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

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

 
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 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 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 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