Gas-Phase Ion Chemistry in Interstellar, Circumstellar, and Planetary Environments by Nicholas J. Demarais B.S., Minnesota State University, Mankato, 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 2014 This thesis entitled: Gas-Phase Ion Chemistry in Interstellar, Circumstellar, and Planetary Environments written by Nicholas J. Demarais has been approved for the Department of Chemistry and Biochemistry 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 scholarly work in the above mentioned discipline. Demarais, Nicholas J. (Ph.D., Physical Chemistry) Gas-Phase Ion Chemistry in Interstellar, Circumstellar, and Planetary Environments Thesis directed by Dr. Veronica M. Bierbaum Abstract In the last century, astronomers, physicists, and chemists have shown that the environ- ments of space are complex. Although we have learned a great amount about the interstellar medium, circumstellar medium, and atmospheres of other planets and moons, many mys- teries still remain unsolved. The cooperation of astronomers, modelers, and chemists has lead to the detection of over 180 molecules in the interstellar and circumstellar medium, and the evolution of the new scientific field of astrochemistry. Gas-phase ion chemistry can determine the stability of ions in these complex environments, provide chemical networks, and guide searches for new interstellar molecules. Using the flowing afterglow-selected ion flow tube (FA-SIFT), we have characterized the reactions of positive and negative ions that are important in a variety of astrochemical environments. The detection of CF+ in photodissociation regions highlights the importance of fluorinated species in the interstellar medium. The viability of CF+ as a possible diffuse interstellar band (DIB) carrier is discussed as related to reactions with neutral molecules in various interstellar conditions; the reactions of CF+ with twenty-two molecules of interstellar relevance were investigated. + The chemical reactions of HCNH with H2, CH4, C2H2, and C2H4 were reexamined to provide insight into the overprediction of HCNH+ in Titan’s ionosphere by current astro- chemical models. In addition, this work suggests other chemical reactions that should be included in the current models to fully describe the destruction rates of HCNH+ in Titan’s ionosphere. The reactions of polycyclic aromatic hydrocarbon (PAH) ions with H atoms and other iv small molecules were carried out to determine the stability of these species. In diffuse regions, where the photon flux is high, PAH cations are the dominant ionization state. This work continues our previous research to include PAHs of differing geometries as well as nitrogen- containing PAHs. Extension to larger PAH cations was made possible by the integration of the laser induced acoustic desorption (LIAD) source with the FA-SIFT. In addition, in dense environments, where the photon flux is low, anionic PAHs may exist. The detection of negative ions in the past 10 years has highlighted the importance of their inclusion in astrochemical models. We have investigated the chemistry of deprotonated PAHs with molecules of interstellar relevance to determine their chemical stability in dense regions of the interstellar and circumstellar medium. In addition to PAH anions, H− is an important species in dense interstellar environ- ments. While the reaction of hydride anion has been recognized as a critical mechanism in − − the initial cooling immediately after the Big Bang, H + H −→ H2 + e , chemistry with neutral molecules was largely unknown. The chemistry of H− with various classes of organic molecules was investigated and conclusions are drawn based on reaction mechanisms. Dedication To my family. “The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of star stuff.” —Carl Sagan Acknowledgements First and foremost, I would like to express my sincere gratitude to my adviser Veronica Bierbaum. Thank you for pushing me to become a better scientist, researcher, writer, and critic. I appreciate all of the time you have spent guiding and mentoring me. I will never forget your acute attention to detail and I will carry that with me throughout the rest of my career. Thank you for allowing me to fail and learn from my mistakes. In addition, I would like to acknowledge and thank my unofficial adviser, Theodore Snow. Thank you for exposing me to the field of astrophysics and introducing me to one of the most fascinating scientific mysteries, the diffuse interstellar bands. I appreciate your patience and guidance in my understanding of astrophysics and your ability to see the big picture impact through all of the chemistry. To both of you, I will never be able to repay to you what you have given me. Thank you. Second, I need to thank all of the behind-the-scenes help that I have received in my tenure at the University of Colorado, Boulder. Thank you to Don David, Ken Smith, and everyone in the CIRES integrated instrument development facility. You all were integral in maintaining the FA-SIFT, helping with repairs and troubleshooting, and designing and implementing the laser induced acoustic desorption technique. I would not have been able to finish my degree without your expert knowledge and immense amount of patience. A special thank you is extended to Hilkka Kentt¨amaa and her research group at Purdue for allowing me to visit their laboratory and providing invaluable insight into the LIAD technique. In addition, I want to thank Marshall Wilkinson and everyone in the ChemStore and purchasing vii department. Thank you for all the time and effort you put into obtaining all of the dangerous chemicals that I needed. Lastly, I have to thank all of the great people I have met and have had the opportunity to interact with. Thank you to my lab mates over the years: Oscar Martinez Jr., John Garver, Callie Cole, Charles Nichols, Ditte Thomsen, Zhibo Yang, Nadine Wehres, Jeniffer Herbst, and Zhe-Chen Wang. Thank you all for your collaborations and discussions, guidance and wisdom, and for being great friends. I never thought I would meet a group of people who love sugar as much as I do. In addition, I would like to thank everyone involved in the ion supergroup: the Ellision lab, Lineberger lab, and Weber lab. Thank you all for you help and guidance, and for allowing me to present my research. The last group of people I have to thank are my classmates. I owe a huge thank you to all of you. We worked together, made it through, and now it’s on to the next challenge. Congratulations to all of you, and good luck in your next endeavor. viii Contents Chapter 1 Gas-Phase Ion Chemistry in Interstellar, Circumstellar, and Planetary Environments 1 1.1 Introduction.................................... 1 1.2 InterstellarandCircumstellarMedium . ....... 5 1.2.1 DiffuseAtomicClouds .......................... 5 1.2.2 DiffuseMolecularClouds. 8 1.2.3 TranslucentClouds ............................ 8 1.2.4 DenseMolecularClouds ......................... 9 1.2.5 CircumstellarMedium . .. .. ... .. .. .. .. .. ... .. .. 10 1.3 DiffuseInterstellarAbsorptionBands . ...... 11 1.4 UnidentifiedInfraredEmissionBands . ..... 14 1.5 AtmosphereofTitan ............................... 14 1.6 Conclusion..................................... 15 1.7 References..................................... 19 2 Methods 24 2.1 Introduction.................................... 24 2.2 Flowing Afterglow-Selected Ion Flow Tube Technique . ......... 24 2.2.1 IonProductionFlowTube . 25 ix 2.2.2 IonSelectionRegion ........................... 27 2.2.3 ReactionFlowTube ........................... 27 2.2.4 IonDetectionRegion........................... 29 2.3 LaserInducedAcousticDesorption . .... 29 2.4 IonFormation................................... 35 2.5 HydrogenAtomGeneration . 36 2.6 ReactionRateConstantDetermination . ...... 37 2.6.1 Ion-MoleculeReactions. 37 2.6.2 Ion-HAtomReactions .......................... 43 2.7 ProductDistributionDetermination. ....... 45 2.8 Radiative Association Rate Constant Determination . .......... 45 2.9 Collision Rate Constant and Reaction Efficiency Determination ....... 48 2.10 ComputationalMethods . .. 49 2.11References..................................... 50 3 Gas-Phase Reactions of Polycyclic Aromatic Hydrocarbon Cations andtheirNitrogen-ContainingAnalogswithHAtoms 53 3.1 Introduction.................................... 53 3.2 Methods...................................... 54 3.2.1 ExperimentalMethods . 54 3.2.2 ComputationalMethods . 57 3.3 ResultsandDiscussion . .. 59 3.3.1 SizeandGeometryDependence . 59 3.3.2 PAHversusPANHCations ....................... 63 3.4 Conclusion..................................... 64 3.5 References..................................... 66 x 4 Chemistry of CF+ anditsRelevancetotheInterstellarMedium 70 4.1 Introduction.................................... 70 4.2 Methods...................................... 72 4.2.1 ExperimentalMethods . 72 4.2.2 ComputationalMethods . 73 4.3 ResultsandDiscussion . .. 74 4.3.1 Triatomics................................. 76 4.3.2 Oxygen-ContainingOrganics. .. 78 4.3.3 CX4/NX3 ................................. 81 4.3.4 Hydrocarbons............................... 84 4.3.5