Midplane models of protoplanetary disks iind that the cold temperatures in
the outer parts of the disk ensure that virtually all molecules are accrete
d onto the grains. However, molecules in the gas are observed at these radi
i. One possible explanation is that the emission arises from above the midp
lane, possibly in a heated layer at the surface of a flared disk. Models wh
ich take into account the vertical chemical distribution of molecules and c
an calculate column densities are therefore required for comparison with ob
servations. We present the results of a calculation of the time-dependent t
wo-dimensional chemical structure of a flared protoplanetary disk which inc
ludes photoprocesses driven by both the stellar and interstellar radiation
fields. Three layers are found in the disk consistent with previous work. I
n the upper layer photodissociation produces large abundances of atoms and
ions. Below this molecules are shielded and can avoid dissociation, althoug
h sufficient radiation is present to remove molecules from the grain surfac
es by photodesorption. The majority of the observable species come from thi
s layer. Closer to the midplane of the disk, freezeout removes molecules fr
om the gas. We find that photodesorption can account for the observed colum
n densities if the photodesorption yield is higher than 10(-3) molecules pe
r photon. These results indicate that many observed molecules trace the phy
sical and chemical conditions in the surface regions rather than the midpla
ne although the contribution of the heated surface layer to the column dens
ities is minimal.