Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2013. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references. / 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. / by Peng Zou. / Ph.D.

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / Chapter 1. Palladium-Catalyzed Cross-Coupling of Aryl Chlorides and Triflates with Sodium Cyanate: A Practical Synthesis of Unsymmetrical Ureas. An efficient method for palladium-catalyzed cross-coupling of aryl chlorides and triflates with sodium cyanate is reported. The protocol allows for the synthesis of unsymmetrical N,N'-di- and N,N,N'-trisubstituted ureas in one pot, and is tolerant of a wide range of functional groups. Insight into the mechanism of aryl isocyanate formation is gleaned through studies of the transmetallation and reductive elimination steps of the reaction, including the first demonstration of reductive elimination from an arylpalladium isocyanate complex to produce an aryl isocyanate. Chapter 2. Palladium-Catalyzed Synthesis of N-Aryl Carbamates. An efficient synthesis of aryl carbamates was achieved by performing palladiumcatalyzed cross-coupling of ArX (X = CI, OTf) with sodium cyanate in the presence of alcohols. The use of aryl triflates as electrophilic components in this transformation allowed for an expanded substrate scope for the direct synthesis of aryl isocyanates. This methodology provides direct access to major carbamate protecting groups, Sthiocarbamates, and diisocyanates, which are precursors to polyurethane materials. Chapter 3. Structural Reevaluation of the Electrophilic Hypervalent Iodine Reagent for Trifluoromethylthiolation. Hypervalent iodine [lambda]3-benziodoxoles are common electrophilic transfer reagents known for their enhanced stability compared to their non-cyclic analogues. Here we present data showing that chlorobenziodoxole reacts with two different thiolate nucleophiles (thiocyanate and trifluoromethylthiolate) resulting in the formation of stable thioperoxy complexes rather than the expected benziodoxole derivatives. We further report a revised structure for the earlier described electrophilic trifluoromethylthiolation reagent (1), previously believed to contain the benziodoxole framework. Our findings, which are based on a combination of analytical techniques, including the recently introduced crystalline sponge method for X-ray analysis, unambiguously demonstrate that 1 is a thioperoxy compound both in solution and the solid state. Chapter 4. Organometallic Palladium Reagents for Cysteine Bioconjugation. Organometallic palladium reagents for the selective S-arylation of biomolecules are described. This new bioconjugation toolkit provides a highly versatile technique for the fast functionalization of cysteine with aromatic scaffolds under a broad range of reaction conditions (e.g., pH, solvent, temperature). The resulting bioconjugates are stable under basic and acidic conditions, as well as in the presence of external thiol nucleophiles. The substitution pattern on the aryl ring can be varied to achieve high levels of stability toward oxidation. Lastly, new types of bio-therapeutics - stapled peptides and linker-free antibody-drug conjugates - could be synthesized using the new method. / by Ekaterina V. Vinogradova. / Ph. D. in Organic Chemistry

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / We explore strategies to exploit the rich chemical reactivity available to inorganic coordination complexes in order to realize chemiresistive detectors, electronic device elements that undergo a change in resistance in the presence of analyte, through either incorporation of a conductive material (i.e., carbon nanotubes) or reliance on intrinsic conductivity. We seek to elucidate fundamental principles that govern these chemical detectors and use these insights to aid our design of effective chemical detection systems. In Chapter 1, we give an overview of chemiresistors in chemical detection with an emphasis on those based on carbon nanotubes. In Chapter 2, we employ metalloporphyrin complexes bearing late first-row transition metal centers in composites with single-walled carbon nanotubes (SWCNTs) in a chemiresistive sensor array capable of classifying various volatile organic compounds (VOCs) through the use of statistical analyses. In this study, we hypothesize that a swelling-based transduction mechanism is a significant contributor to the observed response. In Chapter 3, we demonstrate that the metalloporphyrin-SWCNT chemiresistor can be optimized through rational design for the detection of amines relevant to meat spoilage. Within the meso-tetraarylporphinatocobalt manifold, increasing the electron deficiency of the metal center through synthetic tuning can increase the device's sensitivity to amines, allowing for a detector to monitor the decomposition of meat. In Chapter 4, we describe the design of a sensor for carbon monoxide, fabricated from carbon nanotubes and an organocobalt(III) complex. This work represents the first example of a carbon monoxide detector based on carbon nanotubes functionalized with a molecular species. In Chapter 5, we immobilize a composite of SWCNTs and poly(4-vinylpyridine) onto glass substrates decorated with gold electrodes and then incorporate PdCl₂ into the devices to give chemiresistive detectors for vapors of thioethers. We also show that incorporating permanaganate into the polymer leads to a chemiresistive detector for VOCs susceptible to oxidation. In Chapter 6, we employ 2-D metal-organic frameworks as chemiresistors for the detection of volatile compounds, exploiting their intrinsic conductivity. These materials are the first of their class to be utilized as chemiresistive detectors because of their uniquely high conductivities. / by Sophie Liu. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references. / Chapter 1. In this introductory chapter, we present the general properties of conjugated polymers for sensory and electronic applications, with a special emphasis placed on electron-deficient materials. Chapter 2. In this chapter is presented the synthesis, characterization, and applications of a series of electron-deficient poly(p-phenylene vinylene)s (PPVs) homopolymers and copolymers. Poly(p-phenylenevinylene)s containing trifluoromethyl substituted aromatic rings (CF3- PPVs) exhibited high photooxidative stability to give robust materials suitable for molecular electronic device applications. Chapter 3. Hyperconjugative and Inductive Perturbations in Poly(p-phenylene vinylenes) New approaches that produce high fluorescence quantum yields and also tune electron affinity of conjugated polymers are presented. Novel three-dimensional poly(phenylene vinylenes) having [2.2.2] bicyclic ring system were synthesized to give highly efficient solid- state fluorescence and hyperconjugative and inductive electronic perturbations. The ability of hyperconjugative and inductive perturbation to tune the polymers' sensory applications was determined by investigating the fluorescence quenching responses to electron-rich and electron-deficient analytes in solution and solid thin films. Chapter 4. High Ionization Potential Conjugated Polymers In this chapter is presented a series of poly(p-phenylene ethynylenes) (PPEs) with high ionization potentials. Their photophysical properties were investigated using steady-state and time-resolved fluorescence techniques. / (cont.) The ionization potentials of the polymer thin films were determined using ultraviolet photoelectron spectroscopy (UPS), and those with the highest ionization potentials displayed high sensitivity for the detection of electron-donating aromatic compounds. The effects of sterics and electronic properties on the polymers' sensory responses were investigated by fluorescence quenching experiments in both solution and solid thin films. In addition, in some cases the excited state charge-transfer complexes (exciplexes) of the PPEs with analytes were observed. These effects provide promising opportunities for the formation of sensitive and selective chemical sensors. Chapter 5. Highly Emissive Conjugated Polymer Excimers Conjugated polymers often display a decrease of fluorescence efficiency upon aggregation due in large part to enhanced interpolymer interactions that produce weakly emissive species generally described as having excimer character. We have found that poly(phenylene ethynylene)s with fused pendant [2.2.2] ring structures having alkene bridges substituted with two ester groups function to give highly emissive, broad, and red-shifted emission spectra in the solid state. To best understand the origin of this new solid-state emissive species, we have performed photophysical studies of a series of different materials in solution, spin-coated thin films, solid solutions, and Langmuir films. We conclude that the new, red-shifted, emissive species originate from excimers produced by interchain interactions being mediated by the particular [2.2.2] ring system employed. / (cont.) The ability to predictably produce highly emissive excimers from conjugated polymers is important for the understanding how solid-state structures can control emissive behaviors. Chapter 6. Electron-Deficient Polyelectrolytes For Biosensory Applications In this chapter is described a novel photo-oxidizing water-soluble fluorescent polymer that was designed for the detection of electron-rich biological analytes. The polymer fluorescence is strongly quenched through an efficient photoinduced electron transfer from electron-donating aromatic moieties in amino acids, neurotransmitters, and proteins to the photo-oxidizing polymer. These efficient fluorescence quenching responses may be further enhanced by rapid exciton migration in the polymer backbone and further facilitated by ion- pairing between the polymer and quencher. / by Youngmi Kim. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999. / Includes bibliographical references. / by Kent E. Pryor. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995. / Includes bibliographical references. / by Roelof Jan Pieters. / Ph.D.

Thesis (B.S.) Massachusetts Institute of Technology. Dept. of Chemistry, 1949. / MIT copy bound with: Acid hydrolysis of aḏm̲ethyl glucoside and 6ṯosyl aḏm̲ethyl glucoside / George W. Pratt, Jr. 1949. / Bibliography: leaf [23]. / by Mary C. Cretella. / B.S.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The synthesis and reactions of 2-iodoynamides were investigated. 2-Iodoynamides undergo efficient and regioselective [2 + 2] cycloaddition with ketene to produce cyclobutenones that are useful synthetic building blocks. Reaction of 2-iodoynamides and vinylketenes generated in situ from cyclobutenones proceeds via a pericyclic cascade mechanism to produce highly substituted 2-iodoanilines. Tandem strategies for the synthesis of highly substituted indoles involving this benzannulation reaction were investigated. In addition, the synthesis of furo[2,3-g]thieno[2,3- e]indole, a new tetracyclic aromatic compound, was achieved via a strategy based on benzannulation with ynamides. / by Yu-Pu Wang. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Vita. / Includes bibliographical references. / Chapter 1. An Introduction to Zinc Metalloneurochemistry and Zinc Detection in Biology. This chapter presents an overview of zinc neurophysiology and pathology, which provides motivation for the design of new tools and tactics for zinc detection in vivo. A historical account of biological zinc detection is also given, followed by a summary of recent progress in the development and use of fluorescent Zn(II) sensors for in vivo studies. A summary of project goals and thesis organization is also included. Chapter 2. Zinc Sensors Based on Monosubstituted Fluorescein Platforms I: Routes to Electronic Variation, Syntheses and Spectroscopic Characterization. In this work, a convergent synthetic approach for the assembly of fluorescent zinc sensors from aniline-derivatized ligands and a fluroescein carboxaldehyde platform is presented. These sensors are based on the previously reported ZP4 motif and incorporate a di(2-picolyl)amine moiety in the aniline-based ligand framework. The effects of electronic variation, achieved by halogenation of either the zinc-binding unit or the fluorophore platform, on the fluorescence properties and aniline nitrogen atom pKa values are considered. / (cont.) Chapter 3. Spectroscopic Characterization and Biological Applications of Halogenated Zinpyr Sensors. In this chapter, the effects of fluorescein halogenation on the photophysical properties and protonation equilbria of symmetrical Zinpyr derivatives, which contain two di(2-picolyl)amine-based ligand appendages, are considered. These sensors have sub-nM affinity for Zn(II) and are selective for Zn(II) over biologically relevant alkali and alkaline earth metals. Fluorescein halogenation influences background fluorescence, dynamic range, tertiary amine pKa, and both excitation and emission wavelengths. Extensive biological work, including cytotoxicity assays and confocal imaging, are also presented. Studies in a number of cell lines, including neurons, show that ZP3 is a versatile Zn(II) imaging tool. Chapter 4. Zinc Sensors Based on Monosubstituted Fluorescein Platforms II: Modulation of Zinc Affinity and Biological Applications. To access ZP sensors with lower Zn(II) affinity, pyrrole moieties were incorporated into an aniline-based ligand unit to give sensors ZP9 and ZP10. The photophysical characterization and metal binding properties of these sensors are described. / (cont.) The pyrrole-for-pyridyl substitution affords Zn(II) sensors with improved Zn(II) selectivity and sub-[M dissociation constants. Biological imaging studies revealed that asymmetrical ZP probes, including ZP4, are cell permeable and Zn(II) responsive in vivo. Both ZP4 and ZP9 detect endogenous Zn(II) in acute hippocampal slices from the adult rat. Chapter 5. The Zinspy Family of Fluorescent Zinc Sensors: Syntheses and Spectroscopic Investigations. Four fluorescent sensors designed for Zn(II) detection and which contain a fluorescein reporting group and a pyridyl-amine-thioether derivatized ligand moiety were prepared and their photophyiscal properties characterized. These "Zinspy" sensors are water soluble and generally display -1.4 to -4.5-fold fluorescence enhancement upon Zn(II) coordination, depending upon fluorescein halogenation and the number and nature of the Zn(II)-binding appendages. The Zinspy sensors exhibit improved selectivity and lower affinity for Zn(II) compared to the di(2-picolyl)amine-based Zinpyr family members. Chapter 6. Zinspy Sensors with Enhanced Dynamic Range: Imaging Zinc Uptake and Mobilization with a Low Affinity Probe. / (cont.) This chapter describes the preparation and characterization of Zinspy sensors containing non-coordinating thiophene heterocycles in the metal-binding unit. These probes show improved dynamic range relative to thioether-containing ZS sensors, low M dissociation constants for Zn(II) and improved Zn(II) selectivity. Stopped-flow kinetics investigations indicate fast association rates and reversible Zn(II) coordination with kon > 1.8 x 106 M'-s- and koff > 3 s-1 at 25 C. ZS5 is cell permeable, Zn(II)-responsive in vivo and localizes to the mitochondria of certain cell types. ZS5 can detect Zn(II) released from neurons following nitrosative stress. Chapter 7. QZ1 and QZ2, Rapid Reversible Quinoline Derivatized Fluoresceins for Sensing Biological Zinc. Two fluorescein-based dyes derivatized with 8-aminoquinoline were prepared and their photophysical, thermodynamic and zinc-binding kinetic properties determined. Because of their low background fluorescence and highly emissive Zn(II) complexes, QZ1 and QZ2 display a large dynamic range, with -42- and -150-fold fluorescence enhancements upon Zn(II) coordination, respectively. / (cont.) These sensors have micromolar dissociation constants for Zn(II), improved selectivity and bind Zn(II) rapidly and reversibly with kon values >106 M-'s-1 and koffvalues of ~150 s-1. Biological imaging studies with ZP3 and QZ2 show that binding affinity is an important parameter for metal ion detection in vivo. QZ1 and QZ2 also respond to two-photon excitation and two-photon microscopy was used to visualize Zn(II) with QZ2 in live HeLa cells. Chapter 8. A "Turn-On" Fluorescent Sensor for the Selective Detection of Mercuric Ion in Aqueous Media. This chapter describes the synthesis, photophysical characterization and metal-binding properties of mercury sensor 1 (MS1). This sensor is based on a fluorescein platform and has a thioether-rich metal-binding unit, which conveys high selectivity for Hg(II). To the best of our knowledge, MS1 was the first reversible fluorescent Hg(II) sensor to give fluorescence turn-on in water. MS1 can detect low ppb levels of Hg(II) in aqueous solution at neutral pH. Chapter 9. Selective Hg(II) Detection in Aqueous Solution with Thiol Derivatized Fluoresceins. The syntheses and photophysical properties of MS2 and MS3, two asymmetrically derivatized fluorescein-based dyes designed for Hg(II) detection, are described. / (cont.) These sensors each contain a single pyridyl-amine-thiol metal-binding moiety, form 1:1 complexes with Hg(II) and exhibit selectivity for Hg(II) over other Group 12 metals, alkali and alkaline earth metals, and most divalent first-row transition metals. Both dyes display superior brightness ( x ) and fluorescence enhancement following Hg(II) coordination in aqueous solution. At neutral pH, electron transfer (PET) quenching of the free dye is enhanced, and the Hg(II)-induced turn-on also benefits from alleviation of this pathway. MS2 can detect ppb levels of Hg(II) in aqueous solution, demonstrating its ability to identify environmentally relevant concentrations of Hg(II). Chapter 10. MS4, A Seminaphthofluorescein-Based Chemosensor for the Ratiometric Detection of Hg(II). The synthesis and photophysical characterization of MS4, an aniline-derivatized seminaphthofluorescein-based dye that contains a pyridyl-amine-thioether ligand analogous to that employed in the Zinspy Zn(II) sensor family (Chapter 5) are reported. Sensor MS4 provides single-excitation, dual-emission ratiometric detection of Hg(II) in aqueous solution. An -4-fold ratiometric change (624/524) is observed upon introduction of Hg(II) to an aqueous chloride-containing solution of MS4 at pH 8. / (cont.) In this milieu, MS4 shows selectivity for Hg(II) over a background of alkali and alkaline earth metals, a number of divalent first-row transition metals and its Groupl2 congeners Zn(II) and Cd(II). Chapter 11. Turn-On and Ratiometric Mercury Sensing in Water with a Seminaphthofluorescein-Based Probe. The synthesis and characterization of MS5 are presented in this chapter. This sensor incorporates the aniline-derivatized thioether ligand used in the preparation of MS1 and the seminaphthofluorescein platform described in the design of MS4. MS5 gives selective fluorescence turn-on for Hg(II) at pH > 7. At pH > 8, single-excitation dual-emission ratiometric Hg(II) detection is possible by comparison of the (624 / 524) ratio before and after Hg(II) coordination. Studies of the pH dependence suggest that the seminaphthofluorescein dianion is critical for generating the ratiometric response. X-ray crystallographic studies with a salicylaldehyde-based model complex are presented to help elucidate the nature of Hg(II) coordination to MS1 and MS5. MS5 can respond to Hg(II) added to natural water samples, which points to its potential utility in the field. / (cont.) Appendix 1. Miscellenous Fluorescein-Based Ligands. This appendix details the preparation and, in some cases, characterization of potential fluorescein based sensors for either Zn(II) or Hg(II) detection that were not described in earlier chapters. Many of these compounds give fluorescence turn-off or no fluorescence change with analyte binding. Sensors ZP11 and MS6 are lower-affinity probes that give fluorescence turn-on for Zn(II) and Hg(II), respectively. Appendix 2. Theoretical Investigations of Fluorescein Derivatives. In this chapter, we present the results from DFT and TDDFT calculations on fluorescein and its derivatives. These studies include establishing protocols for fluorescein pKa determination and TDDFT analysis. The absorption spectra of the fluorescein dianion and monoanion were assigned and a detailed molecular orbital analysis for a fluorescein dianion analog was conducted. These studies indicate that oxygen atoms in the xanthenone moiety influence the amount of C1 character in the donor and acceptor molecular orbitals responsible for fluorescein absorption. / by Elizabeth M. Nolan. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1999. / Vita. / Includes bibliographical references. / The synthesis and structure of several Zr(IV) carboxylate complexes are described in which the bridging carboxylate is the dianion of 111-xylylenediamine bis(Kemp's triacid imide) (H2XDK) or the more soluble propyl derivative (H2PXDK). Reaction of either H2XDK or H2PXDK with [Zr(CH2Ph)4] or [Zr(NMe2)4] afforded [Zr(CH2Ph)2(XDK)] or [Zr(NMe2)2(XDK)]. [Zr(CH2Ph)2(XDK)] is a rare example of an alkyl zirconium carboxylate complex. [Zr(CH2Ph)2(XDK)] reacts with various pyridine derivatives to yield the 7-coordinate pyridine adduct. An aryl isocyanide (2 equiv) reacts with [Zr(CH2Ph)2(XDK)] to afford the iminoacyl complex [Zr{11 2 -2,6- Me2PhNCCH2Ph}2(XDK)]. [Zr(CH2Ph)2(XDK)] is unreactive, however, towards weak sigma donors such as CO. The eight-coordinate complex [Zr(XDK)2] was formed by either treating [Zr(NMe2)4] with H2XDK (2 equiv) or [Zr(CH2Ph)2(XDK)] with H2XDK. Several of these complexes have been characterized by X-ray crystallography. [Zr(CH2Ph)2(XDK)] is electrophilic since the ipso carbon of one benzyl group is interacting with the Zr center as revealed by the acute Zr-C-C(ipso) angle in the X-ray structure of [Zr(CH2Ph)2(XDK)]. These studies have shown that 6-coordinate Zr carboxylate complexes are electrophilic. Complexes of this type are most stable when they possess high coordination numbers; this trend is exemplified by the stability of [Zr(XDK)2] and [Zr(eta)rt2-2,6-Me2PhNCCH2Phh(XDK)]. / by Dietrich P. Steinhubel. / Ph.D.