MUlti-faceted Studies on Highly Oxidized Organic Molecules MUSHrOOM

Introduction and Aims

Highly oxidized organic molecules (HOMs) are a key set of compounds in the atmosphere that have attracted considerable recent attention.1-2 The low volatility of these compounds means that they have an important role in aerosol formation and growth with a consequent impact on air quality and climate.

HOMs can be formed from simple organic species by a process known as auto-oxidation. For a simple molecule such as butane this could consist of the following chemistry:

R1  OH + n-C4H10  H2O + CH3CH2CH2CH2O2


The initial radical formed (R), rapidly reacts with oxygen to give CH3CH2CH2CH2O2 (RO2) via reaction 1. Now there is a competition between bimolecular reactions of RO2 with a range of atmospheric species (e.g. NO, NO2, HO2, RO2) and an internal abstraction to give a hydroperoxy radical CH3CHCH2CH2OOH (R2). This process can then be repeated (addition of O2 to the carbon centre radical and internal abstraction) gradually introducing more functionality into the molecule and reducing the volatility.

A crucial part of this mechanism is quantifying the competition between the internal isomerization (R2) and the other reactions of RO2 species such as reactions R3 and R4:


R4  CH3CH2CH2CH2O2 + HO2 → products

Reaction R3 is a very exothermic reaction and the energy released can induce chemistry in the products, so called chemical activation (CA). CA is something that we are currently looking at via an EPSRC project Complex Chemistry and Chemical Activation in conjunction with colleagues at the University of Oxford. Reaction R4 can lead to a variety of products as illustrated in our earlier study on CH3C(O)O2 + HO2.3 The supervisors are involved in a related NERC proposal, PEROXY, led by Prof Heard, with colleagues in the University of Manchester, which looks at various aspects of RO2 chemistry including field work.

The aims of MUSHrOOM are to look in more detail at the critical process of the type shown in R2 using a range of experimental methods and also to build up a database of kinetics on RO2 reactions competing with reaction R2. The PEROXY proposal seeks to carry out some of these reactions in the HIRAC chamber using techniques similar to those of Winiberg et al. You will be involved in these studies, but a significant component of your experimental work will utilize other experimental techniques such as laser flash photolysis and laser induced fluorescence to study the critical steps of the reactions in more detail. There will also be scope to include theoretical calculations, modelling and potentially some field-work in the project, depending on your interests and how the project progresses.


Supervision Team and Methodology

The supervisory team is well-placed to study this chemistry. The mechanism of auto-oxidation was developed within combustion chemistry and Prof Seakins has studied such chemistry in dimethylether combustion, and brings expertise in laboratory kinetics of combustion and atmospheric chemistry.4-5 Prof Heard is the PI on the PEROXY NERC proposal looking at RO2 chemistry and Dr Stone and Prof Heard have particular expertise in monitoring RO2 species.6-7  Dr Stone has very recently been awarded a NERC grant looking at the lifetime of OH radicals in the atmosphere, involving the type of chemistry exemplified by the first part of reaction R1. Prof Seakins and Dr Stone are currently supervising a Panorama studentship on the reactions of OH with complex hydrocarbons; your project will focus on the subsequent steps in the oxidation.

In addition to the supervisory team, your PhD research will be supported by several experienced post-doctoral and PhD researchers who will be able to provide hands-on support for operation of laser systems and the HIRAC chamber. We appreciate that many applicants may only have had limited or no experience operating such instrumentation, rest assured that there is plenty of support!

The main focus of the project will be laboratory studies of gas phase species using two complementary approaches. The HIRAC chamber3, 8 looks at overall reactions. The nature of the chamber allows us to deploy a wide range of experimental techniques. However, we also need to focus on specific elementary reactions and here laser flash photolysis combined with various monitoring methods generally gives more information.4-5 You will gain skills in a wide range of monitoring techniques involving both optical and mass spectrometry. Depending on your interests and how the project progresses, there will be scope to gain additional experience in modelling, calculations, fieldwork and aerosol chemistry.



It’s not possible at this stage to give a detailed programme; research projects evolve depending on the results and your developing interests. However, we can give a good idea of the initial year or so of the project:

  1. Gaining experience on both the HIRAC chamber and laser flash photolysis experiments.
  2. Working on RO2 + NO reactions and exploring the role of chemical activation on the RO fragment.
  3. Completing an RO2 + HO2 similar to that of Winiberg et al. utilizing the full range of HIRAC instrumentation.
  4. Starting studies on RO2 to QOOH isomerization reactions initially using laser flash photolysis methods.

As mentioned above, there is then scope to explore some other areas as the project develops.



  1. Bianchi, F.; Kurten, T.; Riva, M.; Mohr, C.; Rissanen, M. P.; Roldin, P.; Berndt, T.; Crounse, J. D.; Wennberg, P. O.; Mentel, T. F., et al., Highly oxygenated organic molecules (hom) from gas-phase autoxidation involving peroxy radicals: A key contributor to atmospheric aerosol. Chem. Rev. 2019, 119 (6), 3472-3509.
  2. Rissanen, M., Anthropogenic volatile organic compound (avoc) autoxidation as a source of highly oxygenated organic molecules (hom). J. Phys. Chem. A 2021, 125 (41), 9027-9039.
  3. Winiberg, F. A. F.; Dillon, T. J.; Orr, S. C.; Gross, C. B. M.; Bejan, I.; Brumby, C. A.; Evans, M. J.; Smith, S. C.; Heard, D. E.; Seakins, P. W., Direct measurements of OH and other product yields from the HO2 + CH3C(O)O2 reaction. Atmos. Chem. Phys. 2016, 16, 4023-4042.
  4. Eskola, A. J.; Carr, S. A.; Shannon, R. J.; Wang, B.; Blitz, M. A.; Pilling, M. J.; Seakins, P. W.; Robertson, S. H., Analysis of the kinetics and yields of OH radical production from the CH3OCH2 + O2 reaction in the temperature range 195-650 K: An experimental and computational study. J. Phys. Chem. A 2014, 118 (34), 6773-6788.
  5. Glowacki, D. R.; Lockhart, J.; Blitz, M. A.; Klippenstein, S. J.; Pilling, M. J.; Robertson, S. H.; Seakins, P. W., Interception of excited vibrational quantum states by O2 in atmospheric association reactions. Science 2012, 337 (6098), 1066-1069.
  6. Onel, L.; Brennan, A.; Seakins, P. W.; Whalley, L.; Heard, D. E., A new method for atmospheric detection of the CH3O2 radical. Atmos. Meas. Tech. 2017, 10 (10), 3985-4000.
  7. Mir, Z. S.; Lewis, T. R.; Onel, L.; Blitz, M. A.; Seakins, P. W.; Stone, D., CH2OO criegee intermediate UV absorption cross-sections and kinetics of CH2OO + CH2OO and CH2OO + i as a function of pressure. PCCP 2020, 22 (17), 9448-9459.
  8. Glowacki, D. R.; Goddard, A.; Hemavibool, K.; Malkin, T. L.; Commane, R.; Anderson, F.; Bloss, W. J.; Heard, D. E.; Ingham, T.; Pilling, M. J., et al., Design of and initial results from a highly instrumented reactor for atmospheric chemistry (HIRAC). Atmos. Chem. Phys. 2007, 7 (20), 5371-5390.