The Pennsylvania State University. The Graduate School. Department of Chemistry ARTIFICIAL ASSEMBLY OF PRECISE FUNCTIONAL NANOSTRUCTURES.

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1 The Pennsylvania State University The Graduate School Department of Chemistry ARTIFICIAL ASSEMBLY OF PRECISE FUNCTIONAL NANOSTRUCTURES A Thesis in Chemistry by Andrea Nicole Giordano 2010 Andrea Giordano Submitted in Partial Fulfillment of the Requirements for the Degree of Master of Science August 2010

2 ii The thesis of Andrea Giordano was reviewed and approved* by the following: Paul S. Weiss Distinguished Professor of Chemistry & Physics Thesis Advisor Lasse Jensen Assistant Professor of Chemistry Will Noid Assistant Professor of Chemistry Ken Feldmann Professor of Chemistry Graduate Program Head *Signatures are on file in the Graduate School

3 iii ABSTRACT We used a cyrogenic, ultrastable scanning tunneling microscope (STM) to investigate fundamental questions in the field of surface science. We examined the molecular orientations of bicomponent alkanethiolate self-assembled monolayers (SAMs) through simultaneous constantcurrent topographic and local barrier-height imaging, which allowed us to develop a STM-based technique to probe both interfaces concurrently. This enabled us to resolve the controversy in topographic image contrast assignment and to make molecular orientation measurements. The measured molecular orientations were found to be in agreement with previous infrared spectroscopy and grazing incidence X-ray diffraction experiments. For longer-chain highcoverage SAMs, such as octanethiolate/decanethiolate SAMs, the domains presenting a ( 3 3)R30 superstructure in the exposed methyl interface also have a buried thiolate headgroup ( 3 3)R30 structure. For domains containing a c(4 2) overlayer in the exposed interface, a more complex buried structure was observed. We investigated the interactions of thiophene with a deuterated Pd{110} surface. Thiophene-induced microfaceting of a D/Pd{110}-(1 2) surface in the 110 direction by subsurface deuterium was observed. The propagating facets were found to be out of plane with respect to the underlying Pd{110} substrate by 3.2 ± 0.8. The microfacets were formed as a consequence of bulk deuterium diffusing up to the subsurface sites, which caused the surface configuration to change from a (1 2) to a (1 1) structure. We observed that at 4 K, the formation of the microfacets requires the adsorption of thiophene, which lowers the barrier for the population of subsurface sites by bulk deuterium atoms. Conductance spectroscopy revealed the onset voltage to bulk deuterium diffusion to be 0.38 ± 0.02 ev.

4 iv TABLE OF CONTENTS LIST OF FIGURES... v LIST OF TABLES... viii LIST OF ABBREVIATIONS... ix ACKNOWLEDGEMENTS... x Chapter 1 Atomic-Scale Studies of Molecules Using Scanning Tunneling Microscopy Scanning Tunneling Microscopy, Scanning Tunneling Spectroscopy, and Local Barrier-Height Imaging Thesis Overview... 4 Chapter 2 Heads and Tails: Simultaneus Exposed and Buried Interface Imaging of Monolayers Introduction Sample Preparation and Experimental Methods Results and Discussion Achieving the Optimum Tip-State Measuring Molecular Orientations Comparing Molecular Orientations of C6/C8 and C8/C10 Bicomponent SAMs on Au{111} Conclusions Chapter 3 Interactions of Thiophene and Deuterium on Pd{110} Introduction Adsorbate-Induced Microfaceting on D/Pd{110}-(1 2) Introduction Sample Preparation and Experimental Methods Results and Discussion Conclusions Chapter 4 Conclusions and Propsed Future Directions References... 48

5 v LIST OF FIGURES Figure 1-1: Schematic of topographic imaging in STM. Adjustments in the tunneling gap distance in constant-current topographic imaging in mode are depicted by the trajectory of the STM tip (black dashed line) Figure 2-1: Schematic of an octanethiolate (C8) SAM on a Au{111} surface. Black Carbon; White Hydrogen; Purple Sulfur; Yellow--Gold... 8 Figure 2-2: Schematic depicting the unit cells for ( 3 3)R30 (red diamond) and c(4 2) (green rectangle) superstructures on a Au{111} surface. Yellow circles represent the Au atoms and the purple circles represent the S head groups of the alkanethiol SAM. The black diamond shows the unit cell for the Au{111} surface Figure 2-3: Schematic of a C6/C8 bicomponent SAM shows constant-current topographic mode imaging the exposed methyl termini and local barrier height mode imaging of the of buried S-Au interface. The perspective images of a C6/C8 SAM represent simultaneous imaging of the methyl termini in topography (red) and the S- Au interface in LBH (blue) imaging modes (25Å 30Å, V s = 1.2 V, I t = 11 pa) Figure 2-4: Topographic and LBH images of a C6/C8 bicomponent SAM displaying the importance of achieving an optimum tip state. (a) Topographic STM image (26 Å 25 Å, V s = 1.2 V, I t = 11 pa) where the black dots are the assigned to local maxima. (b) Simultaneous LBH STM image acquired with (a). The red dots are the assigned LBH maxima. (c) Topographic STM image (26 Å 25 Å, V s = 0.8 V, I t = 11 pa) in the same area as (a). The change in bias voltage has induced a tip change that images each molecule more sharply. (d) Simultaneous LBH STM image acquired with (c). This image shows additional LBH maxima, with unknown identities. (e) Topographic STM image (37 Å 37 Å, V s = 1.2 V, I t = 11 pa) in an area macroscopically distant from (a)-(d). This image shows the maxima of the C6 molecules are not resolved due to the unfavorable tip state. (f) Simultaneous LBH STM images acquired with (e). This tip state gives a shift in the brighter protrusions and the identity of this shift is unknown. For the purpose of this experiment, we only use data from tips similar to that used to acquire images (a) and (b) Figure 2-5: Topographic STM image (270 Å 270 Å, V s = 1.2 V, I t = 11 pa) of a C7/C9 bicomponent SAM showing two rotational domains containing c(4 2) superstructures. The blue and red squares show high-resolution STM images (both 25 Å 25 Å, V s = 1.2 V, I t = 11 pa) of areas with a few C7 molecules showing their directionality. The top black arrow shows the 11 0 and the direction of the herringbone pattern (indicative of c(4 2) superstructure). The bottom black arrow indicates the direction of the herringbone pattern, which is rotated 60 with respect to the 11 0 direction

6 vi Figure 2-6: Coordinate systems used to make head-to-tail assignments for single alkanethiol molecules. (a) Molecular orientation coordinate system. The polar tilt and azimuthal angles are represented by α and θ, respectively. The surface projection of the shift between the S head group and the methyl terminus of a single alkanethiol molecule is denoted by δ. (b) Coordinate system used to measure and bin δ values. The red and black dots represent the LBH and topographic maxima, respectively. The red circle, X, denotes the origin and the colored circles and letters allow us to categorize the molecular azimuthal directions from X Figure 2-7: Alkanethiolate molecular extremities located and highlighted by digital image processing. (a) Topographic STM image (26 Å 25 Å, V s = 1.2 V, I t = 11 pa) of a C6/C8 SAM. (b) Barrier height STM image acquired simultaneously with a. (c) Topographic STM image (25 Å 30 Å, V s = 1.2 V, I t = 11 pa) of an adjacent rotational domain with respect to a. (d) Barrier height STM image acquired simultaneously with c. (e) Topographic STM image (35 Å 34 Å, V s = 1.2 V, I t = 11 pa) of a macroscopically different area from a-d. (f) Barrier height STM image (35 Å 30 Å, V s = -1.2 V, I t = 10 pa) of a C8/C10 SAM. The black and red dots represent the topographic and LBH local maxima, respectively, acquired simultaneously in a, c, e, and f. Only the LBH maxima are displayed in b and d. This figure exhibits only areas of ( 3 3)R Figure 2-8: Digital imaging processing of C6/C8 bicomponent SAM demonstrating the smoothing function applied using Matlab software. (A) Raw STM topographic image (25 Å 30 Å, V s = 1.2 V, I t = 11 pa). (B) The STM image shown in (A) after performing smoothing in Matlab. (C) Display of the superimposed topographic local maxima from images (A) and (B). The graph to the right compares the blue and red height traces in (A) and (B), respectively. The good agreement between local maxima and the height traces shows that the smoothing function does not alter the position of the maxima or the apparent height differences Figure 3-1: Proposed mechanism for hydrogenation of thiophene. Scheme shows two competing pathways for the reaction to proceed. Adapted from reference [39] Figure 3-2: Schematic of hydrogen migration from the bulk to subsurface sites. The STM tip is utilized to inject electrons into the bulk Pd, exciting the bulk hydrogen. This enables hydrogen to overcome the diffusion barrier and to migrate to the stable subsurface site, directly underneath the topmost Pd atoms Figure 3-3: Pd{110}-(1 2) surface reconstruction induced by deuterium. (a) STM topographic image (V s = 0.01 V; I t = 1.4 na; 22 Å 22 Å) of an atomically resolved Pd{110}-(1 2) surface. Inset shows model (1 2) structure. (b) Apparent height profile acquired along the dashed red line in (a) Figure 3-4: Adsorption of thiophene on D/Pd{110}-(1 2) and on clean Pd{110}-(1 1). (a) STM topographic image (V s = V; I t = 0.2 na; 73 Å 73 Å) of thiophene adsorbed on D/Pd{110}-(1 2) surface at low coverage. This image shows thiophene s two preferred adsorption sites, between paired rows in the troughs and atop the paired rows (denoted by the red arrow). The black arrow indicates surface-

7 vii bound sulfur impurities. (b) STM topographic image (V s = 0.01 V; I t = 0.9 na; 22 Å 22 Å) of an isolated thiophene molecule adsorbed on clean Pd{110}-(1 1). (c) Simultaneously obtained (with (b)) differential conductance image illustrating enhancement of the LDOS of thiophene, where the observed lobes are π * empty states due to imaging at a positive sample bias Figure 3-5: Schematic of Ni{110} surface showing the two proposed adsorption sites for thiophene (red ovals). Due to the symmetry of the crystal, the two adsorption sites are equivalent. The proposed adsorption orientations of thiophene are labeled 1 and 2. Adapted from reference [66] Figure 3-6: Populating subsurface sites with deuterium of Pd{110}. The left STM topographic image (V s = 0.5 V; I t = na; 260 Å 260 Å) was acquired before changing the sample bias voltage to 1 V. After the sample bias voltage was set to 1 V, the tip hovered in the center of the image (its resting position) for 2 minutes. The right STM image shows a diffuse protruding region in the center of the image, where the tip hovered Figure 3-7: A series of sequential topographic STM images (V s = 1.0 V; I t = 0.05 na; 260 Å 260 Å) that shows the evolution of the microfacets along the 11 0 direction. Frame 0 shows some protrusions in the center of the image due to the STM tip resting for <10 ms before and between frame acquisitions. By frame 30, the subsurface sites have been populated by deuterium and the facets propagated in the direction of the Pd{110} substrate Figure 3-8: Determining the onset voltage required to populate the subsurface sites with deuterium in the presence of thiophene. (a) STM topographic (derivative) image (V s = 0.05 V; I t = 0.05 na; 348 Å 348 Å) demonstrating our ability to create areas of microfacets locally (β region), while not disturbing the (1 2) reconstruction (α area). (b) Topographic STM image (V s = 0.05 V; I t = 0.05 na; 260 Å 260 Å) of region β in (a). This image was plane-subtracted to show that the out-of-plane angles are self-consistent. The high-resolution STM topographic image inset (V s = 0.01 V; I t = 1.4 na; 22 Å 22 Å) was acquired over the area in (b) denoted by a red dashed box. The inset resolves the Pd atoms in the (1 1) structure, indicating a thiophene-induced reconstruction. In both images (a) and (b), the protrusions are adsorbed thiophene molecules. (c) A typical I(V) spectrum acquired over the α region in (a) (V gap = 0.05 V; I gap = 0.05 na). The forward sweep from negative to positive bias voltage is shown in red, and the reverse sweep from positive to negative bias voltage is shown in blue. The black dashed vertical line at 0.38 ev represents the onset voltage required for bulk deuterium to diffuse to the subsurfaces sites. The onset voltage value (0.38 ± 0.02 ev) was determined from the average of 45 forward spectra. (d) Conductance spectra acquired over the (1 1) region of the inset of (b). The forward and reverse sweeps completely overlap indicating that microfaceting is complete in this area. The features at ca. ±0.045 ev were observed in the reverse sweep (blue) in (c), and were attributed to the surface electronic state of the Pd{110} substrate

8 viii LIST OF TABLES Table 2-1: Molecular orientation measurements for Figures 2.7a and 2.7c. Each value is an average of every measurement in the same azimuthal direction according to the coordinate system in Figure 2.6b. The red boxes denote the assigned orientation direction. Standard deviations are shown where possible and α values are measured with respect to the horizontal direction Table 2-2: Total number of δ measurements used to obtain the standard deviation values in Table Table 2-3: Molecular orientation measurements for Figures 2.7e and 2.7f. Each value is an average of every measurement in the same azimuthal direction according to the coordinate system in Figure 2.6b. The red boxes denote the assigned orientation direction. Standard deviations are shown where possible and α values are measured with respect to the horizontal direction Table 2-4: Comparison between assigned molecular orientations for C6/C8 and C8/C10 bicomponent SAMs. Standard deviations are shown where possible. The α values are measured with respect to the Au{111} direction... 27

9 ix LIST OF ABBREVIATIONS AC C1 C4 C6 C7 C8 C9 C10 DFT di/dv GIXD IR I/V LBH LDOS NIXSW SAM STM STS TPD Alternating current Methylthiolate Butanethiolate Hexanethiolate Heptanethiolate Octanethiolate Nonanethiolate Decanethiolate Density functional theory Differential conductance spectroscopy Grazing incidence X-ray diffraction Infrared spectroscopy Conductance spectroscopy Local barrier-height Local density of states Normal incidence X-ray standing waves Self-assembled monolayer Scanning tunneling microscopy Scanning tunneling spectroscopy Temperature programmed desorption

10 x ACKNOWLEDGEMENTS It is a pleasure to thank the many people who make this thesis possible. I would like to begin by thanking Professor Paul S. Weiss for giving me the opportunity to work in his lab. I am grateful to my advisor for his understanding and encouragement during my decision to switch out of the field of surface science. His scientific perspective and inspiration have been of great value for me. I would also like to thank my thesis committee, Professors Lasse Jensen and Will Noid, for their scientific insights and advice. I am grateful for the support provided by The National Science Foundation ( ), U.S. Department of Energy (DE-FG02-08ER46546), and The Petroleum Research Fund American Chemical Society (47099-AC5). In addition, I am grateful for the Robertson Award from The Pennsylvania State University Chemistry Department. I am indebted to many Weiss group members for providing a stimulating and fun environment in which to learn and grow. I would like to thank Adam Kurland, Patrick Han, John C. Thomas, and Meaghan Blake, who have been consistently giving me helpful advice whenever I need it. I would also like to thank my undergraduate advisor, Professor Jordan Poler, and friend, Professor Harsh Chaturvedi, for all their insightful discussions and advice during my academic career. I especially wish to thank my parents, who raised me, supported me, taught me, and loved me. To them I dedicate this thesis.

11 1 Chapter 1 Atomic-Scale Studies of Molecules Using Scanning Tunneling Microscopy 1.1 Scanning Tunneling Microscopy, Scanning Tunneling Spectroscopy, and Local Barrier-Height Imaging The advent of scanning tunneling microscopy (STM) in 1981 by Binnig and Rohrer gave scientists a real-space atomic-scale view of surfaces and revolutionized the field of surface science [1]. This technique has provided atomically resolved surface images, catalytic surface reaction observations, single-adsorbate manipulation, and the capability of single-molecule spectroscopic measurements [2-4]. Scanning tunneling microscopy s sensitivity to surface features will be utilized in this thesis to gain fundamental insight into two systems: bicomponent alkanethiolate self-assembled monolayers (SAMs), and thiophene on deuterated Pd{110}. Scanning tunneling microscopy exploits the quantum mechanical phenomenon of electron tunneling through a barrier (vacuum or air) when a voltage bias is applied between the surface and a proximate STM tip. This measures a convolution of the topographic and electronic structure of the surface. Topography is typically acquired in constant-current imaging mode, where the feedback loop is used to adjust the tunneling gap distance, in order to maintain a constant current within the tunneling junction (Figure 1-1). Adjustments in the tunneling gap distances are a consequence of the exponential dependence of the tunneling current (I) on the

12 Figure 1-1: Schematic of topographic imaging in STM. Adjustments in the tunneling gap distance in constant-current topographic imaging in mode are depicted by the trajectory of the STM tip (black dashed line). 2

13 3 tunneling gap distance (z) as indicated by Equation 1 [1, 5]. This enables STM to resolve apparent height differences between adsorbates on the surface or between different adsorbates. Below is the generalized tunneling equation, where Κ is the decay constant, φ is the effective local potential barrier height, m is the mass of an electron, and ħ is the reduced Planck s constant [1]. I e 2Κz (1) Κ = (2mϕ)1/ 2 ϕ = 2 d lni 8m dz 2 (2) (3) In addition, electronic information can be acquired by scanning tunneling spectroscopy (STS), which includes conductance spectroscopy (I/V) and differential conductance spectroscopy (di/dv). In di/dv spectroscopy, a sinusoidal modulation is applied to the bias voltage by the lockin amplifier. When the modulated current signal returns back to the lock-in amplifier, it is compared with a sinusoidal reference signal to extract the first harmonic frequency of the current signal. The first harmonic of the current signal corresponds to di/dv, which reveals information about the local density of states (LDOS) of the sample. Topography and STS were used to probe adsorbates, including thiophene and deuterium, interacting with a Pd{110} surface, which is discussed in Chapter 3. Local barrier-height (LBH) imaging is another capability of STM. This technique measures the local barrier for an electron to be ejected from the adsorbate. The LBH (φ) is proportional to the square of the total derivative of the natural log of the current signal with respect to the tunneling gap distance (dlni/dz) as shown in Equation 3. Following Equation 2, the decay constant (Κ) for an electron to cross the local barrier depends on φ, and thus on the tunneling current from Equation 1. The magnitude of the LBH can be measured directly by

14 4 modulating the tunneling gap distance. A small AC modulation of the tunneling gap distance at a frequency of khz results in a change in the tunneling gap distance by Å. By monitoring the change in the current with respect to the modulation of the tunneling gap distance, it is possible to image buried interfaces with the correct imaging conditions. In this thesis, we used LBH imaging to probe the interfaces of alkanethiolate self-assembled monolayers (SAMs), and addressed the controversy of contrast assignment in STM topographic images of SAMs in Chapter 2. Our STM experiments were carried out at cryogenic temperatures (4 K), which provided three key advantages. First, the low temperature reduced the amount of thermal drift between the surface and the tip, resulting in maximum control of the STM tip. This capability is essential for precise spectroscopic measurements over a point location, and for single molecule or atom manipulation. In addition, the narrowing of the electron distribution of both the tip and surface at low temperatures greatly enhances the imaging, as well as spectroscopic resolutions. Finally, most thermally-activated diffusion is quenched at 4 K, which enabled us to perform experiments on isolated adsorbates. 1.2 Thesis Overview The research presented in this thesis was performed using a cyrogenic, ultrastable STM to investigate fundamental questions in the field of surface science [6]. In Chapter 2, we examine the molecular orientations of bicomponent alkanethiolate SAMs through simultaneous constantcurrent topographic and LBH imaging. The molecular orientation measurements were in good agreement with previous infrared and grazing incidence X-ray diffraction experiments [7-9]. The contrast assignment of topographic images of SAMs is also addressed.

15 5 Investigations into the interactions of thiophene with a deuterated Pd{110} surface is discussed in Chapter 3. Deposition of deuterium, followed by thiophene molecules, on Pd{110} leads to an adsorbate-induced microfaceting of the surface from a (1 2) to a (1 1) reconstruction. These observations provide insight into the interaction of thiophene with Pd{110}, which can ultimately be used for mechanism determination and catalyst design. Chapter 4 provides conclusions from the individual chapters and future experimental directions are outlined.

16 6 Chapter 2 Heads and Tails: Simultaneous Exposed and Buried Interface Imaging of Monolayers 2.1 Introduction Self-assembled monolayers of alkanethiols are intensely studied for their potential applications in molecular electronics, biosensors, and nanofabrication [10, 11]. Alkanethiolate SAMs on Au{111} are the most studied family of SAMs, but there are many structural and functional group variations [12]. Fundamental issues, however, need to be addressed in this system before SAMs are employed in the aforementioned potential technologies [10-15]. For example, the high-coverage self-assembly of simple linear alkanethiol molecules on Au{111} surfaces involves a multitude of more complex stages such as lifting of the (22 3) Au reconstruction, upright molecular alignment at specific orientations, and the formation of both the ( 3 3)R30 and c(4 2) superstructures in neighboring domains [14]. Fundamental questions, such as why more than one superstructure forms and what happens to the additional Au atoms after assembly, remain to be understood [15-18]. Alkanethiolate SAMs on Au{111} form by spontaneous chemisorption of the sulfur head-group on surface Au atoms as shown in Figure 2-1 [12]. Investigations of adsorption kinetics by second-harmonic generation, x-ray photoelectron spectroscopy, and near edge x-ray absorption fine structure studies revealed a two-step mechanism for the formation of alkanethiolate SAMs [19-21]. The initial adsorption step occurs within fractions of a second to minutes and is kinetically driven [22]. The second step is surface crystallization, in which the

17 7 alkanethiol molecules reach their final tilt structure, forming a two-dimensional crystal [12]. The driving force for this assembly is both thermodynamic and kinetic, utilizing the strength of the S-Au bond (40 kcal/mol) and the favorable van der Waals interactions between the methylene groups of the alkanethiol molecules [23]. Full monolayers of long-chain alkanethiolate SAMs on Au{111} form domains of ( 3 3)R30 and c(4 2) superstructures, where the ( 3 3)R30 structure is dominant for shorter alkanethiols ( n 10 carbons) [24-26]. The unit cells for both superstructures are shown in Figure 2-2. Multi-component SAMs can be achieved through coadsorption of two or more adsorbates, and will be employed in the STM experiments discussed below. Changing the terminal functional group, alkyl chain length, or internal functional group of the alkanethiol molecule leads to variation in the overall film morphology and interfacial properties [12]. Ensemble techniques, such as normal incidence X-ray standing waves (NIXSW) and grazing incidence X-ray diffraction (GIXD), have been employed to investigate whether a monoor dithiolate species predominates for various chain lengths in SAMs on Au{111} [16, 18, 27, 28]. Based on NIXSW predictions, Yu et al. hypothesized that the number of sulfur atoms bound to a Au adatom could be correlated with the observation of two superstructures in neighboring domains [18]. The current consensus regarding the S-Au interface in SAMs involves a S-bound- Au adatom species [29, 30]. There is strong experimental evidence for the formation of Au adatom-dithiolate species for low coverage of short chain alkanethiols (n 4 carbons) [28-30]. For high-coverage systems, the NIXSW and GIXD techniques give inconsistent results due to the coexistence of ( 3 3)R30 and c(4 2) superstructures across the measurement area [15]. Grazing incidence X-ray diffraction coupled with density functional theory (DFT) simulations predict a Au adatom-dithiolate species for methylthiolate (C1) and hexanethiolate (C6) in both the ( 3 3)R30 and c(4 2) overlayers [16]. In contrast, NIXSW data detects a Au adatom-

18 8 Figure 2-1: Schematic of an octanethiolate (C8) SAM on a Au{111} surface. Black Carbon; White Hydrogen; Purple Sulfur; Yellow Gold.

19 Figure 2-2: Schematic depicting the unit cells for ( 3 3)R30 (red diamond) and c(4 2) (green rectangle) superstructures on a Au{111} surface. Yellow circles represent the Au atoms and the purple circles represent the S head groups of the alkanethiol SAM. The black diamond shows the unit cell for the Au{111} surface. 9

20 10 monothiolate species for C1, butanethiolate (C4), C6, and octanethiolate (C8) in both the ( 3 3)R30 and c(4 2) superstructures [18, 27]. The discrepancy between X-ray experiments is attributed to the ensemble nature of these techniques. Thus, the application of a single-molecule technique, such as STM, can elucidate the S-Au lattice for high-coverage SAMs. To utilize STM for this type of experiment, the controversy over contrast interpretation of topographic STM images of SAMs must first be resolved. Experimental evidence supporting STM s sensitivity to imaging the exposed methyl termini was demonstrated by resolving the apparent height difference in bicomponent SAMs [31, 32]. Earlier STM work suggested the imaged interface to be the buried S-Au interface, using perturbative tunneling conditions that induced degradation of the crystallinity of the SAM [33, 34]. Other reports in the literature suggest STM s sensitivity to either interface is tip-dependent [32, 35]. In this chapter, we addressed the image contrast controversy enabling STM to be used for direct measurement of the buried S-Au interface. We used a low-temperature (4 K), ultrastable STM to study both the exposed methyl termini and the buried S-Au interface by simultaneously imaging in constant- current topographic mode and local barrier height (LBH) imaging mode (described in Section 1.1) [6]. The STM tip state was controlled through in situ voltage pulses, achieving the desired tip state, in which topography images the methyl termini and, LBH images the S-Au interface, as shown in Figure 2-3 [36]. Bicomponent SAMs of alkanethiols of different chain lengths were used to determine molecular orientations of the alkanethiolates, due to their apparent height differences, enabling us to monitor the STM tip state. These results were compared with results previously obtained infrared spectroscopy (IR) and GIXD values [7-9]. Data collected from a C8/ decanethiolate (C10) bicomponent SAM reveals that domains of ( 3 3)R30

21 11 Figure 2-3: Schematic of a C6/C8 bicomponent SAM shows constant-current topographic mode imaging the exposed methyl termini and local barrier height mode imaging of the of buried S-Au interface. The perspective images of a C6/C8 SAM represent simultaneous imaging of the methyl termini in topography (red) and the S-Au interface in LBH (blue) imaging modes (25Å 30Å, V s = 1.2 V, I t = 11 pa).

22 12 superstructures exhibit the same ( 3 3)R30 lattice structure for the buried S-Au interface, but domains of c(4 2) supersturecture exhibit a more complex buried interface. 2.2 Sample Preparation and Experimental Methods The Au{111} substrate (Agilent Technology, Tempe, AZ) was hydrogen-flame-annealed prior to SAM preparation to remove any organic material and anneal terraces. The Au{111} substrates were immersed in 1 mm alkanethiol (Sigma-Aldrich, St. Louis, MO) solution for 24 hours at room temperature. The sample was removed from solution and rinsed with room temperature ethanol (Pharmco, Brookfield, CT) before being dried with high purity argon gas. The SAM was then introduced into the ultrahigh vacuum chamber. Bicomponent SAMs were prepared through codeposition of C6/C8, heptanethiol (C7)/nonanethiol (C9), and C8/C10 in a 1:9 mole ratio. The presence of the shorter alkanethiolate species in the bicomponent SAMs introduces an important structural effect: due to the polar tilt in SAMs, the methyl termini of the shorter molecules are constrained for lateral shifts relative to the methyl termini from the surrounding molecules (Figure 2-3). This lateral shift enables us to monitor the STM tip state and to assign molecular orientations (polar tilt and azimuthal angles) from the local maxima. A custom-built, Besoke-style, low-temperature, extreme high vacuum STM was employed for all topographic and LBH measurements [6]. Simultaneous constant-current topographic and LBH images were acquired at a current set point of 11 pa and a sample bias of +1.2 V. A Pt/Ir STM tip was cut under ambient conditions and prepared in situ with voltage pulses. All LBH images are obtained through the application of a small AC modulation of the tunneling gap distance, with amplitudes of Å and frequencies of khz. The

23 13 derivative of the modulated current signal is measured with a lock-in amplifier (Sanford Research Systems SR850 DSP, Sunnyvale, CA). Molecular orientation measurements were conducted by applying an automated digital image processing routine to all STM images. This routine was developed in Matlab R2008b (The Math-Works, Natick, MA) to remove intensity peaks and high-frequency noise from images that could impair our ability to pick local maxima reliably. Our STM data were collected by rastering (pixel by pixel), therefore the raw data were represented in pixel values. A matrixsmoothing algorithm was applied to the raw data to transform then into an n n intensity map. This algorithm applies a nonweighted moving average to every line in the horizontal direction and every row in the vertical direction. After application of the smoothing function, a second algorithm, localmaximum, was utilized to locate and to index local maxima across the image matrix. These data analysis methods were repeated for each set of topographic and LBH data, and the maxima from both modes were superimposed for molecular orientation measurement. 2.3 Results and Discussion Achieving the Optimum Tip-State An optimum STM tip for these experiments is one that simultaneously images the exposed methyl termini in topographic mode and the buried S-Au interface in LBH mode. The ( 3 3)R30 phase of a C6/C8 SAM imaged in Figure 2-3 shows an optimum STM tip, where a topographic image (red) resolves both the apparent height difference and lateral shift in the exposed methyl termini lattice. The LBH imaging mode (blue) shows a periodic structure with no lateral shifts, which is consistent with imaging the buried S-Au interface based on previous

24 14 Figure 2-4: Topographic and LBH images of a C6/C8 bicomponent SAM displaying the importance of achieving an optimum tip state. (a) Topographic STM image (26 Å 25 Å, Vs = 1.2 V, It = 11 pa) where the black dots are the assigned to local maxima. (b) Simultaneous LBH STM image acquired with (a). The red dots are the assigned LBH maxima. (c) Topographic STM image (26 Å 25 Å, Vs = 0.8 V, It = 11 pa) in the same area as (a). The change in bias voltage has induced a tip change that images each molecule more sharply. (d) Simultaneous LBH STM image acquired with (c). This image shows additional LBH maxima, with unknown identities. (e) Topographic STM image (37 Å 37 Å, Vs = 1.2 V, It = 11 pa) in an area macroscopically distant from (a)-(d). This image shows the maxima of the C6 molecules are not resolved due to the unfavorable tip state. (f) Simultaneous LBH STM images acquired with (e). This tip state gives a shift in the brighter protrusions and the identity of this shift is unknown. For the purpose of this experiment, we only use data from tips similar to that used to acquire images (a) and (b).

25 15 NIXSW measurements [27]. The desired tip state was characterized by comparing of the number of local maxima in both topographic and LBH images. Only images that exhibited an equal number of maxima in both imaging modes were used in the analysis, as shown in Figure 2-4, where the black and red dots represent the topographic and LBH local maxima, respectively Measuring Molecular Orientations Molecular orientations of alkanethiolates in bicomponent SAMs were determined through simultaneous imaging in topographic and LBH modes in order to locate the exposed and buried interfaces. Areas with neighboring rotational domains, as shown in Figure 2-5, were selected to test whether the observed lateral shifts of the topographic maxima are a consequence of differing molecular orientations between rotational domains. The C7/C9 bicomponent SAM in Figure 2-5 shows two c(4 2) rotational domains, evidenced by the observed 60 rotation in the herringbone pattern. This 60 rotation arises from the three-fold symmetry of alkanethiolate SAMs on Au{111} [37]. The lateral shifts observed in the topographic maxima of the isolated C7 molecules shows the corresponding directionality of the lattice (insets of Figure 2-5). This is consistent with the observed rotational domains developing from different molecular orientations of the alkanethiol molecules. The 60 rotation between domains produces a structural effect that enables us to test the validity of our molecular orientation measurements; we expect the measured azimuthal angles (defined in Figure 2-6a) between neighboring rotational domains to exist in multiples of 60. The coordinate system developed to describe the molecular orientations of alkanethiols is shown in Figure 2-6a. The azimuthal and polar angles are denoted by α and θ, respectively, and δ denotes the surface projection of the shift between the Au-bound S and the methyl terminus of a single alkanethiol molecule. For a complete description of the molecular orientation, an

26 Figure 2-5: Topographic STM image (270 Å 270 Å, V s = 1.2 V, I t = 11 pa) of a C7/C9 bicomponent SAM showing two rotational domains containing c(4 2) superstructures. The blue and red squares show high-resolution STM images (both 25 Å 25 Å, V s = 1.2 V, I t = 11 pa) of areas with a few C7 molecules showing their directionality. The top black arrow shows the 11 0 and the direction of the herringbone pattern (indicative of c(4 2) superstructure). The bottom black arrow indicates the direction of the herringbone pattern, which is rotated 60 with respect to the 11 0 direction.

27 17 a b Figure 2-6: Coordinate systems used to make head-to-tail assignments for single alkanethiol molecules. (a) Molecular orientation coordinate system. The polar tilt and azimuthal angles are represented by α and θ, respectively. The surface projection of the shift between the S head group and the methyl terminus of a single alkanethiol molecule is denoted by δ. (b) Coordinate system used to measure and bin δ values. The red and black dots represent the LBH and topographic maxima, respectively. The red circle, X, denotes the origin and the colored circles and letters allow us to categorize the molecular azimuthal directions from X.

28 18 additional angle, the axial twist angle, is required. We do not address this quantity here due to the nature of our method, which only measures the molecular extremities (α, θ, and δ), and not the internal configuration of the alkanethiols. Due to the insensitivity of our technique to the axial twist angle, we exclude areas that contain c(4 2) superstructures from orientation measurements. This is a consequence of different possible molecular twists orientations and the complex S-Au configuration, and leads to complicated data interpretation [16, 18]. Additionally, the topographic image contrast of c(4 2) superstructures is highly sensitive to the tunneling gap conditions [38]. This leads to our inability to locate the local maxima over c(4 2) domains consistently. Thus, we only analyzed data for ( 3 3)R30 superstructure domains. Simultaneous acquisition of topographic and LBH images yields two sets of local maxima that can be superimposed on the topographic image for data interpretation (Figure 2-7a). We assign the local maxima of the topographic imaging mode to be the positions of the methyl termini (black dots in figures) and local maxima assigned in LBH imaging mode to be the positions of the sulfur head-groups (red dots in figures). As exemplified by the black and red dots in Figure 2-7a, superimposing the two sets of local maxima does not straightforwardly reveal each thiolate s corresponding methyl terminus. The method used make the head-to-tail assignments is described by the coordinate system shown in Figure 2-6b. To make molecular head-to-tail assignments, the surface projection (δ) can be measured by anchoring the red dot of the molecule of interest (position X in Figure 2-6b) as the origin and measuring every distance between the black dot and its nearest neighbors, next-nearest neighbors, and next-next-nearest neighbors (represented by blue, black, and green circles, respectively in Figure 2-6b). The distance from every red maximum to every black maximum was measured, averaged, and binned by direction using the lettered directions shown in the coordinate system.

29 19 Figure 2-7: Alkanethiolate molecular extremities located and highlighted by digital image processing. (a) Topographic STM image (26 Å 25 Å, Vs = 1.2 V, It = 11 pa) of a C6/C8 SAM. (b) Barrier height STM image acquired simultaneously with a. (c) Topographic STM image (25 Å 30 Å, Vs = 1.2 V, It = 11 pa) of an adjacent rotational domain with respect to a. (d) Barrier height STM image acquired simultaneously with c. (e) Topographic STM image (35 Å 34 Å, Vs = 1.2 V, It = 11 pa) of a macroscopically different area from a-d. (f) Barrier height STM image (35 Å 30 Å, Vs = -1.2 V, It = 10 pa) of a C8/C10 SAM. The black and red dots represent the topographic and LBH local maxima, respectively, acquired simultaneously in a, c, e, and f. Only the LBH maxima are displayed in b and d. This figure exhibits only areas of ( 3 3)R30.

30 20 Figure 2-8: Digital imaging processing of C6/C8 bicomponent SAM demonstrating the smoothing function applied using Matlab software. (A) Raw STM topographic image (25 Å 30 Å, V s = 1.2 V, I t = 11 pa). (B) The STM image shown in (A) after performing smoothing in Matlab. (C) Display of the superimposed topographic local maxima from images (A) and (B). The graph to the right compares the blue and red height traces in (A) and (B), respectively. The good agreement between local maxima and the height traces shows that the smoothing function does not alter the position of the maxima or the apparent height differences.

31 21 After simultaneous acquisition of topography and LBH of a bicomponent SAM in areas of ( 3 3)R30 superstructures with adjacent rotational domains, we used a digital image processing routine to assign the local maxima (Figure 2-8). Matlab software was used to smooth, apply drift correction, and select local maxima in both the topographic and LBH images. The smoothing process applied a moving average to each row and column of the raw image to filter the data without altering the apparent height differences between alkanethiolates (shown in Figure 2-8d). The stability of our instrument at 4 K minimizes the amount of thermal drift during an experiment (typical LBH image acquired in ~15 min) but a drift correction was applied to compensate for residual drift and non-orthogonalities of the scanner tube. The molecular orientation measurements and digital image processing were performed on C6/C8 and C8/C10 bicomponent SAMs on Au{111} and the results are discussed below Comparing Molecular Orientations of C6/C8 and C8/C10 Bicomponent SAMs on Au{111} Three criteria were employed to make molecular orientation assignments: (1) the polar tilt (θ) and azimuthal angles (α) must be consistent between the corresponding C6 and C8 alkanethiolates; (2) the ratio of measured surface projections (δ C8 /δ C6 ) must be in good agreement with the ratio between the molecular chain lengths (l C8 /l C6 ); and (3) the resulting assignment of the molecular orientation must be consistent with the shift in the maximum of the shorter alkanethiolate imaged in topographic mode. These criteria were used to select the correct molecular orientation for C6/C8 and C8/C10 bicomponent SAMs. It was assumed that the molecular orientations of the shorter and longer alkanethiolates in the same rotational domain were identical. Figure 2-7 displays the topographic and LBH images for C6/C8 (Figure 2-7 a-d) and C8/C10 (Figure 2-7 e-f) bicomponent SAMs.

32 22 Table 2-1 presents the measured θ, δ, and α values determined and categorized by the binning system described in Section The top half of Table 2-1 lists the data for a C6/C8 bicomponent SAM shown in Figure 2-7a, where directions b, g, and q are plausible based on the close agreement of the ratio of δ C8 /δ C6 with the ratio of l C8 /l C6. When considering the polar tilt angle (θ), direction b can be eliminated due to the fact that θ = 16 ± 2, which is inconsistent with the experimentally accepted range of 28 < θ < 40 [7-9]. Analysis of Figure 2-7a does not allow immediate elimination of either direction g or q, but direction g has a better δ C8 /δ C6 agreement with l C8 /l C6, therefore direction g was assigned to be the correct molecular orientation. The bottom half of Table 2-1 corresponds to the measurements performed on data in Figure 2-7c, which is a rotational domain adjacent to the area imaged in Figure 2-7a. The plausible directions based on agreement between the ratios δ C8 /δ C6 and l C8 /l C6 are directions a and b, but both can be eliminated due to their small polar tilt angle values. The next best directions with reasonable δ C8 /δ C6 ratios are directions i and k. While direction g in Figure 2-7a shows very good agreement between δ C8 /δ C6 and l C8 /l C6, directions i and k in Figure 2-7c show a larger δ C8 /δ C6 deviation from l C8 /l C6. We believe a slight thermal drift caused this during data acquisition of Figure 2-7c, in the direction parallel to the tilt direction. This is evident from the vertical stretch of the figure. In effect, this thermal drift caused some data loss for our tilt measurement. Direction k can be eliminated for its inconsistent azimuthal angle with respect to the rest of the lattice in Figure 2-7c. Thus, direction i remains the only as the possible direction for the molecular orientation in this C6/C8 bicomponent SAM. The standard deviations associated with the α, θ, and δ measurements in Table 2-1 were calculated using the total number of δ measurements obtained (tabulated by direction in Table 2-2). Measurements over adjacent rotational domains of the C6/C8 SAM yield identical polar tilt angle values (33 ± 1 for Figure 2-8a and 32 ± 2 for Figure 2-8c) within experimental error.

33 Table 2-1: Molecular orientation measurements for Figures 2-7a and 2-7c. Each value is an average of every measurement in the same azimuthal direction according to the coordinate system in Figure 2-6b. The red boxes denote the assigned orientation direction. Standard deviations are shown where possible and α values are measured with respect to the horizontal direction. 23

34 24 Table 2-2: Total number of δ measurements used to obtain the standard deviation values in Table 2-1.

35 25 The measured azimuthal angles in both rotational domains show that the domains are out of phase by 65 ± 7, in agreement with the previously observed 60 rotation between domains in Figure 2-5. This result enables us to conclude that simultaneous topographic and LBH imaging probes the exposed methyl termini and the buried thiolate head-groups, respectively. Another molecular orientation measurement of the C6/C8 SAM was made in a region macroscopically distant (Figure 2-7e) from the areas imaged in Figure 2-7 a-d. The top half of Table 2-3 shows the molecular orientation measurements made, and the selection process described previously was completed. Direction q was assigned as the molecular orientation for this region of the C6/C8 SAM. Direction q has a much larger θ value (41 ± 3 ) than the neighboring rotational domains (33 ± 1 and 32 ± 2 ). This result indicates that there are significant variations over distant regions of the same SAM, but all results fall within the experimentally accepted range for θ [7-9]. Figure 2-7f shows the LBH image with local maxima for a C8/C10 bicomponent SAM. The lower half of Table 2-3 presents the molecular orientation measurements, where direction i was assigned to be the correct orientation based on our criteria for orientation assignment. The measured molecular orientations for different regions of C6/C8 and C8/C10 SAMs are summarized in Table 2-4. The polar tilt angle for all systems studied yields θ values in good agreement with experimentally accepted values observed by IR and GIXD techniques [7-9, 25]. The measured azimuthal angles for various areas within the same SAM and for different bicomponent SAMs are found to be similar, with all α < 10 with respect to the Au direction. This result contradicts previously reported GIXD data, in which Fenter et al. observed an alkyl chain length dependence of the azimuthal orientation angle, where α C8 > 15 with respect to the Au 110 direction [9]. It should be noted that the alkyl chain lengths for C8 and C10

36 Table 2.3. Molecular orientation measurements for Figures 2-7e and 2-7f. Each value is an average of every measurement in the same azimuthal direction according to the coordinate system in Figure 2-6b. The red boxes denote the assigned orientation direction. Standard deviations are shown where possible and α values are measured with respect to the horizontal direction. 26

37 27 Table 2-4. Comparison between assigned molecular orientations for C6/C8 and C8/C10 bicomponent SAMs. Standard deviations are shown where possible. The α values are measured with respect to the Au{111} 1 10 direction.

38 28 alkanethiolates are in the intermediate chain length regime, leading to a delicate balance between intermolecular interactions and thiolate head group-substrate interactions [10]. Slight changes in these interactions can give different molecular orientations, making alkanethiolates in this intermediate regime less predictable [10]. For determination of the specific molecular orientation for alkanethiolates in the intermediate alkyl chain length regime, such as the C8/C10 SAM, more statistically significant analysis is necessary. 2.4 Conclusions The employment of dual imaging mode STM facilitated molecular orientation measurements of alkanethiol molecules in bicomponent SAMs, by locating the extremities of each molecule. Simultaneous imaging in constant-current topographic and LBH modes allowed us to develop a STM-based technique probing both interfaces concurrently. This enabled us to resolve the controversy in image contrast assignment that had previously hindered STM from answering fundamental questions regarding the structure of an alkanethiolate SAMs on Au{111}. The validity of our method for determining molecular orientation of alkanethiol molecules in a bicomponent SAM was assessed by comparing local-orientation measurements with ensemble orientation measurements previously observed in IR and GIXD experiments [7-9]. Our measurements show that for longer-chain high-coverage SAMs, such as C8/C10 SAMs, the domains presenting a ( 3 3)R30 superstructure in the exposed methyl interface also have a buried thiolate head-group ( 3 3)R30 structure. For domains containing a c(4 2) overlayer in the exposed interface, a more complex buried structure is observed. This is consistent with predictions by Yu et al. based on NIXSW observations [18]. Utilizing simultaneous LBH imaging mode with constant-current topographic imaging mode to probe both

39 the buried and exposed interfaces in alkanethiolate SAMs adds a third dimension to STM s sensitivity to this system and offers a solution for studying problems of greater complexity. 29

40 30 Chapter 3 Interactions of Thiophene and Deuterium on Pd{110} 1.1 Introduction A fundamental understanding of the mechanisms involved in heterogeneous catalysis is critical for optimizing significant industrial catalytic reactions such as hydrogenation. To date, the isolation of hydrogenation intermediates of aromatic heterocycles model compounds due to their stabilizing π-ring system has not been accomplished, and thus the actual mechanism remains unknown [39]. The current proposed mechanisms for the hydrogenation of thiophene stem from temperature-programmed desorption (TPD) studies, which monitored the reactants and products but not the intermediates of the reaction [39]. Pd-catalyzed hydrogenation of aromatic heterocycles, such as thiophene, is hypothesized to occur via reaction with subsurface hydrogen, since surface hydrogen is strongly chemisorbed and thus unavailable for reaction [40]. Theoretical calculations predict a charge transfer between the subsurface hydrogen and the topmost Pd atom, creating a subsurface hydride, which has been experimentally isolated using differential conductance STM measurements [41-43]. The overall goal of these latter experiments is to elucidate the mechanism for thiophene hydrogenation by identifying the reaction intermediates. The proposed thiophene hydrogenation mechanisms, determined by TPD, are shown in Figure 3-1. The hydrogenation of thiophene to 1,3-butadiene has two competing pathways. The top scheme indicates hydrogen addition to the 1,5 position on the ring, followed by the breaking

41 Figure 3-1: Proposed mechanism for hydrogenation of thiophene. Scheme shows two competing pathways for the reaction to proceed. Adapted from reference [39]. 31

42 32 of the C-S bonds, while the bottom scheme alludes to breaking the C-S bonds first, then hydrogen addition to the adsorbed butadiene fragment. To determine the dominant mechanism, a technique that can observe the intermediates of the reaction is required. This method must be a local probe as opposed to an ensemble technique such as TPD, photoelectron spectroscopy, or infrared spectroscopy. These latter techniques give an average measurement of the surface environment, which provide a convolution of reactants, intermediates, and products on the surface. Scanning tunneling microscopy is a local probe with the capabilities of topographic imaging and STS. In addition, STM can isolate and differentiate between the intermediates formed, thereby, facilitating mechanism determination. Previously, our group has observed and manipulated subsurface hydride with STM [42, 43]. We found that by injecting electrons from the STM tip to the surface, the bulk hydrogen is sufficiently excited to overcome the diffusion barrier to move and ultimately to reach a stable subsurface site. In so doing, we selectively excited bulk hydrogen to subsurface sites, as shown in Figure 3-2 [42, 43]. In this chapter, we discuss preliminary experiments conducted to elucidate the mechanism of hydrogenation by subsurface deuterium. Specifically, this chapter discusses the observation of thiophene-induced microfaceting of a deuterium-covered Pd{110} surface. This experiment reflects the multitude of events occurring at the surface of this system and reveals the complexity of surface-catalyzed hydrogenation reactions by subsurface hyride.

43 Figure 3-2: Schematic of hydrogen migration from the bulk to subsurface sites. The STM tip is utilized to inject electrons into the bulk Pd, exciting the bulk hydrogen. This enables hydrogen to overcome the diffusion barrier and to migrate to the stable subsurface site, directly underneath the topmost Pd atoms. 33

44 Adsorbate-Induced Microfaceting on D/Pd{110}-(1 2) Introduction Previous literature on a variety of surfaces, such as Ag{110}, Pd{110}, Ag{111}, and Si{111}, demonstrated that adsorbate-induced reconstruction occurs via molecular chemisorption and epitaxial growth [44-51]. In both of these mechanisms, reconstruction is observed in the same plane as the underlying substrate. The reconstruction of the Pd{110} surface has been reported with and without the presence of hydrogen or deuterium adsorption, indicating that the (1 1) structure is metastable; therefore, it is not surprising that additional adsorption can drive the surface to an energetically more favorable configuration [52-54]. Experiments of H (D) on Pd{110} have focused on understanding the variety of observed adsorbate-induced in-plane surface reconstructions [52, 55-63]. In addition, uptake of H or D to the subsurface sites from the bulk Pd results in a 6% outward relaxation relative to the bulk Pd lattice constant [63]. Previously, we measured the outward relaxation directly with di/dv STM imaging of subsurface H in Pd{111} [42]. This outward relaxation of the substrate lattice has also been observed on vicinal Cu{100} in the presence of oxygen [64]. In this work, we observe a thiophene-induced reconstruction from D/Pd{110}-(1 2) to an out-of-plane faceted D/Pd{1110}-(1 1) reconstruction.

45 Sample Preparation and Experimental Methods All experiments were performed using our ultrastable, custom-built STM [6]. The Pd{110} single-crystal (MaTecK, GmbH) was prepared by cycles of Ar + sputtering at 875 K, oxygen treatment (~ Torr at 875 K), and flash annealing to 1175 K. The tungsten STM tip was prepared using in situ high voltage pulses [65]. Our STM has an additional capability of sample rotation, providing a direct line of sight from the sample to the room temperature section of the chamber. This additional degree of freedom enables direct deposition of gas-phase molecules from the room temperature chamber to the sample held at 4 K [6]. Deposition of molecular deuterium (Matheson Tri Gas, Parsippany, NJ) onto the sample at 4 K was achieved using a high-precision sapphire leak valve. Thiophene (Supelco, Bellefonte, PA) was further purified by several freeze-pump-thaw cycles and deposited on the sample at 4 K by an identical high-precision leak valve. The purity of both deuterium and thiophene deposited on Pd{110} were monitored by a quadrupole residual gas analyzer (QMA 125, Balzers, Liechtenstein) and standard deposition parameters were 180 L for deuterium and 480 L for thiophene. While these parameters were calibrated using the inverted magnetron cold cathode ion gauge at the main chamber, the actual deposition on the sample could be up to five orders of magnitude lower, due to the efficiency of crypumping [6]. Differential conductance imaging was acquired by superimposing an AC modulation (ν AC = 1 khz, V rms = 25 mv) on the bias voltage. The signal was monitored using a lock-in amplifier (SR850, Standford Research Systems, Sunnyvale, CA) and compared with a reference signal to extract the first harmonic signal of the current (di/dv). Topography and di/dv images were obtained simultaneously.

46 Results and Discussion Deposition of deuterium on a clean Pd{110} surface leads to the typical (1 2) reconstruction, as shown in Figure 3-3a. The height profile (Figure 3-3b) for the dashed red line in Figure 3-3a emphasizes the row-pairing of the (1 2) surface reconstruction. Several similar images were acquired, and demonstrated that our preparation method produces minimal contamination by subsurface impurities, such as atomic sulfur. Similar contamination has been observed previously on Ni{110} and Pd{111} surfaces, and we observed minimal sulfur contamination on Pd{110} surface before thiophene deposition [6, 42, 43]. After the (1 2) surface reconstruction was confirmed, thiophene was deposited on the surface at 4 K. Figure 3-4a illustrates thiophene s two preferred adsorption orientations, between paired rows in the troughs and atop the paired rows (molecule highlighted by red arrow). In previous studies of thiophene on Ni{110}, two distinctive bonding orientations were observed, as shown in Figure 3-5 [66]. The black arrow in Figure 3-4a denotes surface-bound sulfur impurities. The electronic-structure perturbations induced by thiophene adsorption on D/Pd{110} were observed in the differential conductance image shown in Figure 3-4c. The observed lobes of adsorbed thiophene were assigned to be the π * -orbitals, since imaging at a positive sample bias voltage probes the empty electronic states of the system. This observation is consistent with STM simulations of thiophene on Pd{111} [67]. The simultaneously obtained topographic image is displayed in Figure 3-4b. In these experiments, higher sample bias voltages (~1 V) resulted in loss of molecular detail during imaging. The high bias voltages created features in the center of the image, where the STM tips rests between images. After hovering the STM tip over the center of the image for two minutes at 1 V, perturbations appear in this area, as shown in Figure 3-6. Additional

47 37 b Figure 3-3: Pd{110}-(1 2) surface reconstruction induced by deuterium. (a) STM topographic image (V s = 0.01 V; I t = 1.4 na; 22 Å 22 Å) of an atomically resolved Pd{110}- (1 2) surface. Inset shows model (1 2) structure. (b) Apparent height profile acquired along the dashed red line in (a).

48 38 Figure 3-4: Adsorption of thiophene on D/Pd{110}-(1 2) and on clean Pd{110}-(1 1). (a) STM topographic image (V s = V; I t = 0.2 na; 73 Å 73 Å) of thiophene adsorbed on D/Pd{110}-(1 2) surface at low coverage. This image shows thiophene s two preferred adsorption sites, between paired rows in the troughs and atop the paired rows (denoted by the red arrow). The black arrow indicates surface-bound sulfur impurities. (b) STM topographic image (V s = 0.01 V; I t = 0.9 na; 22 Å 22 Å) of an isolated thiophene molecule adsorbed on clean Pd{110}-(1 1). (c) Simultaneously obtained (with (b)) differential conductance image illustrating enhancement of the LDOS of thiophene, where the observed lobes are π * empty states due to imaging at a positive sample bias.

49 Figure 3-5: Schematic of Ni{110} surface showing the two proposed adsorption sites for thiophene (red ovals). Due to the symmetry of the crystal, the two adsorption sites are equivalent. The proposed adsorption orientations of thiophene are labeled 1 and 2. Adapted from reference [66]. 39

50 Figure 3-6: Populating subsurface sites with deuterium of Pd{110}. The left STM topographic image (V s = 0.5 V; I t = na; 260 Å 260 Å) was acquired before changing the sample bias voltage to 1 V. After the sample bias voltage was set to 1 V, the tip hovered in the center of the image (its resting position) for 2 minutes. The right STM image shows a diffuse protruding region in the center of the image, where the tip hovered. 40

51 41 hovering and scanning produced more prominent features in the center of the image. These features were attributed to the population of subsurface sites by deuterium from the bulk Pd. This observation is in agreement with our previous work reporting the observation and manipulation of subsurface hydride on Pd{111} by ballistic scattering of tunneling electrons [42]. Sykes et al. showed outward relaxation of the Pd lattice on the order of a few hundredths of an Ångstrom, but here we observed a significant restructuring of the surface, as evident by the sequence of images in Figure 3-7. This change in the morphology of the surface is both energetically and kinetically driven, as seen by fast growth of the features at high sample bias voltages, and, given enough hovering time, at lower sample bias voltages. It should be noted that this phenomenon is not observed in the absence of adsorbed thiophene molecules. Therefore, we hypothesize that the adsorbed thiophene molecules lower the overall barrier to bulk deuterium diffusion. This perturbation to the diffusion barrier may have a coverage dependence, which is implied by the recent work by Domen and coworkers [68]. In Figure 3-7, the surface reconstruction leads to propagation of new faceted steps along the 110 direction. This microfaceting was observed over 50 consecutive frames acquired at 1 V and was nearly complete by frame 30 (Figure 3-7). During microfaceting, little molecular diffusion was observed. Several time-lapse sequences of STM images acquired at a variety of sample bias voltages exhibit that faceting is reliably induced at sample bias voltages > ± 500 mv. Microfaceting of the Pd{110} surface was found to be localized to the area on the surface that was imaged at a sample bias voltage >500 mv and in the center of the image, where the STM tip hovers between images. Imaging a small area at high sample bias voltage, and then imaging a larger area at lower sample bias voltage, demonstrates the localization of faceting as shown in Figure 3-8a. In Figure 3-8a, the region of microfaceting (D/Pd{110}-(1 1) reconstruction) is

52 Figure 3-7: A series of sequential topographic STM images (V s = 1.0 V; I t = 0.05 na; 260 Å 260 Å) that shows the evolution of the microfacets along the 11 0 direction. Frame 0 shows some protrusions in the center of the image due to the STM tip resting for <10 ms before and between frame acquisitions. By frame 30, the subsurface sites have been populated by deuterium and the facets propagated in the 11 0 direction of the Pd{110} substrate. 42

53 43 Figure 3-8: Determining the onset voltage required to populate the subsurface sites with deuterium in the presence of thiophene. (a) STM topographic (derivative) image (V s = 0.05 V; I t = 0.05 na; 348 Å 348 Å) demonstrating our ability to create areas of microfacets locally (β region), while not disturbing the (1 2) reconstruction (α area). (b) Topographic STM image (V s = 0.05 V; I t = 0.05 na; 260 Å 260 Å) of region β in (a). This image was plane-subtracted to show that the out-of-plane angles are self-consistent. The highresolution STM topographic image inset (V s = 0.01 V; I t = 1.4 na; 22 Å 22 Å) was acquired over the area in (b) denoted by a red dashed box. The inset resolves the Pd atoms in the (1 1) structure, indicating a thiophene-induced reconstruction. In both images (a) and (b), the protrusions are adsorbed thiophene molecules. (c) A typical I(V) spectrum acquired over the α region in (a) (V gap = 0.05 V; I gap = 0.05 na). The forward sweep from negative to positive bias voltage is shown in red, and the reverse sweep from positive to negative bias voltage is shown in blue. The black dashed vertical line at 0.38 ev represents the onset voltage required for bulk deuterium to diffuse to the subsurfaces sites. The onset voltage value (0.38 ± 0.02 ev) was determined from the average of 45 forward spectra. (d) Conductance spectra acquired over the (1 1) region of the inset of (b). The forward and reverse sweeps completely overlap indicating that microfaceting is complete in this area. The features at ca. ±0.045 ev were observed in the reverse sweep (blue) in (c), and were attributed to the surface electronic state of the Pd{110} substrate.