http://hdl.handle.net/1721.1/7646 2013-06-20T06:54:21Z http://hdl.handle.net/1721.1/79328 Small molecule binding to electrophilic trigonal pyramidal platinum, palladium, and nickel Tsay, Charlene Chapter 1 A general introduction to the concepts and background of several types of transition metal complexes that motivate and inform the research described herein. These include a-complexes and molecular adducts of dinitrogen, dihydrogen, and carbon dioxide. Chapter 2 Trigonal bipyramidal platinum(II) complexes of the monoanionic, tetradentate, triphosphine [SiPR₃ ([SiP₃R]- = [(2-R₂PC₆H₄)₃Si]-; R = Ph, iPr) ligand are prepared and shown to provide access to cationic species with divergent behavior. The less electron-rich phenyl-substituted ligand renders the platinum center extremely electrophilic, leading to structurally characterized examples of weakly-donating ligands bound in the fifth, apical coordination site. Of particular interest is the structure of the toluene adduct, which suggests a possible interaction between the platinum center and an aryl C-H bond. When the ligand phosphines are instead substituted by the more electron-rich isopropyl groups, the electrophilicity of the cationic platinum is shown to be mitigated, allowing access to a four-coordinate, trigonal pyramidal platinum center. The crystallographically characterized geometry for this divalent platinum is in contrast to the canonical square planar configuration for d⁸, 16-electron transition metal complexes. The palladium analogue is also synthesized and shown to possess the same coordination. Chapter 3 Cationic nickel complexes of the [SiPR₃] ligand are synthesized and, in contrast to their platinum and palladium congeners, facilitate the surprising binding of molecular dinitrogen to electrophilic nickel(II) centers. The extremely high stretching frequencies of these bound N₂ moieties attest to their minimal activation, and the stability of these complexes is shown to arise from increased adonation from the N₂ to the cationic nickel center, which compensates for the relative lack of it back-bonding that stabilizes N₂ adducts in less electrophilic systems. These cationic nickel species are additionally shown to form thermally stable adducts of molecular dihydrogen. The relative binding strengths of N₂ and H₂ to these nickel centers are explored and shown to be modulated by the ligand phosphine substituents. Furthermore, evidence of linear binding of carbon dioxide is presented, representing an electrophilic approach to carbon dioxide activation that is in contrast to the low-valent, nucleophilic metal paradigm. Chapter 4 The four-coordinate neutral nickel boratrane (TPiPrB = (2-iPr₂PC₆H₄)₃B) reported in the literature represents an isostructural counterpart to the cationic {[SiiPr₃]Ni}+ species presented in Chapter 3. Though these two compounds are formally separated by two oxidation states of nickel, the Lewis-acidic nature of the Z-type borane ligand in (TP'PrB)Ni renders it valence-isoelectronic with {[SiiPr3]Ni}+. The reactivity toward N₂ and H₂ of (TPiPr'B)Ni, as well as that of the new compound (TPPhB)Ni, is explored and discussed in context of what is observed for the {[SiPR3]Ni}+ system. The neutral (TPiPr'B)Ni, while presumably a better [pi] back-bonder than cationic {I[SiPip' 3]Ni}T, is demonstrated not to bind N2, though a very weak, fluxional interaction with H₂ at low temperature is hypothesized. The more electrophilic (TP PhB)Ni exhibits room temperature interactions with both N₂ and H₂, though the nature of these interactions has yet to be confirmed. These results thus underline the importance of [sigma]-donation in stabilizing N₂ and H₂ adducts of poorly 7r back-bonding metal centers. Chapter 5 Cobalt(I) complexes of [SiPR3] provide an additional isostructural, isoelectronic point of comparison to the cationic nickel species presented in Chapter 3. The dinitrogen adducts [SiP'i' 3]Co(N2) and [SiPPh3]Co(N₂), previously reported from our laboratory, feature strongly bound N₂ ligands that are not labile to vacuum. The corresponding dihydrogen adducts are generated slowly under an H₂ atmosphere. The intact nature of both dihydrogen ligands, which also are not labile to vacuum, is reflected in their NMR spectroscopic parameters. The thermal stability of these compounds enabled crystallization of [SiPi'' 3]Co(H₂) which, along with the related (TP'i'B)Co(H₂) complex also developed in our laboratory, represent the first structurally characterized dihydrogen adducts of cobalt. Additional comparisons are made between the relative N₂ and H₂ binding strengths of this system and those of the structurally and electronically related family of [SiPR3] and (TpRB) metal complexes. Appendix A The asymmetric dinucleating ligand [NOPPh], designed to contain both a hard, N-donor binding site and a soft-P-donor binding site, is synthesized and shown to form a diiron complex that features asymmetric bonding to the bridging acetates. The corresponding symmetric, allphosphine dinucleating ligand [POPPh], proves to be more conducive to further study, and provides access to the symmetric diiron, di-([mu]-bromide) starting material {[POPPh ]Fe 2Br2} {BArF4 }. Addition of hydrazine generates the asymmetric, unbridged N₂H₄ adduct, which features localized diamagnetic and paramagnetic iron centers. The conformation of this species additionally demonstrates the flexibility of this ligand framework. Reduction of the diiron(II) starting material in the presence of PMe₃ results in formation of a putative asymmetric iron(O)/iron(I) dimetallic complex, in which an N₂ molecule is bound to the diamagnetic iron center, while the PMe₃ is ligated to the high-spin iron center and rendered NMR silent. The N₂ ligand is shown to be reversibly displaced by H₂ , suggesting the formation of a dihydrogen adduct, as well as by CO₂, which is postulated to bind as a bent, [eta]²(C,O) ligand. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013.; Vita. Cataloged from PDF version of thesis.; Includes bibliographical references. 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79264 Enzyme-based reporters for mapping proteome and imaging proteins in living cells Zou, Peng, 1985- Each eukaryotic cell is exquisitely divided into organellar compartments whose functions are uniquely defined by the set of proteins they possess. For each individual protein, precise targeting to a specific sub-cellular location and trafficking between compartments are often key to its proper function. In fact, many human diseases are linked to mutations that cause mistargeting and/or defective trafficking. This thesis describes the development of enzyme-based reporters for measuring protein localization and trafficking. We employ two complementary approaches: a top-down approach, involving proteomics, to simultaneously acquire the subcellular localization information for hundreds of proteins; and a bottom-up approach, involving fluorescence imaging, to record detailed spatial information for proteins on an individual basis. This thesis is therefore divided into the following two parts. Part A describes a promiscuous protein labeling technique for proteomic mapping of organelles. This method capitalizes on peroxidase as a source of free radical generator. Compared to traditional sub-cellular fractionation methods, this novel approach obviates the need of organelle purification, thereby not only eliminating the potential artifacts associated with purification, but also greatly improving the temporal resolution of the proteomic mapping. Applying this technique to study the proteome of mitochondrial matrix and endoplasmic reticulum lumen has led to the discovery of several mitochondrial proteins whose localizations have previously been unknown or ambiguous. Part B discusses the development and application of site-specific protein labeling methods for studying receptor trafficking mechanisms. Building upon previous work in our lab, we utilized the Escherichia coli biotin ligase BirA and its acceptor peptide to site-specifically label the low-density lipoprotein receptor and studied its internalization and trafficking both at the ensemble imaging and single-molecule level. We discovered that this receptor internalizes as an oligomer into cells. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013.; Vita. Cataloged from PDF version of thesis.; Includes bibliographical references. 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79263 Cellular delivery and site-specific targeting of organic fluorophores for super-resolution imaging in living cells Uttamapinant, Chayasith Recent advances in super-resolution fluorescence microscopy have pushed the spatial resolution of biological imaging down to a few nanometers. The key element to the development of such imaging modality is synthetic organic fluorophores with suitable brightness and photostability. However, organic fluorophores are very difficult to use in live cells because of their chemical compositions. Many excellent fluorophores, such as cyanine and Alexa Fluor dyes, are highly charged with sulfonate groups and do not cross the plasma membrane. Even if the fluorophores get inside cells, there exist few methods that can be used to target these nongenetically encoded probes to specific cellular proteins with high specificity and minimal interference. We describe herein the development of new methods for cellular delivery and sitespecific targeting of organic fluorophores to proteins in living cells. Building on our lab's previous work on engineering new substrate specificity for E. coli lipoic acid ligase (LplA), we created a mutant ligase that catalyzes covalent conjugation of a 7-hydroxycoumarin fluorophore onto a 13-amino acid peptide substrate, called LAP. We showed that enzymatic fluorophore ligation is compatible with the living cell interior and is highly specific for LAP fusion proteins. To extend the repertoire of fluorophores targetable by LplA inside cells, we devised a two-step labeling approach based on enzymatic azide ligation, followed by chemoselective derivatization with any membrane-permeable fluorophore via strain-promoted cycloaddition. As an auxiliary tool for enzymatic probe ligation, we also developed a very efficient and biocompatible variant of copper-catalyzed azide-alkyne cycloaddition that can be used for modification of cell-surface proteins. To overcome the lack of membrane permeability of sulfonated fluorophores, we identified a chemical reaction that efficiently masks charged sulfonate groups as esterase-labile sulfonate esters. Such masked sulfonated fluorophores enter cells readily and can be sitespecifically targeted to intracellular proteins. Our efforts in developing protein labeling and fluorophore delivery methods culminated in their application to super-resolution imaging of cellular proteins in living cells. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013.; Vita. Cataloged from PDF version of thesis.; Includes bibliographical references. 2013-01-01T00:00:00Z http://hdl.handle.net/1721.1/79260 Bromonium-Initiated Epoxide-Opening Cascades : total Synthesis of ent-Dioxepandehydrothyrsiferol and Synthetic Studies toward (+)-Scholarisine A Tanuwidjaja, Jessica CHAPTER I. Bromonium-Initiated Epoxide-Opening Cascades: Total Synthesis of ent-Dioxepandehydrothyrsiferol Our foray into the total synthesis of ent-dioxepandehydrothyrsiferol has led to the discovery and development of the bromonium-initiated epoxide-opening cascade. This transformation constructs the signature trans-anti-trans tricyclic portion of the natural product containing the bromo-oxepane in a single step. Further explorations into this cascade also revealed feasibility of incorporation of exogenous trapping nucleophiles into the reaction. [chemical formulae] CHAPTER 11. Synthetic Studies toward (+)-Scholarisine A. A concise and scalable route toward the monoterpene indole alkaloid (+)- scholarisine A has been developed. Synthetic highlights of the route include: 1) cisselective Diels-Alder cycloaddition reaction to construct strained 5,6-fused hydrindanones, 2) a novel indole formation via an in-situ aza-Wittig reaction, and 3) a selective enolization and hydrolysis sequence of a diketone substrate to provide rapid access to a key tetracyclic intermediate. Studies to access the natural product via latestage intramolecular indole alkylations are presented. [chemical formulae] Thesis (Ph. D. in Organic Chemistry)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013.; Vita. Cataloged from PDF version of thesis.; Includes bibliographical references. 2013-01-01T00:00:00Z