CHARACTERIZING STRUCTURE REARRANGEMENT AND FRAGMENTATION KINETICS FOR BIOMOLECULES IN GAS PHASE BY SPECTROSCOPY By NING ZHAO A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2016 © 2016 Ning Zhao To my family ACKNOWLEDGEMENTS I am very appreciating that I have had the opportunity to pursue the Ph.D. in chemistry from University of Florida. First I would like to thank my wife Chen Cao for her love and the new family member Claire Zhao. I would thank my parents and my parents in law for their unending support and encouragement. I am so grateful for everything they give me. Respecting to my research, I would sincerely thank my advisor Dr. Nick Polfer. Because not only he provides me interesting projects and teaches me think research more deeply, but also his standard requirement and critics push me to improve myself everyday. His kind personality always encourages me to overcome the research problems and has truly been a huge influence on my growth as a scientist and person. It is such a great honor to be a member of the Polfer group. Also, I would like to thank all the Polfer group members in past or in present. Almost everyone gave me direct helps and advices for my research. I learned so much experimental techniques and theoretical knowledge from Dr. Kerim Gulyuz, Dr. Corey Stedwell, Dr. Amanda Patrick, Dr. Yanglan Tan and Da Wang. From the direct teaching from Corey, I learned from how to use SOLIDWORKS to design staff to how to conduct experiments. Without the discussion with Amanda, I could not overcome some critical research problems. I would also thank current group members: Matt Bell for implementing software programs for data acquisition and data analysis, Adam Cismesia for guidance and maintenance of new instruments, Laura Bailey for spectroscopy setup and Larry Tesla for calculation and simulation setup. Without them, I could not complete my research projects. 4 I would like to thank all faculties and staffs that gave me direct help during my Ph.D. research. I would like to thank Dr. Nicolo Omenetto for spectroscopy teaching and test, Dr. Ion Ghiviriga for all the NMR experiments. I would like to thank Brian Smith and Todd Proxx in machine shop for implementation of designs. Last but not least, I would like to thank graduate students from other research groups that helped me finish experiments. Especially, I would like to thank Dr. Xinxing Zhang from Butcher group for help on synthesis and UV/Vis test. Finally, I would like to thank all my committee members for the help in my Ph.D. research. 5 TABLE OF CONTENTS page ACKNOWLEDGEMENTS ............................................................................................... 4 LIST OF TABLES ............................................................................................................ 9 LIST OF FIGURES ........................................................................................................ 10 LIST OF ABBREVIATIONS ........................................................................................... 14 ABSTRACT ................................................................................................................... 17 CHAPTER 1 MASS SPECTROMETRY AND SPECTROSCOPY: TOOLS FOR STRUCTURAL ANALYSIS ON BIOMOLECULES .................................................. 19 Introduction ............................................................................................................. 19 Amino Acids ............................................................................................................ 19 Peptides and Proteins ............................................................................................. 20 Saccharides ............................................................................................................ 22 Mass Spectrometry ................................................................................................. 23 Peptide Dissociation and Rearrangement Chemistry ............................................. 24 Oligosaccharide Dissociation and Rearrangement Chemistry ................................ 25 Spectroscopy .......................................................................................................... 26 Infrared Multiple Photon Dissociation .................................................................. 26 Ultraviolet Photon Dissociation ............................................................................ 28 Perspective Overview ............................................................................................. 29 2 INSTRUMENTAL METHODOLOGY FOR PHOTODISSOCIATION SPECTROSCOPY EXPERIMENTS ....................................................................... 40 Mass Spectrometry ................................................................................................. 40 Encapsulated Spray Electrospray Ionization ....................................................... 40 Metal Capillary ..................................................................................................... 42 Ion Funnel ............................................................................................................ 42 Quadrupole Mass Filter ....................................................................................... 43 Quadrupole Ion Trap ........................................................................................... 44 Time-of-Flight ...................................................................................................... 46 Homebuilt ESI-QMF-QIT-ToF .............................................................................. 47 Fourier Transfer Ion Cyclotron Resonance .......................................................... 47 Spectroscopy Light Sources ................................................................................... 48 Optical Parametric Oscillator ............................................................................... 48 Excimer Ultraviolet Laser ..................................................................................... 49 Carbon Dioxide Laser .......................................................................................... 50 6 3 IDENTIFYING RADICAL REARRANGEMENT STRUCTURES VIA IRMPD SPECTROSCOPY .................................................................................................. 58 Introduction ............................................................................................................. 58 Experimental Methods ............................................................................................ 59 Sample Preparation ............................................................................................. 59 Gas Phase Acidification Setup ............................................................................ 60 UVPD Setup ........................................................................................................ 61 IRMPD Yield ........................................................................................................ 61 Computations ...................................................................................................... 61 Experimental Results .............................................................................................. 62 IRMPD of Protonate Acetyl Tryptophan (m/z = 247) ............................................ 62 Stucture Elucidation of Protonated Acetyl Tryptophan Radical (m/z = 246) ........ 63 UVPD of Iodized Tyrosines .................................................................................. 64 IRMPD Sepctroscopy of m/z = 136 Ion ................................................................ 65 Structural Elucidation of m/z = 135 Radical Ion ................................................... 65 Structural Elucidation of m/z = 134 Radical Ion ................................................... 67 Structural Elucidation of m/z = 262 Ion ................................................................ 68 Structural Elucidation of m/z = 261 Radical Ion ................................................... 68 Summary and Conclusions ..................................................................................... 70 4 FRAGMENTATION KINETICS STUDIED IN MASS SPECTROMETRY IN SUBMICRO SECOND SCALE ............................................................................... 85 Introduction ............................................................................................................. 85 Experimental Methods ............................................................................................ 86 Smaple preparation ............................................................................................. 86 Data Acquisition Setup ........................................................................................ 86 Simulations ............................................................................................................. 87 Experimental Results .............................................................................................. 87 Identification of Unstable Radical Mediates ......................................................... 87 Formation of Radical Species .............................................................................. 88 Data Analysis Method .........................................................................................