Ab initio methods such as quadratic configuration and coupled cluster combined with the complete Pople basis set, 6-311++G(3df,3pd), were employed to calculate reaction thermochemistry and corresponding equilibrium constants for a series of reactions between arsenic, selenium, and various atmospheric gases at standard temperature and pressure. Theoretical kinetic investigations of formation reactions for the arsenic and selenium species found to be stable at atmospheric conditions were carried out as well. Reaction pathways in the troposphere involving these trace species from coal combustion flue gases have been predicted. Understanding the speciation and ultimate fate of these trace contaminants will aid in the design of more effective control strategies.