Recent studies have found that there remain many unresolved gaps in the atmospheric chemistry employed in regional air quality models. These deficiencies include under-prediction of the response of ozone to emission changes; over-prediction of the oxidation rate of nitrogen dioxide and substantial errors in the estimated vertical concentrations of ozone, nitrogen oxides (NOx), peroxy acetyl nitrate in comparison with field observations such as those obtained by the International Consortium for Atmospheric Research on Transport and Transformation (ICARTT) in 2004. Although there are uncertainties attributable to emissions, including their quantity and speciation (especially with respect to the reactivity of volatile organic compounds VOC), meteorology, and to sub-grid scale effects, these disagreements between measurements and models suggest that there remain significant gaps in regional atmospheric chemical mechanisms. Analyses of field measurements and atmospheric chemistry simulations are necessary to improve the models. Therefore, this study focuses on interpretation of 2006 data from NATIVE and sonde launches at Beltsville, MD (39N, 77W), and air quality model analysis with the latter involving the inter-comparison of specific mechanisms such as the Regional Atmospheric Chemical Mechanism, version 2 (RACM2) and focusing on VOC, NOx and HOx transformations.