Abstract. The CMAQ model in combination with observations for INTEX-NA/ICARTT 2004 are used to evaluate recent advances in isoprene oxidation chemistry and provide constraints on isoprene nitrate yields, isoprene nitrate lifetimes, and NOx recycling rates. We incorporate recent advances in isoprene oxidation chemistry into the SAPRC-07 chemical mechanism within the US EPA Community Multiscale Air Quality (CMAQ) model. The results show improved model performance for a range of species compared against aircraft observations from the INTEX-NA/ICARTT 2004 field campaign. We further investigate the key processes in isoprene nitrate chemistry and evaluate the impact of uncertainties in the isoprene nitrate yield, NOx (NOx = NO + NO2) recycling efficiency, dry deposition velocity, and RO2 + HO2 reaction rates. We focus our examination in the Southeastern United States, which is impacted by both abundant isoprene emissions and high levels of anthropogenic pollutants. We find that NOx concentrations increase by 4–9% as a result of reduced removal by isoprene nitrate chemistry. O3 increases by 2 ppbv as a result of changes in NOx. OH concentrations increase by 30%, which can be primarily attributed to greater HOx production. We find that the model can capture observed total alkyl and multifunctional nitrates (∑ANs) and their relationship with O3, by assuming either an isoprene nitrate yield of 6% and daytime lifetime of 6 h or a yield of 12% and lifetime of 4 h. Uncertainties in the isoprene nitrates can impact ozone production by 10% and OH concentrations by 6%. The uncertainties in NOx recycling efficiency appear to have larger effects than uncertainties in isoprene nitrate yield and dry deposition velocity. Further progress depends on improved understanding of isoprene oxidation pathways, the rate of NOx recycling from isoprene nitrates, and the fate of the secondary, tertiary, and further oxidation products of isoprene.