POLARIZATION PHENOMENA IN ORGANIC NANOSTRUCTURES by Donna Kunkel A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfilment of Requirements For the Degree of Doctor of Philosophy Major: Physics and Astronomy Under the Supervision of Professor Axel Enders Lincoln, Nebraska August, 2014 POLARIZATION PHENOMENA IN ORGANIC NANOSTRUCTURES Donna Kunkel, Ph.D. University of Nebraska, 2014 Adviser: Axel Enders This thesis explores the self-assembly and surface interactions of two classes of or- ganic molecules through scanning tunneling microscopy. The primary scientific goal of this thesis is to better understand the electric polarization in surface-supported or- ganic molecules, whether inherent to a molecule or acquired through intermolecular interactions. First, a class of dipolar molecules, the quinonoid zwitterions, are examined on three noble metal surfaces. Two-dimensional islands of hydrogen-bonded molecules, with aligned dipole moments, are formed on Au(111). However, other structures with zero net dipole moment are observed on Ag(111) and Cu(111). Modifying the molecules with longer substituent tails results in the formation of one-dimensional chains irrespective of the surface. Our calculations show that the dipole moment is not the driving factor determining the self-assembly of these molecules. Instead a more complicated picture emerges in which extensive charge transfer with the surface drastically reduces the dipole moment of the molecule by nearly 9 D, so that dipolar energies become small compared to typical chemical bond energies such as hydrogen bonds. Second, the self-assembly of three molecules, croconic acid, rhodizonic acid, and 3-hydroxyphenalenone (3-HPLN) are studied on three noble metal surfaces. These molecules were chosen due to their ferroelectric bulk properties, which arise from switchable hydrogen bonds. On Ag, croconic acid forms two-dimensional hydrogen bonded sheets which are, in theory, capable of proton transfer. While these com- pounds form hydrogen bonded structures on Ag(111) and Au(111), on the more reactive Cu(111) surface metal-organic frameworks involving surface metal atoms are observed for rhodizonic acid, highlighting the importance of surface chemistry. Ad- ditionally, on an insulating buffer layer, CuN, croconic acid forms a densely packed hydrogen bonded structure, which more closely resembles its bulk phase, demonstrat- ing the effect of charge transfer on self-assembly. Additionally, hydrogen bonded co-crystals of 3-HPLN and croconic acid are syn- thesized on Au(111). Co-crystals of quinonoid zwitterions and croconic acid are also reported. Guided by the surface science studies, related 3D organic co-crystals were grown. Finally, the topic 2D magic organic clusters is presented as a new branch of research. Five new organic magic clusters are described. The research presented in this thesis has relevance to a broad range of applications including data storage devices and molecular electronics. iv ACKNOWLEDGMENTS First and foremost, I want to offer sincere and heartfelt thanks to my thesis adviser, Dr. Axel Enders. His passion for science and learning is nothing short of inspiring. Throughout the years, he has always provided me with kind words of encouragement and wise words of guidance. As a scientist, he has served as an exceptional role model. On a personal note, his warm and gregarious personality has made working with him an absolute pleasure. I would also like to thank my committee members, Dr. Peter Dowben, Dr. Stephen Ducharme, and Dr. Eva Franke-Schubert for their service both as committee members as well as mentors. Furthermore, I would like to thank my numerous collaborators. Chief among them, Dr. Eva Zurek, Scott Simpson, and Dr. James Hooper have continuously proven to be excellent scientists whose tireless research has provided theoretical insights which add significant value to my thesis. Additionally, I want to thank Dr. Alexander Sinitskii and his students Timothy Vo and Wayz Khan for their collaborations. Aside from the committee service, I also would like to thank Dr. Stephen Ducharme and his student Shashi Poddar, and Dr. Peter Dowben for their scientific collaborations. I wish to acknowledge my former lab mates Geoffrey Rojas and Xumin Chen for training me on the instrumentation. I would also like to thank my fellow researcher Sumit Beniwal for continually helping in every aspect of research. By aiding me in everything from routine maintenance to providing valuable scientific discussions Sumit has made this thesis possible. Additionally, his humor and friendship has made conducting research for this thesis enjoyable. Finally, I wish to sincerely thank my friends and family for providing unconditional support during my graduate years. With that, to everyone mentioned above: Thank you! v PUBLICATIONS RELATED TO THIS RESEARCH 11. S. Beniwal, S. Chen, X.-C. Zeng, S. Simpson, J. Hooper, E. Zurek, D. A. Kunkel, A. Enders Kagome Lattice of π-π Stacked 3-Hydroxyphenalenone on Cu(111) accepted Chem. Commun. (2014) 10. J. Hooper, D. A. Kunkel, S. Simpson, S. Beniwal, A. Enders, E. Zurek Chi- ral Surface Networks of 3-HPLN - A Molecular Analog of Rounded Triangle Assembly? Surface Science, in print (2014) 9. T. H. Vo, M. D. Morton, M. Shekkirev, D. A. Kunkel, E. Berglund, P. Wilson, A. Enders, A. Sinitskii Bottom-up Synthesis of Narrow Nitrogen-doped Graphene Nano-ribbons Chem. Commun. 50 4172-4174 (2014). 8. T. H. Vo, M. Shrekhirev, D. A. Kunkel, M. D. Morton, E. Berglund, L. Kong, P. M. Wilson, P. A. Dowben, A. Enders, A. Sinitskii Large-Scale Solution of Narrow Graphene Nanoribbons, Nat. Commun. 5 3189 (2014). 7. D. A. Kunkel, J. Hooper, S. Simpson, S. Beniwal, K. L. Morrow, D. C. Smith, K. Cousins, S. Ducharme, E. Zurek, A. Enders Rhodizonic Acid on Noble Metals: Surface Reactivity and Coordination Chemistry, J. Phys. Chem. Lett. 4, 3413 (2013). 6. S. Simpson, D. A. Kunkel, J. Hooper, J. Nitz, P. A. Dowben, L. Routaboul, P. Braunstein, B. Doudin, A. Enders, E. Zurek, Coverage-Dependent Interactions at the Organics-Metal Interface: Quinonoid Zwitterions on Au(111), J. Phys. Chem. C 117, 16406 (2013). 5. D. A. Kunkel, J. Hooper, S. Simpson, G. A. Rojas, S. Ducharme, T. Usher, E. Zurek, A. Enders Proton Transfer in Surface-Stabilized Chiral Motifs of Cro- conic Acid, Phys. Rev. B 87, 041402 (2013). 4. P. A. Dowben, D. A. Kunkel, A. Enders, Luis G. Rosa, L. Routaboul, B. Doudin, P. Braunstein The Dipole Mediated Surface Chemistry of p-Benzoquinonemonoimine Zwitterions, Top. Cat.56, 1096 (2013). 3. D. A. Kunkel, S. Simpson, J. Nitz, G. A. Rojas, E.Zurek, L. Routaboul, B. Doudin, P. Braunstein, P. A. Dowben, A. Enders Dipole Driven Schemes of Quinonoid Zwitterions on Surfaces, Chem. Commun. 48, 7143 (2012). 2. G. Rojas, S. Simpson, X. Chen, D. A. Kunkel, J.Nitz, J. Xiao, P. A. Dow- ben, E. Zurek, and A. Enders Surface State Engineering of Molecule-Molecule Interactions, Phys. Chem. Chem. Phys. 14, 4971-4976 (2012). 1. G. Rojas, X. Chen, D. Kunkel, M. Bode, A. Enders Temperature Dependence of Metal-Organic Heteroepitaxy, Langmuir 27, 14267-14271 (2011). vi Contents Contents vi 1 Introduction 1 2 Fundamentals 5 2.1 Intermolecular Interactions........................ 5 2.1.1 Dipole-Dipole Interactions .................... 6 2.1.2 Resonance Assisted Hydrogen Bonding ............. 13 2.2 Review of Experiments of Dipolar Molecules on Surfaces ....... 17 2.2.1 Electronic Effects of Dipolar Molecules on Surfaces ...... 17 2.2.2 Self-Assembly of Dipolar Molecules ............... 20 2.3 Molecule Surface Interactions ...................... 27 2.3.1 Short Review of Clean Metal Surfaces .............. 28 2.3.2 Molecule-Substrate Interaction Strengths ............ 30 2.3.3 Energy Level Alignment ..................... 30 2.3.4 Interface Charge Transfer .................... 33 2.3.5 Pauli Repulsion .......................... 35 2.3.6 Unified IDIS-Pillow-Permanent Dipole Model ......... 37 2.3.7 Experimental Confirmation of the IDIS Model ......... 39 vii 2.3.8 Challenges to Interface Modelling ................ 40 2.4 Experimental Methods .......................... 41 2.4.1 Basic Principles of Scanning Tunneling Microscopy ...... 42 2.4.2 Applications of Scanning Tunneling Microscopy ........ 43 2.4.3 Experimental Apparatus ..................... 48 3 Investigation of Strongly Dipolar Organic Molecules on Surfaces 49 3.1 Overview of Quinonoid Zwitterions ................... 49 3.2 Experimental Observations of Quinonoid Zwitterions on Metal Surfaces 54 3.2.1 Parent Quinonoid Zwitterions .................. 55 3.2.2 Ethyl and Butyl Quinonoid Zwitterions ............. 66 3.3 Discussion of Self-Assembly ....................... 71 3.3.1 Single Molecule Adsorption Phenomena ............. 71 3.3.2 Coverage Dependent Bond Strength of PZI on Au(111) .... 77 3.3.3 Amine Deprotonation ....................... 78 3.3.4 Long Range Surface Mediated Interactions ........... 80 3.4 Does the Dipole Moment Drive Quinonoid Zwitterion Self-Assembly? 81 4 2D Single Component, Organic Hydrogen Bonded Networks 84 4.1 STM Investiagations of Surface Supported Croconic Acid ....... 88 4.1.1 Croconic Acid on Ag(111) .................... 89 4.1.2 Croconic Acid on Au(111) .................... 95 4.1.3 Metal Organic Networks of Croconic Acid/Cu ......... 97 4.1.4 Croconic Acid on an Insulating Copper Nitride Buffer Layer . 98 4.2 STM Studies of Surface Supported Rhodizonic Acid .......... 106 4.2.1 First Crystallization of Rhodizonic Acid on Au(111) ...... 106 4.2.2 Metal