Open Source License? Yes  
Impact Integration in to two established codebases, and community engagement to develop broader standards with respect to data communication for atomic simulations. 
URL https://doi.org/10.21105/joss.05186
 
Title EmbASI 
Description EmbASI is a python-based wrapper for QM/QM embedding simulations using the ASI (Atomic Simulation Interface). The wrapper handles communication between QM code library calls through C-based callbacks, and imports/exports relevant matices such as density matrices and hamiltonians required for embedding schemes such as Projection-Based Embedding (PbE). Atomic information is communicated through Atomic Simulation Environment (ASE) atoms objects. 
Type Of Technology Software 
Year Produced 2025 
Open Source License? Yes  
Impact N/A 
 
Description Hosting of Nuffield Summer Studentships 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The activity involves the hosting of A-level students interested in studying Chemistry for a 3- or 4-week placement in the research group. The placement students are from historically under-represented groups at University (Minority groups, or no previous family history of university attendance). The placements allow the students to see and participate in the university working environment, and involves working on a small project that is then formally documented and presented at an award day organised for the Nuffield Foundation. In 2021, we remotely hosted 3 students in the group from across Wales. In 2022, we hosted 3 students in person in the group from the local area. In 2023, we hosted 3 students in person in the group from the local area. In 2024, we hosted 2 students in person in the group from the local area.
Year(s) Of Engagement Activity 2021,2022,2023,2024
 
Description Participation in FLF Development Network podcast series 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact With support from the FLF Development Network, and via coordination from fellow FLFs, we planned, recorded, and disseminated a 6-part podcast series named "Next Generation Research". I participated centrally in one episode, discussing the FLF project and its impact on society. The podcast was supported by participation of colleagues, and looked at the current and future opportunities generated by the work. I then was participant in an event at the FLF Annual conference where we discussed impact, in front of an audience of ~300 Fellows.
Year(s) Of Engagement Activity 2023,2024
URL https://pod.link/1691506840/episode/eb00155f03e0b57a862ab268253a136d