  CO is commonly used as a tracer of the total gas mass in both the
interstellar medium and in protoplanetary disks. Recently there has been much
debate about the utility of CO as a mass tracer in disks. Observations of CO in
protoplanetary disks reveal a range of CO abundances, with measurements of low
CO to dust mass ratios in numerous systems. One possibility is that carbon is
removed from CO via chemistry. However, the full range of physical conditions
conducive to this chemical reprocessing is not well understood. We perform a
systematic survey of the time dependent chemistry in protoplanetary disks for
198 models with a range of physical conditions. We varying dust grain size
distribution, temperature, comic ray and X-ray ionization rate, disk mass, and
initial water abundance, detailing what physical conditions are necessary to
activate the various CO depletion mechanisms in the warm molecular layer. We
focus our analysis on the warm molecular layer in two regions: the outer disk
(100 au) well outside the CO snowline and the inner disk (19 au) just inside
the midplane CO snow line. After 1 Myr, we find that the majority of models
have a CO abundance relative to H$_2$ less than $10^{-4}$ in the outer disk,
while an abundance less than $10^{-5}$ requires the presence of cosmic rays.
Inside the CO snow line, significant depletion of CO only occurs in models with
a high cosmic ray rate. If cosmic rays are not present in young disks it is
difficult to chemically remove carbon from CO. Additionally, removing water
prior to CO depletion impedes the chemical processing of CO. Chemical
processing alone cannot explain current observations of low CO abundances.
Other mechanisms must also be involved.
