Surface and Interface Toolkit for the Materials Chemistry Community
Lead Research Organisation:
University College London
Department Name: Chemistry
Abstract
We propose to develop a software suite that will support advanced and complex surface and interface simulations of materials employed across the fields of energy, catalysis and life sciences. Surfaces and interfaces of materials control important processes, including corrosion, catalysis, electronic and photovoltaic device operation. Surface and interface studies pose greater challenges than the respective bulk investigations, but a wealth of new experimental techniques to interrogate surfaces need now to be fully complemented with tools for their systematic investigation in silico.
Mechanistic studies of two-dimensional systems using modern computers have become vastly complex, onerous and often repetitive, where similar tasks or materials or problems are carried out by researchers, often without a simple opportunity to share the primary research or expertise to exploit obtained data to the full potential. With the developments planned we aim to streamline the basic computational research on surfaces and interfaces by expanding the capability of leading simulation software to deal with surfaces and interfaces, and developing and providing data for a new database of surfaces and interfaces - Surface and Interface Toolkit for the Materials Chemistry Community (SAINT Toolkit for the MCC). We have chosen surface reactivity as our first target application, the software infrastructure created in the course of the project, however, will be readily extended to adjacent fields of materials chemistry in the future.
The problem of accurate and predictive surface thermochemistry is now coming to the forefront of our research with two main challenges:
- Lack of high quality readily accessible models for excited states in surfaces and interfaces with applications in photocatalysis and energy harvesting materials; reactivity of metallic surfaces; accurate energetics of surface defects, active sites and reactants
- Lack of surface and interface databases that would allow access to results of simulations; quality control and comparison of massive data sets obtained in such simulations; predictive screening of reactants and materials
The key problem of "how to handle big datasets" relevant to particular catalytic applications, or more general chemical questions calls for the development of an Expert System that will answer questions of the type:
- Which material/surface under what conditions would have a specific physical or chemical property, for example the ability to catalyse a particular reaction?
- How can a surface or interface be modified to promote a particular physical property or reactivity
The software infrastructure created and enhancement to internationally leading software we plan will be readily extended to adjacent fields of materials chemistry and beyond in the future. We will strive to make the new software freely available and open source. It will have general impact in the field of surface and interfacial science and will enhance the efficacy of our communities' exploitation of supercomputers in this key field.
Mechanistic studies of two-dimensional systems using modern computers have become vastly complex, onerous and often repetitive, where similar tasks or materials or problems are carried out by researchers, often without a simple opportunity to share the primary research or expertise to exploit obtained data to the full potential. With the developments planned we aim to streamline the basic computational research on surfaces and interfaces by expanding the capability of leading simulation software to deal with surfaces and interfaces, and developing and providing data for a new database of surfaces and interfaces - Surface and Interface Toolkit for the Materials Chemistry Community (SAINT Toolkit for the MCC). We have chosen surface reactivity as our first target application, the software infrastructure created in the course of the project, however, will be readily extended to adjacent fields of materials chemistry in the future.
The problem of accurate and predictive surface thermochemistry is now coming to the forefront of our research with two main challenges:
- Lack of high quality readily accessible models for excited states in surfaces and interfaces with applications in photocatalysis and energy harvesting materials; reactivity of metallic surfaces; accurate energetics of surface defects, active sites and reactants
- Lack of surface and interface databases that would allow access to results of simulations; quality control and comparison of massive data sets obtained in such simulations; predictive screening of reactants and materials
The key problem of "how to handle big datasets" relevant to particular catalytic applications, or more general chemical questions calls for the development of an Expert System that will answer questions of the type:
- Which material/surface under what conditions would have a specific physical or chemical property, for example the ability to catalyse a particular reaction?
- How can a surface or interface be modified to promote a particular physical property or reactivity
The software infrastructure created and enhancement to internationally leading software we plan will be readily extended to adjacent fields of materials chemistry and beyond in the future. We will strive to make the new software freely available and open source. It will have general impact in the field of surface and interfacial science and will enhance the efficacy of our communities' exploitation of supercomputers in this key field.
Planned Impact
The impact of the work of our Materials Chemistry Consortium is substantial and widespread, and the surface and interface studies embrace more than 50% of our projects. The newly developed SAINT Toolkit for the materials chemistry community will bring a new dimension to this research, greatly enhancing our ability to model complex and diverse chemical systems of tremendous interest in the efficient manner. Materials performance, which is crucially dependent upon properties of their surfaces and interfaces, underpins a large number of industrial processes, which are instrumental in maintaining global wealth and health, as well as playing a key role in developing process that are both environmentally and economically sustainable. The work enabled by the developed software will have impact on the industrial sector, including chemicals, energy, and electronics industries, on society in more generally and on academic communities in chemistry, physics and materials and computational science. The MCC consortium will exploit the SAINT Toolkit for the materials chemistry community to help to ensure the continual leadership of UK science in a strongly competitive field.
The specific areas of impact will be:
(i) Industry, where surface and interface modelling and simulation are now integral tools in the design and optimisation of materials. All the themes of the Consortium typically have a focus on surfaces and interfaces, and have direct relevance to industries; Consortium members have active colorations with several UK industries, e.g. Johnson Matthey, GlaxoSmith Kline, and BP. The project will therefore contribute to the continuing competitiveness of the UK economy
(ii) The General Public and policy makers to whom the work of the Consortium with the development of the SAINT Toolkit for the materials chemistry community will be communicated by the website and a variety of outreach events with which we will promote the key role of materials developments and computational modelling in areas of general interest to the public including energy technologies and policy. The new software and in particular the database will be made available to the public, so that it could also, importantly, be exploited by the wider community, for example, in science lessons in schools and definitely in undergraduate university science courses, thus increasing awareness by the general public of latest science and their importance for the successful industrial production and development.
(iii) Academic Groups - both experimental and computational - where the extensive network of the Consortium will ensure the effective dissemination of the new software and its applications with much of the work of the Consortium feeding into other projects. The software developed will thus be of wide benefit. To maximise the outreach the developed software will be used in teaching at the workshop planned to be held in the course of the project, CCP5 Summer School, and in the Molecular Modelling and Materials Science Industry Doctoral Training Centre based at UCL Chemistry.
We will invite representatives of our industrial partners to attend our meetings and workshops. Direct impact will be leveraged through targeted workshops aimed at both academia and industry to disseminate know-how and facilitate specific collaborations. Industry will gain from highly skilled, talented young researchers trained by the programme, graduating PhD students and PDRAs. Outreach activities to the general public will both inform them of the importance and benefits of engineering and the physical sciences and encourage young people to choose careers in this area.
The specific areas of impact will be:
(i) Industry, where surface and interface modelling and simulation are now integral tools in the design and optimisation of materials. All the themes of the Consortium typically have a focus on surfaces and interfaces, and have direct relevance to industries; Consortium members have active colorations with several UK industries, e.g. Johnson Matthey, GlaxoSmith Kline, and BP. The project will therefore contribute to the continuing competitiveness of the UK economy
(ii) The General Public and policy makers to whom the work of the Consortium with the development of the SAINT Toolkit for the materials chemistry community will be communicated by the website and a variety of outreach events with which we will promote the key role of materials developments and computational modelling in areas of general interest to the public including energy technologies and policy. The new software and in particular the database will be made available to the public, so that it could also, importantly, be exploited by the wider community, for example, in science lessons in schools and definitely in undergraduate university science courses, thus increasing awareness by the general public of latest science and their importance for the successful industrial production and development.
(iii) Academic Groups - both experimental and computational - where the extensive network of the Consortium will ensure the effective dissemination of the new software and its applications with much of the work of the Consortium feeding into other projects. The software developed will thus be of wide benefit. To maximise the outreach the developed software will be used in teaching at the workshop planned to be held in the course of the project, CCP5 Summer School, and in the Molecular Modelling and Materials Science Industry Doctoral Training Centre based at UCL Chemistry.
We will invite representatives of our industrial partners to attend our meetings and workshops. Direct impact will be leveraged through targeted workshops aimed at both academia and industry to disseminate know-how and facilitate specific collaborations. Industry will gain from highly skilled, talented young researchers trained by the programme, graduating PhD students and PDRAs. Outreach activities to the general public will both inform them of the importance and benefits of engineering and the physical sciences and encourage young people to choose careers in this area.
Organisations
Publications
Durrant TR
(2018)
Relation between image charge and potential alignment corrections for charged defects in periodic boundary conditions.
in The Journal of chemical physics
Escher S
(2021)
Approaching Bulk from the Nanoscale: Extrapolation of Binding Energy from Rock-Salt Cuts of Alkaline Earth Metal Oxides
in South African Journal of Chemistry
Kühne T
(2020)
CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations
in The Journal of Chemical Physics
Lu Y
(2023)
Multiscale QM/MM modelling of catalytic systems with ChemShell.
in Physical chemistry chemical physics : PCCP
Poli E
(2019)
The Role of Cation-Vacancies for the Electronic and Optical Properties of Aluminosilicate Imogolite Nanotubes: A Non-local, Linear-Response TDDFT Study.
in Frontiers in chemistry
Description | The overall objective is to enable more efficient and new science by the development of software and a web-database for modelling the structure, physical properties and reactivity of inorganic surfaces. The funding has allowed us to develop new functionality in two internationally recognised materials modelling codes (a) CP2K and (b) CHEMSHELL, and to develop the web-page toolkit and searchable web-database for inorganic surfaces. In the latter, surface models can be generated, from bulk models that are uploaded into the database, using the toolkit; both bulk and surface models can be viewed online as rotatable ball and stick models; grids of binding energies and structural data of three different probe molecules can be generated and viewed; simulations using the dedicated nodes and the CRYSTAL electronic structure code can be launched from the webpage, i.e. multiple simulations launched after selecting options for bulk (converge with respect to k-points), surface (converge with respect to k-points and atomic layers) and binding energies (set of simulations for each point on a grid across the exposed surface); searches can also be performed on the data within the database; downloaded input files for many commonly used materials software; and the latest version is now installed on the same hardware that hosts the HIVE database for nanoclusters (previously developed as part of the WASP@N project) but with additional nodes (and replacement head node). |
Exploitation Route | The toolkit and database is freely available and accessible via the internet. The original target audience is that of the members of UK's Materials Chemistry HEC consortium who will be able to use it to initiate projects more efficiently by downloading suitable initial models and then, once their research is published, upload their data for other to exploit. The feature of running simulations from the webpage will initially be restricted to selected users until a critical mass of data is generated. The toolkit has already been been used in training postgraduate students (MSc and PhD level) and it is expected to be of interest to industry. |
Sectors | Chemicals Education Electronics Energy Environment Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology Transport |
URL | https://saint.chem.ucl.ac.uk/ |
Description | The SAINT website provides both tools and data for visualization, modelling and analysis of surfaces of materials and surface reactivity. This site is attracting users, particularly academic and is anticipated that industry and interested general public will also find the site beneficial. The tools and visualizer on the SAINT website have been used in the Materials and Molecular Modelling postgraduate course taught at UCL; some of the cohort will either continue in academia or go into industry where they will be able to exploit this facility. Software developments were completed in both CP2K and CHEMSHELL, which are codes used by both academia and industry. |
First Year Of Impact | 2021 |
Sector | Aerospace, Defence and Marine,Chemicals,Education,Electronics,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Transport |
Impact Types | Economic |
Description | COVID 19 Grant Extension Allocation University College London |
Amount | £10,872,785 (GBP) |
Funding ID | EP/V520342/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 05/2020 |
End | 09/2021 |
Title | SAINT website database for atomic models of surfaces and interfaces |
Description | Database, website interface and additional software developed in collaboration with our partners. Website interface enables users (including general public) to access the database of atomic structures for bulk phases of crystalline materials and their surfaces. From the website interface it is possible to set running electronic structure calculations/simulations on the dedicated nodes reserved for this project. There are a number of user access levels: the lowest level allows a user to register, search the database, create a surface model by selecting the bulk unit cell and specifying which surface, visualise the atomic structure of either the bulk phase or the surface, visualise contour maps above a surface model that provides a measure of its reactivity; download the atomic coordinates for further analysis or calculation; whereas the highest level user can also optimise bulk and surface structures, add new data into the database, run calculations required to generate data for maps of the reactivity of a surface. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Access to the research database is currently only through the website interface. The website went live 2019, although there is not yet a hyperlink to it as it is still under construction. Impact with regards to users of this site is expected to increase with time (we have not yet begun to advertise its existence, but have used the tools that are part of this website for an exercise that Master postgraduate students need in order to complete assessed coursework). There are currently 34 registered users of the SAINT website/database. Community of materials researchers who model surfaces and reactions thereon can use this database to: (a) generate surface models for use in their research/simulations; (b) retrieve models already in the database for use in their research/simulations; (c) find the best surface in the database that is likely to be a suitable candidate for a certain type of reactivity (maps of energy absorption of three different probe molecules are also a key part of this database). |
URL | https://saint.chem.ucl.ac.uk/ |
Title | Py-ChemShell 2023 release (v23.0) |
Description | Py-ChemShell is the python-based version of the ChemShell multiscale computational chemistry environment, a leading package for combined quantum mechanical/molecular mechanical simulations. |
Type Of Technology | Software |
Year Produced | 2023 |
Open Source License? | Yes |
Impact | The 2023 release of Py-ChemShell contained a number of major new features developed through and in support of the BBSRC "BEORHN" grant, EPSRC "UEMBioMat" and "FEHybCat" grants, InnovateUK "QuPharma" grant, ExCALIBUR "PAX-HPC" and CoSeC support for the Materials Chemistry Consortium. These include improved handling of biomolecular forcefields for QM/MM, of general interest for enzyme modelling, a generic n-layer subtractive embedding scheme, an interface to the basis set exchange, and new interfaces to CASTEP (for periodic QM/MM), TURBOMOLE and PySCF. |
URL | https://www.chemshell.org |
Title | Py-ChemShell third beta release (v21.0) |
Description | Py-ChemShell is the python-based version of the ChemShell multiscale computational chemistry environment, a leading package for combined quantum mechanical/molecular mechanical simulations. |
Type Of Technology | Software |
Year Produced | 2021 |
Open Source License? | Yes |
Impact | The third beta release of Py-ChemShell was the first release to support automated import of biomolecular forcefields (CHARMM and AMBER) for QM/MM calculations, and features a new integrated workflow for setup of biomolecular systems. This is a major milestone for users in the biomolecular modelling community to transition from the original Tcl-based version of the software. It also features periodic QM/MM embedding for surface-adsorbate systems developed under the "SAINT" project. |
URL | https://www.chemshell.org |
Description | A School on "Computational Modeling and Simulations of Materials for Energy and Environment", December, 2022 at JNCASR |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Indian school, where international experts in materials modelling were invited to teach approximately 30 to 40 postgraduates from research groups based in universities not just within Bangalore but also from other provinces across India. Postgraduates given the opportunity to learn from leading international experts; it is expected that they will apply the knowledge and new skills learnt during this event to their own research. I presented the theory of modelling materials using novel interatomic potentials that my group have developed. I also demonstrated how to use the software/database developed in the WASP@N and SAINT projects. |
Year(s) Of Engagement Activity | 2022 |
Description | CoSeC presentation at MCC meeting, January 2020 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal gave a presentation on recent CoSeC and SAINT developments at the Materials Chemistry Consortium meeting at UCL, 6 January 2020 |
Year(s) Of Engagement Activity | 2020 |
Description | Invited Lecturer at the summer school "Hands-on DFT and beyond" held in Barcelona (26 August - 6 September, 2020) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | European summer school, where international experts in materials modelling were invited to teach approximately 30 to 40 postgraduates from research groups typically based in Europe. Lectures on the theory were presented in the morning sessions and hands on exercises using internationally leading materials software were conducted in the afternoon. Postgraduates given the opportunity to learn from leading international experts; it is expected that they will apply the knowledge and new skills learnt during this event to their own research. I presented the theory of global optimisation as applied to predicting atomic structures of clusters and crystalline materials (bulk phases and surfaces thereof) as well as how to use the software/database developed in the WASP@N and SAINT projects. I was also able to catch up on collaborative efforts/projects with some of the other invited lecturers and established a new collaboration with one lecturer who I had not met before attending this event. |
Year(s) Of Engagement Activity | 2019 |
URL | https://th.fhi-berlin.mpg.de/meetings/dft2019/ |
Description | Invited Lecturer at the winter school "Modeling and Simulations of Materials for Energy and Environment" held in JNCASR, Bangalore (12 - 14 December 2018) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Indian school, where international experts in materials modelling were invited to teach approximately 30 to 40 postgraduates from research groups based in universities not just within Bangalore but also from other provinces across India. Postgraduates given the opportunity to learn from leading international experts; it is expected that they will apply the knowledge and new skills learnt during this event to their own research. I presented the theory of global optimisation as applied to predicting atomic structures of clusters and crystalline materials (bulk phases and surfaces thereof) as well as how to use the software/database developed in the WASP@N and SAINT projects. |
Year(s) Of Engagement Activity | 2018 |
Description | Invited talk at 3rd EMMC (European Materials Modelling Council) International Workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | The non-profit Association, EMMC ASBL, was created in 2019 to ensure continuity, growth and sustainability of EMMC activities for all stakeholders including modellers, materials data scientists, software owners, translators and manufacturers in Europe. The EMMC considers the integration of materials modelling and digitalisation critical for more agile and sustainable product development. |
Year(s) Of Engagement Activity | 2021 |
URL | https://emmc.eu/ |
Description | PRACE Winter School: Catalysis for Europe's Green Transition - ChemShell talks, Nov 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | As part of the PRACE Winter School on Catalysis for Europe's Green Transition, Tom Keal and Kakali Sen of STFC Scientific Computing presented talks on "Introduction to QM/MM modelling of catalytic systems with ChemShell" and "Modelling Enzyme Reactivity by Combining QM/MM with Serial Crystallography". |
Year(s) Of Engagement Activity | 2022 |
Description | Presentation at Cluster-Surface Interaction Workshop 2022, Genoa |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Present, to fellow international experts in the field, (a) cluster-surface research achieved using UK HPC resources provided via membership of the MCC and (b) the web-database and toolkits developed in the WASP@N and SAINT projects. |
Year(s) Of Engagement Activity | 2022 |
URL | https://csi2022.unige.it/ |
Description | Presentation of the toolkit features at an international conference |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Helen Duncan gave a presentation on the SAINT toolkit during the Materials Research Society's Winter meeting in Boston/online |
Year(s) Of Engagement Activity | 2020 |
Description | Royce Industrial Engagement Workshop - Combining Ab Initio and Atomistic Methods |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | As part of the CCP5/Royce Industrial Engagement Event, Thomas Keal chaired a session and presented on "Predictive Power and Capability: Combining Ab Initio and Atomistic Modelling" |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.royce.ac.uk/events/the-power-of-materials-modelling-for-industrial-applications-an-indus... |
Description | Seminar by PI to the Department of Chemistry, University of Bath |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Departmental seminar with the aim to generate new collaboration and to advertise the work of the WASP@N, SAINT, MMM DDWG and PAX-HPC projects as well as to encourage applications to join the MCC (largest EPSRC funded HEC that shares best HPC practise and distributes national HPC resources). |
Year(s) Of Engagement Activity | 2023 |
Description | Tom Keal UCL Inaugural Lecture 2023 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Tom Keal gave his inaugural professorial lecture "Scaling up computational chemistry: from small molecules to complex systems " at UCL Department of Chemistry on 27 April 2023. The event was arranged as a workshop by the Thomas Young Centre with additional speakers Michael Buehl (St Andrews), Kakali Sen (STFC), Xingfan Zhang (UCL) and Keith Butler (QMUL). The inaugural lecture covered a range of topics including the redevelopment of ChemShell and recent work from the EPSRC "UEMBioMat" and "FEHybCat" grants, BBSRC "ENCATS" and "BEORHN" grants, and CoSeC support. |
Year(s) Of Engagement Activity | 2023 |
URL | https://thomasyoungcentre.org/event/tyc-inaugural-lecture-thomas-keal/ |
Description | Workshop at the Telluride Science and Innovation Centre, July 2022 |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Present, to fellow international experts in the field, (a) research achieved using UK HPC resources provided via membership of the MCC, (b) the web-database and toolkits developed in the WASP@N and SAINT projects, and (c) discuss solutions to problems found in new on-going work. |
Year(s) Of Engagement Activity | 2022 |