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Open Moore Thesis08.Pdf The Pennsylvania State University The Graduate School Department of Chemistry CREATING AND PROBING MOLECULAR ASSEMBLIES FOR SINGLE-MOLECULE DEVICES A Dissertation in Chemistry by Amanda Michelle Moore © 2008 Amanda Michelle Moore Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy August 2008 ii The dissertation of Amanda Michelle Moore was reviewed and approved* by the following: Paul S. Weiss Distinguished Professor of Chemistry and Physics Dissertation Advisor Chair of Committee Thomas E. Mallouk DuPont Professor of Materials Chemistry and Physics David L. Allara Professor of Polymer Science and Chemistry Mary Jane Irwin Evan Pugh Professor of Computer Science and Engineering A. Robert Noll Chair of Engineering Ayusman Sen Professor of Chemistry Head of the Department of Chemistry *Signatures are on file in the Graduate School iii ABSTRACT We explored the creation and conductance of molecular assemblies by looking at both the larger body of work that has been performed to characterize molecular devices, and through probing isolated single-molecule assemblies and creating cluster tether schemes. We have characterized the bistable conductance switching exhibited by oligo(phenylene-ethynylene) molecules. This conductance switching has been hypothesized to occur through a variety of interactions including reduction, rotation, neighboring molecule interactions, bond fluctuations and changes in hybridization. Using molecular design, we tailored the switch molecules to enable the testing of each mechanism. The hypothesis most consistent with our and others’ data is that of hybridization change at the molecule-substrate interface. The oligo(phenylene-ethynylene) switches also exhibited motion within the host self-assembled monolayers at substrate step edges. This was observed as three apparent heights in our analyses of scanning tunneling microscope data. We have characterized the ‘third’ apparent height as arising from the switch molecules place-exchanging up and down substrate step edges. Only switches residing at substrate step edges have the ability to exhibit three apparent heights, as compared to those isolated at domain boundaries, which only exhibit two possible apparent heights. The oligo(phenylene-ethynylene) molecules were further characterized to show that the switching and motion events occur on time scales faster (ms) than those of scanning tunneling microscopy imaging (min) using height vs. time measurements. iv We have expanded the capabilities of scanning tunneling microscopy to include measurements using microwave frequencies. Using AC measurements, we were able to compare the polarizabilities of several self-assembled monolayers. We applied the microwave frequencies to the systems of the oligo(phenylene-ethynylene) switches and gained predicative abilities of which molecules were likely to exhibit conductance switching or motion. In addition to our studies of isolating and studying switch molecules, we have developed capture surfaces for superatom clusters, which have element-like properties. We used barium ions to model the capture for alkaline-earth-metal-like clusters. We are developing the captures surfaces both to identify the cluster properties and to tether them for measurement with scanning tunneling microscopy. These studies demonstrate our abilities to capture, to isolate and to measure properties of molecules on the single-molecule scale. v TABLE OF CONTENTS LIST OF FIGURES . .viii LIST OF TABLES. .xii LIST OF ABBREVIATIONS. xiii ACKNOWLEDGMENTS. .xv CHAPTER 1 CREATING AND IMAGING MOLECULAR ASSEMBLIES. 1 1.1 Introduction. 1 1.2 Self-Assembled Monolayers. 2 1.2.1 Insertion into Self-Assembled Monolayers. 5 1.2.2 Mixed Alkanethiolate Monolayers. 7 1.3 Scanning Tunneling Microscopy. 8 1.3.1 Scanning Tunneling Microscopy Operation . 10 1.4 Microwave-Frequency Alternating Current Scanning Tunneling Microscopy. 13 1.5 Dissertation Overview. .19 CHAPTER 2 MOLECULAR DEVICES . 22 2.1 Introduction. 22 2.1.1 The Drive Towards Single-Molecule Electronics . 22 2.2 Molecules and Measurements at the Single-Molecule Scale. 31 2.2.1 Scanning Tunneling Microscopy. 31 2.2.2 Conductive Probe Atomic Force Microscopy. 37 2.2.3 Mechanically Controlled Break Junctions. 39 2.2.4 Scanning Tunneling Microscopy Tip Break Junctions. .41 2.2.5 Electromigration Junctions. .42 2.3 Converting to the Nanoscale. 45 2.3.1 Mercury Drop Junction. .45 2.3.2 Nanopores. .46 2.3.3 Particle Bridge. 47 2.3.4 Crossed-Wire Junction. 48 2.3.5 Nanorod Junction. .50 2.3.6 Tip-End Junction. .52 2.4 Connecting to the Outside World. 54 2.4.1 Molecular Rulers. .55 2.4.2 Directed Diblock Copolymers. 57 vi 2.4.3 Imprint Lithography. 58 2.4.4 On-Wire Lithography. 59 2.5 Conclusions and Future Molecular Devices Direction. 60 CHAPTER 3 TESTING HYPOTHESIZED SWITCHING MECHANISMS FOR SINGLE OLIGO(PHENYLENE-ETHYNYLENE) MOLECULES. 62 3.1 Introduction. 62 3.2 Experimental Procedure. .67 3.2.1 Sample Preparation. .67 3.2.2 Scanning Tunneling Microscopy. 70 3.2.3 Apparent Height Determination. 70 3.3 Results and Discussion. 73 3.3.1 Reduction and Functional Group Rotation Mechanisms. 74 3.3.2 Backbone Ring Rotation Mechanism. .75 3.3.3 Neighbor Molecule Interactions Mechanism. 76 3.3.4 Bond Fluctuations. .79 3.3.5 Hybridization Change. .84 3.3.6 Experiments with Restricted Motion. 86 3.4 Conclusions and Future Direction. .89 CHAPTER 4 MOTION UP AND DOWN SUBSTRATE STEP EDGES BY OLIGO(PHENYLENE-ETHYNYLENE) MOLECULES. 91 4.1 Introduction. .91 4.2 Experimental Procedure. 94 4.2.1 Sample Preparation. .94 4.2.2 Scanning Tunneling Microscopy. 96 4.2.3 Apparent Height Determination. 96 4.3 Results and Discussion. 99 4.4 Conclusions and Future Directions. 110 CHAPTER 5 REAL-TIME MEASUREMENTS OF CONDUCTANCE SWITCHING AND MOTION OF SINGLE OLIGO(PHENYLENE-ETHYNYLENE) MOLECULES. 111 5.1 Introduction. 111 5.2 Experimental Procedure. 115 5.2.1 Sample Preparation. .115 5.2.2 Scanning Tunneling Microscopy. 115 5.2.3 Height vs. Time Spectroscopy Acquisition. .115 5.3 Results and Discussion. 117 5.4 Conclusions and Future Direction. .125 CHAPTER 6 IMAGING SINGLE-MOLECULE POLARIZABILITY AND BURIED INTERFACE DYNAMICS. .126 6.1 Introduction. 126 6.1.1 Sample Preparation. .129 vii 6.1.2 Scanning Tunneling Microscopy. 131 6.1.2.1 Alternating Current Scanning Tunneling Microscopy Imaging and Spectral Acquisition. 132 6.1.3 Single-Molecule and Microwave Magnitude Extraction. 132 6.2 Results and Discussion . .133 6.2.1 Probing the Polarizability of Self-Assembled Monolayers . .133 6.2.2 Buried Interface Dynamics of Oligo(phenylene-ethynylene) switches . 142 6.3 Conclusions and Future Direction . 155 CHAPTER 7 DEVELOPMENT OF CLUSTER CAPTURE SURFACES . .156 7.1 Introduction . .156 7.2 Experimental Procedure . 158 7.2.1 Sample Preparation. .158 7.2.2 Time-of-Flight Secondary Ion Mass Spectrometry . .161 7.2.3 X-Ray Photoelectron Spectroscopy . .161 7.3 Results and Discussion . .163 7.3.1 Electrostatic Capture Surfaces. 163 7.3.2 Minimizing Nonspecific Adsorption. 167 7.4 Conclusions and Future Direction . ..
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