Mechanism generation for aqueous-phase oxidation of organics: development and application for global model simulations

The formation, degradation, and physical properties of organic aerosol (OA) constituents strongly depend on multiphase chemical kinetics. Gas-phase oxidation of OA precursors has been extensively investigated in recent decades. However, laboratory kinetic data on the aqueous-phase oxidation of the organics are scarce. As a result, the aging of organics in cloud droplets and deliquescent aerosols is commonly simplified in model simulations. In studies that aim to characterize the constituents and the phase state of organics specifically, this limitation may be overcome by introducing reactions based on structure-activity relationships (SAR). In models with sophisticated gas-phase oxidation and partitioning schemes, organics of various sizes and oxidation states are present in the condensed phase. Thus, an oxidation mechanism for hundreds of species needs to be constructed. However, manual mechanism development is time-consuming and error-prone. The use of new or updated SAR methods may lead to different dominant reaction routes, further increasing the required time investment. Alternatively, various SAR methods can be combined in a code framework in order to automatically generate self-contained mechanisms for a given list of compounds, within seconds. Updates of the SARs can be implemented in the underlying code framework.
In this study, we construct and apply a mechanism generator for the application in global model simulations. It focuses on the chemical processing in aqueous media such as cloud droplets and deliquescent aerosols. The generator is developed in conjunction with the MESSy model. As a result, the output of the generator is fined-tuned to be used with the MESSy submodels. However, mechanisms can be generated without MESSy by user input of molecule structures. This feature is intended to simplify the wide range application of the generator results. Molecular structure input is given by SMILES strings and output can be generated in either SMILES or InChI-Key format. Currently, the generator is restricted to a predefined set of input molecule types. This is due to the limitations of the available SARs. The generator considers the following reaction types: 1) OH-oxidation 2) photolysis 3) hydrolysis of nitrates and 4) peroxy-radical reactions. Minor reaction pathways are neglected to minimize the effect of the new chemistry on model performance.
An aqueous-phase mechanism for the most water-soluble organics has been generated and used to simulate aerosol and cloud chemistry within MESSy. Test simulations with the expanded aqueous-phase mechanism revealed a change in the distribution of aerosol constituents. The results suggest that in aerosols larger organics are efficiently degraded and the average molecular size of organics is smaller. However, the change in aerosol mass by outgassing of organics is less pronounced than expected. The mechanism generator does not construct phase-partitioning "reactions" as the respective constants are missing. Thus, in the generated mechanism solely compounds that have a predefined partitioning may outgas. Consequently, future developments will focus on the estimation of partitioning constants upon generation of a novel molecule. In general, the range of application of the generator may be extended for further reactions.