We document the implementation of the Common Representative Intermediates Mechanism version 2, reduction 5 (CRIv2-R5) into the United Kingdom Chemistry and Aerosol model (UKCA) version 10.9. The mechanism is merged with the stratospheric chemistry already used by the StratTrop mechanism, as used in UKCA and the UK Earth System Model (UKESM1), to create a new CRI-Strat mechanism. CRI-Strat simulates a more comprehensive treatment of non-methane volatile organic compounds (NMVOCs) and provides traceability with the Master Chemical Mechanism (MCM). In total, CRI-Strat simulates the chemistry of 233 species competing in 613 reactions (compared to 87 species and 305 reactions in the existing StratTrop mechanism). However, while more than twice as complex than StratTrop, the new mechanism is only 75% more computationally expensive. CRI-Strat is evaluated against an array of in situ and remote sensing observations and simulations using the StratTrop mechanism in the UKCA model. It is found to increase production of ozone near the surface, leading to higher ozone concentrations compared to surface observations. However, ozone loss is also greater in CRI-Strat, leading to less ozone away from emission sources and a similar tropospheric ozone burden compared to StratTrop. CRI-Strat also produces more carbon monoxide than StratTrop, particularly downwind of biogenic VOC emission sources, but has lower burdens of nitrogen oxides as more is converted into reservoir species. The changes to tropospheric ozone and nitrogen budgets are sensitive to the treatment of NMVOC emissions, highlighting the need to reduce uncertainty in these emissions to improve representation of tropospheric chemical composition.

The role of stomata in regulating photosynthesis and transpiration, and hence governing global biogeochemical cycles and climate, is well-known. Less well-understood, however, is the importance of stomatal control to the exchange of other trace gases between terrestrial vegetation and the atmosphere. Yet these gases determine atmospheric composition, and hence air quality and climate, on scales ranging from local to global, and seconds to decades. Vegetation is a major sink for ground-level ozone via the process of dry deposition and the primary source of many biogenic volatile organic compounds (BVOCs). The rate of dry deposition is largely controlled by the rate of diffusion of a gas through the stomata, and this also governs the emission rate of some key BVOCs. It is critical therefore that canopy-atmosphere exchange models capture the physiological processes controlling stomatal conductance and the transfer of trace gases other than carbon dioxide and water vapour. We incorporate three of the most widely used coupled stomatal conductance-photosynthesis models into the one-dimensional multi-layer FORest Canopy-Atmosphere Transfer (FORCAsT1.0) model to assess the importance of choice of parameterisation on simulated ozone deposition rates. Modelled GPP and stomatal conductance across a broad range of ecosystems differ by up to a factor of 3 between the best and worst performing model configurations. This leads to divergences in seasonal and diel profiles of ozone deposition velocity of 1-30% and deposition rate of up to 10%, demonstrating that the choice of stomatal conductance parameterisation is critical in understanding ozone deposition.