University of Notre Dame
KautzN092010.pdf (26.53 MB)

Scanning tunneling microscopy studies of reactive gas-phase interactions with alkanethiol self-assembled monolayers

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posted on 2010-09-01, 00:00 authored by Natalie A Kautz
This thesis studies the reactions and structural changes in alkanethiol self-assembled monolayers (SAMs) on Au(111) resulting from exposure to gas-phase atomic hydrogen. Hydrogen atoms remove the alkanethiol molecules and we investigate how the local surface environment influences monolayer erosion. A scanning tunneling microscope (STM), attached to a molecular beam chamber, allows us to monitor in situ the exact same area of a surface before, during and after exposure. Initially extensive damage to the monolayer is observed in the form of both dark and bright features in STM images. Molecules positioned along surface defects (domain boundaries, gold-terrace step edges) are preferentially removed before molecules located in close-packed areas. While the overall net reaction is to remove the octanethiol SAM, molecules remaining on the gold surface undergo significant rearrangement: domain boundaries anneal into close-packed areas, film defects diffuse to monolayer edges, and molecules located along the edge of close-packed features reorganize and change the shape of the remaining monolayer. This annealing and restructuring likely results from increased mobility of surface-bound alkanethiolates in the vicinity of monolayer defects, or from diffusion and readsorption of transiently formed alkanethiol molecules. Increasing exposure also results in an accelerated rate of observed surface changes, indicating that the reactivity of the surface increases as a result of gas-surface reactions. We compare our results with kinetic Monte Carlo simulations to determine that the edge of defect sites are upwards to 100 times more reactive than close-packed monolayer areas. Monolayer erosion also revealed the formation of bright gold islands. Recent theoretical and experimental studies have suggested gold adatoms are incorporated into the alkanethiol--gold interface. The gold adatoms remain on the surface after alkanethiol monolayer removal and form features that we can observe using STM: formation of single-atom thick gold islands, decreasing size of surface vacancy pits, and faceting of terrace step edges. Compared to the alkanethiol-terminated surface, these features indicate a net increase in the amount of gold present on the surface, compared to the alkanethiol-terminated bulk structure. Varying the length of the alkane chain does not affect the total adatom coverage, as adatom coverage for ethanethiol (0.172 &177; 0.039), octanethiol (0.143 &177; 0.033), and dodecanethiol (0.154 &177; 0.024) SAMs are within experimental error of one another. This corresponds to one gold adatom for every six atoms in the bulk-terminated surface, and thus one gold adatom for every two alkanethiol molecules.


Date Modified


Defense Date


Research Director(s)

S. Alex Kandel

Committee Members

Prashant Kamat Gregory V. Hartland Paul Bohn


  • Doctor of Philosophy

Degree Level

  • Doctoral Dissertation


  • English

Alternate Identifier



University of Notre Dame

Program Name

  • Chemistry and Biochemistry (BIOCHEM)

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