Scanning Tunneling Microscope Development and Use in Hydrogen Reaction Studies of Alkanethiol Self-Assembled Monolayers on Au(111)

This thesis explores the development of home-built precision instrumentation and the nature of reaction between alkanethiols and atomic hydrogen gas using scanning tunneling microscopy (STM). STM is a powerful technique, but due to the nature of the instrument it is also an expensive one. The STM used in this work has been built by or machined from commercially available parts. The development of 3D printing offers a new avenue for instrument design. If parts can be 3D printed, this instrument can be built and implemented at a significantly cheaper price than commercially available. 3D printing allows instruments to be replicated with a single geometry file and adjustments can easily be made as needed. The transfer system involved with the STM as well as the instrument housing have been 3D printed as this technology offers a level of customization that is unmatched by machining alone. 3D metal printing parts allows for complex and intricate parts to be made at a fraction of the cost of commercially available systems. This transfer system and its parts are explored. The instrumentation build is also examined.

With a functional instrument and means of introducing samples to a vacuum chamber, reactions of alkanethiols on Au(111) with atomic hydrogen can be examined on an atomic scale. 8-mercapto-1-octanol was investigated due to its similarity with a better studied molecule, 1-octanethiol. The 8-mercapto-1-octanol surface lacks long range order that was characteristic of 1-octanethiol. Despite the difference in surface features, the reaction pathway of 8-mercapto-1-octanol is similar to that of 1-octanethiol. 1-octanethiol on Au(111) has been studied robustly, but the system is still not fully understood. A temperature increase of a few degrees Celsius resulted in a significant change in the dynamics of the reaction between 1-octanethiol and atomic hydrogen because of a phase that does not occur at room temperature. This new phase can be visually distinguished from the other phases using STM. The change of the reaction pathway and how it differs from previous studies is explored. In addition future molecules that contain two sulfur groups rather than one that 1-octanethiol and 8-mercapto-1-octanol have and their potential reactivity is briefly discussed along with the prospect of repeating experiments at cryogenic temperatures.