As analogs to the solar nebula, circumstellar disks offer a unique opportunity to study the conditions during the star and planet formation process. Interpretation of molecular line observations is dependent on the development of extensive models of the chemistry and radiative transfer in accretion disks. In this study, several millimeter-wave molecular lines were observed toward a sample of disks encircling T Tauri and Herbig Ae stars with the Owens Valley Millimeter Array. The intent of these studies is the quantitative examination of the chemistry of the biogenic elements (C, N, O, S) in accretion disks. Toward this goal, radiative transfer models were modified for direct comparison with the observations to aid in the interpretation of molecular line emission and comparison with the predictions of chemical models, as discussed in Chapter 2. Chapter 3 presents a survey of CN, HCN, CO and HCO+ in 7 Herbig Ae and T Tauri star disks, which was performed in order to probe the effects of UV fields on disk chemistry. In this study, CN and HCO+ are found to be sensitive to the strength of the local UV field. The first interferometric studies of deuterium in disks were performed and are discussed in Chapter 4. HDO and DCN were detected toward the T Tauri disk LkCa 15 and the Herbig Ae disk HD 163296. The deuterium enrichments are similar to that of molecular clouds, hot cores, and comets, consistent with comet formation in the outer regions of disks. The distribution of HDO in LkCa 15 was found to be similar to predictions from chemical models, which suggest a steep gradient as a function of disk radius. Chapter 5 presents Keck LWS observations of the 8-13 micron silicate emission feature toward several T Tauri and Herbig Ae stars at various stages of the star formation process indicate an evolutionary trend similar to that previously seen with ISO for disks around intermediate mass stars. However, emission from crystalline silicates was only detected toward one low mass star, Hen 3-600A, possibly indicating that crystallization processes occur less frequently, or are more difficult to observe at mid-infrared wavelengths, in these disks. Finally, in Chapter 6, a summary of protoplanetary disk chemistry is presented and the future of the field is discussed.
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