Article pubs.acs.org/JPCC
Reactivity of Self-Assembled Monolayers: Local Surface Environment Determines Monolayer Erosion Rates Natalie A. Kautz† and S. Alex Kandel* Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States ABSTRACT: We use scanning tunneling microscopy (STM) to study octanethiol self-assembled monolayers (SAMs) on Au(111) exposed to atomic hydrogen. While the overall net reaction is to remove octanethiol molecules from the underlying gold surface, the monolayer structure heavily influences the rate of this reaction and molecules located along surface defects are preferentially removed before those located in close-packed areas. Octanethiol molecules remaining on the gold surface can go through significant rearrangement: domain boundaries can change both size and structure, annealing into surrounding close-packed domains; film defects diffuse to the edge of close-packed areas; and molecules located along the edge of close-packed domains shift position, changing the size and shape of the remaining close-packed features. Monolayer reactivity increases with increasing hydrogen-atom exposure, and we compare the experimental results with kinetic Monte Carlo simulations. We find that the edges of defect sites are potentially over 500 times more reactive than close-packed monolayer areas.
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INTRODUCTION In this manuscript, we present a scanning tunneling microscopy (STM) study of the reaction of gas-phase hydrogen atoms with alkanethiolate self-assembled monolayers (SAMs) on Au(111). Alkanethiolates are often picked as model surfaces because of their complexity (compared to single-crystal solids), made tractable by their relatively high degree of order and the extensive literature characterizing their structure. In particular, gas-surface reactions with alkanethiolate monolayers have been the subject of considerable experimental1−35 and theoretical27−29,31,36−47 investigation. The reaction of gas-phase atomic hydrogen with alkanethiolate monolayers has been characterized by Gorham et al. using X-ray photoelectron spectroscopy.17 Hydrogen atoms remove the monolayer and expose the underlying gold surface through one of two reaction mechanisms: (1) hydrogenation of the sulfur− gold bond H• + R−S−Au → Au + R−SH or (2) hydrogen abstraction from the alkane chain. H• + R−H → H2 + R•
Increasing the hydrogen-atom exposure results in desorption of H2S from the surface as the sulfur−gold bond breaks and the slow erosion of the remaining hydrocarbon species over longer time scales. For both the hydrogenation and hydrogen abstraction reactions, hydrogen atoms remove the monolayer and expose the underlying gold surface. The current manuscript is focused on how the rates and mechanisms of gas−surface reactions are affected by the local surface environment. Alkanethiolate monolayers present surfaces with a diverse array of possible structures. At high surface coverage, they are characterized by the short-range order of molecules in dense, close-packed arrays. Close-packed areas, however, typically extend only 10−100 nm before they are broken up by misalignments in packing or orientation, or by defects in Au(111) substrate. Heterogeneity in the monolayer structure will result in a significant number of surface sites with more open structures that are more susceptible to attack by gasphase species. Defect sites are sites that may allow hydrogen atoms to bypass the film thickness, and film thickness, viewed in the light of the results of ref 17, may determine reaction pathway and reaction rate. Our approach is to use scanning tunneling microscopy (STM) to monitor the same area of the surface both before and after exposure to atomic hydrogen. 1−3 As alkanethiol monolayers are exposed to gas-phase hydrogen, we observe large-scale modifications of surface structure as the surface progresses from full alkanethiolate coverage to a totally reacted surface free of organic species. We characterize these changes, quantify them as a function of hydrogen-atom exposure, and compare the results to kinetic Monte Carlo simulations of
The relative importance of each of these mechanisms is determined by the length of the alkanethiolate chain. For medium-length alkanethiol molecules (9−12 carbon atoms), the incident hydrogen atom is able to permeate through (or along) the alkane chain to the monolayer interface, breaking the sulfur− gold bond and resulting in desorption of a complete alkanethiol molecule. Longer alkane chains (16−18 carbon atoms) inhibit the incident hydrogen atom from reaching the interface; abstraction of a hydrogen atom from the carbon chain, forming a surface radical, is much more likely. This surface radical can then interact with neighboring alkane chains, forming a crosslinked hydrocarbon species, and preventing alkanethiol desorption. © 2012 American Chemical Society
Received: November 21, 2011 Revised: January 11, 2012 Published: January 30, 2012 4725
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surface defect sites: domain boundaries, step edges, or vacancies caused by reaction. In our experimental data, we find that each of these sites qualitatively appears to be much more reactive than close-packed areas, with no clear difference between them.) Depending upon the local surface environment, each incidental hydrogen atom will have a probability of reacting and removing the molecule from the surface, and we can control the relative rate of reaction between these two environments. This reaction rate ratio is the primary adjustable parameter in these simulations. Between short intervals of hydrogen-atom exposure, the surface is allowed time to anneal. This process is simulated after calculating an interaction energy for each molecule based on its number of neighbors: each pairwise interaction lowers the energy one unit, with eight such interactions for molecules in the middle of close-packed regions. (Note that, in alkanethiol SAMs, high-density phases are hexagonally close-packed, and each alkanethiol has six neighboring molecules. In our simulation, the molecules in close-packed regions have eight adjacent neighbors, one located on each side and each corner. While our close-packed regions do not model the experimental surface exactly, the overall behavior is the same.) Periodic boundary conditions were used to avoid the creation of defects due to geometric constraints at the image edges. Surface annealing is implemented using a Metropolis algorithm, with random motions generated and either (1) always allowed if they lower energy or (2) allowed if they raise energy, according to a probability decreasing exponentially with the ratio between the energy increase and a selected temperature parameter. Reaction and annealing are repeated until the monolayer is completely removed from the surface (i.e., every pixel in the mask is zero) or until the simulated coverage falls below a set threshold. Simulations were run for various initial surface structures, as well as different ratios of reactivity between molecules in close-packed regions and defect sites. Simulation results were then compared with the experimental STM images.
reaction rates. Our conclusion is that the rate of reaction and the effect of reaction on surface morphology are determined overwhelmingly by the presence of defects in the original monolayer.
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EXPERIMENTAL SECTION Experiments were performed in situ using a home-built, UHV scanning tunneling microscope (STM) attached to a differentially pumped molecular beam chamber.2,3,48 The molecular beam source and skimmer, described in detail in ref 48, were replaced with an Oxford Scientific OS-Crack Thermal Gas Cracker and two mechanical shutters, used to control sample exposure to hydrogen atoms. Molecular hydrogen, with a back pressure of 1 × 10−6 Torr, flowed through a heated (1800− 2000 K) tungsten capillary to produce hydrogen atoms. Under these conditions, we expect 6−27% of the gas dissociates into atomic hydrogen with an average kinetic energy of 0.07−0.08 eV, resulting in a mixture of both atomic and molecular hydrogen dosing the sample surface.49 Octanethiol self-assembled monolayers (SAMs) were prepared on flame-annealed Au(111)-on-mica substrates in air by vapor deposition at 70 °C for ∼24 h.50 Samples were rinsed thoroughly with ethanol and dried in air (∼5 min) before being placed in the UHV STM chamber for the experiment. STM images, taken with a bias voltage of 0.5 V and a tunneling current of 10 pA, showed large areas of hexagonally closepacked molecules. Typical monolayer defects were also observed, including the formation of domain boundaries and the presence of single-atom thick vacancy islands in the gold surface. Prior to hydrogen-atom exposure, an area of the surface is selected that (1) accurately represents the overall monolayer structure and (2) contains a recognizable feature (such as a small terrace or large vacancy island) that indicates we remain in the same area of the surface, despite multiple changes occurring within the monolayer. We confirmed that the SAM is stable at room temperature in UHV by initially scanning the area multiple times to ensure no structural changes occurred; the surface was then exposed to hydrogen atoms (at an incidental angle of ∼45°) for 4−180 s by opening the mechanical shutters. To minimize the influence of tip shadowing, occurring when the STM tip blocks the line-of-sight between the hydrogen-atom source and the surface and results in lower hydrogen-atom exposure, the tip was withdrawn and removed from the imaging area during dosing. After exposure, the tip was moved back to the imaging area for scanning and the procedure was repeated until the entire monolayer was removed and the underlying gold surface exposed.3 The STM data presented are taken from a series of images monitoring monolayer removal and were processed using a masked high-pass filter applied in the fast-scan direction.51 This processing removed noise due to low-frequency floor vibrations from each image. Theoretical simulations were also performed using a kinetic Monte Carlo simulation, written to run using Matlab. We defined the initial surface structure, using a mask to describe monolayer (one) and defect (zero) locations; hydrogen-atom exposure is simulated using a random number generator. Incoming hydrogen atoms will hit a molecule on the surface that falls into one of two categories: (1) close-packed regions, where the molecule is completely surrounded by neighboring molecules, and (2) defect sites, where the molecule is located along the edge of a close-packed region and therefore sits next to unoccupied sites. (We do not distinguish between the different types of
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RESULTS Octanethiol self-assembled monolayers are removed from the gold surface with extended hydrogen-atom exposure, and an example is shown in the series of images presented in Figure 1. These images were processed to increase the display contrast by subtracting a constant value from each point on the upper terrace. This effectively makes each image flatter, though it does introduce a dim/bright subtraction artifact at the step edge itself. The reaction process is similar to that observed in ref 1. Prior to any dosing (Figure 1a), a region of the surface containing multiple gold terraces, single-atom surface vacancies, and areas of close-packed octanethiol molecules separated by domain boundaries was chosen. Even a small amount of exposure in Figure 1b results in changes to the monolayer. Dissociation of octanethiol molecules along monolayer defects (domain boundaries, step edges) and in close-packed regions has resulted in the formation of regions with apparently lower topographic height. Domain boundary structure and shape has also been modified. These changes become larger and more prevalent with additional hydrogen-atom dosing in Figure 1c−f. Octanethiol molecules continue to erode along domain boundaries and step edges, resulting in an increase in size and a change in shape of the dark defects first appearing in Figure 1b, and a decrease in the overall area of the close-packed film. A few small regions likely correspond to low-density 4726
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Figure 1. A series of 1110 Å × 1115 Å images showing an octanethiol SAM before (a) and after 48 s (b), 200 s (c), 592 s (d), 862 s (e), and 1042 s (f) of hydrogen-atom exposure. See text for description of image processing.
Figure 2. (a) Map of the surface defects that occur in Figure 1a, with solid lines showing substrate step edges and dashed lines showing octanethiolate domain boundaries. Panels b−f match the corresponding panels in Figure 1, with areas covered by alkanethiolates colored white and areas where reaction has occurred colored black.
“striped” alkanethiolate phases, for example, near the pit defect in the middle of the upper edge of Figure 1f. Other regions might contain disorganized or mobile low-density alkanethiolates. Other regions could be bare Au(111); while this is unlikely at the start of the reaction when few alkanethiols have been removed, it is increasingly more likely as exposure continues and reaction progresses. We acquire images past the point of Figure 1f, until all visible alkanethiol is gone and the surface stops changing. Analysis of the images in Figure 1, as well as of similar data sets acquired in other experiments, created binary masks for each image, with the mask set to white (1) in areas where closepacked alkanethiolates remained on the surface and to black (0) in areas where the monolayer has reacted. These masks are shown in Figure 2. Only the two main terraces were analyzed. The lower terrace in the bottom left of the images and the small substrate vacancy islands are shown in black as well and are not included in subsequent calculations. A consistent observation is that molecules remaining on the surface are mobile, and several local annealing effects are observed. Domain boundaries order into close-packed features, dark vacancy defects located in close-packed regions change location, and the perimeter of close-packed octanethiol molecules (monolayer edge) changes shape. This behavior is highlighted in Figure 3, which compares regions of the monolayer that have disappeared with increased hydrogenatom exposure (orange), shown alongside areas that have appeared to fill in during the course of the reaction (blue). The close proximity of many blue and orange areas results from domain boundaries that have shifted, eroding in some areas
Figure 3. Map showing differences in monolayer coverage between Figure 1c and d. Orange areas indicate regions of the monolayer that are present in Figure 1c but disappear in Figure 1d. Blue areas show regions that were not present in Figure 1c but appear in Figure 1d. Blue areas result from the annealing of the monolayer that occurs as the reaction progresses. Step edges (solid black lines) and domain boundaries (dashed lines) originally appearing in Figure 1a are shown in each image. 4727
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while filling in others. Isolated blue features, in contrast, show vacancy defects that have annealed out to form close-packed regions as the reaction progresses. Figure 4 illustrates the time dependence of the reaction by displaying a map of the monolayer area for each image in Figure
Figure 5. The normalized monolayer area (black circles) for each image in Figure 1 plotted against the length of hydrogen-atom exposure. The experimental data is concave-down, which can be seen in comparison to the best-fit line (red) and exponential (blue).
and spread from steps and domain boundaries. We quantify the relative reactivity between these two surface sites using kinetic Monte Carlo simulations. An example simulation is shown in Figure 6. In this figure, a series of images were selected from a
Figure 4. The total monolayer area for each image in Figure 1b−f is shown with sequential images overlaid on top of each other. The edge of each close-packed region is tinted (blue-dark green-green-yellowwhite) to show how it changes versus exposure time. The greatest monolayer erosion occurs in the vicinity of steps and defects, though, once again, evidence of annealing is present in the shifting of monolayer edges as reaction progresses.
1b−f (and each mask in Figure 2b−f), respectively colored blue, dark green, green, yellow, and white. The edge of each closepacked area is drawn as a solid colored line shaded toward the interior of the monolayer, and areas without octanethiol molecules (or not included in the image analysis) contain no color. Sequential images are laid on top of one another to show changes in the exact same portion of monolayer after additional dosing. Step edges (solid white line) and domain boundaries (dashed white lines) appearing before hydrogen-atom exposure are also shown. In Figure 5, the monolayer area (black circles) for each image in Figure 1 is plotted over time. As hydrogen-atom exposure increases, monolayer coverage decreases. We also observe a distinct concave-downward slope which does not correspond to an exponential (blue) or linear (red) fit. Similar plots of coverage versus exposure, measured in separate experiments on different octanethiol monolayers, yield similar concave-down functional forms. For these data sets, we assume all reacted regions are bare gold; that is, they do not contain low-density alkanethiols. This will underestimate the coverage but likely only slightly: while there are a variety of medium-density alkanethiolate phases, the common low-density striped phases have coverages more than 4 times lower than the close-packed phases.52 Additionally, the extent of low-density alkanethiolates coverage will decrease as the reaction progresses, which means the concave-down shape will, if anything, be underestimated. Qualitatively, we observe from the STM images that molecules located along defect sites are more reactive than close-packed areasthis is apparent by observing how vacant areas begin at
Figure 6. Monolayer erosion simulated by kinetic Monte Carlo. The original monolayer (white) is presented in part a, along with a solid line that shows the initial surface defect used to start the simulation. For this simulation, sites located on this defect or adjacent to any newly formed monolayer vacancy (black) are ∼4500× more reactive than those located in the close-packed areas (white). Changes in the monolayer with increasing reaction are shown in panels b−f. 4728
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regions) produces an exponential dependence of coverage on exposure time, whereas larger ratios produce increasingly concavedown functional forms that better match the experimental data. We plot the normalized monolayer area for each frame of the simulation, producing a graph similar to Figure 5. We can only roughly estimate the intensity of our hydrogen-atom source, and the dose rate of H atoms is also dependent to a large degree on instrumental alignment. As a result, we cannot compare the time axes of the experimental and simulated data directly. To adjust for this, we scale the time (x) axis of the simulation to best fit the experimental data. This process was repeated for each simulation. The results for 91 simulations with reactivity ratios spaced logarithmically between 1 (close-packed and defect sites have identical reactivity) and 8100 as well as a simulation with an infinite ratio (molecules at close-packed sites do not react at all) are plotted in Figure 8. The best match to the shape of the
simulation where molecules located along defect sites are 4500 times more reactive than those in close-packed monolayer areas; molecules are displayed in white, areas of black contain no monolayer, and the original surface defect is shown as the solid line in image a. As the reaction proceeds (Figure 6b−f), we observe features directly comparable to those in the masks of experimental STM images in Figure 2: monolayer erosion along defect sites and in close-packed areas, changing size and shape of pre-existing domain boundaries, and complete monolayer removal over long exposure times. The time dependence of this simulated surface reaction is shown in a single panel in Figure 7, which was generated in the same fashion as the map for experimental data in Figure 4.
Figure 8. Kinetic Monte Carlo simulations of monolayer coverage versus exposure time, compared to the experimental data of Figure 5 (black points). The best fit (dark red) occurs with reactivity ∼4500 times greater at defect sites compared to close-packed sites. Light red curves have edge-to-close-packed reactivity ratios of 500 or greater, while light blue curves have ratios between 1 and 500.
Figure 7. The monolayer area for each image in Figure 6b−f is colorcoded (blue-dark green-green-yellow-white) and presented as in Figure 4. The original domain boundary is shown by the white line.
The variables in the kinetic Monte Carlo simulation are (1) the ratio of reactivity between defect and close-packed sites; (2) the relative rates of annealing and reaction; (3) the annealing temperature; and (4) the size and shape of initial defects used to start simulations. All of these parameters were varied, and we find that, within reasonable bounds, only the first simulation parameterthe relative reaction rate of defect sites versus close-packed siteshas any significant effect on how the total monolayer coverage changes with exposure time. The inclusion of annealing is not necessary to fit the coverage-versus-exposure data; however, the annealing rate affects how the morphology of the unreacted monolayer changes with exposure time. Without any annealing, vacancies grow in a dendritic fashion and extend over the entire surface. This is in contrast to the clustering of vacancies observed in the experimental data and reproduced in simulations performed with annealing; for the simulation in Figure 6, there are approximately 100 annealing steps (not all successful) between each defect-site reaction event. In a similar fashion, simulations with annealing rates 10 times larger than that of Figure 6 result in agglomeration of defects beyond what is observed experimentally but again do not affect the time dependence of monolayer coverage. A 1:1 ratio of defect to nondefect reactivity (molecules near defects are no more likely to react than molecules in close-packed
experimental coverage data is achieved with a ratio of 4500 and shown as a dark red line. Reasonably good fits to experiment result from ratios of 500 or greater (shown in light red), while ratios below 500 (light blue) do not match observation nearly as well. Similar reactivity ratios were required to adequately match additional data sets from other experiments.
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DISCUSSION The key observation in this study is that the monolayer coverage decreases with exposure time in a faster-thanexponential fashion, and the concave-down shape of the coverage-vs-time curve shows that reaction rate accelerates as reaction proceeds. This behavior cannot result from simple kinetics of a single surface species. Acceleration is explained well, however, by an increased reaction rate for molecules near defect sites; as the reaction proceeds, the number of defect sites, and thus the reaction rate, increases. This is borne out by the kinetic Monte Carlo simulations in Figure 8, which reproduce the experimental coverage for greater than 500-fold increases in reactivity for molecules adjacent to monolayer defects. This reaction ratio is the only adjustable parameter in the simulations required to reproduce the experimental dependence of coverage on exposure. 4729
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The inclusion of annealing in the Monte Carlo simulation does not affect coverage versus exposure, but it is necessary to produce calculated images (Figure 6) with morphologies that match those of the experimental data (Figure 2). Annealing is also apparent experimentally in the composite images presented in Figures 3 and 4, which show that the boundaries are fluid between the remaining monolayer and surrounding surface vacancies: small vacancies can anneal out completely, and vacancy defects not only expand but also shift position as reaction occurs. The two important aspects of alkanethiolate monolayer reactivity, therefore, are the following: (1) molecules are hundreds or thousands of times more likely to be removed from the surface when they are adjacent to monolayer defects and (2) the surface that remains is increasingly dynamic, with molecules able to shift position. Both of these are consistent with the reaction mechanism proposed for this system by Gorham et al., which states that hydrogen atoms are able to penetrate through the alkane chain and directly break the sulfur−gold bond for alkanethiol SAMs with medium-length carbon chains.17 For the self-assembled films used in our experiments, then, we expect monolayer removal to occur primarily by hydrogenation of sulfur and desorption of a complete octanethiol molecule. For steric reasons, we expect a moderate increase in sulfur hydrogenation rate for alkanethiolate molecules located at domain boundaries or near substrate steps, as these environments are more likely to expose the sulfur atom to attack from the gas phase. However, it is the second step of the reaction desorption of a newly formed alkanethiol from the surface that we believe is responsible for the very large enhancement of reaction rate observed for molecules near defects or alreadyextant vacancies. We posit that reaction will occur for molecules in close-packed regions at rates many times greater than what is observed but that the alkanethiol created after sulfur hydrogenation will be unable to desorb because of van der Waals interactions with neighbors on all sides. Initially, molecular desorption is only possible along native monolayer defects (domain boundaries and step edges), though continued reaction creates additional sites from which molecules can desorb. Increased molecular mobility, in addition to allowing increased desorption, also explains the structural changes observed during reaction. We have discussed these changes in previous publications,1 and similar features are observed in Figure 1, including domain boundary rearrangement and annealing of domain boundaries into close-packed areas. This can be explained either by molecular diffusion of molecules in low-density alkanethiol phases53−55 or by readsorption of octanethiol that is formed through sulfur hydrogenation but not able to desorb from the surface. In conclusion, we have determined that defect sites in octanethiolate monolayers are the primaryand possibly the solecause of reactivity when the surface is exposed to gasphase hydrogen atoms. While increased access to the sulfur− gold bond by incident hydrogen is one possible cause of increased reactivity, we propose that desorption of the octanethiol molecule formed is the limiting step that essentially does not occur for reaction of molecules within close-packed regions. Alkanethiol or similar surfaces could potentially be hundreds or thousands of times more stable in reactive environments if they could be designed to contain fewer initial defects; conversely, this property can be exploited where quick removal of molecules is desired.
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Present Address †
University of Chicago, Department of Chemistry, Chicago, IL 60637. Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS This work was supported by the National Science Foundation (NSF grants CHE-034857 and CHE-0848415). REFERENCES
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