Ultra-high dose rate FLASH radiotherapy, a promising cancer treatment approach, offers the potential to reduce healthy tissue damage during radiotherapy. As the mechanisms underlying this process remain unknown, several hypotheses have been proposed, including the altered production of radio-induced species under ultra-high dose rate (UHDR) conditions. This study explores realistic irradiation scenarios with various dose-per-pulse and investigates the role of pulse temporal structure. Using the Geant4 toolkit and its Geant4-DNA extension, we modeled the Oriatron eRT6 linac, a FLASH-validated electron beam, and conducted simulations covering four distinct dose-per-pulse scenarios - 0.17 Gy, 1 Gy, 5 Gy, and 10 Gy - all featuring a 1.8 µs pulse duration. Results show close agreement between simulated and experimental dose profiles in water, validating the eRT6 model for Geant4-DNA simulations. We observed important changes in the temporal evolution of certain species, such as the earlier fall in hydroxyl radicals ([Formula: see text]) and reduced production and lifetime of superoxide ([Formula: see text]) with higher dose-per-pulse levels. The pulse temporal structure did not influence the long-term evolution of species. Our findings encourage further investigation into different irradiation types, such as multi-pulse configurations, and emphasize the need to add components in water to account for relevant cellular processes.