Observations of molecules in planet-forming circumstellar disks are powerful diagnostic tools, enabling characterization of both gas composition andunderlying physical conditions using molecular excitation. My thesis has primarily focused on the role of disk structure and ionization for the chemistry of disks and the corresponding submillimeter emission. Changes in the overall morphology of disks, including inner holes or gaps, significantly alters the stellar irradiation of the disk, which will affect the disk heating, especially at the walls of an inner hole (Chapter 2). I have modeled the 3D chemistry of gapped disks, carved out by planets, including for the first time heating by a luminous protoplanet. The planet sublimates ices beyond expected disk ;;snow-lines;; leading to observable signatures detectable with ALMA (Chapter 3). Regarding ionization, I have studied disk ionization by cosmic rays (Chapter 4), short-lived radionuclides (Chapter 5), and X-rays from the central star (Chapter 6). In Chapter 6, I investigated the molecular dependence on each of these processes and made testable predictions for sensitive submillimeter observations to map out disk ionization, which I applied to the TW Hya disk, finding a substantially lower than interstellar cosmic ray rate (Chapter 7). One of the major implications of this work is related to the formation chemistry of water, which requires ionization to proceed. In the absence of water-formation in the solar nebula protoplanetary disk, this work demonstrates that there must be a substantial inheritance of water from earlier evolutionary stages, pre-dating the Sun;;s formation (Chapter 8). Together, these projects have also enabled the development of a comprehensive 2D and 3D disk modeling framework, useful for parameter space studies and source-targeted modeling.
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Molecular Signposts of the Physics and Chemistry of Planet Formation.
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