The role of boundary layer dynamics on the diurnal evolution of isoprene and the hydroxyl radical over tropical forests

We investigate diurnal variability of isoprene and related chemical species in the Amazonian region. The dynamics and chemistry of an atmospheric boundary layer are studied with a large-eddy simulation code and a mixed-layer model which are guided by observations available for the same area. The main features of isoprene and related species are reproduced well, but their evolution raises questions regarding the physical and chemical processes responsible for the observed diurnal behaviors. To address these questions, we systematically examine the role of (1) the exchange of chemical species between the free troposphere and the atmospheric boundary layer (entrainment), (2) surface isoprene and nitric oxide emissions, and (3) new chemical pathways to recycle the hydroxyl radical. The entrainment flux of isoprene is shown to be equally important as surface isoprene emissions in determining the isoprene temporal evolution. Varying the relationship between the initial isoprene mixing ratio in the boundary layer and that in the overlying free troposphere in the early morning results in an 50% increase/decrease in isoprene mixing ratio or more within the atmospheric boundary layer at noon. Entrainment of free tropospheric nitrogen oxides creates changes of similar magnitude to the boundary layer isoprene mixing ratio. These effects of entrainment and surface emissions on isoprene are found for two different chemical regimes. The introduction of an OH recycling pathway in the chemical mechanism increases midday OH. Our findings show that atmospheric dynamics and chemistry are equally important for interpreting the diurnal observation of reactants and for including in regional-scale modeling efforts where turbulence is parameterized.