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

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.

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.