A version of the Master Chemical Mechanism (MCM) v3.1, refined on the basis of recent chamber evaluations, has been incorporated into a Photochemical Trajectory Model (PTM) and applied to the simulation of boundary layer photochemistry in the Portuguese west coast region. Comparison of modelled concentrations of ozone and a number of other species (NO(x) and selected hydrocarbons and organic oxygenates) was carried out, using data from three connected sites on two case study days when well-defined sea breeze conditions were established. The ozone concentrations obtained through the application of the PTM are a good approximation to the measured values, the average difference being ca. 15%, indicating that the model was acceptable for evaluation of the details of the chemical processing. The detailed chemistry is examined, allowing conclusions to be drawn concerning chemical interferences in the measurements of NO(2), and in relation to the sensitivity of ozone formation to changes in ambient temperature. Three important, and comparable, contributions to the temperature sensitivity are identified and quantified, namely (i) an effect of increasing biogenic emissions with temperature; (ii) an effect of increasing ambient water vapour concentration with temperature, and its influence on radical production; and (iii) an increase in VOC oxidation chain lengths resulting from the temperature-dependence of the kinetic parameters, particularly in relation to the stability of PAN and its higher analogues. The sensitivity of the simulations to the refinements implemented into MCM v3.1 are also presented and discussed.