Quantum mechanics

Ecology

Biology

Computer science

Botany

Substrate (aquarium)

Software

Physics

Apex (geometry)

Organic chemistry

Mathematics

Xenobiotic

Aqueous solution

Enzyme

Environmental science

Geometry

Kinetics

Chemistry

Programming language

Biological system

Molecules

The APEX (aqueous photochemistry of environmentally occurring xenobiotics) software computes the phototransformation kinetics of compounds that occur in sunlit surface waters. It is free software based on Octave, and was originally released in 2014. Since then, APEX has proven to be a remarkably flexible platform, allowing for the addressing of several environmental problems. However, considering APEX as a stand-alone software is not conducive to exploiting its full potentialities. Rather, it is part of a whole ecosystem that encompasses both the software and the laboratory protocols that allow for the measurement of substrate photoreactivity parameters. Coherently with this viewpoint, the present paper shows both how to use APEX, and how to experimentally derive or approximately assess the needed input data. Attention is also given to some issues that might provide obstacles to users, including the extension of APEX beyond the simple systems for which it was initially conceived. In particular, we show how to use APEX to deal with compounds that undergo acid–base equilibria, and with the photochemistry of systems such as stratified lakes, lakes undergoing evaporation, and rivers. Hopefully, this work will provide a reference for the smooth use of one of the most powerful instruments for the modeling of photochemical processes in freshwater environments. All authors have read and agreed to the published version of the manuscript.

A Critical View of the Application of the APEX Software (Aqueous Photochemistry of Environmentally-Occurring Xenobiotics) to Predict Photoreaction Kinetics in Surface Freshwaters