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Junhua Thesis First Draft Enediyne to Polyyne: Spontaneity in the Biosynthesis of Uncialamycin and Intermolecular Trapping of Benzynes Generated from the Hexadehydro-Diels–Alder Reaction A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA Junhua Chen IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Thomas R. Hoye, Advisor August 2016 © Junhua Chen 2016 i Acknowledgements As my time as a graduate student is coming to an end, I start to reflect on this wonderful journey that is only made possible by the love, tutelage, and support of so many people. First and foremost, I would like to thank my parent, Yongming Chen and Xiaomei Zhou. They were my first teachers, my role models, and the ones to shape who I am now. When I was little, my father would place me on his lap and started to sketch out a three- dimensional perspective of a random object on a piece of paper. In the hindsight, that could have been the initial driving force that ultimately led me to the ubiquitous tetrahedron skeletons in organic chemistry. As a role model, there were countless nights when my father would study coding language to materials for becoming a registered cost engineer. He would always advise me to solve problems independently and understand the underlining logic behind the theories I learned from school. He instilled me with an image of being responsible to his family, his parents, and to his job. I would like to thank my mother for her tremendous dedication to family, her love and support for me to travel across the ocean to pursue my goal, and for taking care of my father and I day by day. I would also thank my extended family of my uncle Yongju, my aunt Shuping, and my cousin Tingliang. They make sure I know they are here in this foreign country when I need them. In addition, I would thank my two roommates during different times in Minnesota and my good friends, Xu Zou and Shengbo Hu, for the laughs and dinner we had together. I would like to thank my advisor, Prof. Thomas R. Hoye, for showing me the art of teaching and his contagious passion for guiding young students. Tom demonstrates what a true scholar is. He always pays great attention to detail, from “How to balance that equation” to frowning at a mechanism that involves a plausible hydrolysis step in an anhydrous solvent, from the thirty-minute analysis of a GC-MS trace at a subgroup meeting to the absolute level of precision for NMR interpretation. He is an extraordinary advisor. Patient and approachable does not suffice to describe him at all. He provides sufficient space for each individual to develop their own professional character, and yet offers enlightening advice to make us better chemists, from registering for the computational chemistry class during my first year, to being less obsessive in a tunnel vision. I cannot say how much Tom has influenced me on teaching and mentoring, as I was surprised to hear myself saying the ii same phrases and the same kind of advice to the undergraduate student I was working with and other new graduate students in the Hoye group. Additionally, I thank Tom for his commitment and advice on my career plan during my later stage in the graduate school. I would also like to thank my committee members, Prof. Joseph Topczewski, William Pomarantz, and Daniel Harki for their patience and suggestion for the final thesis submission, as well as Prof. Wayland Noland and George Barany for their constructive advice throughout my written and oral preliminary examinations. I would like to thank Prof. Jane Wissinger. The experience of working as a lab TA is highly valuable. I appreciate and admire her passion with course innovation. To the faculty members who had taught their courses to me, I thank Prof. Valerie Pierre, Christopher Douglas, Andrew Harned, Christopher Cramer, Steven Kass, and one more time, Tom. Throughout the two additional semesters when I was the course TA for Tom, I was able to reinforce what I learned by creating problems for problem sets, mid-term and final examinations and the useful advice he gave me not as my research advisor, but as an instructor. I would also like to thank Dr. Letitia Yao and all the NMR TAs for maintaining the NMR facilities and their knowledge for data collection. I have the great honor to mentor a highly motivated and talented undergraduate student, Vignesh Palani, for three years, and to witness his growth from an eager freshman to become a mature and insightful chemist with a bright future ahead. Our relationship has evolved from one-way instillation of knowledge and experience to a mutually instructive team. I greatly appreciate his work under all circumstances and it had been a joy to work with him. His contribution to benzyne chemistry has been immensely inspiring and constitutes an important portion of this Thesis and beyond. The development of the HDDA chemistry would have been possible without the endeavor by the original “team benzyne”: Dr. Beeru Baire, Dawen Niu, Patrick, and Brian woods. Their work has paved the foundation on which more elaborated and exotic precursors as well as trapping reactions were designed and implemented. I would also like to thank the senior graduate students of the Hoye group during my time as an immature new graduate student. I thank Dr. Dawen Niu and Patrick Willoughby once again, who were with me on the same subgroup at the beginning, for introducing me the way to conduct iii research in the Hoye group. I thank Dr. Cagui Izgu for showing me how a senior graduate student is focused and productive with research, and his friendship as well. I thank Dr. Matthew Jansma for being a role model not only to me, but many other Hoye group members. His bench skills and hard working have defined an outstanding experimentalist. I also thank other previous Hoye group members Dr. Susan Brown, Mandy Schmit, Susie Emond, and Adam Wohl for creating a positive environment overall within the Hoye group. And for the cordial relationship with the current Hoye group member, I have been having fruitful and pleasant conversations with Sean Ross on our research projects on a daily basis. I would like to thank Severin Thompson for some suggestions on my computational work, and Jutian Zhang for maintaining the essential GC-MS instrument, as well as their friendship to make Smith 415 a great place to stay. I would also like to thank Dr. Andrew Michel for his extraordinary work with the LC-MS, and later Xiao Xiao and Dr. Bryce Sunsdale for their continuing effort under compromised conditions. iv Abstract The enediyne natural products are potent antitumor antibiotics. According to the presence of a bicyclo[7.3.0]-dodecadienediyne or a bicyclo[7.3.1]-tridecadiynene unit, they are further divided into nine-membered or ten-membered sumfamilies. Enediynes are capable of causing single or double DNA strand lesion due to their propensity to undergo cycloaromatization reactions to generate 1,4-benzenoid diradical species under biological conditions. We envision that the establishment of the enediyne skeleton of uncialamycin, a ten-membered enediyne, is biosynthetically derived from a linear precursor via an hetero- intramolecular Diels–Alder reaction without enzymatic catalysis. Hence, we aim to synthesize a key intermediate in order to examine this proposal. Meanwhile, a related study on the generic biosynthesis of the nine-membered enediynes had resulted in the serendipitous discovery of the underutilized hexadehydro- Diels–Alder (HDDA) reaction. During such an event, a 1,3-diyne moiety engages an intramolecularly placed alkyne moiety in a formal [4+2]-cycloaddition reaction to produce a fused bicyclic benzyne intermediate, which is subsequently trapped in situ to yield highly substituted benzenoid products. We are dedicated to the investigation of mode of reactivity between the HDDA-generated benzynes and sulfur-based nucleophiles. Thus, consistent with the prior reports, sulfides react with benzyne to form the S-arylsulfonium ylides, which we further utilize in the development of a highly versatile three-component process. We describe the first examples of the reactions between aromatic thioamides and the HDDA-generated benzynes to form dihydrobenzothiazines through an unusual thiolate- relayed 1,3-proton migration of the pivotal ortho-mercaptoaryliminium betaine intermediate. The trapping reaction manifold with thioamide is found to be altered by tuning the electronic property to give rise to 2,2-disubstituted benzothiazoline derivatives. On the other hand, vinyl sulfoxides are shown to participate a tandem three-component reaction the produce ortho-sulfanylaryl ethers and benzooxathiine derivatives. These new trapping reactions are not only rich in mechanistic content, but also show potential in drug discovery industry. v Table of Contents Acknowledgement i Abstract iv Table of Contents v List of Figures viii List of Tables xi List of Abbreviations xii Structures are numbered according to the following format: Chapter 1, 1xxx; Chapter 2, 2xxx; … Chapter 7, 7xxx. Part I: Spontaneity in the Biosynthesis of Uncialamycin Chapter 1. Enediyne Natural Products and Their Biosyntheses 2 1.1 The enediyne Natural Products 2 1.2 Mode of Action 4 1.3 Previous Chemical Syntheses of the Ten-Membered Enediyne Core 7 1.4 Previous Studies toward the Biosynthesis of Enediynes in the Pre-genomic Era 12 1.5 Enediyne Gene Clusters 14 1.6 Isolation of Possible Biosynthetic Intermediates 17 1.7 Divergence between Nine-Membered and Ten-Membered Enediyne Warheads 19 Chapter 2. Spontaneity in the Biosynthesis of Uncialamycin 22 2.1 Biosynthetic Hypothesis 22 2.2 Progress toward the Synthesis of the Proposed Biosynthetic Precursor 23 Part II: Intermolecular Trapping of the Benzynes Generated from the Hexadehydro- Diels–Alder Reaction Chapter 3.
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