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Copyright by Valoris Reid Smith 2006 Copyright by Valoris Reid Smith 2006 The Dissertation Committee for Valoris Reid Smith certifies that this is the approved version of the following dissertation: From DNA Bases to Ultracold Atoms: Probing Ensembles Using Supersonic Beams Committee: Manfred Fink, Supervisor Michael Downer Lothar Frommhold Daniel Heinzen Philip Varghese From DNA Bases to Ultracold Atoms: Probing Ensembles Using Supersonic Beams by Valoris Reid Smith, B.S. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2006 To my family Acknowledgments None of this work would have been accomplished without the help and support of many, many people. Most importantly, I gratefully acknowledge my supervisor, Manfred Fink, for granting me the opportunity to carry out research under his guid- ance. Whenever things were not working, he was ready with a creative solution. His enthusiasm and profound understanding of the underlying physics serve as an exam- ple for all of those who work with him. I am also deeply indebted to him for sending me to the Max Born Institute in Berlin, which further broadened my horizons. In his lab, I have also had the opportunity to work with other wonderful people, including Watson Henderson, Ned Flagg, Robert Spitzenpfeil, Michael Eckart, Noel Ramos, F.E. (Siggie) Ziegler, and Zhaowen Tang. I am grateful to Professor Ingolf-Volker Hertel for having permitted my visit to MBI last year. Many thanks to those who were so hospitable to a stranger: Dr. Claus-Peter Schulz, Dr. Helmut Lippert, Dr. Tim Laarman, Dr. Mark Boyle, and Roman Peslin. I also thank those who worked on the DNA base experiments with me, especially Dr. Thomas Schultz, Elena Samoylova, Pierre-Alain Henry, Professor Wolfgang Radloff, Dr. Volker Stert, and Dr. Frank Noack. I feel fortunate to have been a part of the institute and of A-2. I am also grateful to Greg Sitz, John Keto, Jerry Kim, Arban Uka, Leah Shackman, Kay Hoffman, Ignacio Gallardo, David Stoker, and Brendan Murphy for the steady stream of advice and equipment that flowed my way. I appreciate v the UT Physics Machine shop and Cryo shop for their dedication and excellent workmanship and the staff of the fifth floor for always maintaining the highest levels of professionalism and friendliness. Thanks to the wonderful friends in the physics and engineering departments that have made this process as painless as possible by remaining endlessly entertaining and supportive. My special thanks to my family for their love, support and sacrifice. Finally, I would like to thank my husband, Greg, whose patience, love, and understanding are without equal. Valoris Reid Smith The University of Texas at Austin August 2006 vi From DNA Bases to Ultracold Atoms: Probing Ensembles Using Supersonic Beams Publication No. Valoris Reid Smith, Ph.D. The University of Texas at Austin, 2006 Supervisor: Manfred Fink This thesis discusses two ensembles, the study of which was dependent upon the controllable production of cold gas-phase samples using supersonic beams. The experiments on DNA bases and base clusters were carried out in Germany at the Max Born Institute. The experiments anticipating the construction of a molecular beam slower were carried out in the United States at the University of Texas at Austin. Femtosecond pump-probe techniques were employed to study the dynamics and electronic character of DNA bases, pairs and clusters in the gas phase. Experi- ments on DNA base monomers confirmed the dominance of a particular relaxation pathway, the nπ* state. Competition between this state and another proposed re- vii laxation pathway was demonstrated through observations of the DNA base pairs and base-water clusters, settling a recent controversy. Further, it was determined that the excited state dynamics in base pairs is due to intramolecular processes rather than intermolecular processes. Finally, results from base-water clusters con- firm that microsolvation permits comparison with biologically relevant liquid phase experiments and with ab initio calculations, bridging a long-standing gap. A purely mechanical technique that does not rely upon quantum or elec- tronic properties to produce very cold, very slow atoms and molecules would be more generally applicable than current approaches. The approach described here uses supersonic beam methods to produce a very cold beam of particles and a ro- tating paddle-wheel, or rotor, to slow the cold beam. Initial experiments testing the possibility of elastic scattering from a single crystal surface were conducted and the implications of these experiments are discussed. viii Contents Acknowledgments v Abstract vii List of Figures xiii I Femtosecond Studies of DNA Bases and Base Clusters 1 Chapter 1 Introduction 2 A Discussion of Molecular Physics . 7 Chapter 2 Experimental Setup 10 I Overview . 10 II Nozzle apparatus . 12 III Vacuum system . 14 IV Lasers . 15 A The Roles of the Pump and Probe Wavelengths . 18 V Detectors . 19 A Wiley-McLaren Time-of-Flight ion detector . 19 B Magnetic bottle electron spectrometer . 22 ix Chapter 3 DNA Base Monomers 24 I Background . 24 II Our experimental techniques: . 27 A Time Resolved Mass Spectra (TRMS) . 27 B Femtosecond Electron-Ion COincidence (FEICO) . 30 III Results . 37 A Adenine . 37 B Thymine . 43 C Cytosine . 46 IV Conclusions . 48 Chapter 4 DNA Base Clusters 49 I Why clusters? . 49 II How to study clusters . 50 III Homodimers . 51 A Adenine Dimer . 51 B Thymine dimer . 54 IV Heterodimers . 56 V Water Clusters . 59 A Monomer Water Clusters . 59 B Dimer Water Clusters . 63 VI Conclusions . 66 II Scattering a supersonic beam from a single crystal surface 68 Chapter 5 Introduction 69 x I Overview of Research . 69 A Supersonic Beams . 69 B Crystal Surfaces . 71 C Atom-Surface Interactions . 72 D Cold Atoms and Molecules . 73 Chapter 6 Experimental Setup 75 I Overview . 75 II Vacuum System . 76 III Nozzles and Cooling System . 79 IV Rotor . 80 V Particle Detection . 82 VI Crystal Chamber . 83 A Cleaning with a laser . 86 Chapter 7 Scattering from a stationary crystal 88 I Overview . 88 II Theory . 90 III Experimental technique . 93 IV Results . 94 A Initial scattering attempt . 94 B Ion gauge detection of the beam . 95 V Conclusions . 98 Appendices 99 A Quartz nozzle . 100 B Chopper . 101 xi C Crystal Chamber . 102 1 Previous approach to heating . 102 2 Previous approach to cooling . 103 3 Previous approach to rotation . 103 References 104 Vita 112 xii List of Figures 1.1 DNA . 4 1.2 DNA bases . 5 1.3 Canonical DNA pairs . 6 1.4 Avoided Crossings . 8 2.1 Experimental Schematic at MBI . 11 2.2 A schematic of the oven and nozzle apparatus. 13 2.3 Photo of Vacuum system . 14 2.4 Photo of the Clark laser system . 16 2.5 Schematic of our optical setup . 17 2.6 Wiley McLaren Spectrometer . 20 3.1 A cartoon of the SDDJ paradigm . 26 3.2 The relaxation channels of Adenine . 27 3.3 Mass spectrum containing water clusters . 28 3.4 A comparison of ionization at t0 and at a later time . 29 3.5 A typical electron-ion coincidence spectrum . 31 3.6 NO electron spectrum . 34 3.7 Electron spectra taken on different days . 35 xiii 3.8 Dynamics of A, λpr = 800nm ...................... 38 3.9 Dynamics of A, λpr = 400nm ...................... 39 3.10 Electron spectrum of A, λpr = 800nm ................. 40 3.11 Electron spectrum of A, λpr = 400nm ................. 41 3.12 Electron spectra of A at different delays . 43 3.13 Dynamics of T, λpr = 800nm ...................... 44 3.14 Dynamics of T, λpr = 400nm ...................... 45 3.15 Electron Spectrum of T . 46 3.16 Dynamics of C . 47 4.1 Dynamics of A2 .............................. 52 4.2 Electron spectrum of A2 ......................... 53 4.3 Dynamics of T2 .............................. 54 4.4 Electron spectrum for T2 ........................ 55 4.5 Electron spectrum of AT, A and T . 57 4.6 Dynamics of AT . 58 4.7 Electron spectra of A(H2O)n ...................... 61 4.8 Dynamics of T(H2O)n .......................... 62 4.9 Dynamics of C(H2O)n .......................... 64 4.10 Dynamics of A, A2, A(H2O)3, and A2(H2O)3 ............. 65 6.1 Experimental Overview, large scale . 76 6.2 Experimental Overview, small scale . 77 6.3 Rotor Schematic . 80 6.4 Sample holder schematic . 84 7.1 Chopper Rod . 101 xiv Part I Femtosecond Studies of DNA Bases and Base Clusters 1 Chapter 1 Introduction The earth was nearly uninhabitable after formation. It was rocky, comprised of silicates and an iron core condensed from the solar nebula, and added to by bom- barding meteorites. In the Hadean eon, the earth did not even have water, liquid or otherwise, until sufficient impact with comets and meteorites left behind water ice and various hydrocarbons, important for generation of life. Its initial atmosphere consisted of hydrogen and helium and then later, CO2, water vapor and ammonia emitted from volcanoes. Oxygen and ozone as significant parts of the atmosphere did not emerge until after photosynthesis and plant life arose. Without the ozone layer, the sun’s rays entered the atmosphere and impacted the earth’s surface, largely unimpeded. We consider the ozone layer vital because it protects us and other living things by absorbing the harmful UV rays of the sun. When a high energy UV photon is absorbed by a biomolecule, it promotes the molecule into a more reactive excited state. In this state, the molecule can transform to a different structure, can react with other molecules to create new ones, or can dissociate. Any of these destructive processes can lead to potentially harmful effects.
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