Land use change from natural to impervious surfaces modifies the surface energy balance and hence the dynamical properties of the overlying atmosphere. The urban heat island is manifested in the formation of an urban boundary layer with distinct thermodynamic features which in turn govern transport processes of air pollutants. A detailed representation of urban areas in mesoscale models however needs to involve the introduction of sophisticated urban canopy parametrizations, coupled to the land surface model. This presentation discusses the impact of the urban morphology on the chemical and dynamical properties of the urban boundary layer for two major urban agglomerations in Germany using state of the art chemical transport models WRF-Chem and COSMO-MESSy at convective scale. Two case studies are in the focus, describing the effect of urban greening on urban heat island and air quality for the region of Stuttgart on the one and the impact of urban densification on exchange processes between surface, urban atmosphere and rural surrounding for the Rhine-Main area on the other hand. Facilitating the output from these models as boundary conditions for the microclimate model ENVI-met, we assess the impact of certain tree species on temperature and ozone concentration at street level. Doing this, we found that certain tree species, if under heat stress, emit biogenic volatile organic compounds, which together with traffic emissions amplify the chemical formation of tropospheric ozone which in the end is harmful for human health.