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Gas-Phase Ion Chemistry: Kinetics and Thermodynamics

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Gas-Phase Ion Chemistry: Kinetics and Thermodynamics by Charles M. Nichols B. S., Chemistry – ACS Certified University of Central Arkansas, 2009 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry and Biochemistry 2016 This thesis entitled: Gas-Phase Ion Chemistry: Kinetics and Thermodynamics Written by Charles M. Nichols has been approved for the Department of Chemistry and Biochemistry by: _______________________________________ Veronica M. Bierbaum _______________________________________ W. Carl Lineberger Date: December 08, 2015 A final copy of this thesis has been examined by all signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline. Nichols, Charles M. (Ph.D., Physical Chemistry) Gas Phase Ion Chemistry: Kinetics and Thermodynamics Thesis directed by Professors Veronica M. Bierbaum and W. Carl Lineberger Abstract: This thesis employs gas-phase ion chemistry to study the kinetics and thermodynamics of chemical reactions and molecular properties. Gas-phase ion chemistry is important in diverse regions of the universe. It is directly relevant to the chemistry occurring in the atmospheres of planets and moons as well as the molecular clouds of the interstellar medium. Gas-phase ion chemistry is also employed to determine fundamental properties, such as the proton and electron affinities of molecules. Furthermore, gas-phase ion chemistry can be used to study chemical events that typically occur in the condensed-phase, such as prototypical organic reactions, in an effort to reveal the intrinsic properties and mechanisms of chemical reactions. Mass spectrometry is used to investigate the reactivity and fundamental properties of ions. Kinetic data for reactions between cations or anions with neutral atoms or molecules is acquired using the selected ion flow tube (SIFT). These data are interpreted mechanistically and thermodynamically using literature data and theoretical computations. Additionally, the proton affinities of a series of anions are determined using a triple quadrupole mass spectrometer by investigating the collision induced dissociation of proton-bound, anionic heterodimers. The SIFT is coupled with a variety of ion-generation techniques. This thesis reports the design and operation of a new electrospray ion source for the SIFT in detail. The electrospray ionization technique allows ions that are pre-formed in the condensed-phase to be transmitted into the gas-phase for studies of their reactivity. To my friends, family, teachers, and Alex. Thanks for all of your support. Acknowledgements The completion of this thesis would not be possible without the assistance of so many people in my life. First and foremost, I’d like to thank my scientific mentor and advisor, Veronica ‘Ronnie’ Bierbaum. I couldn’t have picked a better research advisor for my time at the University of Colorado. Thank you for your support and guidance over the last six years. I wouldn’t be the speaker, writer, or scientist that I am today without your help. I feel lucky to have Carl Lineberger as a co-advisor. His comments and insight into public speaking, experimental phenomena, and data analysis have been invaluable. Mathias Weber supported me through three oral examinations, a process that proved to be one of the hardest obstacles in my life. I must also thank William Old for helping me initiate the kinetic method experiments on East campus, and for helping me find the postdoc position at Vanderbilt University. To Barney Ellison, thanks for your patience when the lab sink would overflow or the water line of a diffusion pump would pop off and flood your lab. I owe you a copy of Pedley. To my undergraduate advisor, Bill Taylor, thanks for introducing me to gas-phase ion chemistry, and becoming a friend over the years. I don’t know what I would have done without my coworkers in the Bierbaum lab. To John, Callie, Nick, Ditte, Jennifer, Zhibo, Zhe-Chen, Nadine, and Scott, thanks for making the group office an awesome workplace! I appreciate all of the scientific and instrumental discussions, as well as the snack and coffee breaks. Many thanks to the Lineberger, Ellison, and Weber research labs for being part of the ion chemistry “supergroup.” The supergroup has been a great way to practice public speaking, receive feedback on my work, and to keep up with some of the research that is taking place on campus. The work that follows would not have been possible without funding, and therefore I must thank the National Science Foundation and the Air Force Office of Scientific Research (Grants CHE-1012321, CHE- 1300886, ACI-1053575, and FA-9550-12-1-0125). I must thank the support staff for their assistance. In the CIRES shop, Don has always been fun to talk with about instrumentation and electronics in general. The staff in the chemistry department also provided much assistance from purchasing orders to academic advising. Furthermore, I’m lucky to have access to v the JILA staff; the electronics, machine shop, and computer staff have helped me resolve many problems on the fly. I must give a special thanks to Casey Christopher. Casey helped me with homework in the first three semesters, teaching me linear algebra and other math tricks. Without his generous assistance, I’m not sure that I would be here today. Casey and Jon were my roommates for four unforgettable years; thanks for putting up with me, and reintroducing me to the joy of board-games. The rest of the Boulder crew, Michael, Brett, Joe, Phil, Kristin, Laura, Daniel, Mindy, Jessie, Jessica, Joel, Kelsey, Rajine, Silvio, and everyone else… I had such a good group of friends during my time in Boulder; I’ll always remember our snowboarding, hiking, backpacking, and camping adventures. Alex has been both supporting and loving since we began dating approximately three years ago. I don’t know what I would do without you. I can’t wait to start a new life down in Nashville together. Finally, I need to thank my family. To my mom and dad, Roy and Melissa, thanks for all of your unconditional support throughout my life. My two sisters, Jessica and Rebekah, and brother-in-laws, thanks for putting up with and supporting me. To my two awesome nephews and my adorable niece, hopefully I’ll get to see more of you while living in Nashville. Thanks to all of my cousins, cousin-in-laws, and cousins’ babies, I’m lucky to have such a large supportive family. My cousin Jim in particular has joined me on so many adventures that I think of him like a brother. Finally, thanks to my grandma, Tater Bug. You have been one of the biggest supporters in my life. Thanks for everything, including the strong family values you have instilled in me. vi Publications John M. Garver, Zhibo Yang, Charles M. Nichols, Benjamin B. Worker, Scott Gronert, Veronica M. Bierbaum; “Resolving the α-Effect in Gas-Phase SN2 Reactions: A Marcus Theory Approach,” Int. J. Mass Spectrom., 2012, 316, 244 John M. Garver, Zhibo Yang, Nadine Wehres, Charles M. Nichols, Benjamin B. Worker, Veronica M. Bierbaum; “The α-Effect in Elimination Reactions and Competing Mechanisms in the Gas-Phase,” Int. J. Mass Spectrom., 2012, 330, 182 Charles M. Nichols, Zhibo Yang, Benjamin B. Worker, Denver R. Hager, Nico M. M. Nibbering, Veronica M. Bierbaum; “Gas-Phase Reactions of the Atomic Oxygen Radical Cation with Halogenated Compounds,” Phys. Chem. Chem. Phys., 2013, 15, 561 Charles M. Nichols, Zhibo Yang, Veronica M. Bierbaum; “Gas-phase Organic Reactions of the Atomic Oxygen Radical Cation,” Int. J. Mass Spectrom., 2013, 353, 1 Ditte L. Thomsen, Jennifer N. Reece, Charles M. Nichols, Steen Hammerum, Veronica M. Bierbaum; “Investigating the α-Effect in Gas-Phase SN2 Reactions of Microsolvated Anions,” J. Am. Chem. Soc., 2013, 135, 15508 Ditte L. Thomsen, Charles M. Nichols, Jennifer N. Reece, Steen Hammerum, Veronica M. Bierbaum. “The α- Effect and Competing Mechanisms: The Gas-Phase Reactions of Microsolvated Anions with Methyl Formate,” J. Am. Soc. Mass Spectrom., 2014, 25, 159. Ditte L. Thomsen, Jennifer N. Reece, Charles M. Nichols, Steen Hammerum, Veronica M. Bierbaum; “The α- Effect in Gas-Phase SN2 Reactions of Microsolvated Anions: Methanol as a Solvent,” J. Phys. Chem. A, 2014, 118, 8060. Scott Gronert, John M. Garver, Charles M. Nichols, Benjamin B. Worker, Veronica M. Bierbaum; “Dehalogenation of Arenes via SN2 Reactions at Bromine: Competition with Nucleophilic Aromatic Substitution,” J. Org. Chem., 2014, 79, 11020 Charles M. Nichols, William M. Old, W. Carl Lineberger, Veronica M. Bierbaum, “Gas-Phase Acidities of Nitrated Azoles as Determined by the Extended Kinetic Method and Computations,” J. Phys. Chem. A, 2015, 119, 395 Daniel J. Nelson, Wilson K. Gichuhi, Charles M. Nichols, Veronica M. Bierbaum, and W. Carl Lineberger; “Structure and Thermochemistry of o-, m-, and p-Dehydromethylphenol” – In preparation. Charles M. Nichols, Zhe-Chen Wang, Zhibo Yang, W. Carl Lineberger, Veronica M. Bierbaum, “Experimental and ─ theoretical studies of the reactivity and thermochemistry of dicyanamide: N(CN)2 ” – In preparation. Charles M. Nichols, Zhe-Chen Wang, W. Carl Lineberger, Veronica M. Bierbaum, “Gas-Phase Reactions of the deprotonated nucleobases with H, N, and O atom” – In preparation. vii Table of Contents 1 Introduction: Gas-Phase Ion Chemistry ..........................................................................................
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