Embedded Cluster Modelling for Realistic Solid-State Systems

Lead Research Organisation: CARDIFF UNIVERSITY
Department Name: Chemistry


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.


10 25 50

publication icon
Beynon O (2023) Evaluating the Role of Anharmonic Vibrations in Zeolite ß Materials in The Journal of Physical Chemistry C

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

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

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

publication icon
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

publication icon
Kabalan L (2023) Investigation of the Pd(1-x)Znxalloy phase diagram usingab initiomodelling approaches. in Journal of physics. Condensed matter : an Institute of Physics journal

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. However, the project is still in the early stages and therefore the outcomes are still developing.
Exploitation Route The outlined new software is 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.
Sectors Chemicals

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 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.
Collaborator Contribution Our collaborators have provided their support in time and expertise, without which the project would have been far less productive. Secondments are organised for the forthcoming period (2024).
Impact Publications: 10.21105/joss.05186
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
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
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.
Year(s) Of Engagement Activity 2021,2022,2023
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.
Year(s) Of Engagement Activity 2023
URL https://pod.link/1691506840/episode/eb00155f03e0b57a862ab268253a136d