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1 Theoretical Studies of Reactive Intermediates in Complex Reaction Mechanisms Dissertation Presented in Partial Fulfillment Of Theoretical Studies of Reactive Intermediates in Complex Reaction Mechanisms Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By William H. Coldren Graduate Program in Chemistry The Ohio State University 2018 Dissertation Committee Professor Christopher M. Hadad, Advisor Professor Jon R. Parquette Professor David A. Nagib Professor Karl A. Werbovetz 1 Copyrighted by William H. Coldren 2018 2 Abstract The mechanistic transformations of three fundamental classes of reactive intermediates are explored: singlet and triplet carbenes, carbene radical cations, and carbon-centered radicals. Through a marriage of theory and ultrafast spectroscopy, the identities of unique carbene species and photochemical transformations were characterized from nitrogenous (diazo and diazirine) precursors. The photochemistry of a novel trifluoro-diazo, carbenic precursor (ethyl 2-diazo-3,3,3-trifluoropropanoate) is explored by ultrafast time-resolved infrared spectroscopy in multiple solvents and the results do not reveal a prototypical 1,2-migration product via rearrangement in the excited state or through a carbene intermediate. The primary photochemical process is the interconversion of a diazo functional group to the corresponding diazirine. A completely new mechanistic pathway is detailed for the conversion of diazo and diazirine containing nitrogenous precursors to their corresponding products. This theoretical report accounts for the partially unexplained and curious bifurcation in photochemical vs thermal decomposition of nitrogenous precursors. Using a phenanthrene precursor, the first ultrafast time-resolved spectroscopic observation of a vinyl carbene (singlet a-methylbenzylidenecarbene) is reported and the results are supported and rationalized by computational data. ii Electronic factors affecting the regioselectivity of aryl radical hydrogen-atom abstraction reactions in benzyl-alkyl tethered species is explored in order to guide efforts of selective remote C–H functionalizations. The system can be biased towards or away from the standard abstraction pathway by the use of electron-donating and electron- withdrawing groups strategically placed on the benzene ring. The mechanistic aspects of the oxidative transformation of C2 symmetric o- aminophenol species and C3 symmetric formyl fragments to form benzobisxazole based covalent organic frameworks (COFs). Computational data strongly suggest that such reactions occur via a putative radical species that is stabilized by an active captodative effect. The nature of the catalysts used affects the efficiency of this reaction and the overall crystallinity and porosity of desired COFs. Preliminary investigations into the difficulty of resurrecting aged huAChE based on the nature of organophosphorus chemical nerve agents are presented. The active site is severely contracted for a methyl phosphonate aged enzyme compared to an alkyl phosphate aged enzyme. In silico prediction of factors influencing the binding and activity of novel quinone methide precursors as potential therapeutics is investigated with biophysical molecular dynamics simulations and in the case of one substrate, the efficacious enantiomer was predicted a priori to experimental in vitro screening. iii Dedication To my parents, John and Karen Coldren, and all of my family and friends, without whom none of my success would be possible. “He who has a why to live can bear almost any how.” – Friedrich Nietzsche “The fundamental laws necessary for the mathematical treatment of a large part of physics and the whole of chemistry are thus completely known, and the difficulty lies only in the fact that application of these laws leads to equations that are too complex to be solved.” – Paul Dirac iv Acknowledgments As I’ve finally reached this moment in time where my graduate career is almost at a close, I am reminded, humbled, and blessed by the many outstanding people who have made my accomplishments possible. This acknowledgment section could take up an entire chapter’s worth of space and still not adequately cover the extent of my gratitude towards all those mentioned. Brevity was never my thing as anyone who knows me could surely tell you (I think the tremendous amount of epic fantasy literature I have read has contributed to this shortcoming), but I will endeavor to do my best. Buckle up… I would like to thank my mother and father for their constant love, encouragement, patience, and support throughout my life. Their support has allowed me to defeat every obstacle, no matter the size, that has obstructed my path. To the D’Elias, Mr. and Mrs. D’Elia, Patrick and Becky, Scott and Catherine whom I consider to be as close as family; my gratitude for your selflessness, love, kindness, prayers, and support I cannot sufficiently put into words. To Dr. Francis Marchlinski, Dr. Anjali Tiku Owens, Monica Pammer, Erica Zado, Amy Beatty Marzolf, Dr. Stephanie Clouse, and Dr. Heidi Johnson as well as many other talented and compassionate electrophysiologists, nurses, especially my good friend Rachel Zekany, and the many other healthcare professionals at the University of Pennsylvania. You helped me through some of the most challenging periods of my life v and enabled me to live and accomplish my goals and live out my passion. You've instilled in me a desire to do everything that is within my power to help others. To Mr. Spahr, my first chemistry instructor and one of the most influential instructors I have ever met. I was hooked on the subject from the first day of class. I decided my sophomore year of high school that I was going to study chemistry, and it would be my passion for life. The critical thinking skills you instilled in me, and the sheer amount of talent and excitement you brought to the classroom is something I will take with me wherever I go. I'd like to thank my undergraduate research advisor Dr. Daniel Falvey and my graduate mentor Dr. Raffaele Perrotta who introduced me to the world of reactive intermediates and computational chemistry and guided me on my way to my graduate studies. To Dr. Christopher Hadad whose unending patience, unparalleled expertise, guidance, and willingness to help and mentor me throughout my graduate career has entirely enabled the successful completion of my Ph.D. The lessons I have learned I will keep for a lifetime. You have been an absolutely outstanding advisor. I owe you a debt that I can never possibly repay. Thank you, you are an inspiration of excellence. To Dr. Matthew Platz, my only regret is that our time at OSU didn’t overlap for longer. You are monumental in the field of reactive intermediate chemistry. It has been an absolute pleasure speaking and collaborating with you. To my graduate teaching mentors, Dr. Christopher Callam and Dr. Noel Paul, your commitment to excellence is an inspiration. You have a fantastic ability to draw out vi the best in the people around you. Dr. Callam, your love of everything chemistry and tremendous knowledge along with the willingness to discuss life and science has been a blessing. To the Hadad Group, especially Dr. Hoi Ling (Calvin) Luk, Dr. Shubham Vyas, and Dr. Shameema Oottikkal who spent the time to answer my questions and guided me at the beginning and throughout my graduate career. I’d also like to thank my classmates and colleagues: Dr. Ryan McKenney, Dr. Thomas Corrigan, Dr. Qinggeng Zhuang, Andrew Franjesivic, Ola Nosseir, Dr. Jojo Joseph, Sarah Border, Dr. Amneh Young, Dr. Ben Garrett, and Dr. Shane Polen. Also, to the new class of graduate students, especially Remy Lalisse and Joe Fernandez, may your careers and computational endeavors be fruitful. The thoughtful scientific discussion and support provided by those above was invaluable. To Dr. Krista Cunningham who cheered me on every step of the way to the finish line, your compassion and friendship is absolutely irreplaceable. Also, to all of my friends that helped me along my journey, putting up with my insanity. Thanks to Ryan Letourneau and the rest of the gang, your humor helped keep me afloat during my graduate career and while completing this thesis. A final thanks to the agencies that supported this research: The Ohio Supercomputing Center, the National Science Foundation, and the National Institutes of Health. vii Vita September 21, 1989 ......................................Born – Chester County, Pennsylvania USA June, 2008 ....................................................Lancaster Catholic High School May, 2012 ....................................................B.S., Chemistry, University of Maryland, College Park 2012–2016 ...................................................Graduate Teaching Associate, Department of Chemistry, The Ohio State University 2016–2018 ...................................................Graduate Research Associate, Department of Chemistry, The Ohio State University Publications 1. Perrotta, R. R.; Winter A. H.; Coldren, W. H.; Falvey, D. E. “2-(3,5- Dinitrophenyl)-1,3-dithiane Carbanion: A Benzylic Anion with a Low Energy Triplet State” J. Am. Chem. Soc. 2011, 133, 15553–15558. 2. Kaur, D; Luk, H.; Coldren, W.; Srinivas, P. M.; Sridhar, L.; Prabhakarm S.; Raghunathan, P.; Guru Row, T. N.; Hadad, C. M.; Platz, M. S.; Eswaran, S. V. “Concomitant Nitrene and Carbene Insertion Accompanying Ring Expansion: Spectroscopic, X-ray, and Computational Studies” J. Org. Chem. 2014, 79, 1199– 1205. 3. Feng, C.; Chan, D.; Joseph, J.; Muuronen, M.; Coldren, W. H.; Dai,
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