Chemistry in Protoplanetary Disks

This comprehensive review summarizes our current understanding of the evolution of gas, solids and molecular ices in protoplanetary disks. Key findings related to disk physics and chemistry, both observationally and theoretically, are highlighted. We discuss which molecular probes are used to derive gas temperature, density, ionization state, kinematics, deuterium fractionation, and study organic matter in protoplanetary disks.Comment: 83 pages, 8 figures, 5 tables, to be published in a Thematic Issue "Astrochemistry" in Chem. Reviews (December 2013). This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Chemical Reviews, copyright (c) American Chemical Society after peer revie

Gas mass tracers in protoplanetary disks: CO is still the best

Protoplanetary disk mass is a key parameter controlling the process of planetary system formation. CO molecular emission is often used as a tracer of gas mass in the disk. In this study we consider the ability of CO to trace the gas mass over a wide range of disk structural parameters and search for chemical species that could possibly be used as alternative mass tracers to CO. Specifically, we apply detailed astrochemical modeling to a large set of models of protoplanetary disks around low-mass stars, to select molecules with abundances correlated with the disk mass and being relatively insensitive to other disk properties. We do not consider sophisticated dust evolution models, restricting ourselves with the standard astrochemical assumption of $0.1~\mu$m dust. We find that CO is indeed the best molecular tracer for total gas mass, despite the fact that it is not the main carbon carrier, provided reasonable assumptions about CO abundance in the disk are used. Typically, chemical reprocessing lowers the abundance of CO by a factor of 3, compared to the case of photo-dissociation and freeze-out as the only ways of CO depletion. On average only 13% C-atoms reside in gas-phase CO, albeit with variations from 2 to 30%. CO$_2$, H$_2$O and H$_2$CO can potentially serve as alternative mass tracers, the latter two being only applicable if disk structural parameters are known.Comment: Accepted for publication in Ap