Transition metal controlled nitrogen chemistry in zeolite and protein environments using a unified quantum embedding model

Lead Research Organisation: Science and Technology Facilities Council
Department Name: Scientific Computing Department

Abstract

Nitrogen compounds play a crucial role in the earth's ecosystems, being continually converted from one form to another as they pass from the atmosphere to living organisms on land and in the sea. Nitric oxide gas (NO), for example, is a key intermediate in the global nitrogen cycle, and plays important roles in many processes in almost all forms of life, often acting as a signalling molecule. However, emissions of NO and the toxic gas nitrogen dioxide (collectively known as NOx) from heavy industry and motor vehicles alter the composition of nitrogen compounds in the atmosphere and are highly damaging both directly and indirectly to the human respiratory system. The removal of NOx from exhaust emissions is a pressing environmental concern and an important target for industrial catalysis research, an area of extreme importance to the UK economy.

We propose to study the chemistry of nitrogen oxides in biological and industrial environments where a full understanding of how the gases are controlled is crucial but still lacking. In both cases the chemistry is controlled by transition metals: cytochrome c' proteins have evolved an extraordinary degree of control of NO through binding to an iron complex which discriminates against other diatomic gases, while in zeolite catalysts (microporous aluminosilicate structures) NOx gases can be converted into safer by-products at copper centres through the addition of ammonia in a process known as selective catalytic reduction (SCR). The precise mechanisms, however, are not currently proven.

We will investigate the chemistry of nitrogen dioxide and nitrogen oxide in both systems by computational simulations performed on high performance clusters. The resulting data will be used to model spectroscopic signatures, i.e. how electromagnetic radiation (such as light or X-rays) interacts with matter. These will be compared with the results of infrared, Raman, UV-visible and X-ray absorption experiments on the two systems to better understand the processes involved in the chemical reactions, which will inform the future design of improved zeolite catalysts and bioengineered proteins.

We will use quantum mechanical/molecular mechanical (QM/MM) modelling to identify the reaction mechanisms and calculate spectroscopic signatures of the two systems. In this approach the zeolite and protein active sites will be treated using a highly accurate, but computationally expensive, quantum mechanical level of theory, embedded in an environment described by an efficient classical calculation. New QM/MM methods will be implemented that can enable larger QM regions to be calculated and more accurate spectroscopic signatures including anharmonic vibrational effects. Importantly, our approach for combining computational modelling with experimental results will be generally applicable to any chemical processes in complex systems, including other industrial catalysts and biomolecules.

Planned Impact

Our research is well-aligned to EPSRC strategic priorities, including long-term multidisciplinary research, engagement and development of large scale facilities and conducting transformative research through advanced computational chemistry. The proposed work will have wide-ranging impacts across academia and industry, where materials and biomolecular research underpin many sectors of the economy. Catalysis is a particularly important strategic area of research, and the investigations into zeolite catalysis will inform the industrial development of new catalysts for the removal of NOx from exhaust emissions, both through the publication of the results in the academic literature and directly through work undertaken by our project partners Johnson Matthey. The proposed software developments will also be applicable to other areas of catalysis research including the emerging field of bio-catalysis, where the techniques we will apply to cytochrome c' proteins will be directly transferable to other haem-containing systems. QM/MM methods are also applicable to other life science industries, and the development of more efficient QM/MM approaches will increase its appeal in areas such as drug discovery.

The development of new tools for the calculation of spectroscopic signatures will be of benefit for all researchers investigating IR, Raman, UV-visible and X-ray absorption spectroscopy of complex systems which require an efficient QM/MM approach, including large facility users in the UK and worldwide. We will contribute new capabilities to the ChemShell QM/MM package for chemical modelling of materials and native and synthetic enzymes, with benefit to other UK EPSRC researchers, academics and industrial scientists. The new code will be placed in the CCPForge repository and will be available free of charge under an open source licence. To maximise the impact of the developments software workshops and training programmes will be provided through the CCP networks to users both in academia and industry. The work, as noted, will also be disseminated via the UK Catalysis Hub.

The general public will benefit from outreach activities at STFC and UCL and through educational materials for schools based on the applications to zeolites and proteins.

Publications

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Deng W (2021) Revealing the Mechanism of Isethionate Sulfite-Lyase by QM/MM Calculations in Journal of Chemical Information and Modeling

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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

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Keal T (2022) Materials and Molecular Modeling at the Exascale in Computing in Science & Engineering

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Lu Y (2019) Open-Source, Python-Based Redevelopment of the ChemShell Multiscale QM/MM Environment. in Journal of chemical theory and computation

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Lu Y (2023) Multiscale QM/MM modelling of catalytic systems with ChemShell. in Physical chemistry chemical physics : PCCP

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Zhang X (2022) Toward a Consistent Prediction of Defect Chemistry in CeO 2 in Chemistry of Materials

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Zhang X (2023) Bulk and Surface Contributions to Ionisation Potentials of Metal Oxides in Angewandte Chemie International Edition

 
Description - Significant methodological developments, including new materials modelling functionality targeted at zeolite applications and a new biomolecular modelling workflow have been implemented and released to users as part of the Py-ChemShell beta release cycle, including appropriate tutorials
- Applications work on the zeolite and protein applications were undertaken as planned and the findings are being written up in multiple journal articles.
Exploitation Route The method developments associated with the grant are available to the large ChemShell user community via our regular public releases.
Sectors Chemicals

Digital/Communication/Information Technologies (including Software)

Energy

Environment

Manufacturing

including Industrial Biotechology

Pharmaceuticals and Medical Biotechnology

 
Description The new multiscale biomolecular workflows developed in this project are already being used for a commercial project involving major pharmaceutical companies working with STFC and other collaborators to accelerate drug discovery with quantum computing algorithms. More generally, all the software developments from the project have now been released in the latest version of ChemShell, which is used in both academic and industrial settings, and is available to all under an open source licence.
First Year Of Impact 2022
Sector Digital/Communication/Information Technologies (including Software),Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description BEORHN: Bacterial Enzymatic Oxidation of Reactive Hydroxylamine in Nitrification via Combined Structural Biology and Molecular Simulation
Amount £368,451 (GBP)
Funding ID BB/V016660/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 06/2025
 
Description Particles At eXascale on High Performance Computers (PAX-HPC)
Amount £3,041,190 (GBP)
Funding ID EP/W026775/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 12/2021 
End 11/2024
 
Description Predictive multiscale free energy simulations of hybrid transition metal catalysts
Amount £682,674 (GBP)
Funding ID EP/W014378/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 06/2022 
End 06/2026
 
Description Quantum Enhanced Computing Platform for Pharmaceutical R&D - QuPharma
Amount £4,700,000 (GBP)
Funding ID TS/W006286/1 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 03/2022 
End 02/2025
 
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 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  
URL https://rs.figshare.com/articles/dataset/SI_data_zip_from_Computational_infrared_and_Raman_spectra_b...
 
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  
URL https://rs.figshare.com/articles/dataset/SI_data_zip_from_Computational_infrared_and_Raman_spectra_b...
 
Description Dalton development team 
Organisation University of Oslo
Country Norway 
Sector Academic/University 
PI Contribution We develop an interface to the Dalton and LSDalton electronic structure packages in our ChemShell software for QM/MM calculations
Collaborator Contribution They have made a number of modifications to the Dalton and LSDalton codes in order to facilitate interface development.
Impact The Dalton & LSDalton interfaces in Tcl & Py-ChemShell
Start Year 2011
 
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 first beta release (v19.0) 
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 2019 
Open Source License? Yes  
Impact The first beta release of Py-ChemShell was the first to include full functionality for materials modelling and so began the transition of the userbase from the original Tcl-based version of the software. 
 
Title Py-ChemShell second beta release (v20.0) 
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 2020 
Open Source License? Yes  
Impact The second beta release of Py-ChemShell was the first release to be recommended for production calculations on materials systems, so continuing the transition for users from the original Tcl-based version of the software. 
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 Bristol Chemshell training Feb 2019 
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 and You Lu gave a 2-day training course in the use of ChemShell for materials and biomolecular modelling to a group of 15 researchers at the University of Bristol
Year(s) Of Engagement Activity 2019
 
Description CCPBioSim Biomolecular QM/MM Modelling with ChemShell workshop, June 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 CCPBioSim held a training day on combined quantum mechanical/molecular mechanical (QM/MM) modelling of biomolecular systems at the University of St Andrews on 14 June 2018 as part of the ScotCHEM 2018 conference. In the morning session we discussed the principles of QM/MM modelling and introduced the ChemShell software package. ChemShell is a scriptable computational chemistry environment which provides a flexible way to link QM and MM codes together to perform QM/MM calculations. There was then an opportunity to learn the basics of ChemShell in the first practical. In the second lecture we described in more depth how QM/MM biomolecular calculations are set up and performed, using a cytochrome P450 system as a case study. The second practical explored modelling of enzymatic reactions with ChemShell on STFC's SCARF cluster.
Year(s) Of Engagement Activity 2018
URL https://www.scotchem.ac.uk/st-andrews-2018/
 
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 presentation at MCC conference, Lincoln, September 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tom Keal gave a presentation on recent ChemShell developments at the Materials Chemistry Consortium conference at the University of Lincoln on 4 September 2018.
Year(s) Of Engagement Activity 2018
 
Description ChemShell presentation visiting Peking University Shenzhen Graduate School, November 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact You Lu gave an 1.5 hours talk about STFC, Daresbury Laboratory, QM/MM methods, and ChemShell's mechanisms, capabilities, history, current status, and future plans.
Year(s) Of Engagement Activity 2019
 
Description ChemShell presentation visiting Shanghai University, December 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact You Lu gave an 1.5 hours lecture about UKRI, STFC, Daresbury Laboratory, computational chemistry, QM/MM methods, and ChemShell's mechanisms and capabilities.
Year(s) Of Engagement Activity 2019
 
Description ChemShell training at Imperial College (DL_SOFTWARE workshop) - December 2019 
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 Tom Keal and You Lu gave ChemShell training as part of the DL_SOFTWARE workshop held at Imperial College, and discussed plans for future research with the trainees.
Year(s) Of Engagement Activity 2019
 
Description ChemShell training workshop at PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development 
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 A ChemShell biomolecular QM/MM training day was held online as part of the PRACE Autumn School 2021: Fundamentals of Biomolecular Simulations and Virtual Drug Development (20-24 Sep 2021), featuring an introduction to the DL_Software suite by Ilian Todorov, and talks and demonstrations of the ChemShell QM/MM package by Tom Keal, Kakali Sen and You Lu.
Year(s) Of Engagement Activity 2021
URL https://events.prace-ri.eu/event/1222/
 
Description ChemShell training workshop at the CCPBioSim training week, September 2021 
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 As part of the CCPBioSim training week 2021, a training session on ChemShell for biomolecular QM/MM calculations was held, with talks and demonstrations from Tom Keal, Kakali Sen, You Lu and Sarah Fegan of STFC.
Year(s) Of Engagement Activity 2021
URL https://www.ccpbiosim.ac.uk/events/workshop-course-material/eventdetail/135/-/ccpbiosim-training-wee...
 
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 DL ChemShell training January 2019 
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 and You Lu gave ChemShell training to a group of 6 researchers from UCL
Year(s) Of Engagement Activity 2019
 
Description MCC ChemShell training September 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 ChemShell training was provided on 3rd September 2018 as part of an MCC training workshop at the University of Lincoln. The training consisted of a presentation introducing the ChemShell QM/MM modelling environment and hands-on practical experience.
Year(s) Of Engagement Activity 2018
 
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 Multiscale modelling presentation, DLS, November 2018 
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 "Multiscale modelling of biomolecules and materials" at the Simulations for Experimentalists and Industrialists training course at Diamond Light Source, 7 November 2018
Year(s) Of Engagement Activity 2018
 
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 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 STFC Seminar talk on DL_PY2F 
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 an STFC seminar on DL_PY2F--A general-purpose Python/FORTRAN interoperability library, and its use to couple codes within the ChemShell computational chemistry environment
Year(s) Of Engagement Activity 2021
 
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/