Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2006. / Includes bibliographical references. / Colloidal semiconductor nanocrystals (NCs) or quantum dots (QDs) can be synthesized to efficiently emit light from the ultraviolet, across the entire visible spectrum, and into the near infrared. This is now possible due to the continual development of new core and core-shell NC structures to meet specific color needs in areas as diverse as optoelectronic devices to biological imaging. Core-shell semiconductor NCs are unique light emitters. They are more stable overtime to photobleaching compared to organic dyes. Their emission is efficient and their spectral full width at half maximum remains highly narrow as their size is synthetically changed to provide desired peak wavelengths of emission to within plus or minus a couple of nanometers. They can be purified and manipulated in solution and their chemical interaction with the environment is the same for all sizes and can be modified using chemical techniques. These unique properties make semiconductor NCs ideal for use in light emitting devices (QD-LEDs). This work shows how electroluminescence can be extended into the near infrared region of the spectrum by employing infrared emitting NCs as well as into the blue region of the spectrum by designing and synthesizing NCs specifically for this application. / (cont.) Once efficient and color saturated electroluminescence at the visible spectrum's extremes had been realized it was a natural extension to begin exploring the potential of QD-LED devices to satisfy the technological requirements of flat panel displays and imaging applications. This led to the synthesis of a new green-emitting core-shell NC material to meet the specific color needs for flat panel display applications. At the same time we developed a new QD-LED device fabrication method to allow the patterning of the NC monolayer in our devices. Micro-contact printing the NC monolayer instead of using phase separation provided efficient and highly color saturated QD--LEDs in the red, green, and blue, and allowed us to pattern these monolayers towards the development of pixelated QD-LEDs such as needed for flat panel display applications. Along the way, the synthesis of colloidal NCs was studied to allow for more control in synthesizing higher quality materials in the future. The simple synthesis of PbSe NCs was used as a model system to begin to understand the mechanism of how the molecular precursors are reduced in solution to produce solid crystalline material in the presence of phosphorous containing molecules. / by Jonathan S. Steckel. / Ph.D.

Thesis: S.M., Massachusetts Institute of Technology, Department of Chemistry, 2014. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references. / The chemistries of fluorine, F₂, and xenon difluoride, XeF₂, with clean Si are basically the same, while their chemistries diverge dramatically past I ML F coverage. With a clean Si surface, F₂ and XeF₂ react utilizing an atom abstraction mechanism, where a surface dangling bond abstracts a F atom from the incident molecule, scattering the F atom or XeF fragment into the gas phase. Past 1 ML coverage, further exposure to F₂ results in no increase in F coverage, indicating that reaction of F₂ with the fluorinated Si surface does not occur. In contrast, further exposure to XeF₂ results in additional reaction, increasing the coverage sufficiently beyond 1 ML F to produce the volatile etch product, SiF 4. The experiments described in this thesis explain the observed difference in reactivity of F₂ and XeF₂ with a fluorinated Si surface as vibrational excitation of the Si lattice, induced by the initial collisions of XeF₂ with the surface that enable a barrierless reaction of the fluorine carried on the Xe with the Si-Si bonds of the surface or lattice. The possibility of enhancement of the reactivity of F₂ by vibrational excitation of the fluorinated Si lattice is studied using the van der Waals dimer Kr(F₂). Kr(F₂) is produced by coexpansion of F₂ and Kr in a molecular beam. It has the mass of bound KrF₂ with the chemical properties of F₂. Any increase in Si reactivity using Kr(F₂) compared to that of F₂ can be attributed to the mass of the molecule, since the dimer is basically a heavy F₂ molecule. After exposure of the fluorinated Si to Kr(F₂) molecules, the final F coverage is measured. With an estimate of Kr(F₂) exposure already calculated, the reaction probability is then found. The Kr(F₂) species is shown to have a reaction probability (Pads = 0.04) that is several orders of magnitude greater than that measured for F₂ (Pads ~10-4) and around 20 times less than that for XeF₂ (Pads = 0.9.) A simple classical model is presented to explain the reactivity difference of F₂ and XeF₂ with Si. Using simulation, the amount of energy transferred by a given mass to the Si surface, along with number of collisions and Si lattice excitation time, is determined. From the simulation, XeF₂ suffers 2-3 more collisions with Si than does F₂ . Since more collisions are occurring using XeF₂, the Si lattice is deformed for a longer period of time. Therefore, the Si-Si lattice bonds are stretched and compressed for a longer period of time, an advantageous situation for further reaction with the fluorine bound to the Xe. Excitation of the surface lattice may play a role in the reactivities of XeF₂ and F₂ with Si. This mechanism has not been fully investigated previously, and may account for the large difference in reactivity that is observed for these species. This study shows for the first time that the energy transferred to a surface as a result of a molecule's initial collision with it plays a critical role in the reaction probability in a molecule-surface interaction. Furthermore, this mechanism should apply to other semiconductor etchants, and must be considered in future kinetic models of such etchant systems. / by Michael Ryan Blair. / S.M.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Bacteriorhodopsin (bR) is comprised of 7 trans-membrane helices that enclose a retinylidene chromophore formed by a Schiff base (SB) between the retinal and Lys216. Due to bR's relative availability, it serves as a model for other members of the rhodopsin family, ion channels and GPCRs. Since its discovery in the 1970's, bR has been intensely studied by various methods including: X-ray crystallography, EM, FT-IR, molecular simulations, and NMR, etc. Despite numerous advances, details of its pump mechanism remain elusive due to experimental limitations in sensitivity and/or resolution. Here, dynamic nuclear polarization (DNP) is employed to boost the ¹H NMR signal. With an enhancement of 75, multidimensional spectra of low gyromagnetic nuclei were made possible. The cryogenic experimental temperature also traps the various bR photocycle intermediates, allowing them to be studied in situ. We are able to answer the one lingering question regarding bR's primary proton transfer pathway and conduct distance measurements near the active site. The pathway of bR's primary proton transfer has been the subject of scrutiny for many years. DNP MAS NMR bond length measurements of the SB proton reveal an elongated N-H bond in L, the transfer of ¹H in deprotonated MO, and a tight N-H bond in N intermediate. The ¹H chemical shift of ~3.6 ppm in M₀ indicates an alcohol hydrogen donor partner. This strongly supports the SB H+ being relayed from the SB to Asp85 via Thr89 as the pathway for bR's primary proton transfer. Distance measurements obtained here are the first set of long-range DNP MAS NMR measurements conducted on a uniformly labeled bR system. We find that the SB-D85 distance shrinks in the first half of the photocycle and is released after the primary proton transfer. The decrease in distance between the two indicates helix C and helix G are moving toward each other, which could be the reason why functional L is difficult to achieve. The subsequent release of helix G provides an additional gate to the release of the torsion energy in the chromophore. Meanwhile, the SB-D212 distance hardly changes. / by Qing Zhe Ni. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2005. / Vita. / Includes bibliographical references. / We have designed and synthesized novel molecules capable of selectively killing tumor cells that aberrantly express steroid hormone receptors. Many human breast cancers express high levels of the estrogen receptor (ER), and most prostate cancers express the androgen receptor (AR). We reasoned that the potential genotoxic effect of DNA adducts would be increased in target cells if these adducts were camouflaged by their association with receptor proteins. This association could shield the DNA adducts from repair proteins and thus increase the toxicity towards a tumor cell. Furthermore, these hormone receptors are transcription factors and an interaction between the protein and the DNA adduct could disrupt cellular signaling events, thus leading to further toxicity. We have synthesized bifunctional agents that contain an aniline mustard linked to ligands for tumor specific hormone receptors. To target ER(+) breast cancers, an aniline mustard was linked to estradiol at the 7[alpha] position (E2-7[alpha]), and to target AR(+) prostate cancer, the aniline mustard was linked to estradien-3-one at the 11[beta] position (11[beta]). Competitive binding experiments show that E2-7[alpha] and 11[beta] compete well with the natural ligands for the ER and AR, respectively. Clonal survival studies have shown that hormone receptor expressing malignant cell lines are more sensitive to our compounds than a corresponding receptor deficient line. [¹⁴C]-E2-7[alpha] and [¹⁴C]- 11[beta] have been formulated in Cremophor-EL and exhibit good bioavailability and stability when injected into mice intraperitoneally. E2-7[alpha] inhibits the growth of ER(+) HeLa cells and 11[beta] inhibits the growth of AR(+) LNCaP cells, both in xenograft mouse models. / (cont.) The compounds are well tolerated by mice after the therapeutic regimens. Stable DNA adducts have been isolated and detected by electrospray mass spectrometry and accelerator mass spectrometry has provided us with a means of quantifying the number of DNA adducts formed in vivo. E2-7[alpha] DNA adducts are repaired, in part, by nucleotide excision repair but the adducts persist longer in ER(+) cells than in ER(-) ones. Melphalan adducts, however, are repaired with equal rates in both cell lines. This result provides evidence in support of the repair shielding hypothesis and suggests that it may be a contributing mechanism to the increased toxicity observed for the ER(+) cell line in the clonal survival study. / by Shawn M. Hillier. / Ph.D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Vita. / Includes bibliographical references (p. 45-49). / Photoluminescent energy transfer in conjugated polymer-dye blend films was studied by means of steady-state fluorescence spectroscopy in order to identify efficient energy acceptors with red-shifted emissions relative to donor emission. A dialkoxy substituted poly(phenylene- ethylene) (PPE) and its pentiptycene derivative were used as the energy donor, and xanthene, cyanine, phenoxazine, and squaraine dyes were utilized as energy acceptors. Energy transfer efficiency was investigated by exciting the polymer and monitoring the quenching of polymer emission, along with the enhanced dye emission. Squaraine dyes exhibited up to 110 times greater emission than the intrinsic dye emission, even though they have little spectral overlap with the polymer donor. Moreover, even after normalization for the degree of spectral overlap, the sensitized emission intensity of squaraine was unusually high relative to those of the other dyes. This result suggested that an alternative Dexter mechanism substantially contributes to efficient energy transfer beyond the "through-space" dipolar mechanism of the Forster theory. This process is additionally assisted by the internal free volume within specific polymer hosts that prevent phase separation and self-aggregation of dyes, as well as preserving the dye emissive within the interstitial cavity. / (cont.) Lastly, other factors that influence energy transfer, such as optimum doping concentration and the specific affinity of dyes to polymers, were investigated. The results provide crucial insights into the identification or design of competent energy acceptors and donors. / by Inja Song. / S.M.

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

Thesis: Ph. D. in Organic Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Chapter 1: Photoredox Activation of SF₆ for Fluorination [chemical formula] We report the first practical use of SF₆ as a fluorinating reagent in organic synthesis. Photoredox catalysis enables the in situ conversion of SF6, an inert gas, into an active fluorinating species using visible light and photoredox catalysis. Under these conditions, deoxyfluorination of allylic alcohols is affected with high chemoselectivity and is tolerant of a wide range of functional groups. Application of the methodology in a continuous-flow setup achieves comparable yields to those obtained with a batch setup, while providing drastically increased material throughput of valuable allylic fluoride products. Further studies are necessary to reveal mechanistic details but preliminary experiments indicate that the mechanism of this deoxyfluorination may share features with that of the chlorination of alcohols with thionyl chloride proceeding through activation of the alcohol and subsequent substitution. Although several substrates exhibit a preference for retention of stereochemistry, similar to reactions with thionyl chloride, additional investigations revealed that this selectivity is also dependent on the structure of the substrate. Chapter 2. Automated On-demand Titration of Organometallic Reagents in Continuous Flow [chemical formula] The development of the first automated organometallic titration system using continuous flow is described. In this system, the desired organometallic reagent at variable flow rate is combined with a constant stream of colorimetric indicator and the end-point of the titration is monitored via inline UV/Vis spectroscopy and LabVIEW interface. Through an iterative process, precisions of 2±% can be achieved. In the described configuration, three titrants (N-pivaloyl-o-toluidine, 4-phenylbenzylidene benzylamine, salicylaldehyde phenylhydrazone) can be used for the titration of a wide array of organometallic species (RLi, RMgX, MHMDS) in molarities ranging from 0. 1M to 4.9M. In removing user intervention from the titration process, the developed system greatly reduces the safety hazards associated with handling pyrophoric organometallics and minimizes user-related error. Additionally, the UV/Vis spectrometer enables a level of precision to be achieved that is unattainable with the naked eye. The system also provides the possibility to be integrated with batch and continuous flow reactions, allowing organometallic reagents to be used in at highly accurate concentrations and without re-exposure to the user. Chapter 3. Progress Toward an Enantioselective Synthesis of Bedaquiline [chemical formula] Herein we describe progress toward an enantioselective synthesis of bedaquiline, a novel pharmaceutical used for the treatment of multi-drug resistant tuberculosis. In our efforts, several provisional routes have been investigated and assessed for feasibility. Although decarboxylative arylation, hydrogen atom-transfer, and sulfur-ylide epoxidation proved ineffective for the in these routes, our latest efforts are focused on a much more precedented asymmetric epoxidation which will be the subject of future work. During these investigations, the synthesis of the final epoxide intermediate of our route has been achieved on multi-gram scale, albeit in a racemic fashion. Our proposed route uses readily available, inexpensive starting materials, and would afford bedaquiline in six steps. / by T. Andrew McTeague. / Ph. D. in Organic Chemistry

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1994. / Includes bibliographical references (leaf 218). / by George William Adamson. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010. / Vita. Cataloged from PDF version of thesis. / Includes bibliographical references (p. 221-228). / Single-shot femtosecond spectroscopy has been developed and employed for the study of phase transitions of solid-state materials. Using two crossed echelons, a two dimensional spatial delay gradient was generated across a single probe pulse profile. This novel scheme enables us to monitor irreversible change in solids by acquiring many time-resolved data points with a single laser pulse. With the integration with a non-collinear optical parametric amplifier (NOPA) and a conventional pump-probe instrument, ultrafast dynamics of coherent lattice vibrations and photo-induced phase transitions were examined in two different systems. Ultrafast dynamics such as coherent lattice vibrations and bond softening were investigated for Bi thin films and bulk single crystals. Depending on the thickness, transient reflectivity was changed significantly. The variations are ascribed to different electronic structures possibly originating from quantum confinement. Bond softening exhibits a strong thickness dependence due to hot carrier dynamics as well as to the different electronic structures. At high pump fluences, no phonon oscillations were observed suggesting a phase transition to liquid or to a higher symmetry crystalline phase (reverse Peierls distortion). Together with thermal modeling, double pump measurements reveal nonthermal melting occurring in bulk and thin Bi films. A higher threshold fluence for nonthermal melting is observed in bulk bismuth as compared to thin films, suggesting ultrafast carrier dynamics such as ballistic transport. In addition to nonthermal effects, thermal effects such as inelastic electron-phonon scattering and nonradiative recombination play a crucial role in melting and cooling at later times after nonthermal melting takes place. A quasi one-dimensional platinum iodide complex showed strong oscillations in reflectivity which are attributed to oscillatory motions of wave packets on a selftrapped exciton (STE) potential surface., As optical excitation increased, electron transfer from Pt 2+ to an adjacent Pt4+ occurred over a wider range of lattice sites and weakened the oscillations. Above a certain pump fluence, oscillations disappeared completely indicating that the mixed valence, charge density wave state changed to monovalent, Mott-Hubbard phase. The reverse phase transition, i.e., from the MottHubbard phase to the charge density wave state began within 3 ps of the optical pump. / by Taeho Shin. / Ph.D.

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.