Transition Metal and Lanthanide Complexes for Catalysis and Protein Structure Determination Thesis submitted in partial fulfillment of the requirements of: Doctor of Philosophy By Bradley Yat Wah Man The University of New South Wales School of Chemistry Supervisors: Professor Barbara Messerle Professor Gottfried Otting June 5, 2010 Dedicated to the memory of my grandmother Man Wen Fang, whose hopes has inspired me through the tough times. Preface This thesis is a report of original research undertaken by the author and is submitted for admission to the degree of Doctor of Philosophy at the University of New South Wales. This work was completed in the School of Chemistry at the University of New South Wales during the period of March 2006 to March 2010. The works and results presented in this thesis are those of the author, unless otherwise acknowledged. Sections of this work that have been published: 3-Mercapto-2,6-pyridinedicarboxylic acid, A Small Lanthanide Binding Tag for Protein Studies by NMR Spectroscopy Bradley Man, Xun-Cheng Su, Haobo Liang, Shane Simonsen, Thomas Huber, Barbara A. Messerle and Gottfried Otting Chemistry: A European Journal, 2010, 16(12), 3827 – 3832 A Dipicolinic Acid Tag for Rigid Lanthanide Tagging of Proteins and Paramagnetic NMR Spectroscopy Xun-Cheng Su, Bradley Man, Sophie Bereen, Haobo Liang, Shane Simonsen, Christophe Schmitz, Thomas Huber, Barbara A. Messerle and Gottfried Otting Journal of the American Chemical Society, 2008, 130(2), 10486 – 10487 Sections of this work have been presented at scientific conferences: Functionalized Rhodium(I) complexes: structure and catalysis Bradley Man, Barbara Messerle. i Australian Organometallic Meeting 5, Sydney, New South Wales 2010. Oral Presentation. A New Thiol Modified Dipicolinic Acid Tag for Protein Studies with Pseudocontact Shifts Bradley Man, Barbara Messerle, Gottfried Otting, Shane Simonsen, Xun-Cheng Su 7th Biannual Meeting of the Australian and New Zealand Nuclear Magnetic Resonance Society (ANZMAG), Couran Cove, Queensland 2008. Poster presentation. Small Molecular Tags for Protein Structure Determination Bradley Man, Barbara Messerle, Gottfried Otting, Xun-Cheng Su 23rd International Conference on Organometallic Chemistry, Rennes, France 2008. Poster Presentation. Paramagnetic Complexes for Protein Structure Determination Bradley Man, Barbara Messerle, Gottfried Otting, Shane Simonsen, Xun-Cheng Su 21st International Congress for Heterocyclic Chemistry, Sydney, New South Wales 2007. Poster Presentation. Paramagnetic Complexes for Protein Structure Determination Bradley Man, Barbara Messerle, Gottfried Otting, Shane Simonsen, Xun-Cheng Su Conference of the Inorganic Chemistry Division ,Hobart, Tasmania 2007. Poster Presentation. ii Abstract “A short saying often contains much wisdom” Sophocles The aims of this thesis are to explore the application of transition metal and lanthanide complexes in the areas of structural biology and catalysis. This PhD thesis is therefore divided into two sections; the emphasis of the first section is on the synthesis and development of small organic molecules as paramagnetic probes with applications in protein structure refinement. The second section is on the synthesis and characterization of a series of rhodium(I) complexes bearing either functionalized tridentate pyrazolyl or tridentate imidazolyl donor ligands. The reactivity of this series of rhodium(I) complexes as catalysts for the intramolecular cyclization of alkynoic acids was investigated. The first section of the thesis involved the synthesis of two thiol modified dipicolinic acid based tags, 4-mercaptomethyl-2,6-pyridinedicarboxylic acid (4MMDPA, 5) and 3-mercapto-2,6-pyridinedicarboxylic acid (3MDPA, 9) were described. The ligands 4MMDPA (5) and 3MDPA (9) were attached to the N-terminal domain of the arginine repressor from E. coli. (ArgN). Lanthanide complexes of the ArgN-4MMDPA adduct were synthesized in situ and the efficiency of the ligand (5) as a paramagnetic probe was assessed using 15N-HSQC spectra. The HSQC spectra showed that the 4MMDPA- Ln3+ complex was able to rigidly bind to the protein, the first ligand to be reported with rigid binding with only a single attachment point. Similar studies on the lanthanide and transition metal complexes of the ArgN-3MDPA adduct showed that the 3MDPA (9) tag was able to bind to both lanthanide and transition metal ions. Due to the reduced magnitude of the tensors observed for the 3MDPA tag (9), the rigidity of the binding could not be adequately assessed. The incorporation of unnatural amino acids in proteins via a modified protein expression system was proposed as an alternative method to introduce paramagnetic labels without the need of post translational iii modifications. Synthetic routes to a series of unnatural amino acids 11, 15 and 19 based on previously described lanthanide and transition metal binding motifs were developed. The second half of the project describes the synthesis and the characterization of a series of rhodium(I) complexes bearing the tris(pyrazolyl)toluidine ligand (p-tpt, 24a; o-tpt, 24b) and the tris(N-methylimidazolyl)methanol ligand (tim, 23). The structures of the rhodium(I) complexes containing these ligands (27, 28 and 29b) in the solid state showed that the ligands were all bound to the rhodium centre in a bidentate (2) binding mode centre via two of the three available nitrogen donors. In solution, fluxional behavior was observed in the 1H NMR spectrum for the rhodium(I) complexes bearing the tris(pyrazolyl)toluidine ligands (27 – 29). Detailed analysis of the rhodium(I) complexes bearing the o-tris(pyrazolyl)toluidine ligand (27b, 28b and 29b) in the solution state at low temperatures showed that there is restricted rotation of the aryl ring about the C-C bond between the aryl ring and the bridging carbon, leading to observation of two species in the 1H NMR spectrum. The application of rhodium(I) complexes bearing pyrazolyl donors (29a and 29b) and imidazolyl donors (37 and 40) as catalysts for the intramolecular cyclization of aliphatic and aromatic alkynoic acids was investigated. It was found that rhodium(I) complexes bearing imidazolyl donors 37 and 40 were highly active catalysts for the intramolecular cyclization of aliphatic alkynoic acids. Despite the structural similarities between the rhodium(I) imidazolyl complexes containing the bidentate and tridentate ligands, differences in catalytic activity were observed, attributed to the interference of the unbound imidazolyl donor with the substrate during the catalytic cycle. The rhodium(I) complex bearing the pyrazolyl donors (29a) was found to be a highly active catalyst for the intramolecular cyclization of terminal aromatic alkynoic acids, while rhodium(I) complexes bearing bidentate imidazolyl ligands were highly active catalysts for the intramolecular cyclization of non-terminal aromatic alkynoic acids. All rhodium(I) complexes (29a, 37 and 40) investigated as catalysts for the intramolecular cyclization of both non-terminal and terminal aromatic alkynoic acids displayed high level of regioselectivity in the formation of exo-dig vs. endo-dig product. A study of the dependence of the regioselectivity and the efficiency of cyclization on the electronic iv nature of the substrates indicated that electron withdrawing groups at the terminal alkyne substituent generally increased the rates of cyclization. The regioselectivity of the cyclization was also influenced by the relative difference in the electron density between the alkyne carbons. v Acknowledgements “Dreams take long term commitment. From the first to the last we need focus, discipline, persistence, and the ability to keep sight of the vision of what we are slowly creating.” Dennis Wholey Each chapter starts off with a quote, and each describing the theme of the chapter. The quote for the acknowledgement more or less summarizes this entire volume of work. Along the way, this thesis felt like folly and many times along the way, the urge to throw it all in was high. Through the support of family, friends and a bit of positive thinking, it all came through in the end. First I would like to thank my supervisors Prof. Barbara Messerle and Prof. Gottfried Otting for giving me such an opportunity to work on such a wonderful project. Without their tireless guidance and support this project could not have been possible. I would acknowledge the contributions the BAM and GO research group has offered during the PhD. In particular, I would like to thank Dr Jason Harper, Dr Jim Hook, Dr Donald Thomas, Dr Richard Hodgson, Dr Rebecca Wilson, Dr Shane Simonsen and Dr Laurent Poorters. These wonderful people always found the time to teach me everything they knew and without them, I could not have become the chemist I am today. They have also on numerous occasions provided many words of encouragement and wisdom, without which I could not have completed this PhD. I would like to thank all of my friends, especially Debbie Mackay, Chris Haines, and Richard Parry, Murray Adams, Eric Majka, Matthew Stone, Alison Manion and Kate Odenthal. I would like to thank Richard for showing me the strength to get through some of the toughest times time I had in the last two years. I would like to thank Chris, for showing me that life should be viewed for all its potentials, not for what went vi wrong. Deb, Murray and Alison were great friends during my PhD, always offering advice, always happy to take care of a friend going through tough times, and most importantly, always