Predictive multiscale free energy simulations of hybrid transition metal catalysts
Lead Research Organisation:
Science and Technology Facilities Council
Department Name: Scientific Computing Department
Abstract
Catalysis is a key area of fundamental science which underpins a high proportion of manufacturing industry. Developments in catalytic science and technology will also be essential in achieving energy and environmental sustainability. Progress in catalytic science requires a detailed understanding of processes at the molecular level, in which computation now plays a vital role. When used in conjunction with experiment, computational modelling is able to characterise structures, properties and processes including active site structures, reaction mechanisms and increasingly reaction rates and product distributions. However, despite the power of computational catalysis, currently available methods have limitations in both accuracy and their ability to model the reaction environment. Also, it is practically difficult to model hybrid catalysts, which combine elements of different types of catalyst (e.g. unnatural metal centres incorporated in natural enzymes). Advances in technique are essential if the goal of catalysis by design is to be achieved.
A powerful, practical approach to modelling catalytic processes is provided by Quantum Mechanical/Molecular Mechanical (QM/MM) methods, in which the reaction and surroundings are described using an accurate quantum mechanical approach, with the surrounding environment modelled by more approximate classical forcefields. QM/MM has been widely and successfully employed in modelling enzymatic reactions (recognised in the 2013 Nobel prize for Chemistry) but has an equally important role in other areas of catalytic science.
The flagship ChemShell code, developed by the STFC team in collaboration with UCL, Bristol and other groups around the world, is a highly flexible and adaptable open source QM/MM software package which allows a range of codes and techniques to be used in the QM and MM regions (www.chemshell.org). The software has been widely and successfully used in modelling enzymatic reactions and catalytic processes in zeolites and on oxide surfaces. It will provide the ideal platform for the developments we are proposing which will take computational catalysis to the next level. These will include the use of high level QM techniques to achieve chemical accuracy, accurate modelling of solvent effects, calculation of spectroscopic signatures allowing direct interaction with experiment, and dynamical approaches for free energy simulations. Crucially, we will bring together methods from different spheres of computational catalysis to enable modelling of hybrid catalytic systems. We will develop flexible and rigorous methods that meet the twin challenges of high-level QM treatment for accuracy with the ability to sample dynamics of the reacting system. Together these methods will allow accurate and predictive modelling of catalytic reactions under realistic conditions. The project will also anticipate the software developments needed to exploit the next generation of exascale high performance computing.
We will apply these new techniques to model the catalytic behaviour of a range of engineered heterogeneous, homogeneous and biomolecular catalysts, currently under study in the UK Catalysis Hub. The Hub supports experimental and computational applications across the whole UK catalysis community. This project will provide method development and software engineering that is not covered by the Hub, and thus will complement EPSRC investment in the Hub. Specific systems include methanol synthesis using homogeneous ruthenium complexes, Cu-based artificial enzymes for enantioselective Friedel-Crafts reactions, fluorophosphite-modified rhodium systems for hydroformylation catalysis of alkenes, and non-canonical substitutions in non-heme iron enzymes for C-H functionalisations. These highly topical and potentially industrially relevant systems will allow us both to test and exploit the new software, which promises a step change in our ability to model catalytic systems and reactions.
A powerful, practical approach to modelling catalytic processes is provided by Quantum Mechanical/Molecular Mechanical (QM/MM) methods, in which the reaction and surroundings are described using an accurate quantum mechanical approach, with the surrounding environment modelled by more approximate classical forcefields. QM/MM has been widely and successfully employed in modelling enzymatic reactions (recognised in the 2013 Nobel prize for Chemistry) but has an equally important role in other areas of catalytic science.
The flagship ChemShell code, developed by the STFC team in collaboration with UCL, Bristol and other groups around the world, is a highly flexible and adaptable open source QM/MM software package which allows a range of codes and techniques to be used in the QM and MM regions (www.chemshell.org). The software has been widely and successfully used in modelling enzymatic reactions and catalytic processes in zeolites and on oxide surfaces. It will provide the ideal platform for the developments we are proposing which will take computational catalysis to the next level. These will include the use of high level QM techniques to achieve chemical accuracy, accurate modelling of solvent effects, calculation of spectroscopic signatures allowing direct interaction with experiment, and dynamical approaches for free energy simulations. Crucially, we will bring together methods from different spheres of computational catalysis to enable modelling of hybrid catalytic systems. We will develop flexible and rigorous methods that meet the twin challenges of high-level QM treatment for accuracy with the ability to sample dynamics of the reacting system. Together these methods will allow accurate and predictive modelling of catalytic reactions under realistic conditions. The project will also anticipate the software developments needed to exploit the next generation of exascale high performance computing.
We will apply these new techniques to model the catalytic behaviour of a range of engineered heterogeneous, homogeneous and biomolecular catalysts, currently under study in the UK Catalysis Hub. The Hub supports experimental and computational applications across the whole UK catalysis community. This project will provide method development and software engineering that is not covered by the Hub, and thus will complement EPSRC investment in the Hub. Specific systems include methanol synthesis using homogeneous ruthenium complexes, Cu-based artificial enzymes for enantioselective Friedel-Crafts reactions, fluorophosphite-modified rhodium systems for hydroformylation catalysis of alkenes, and non-canonical substitutions in non-heme iron enzymes for C-H functionalisations. These highly topical and potentially industrially relevant systems will allow us both to test and exploit the new software, which promises a step change in our ability to model catalytic systems and reactions.
Organisations
- Science and Technology Facilities Council (Lead Research Organisation)
- University of York (Project Partner)
- University of Stuttgart (Project Partner)
- CARDIFF UNIVERSITY (Project Partner)
- University of Glasgow (Project Partner)
- Imperial College London (Project Partner)
- Heriot-Watt University (Project Partner)
- University of Oxford (Project Partner)
- University of Bristol (Project Partner)
- University of Bath (Project Partner)
- Loughborough University (Project Partner)
- Johnson Matthey (Project Partner)
- Victoria University of Wellington (Project Partner)
- University of Edinburgh (Project Partner)
- Manchester Institute of Biotechnology (Project Partner)
Publications
Abdul Nasir J
(2022)
Influence of Solvent on Selective Catalytic Reduction of Nitrogen Oxides with Ammonia over Cu-CHA Zeolite
in Journal of the American Chemical Society
Abdul Nasir J
(2024)
The Rôle of Iron in Zeolite Beta for deNOx Catalysis
in Journal of Catalysis
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
Liu T
(2025)
Origins of Intrinsic p-type Conductivity, p-n Transition and Substoichiometry in SrO
in Journal of Materials Chemistry A
Lu Y
(2023)
Multiscale QM/MM modelling of catalytic systems with ChemShell.
in Physical chemistry chemical physics : PCCP
Zhang X
(2023)
Toward a Consistent Prediction of Defect Chemistry in CeO2.
in Chemistry of materials : a publication of the American Chemical Society
Zhang X
(2023)
Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides
in Angewandte Chemie
Zhang X
(2024)
Environment-Driven Variability in Absolute Band Edge Positions and Work Functions of Reduced Ceria.
in Journal of the American Chemical Society
Zhu L
(2024)
Formation of intrinsic point defects in AlN: a study of donor and acceptor characteristics using hybrid QM/MM techniques
in Journal of Materials Chemistry A
| Description | A key methodological objective of the project is complete at the time of writing (March 25), namely the implementation of a general molecular dynamics driver within Py-ChemShell. This will be released later this year, and greatly increases the functionality of the software |
| Exploitation Route | QM/MM MD is potentially applicable to all the chemistry, biochemistry and materials science challenges that ChemShell has been developed to address and so has very widespread academic and industrial relevance. |
| Sectors | Agriculture Food and Drink Chemicals Digital/Communication/Information Technologies (including Software) Energy Environment Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | Development in this project complements and underpins our parallel scientific software development work targeting quantum computing, working with commercial quantum computing partners and end users in the pharmaceutical and chemical industries. |
| First Year Of Impact | 2024 |
| Sector | Chemicals,Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology |
| Impact Types | Economic |
| Title | Vastly parallelised vibrational self-consistent field calculations under ChemShell |
| Description | A vastly parallelised vibrational self-consistent field computation infrastructure has been built and tested against molecular and catalytic material systems under ChemShell. New numerical solutions to vibrational self-consistent field theory have also been developed. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | This new development enables new vibrational spectroscopy scientific studies and allows researchers to study much larger-scaled anharmonic vibrational effects, IR, Raman, and environmental impacts using hybrid QM/MM approaches. |
| 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 |
| Description | An invited talk at MCC Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | This Workshop on the Modelling of Point Defects took place in Lancaster on 9-11 Jan 2024 with <100 participants. It aimed at introducing the most recent advances in research and method development in the area of simulating defected material systems. During the workshop, there was also an extensive discussion about the relevant trends and challenges among the participants. I was invited to give a talk, titled Recent Advances in Py-ChemShell for Modelling Hetero-and Homogeneous Catalysis, to summarise the advances in the methodology and software development of ChemShell. The talk received very positive feedbacks and aroused the audience's interests in using ChemShell to perform QM/MM calculations. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://mcc.hec.ac.uk/events/mcc-workshop-on-the-modelling-of-point-defects/ |
| Description | ChemShell presentation at MCC Workshop on the Modelling of Point Defects 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | You Lu gave a talk on ChemShell QM/MM simulations for defect calculations at the MCC Workshop on the Modelling of Point Defects , 9-11 January 2024, Lancaster. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.mccdefectworkshop.com/ |
| Description | ChemShell training workshop at the CCPBioSim training week, September 2024 |
| 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 | As part of the CCPBioSim training week 2024, a training session on ChemShell for multiscale QM/MM calculations was held, with talks from Tom Keal and Kakali Sen of STFC and Warispreet Singh of Northumbria University. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.ccpbiosim.ac.uk/events/past-events/eventdetail/125/-/training-week-2024 |
| Description | CoSeC presentation at MCC summer conference 2023 |
| 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 CoSeC support for MCC at the MCC summer conference at Daresbury on 30 June 2023. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://mcc.hec.ac.uk/events/mcc-conference-2023/ |
| Description | MMM Hub Software Spotlight: Chemshell |
| 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 | As part of the MMMHub software spotlight online workshop series, Dr You Lu from STFC showcased the capabilities of the ChemShell package from a research perspective, as well as spending time looking at exactly how the code can be efficiently run in practice - in particular multinode jobs on Young. Approx 30 people attended online. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://thomasyoungcentre.org/event/mmm-hub-software-spotlight-chemshell/ |
| Description | PAX-HPC training workshop at the South African High Performance Computing conference 2024 |
| 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 | A team from the PAX-HPC project (Scott Woodley, Alexey Sokol and Karen Stoneham from UCL, Tom Keal, Rajany KV, and Marcello Puligheddu from STFC, and Matt Smith and Hossein Ehteshami from York University) organised and delivered a training workshop at the South African national supercomputing conference CHPC 2024 in Port Elizabeth on 1st December 24. Training was provided for GULP, CASTEP, CP2K and ChemShell, covering the full range of materials modelling approaches targeted by the PAX-HPC project. The audience came from a number of universities across South Africa and further afield and resulted in discussions around future research using these software projects and methods. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://chpcconf.co.za/ |
| 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/ |
