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The Supramolecular Chemistry of Cucurbituril Molecules

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The Supramolecular Chemistry of Cucurbituril Molecules THE SUPRAMOLECULAR CHEMISTRY OF CUCURBITURIL MOLECULES SUSANA LORENZO A thesis submitted in fulfilment Of the requirements for the degree of Doctor of Philosophy School of Chemistry University of New South Wales March, 2006 Page i ABSTRACT The set of molecules cucurbit[n]uril (Qn) are macrocycles composed of n glycoluril monomers linked by methylene groups. These molecules have two oxygen-ringed portals of a diameter slightly smaller than their internal cavity diameter. This thesis describes syntheses, crystallisations, crystal structure determinations, crystal packing analyses and force field calculations exploring the supramolecular chemistry of Qn molecules and their derivatives. Qn acts as a host for guest molecules and at the outset of this project no metal containing molecule had been encapsulated in a Qn molecule. One aim of this project was to prepare such complexes. This was achieved with the synthesis and characterisation of crystalline {[cis-SnCl4(H2O)2]@Q7}2(SnCl6)3(H3O)6(H2O)23. Other compounds prepared and characterised crystallographically in the course of this project are: [(Q6)(Na3(H2O)8)]2[CoCl4]4[Co(H2O)6]2[CoCl(H2O)5]2(Cl)4, (Q5@Q10)(CH3COOH)(Cl)2(H3O)2(H2O)26, (Cl@Q5)4Q6(SnCl6)8(H3O)20(H2O)24, (Q8)3(PtCl6)4(H3O)8(H2O)x, (Q8)2(PtCl6)3(H3O)6(H2O)18, (Q7)(Cr3O10)(H3O)2(H2O)x and (Q6)(SnCl6)(H3O)2(H2O)x. While the smaller Qn (n = 5–8) retain their circular forms, the larger Qn (n > 8) are less rigid and distort to accommodate larger guests. After analysis of the crystal structures of these Qn compounds and those listed in the Cambridge Structural Database, the principal packing motifs of the Qn molecules were elucidated. The most common is the portal-to-side interaction in which the portal oxygen atoms of one Qn approach the hydrogen atoms around the equator of another Qn. Force-field calculations on guest@Qn complexes were conducted to determine the mechanism for the formation of these complexes. A comparison of the intermolecular interactions of phenylated systems and comparable fluorinated phenyl systems was made using both crystal packing analyses and force- field energy calculations. Intermolecular energy parameters for these calculations were derived and validated in this work. The principal fluorinated species studied was the – [B(C6F5)4] anion. Examination of its crystal structures found that the substitution of the hydrogen atoms by fluorine atoms is influential enough to alter the predominant Page ii intramolecular conformation. It is the ‘flipper’ conformer, between pairs of perfluorophenyl groups, that is overwhelmingly the favoured conformation and this has – a strong effect on the types of phenyl embraces that a [B(C6F5)4] anion will form. While the parallel 4PFE, the offset parallel 4PFE and the orthogonal 4PFE are all observed the 6PFE is not. Page iii ACKNOWLEDGEMENTS There are many people who have contributed to my project over the years and I would like to take this opportunity to thank them. Firstly to my collaborators at the Australian Defence Force Academy, Dr. Rodney Blanch, Dr. Anthony Day and Dr. Alan White for their introduction to and advice on cucurbituril chemistry. In particular I would like to thank Dr. Anthony Day for the supply of cucurbituril compounds and help with synthetic preparations. Dr. Gareth Lewis, Dr. John McMurtrie, Don Craig and Dr. Peter Turner have provided me with tuition and invaluable assistance in crystallographic techniques. Their help has contributed enormously to this project and I cannot thank them enough. Thanks also to Dr. Jim Hook for his assistance with NMR techniques. Over the years Dr. Marcia Scudder has acted as a second supervisor to me. She has provided me with instruction in many aspects of my research, from computational to crystallographic techniques and provided a wealth of information on general matters of my research. Marcia has been overwhelmingly generous with her time and so a simple ‘thankyou’ seems too weak a word to express my gratitude. Thankyou anyway. My supervisor, Emeritus Prof. Ian Dance, is a tremendous role model for any aspiring researcher and I consider it a privilege to have been his student. Along with his extensive knowledge, it is his enthusiasm for his work, his energy and optimism that I consider to be his greatest attributes and those of an excellent supervisor. He applied all his talents with gusto during my PhD and I offer my deepest gratitude for all he has done for me. I wish him all the best in (partial) retirement. I’d also like to take the time to thank those who have made my time as a PhD student memorable and a lot of fun. They include: Scott Watkins, David Lonnon, Garth Jones, Antonella Petrella, Lakmini Weerakoon, Vanessa Russell, John McMurtrie and Catrin Hasselgren-Harby. Page iv In particular I’d like to thank Nathan Paris for his long friendship and his genuine encouragement, advice and support, especially in recent times, and also to Doug Lawes for his perpetual kindness and willingness to help out a friend in need. My family represents a great source of strength for me and I have drawn on this heavily during my student career. I’d like to finish off this page of thankyous by saying how grateful I am to them for the important role they have played in my life. Page v TABLE OF CONTENTS. ABSTRACT..................................................................................................................... I ACKNOWLEDGEMENTS......................................................................................... III TABLE OF CONTENTS...............................................................................................V ABBREVIATIONS ................................................................................................... XIV CHAPTER 1: INTRODUCTION TO SUPRAMOLECULAR CHEMISTRY .................................1 1.1: Supramolecular Chemistry..................................................................................... 1 1.2: Host-Guest Complexes. ......................................................................................... 2 1.3: Supramolecular Devices. ....................................................................................... 4 1.4: The Role of Crystallography in the Study of Supramolecular Chemistry. ............ 5 1.4.1: Crystal engineering. ........................................................................................ 6 1.4.2: Polymorphism. ................................................................................................ 6 1.5: Conclusion. ............................................................................................................ 7 REFERENCES.............................................................................................................. 9 CHAPTER 2: INTRODUCTION TO CUCURBITURIL CHEMISTRY........................................11 2.1: Introduction.......................................................................................................... 11 2.2: Cucurbituril as a Host Molecule. ......................................................................... 13 2.2.1: Interactions between host and guest molecules. ........................................... 15 2.2.2: Methods of detection of host-guest complexes............................................. 18 2.2.3: Altered guest properties due to complex formation...................................... 19 2.2.4: Chemistry inside the Qn cavity: Qn as a catalyst. ........................................ 21 2.2.5: The host-guest complexes of other macrocycles. ......................................... 22 2.3: Cation Binding to Portals..................................................................................... 24 2.4: The Practical Applications of Qn Chemistry. ...................................................... 26 2.5: The Synthesis of Qns. .......................................................................................... 29 Page vi 2.5.1: The synthesis of substituted Qns. ................................................................. 31 2.6: Computational Studies of Qns. ........................................................................... 33 2.7: Aims of this Project. ............................................................................................ 34 REFERENCES............................................................................................................ 35 CHAPTER 3: CRYSTAL STRUCTURE ANALYSIS OF LITERATURE STRUCTURES.........43 3.1: Introduction.......................................................................................................... 43 3.1.1: The crystal packing of the uncoordinated Qn molecules.............................. 44 3.2: The Metal-Chalcogenide Clusters........................................................................ 48 3.2.1: Columns of parallel Qns. .............................................................................. 51 3.2.2: Zig-zag chains of Qns. .................................................................................. 54 3.2.3: Other packing motifs. .................................................................................. 58 3.2.4: Concluding remarks...................................................................................... 61 3.3: Host-Guest Complexes. ....................................................................................... 62 3.4: Metal Complexes not Coordinated to Qn. ........................................................... 70 3.4.1: Introduction..................................................................................................
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