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Self-Assembly Using Alkene/Imine Orthogonal Dynamic Covalent Chemistry and Arylene-Ethynylene Macrocycle/DNA Hybrids”

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Self-Assembly Using Alkene/Imine Orthogonal Dynamic Covalent Chemistry and Arylene-Ethynylene Macrocycle/DNA Hybrids” Self-Assembly Using Alkene/Imine Orthogonal Dynamic Covalent Chemistry and Arylene-Ethynylene Macrocycle/DNA Hybrids by Kenji D. Okochi B.S. Tulane University, New Orleans, LA, 2007 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirement for the degree of Doctor of Philosophy Department of Chemistry and Biochemistry 2016 This thesis entitled: “Self-Assembly Using Alkene/Imine Orthogonal Dynamic Covalent Chemistry and Arylene-Ethynylene Macrocycle/DNA Hybrids” written by Kenji D. Okochi has been approved for the Department of Chemistry and Biochemistry ______________________________________ Wei Zhang, Ph. D. ______________________________________ David Walba, Ph. D. Date__________________________ The final copy of this thesis has been examined by the signatories and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline. ii Thesis Abstract Okochi, K. D. (Ph.D., Department of Chemistry and Biochemistry) Self-Assembly Using Alkene/Imine Orthogonal Dynamic Covalent Chemistry and Arylene-Ethynylene Macrocycle/DNA Hybrids Thesis directed by Professor Wei Zhang The controllable assembly of materials on the atomic or molecular level remains one of the grand challenges of chemistry. While top-down techniques such as lithography are capable of creating order over the long range, short range assembly on the order of up to 10 nanometers is currently beyond the scope of the most advanced lithographic capabilities. Self-assembly using bottom-up strategies have the potential to fill in this void, and there remains a fundamental need to have multiple strategies for the creation of materials at this scale. Herein we present research focusing on two areas of self-assembly: Alkene/imine ODCC and arylene-ethynylene macrocycle/DNA hybrids that can mediate assembly of gold nanoparticles. Dynamic covalent chemistry (DCvC) is one technique available to chemists to synthesize matter in a controllable manner using bottom-up assembly. However, to date, the majority of DCvC reactions rely on one type of chemistry (homo-sequenced), iii resulting in structures with high symmetry. In contrast, the incorporation of two types of DCvC (hetero-sequenced) into one reaction has been relatively less explored. We first demonstrated that alkene metathesis and imine metathesis DCvC can be utilized in a one-pot fashion to synthesize discrete 2-D phenylene-based macrocycles. Next we showed that macrocycles made in this manner could form a 1-D polymer of macrocycles using alkyne metathesis DCvC and also prepare 3-D and 3-component shape-persistent architectures from simple building blocks. Organic/DNA hybrids offer the potential for material whose self-assembly properties are imparted both by the hydrophobicity and directionality of the organic component as well as the base-pairing capabilities of the DNA. While most research has focused on either small molecule/DNA hybrids or polymer/DNA hybrids, discrete oligomeric architectures provided by DCvC such as arylene-ethynylene macrocycles, offer an intriguing intermediate hybrid that could be incorporated into gold nanoparticle lattices for plasmonic applications. We first explored the synthetic conditions of the on-bead amide coupling using a small library of simple organic substrates and achieved good yields. Next we demonstrated that arylene-ethynylene macrocycle/DNA hybrids can be prepared using the methodology we had developed for small molecules, and that the resulting macrocycle/DNA material can be used to assemble gold nanoparticles into both bulk aggregates and discrete assemblies of iv dimers depending on the DNA sequence; complementary sequences yielded bulk aggregates, while poly-adenines yielded dimers. v DEDICATION Dedicated to my collaborators vi Acknowledgements I would first like to thank Prof. Wei Zhang for his leadership and vision. Wei’s high standards of scientific rigor has made me a much better scientist than I would otherwise be, and I am grateful for having him as an advisor. I would like to thank my fellow members of the Zhang group who I have had the pleasure of working with over the past six years: Yinghua (Alice) Jin, Ryan McCaffrey, Youlong Zhu, Chao Yu, Michael Ortiz, Chengpu Zhu, Yu Gong, Shouhong Fan and David Tran. I would also like to thank past members of the Zhang group: Jyothish Kuthanapillil, Chenxi Zhang, Qi Wang, Philip Taynton, Ya Du, Ryan Denman, Athena Jin, Guolong Lu, Lili Tan, Kun Xun, Prof. Dazhi Tan, and Prof. Huagang Ni. I would especially like to thank Dr. Haishen Yang for his guidance in helping me become a better chemist. In my time at CU Boulder, I have had the opportunity to work with a number of hard-working undergraduates: Gun Han, Ian Aldridge, Yuliang Liu, and Alex Herron, thank you guys for your help. I have been very fortunate in that I have been able to work with high caliber and helpful collaborators. While most Ph.D. students are a member of one or two groups, I feel like I have been part of at least four groups in my time here due to my collaborations. I wish to thank Prof. Jennifer Cha, Prof. Marvin Caruthers, and Prof. Robert Kuchta for allowing me to collaborate with their students and post-docs. I would particularly like to thank Prof. Dylan Domaille, Dr. Luca Monfregola, Sarah vii Dickerson, and Ryan McCaffrey for their time, energy, patience and expertise on the DNA project. I’d also like to thank Prof. Daniel Feldheim and Prof. Bruce Eaton for letting me use their lab equipment. I wish to thank my family, my parents, Andy and Nancy, and my sisters Mina and Rena for supporting me throughout my life. Most of all I wish to thank my wonderful wife, Christine, who has put up with my crazy hours and work schedule to somehow keep our home standing, particularly with the addition of our twin sons/DNA hybrids, Andrew and Bryant (1/26/16). I wish to thank the National Science Foundation for financial support as well as the University of Colorado Boulder and the Department of Chemistry and Biochemistry. viii CONTENTS CHAPTER 1 ..................................................................................................................................1 1.1 Introduction .........................................................................................................................1 1.2 Orthogonal dynamic covalent chemistry .........................................................................3 1.3 Organic/DNA hybrids .......................................................................................................7 1.3.1 Solution-phase convergent ........................................................................................10 1.3.2 Solid-state divergent ..................................................................................................14 1.3.3 Solid-state convergent ................................................................................................17 1.4 Conclusion .........................................................................................................................19 1.5 Scope of thesis ...................................................................................................................20 1.6 Organization of thesis ......................................................................................................20 1.7 References ..........................................................................................................................21 CHAPTER 2 ................................................................................................................................24 2.1 Introduction .......................................................................................................................24 2.2 Model studies .....................................................................................................................25 2.3 Synthesis of ODCC monomers ........................................................................................28 2.4 Alkene/imine ODCC ........................................................................................................30 2.4.1 ODCC macrocyclization trial 1 .................................................................................30 2.4.2 ODCC macrocyclization trial 2 .................................................................................32 2.4.3 ODCC macrocyclization trials 3 and 4 ....................................................................34 2.5 Asymmetric macrocycles ................................................................................................38 2.6 Polymers of ODCC macrocycles ....................................................................................41 2.6.1 Synthesis of ODCC macrocyclic monomers ...........................................................41 2.6.2 ODCC macrocyle aggregation study .......................................................................45 2.6.3 ODCC macrocyclization study .................................................................................46 2.6.3.1 Polymerization by alkyne metathesis ..............................................................48 2.6.3.2 Polymerization by Glaser coupling ..................................................................48 ix 2.7 Conclusions ........................................................................................................................49 2.8 Experimental section ........................................................................................................50
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