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UC Santa Barbara Dissertation Template UNIVERSITY OF CALIFORNIA Santa Barbara Interplay of molecular structure and photon response in select alternative nucleobases and pigments A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry by Gregory Michael Gate Committee in charge: Professor Mattanjah de Vries, Chair Professor Steven Buratto Professor Martin Moskovits Professor Joan-Emma Shea December 2020 The dissertation of Gregory Michael Gate is approved. ____________________________________________ Steven Buratto ____________________________________________ Martin Moskovits ____________________________________________ Joan-Emma Shea ____________________________________________ Mattanjah de Vries, Committee Chair December 2020 Interplay of molecular structure and photon response in select alternative nucleobases and pigments Copyright © 2020 by Gregory Michael Gate iii ACKNOWLEDGEMENTS To my family, who have supported me throughout this entire process. They have patiently tolerated my frantic stress and grumpiness induced by grad school and the Army Reserves. To my friends who did their best to stay in touch thank you for always encouraging me and picking me when I was down. To the United States Army, for making me a better and stronger person, and continually taking me out of my academic bubble. To Mattanjah, for developing me into a scientist, and listening to my crazy ideas. To Michael, for encouraging my crazy ideas putting up with me for the past 5 years. And to all my intramural teams, to include Bucky Ballers I – XV, Bucky Ballers, and ’96 Bullets thank you for keeping me sane and giving me something to look forward to throughout the week. We will forever be chasing those shirts. iv VITA OF GREGORY MICHAEL GATE December 2020 EDUCATION Doctor of Philosophy in Chemistry, University of California, Santa Barbara, December 2020 Advisor: Prof. Mattanjah S. de Vries Bachelor of Science in Biochemistry, Santa Clara University, June 2014 (cum laude) Advisor: Prof. Steven W. Suljak RESEARCH EXPERIENCE Ph.D. Candidate, Physical Chemistry December 2015 – December 2020 de Vries Lab, Department of Chemistry and Biochemistry, UCSB • Focus on photodynamics of canonical and non-canonical nucleobases • Do cold, gas-phase spectroscopy in high vacuum to study photodynamics of isolated organic molecule free from thermal and solvent effects • Employ laser desorption jet-cooled mass spectrometry to get large organic molecule in the gas phase and do action spectroscopy • Utilize resonance enhanced multiphoton ioinization for high resolution spectroscopy in the ultraviolet, visible, and infrared regions • Utilize digital delay generator, digital oscilliscopes, and photodiode arrays to achieve time control resolution down to single nanoseconds • Use Python, Mathematica, and Labview to run experiments and do data analysis Research Assistant, Organic Synthesis Fall 2014, Spring 2015 Fuller Lab, Chemistry and Biochemistry Department, SCU • Used solid-phase synthesis technique to synthesize peptoids with heterocycle backbone to mimic peptides with biological activity • Used high pressure liquid chromatography and liquid chromatography-tandem mass spectrometry to purify and analyze peptoids • Tested peptoids for biological activity Research Assistant, Peptide Analysis and Aptamer Selection Fall 2011 – June 2014 Suljak Lab, Chemistry and Biochemistry Department, SCU • Used manual and automated solid-phase peptide synthesis techniques to synthesize various peptides up to 26 amino acids long • Used high pressure liquid chromatography and liquid chromatography-tandem mass spectrometry to purify and analyze peptides for use in biological assays • Monitored fluorescently-tagged aptamer binding to protein using capillary electrophoresis MILITARY EXPERIENCE Observer, Coach, Trainer (OCT) team leader November 2017 – Present v • Lead about 10 soldiers • Senior OCT, responsible for developing and executing OCT training and certifying soldiers • Observe and evaluate other units’ training, ensuring they are trained to standard and mission ready • Ensure all soldiers on team are qualified OCTs to include identifying doctrinal tasks, public speaking, facilitating discussion, setting up a training lane • Attended First Army Academy, learned how to setup training lanes, identify pertinent doctrine, OCT basics • Combat Lifesaver Certified, having knowledge in tourniquet application, sucking chest wound, collapsed lung, Tactical Casualty Care Combat engineer platoon leader June 2014 – November 2017 • Led over 25 enlisted combat engineers • Helped develop weekend-long training events for up to 90 soldiers, and ensured all necessary equipment and supplies were allocated and accounted for • Ensured all soldiers were proficient in their combat engineer duties including infantry tactics, engineer recon, obstacle breaching, and urban breaching • Assisted soldiers in their personal and civilian lives including receiving military benefits, job searching, school enrollment • Led soldiers through extended combat exercises ACADEMIC AWARDS • Awarded Graduate Research Mentorship Program Fellowship 2019 • Awarded Outstanding Service to the Department Award 2018 and 2019 • Qualified for the semifinals of UCSB’s Grad Slam 2018 PRESENTATIONS • Photon Science Seminar talk on “Excited State Dynamics of Nucleobase Analogues Near Excitation Threshold” at SLAC 2020 • Presented poster on “Mixing Up the R-Groups on the Purines to Unravel the Photostability Mystery” at Pacific Conference for Spectroscopy and Dynamics 2020 • Gave talk on “Using Photostability to Help Select Life” at Chemical Student Speaker Seminars 2019 • Presented poster on “Looking at the isomeric side of life with isoguanine” at ACS Western Regional Meeting 2018 • Gave talk on “Excited state dynamics of a pair of alternative DNA bases” at Pacific Conference for Spectroscopy and Dynamics 2018 • Presented poster on “Probing Intrinsic Photodeactivation Pathways of Nucleobases and Dyes in a Molecular Beam” at Faraday Discussion 2019 PUBLICATIONS vi • G. Gate, A. Willliams, S. Boldissar, R. Szabla, M.S. de Vries, Evidence for a barrier and intersystem crossing in two tautomers of 2,6-diaminopurine, In Preparation • G. Gate, A. Williams, R. Szabla, M.S. de Vries, Experimental and theoretical photodynamics of xanthine and 9-methylxanthine in the gas phase, In Preparation • G. Gate, A. Fuller, G. Hill, M.S. de Vries, Probing the solvent-free excimer dynamics of DNA using the DNA analogue, PNA, In Preparation • G. Gate, A. Williams, M.R. Haggmark, N. Svadlenak, M.S. de Vries, Nucleobases as molecular fossils of prebiotic chemistry: Excited state dynamics of C2 and C6 substituted purines, Royal Society of Chemistry, Book Title: Prebiotic Chemistry. Editors: Franz Saija and Giuseppe Cassone (In Press 2020) • G. Gate, R. Szabla, M. Haggmark, R. Sobolewski, M.S. de Vries, Photodynamics of alternative DNA base isoguanine, Phys. Chem. Chem. Phys, 2019, 21, 13474 2019 PCCP HOT Article • J. Berenbeim, M. Haggmark, G. Gate, C. Patterson, M. Rode, M.S. de Vries, Excited state intramolecular proton transfer in hydroxyanthraquinones: Toward predicting fading of organic red colorants in art, Science Advances, 2019, 5(9), eaaw5227 • M.R. Haggmark, G. Gate, S. Boldissar, J. Berenbeim, A.L Sobolewski, M.S. de Vries, Evidence for competing proton-transfer and hydrogen-transfer reactions in the S1 state of indigo, Chem. Phys., 2018, 515, 535-542 • J.A. Berenbeim, S. Boldissar, F.M. Siouri, G. Gate, M.R. Haggmark, B. Abalouche, T. Cohen, M.S. de Vries, Excited-State Dynamics of Isocytosine: A Hybrid Case of Canonical Nucleobase Photodynamics, J. Phys. Chem. Lett., 2017, 8(20), 5184-5189 • A. Mohan, A.H.M. Koh, G. Gate, A.L. Alkins, K.N. McCormas, A.A. Fuller, Solid- Phase Synthesis of Azole-Compromising Peptidomimetics and Coordination of a Designed Analog to Zn2+, Molecules, 2018, 23(5), 1035 vii ABSTRACT Interplay of molecular structure and photon response in select alternative nucleobases and pigments by Gregory Michael Gate The spectroscopic analyses of organic molecules relevant to genetic material and the origin of life, as well as various culturally important pigments and dyes are reported. This analysis was conducted in the cold, gas phase using resonance enhanced multiphoton ionization (REMPI). REMPI allows for structural characterization and a temporal description of the excited state dynamics. This experimental technique, when combined with state-of-the-art theoretical calculations, creates a much clearer picture of what is occurring on the molecular and electronic levels. These studies are focused on the excited state dynamics of these systems – how do they react and get rid of their electronic energy after absorption of a photon. A photon is merely a packet of energy, which a molecule then converts to electronic energy upon resonant photon absorption. How these systems react to this added energy is a function of their electronic structure, which is ultimately dependent on their molecular structure. Slight changes in the molecular structure alter the excited state dynamics. It is our goal to develop a model to connect molecular structure to photostability. Several nucleobase analogues have been studied to determine their photostability. These studies were conducted to help understand the role light hardiness played in the evolution of viii life’s genetic material, long before the creation of the ozone layer. Photostability is determined by a system’s excited state lifetime and the presence of any barriers along
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