Single Molecule Study of Beta-Carotene using Scanning Tunneling Microscope (Up-close and Personal Investigation of Beta-Carotene) A dissertation presented to the faculty of the College of Arts and Sciences of Ohio University In partial fulfillment of the requirements for the degree Doctor of Philosophy Timur Skeini June 2010 2 This dissertation titled Single Molecule Study of Beta-Carotene using Scanning Tunneling Microscope (Up-close and Personal Investigation of Beta-Carotene) by TIMUR SKEINI has been approved for the Department of Physics and Astronomy and the College of Arts and Sciences by Saw W. Hla Associate Professor of Physics and Astronomy Benjamin M. Ogles Dean, College of Arts and Sciences 3 ABSTRACT SKEINI, TIMUR, Ph.D., June 2010, Physics and Astronomy Single Molecule Study of Beta-Carotene using Scanning Tunneling Microscope (Up-close and Personal Investigation of Beta-Carotene) (101 pp.) Director of Dissertation: Saw W. Hla We mimic beta-carotene (β-carotene) environment in plant leaves by using Au(111) as a substrate and conduct single molecule level studies in ultra high vacuum at low substrate temperatures of 77 K and 4.2 K. The STM images and manipulations studies identify five mechanically stable beta-carotene conformations on this substrate, with two never before reported by experiments. We confirm beta-carotene single molecule switching and molecular wire functionality. The beta-carotene clusters are disordered and rich in conformations. Single molecule extraction and cluster manipulation experiments indicate that intermolecular interactions of beta-carotene on Au(111) are stronger than molecule-substrate interactions. The mixtures of beta-carotene and chlorophyll-a result in three regions of ordered self-assembled chlorophyll-a, mobile beta-carotene, and their disordered mixtures with a ratio of 43.6±7.8% to 56.4±10.1% (over 9 mixtures), respectively, with 56.0±10.1% of beta-carotene being trans, indicating beta-carotene preferential mixing with chlorophyll-a instead of its own beta-carotene clusters. The results of this dissertation provide information on single molecule level properties of beta-carotene for fundamental understanding as well as for applications in green nano-bio-technology, nano-medicine, molecular electronics, and energy harvesting. Approved: _____________________________________________________________ Saw W. Hla Associate Professor of Physics and Astronomy 4 ACKNOWLEDGMENTS - Advisor Dr. Saw Wai Hla, Group and Involved Students www.phy.ohiou.edu/~hla/ - Dissertation Committee: Dr. Ido Braslavsky, Dr. Alexander Neiman, Dr. Hugh H. Richardson - Department of Physics and Astronomy, Faculty, Staff, Students (Dr. Alexander Govorov, Dr. David F. J. Tees, Dr. Sergio Ulloa, Ennice Swiegart, Tracy Inman and MANY others), Department of Chemistry, ISFS, and others - Ohio University: Condensed Matter Surface Science (CMSS), Quantitative Biology Institute (QBI), Nanoscale Quantum Phenomena Institute (NQPI) - Financial Support: Department Physics and Astronomy, Ohio University; USA Department of Energy (DOE) DE-FG02-02ER46012; National Science Foundation (NSF). - All others who helped in whatever way with my research, this work and for my PhD. - Thank you to the Universe, Life and Everything! 5 DEDICATION 6 TABLE OF CONTENTS Page Abstract ............................................................................................................................... 3 Acknowledgments............................................................................................................... 4 Dedication ........................................................................................................................... 5 List of Tables ...................................................................................................................... 8 List of Figures ..................................................................................................................... 9 Chapter I: Introduction ...................................................................................................... 11 1.1 Background and Motivation ................................................................................... 11 1.2 Overview ................................................................................................................. 14 Chapter II: Instrumentation and Experimental Techniques ............................................. 17 2.1. How an STM Works .............................................................................................. 17 2.2. Lateral Manipulation .............................................................................................. 20 2.3. Electron Induced Manipulation ............................................................................. 22 Chapter III: Background Materials: Molecules of Current Study and the Substrate ........ 24 3.0. Introduction ............................................................................................................ 24 3.1. Beta-Carotene (β-carotene) .................................................................................... 26 3.2. Chlorophyll-a ......................................................................................................... 32 3.3. Au(111) Substrate .................................................................................................. 33 3.4. Molecular Deposition ............................................................................................ 33 Chapter IV: Single Molecule Studies ............................................................................... 35 4.1. Stable Beta-Carotene Conformations on Au(111) ................................................. 36 4.1.1 Trans Conformation ......................................................................................... 36 4.1.2 Cis Conformation ............................................................................................. 38 4.1.3 Twist Conformation ......................................................................................... 39 4.1.4 V-Shape Conformation .................................................................................... 40 4.1.5 V-Twist Conformation ..................................................................................... 42 4.2. Mechanical Properties of Single Molecules .......................................................... 43 4.2.1 Trans Conformation ......................................................................................... 44 4.2.2 Cis Conformation ............................................................................................. 45 4.2.3 Twist Conformation ......................................................................................... 46 7 4.2.4 V-Shape Conformation .................................................................................... 47 4.2.5 V-Twist Conformation ..................................................................................... 48 Chapter V: Single Molecule Conformation Switching ..................................................... 51 5.1. Cis-Trans Isomerization using Tunneling Electrons ............................................. 51 5.2. Cis-Trans Isomerization using Force ..................................................................... 52 5.3. V-Twist Conformation Switching ......................................................................... 54 5.4. Conformation Switching of End Pi-Ring ............................................................... 55 5.5. Single Molecule Dynamics .................................................................................... 57 5.6. Direct Evidence of Beta-Carotene as a Molecular Wire ........................................ 59 Chapter VI: Molecular Assembly – Beta-Carotene Clusters on Au(111) ........................ 61 6.1. Single Molecule Extraction ................................................................................... 63 6.2. Beta-Carotene Clusters .......................................................................................... 69 6.3. Cluster Manipulation ............................................................................................. 74 Chapter VII: Beta-Carotene – Chlorophyll-a Complexes ................................................. 76 7.1. Previous STM Experiments ................................................................................... 76 7.2. Our Results ............................................................................................................ 76 Chapter VIII: Conclusion .................................................................................................. 82 8.1. Beta-Carotene ........................................................................................................ 82 8.2. Beta-Carotene and Chlorophyll-a .......................................................................... 84 Appendix A: Cluster Composition Statistics (Beta-Carotene) ........................................ 86 Appendix B: Mixture Composition Statistics (Beta-Carotene + Chlorophyll-a) ............ 88 Appendix C: Manipulation Statistics ............................................................................... 92 References ......................................................................................................................... 94 8 LIST OF TABLES Page Table I: Cluster percentage composition comparison with literature ........................................... 73 9