University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School January 2012 The lecE tronic Structure of Biomolecular Self- Assembled Monolayers Matthaeus Anton Wolak University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the American Studies Commons, Electrical and Computer Engineering Commons, and the Materials Science and Engineering Commons Scholar Commons Citation Wolak, Matthaeus Anton, "The Electronic Structure of Biomolecular Self-Assembled Monolayers" (2012). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/4258 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. The Electronic Structure of Biomolecular Self-Assembled Monolayers by Matthaeus Wolak A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Electrical Engineering College of Engineering University of South Florida Major Professor: Rudy Schlaf, Ph.D. Vinay Gupta, Ph.D. Li-June Ming, Ph.D. Arash Takshi, Ph.D. Jing Wang, Ph.D. Date of Approval: June 13, 2012 Keywords: peptide nucleic acid, tetraphenylporphyrin, work function, charge injection barrier, interface dipole, XPS Copyright © 2012, Matthaeus Wolak DEDICATION I dedicate my dissertation to my girlfriend Emily Helmrich, and my parents Margarete and Anton Wolak, who supported me throughout the process and always had the right words of encouragement for me. I am very grateful to you and will always appreciate all that you have done for me. There is no doubt in my mind that without your continued support I could not have completed this process. ACKNOWLEDGMENTS I would like to thank Dr. Rudy Schlaf for his guidance and support throughout the process of writing this dissertation and I appreciate his commitment. I am also thankful to the members of my supervisory committee for their help and advice on how to improve my work. Furthermore, I would like to express my gratitude to Dr. Alexander Balaeff and Dr. David Beratan from Duke University for providing me with the DOS calculations used in this dissertation and the fruitful discussions we had. I would also like to thank Dr. Catalina Achim and her students at Carnegie Mellon University for giving me the opportunity to engage in their research and their continuous supply of PNA solutions, which were crucial for my research. I am further thankful to Dr. David Waldeck and Emil Wierzbinski of the University of Pittsburgh for their ellipsometry measurements of the investigated PNA monolayers. Additionally, I would like to thank Dr. Shengqian Ma, who provided me with the tetraphenylporphyrin molecules used in this dissertation and was always willing to engage in helpful discussions. I would also like to thank all the members of the Surface Science Lab of the University of South Florida for their continuous help during my research. TABLE OF CONTENTS LIST OF TABLES ............................................................................................................. iii LIST OF FIGURES ........................................................................................................... iv ABSTRACT ....................................................................................................................... ix CHAPTER 1: INTRODUCTION AND MOTIVATION ....................................................1 1.1: Motivation and Outline of this Dissertation .....................................................1 1.2: Charge Transfer and Electronic Structure of Organic Materials ......................3 CHAPTER 2: FUNDAMENTALS OF ORGANIC SELF-ASSEMBLED MONOLAYERS ......................................................................................................5 2.1: Self-Assembly of Monolayers ..........................................................................5 2.1.1: Thiol Based Self-Assembly on Metals ..............................................8 2.2: Peptide Nucleic Acids .....................................................................................11 2.3: Tetraphenylporphyrin .....................................................................................15 CHAPTER 3: EXPERIMENTAL METHODOLOGY .....................................................20 3.1: Incubation Procedure ......................................................................................20 3.2: Fundamentals of Electrospray ........................................................................22 3.3: Photoemission Spectroscopy ..........................................................................24 3.3.1: The Theory of Photoemission Spectroscopy ...................................24 3.3.2: Dipole Formation at Metal-Organic Interfaces ................................31 3.3.3: XPS-Based Estimation of Film Thickness.......................................34 3.3.4: Chemical Shifts of Core-Level Binding Energies and Curve Fitting .............................................................................................36 3.4: Experimental Setup .........................................................................................37 3.4.1: Sample Preparation ..........................................................................38 3.4.2: PES System Setup ............................................................................39 CHAPTER 4: ELECTRONIC STRUCTURE AT THE INTERFACE BETWEEN AU AND SELF-ASSEMBLED PEPTIDE NUCLEIC ACIDS ...................................41 4.1: Experimental ...................................................................................................42 4.2: The Interfaces Between Au and Cys-A7, Cys-T7, and Cys-Bckb7................47 4.3: The Interfaces of Cys-A7-Fc and Cys-T7-Fc on Au ......................................67 4.4: Charge Injection Barrier Changes as an Effect of PNA Strand Orientation .................................................................................................80 i CHAPTER 5: ELECTRONIC STRUCTURE OF SELF-ASSEMBLED TETRAPHENYLPROPHYRIN MONOLAYERS AND ARRAYS ....................90 5.1: Experimental ...................................................................................................91 5.2: The Interface of Self-Assembled TPP-S on Au ..............................................93 5.3: The Electronic Structure of TPP-CN Arrays Formed on Au ........................105 5.3.1: Bond Formation Between Ag and N..............................................109 5.3.2: Charge Transfer Related Binding Energy Shifts ...........................115 5.3.3: Surface Characterization of TPP-CN Films Deposited on Au ......118 5.3.4: Orbital Band Alignment at the Au/TPP-CN and Au/TPP- CN/Ag+ Interfaces ........................................................................127 CHAPTER 6: CONCLUSIONS AND OUTLOOK ........................................................134 REFERENCES ................................................................................................................137 APPENDICES .................................................................................................................154 Appendix A: Copyright Permission to Use Figure 1 ...........................................155 Appendix B: Copyright Permission to Use Table 1 and Figures 27 and 28 ........156 ii LIST OF TABLES Table 1: Emission lines of the Cys-A7, Cys-T7, and Cys-Bckb7 monolayers in eV. ...... 52 Table 2: Work functions and highest occupied molecular orbital (HOMO) onsets of the Cys-A7, Cys-T7 and Cys-Bckb7 SAMs in eV. ........................................55 Table 3: Nitrogen related peak position for several TPP derivatives in eV .................... 111 iii LIST OF FIGURES Figure 1: Diagram of an ideal SAM of alkanethiolates formed on a gold surface with highlighted anatomy and characteristics .....................................................6 Figure 2: A homodimer formed by two sulfur atoms with a spacing of 2.2 Å exists at the interface while the alkane chains in the overlayer have a spacing of 5 Å. ................................................................................................................11 Figure 3: The backbone structure of DNA (left) and PNA (right) ....................................13 Figure 4: TPP derivatives used in the experiments ............................................................18 Figure 5: The principle of the electrospray process ...........................................................23 Figure 6: The energy levels in a solid sample and the electron distribution generated by photons at an energy hv, depicting the location of the Fermi edge, valence band, core levels and secondary edge in the recorded spectrum. ............................................................................................26 Figure 7: An XP-spectrum of a Cys-T7 SAM depicting the various emissions features ..............................................................................................................27 Figure 8: A typical UP-spectrum of sputter cleaned Au showing the work function onset, the valence band emissions and the Fermi edge .....................................29 Figure 9: The secondary edge as measured on a Cys-T7 monolayer with LIXPS and UPS. ............................................................................................................31