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Computational Studies of Anti-Tumor Drug Tirapazamine and Reactions and Rearrangements of Nitrenes and Carbenes

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COMPUTATIONAL STUDIES OF ANTI-TUMOR DRUG TIRAPAZAMINE AND REACTIONS AND REARRANGEMENTS OF NITRENES AND CARBENES DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Jin Liu, B.S. ***** The Ohio State University 2005 Dissertation Committee: Approved by Professor Matthew S. Platz, Advisor Professor Christopher M. Hadad _________________________________ Professor Sherwin J. Singer Advisor Graduate Program in Chemistry Professor Anne B. McCoy ABSTRACT The two possible mechanisms of action of the anti-cancer drug tirapazamine have been investigated using density functional theory (DFT). Tirapazamine is a novel anti- cancer drug which is inactive in oxygen-rich, healthy cells but is active in oxygen-poor, cancerous cells and induces DNA strand scission. We calculate that the mechanism proceeds via a series of electron-transfer/proton-transfer/fragmentation steps to eventually produce hydroxyl radical in a series of energetically favorable reactions. It has been proposed that the generated hydroxyl radical may then react with the sugar residues of the DNA backbone moiety to produce sugar-centered radicals. A direct mechanism involving hydrogen-atom abstraction from the sugar residues by a tirapazamine-centered radical anion or its conjugate acid is not energetically feasible. However, the hydroxyl radical can remove a hydrogen atom from the amino group of tirapazamine to form an iminyl radical. This radical can remove a hydrogen atom of a DNA sugar in an exothermic process. The calculations predict that tirapazamine, acting as a surrogate for molecular oxygen, can then react exothermically with the sugar-centered radical to oxygenate the radical center and thereby induce the DNA strand break. Related reactions of some tirapazamine analogs were studied, and promising new drug candidates were discussed. ii DFT, CCSD(T), and CBS-QB3 calculations were performed to understand the chemical and reactivity differences between acetylnitrene (CH3C(=O)N) and methoxycarbonylnitrene (CH3OC(=O)N) as well as sulfonylnitrenes. Acetyl azide is calculated to decompose by concerted migration of the methyl group along with nitrogen extrusion. Methoxycarbonyl azide, on the other hand, does have a preference for stepwise Curtius rearrangement via the free nitrene. Methanesulfonyl azide prefers to decompose to form singlet methanesulfonylnitrene rather than to extrude nitrogen in concert with sulfurylimine formation (pseudo Curtius Rearrangement). The bimolecular reactions of acetylnitrene, methoxycarbonylnitrene and methanesulfonylnitrene with propane, ethylene and methanol were calculated and found to have enthalpic barriers that are near zero and free energy barriers are controlled by entropy. Similar calculations were performed on diazoketones, diazoesters and diazoalkanes. We find that conformations in which the migrating group and the diazo moiety have an anti disposition extrude nitrogen and undergo concerted Wolff Rearrangement to ketene and avoid the formation of the free carbene. When these groups have a syn disposition, carbenes are formed, and these intermediates subsequently rearrange. Diazoacetone favors a concerted thermal decomposition and methyl diazoacetate prefer stepwise carbene formation. These preferences are explained with the use of isodesmic equations, and upon consideration of the geometries of the transition states and the free carbenes. iii The reactions with oxygen of triplet carbenes and triplet nitrenes were calculated by DFT, CCSD(T) and CASPT2 methods. The fact that triplet carbenes react faster with oxygen than do triplet nitrenes has been explained on the basis of the strength of the bonds being formed. iv To my parents and Peng v ACKNOWLEDGMENTS Standing at a new milestone of my life, I look back to my journey on the road of science. I can see so many people leading me, supporting me, and encouraging me on this road. I would first thank two of my advisors, Dr. Matthew S. Platz and Dr. Christopher M. Hadad. It is their intellectual support and patient guidance that made this dissertation possible. They set a lifetime’s worth of example for me to follow, as a scientist and as a person. I appreciate that many faculty members in physical division gave me a tremendous education. They led me into the world of physical chemistry through their classes and personal discussions. I would give my special thanks to Dr. Singer and Dr. McCoy as my committee members. I would like to mention all group members in Platz and Hadad group, for their friendship, encouragement, and discussions. I will cherish the wonderful moments we shared. I also would like to thank The Ohio Supercomputer Center for technical support and NSF-funded Environmental Molecular Science Institute at OSU for partial financial support. vi My parents, Qiaoyun Liu and Binyan Liu, know nothing about chemistry. What they know is, love. Their love from my mother land, the other side of the Earth, support me to be a strong person during my five years studies in this foreign country. They are not only my parents, but also my mentors and best friends. I love you both, mom and dad, with all my heart. Finally, I would thank the most important person in my life, Peng Tao. As a lab colleague, your intelligent insight helped me tremendously during my completion of this dissertation; as a friend, you are always with me during my countless tough time; as a life partner, your love and support are incredible. I think I am ready to accept your request and to become the luckiest person in the world, spending the rest of my journey with you. Yes, I do. vii VITA May 19, 1978. Born – Xi’an, China 1996 - 2000. B. S. Chemistry Beijing University, China 2000 – 2005. Graduate Teaching and Research Associate, The Ohio State University. PUBLICATIONS Research Publications 1. Liu, J.; Mandel, S.; Hadad, C. M.; Platz, M. S. “A Comparison of Acetyl and Methoxycarbonylnitrenes by Computational methods and a Laser Flash Photolysis Study of Benzoylnitrene.” J. Org. Chem. 2004, 69, 8583-8593. 2. Liu, J.; Hadad, C. M.; Platz, M. S. “The Reaction of Triplet Nitrene with Oxygen: A Computational Study.” Org. Lett. 2005, 7, 549-552. 3. Mandel, S.; Liu, J.; Hadad, C. M.; Platz, M. S. “A Study of Singlet and Triplet 2,6 – Difluorophenylnitrene by Time Resolved Infrared Spectroscopy” J. Phys. Chem. A 2005, 109, 2816-2821. FIELDS OF STUDY Major Field: Chemistry viii TABLE OF CONTENTS P a g e Abstract. ii Dedication. .iv Acknowledgments . .v Vita . .viii List of Tables. xii List of Figures . xv Chapters: 1. Introduction………………………………………………………………………1 2. Mechanism of action of Tirapazamine…………………………………….…….15 2.1 Introduction………………………………………………………………….15 2.2 Computational methods……………………………………………………...20 2.3 Results………………………………………………………………………..23 2.3.1 Protonation of the triapazamine radical anion…………………...23 2.3.2 Hydrogen atom transfer reactions of TO·⎯, TOH·, TOH·’ with Amino Ribose……………………………………………………28 2.3.3 N-O bond cleavage reactions…………………………………….32 2.3.4 Oxygen transfer from tirapazamine to the desoxyribose ring…....34 2.4 Conclusions…………………………………………………………………..36 2.5 References for Chapter 2…………………………………………………….46 3. Analogs of tirapazamine…………………………………………………………48 3.1 Introduction…………………………………………………………………..48 3.2 Computational methods……………………………………………………...49 ix 3.3 Results………………………………………………………………………..49 3.3.1 Effects of phenyl ring substitution and benzannulation………….49 3.3.2 Lumiflavin N-oxide……………………………………………...61 3.3.3 The action of T and T’…………………………………………………...62 3.4 Conclusions…………………………………………………………………..70 3.5 References for Chapter 3…………………………………………………….71 4. Radical additions to aromatic N-oxides………………………………………….72 4.1 Introduction…………………………………………………………………..72 4.2 Computational methods……………………………………………………...72 4.3 Results………………………………………………………………………..73 4.3.1 Reactions of methyl radical with benzene or pyridine…………...73 4.3.2 Reaction of methyl radical with pyridine N-oxide………………74 4.3.3 Oxygen transfer from pyrazine, 1,4-dioxide to methyl radical…..78 4.3.4 Effect of phenyl ring……………………………………………..81 4.3.5 Effect of substitution……………………………………………..82 4.3.6 Silicon centered radicals…………………………………………84 4.4 Conclusions…………………………………………………………………..85 4.5 References for Chapter 4…………………………………………………….86 5. A comparison of acetyl and methoxycarbonylnitrenes…………………………..87 5.1 Introduction………………………………………………………………87 5.2 Computational methods………………………………………………….90 5.3 Results……………………………………………………………………92 5.3.1 Singlet-triplet energy splittings…………………………………..92 5.3.2 Curtius rearrangement……………………………………………98 5.3.3 Intramolecular C-H insertion…………………………………...107 5.3.4 Bimolecular reactions…………………………………………..108 5.4 Conclusions……………………………………………………………..114 5.5 References for Chapter 5……………………………………………….115 6. Sulfonylnitrenes and azides…………………………………………………….118 6.1 Introduction…………………………………………………………….118 6.2 Computational methods………………………………………………...120 6.3 Results…………………………………………………………………..121 6.3.1 Methylsulfonylnitrene singlet-triplet energy separation………..121 6.3.2 Intramolecular C-H insertion reactions of singlet alkylsulfonylnitrenes……………………………………………124 6.3.3 Pseudo-Curtius rearrangements………………………………...126 x 6.3.4 Bimolecular reactions of singlet methylsulfonylnitrene………..129 6.3.5 Bimolecular reactions of triplet methylsulfonylnitrene………...131 6.3.6 Is thermal rearrangement concerted with nitrogen extrusion…..132 6.3.7 Other modes of thermal decomposition of methanesulfonyl azide…………………………………………………………….134
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  • Chemical Basis of Reactive Oxygen Species Reactivity and Involvement in Neurodegenerative Diseases

    Chemical Basis of Reactive Oxygen Species Reactivity and Involvement in Neurodegenerative Diseases

    International Journal of Molecular Sciences Review Chemical Basis of Reactive Oxygen Species Reactivity and Involvement in Neurodegenerative Diseases Fabrice Collin Laboratoire des IMRCP, Université de Toulouse, CNRS UMR 5623, Université Toulouse III-Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse CEDEX 09, France; [email protected] Received: 26 April 2019; Accepted: 13 May 2019; Published: 15 May 2019 Abstract: Increasing numbers of individuals suffer from neurodegenerative diseases, which are characterized by progressive loss of neurons. Oxidative stress, in particular, the overproduction of Reactive Oxygen Species (ROS), play an important role in the development of these diseases, as evidenced by the detection of products of lipid, protein and DNA oxidation in vivo. Even if they participate in cell signaling and metabolism regulation, ROS are also formidable weapons against most of the biological materials because of their intrinsic nature. By nature too, neurons are particularly sensitive to oxidation because of their high polyunsaturated fatty acid content, weak antioxidant defense and high oxygen consumption. Thus, the overproduction of ROS in neurons appears as particularly deleterious and the mechanisms involved in oxidative degradation of biomolecules are numerous and complexes. This review highlights the production and regulation of ROS, their chemical properties, both from kinetic and thermodynamic points of view, the links between them, and their implication in neurodegenerative diseases. Keywords: reactive oxygen species; superoxide anion; hydroxyl radical; hydrogen peroxide; hydroperoxides; neurodegenerative diseases; NADPH oxidase; superoxide dismutase 1. Introduction Reactive Oxygen Species (ROS) are radical or molecular species whose physical-chemical properties are well-known both on thermodynamic and kinetic points of view.