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CO is commonly used as a tracer of the total gas mass in both theinterstellar medium and in protoplanetary disks. Recently there has been muchdebate about the utility of CO as a mass tracer in disks. Observations of CO inprotoplanetary disks reveal a range of CO abundances, with measurements of lowCO to dust mass ratios in numerous systems. One possibility is that carbon isremoved from CO via chemistry. However, the full range of physical conditionsconducive to this chemical reprocessing is not well understood. We perform asystematic survey of the time dependent chemistry in protoplanetary disks for198 models with a range of physical conditions. We varying dust grain sizedistribution, temperature, comic ray and X-ray ionization rate, disk mass, andinitial water abundance, detailing what physical conditions are necessary toactivate the various CO depletion mechanisms in the warm molecular layer. Wefocus 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 insidethe midplane CO snow line. After 1 Myr, we find that the majority of modelshave 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 witha high cosmic ray rate. If cosmic rays are not present in young disks it isdifficult to chemically remove carbon from CO. Additionally, removing waterprior to CO depletion impedes the chemical processing of CO. Chemicalprocessing alone cannot explain current observations of low CO abundances.Other mechanisms must also be involved.

Unlocking CO Depletion in Protoplanetary Disks I. The Warm Molecular Layer