Template directed synthesis of novel supramolecular architectures

TEMPLATE-DIRECTED SYNTHESIS OF NOVEL SUPRAMOLECULAR ARCHITECTURES SUVANKAR DASGUPTA NATIONAL UNIVERSITY OF SINGAPORE 2012 TEMPLATE-DIRECTED SYNTHESIS OF NOVEL SUPRAMOLECULAR ARCHITECTURES SUVANKAR DASGUPTA (M. Sc., Indian Institute of Technology Madras, Chennai, India) A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF CHEMISTRY NATIONAL UNIVERSITY OF SINGAPORE 2012 Acknowledgements I would like to express my deep and sincere gratitude to people who have helped and inspired me during my Ph.D. studies in the Department of Chemistry, National University of Singapore (NUS). This thesis would not have been possible without their firm support. Foremost, I would like to thank my supervisor Dr. Wu Jishan for offering me the opportunity to study in NUS and giving me continuous support during my Ph.D. study and research. His patience, motivation, enthusiasm, and immense knowledge have been of great value for me. He is not only an extraordinary supervisor, a complete mentor, but also a very nice human being. I could not have imagined having a better supervisor for my Ph.D. study. Besides my advisor, I am deeply grateful to our collaborator, Prof. Huang Kuo-Wei from KAUST Catalysis Center (KCC) & Division of Chemical and Life Sciences and Engineering, Kingdom of Saudi Arabia for his kind assistance in the computational calculations. I would also like to thank all my past and present colleagues: Dr. Yao Junhong, Dr. Zhang Xiaojie, Dr Yin Jun, Dr Zhao Baomin, Dr Luo Jing, Dr Luo Ding, Dr Cui Weibin, Dr Zhang kai, Dr. Li Yuan, Dr. Zeng Lintao, Jiao Chongjun, Li Jinling, Zeng Zebing, Sun Zhe, Mao Lu, Zhu Lijun, Zeng Wangdong, Ni Yong, Sha Zhou, Chang Jingjing, Kam Zhiming, Luo Jie and others. They had helped me a lot not only in chemistry but also in life. I also want to express my appreciation to the members of instruments tests in NMR, Mass and X-ray diffraction lab. They gave me too much help during my research I work. I would also like to thank all the staffs in chemistry administrative office, Lab supplies for their immense support. I would always remain indebted to my friends Suresh, Naresh, Abhinav, Arun, Vinayak, Umang, Nitin, Harleen, Gujju, Prabhat, Bharti, Mohit, Madhulika, Shweta, Nikhil, Shibajida, Animesh, Kesta, Raju, Bikram and Pasari for providing me incredible mental support. Last but not least, I would like to give my deepest appreciation to my parents, sister, brother-in-law, and my cutest nephew Gullu for their love and support throughout my studies. I am equally thankful to my partner Puja and her family for having faith in my abilities to excel and always imbibing positivity in me. Without their presence, I would not have been able to complete my thesis. Above all, I thank the almighty for providing me the courage and strength to battle with tough circumstances while doing Ph.D. II Thesis Declaration The work in this thesis is the original work of SUVANKAR DASGUPTA, performed independently under the supervision of Dr. Wu Jishan, (in the laboratory Organic Electronics & Supramolecular Chemistry), Chemistry Department, National University of Singapore, between August 2007 and December 2011. The content of the thesis has been partly published in: 1) Chapter - Dasgupta, S.; Wu, J. Chem. Sci. 2012, 3, 425-432. 2) Chapter - Dasgupta, S.; Kuo-Wei, H.; Wu, J. Manuscript Submitted. 3) Chapter - Dasgupta, S.; Wu, J. Org. Biomol. Chem. 2011, 9, 3504-3515. Suvankar Dasgupta Name Signature 04/02/2012 Date III Table of Contents Table of Contents Summary IV VIII List of Tables X List of Figures XI List of Schemes XVI List of Abbreviations XIX Chapter Introduction 1.1 Supramolecular Phenomenon 1.2 Self-Assembly in Biological Systems 1.3 Self-Assembly in Chemical Systems 1.3.1 Cyclodextrins 1.3.2 Cucurbiturils 1.3.3 Metal ions 1.3.3.1 Passive Templation 1.3.3.1.1 Tetrahedral Geometries 1.3.3.1.2 Octahedral Geometries 1.3.3.1.3 Square Planar Geometries 10 1.3.3.2 Active Templation 11 1.3.3.2.1 CuI-Catalyzed Azide-Alkyne 1,3-Cycloaddition 11 1.3.3.2.2 Alkyne-Alkyne Couplings 12 IV 1.3.4 π-Electron-Acceptor and π-Electron-Donors 13 1.3.4.1 CBPQT4+ as π-Electron-Deficient Host 14 1.3.4.2 Crown Ethers as π-Electron-Rich Host 17 1.3.5 Amide Hydrogen Bonding 20 1.3.6 Ammonium Hydrogen Bonding 22 1.3.6.1 DBA+ and [24]Crown Ether 24 1.3.6.2 DBA+ and other Crown Ethers 31 1.3.6.3 R2NH2+ and [21]Crown Ethers 34 1.4 Project Objectives 36 Chapter Formation of [2]Rotaxanes by Encircling [20],[21], and [22]Crown Ethers Onto the Dibenzylammonium Dumbbell 2.1 Introduction 39 2.2 Results and Discussion 2.2.1 Synthesis of acyclic diolefin polyethers 41 2.2.2 Synthesis of [2]rotaxanes 43 2.2.3 Synthesis of cyclic polyethers 49 2.2.4 Generation of pseudo[2]rotaxanes 50 2.3 Conclusions 64 2.4 Experimental Section 2.4.1 Materials and methods 65 2.4.2 X-ray crystallographic analysis 66 2.4.3 Synthetic procedures and characterization data 68 Chapter Is It Possible to Generate [2]Rotaxanes by Clipping [19]Crown Ethers Onto The Dibenzylammonium Dumbbell? 3.1 Introduction 79 V 3.2 Results and Discussion 3.2.1 Substrate scope 3.2.1.1 Choice of dumbbells 81 3.2.1.2 Choice of acyclic diolefin polyether 84 3.2.2 RCM reactions 3.3 Conclusion 87 95 3.4 Experimental Section 3.4.1 Materials and methods 95 3.4.2 Synthetic procedures and characterization data 96 Chapter Trifluoromethyl as Stopper for a [2]Rotaxane Encircled with a [20]Crown Ether 4.1 Introduction 99 4.2 Results and Discussion 4.2.1 Synthesis of salts 101 4.2.2 Synthesis of 20C6 and 20C6H2 102 4.2.3 Synthesis of [2]rotaxanes by ring-closing-metathesis 103 4.2.4 Kinetic stability of [2]rotaxane 4-14·BAr4 109 4.3 Conclusion 113 4.4 Experimental Section 4.4.1 Materials and methods 4.4.2 Synthetic procedures and characterization data 114 115 Chapter Template-Directed Synthesis of Kinetically and Thermodynamically Stable Molecular Necklace using Ring Closing Metathesis 5.1 Introduction 119 5.2 Results and Discussion VI 5.2.1 Synthesis of key intermediates 5-5, 5-13 and 5-19 123 5.2.2 Synthesis of threads 5-1 (PF6)4 and 5-2 (PF6)6 125 5.2.3 Synthesis of [5]molecular necklace 5-23 (PF6)4 126 5.2.4 Characterization of [5]molecular necklace 5-23 (PF6)4 129 5.2.5 Attempted synthesis of [7]molecular necklace 136 5.3 Conclusion 137 5.4 Experimental Section 5.4.1 Materials and methods 5.4.2 Synthetic procedures and characterization data 138 138 Chapter Conclusion and Outlook 153 References 158 VII Summary This thesis described the ability of the dibenzylammonium ion to be encircled with crown ethers having less than 24 atoms. It also highlighted the affectivity of a small trifluoromethyl group to act as stopper in a [2]rotaxane interlocked with [20]crown ether. The synthesis of a well-defined, homogeneous, kinetically and thermodynamically stable [5]molecular necklace has also been discussed. Chapter presents a brief overview of the supramolecular phenomenon existing in nature and harnessing the same in chemical systems to obtain inclusion complexes. The journey from inclusion complexes to the mechanically interlocked structures with particular emphasis on the template-directed synthesis of mechanically interlocked structures has been described. The plethora of complimentary synthons available for constructing mechanically interlocked structures has been described briefly except for ammonium-crown ether synthons whose progress is discussed much more elaborately. In chapter 2, the synthesis of [2]rotaxanes with dibenzylammonium ion dumbbell and [20]-, [21]-, [22]crown ethers will be described. 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Macromolecules 2003, 36, 9701-9703. 178 [...]... complexes, the chemists realised the potential of the template- directed8 approach for the synthesis of various kinds of mechanically 2 Chapter 1 Introduction interlocked molecules such as catenanes,9 rotaxanes,10 suitanes,11 trefoil knots,12 Borromean rings13 and Solomon links.14 The last two decades witnessed overwhelming reports on the template- directed synthesis of catenanes and rotaxanes because they... of 5-1 (PF6)4 and 5-23 (PF6)4 H-1H COSY NMR spectrum of 5-23 (PF6)4 distribution of the major peaks 134 135 XV List of Schemes Scheme 1.1 Preparation of cyclodextrin-based [2]rotaxanes with metalloorganic stoppers using a threading-followed-by-stoppering procedure Scheme 1.2 Preparation of CB[6]-based [2]rotaxane by threading-followed-by-stoppering approach Scheme 1.3 15 Synthesis of [2]rotaxanes directed. .. of 1-20 PF6 27 XVI Scheme 1.11 Synthesis of branched [4]rotaxanes 1-36 (PF6)3, 1-37 (PF6)3 and 1-38 (PF6)3 by reversible imine-clipping methodology of compound 31 Scheme 1.12 Synthesis of [2]rotaxane 1-48 PF6 by threading-followed-by-stoppering method 35 Scheme 1.13 Synthesis of [2]rotaxane 1-51 BF4 by threading-followed-by-stoppering method 35 Scheme 1.14 Synthesis of hetero[3]rotaxane 1-54 (PF6)2... discussed IX List of Tables Table 2.1 Effect of solvent system on the association constants Ka of the pseudorotaxane species 2-9f PF6 at 300 K Table 2.2 57 Effect of solvent system on the association constants Ka of the pseudorotaxane species 2-9e PF6 at 300 K 61 X List of Figures Figure 1.1 Conceptual approaches for the synthesis of a [2]rotaxane 4 Figure 1.2 Molecular structure of β-cyclodextrin-based... forming [2]rotaxanes with soft metal ions (MII).58 Molecular structure of [2]rotaxanes based on B) RuII template5 9 and C) CoIII template. 60 Octahedral metal ion templated synthesis of catenanes,61 “figure -of- eight” complex,62 and doubly-threaded complex63 were also reported 1.3.3.1.3 Square Planar Geometries A square planar geometry is preferred by palladium(II) ion which served as template to construct... and formation of pseudo[2]rotaxane from DB24C8and DBA Figure 1.19 20 23 Molecular structure of rotaxane based on the self-assembly of DB24C8 and DBA 25 Figure 1.20 Molecular structures of different 24C8 macrocycle 28 Figure 1.21 Structure of polypseudorotaxanes based on the self-assembly of DB24C8 and DBA Figure 1.22 29 Molecular structure of poly[n+1]rotaxanes based on the self-assembly of DB24C8 and... interlocked structures Therefore, the template- directed approach used in conjunction with DCC is gaining rapid popularity The template- directed approach utilized a diverse range of complementary recognition motifs based on different kinds of non-covalent interactions, of which the most prominent are the hydrophobic interactions (Cyclodextrin and Cucurbituril), coordinations of suitably functionalized ligands... series of [2]rotaxanes, 2-(8b-d) PF6 and 2-(9b-d) PF6 43 Scheme 2.3 Synthetic route to cyclic polyethers 2-(10e-f) and 2-(11e-f) 50 Scheme 2.4 Generation of pseudo[2]rotaxane 2-8f PF6 50 Scheme 2.5 Generation of pseudo[2]rotaxane 2-9f PF6 54 Scheme 2.6 Generation of pseudo[2]rotaxane 2-9e PF6 58 Scheme 3.1 Synthesis of 3-2 BAr4 by protonation followed by counter ion exchange Scheme 3.2 Synthesis of compound... representation of the crystallographic structure of 2-9f PF6 Figure 2.16 57 Stacked 1H NMR spectra of 1-1 PF6, pseudo[2]rotaxane 2-9e PF6 and cyclic polyether 2-11e 59 Figure 2.17 Low resolution ESI-MS spectrum of 2-9e PF6 59 Figure 2.18 Stacked 1H NMR spectra of 2-9e PF6 in different solvents 60 Figure 2.19 Partial 1H NMR spectra of 2-9d PF6 at various temperatures 62 Figure 2.20 Partial 1H NMR spectra of 2-9b... of weak non-covalent interactions along with the practical limitation of the “engineering down” approach5 in the field of nanotechnology, gave chemists the impetus to emulate these non-covalent interactions in chemical systems, giving rise to a new field of chemistry, known as supramolecular chemistry.6 Supramolecular chemistry utilizing non-covalently assisted interactions led to the development of . TEMPLATE- DIRECTED SYNTHESIS OF NOVEL SUPRAMOLECULAR ARCHITECTURES SUVANKAR DASGUPTA NATIONAL UNIVERSITY OF SINGAPORE 2012 TEMPLATE- DIRECTED SYNTHESIS OF NOVEL. IV Table of Contents Table of Contents IV Summary VIII List of Tables X List of Figures XI List of Schemes XVI List of Abbreviations XIX Chapter 1 Introduction 1.1 Supramolecular. Discussion 4.2.1 Synthesis of salts 101 4.2.2 Synthesis of 20C6 and 20C6H 2 102 4.2.3 Synthesis of [2]rotaxanes by ring-closing-metathesis 103 4.2.4 Kinetic stability of [2]rotaxane 4-14·BAr 4