  Observations from Spitzer and ground-based infrared spectroscopy reveal
significant diversity in the molecular emission from the inner few AU of T
Tauri disks. We explore theoretically the possible origin of this diversity by
expanding on our earlier thermal-chemical model of disk atmospheres. We
consider how variations in grain settling, X-ray irradiation, accretion-related
mechanical heating, and the oxygen-to-carbon ratio can affect the thermal and
chemical properties of the atmosphere at 0.25-40 AU. We find that these model
parameters can account for many properties of the detected molecular emission.
The column density of the warm (200-2000K) molecular atmosphere is sensitive to
grain settling and the efficiency of accretion-related heating, which may
account, at least in part, for the large range in molecular emission fluxes
that have been observed. The dependence of the atmospheric properties on the
model parameters may also help to explain trends that have been reported in the
literature between molecular emission strength and mid-infrared color, stellar
accretion rate, and disk mass. We discuss whether some of the differences
between our model results and the observations (e.g., for water) indicate a
role for vertical transport and freeze-out in the disk midplane. We also
discuss how planetesimal formation in the outer disk (beyond the snowline) may
imprint a chemical signature on the inner few AU of the disk and speculate on
possible observational tracers of this process.
