Applications of Computational Chemistry Towards Combatting Challenges in Chemical Warfare and Renewable Energy
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Applications of Computational Chemistry towards Combatting Challenges in Chemical Warfare and Renewable Energy DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Ryan J. Yoder Graduate Program in Chemistry The Ohio State University 2013 Dissertation Committee: Professor Christopher M. Hadad, Advisor Professor Jonathan R. Parquette Professor James P. Stambuli Copyright by Ryan J. Yoder 2013 Abstract Across the globe, chemists are constantly seeking to provide answers to the challenges threatening our society. Both long-term obstacles and short-term hazards are being confronted with the commitment of time, money, and intellectual acumen. The challenges faced in this thesis span both the imminent threat of the deployment of chemical warfare agents, and the long-term challenge of renewable energy. One strategy towards combatting the toxic effects of these chemical warfare agents will focus on reversing the result of exposure to organophosphorus (OP) compounds. The other strategy will examine the use of synthetic molecular baskets as a macromolecule designed to entrap OP compounds before victims can feel their adverse effects. Also in this thesis, our contribution towards the pursuit of sources for renewable energy, namely the synthesis of important small molecules from chemical feedstocks, will be presented. OP compounds are a grave threat to military and civilian populations, especially in the context of increasing acts of terror around the globe. These nerve agents are toxic due to their inhibition of the acetylcholinesterase (AChE) active site. Although some methods of enzyme recovery are known to exist, they succumb to the need to be presented to affected victims in an extremely short amount of time. Currently, there are no known therapeutics to recover aged AChE, a permanently dead form of the enzyme upon prolonged inhibition as a result of OP binding to the enzyme. Part of this thesis will ii present efforts towards the development of a small molecule therapeutic designed as an alkylating agent to reverse the aging process and ultimately recover the active enzyme. Our efforts have focused on the synthesis of a library of quinone methide precursors (QMPs) that have been shown to alkylate a model phosphonate, making them promising candidates for further study with the native enzyme. An alternate strategy to the reversal of the inhibition of the enzyme by OP compounds would be to sequester the nerve agent before it binds with AChE. In collaboration with the Badjic research group at The Ohio State University, molecular baskets have been synthesized to accomplish this goal. A rigorous computational protocol was established to examine the conformational flexibility of the molecular baskets, and further modeling studies were performed to determine the recognition of various OP compounds by molecular baskets. An imidazole-capped basket, mimicking a decarboxylated histidine residue, has been shown to bind the small OP compound, dimethoxy methylphosphonate (DMMP). Finally, this thesis will present efforts in collaboration with the Stambuli research group at The Ohio State University towards the development of a metal catalyst to transform a saturated fatty acid into an unsaturated fatty acid. This novel chemistry would allow access to value-added chemicals as identified by the Department of Energy. Our molecular modeling studies provided important insight to experimental results. These insights included the inability to dehydrogenate a pendant fatty acid and reasoning for the selective dehydrogenation of an acyl phosphine ligand. iii Acknowledgments The work presented in this thesis could not be possible without the contributions of several important people towards my growth as an educator, scientist, and person. First, I must thank my advisor, Dr. Christopher Hadad, for your valuable mentorship and support over the past five years. Your continuing guidance was instrumental in helping me to realize my scientific, academic, and personal goals, and I hope our relationship will only grow in future years. I would also like to thank collaborators at The Ohio State University who played pivotal roles in my maturation as a research scientist, namely Dr. James Stambuli and Dr. Jovica Badjic. To my fellow members of the Hadad Research Group, thank you for your unconditional assistance in allowing me to become a successful researcher. Each of you, whether past or present, remains a part of creating the unique atmosphere that allows our group to function so well. Special thanks go to Dr. Jeremy Beck, Dr. Shubham Vyas, Dr. Daniel Turner, and Dr. Hashem Taha for your patience and mentorship as you passed on the wealth of knowledge you possess. Thank you also to Jason Brown for your friendship and collaboration within the Hadad Group on our nerve agent work. I would also like to thank all of the experimental researchers who assisted in advancing this work through their collaborative efforts. iv Specifically, I would like to thank Katelyn Cody, an undergraduate researcher in Dr. Christopher Callam’s research group at The Ohio State University who I have taken an active role in mentoring the past year. Thank you for your tireless efforts towards completing and presenting our research to many different audiences. Hopefully, I have been a positive influence in your development towards reaching your personal and professional goals. I am thankful to the funding agencies that made this research possible. These agencies include the Defense Threat Reduction Agency (DTRA) and the Ohio Supercomputer Center (OSC). As much as I’ve grown as a scientist during my graduate career, I feel I’ve matured just as much as a teacher. Through the generosity and guidance of several influential mentors, I’ve been able to realize my true calling in life as an educator. Certainly, I must thank Dr. Hadad for allowing me to pursue several opportunities to teach while completing my graduate research. Also, I have to thank Dr. Christopher Callam and Dr. Noel Paul for their mentorship while serving as their Teaching Assistant at The Ohio State University. Although both of you have your own unique style and personality, you each taught me invaluable lessons in and out of the classroom. I hold the utmost respect for both of you and look forward to our friendship continuing for years to come. Thanks also to those at Capital University and Ohio Wesleyan University for allowing me the opportunity to be an adjunct instructor during my graduate career. Thank you especially to my undergraduate advisor, Dr. Katie Hervert, for your continued friendship and support in nurturing my chosen career path. v Finally, thank you to my friends and family for your unconditional love and support over the last five years. To my wife and best friend Stefanie, thank you for helping me through every step of this experience. I know we have had significant challenges to overcome in the last five years, but through our growing love and faith, we have reached a new stage in our life’s journey together. You have undoubtedly been the best thing that has ever happened to me and I promise to continue my career knowing it is in loving devotion to you and our family. Although you may never read or understand the contents of this dissertation, it would not have been possible without the love and support from you, Boo, and Beaker. To my mother and father, thank you for your unending love and support in cultivating my potential to allow me to reach this point in my life. Hopefully I have made you proud by following in your footsteps with a career in academia. Every day of my life I have sought to live by the principles and values you have taught me. I will continue to do so to the best of my abilities as I begin my career and family. Surely, I would not be where I am today without the sacrifices you have made. And lastly, thank you to my twin brother Matt. I would be nowhere without your love, support, and companionship for the last twenty-seven years. My sincere hope is that our relationship will continue to stay strong as we both encounter the exciting changes and challenges ahead in each of our lives, wherever that may lead us. Onward and upward. vi Vita 2004 ............................................................... Urbana High School 2008 ............................................................... B.A. Chemistry, Ohio Wesleyan University 2008 to present ............................................. Graduate Research Associate, Department of Chemistry, The Ohio State University Publications 1) Whittemore, S. M.; Yoder, R. J.; Stambuli, J. P. “Site-Selective Alkyl Dehydrogenation of a Coordinated Acylphosphine Ligand” Organometallics, 2012, 31 (17), 6124. 2) Hermann, K.; Sardini, S.; Ruan, Y.; Yoder, R. J.; Chakraborty, M.; Vyas, S.; Hadad, C. M.; Badjic, J. D. “Method for the Preparation of Derivatives of Heptiptycene: Toward Dual–Cavity Baskets” J. Org. Chem. 2013, 78 (7), 2984. 3) Ruan, Y.; Taha, H. A.; Yoder, R. J.; Maslak, V.; Hadad, C. M.; Badjic, J. D. “The Prospect of Selective Recognition of Nerve Agents with Modular Basket-like Hosts. A Structure–Activity Study of the Entrapment of a Series of Organophosphonates in Aqueous Media” J. Phys. Chem. B. 2013, 117 (11), 3240. vii Fields of Study Major Field: Chemistry viii Table of Contents Abstract ............................................................................................................................... ii Acknowledgments