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The atmospheric chemistry general circulation model ECHAM5/MESSy (EMAC) has been extended by processes that parameterize particle precipitation. Several types of particle precipitation that directly affect NO<sub>y</sub> and HO<sub>x</sub> concentrations in the middle atmosphere are accounted for and discussed in a series of papers. In part 1, the EMAC parameterization for NO<sub>x</sub> produced in the upper atmosphere by low-energy electrons is presented. Here, we discuss production of NO<sub>y</sub> and HO<sub>x</sub> associated with Solar Proton Events (SPEs). A submodel that parameterizes the effects of precipitating protons, based on flux measurements by instruments on the IMP or GOES satellites, was added to the EMAC model. Production and transport of NO<sub>y</sub> and HO<sub>x</sub>, as well as effects on other chemical species and dynamics during the 2003 Halloween SPEs are presented. Comparisons with MIPAS/ENVISAT measurements of a number of species affected by the SPE are shown and discussed. There is good agreement for NO<sub>2</sub>, but a severe disagreement is found for N<sub>2</sub>O similar to other studies. We discuss the effects of an altitude dependence of the N/NO production rate on the N<sub>2</sub>O and NO<sub>y</sub> changes during the SPE. This yields a modified parameterization that shows mostly good agreement between MIPAS and model results for NO<sub>2</sub>, N<sub>2</sub>O, O<sub>3</sub>, and HOCl. With the ability of EMAC to relax the model meteorology to observations, accurate assessment of total column ozone loss is also possible, yielding a loss of approximately 10 DU at the end of November. Discrepancies remain for HNO<sub>3</sub>, N<sub>2</sub>O<sub>5</sub>, and ClONO<sub>2</sub>, which are likely a consequence from the missing cluster ion chemistry and ion-ion recombination in the EMAC model as well as known issues with the model's NO<sub>y</sub> partitioning.