I will discuss a few applications requiring coupling chemistry with gas dynamics in protoplanetary disks. The most common application is to obtain the level of ionization, which determines the coupling between gas and magnetic fields. In the bulk disk, as far as ionization is concerned, equilibrium chemistry holds unless sub-micron sized grains are depleted. This allows magnetic diffusivities to be obtained from a pre-computed look-up table based on a complex chemical network, although magnetic diffusivities could have non-trivial dependence on magnetic field strengths due to small dust grains. More interesting applications involve the transport of chemical species over dynamical timescales, such as those important for heating/cooling in the disk atmosphere, which requires explicitly evolving a (reduced) chemical network with gas dynamics. We further show that a complex network can be reduced to a network with ~20-30 species with ~50-60 gas-phase reactions that still reasonably reproduces the abundances of most major species of interest in the disk atmosphere of the bulk midplane region. However, the intermediate layer is more complex, which may pose a challenge to chemo-dynamical studies.