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The Ionic Building Blocks of Life: Exploring Astrochemistry Through Mass Spectrometry

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THE IONIC BUILDING BLOCKS OF LIFE: EXPLORING ASTROCHEMISTRY THROUGH MASS SPECTROMETRY by Callie A. Cole B.S., Chemistry – ACS Certified University of Montana, Missoula, 2010 Certificate of College Teaching Graduate Teacher Program University of Colorado, Boulder, 2013 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 2015 This thesis entitled: The Ionic Building Blocks of Life: Exploring Astrochemistry through Mass Spectrometry written by Callie A. Cole has been approved for the Department of Chemistry and Biochemistry by: ______________________________________ Veronica M. Bierbaum ______________________________________ Theodore P. Snow ________________________ Date The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of the scholarly work in the above mentioned discipline. ii Cole, Callie A. (Ph.D., Analytical Chemistry) The Ionic Building Blocks of Life: Exploring Astrochemistry through Mass Spectrometry Thesis directed by Dr. Veronica M. Bierbaum ABSTRACT The first polyatomic molecule was discovered in interstellar space in 1968, catalyzing the growth of a new scientific field called astrochemistry. Since its inception, collaborations among laboratory chemists, astrophysical modelers, and observational astronomers in this field have led to the detection of nearly 200 molecules in the interstellar medium (ISM). Similarly, detections of complex biomolecules in cometary dust and meteorites have sparked theories of the origin of terrestrial life, a central focus of the recently-established field of astrobiology. Chemical processing occurs in a variety of environments within our galaxy. The purpose of this work is to explore the chemistry of ions and molecules that are pertinent to a multitude of these regions including nebulae, prestellar cores, and the atmosphere of Saturn’s moon, Titan. This thesis presents mass spectrometric investigations of gas-phase ion chemistry that contribute to the fields of both astrochemistry and astrobiology. Many gas-phase chemical reactions are initiated by ions due to the attractive forces induced by their charge on a reacting partner. This attraction often lowers the barriers of ion-neutral reactions, and can lead to high reaction rates even at low temperatures. The ions examined herein increase in complexity starting with simple species (CN–) and concluding with larger biomolecules, the deprotonated nucleobases. This work begins with a series of Flowing Afterglow-Selected Ion Flow Tube (FA-SIFT) – experiments exploring nitrogen-containing carbanion (CxNy ) chemistry and the formation of – interstellar propene and methyl formate (Chapters 3 and 4). Reactions between CxNy and H atoms – – reveal pathways for destruction of several CxN and CxN2 anions, but no reactions are observed for iii – CxN3 species. Two previously-proposed reactions between organic cations and H2 are shown to be immeasurably slow and unlikely to produce propene. Lastly, a reaction pathway producing protonated trans-methyl formate is experimentally and computationally verified. The later chapters describe studies of heterocyclic biomolecules performed using a modified ion trap apparatus. These ions include deprotonated azoles, pyrimidines, and purines (Chapters 5-7). In addition to their reactivity, the dissociation processes and fragments of these anions provide clues to potential precursors and abiotic syntheses. Notably, nearly all fragments observed are detected interstellar species. iv To my mother, who taught me to view the world with wonder, curiosity, and joy. We are all connected; to each other, biologically. To the earth, chemically. To the rest of the universe, atomically. Neil deGrasse Tyson v ACKNOWLEDGEMENTS There are many individuals who contributed to the completion of this thesis work, but the central figure is my advisor and mentor, Ronnie Bierbaum. Thank you for your guidance, reassurance, and (of course) scientific expertise. I also want to thank Theodore Snow, for his constant smiles of encouragement and his wisdom. You both helped make the University of Colorado my scientific home for the past 5 years. I would also like to thank a scientist and friend, Eric Herbst, for his great advice and suggestions during his visits and at conferences. Lastly, my undergraduate research advisors Chris Palmer and Philip Ramsey deserve my gratitude for introducing me to the chemistry laboratory at the University of Montana. What all five of these people have in common, in addition to their great breadth of scientific knowledge, is their ability to light up a room with their enthusiasm and positivity. Their love of science is contagious, and I thank them all deeply for that. The Bierbaum lab group has always been there for scientific support, as well as afternoon snack breaks and laughs. Oscar Martinez, Nick Demarais, Jennifer Herbst, Zhibo Yang, Charles Nichols, Zhe-Chen Wang, and Nadine Wehres all deserve my thanks. The “supergroup” meetings also allowed me to interact with other graduate students, and to practice public speaking. The supergroup members include those of the Barney Ellison, Mathias Weber, and Carl Lineberger research groups. I thank them for their interesting weekly talks and great research suggestions over the years. In addition, I thank my instructors in the Analytical and Physical Chemistry divisions, and the members of my thesis committee: Maggie Tolbert, Jose Jimenez, and Mathias Weber. Without funding, none of the research in this thesis would be possible. Therefore, I also thank the National Aeronautics and Space Administration (NASA) and the National Science Foundation (Grants CHE- 1012321, CHE-1300886, and DGE-1144083) for their financial assistance. vi My love of teaching and scientific outreach was also greatly enriched during my time at the University of Colorado. Dr. Margaret Asirvatham, Laurel Hyde Boni, Dr. Pam Nagafuji, Alan Foster, and Julie Andrew provided invaluable assistance in setting up (and thinking up) demonstrations and preparing lessons for my teaching efforts. I would like to thank several specific events and schools for the spectacular opportunities they gave me: the CU Teach Program (Julie Andrew), Boulder High School (Dr. Laura Duncan), CU Upward Bound (Tanaya Winder), CU Wizards, the Women in Science Conference, the AP Preparation Program, Longmont and Skyline High Schools (Dr. Richard Martyr), and the Graduate Teacher Program (Dr. Laura Border). Thank you so much for everything you continue to do to spread the love of science to people of all ages! I can’t finish my acknowledgements without thanking those people who helped me blow off steam outside of work. Every morning, I rely on women like Clara Chew, Candace Garbow, and Allison Betts to drag me out of bed and run. Thank you for your constant inspiration! My lunch would taste sour if I had to eat it alone, so thanks to my lunch buddies from the Niels Damrauer group. I really enjoyed my mid-day time with you. My roommate and friend Stephen Hinton has somehow put up with me for four years. I adore him and always will. Sean Bannon has been both supportive and loving to me since before I even began the Ph.D. program here at CU. He is my confidant, friend, and partner. I would not be where I am today without him. Finally, my family has been there through thick and thin, always encouraging me to press on in my pursuits: my mother, Geri, my grandmother, Lois, my twin brother, Ben, my brothers Trevor and Graham, my sister-in-law Tami, my adorable nephew Ryker, and my father, Patrick. Thank you all for your love. I’d like to extend a special thank you to my twin brother Ben (http://www.vogengineering.com), for creating many of the figures and images included in this thesis. vii PUBLICATIONS 1. Cole, C. A. & Wang, Z.-C.; Snow, T. P.; Bierbaum, V. M. Gas Phase Chemical Processes of the Cyanate Ion (OCN–). Journal of Chemical Physics. 2015, in preparation. 2. Wang, Z.-C.; Cole, C. A.; Snow, T. P.; Bierbaum, V. M. Reactions of Azine Anions with Nitrogen and Oxygen Atoms: Implications for Titan and Interstellar Gas-Phase Chemistry. Journal of the American Chemical Society. 2015, in preparation. 3. Cole, C. A.; Wang, Z.-C.; Snow, T. P.; Bierbaum, V. M. Deprotonated Purine Dissociation: Experiments, Computations, and Astrobiological Implications. Journal of Physical Chemistry A. 2015, 119, 334-343. 4. Wang, Z.-C.; Cole, C. A.; Snow, T. P.; Bierbaum, V. M. Experimental and Computational Studies of the Formation Mechanism of Protonated Interstellar Diazines. The Astrophysical Journal. 2015, 798, 102-109. 5. Cole, C. A.; Wang, Z.-C.; Snow, T. P.; Bierbaum, V. M. Anionic Derivatives of Uracil: Fragmentation and Reactivity. Physical Chemistry Chemical Physics. 2014, 16, 17835-17844. 6. Cole, C. A.; Demarais, N. J.; Yang, Z.; Snow, T. P.; Bierbaum, V. M. Heterocyclic Anions of Astrobiological Interest. The Astrophysical Journal. 2013, 779, 181-190. 7. Lin, Z.; Talbi, D.; Roueff, E.; Herbst, E.; Wehres, N.; Cole, C. A.; Yang, Z.; Snow, T. P.; and Bierbaum, V. M. Can Interstellar Propene (CH3CHCH2) Be Formed Via Gas-Phase Reactions? The Astrophysical Journal. 2013, 764, 80-85. 8. Cole, C. A.; Wehres, N.; Yang, Z.; Thomsen, D. L.; Snow, T. P.; Bierbaum, V. M. A Gas-Phase Formation Route to Interstellar Trans Methyl Formate. The Astrophysical Journal Letters, 2012, 754, L5-L9. 9. Yang, Z.; Cole, C. A.; Martinez, O.; Carpenter, M. Y.; Snow, T. P.; Bierbaum, V. M. Experimental and Theoretical Studies of Reactions between H atoms and Nitrogen-containing Carbanions. The Astrophysical Journal. 2011, 739, 19-29. viii TABLE OF CONTENTS CHAPTER 1 The Astrochemistry of Gas-Phase Ions 1.1 Introduction……………………………………………………………. 1 1.2 Astrochemical Background……………………………………………... 5 1.2.1 What is Astrochemistry? ………………………………………….. 5 1.2.2 Why Ions? ………………………………………………………... 7 1.2.3 Chemistry in the Interstellar Medium (ISM)……………………….. 10 1.2.4 Atmospheric Chemistry of Titan…………………………………... 16 1.3 Astrobiology and the Origin of Life…………………………………….
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