Brigham Young University BYU ScholarsArchive Theses and Dissertations 2011-08-09 The Formation and Stability of Radical-Molecule and Radical- Radical Complexes and Their Importance in Atmospheric Processes Jared M. Clark Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biochemistry Commons, and the Chemistry Commons BYU ScholarsArchive Citation Clark, Jared M., "The Formation and Stability of Radical-Molecule and Radical-Radical Complexes and Their Importance in Atmospheric Processes" (2011). Theses and Dissertations. 2679. https://scholarsarchive.byu.edu/etd/2679 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. The Formation and Stability of Radical-Molecule and Radical-Radical Complexes and Their Importance in Atmospheric Processes Jared Matthew Clark A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Jaron C Hansen, Chair Milton L Lee Daniel E Austin Matthew C Asplund Delbert J Eatough Department of Chemistry and Biochemistry Brigham Young University December 2011 Copyright © 2011 Jared M Clark All Rights Reserved This thesis is dedicated to the patience and great goodness of my wife Ruth and my three beautiful children Katie, Nathan, and Alice THE TEST OF A FIRST RATE INTELLIGENCE IS THE ABILITY TO HOLD TWO OPPOSED IDEAS IN THE MIND AT THE SAME TIME, AND STILL RETAIN THE ABILITY TO FUNCTION. ONE SHOULD, FOR EXAMPLE, BE ABLE TO SEE THAT THINGS ARE HOPELESS AND YET BE DETERMINED TO MAKE THEM OTHERWISE. -- F. SCOTT FITZGERALD ABSTRACT The Formation and Stability of Radical-Molecule and Radical-Radical Complexes and Their Importance in Atmospheric Processes Jared Matthew Clark Department of Chemistry and Biochemistry, BYU Doctor of Philosophy This research explores the role that radical-molecule complexes play in the chemistry of Earth's atmosphere. The formation of such complexes can have direct and pronounced effects on the reaction and product outcome of atmospheric chemical reactions. Some attention is also given to the formation of radial-radical pre-reactive complexes in the HO + ClO system. Peroxy radicals (RO2) can form stable complexes with polar compounds such as H2O, NH3, and CH3OH. For the simplest RO2 radical, HO2, complex formation (e.g., HO2−H2O, HO2−NH3, and HO2−CH3OH) gives rise to a significant increase in the HO2 self-reaction rate constant. Although this phenomenon has been observed since the mid-1970s, no satisfactory explanation has been put forward to explain this effect. Herein a rationale for the enhancement of the HO2 self-reaction is given based on extensive geometric, mechanistic and natural bond orbital (NBO) analyses. The apparent lack of a rate enhancement for the methyl peroxy (CH3O2) self- reaction is also presented. The combined insights gained from these two systems are then extended to predict if a water enhancement is expected for the 2-hydroxyethyl peroxy (HOCH2CH2O2) self-reaction kinetics. The computational results of this study are then compared to experimental work and conclusions are drawn towards a general procedure to predict the presence/absence of water initiated rate enhancements in RO2 systems as a whole. Original work regarding the formation of a series of organic RO2−H2O complexes is presented. This work established the effects of different functional groups on the stability of organic peroxy radicals and makes estimates of the associated atmospheric lifetimes and equilibrium constants. This work is further extended to the family of peroxy radicals that form from the atmospheric oxidation of isoprene (the most abundant non- methane biologically emitted hydrocarbon). For the first time, complexes of isoprene peroxy radicals with water are presented along with atmospheric lifetime estimates. Conclusions are made as to the effect of water on the product branching ratio of the isoprene peroxy radical + NO2. The oxidation of hexanal to form hexanal peroxy radicals is discussed within the context of the formation of hexanal peroxy water complexes. Aerosol formation is also perturbed as a result of complexation. Aerosol formation under atmospheric conditions is hypothesized to be initiated by radical- molecule complex formation. For example, in the absence of ammonia, the nucleation of H2SO4 in water vapor to form sulfuric acid aerosols is slow. However, as the concentration of NH3 rises, a marked increase in the rate of sulfuric acid aerosol formation is observed. This work explores the effects of the photolysis products of NH3 (NH2 and NH) on the rate of aerosol formation in systems involving H2SO4, HNO3, HC(O)OH, and CH3C(O)OH. With the exception of H2SO4−NH3 and HNO3−NH3 (geometries already published in the literature), minimum energy structures are presented here for the first time for each of the acid−NHx complexes. Thermochemical data and lifetime estimates are provided for each complex. Conclusions about the relevance of acid−NH2 and acid−NH in the formation of atmospheric aerosols are set forth. Finally, mechanistic insights into the reaction of the hydroxyl radical (OH) and Cl2O are obtained via analysis of the two potential energy surfaces that both involve the formation of HO−Cl2O pre-reactive complexes. Keywords: peroxy radical, radical water complex, atmosphere, ozone, aerosol ACKNOWLEDGEMENTS I express my deepest appreciation and thanks to my dear wife Ruth Clark for her unfailing patience and support throughout my time as a graduate student. Her belief in me made all my efforts leading to the production of this thesis possible. I thank my adorable children for their love and for all of the times they begged me not to go into work, but to stay home and play with them. I would like to thank my graduate advisor, Jaron Hansen, for the untold wealth of knowledge and experience he has given me and for seeing potential in me when I first arrived at BYU. I want to acknowledge my fellow graduate student Taylor Cline for all of the effort and work he put in to help make this dissertation possible. I would also like to thank Marie Chilton for her help with data modeling. TABLE OF CONTENTS LIST OF FIGURES .......................................................................................................... xv LIST OF TABLES ........................................................................................................... xix CHAPTER 1: INTRODUCTION ....................................................................................... 1 1.1 Radical-Molecule Complexes .............................................................................. 1 1.2 Peroxy Radicals ................................................................................................... 2 1.3 Aerosol Formation................................................................................................ 4 1.4 OH + Cl2O Chemistry .......................................................................................... 6 CHAPTER 2: AN NBO ANALYSIS OF THE CATALYTIC EFFECT OF WATER ON THE HO2 SELF-REACTION ............................................................................................. 7 2.1 Abstract ................................................................................................................ 7 2.2 Introduction .......................................................................................................... 7 2.3 Methods ................................................................................................................ 8 2.4 Results and Discussion ....................................................................................... 10 2.4.1 HO2—HO2 Reaction and Hydrogen Bonding ............................................. 11 2.4.2 HO2−HO2 Potential Energy Surface ........................................................... 13 2.4.3 HO2−H2O−HO2 Potential Energy Surface .................................................. 22 2.5 Conclusions ........................................................................................................ 32 2.6 Supplementary Material ..................................................................................... 33 2.6.1 Cartesian Coordinates for Each Optimized Geometry ................................ 33 2.6.2 Harmonic Vibrational Frequencies ............................................................. 37 CHAPTER 3: COMPUTATIONAL STUDY ON THE EXISTENCE OF ORGANIC PEROXY-WATER COMPLEXES (RO2-H2O) ............................................................... 39 3.1 Abstract .............................................................................................................. 39 3.2 Introduction ........................................................................................................ 39 3.3 Methods .............................................................................................................. 42 3.4 Results ................................................................................................................ 45 3.4.1 Foreword ..................................................................................................... 45 3.4.2 Calibration..................................................................................................