In this paper, we aim to investigate the interplay between chemistry, flow dynamics and temperature using high fidelity computational fluid dynamics (CFD) models in an urban environment. A detailed numerical model based on large eddy simulation (LES) is developed considering the temperature and buoyancy effect and the non-equilibrium chemical processes. The model is used to study flow and reaction inside experimental and real-size street canyons. Street canyons are chosen for this study, as they represent the smallest unit of urban environments where detailed flow simulations combined with chemical reactions can be performed with high numerical accuracy. The effect of thermal driven flow is studied in reacting and non-reacting conditions to understand the role of buoyancy in accurately modeling pollutant reaction and dispersion. It is shown that buoyancy has a significant effect on the dynamics of the flow, by altering the main vortex structure inside the canyon and by increasing turbulent kinetic energy. It is also found that the chemical reactions strongly affect final concentrations of pollutants, which indicates the potential need for implementation of more advanced chemical models in future work. The importance of correct boundary conditions to accurately predict pollutant concentrations are discussed. Finally, by comparing the LES results with experimental field measurements in a real street canyon, the limitation of using periodic boundary conditions, as it is commonly used in the literature, is discussed. Moreover, it is shown that implementation of a variable photolysis rate is likely needed.