DEVELOPMENT OF MICROPLASMAS AND ANALYSIS OF COMPLEX BIOMOLECULES USING PLASMA AND SYNCHROTRON RADIATION A Thesis Presented to The Academic Faculty by Joshua Milbourne Symonds In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the School of Physics Georgia Institute of Technology August 2014 © Joshua Milbourne Symonds 2014 DEVELOPMENT OF MICROPLASMAS AND ANALYSIS OF COMPLEX BIOMOLECULES USING PLASMA AND SYNCHROTRON RADIATION Approved by: Dr. Thomas M. Orlando, Advisor Dr. Facundo M. Fernández School of Chemistry and Biochemistry School of Chemistry and Biochemistry Georgia Institute of Technology Georgia Institute of Technology Dr. Jennifer E. Curtis Dr. Edward H. Conrad School of Physics School of Physics Georgia Institute of Technology Georgia Institute of Technology Dr. Phillip N. First School of Physics Georgia Institute of Technology Date Approved: April 29, 2014 ACKNOWLEDGEMENTS In the course of this work, I have primarily labored independently. That is not to say it has been a lonely experience: I have always enjoyed a strong support system, for which I am very grateful. As my advisor, Thom has given me the flexibility to pursue my curiosity, and provided unwavering support for my studies. I have been fortunate to have such a stable environment and so many opportunities to collaborate in the course of my research. My work in mass spectrometry has benefited immensely from my collaboration with Facundo Fernández and his group. He and Asiri Galhena helped me succeed in a highly interdisciplinary project, and contributed enormously to the chemical analysis in my research. I have had a great many wonderful colleagues that have helped me in innumerable ways since my first day in the lab. They have all helped me tremendously along this path. In particular, I would like to thank Gregory Grieves and Aleksandr Aleksandrov for their inexhaustible experience and guidance. I would like to thank Heather Abbott-Lyon, Claire Pirim, and Reuben Gann for being good mentors, counselors, and collaborators for me at various times when I needed it most. Outside of our lab, I would like to thank Richard Rosenberg for an exciting opportunity, a stimulating collaboration, and one of the most scientifically rewarding experiences of my career. Thanks to Mom, Dad, Ben and Daniel for supporting whatever I do. Finally, thanks to Allison, who has been indispensable these past months. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................... iii LIST OF TABLES .............................................................................................................. x LIST OF FIGURES ........................................................................................................... xi LIST OF SYMBOLS AND ABBREVIATIONS .......................................................... xviii SUMMARY ..................................................................................................................... xix CHAPTER 1: INTRODUCTION ....................................................................................... 1 1.1 Motivation for this work ........................................................................................ 1 1.2 Fundamentals of DC plasmas ................................................................................ 5 1.2.1 Before the glow: kinetic theory of gases..................................................... 5 1.2.2 Collisions .................................................................................................... 6 1.2.3 Charge acceleration ................................................................................... 10 1.2.4 Electrical breakdown ................................................................................ 11 1.2.5 Discharge modes ....................................................................................... 13 1.2.6 Organization of a discharge ...................................................................... 15 1.2.7 Hollow cathode discharges ....................................................................... 17 1.2.7.1 The Pendel effect ............................................................................ 18 1.2.7.2 Contraction of the cathode dark space ........................................... 18 1.2.7.3 Enhanced cathode effects ............................................................... 18 iv 1.2.8 Paschen scaling microplasmas ............................................................. 19 → 1.3 Application of microplasmas ............................................................................... 19 1.4 MHCDs ............................................................................................................... 20 1.5 Ionization processes in mass spectrometry ......................................................... 21 1.5.1 Electron ionization .................................................................................... 21 1.5.2 Chemical ionization .................................................................................. 22 1.5.3 Penning ionization .................................................................................... 23 1.5.4 Photoionization ......................................................................................... 23 1.6 Final thoughts ...................................................................................................... 24 CHAPTER 2: EXPERIMENTAL DESIGN ..................................................................... 25 2.1 Microplasma device design and fabrication ........................................................ 25 2.1.1 Silicon-based MHCD ................................................................................ 25 2.1.1.1 Design and fabrication .................................................................... 25 2.1.1.2 Performance .................................................................................... 28 2.1.2 Drilled-foil MHCD ................................................................................... 29 2.1.3 MHCD device holder ................................................................................ 30 2.1.4 Window ..................................................................................................... 33 2.1.5 Other designs ............................................................................................ 34 2.1.5.1 Capillary plasma ............................................................................. 34 2.1.5.2 Glass coverslip MHCD .................................................................. 35 v 2.2 MHCD operation ................................................................................................. 36 2.2.1 Electrical power ........................................................................................ 36 2.2.2 Gas supply ................................................................................................. 38 2.3 Other instrumentation .......................................................................................... 40 2.3.1 Microchannel plate VUV detector ............................................................ 40 2.3.2 Voltage sensing network ........................................................................... 42 CHAPTER 3: CHARACTERIZATION OF THE MHCD SOURCE .............................. 44 3.1 Electrical Characterization .................................................................................. 44 3.1.1 Results and discussion .............................................................................. 44 3.2 Optical Measurement of Device .......................................................................... 47 3.2.1 Results and Discussion ............................................................................. 48 3.3 Optical Emission Spectroscopy ........................................................................... 49 3.3.1 Spectroscopic measurement of gas temperature ....................................... 50 3.3.2 Experimental ............................................................................................. 53 3.3.2.1 Gas supply ...................................................................................... 53 3.3.2.2 Optical spectrometer and light collection ....................................... 53 3.3.3 Theory of fitting rovibrational temperatures to N2 discharge spectra....... 56 3.3.3.1 Vibrational temperature measurement of N2 .................................. 62 3.3.3.2 Rotational temperature measurements of N2 .................................. 63 + 3.3.3.3 Rotational temperature measurement of N2 .................................. 63 vi 3.3.4 Electron density measurement .................................................................. 64 3.3.5 Results and discussion .............................................................................. 65 3.4 Conclusions ......................................................................................................... 70 CHAPTER 4: A MICROPLASMA DISCHARGE IONIZATION SOURCE FOR AMBIENT MASS SPECTROMETRY ............................................................................ 71 4.1 Overview ............................................................................................................. 71 4.2 Experimental ....................................................................................................... 73 4.2.1 Materials and Chemicals ..........................................................................