The work described in this thesis involves a simple model system --- atomic hydrogen and alkanethiol self assembled monolayers (SAMs) --- to probe the most basic interactions of gas-surface reactions. Presented below are the results of experiments that investigate the roles of molecular structure and surface defect structure in the degradation of these monolayers. A large body of previous alkanethiolate SAM studies has probed the mechanisms of monolayer formation and desorption. Chain length dependence on reaction time and reaction pathway was found, with longer chain thiols reacting more slowly through a series of reactions, compared to the quick hydrogenation reaction for shorter chain thiols. Previous work from this lab showed that defect sites are significantly more reactive than close-packed areas of the monolayer, and that the reaction rate accelerates due to increased defect site coverage over the course of a reaction at room temperature. Another recent room temperature study proposed a kinetic model describing the mechanism of erosion happening in two parts, a fast step and a slow step, dependent on the surface phases and on chain length. The studies for this thesis work however, were performed slightly above room temperature, at 27◦C. This slight change in temperature allowed for an additional phase, not seen at 22◦C, to exist on the surface. This new liquid phase revealed new insight into the reaction pathway of the alkanethiolate SAM, and a kinetic model was developed to describe monolayer erosion upon exposure to atomic hydrogen that is dependent on the phase transitions and the build up of vacancies on the surface throughout the reaction. Though it is likely that surface defect structure does cause acceleration of these reactions, the results presented here make a case for the larger role that surface phase transitions play in the mechanisms for alkanethiolate monolayer degradation.These higher temperature experiments with both 1-octanethiol and 8-mercapto-1-octanol surfaces also revealed the sudden appearance of gold islands concomitant with the appearance of a striped phase. These results inform us that gold adatoms are freed up upon the emergence of the striped phase during monolayer erosion, and is evidence of the reconstruction of the underlying Au(111) substrate for the close packed and liquid phases, while the striped phase does not require the incorporation of gold adatoms into the monolayer. Scanning tunneling microscopy (STM) is the main technique used for these experiments. Its 3D real space, high resolution direct imaging capabilities make it an ideal characterization tool for studies that examine the structural changes occurring over the course of a surface reaction. The experiments described in this thesis work were performed on a home-built instrument with a design focused around accessibility, and customizability. Incorporating commercially available parts into the design lowers the cost and allows the instrument setup to be easily replicated, while the use of 3D printed parts allows for small, intricate pieces that simplify the control and handling of the instrument. Both eliminate the need for access to a machining shop, but later versions of the instrument design do require machined parts. The freedom of customizability is another advantage to the design of the chamber parts with. The current set up is customized to include direct access to the sample surface for hydrogen cracking experiments, a low-degree-of-freedom vacuum transfer system, and cryogenic cooling capabilities for future low temperature experiments.