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Application of Radical Chemosensors to Investigate Atmospheric Chemical Mechanisms

Dr Andrew Rickard (WACL, University of York), Dr Victor Chechik (Department of Chemistry, University of York), Professor Paul Seakins (School of Chemistry, University of Leeds)

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The chemistry of the troposphere underlies a range of environmental issues, which have substantial societal and economic impacts. Whether it is a changing climate, a reduction in air quality affecting human health or the degradation of ecosystems due to air pollution, the details of this chemistry determines the severity of the impact.

The complex photo-oxidation cycles involved in the chemical processing of anthropogenic and biogenic hydrocarbon emissions are initiated and mediated by radical intermediates.  Daytime removal of these trace species are predominantly initiated by their reaction with the hydroxyl radical, ·OH, which controls the oxidative capacity of the atmosphere.  Peroxy radicals (e.g., HO2· and generic organic peroxy radicals RO2·) are key reactive intermediates/chain propagators directly involved in the formation of ground-level ozone, photochemical smog and for the production of secondary organic aerosols – significantly impacting upon air quality and human health and, through aerosol production, climate.1

Numerical models of atmospheric chemistry are essential to understanding this complex chemical composition and are key to our ability to understand, predict and hence mitigate air quality problems. Therefore, it is of critical importance that the detailed chemical mechanisms (e.g., the Master Chemical Mechanism2) used in the models adequately and accurately represent the important oxidative processes involved. This is primarily done through direct comparisons with in-situ field measurements of a wide range of species, including radicals, throughout the atmosphere and across the globe. Individual reaction mechanisms of important ozone and aerosol precursors are also evaluated using highly instrumented environmental chambers, where the accurate measurement of radical intermediates are a key diagnostic for understanding the chemical kinetic and mechanistic processes involved in their photochemical degradation.

However, quantitative and speciated measurements of atmospheric radicals pose considerable challenges to analytical chemistry. Owing to their low concentrations, high reactivity, and short lifetimes, free radicals cannot be easily sampled and hence direct offline analysis is extremely difficult.  Although a number of highly sensitive sophisticated techniques have been developed3, selectivity, full structure determination, portability and cost remain challenging obstacles to atmospheric radical analysis.

Aims and Objectives

The overall aim of this project is to build upon previous proof of concept work carried out by the investigators on the development and application of a series of novel organic trapping compounds (or “chemosensors”) that can efficiently and selectively react with a range of important gas-phase atmospheric radical species, producing non-radical reaction products. These products conserve the structure of the original radical and are stable enough for off-line analysis using a range of mass spectrometric techniques (see Figure 1a). This approach allows accurate determination of the radical structures (see Figure 1b). Preliminary results suggest that this method has excellent sensitivity and is well suited for quantitative monitoring of gas-phase radicals.

The student will optimise sampling strategies and detection methodologies in order to investigate the simultaneous, speciated chemical evolution of radical species formed in a broad range of atmospherically important (photo)chemical systems. Experiments will be performed in quartz flow tube and static bag experiments in York (e.g. see Figure 2a), as well as the Highly Instrumented Reactor for Atmospheric Chemistry (HIRAC) chamber4 in the School of Chemistry, University of Leeds (see Figure 2b).  HIRAC is a 2.25 m3 cylindrical stainless steel chamber in which temperature, pressure and photolysis can be controlled so that chemistry can be investigated over a range of atmospherically important conditions.  Radicals can also be produced in steady state and at much higher concentrations than ambient, so the sensitivity of the chemosensor technique can be assessed and directly compared with in-situ spectroscopic detection methods.

Radical formation in several atmospherically important systems will be investigated in both York and Leeds including:

  1. Characterization experiments of so called “simple” atmospheric systems such as the photolysis of formaldehyde and the self-reaction of CH3O2 + CH3O2.

  2. Systematic experiments of structurally diverse alkene ozonolysis systems, which are known to be important atmospheric sources of ·OH, HO2· and RO2.5

  3. OH abstraction reactions of long chain alkanes in order to look at the formation of primary RO2 species and the branching ratio of secondary RO2 species formed via 1,5 hydrogen shifts (see Figure 1b).

  4. Reactions of acyl RO2 + HO2 (e.g. CH3C(O)O2 + HO2) – an important sources of radicals under “low NOx” conditions.6

  5. Detection of radical species involved in low temperature “auto-ignition” chemistry of oxygenates and their role in aerosol formation.7

  6. Formation and structural characterization of ring retained peroxy-bicyclic RO2 systems formed in aromatic photo-oxidation over a range of precursor to NOx conditions.8

As the name suggests, HIRAC is fitted with a full suite of instrumentation to allow accurate and thorough characterisation of the chemistry occurring inside the chamber. This includes high temporal resolution, direct in-situ detection of radical intermediates OH, HO2 and CH3O2. We will use the unique capabilities of HIRAC to inter-compare and evaluate our offline chemosensor systems as well as to quantitatively calibrate them for individual radical species such as OH, HO2 (using water photolysis at 189.4 nm as a HOx source) and a range of RO2 species. Specific RO2 radicals can be generated by the addition of an appropriate hydrocarbon upstream of the HOx radical source, scavenging all OH radicals.

We will use chemical box models incorporating the Master Chemical Mechanism (MCM: http// to design our experiments - modelling the temporal profiles of precursor decay and product formation, intercomparing the model predictions with the measurements in order to better understand the chemistry and to evaluate the chemistry incorporated in the MCM itself.

To carry out the experimental work described above, modifications to the sampling procedure will be necessary in order to increase sampling efficiency and to increase the temporal resolution of measurements for chamber sampling.  Changes to the functional groups on the target-trapping molecule will also be investigated to increase stability and lower the volatility of the trapping material and product, to improve the trapping efficiency of smaller radical species (e.g. H and OH). Refinements to the detection methodologies will also be investigated in terms of sensitivity and speciation through High Pressure Liquid Chromatography coupled to Mass Spectrometry (HPLC/MS) method development.

Once the sensitivity of the radical trapping system has been refined to ca. 1 × 106 molecules cm-3 and below, we will also attempt to measure and speciate ambient levels of RO2 and HO2, as a function of time of day and location, as well as direct comparisons to the Leeds FAGE field instrument for measuring HOx under ambient conditions.9

Potential for high impact outcome

This highly ambitious project aims to achieve a paradigm shift in the accurate detection and speciation of low concentration, highly reactive gas-phase radical species.  Although the methods applied here are based on established techniques used in different disciplines (e.g. some of the investigators have recently pioneered the application of this type of technique to probe radical intermediates in heterogeneous catalysis10), they represent a completely new approach to the detection of free radicals in the atmosphere.  Therefore, we envisage a range of high impact publications will be produced in this project, stimulating interest from across the atmospheric science community and beyond.

The project is very interdisciplinary, representing a unique collaboration and opportunity for knowledge transfer between established atmospheric gas kineticists, model mechanism development experts and physical organic chemists. 

We believe our method has the potential to revolutionize free radical measurements in the gas-phase, and we plan to use the results obtained to expand the scope of the applications, but also establish new collaborations. We envisage future funding applications in areas of kinetics and mechanisms e.g. air quality, wood and tobacco smoke and indoor air measurements as well as fundamental aspects of separation and mass spectrometry.


The student will work under the supervision of Dr. Andrew Rickard (WACL, York -, Dr Victor Chechik (Department of Chemistry, York - and Prof. Paul Seakins (School of Chemistry, Leeds -, and will be primarily based at the Wolfson Atmospheric Chemistry Laboratories, part of the Department of Chemistry, University of York. The project is very interdisciplinary. The student will develop transferrable skills in organic synthesis, experiment design, spectroscopic characterisation techniques, development of analytical methods (e.g., HPLC with mass spectrometry), chemical mechanism development and evaluation, numerical and data skills and kinetic model analysis. Training will be provided in all areas, and we expect to establish collaborations with a number of colleagues in the area of chemical kinetics and mechanism development, with potential opportunity to take part in the chamber campaigns at large, highly instrumented European photo-reactors as part of the Horizons 2020 EUROCHAMP2020 programme (

The Universities of York and Leeds, and the wider NERC SPHERES DTP provide comprehensive training programmes for PhD students with a range of courses on both hard and soft skills.  Dr. Rickard and Prof. Seakins both work for and with the National Centre for Atmospheric Science (NCAS), and thus the student will have access to the wider resources that NCAS provides. You will also have access to training provided by NCAS such as the Arran instrumental Summer School, the Earth System Science Summer School (ES4), and future further developments in computations and data analysis.

The student will be based in the Wolfson Atmospheric Chemistry Laboratories, part of the department of Chemistry, University of York.  These were established in 2013 and comprise a state of the art 800 m2 dedicated research building, the first of its kind in the UK. Supported by a large award from the Wolfson Foundation and a private donor, the Laboratories enable experimental and theoretical studies relating to the science of local and global air pollution, stratospheric ozone depletion and climate change. The Laboratories are operated as collaborative venture between the University of York and the National Centre for Atmospheric Science (NCAS), co-locating around 40 researchers from seven academic groups and from NCAS. The Laboratories are also home to independent research fellows, postdoctoral researchers, PhD students and final year undergraduate research projects.

The student will have the opportunity to present their work to the scientific community at national and international meetings and conferences. They will also be encouraged to take part in outreach events organised by both WACL and NCAS in order to disseminate the research beyond the immediate scientific community (e.g. to policymakers and the general public).

We appreciate that this PhD project encompasses several different science and technology areas, and we don’t expect applicants to have experience in many of these fields. The project is very well supported with experienced scientists and training in these techniques and disciplines is all part of the PhD.

Useful References

  1. Orlando and Tyndall (2012):  Laboratory studies of organic peroxy radical chemistry: an overview with emphasis on recent issues of atmospheric significance. Chem. Soc. Rev., 41, 6294–6317. DOI: 10.1039/c2cs35166h.

  2. Saunders et al., (2003):  Protocol for the development of the Master Chemical Mechanism, MCM v3 (Part A): tropospheric degradation of non-aromatic volatile organic compounds. Atmospheric Chemistry and Physics, 3, 161-180.

  3. Stone et al., (2012):  Tropospheric OH and HO2 radicals: field measurements and model comparisons. Chem. Soc. Rev., 41, 6348-6404. DOI: 10.1039/c2cs35140d.

  4. Glowacki et al., (2007):  Design of and initial results from a Highly Instrumented Reactor for Atmospheric Chemistry (HIRAC)., Atmos. Chem. Phys., 7, 5371–5390.

  5. Alam et al., (2013):  Radical Product Yields from the Ozonolysis of Short Chain Alkenes under Atmospheric Boundary Layer Conditions. J. Phys. Chem. A., 117 (47), 2468–12483. DOI: 10.1021/jp408745h.

  6. Winiberg et al., (2016) Direct Measurements of OH and Other Product Yields from the HO2 + CH3C(O)O2 Reaction. Atmospheric Chemistry and Physics, 16, 4023-4042, doi:10.5194/acp-16-4023-2016.

  7. Crounse et al., (2013): Autoxidation of Organic Compounds in the Atmosphere. . Phys. Chem. Lett., 4, 3513-3520.

  8. Rickard et al., (2009):  Gas phase precursors to anthropogenic secondary organic aerosol: Using the Master Chemical Mechanism to probe detailed observations of 1,3,5-trimethylbenzene photo-oxidation., Atmospheric Environment,  44, 423–5433. doi:10.1016/j.atmosenv.2009.09.043.

  9. Whalley et al., (2013):  Reporting the sensitivity of laser-induced fluorescence instruments used for HO2detection to an interference from RO2 radicals and introducing a novel approach that enables HO2 and certain RO2 types to be selectively measured., Atmos. Meas. Tech., 6, 3425-3440, doi:10.5194/amt-6-3425-2013.

  10. Conte and Chechik (2010), Spin trapping of radical intermediates in gas phase catalysis: cyclohexane oxidation over metal oxides., Chem. Commun., 46, 3991-3993. 10.1039/c0cc00157k.

Related undergraduate subjects:

  • Chemistry