GECKO-A v1.0: exploring VOC oxidation trajectories through comparison with the master chemical mechanism

Abstract

Abstract. Numerical models are crucial tools for understanding complex chemical systems such as the atmosphere, and their sensitivity across a range of conditions. In atmospheric chemistry models, reaction mechanisms are used to represent chemical transformations and define the underlying system of equations. Building highly explicit mechanisms that capture the full complexity of organic oxidation occurring in the atmosphere remains challenging owing to the large number of intermediates involved, the breadth of reaction pathways, and the limited availability of reliable kinetic and thermodynamic data. The Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere (GECKO-A) was developed to address these limitations by enabling the systematic construction of near-explicit mechanisms. Here, we present its first open-source release (v1.0), which incorporates updated chemical protocols and structure-activity relationships, together with its companion box model for mechanism integration. GECKO-A's performance is evaluated through systematic comparisons with the Master Chemical Mechanism (MCM v3.3.1), based on simulations of the oxidation of five representative hydrocarbons (butane, octane, dodecane, toluene, and α-pinene) under environmental conditions ranging from urban to remote. The two approaches yield similar oxidation pathways for small and structurally simple compounds. However, differences increase with the size and complexity of the carbon backbone. In particular, the simplifications inherent to the MCM tend to limit the formation of multifunctional products and promote earlier fragmentation, resulting in notable discrepancies in the predicted volatility of secondary organic carbon and, consequently, in secondary organic aerosol yields.