Determining the kinetics of reactions leading to highly oxidized molecules

Determining the kinetics of reactions leading to highly oxidized molecules


Prof Paul Seakins:

Dr Mark Blitz:


Contact email:


The processing of the atmosphere is largely controlled by radicals, where the OH radical plays the dominant role.[1] The reaction of OH with hydrocarbons in the presence of oxygen leads to peroxy radicals, RO2, and there is a wide range of knowledge on the reactivity of RO2 via their reaction with other RO2, NO and NO2. However, recently it has been identified that for a number of RO2 under atmospheric conditions they can efficiently isomerize via H-shift and further add O2 to form radicals with a hydroperoxide group, OOQOOH:


This isomerization process with O2 addition is well known in combustion chemistry and ultimately leads to autoignition. However, at atmospheric temperatures these hydroperoxides are stable, and further H-shift isomerizations are possible. These products are low vapour compounds with 6 or more oxygen, and are collectively known as highly oxidized molecules (HOM). HOM have recently been identified as large contributors to secondary organic aerosols in forested environments.[2]

The observation of HOM is via sensitive chemical ionization mass spectrometers, where a specific ion generated in the mass spectrometer is used to titrate the HOM. However, HOM are usually identified in field campaigns or atmospheric simulation chambers, and therefore provide little kinetic information on their formation or loss.



In this project, the kinetics of autoxidation is to be determined for a range of OH initiated reactions involving aromatics and terpenes. The key to identifying the kinetics is that under certain conditions the hydroperoxide will result in OH being reformed (recycling), where temperature and [O2] are the experimental parameters that controls this OH recycling. When recycling is distinctly observed the kinetics and mechanism of the system can be identified. In the case of the terpene isoprene, C5H8, we have recently determined the OH kinetics in the presence of C5H8/O2, see figure below.

The OH under these conditions (T = 584 K) is recycling, the red line represents no recycling. The other lines are various recycling models, where the blue is the best description of the system. By recording OH traces over a wide range of recycling conditions a full description of the kinetics and mechanism is determined. In the OH/C5H8/O2 system, the full kinetics have been determined, and allows the OH recycling under atmospheric conditions to be accurately predicted. This result is important as isoprene is the second largest emitted hydrocarbon in the atmosphere after methane and there has been much recent debate about the rate of OH recycling in tropical forested environments.[3-5] For the OH/C5H8/O2 system theoretical calculations have already been performed and they were used in guiding the kinetic assignments of the experimental data traces. For aromatics and other terpenes calculations will be required to guide the kinetic analysis.

While OH is the driver for autoxidation, HO2 is an alternative channel. HO2 can also be measured to reinforce the OH measurements. The co-products of OH and HO2 can potentially be detected by PTR mass spectrometry, which is available.

In addition to determining OH autoxidation kinetics, the photochemistry of the radical intermediates can be determined. In the case of aromatics, it is known that intermediate adducts have significant absorption in the actinic window, but the photolysis channels in the atmosphere are unknown.[6]

The impact of these laboratory generated parameters is assessed in atmospheric models. From the purely chemical model (MCM:, which can assess local air quality and composition, to the 3-D chemical transport models that can assess such things on a global scale.



The student will work under the supervision of Dr Mark Blitz and Prof Paul Seakins within the Atmospheric and Planetary Chemistry research group, School of Chemistry. Within the group there is a wealth of knowledge running many laser based experiments, which require regular maintenance, repair and development. You will learn the skills to carry out experiments to determine the relevant data, which is often discussed in the weekly group meeting. The repair and development of the experiments is carried out in conjunction with the senior members of the group, who can provide help / guidance. Potentially you will be conversing the University Workshops (Mechanical and Electronic) and outside companies with aspects of your experiment. By the end of your PhD you should be independently carrying out experiments, with good knowledge of future experiments.

Computers are used to control the experiment and process the data produced. LabVIEW is used to control the experiment and Origin/MATLAB is used to process the raw experimental data. Gaussian and MESMER is used to theoretically test the experimental data, before using it is put into atmospheric models. The University runs a number of computer courses in order to run the software used in the group. In addition the University also runs workshops on the generic skills for students that ultimately prepares you for your viva, (


Student profile

The majority of this project is laboratory based where lasers will be used to both create / photolyse / monitor species over conditions that will generate the parameters relevant to atmospheric chemistry. These experiments are controlled by hardware and software, so a strong experimental background with good knowledge of computers is desirable. The data collected from these experiments is then processed, parameterized and often modelled using theoretical descriptions. This data processing uses computer software such Gaussian / Origin / MATLAB and code developed within the group, MESMER, So some computer programming skills will be required.



[1] D.E. Heard, M.J. Pilling, Measurement of OH and HO2in the Troposphere, Chemical Reviews 103 (2003) 5163-5198.

[2] M. Ehn, J.A. Thornton, E. Kleist, M. Sipilä, H. Junninen, I. Pullinen, M. Springer, F. Rubach, R. Tillmann, B. Lee, F. Lopez-Hilfiker, S. Andres, I.-H. Acir, M. Rissanen, T. Jokinen, S. Schobesberger, J. Kangasluoma, J. Kontkanen, T. Nieminen, T. Kurtén, L.B. Nielsen, S. Jørgensen, H.G. Kjaergaard, M. Canagaratna, M.D. Maso, T. Berndt, T. Petäjä, A. Wahner, V.-M. Kerminen, M. Kulmala, D.R. Worsnop, J. Wildt, T.F. Mentel, A large source of low-volatility secondary organic aerosol, Nature 506 (2014) 476-479.

[3] J.D. Crounse, F. Paulot, H.G. Kjaergaard, P.O. Wennberg, Peroxy radical isomerization in the oxidation of isoprene, Physical Chemistry Chemical Physics 13 (2011) 13607.

[4] J. Lelieveld, T.M. Butler, J.N. Crowley, T.J. Dillon, H. Fischer, L. Ganzeveld, H. Harder, M.G. Lawrence, M. Martinez, D. Taraborrelli, J. Williams, Atmospheric oxidation capacity sustained by a tropical forest, Nature 452 (2008) 737-740.

[5] J. Peeters, J.-F. Müller, T. Stavrakou, V.S. Nguyen, Hydroxyl Radical Recycling in Isoprene Oxidation Driven by Hydrogen Bonding and Hydrogen Tunneling: The Upgraded LIM1 Mechanism, The Journal of Physical Chemistry A 118 (2014) 8625-8643.

[6] R.F. Hansen, T.R. Lewis, L. Graham, L.K. Whalley, P.W. Seakins, D.E. Heard, M.A. Blitz, OH production from the photolysis of isoprene-derived peroxy radicals: cross-sections, quantum yields and atmospheric implications, Physical Chemistry Chemical Physics 19 (2017) 2332-2345.