We calculate the chemical evolution of protoplanetary disks considering radial viscous accretion, vertical turbulent mixing and vertical disk winds. We study the effects on the disk chemical structure when different models for the formation of molecular hydrogen on dust grains are adopted. Our gas-phase chemistry is extracted from the UMIST Database for Astrochemistry (Rate06) to which we have added detailed gas-grain interactions. We use our chemical model results to generate synthetic near- and mid-infrared LTE line emission spectra and compare these with recent Spitzer observations. Our results show that if H2 formation on warm grains is taken into consideration, the H2O and OH abundances in the disk surface increase significantly. We find the radial accretion flow strongly influences the molecular abundances, with those in the cold midplane layers particularly affected. On the other hand, we show that diffusive turbulent mixing affects the disk chemistry in the warm molecular layers, influencing the line emission from the disk and subsequently improving agreement with observations. We find that NH3, CH3OH, C2H2 and sulphur-containing species are greatly enhanced by the inclusion of turbulent mixing. We demonstrate that disk winds potentially affect the disk chemistry and the resulting molecular line emission in a similar manner to that found when mixing is included.
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