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Thesis advisor: Amir Hoveyda / Chapter 1: E- and Z-, Di- and Trisubstituted Alkenyl Nitriles through Catalytic Cross MetathesisWe have described the development of several catalytic cross-metathesis strategies, which can deliver a considerable range of Z- or E-disubstituted alkenyl nitriles and their corresponding trisubstituted variants. Through careful examination of the steric and electronic attributes of the starting materials, a Mo-based monoaryloxide pyrrolide or chloride complex may be the optimal choice depending on the reaction type. In the event, equimolar amounts of the two substrates are necessary to maximize reaction efficiency; a pyridine ligand is more desirable than a phosphine ligand, as a stabilizing ligand for a Mo-based complex, for improving reaction stereoselectivity. We also highlighted the utility of this approach with the synthesis of several biologically active compounds, such as LR5182 (Cocaine abuse treatment), alliarinoside (anti-feedant), perhydrohistrionicotoxin (natural product), CC-5079 (anti-cancer) and indatraline (anti-depressant). Chapter 2: Traceless Protection for More Broadly Applicable Olefin Metathesis We have devised an operationally simple in-situ protection/deprotection strategy that significantly expands the scope of kinetically controlled catalytic olefin metathesis. Pretreatment of an olefin containing a protic group with commercially available HB(pin) or HB(trip)2 is sufficient for generating the desired product efficiently through the catalytic cross-metathesis reaction. A wide range of stereochemically defined Z- and E-alkenyl halides and boronates as well as Z-trifluoromethyl-substituted alkenes with a hydroxy or carboxylic acid group were prepared. We also discovered that a small amount of HB(pin) may be used for the removal of residual water and impurities, significantly enhancing the efficiency of a multigram-scale olefin metathesis transformation. Chapter 3: E- and Z-Macrocyclic Trisubstituted Alkenes for Natural Product Synthesis and Skeletal Editing We have introduced a reliable catalytic strategy for the synthesis of a variety of macrocyclic trisubstituted olefins in either stereoisomeric form. This was achieved by overcoming the unexpected difficulties through careful mechanistic studies, including addressing complications arising from pre-metathesis alkene isomerization. Macrocyclic ring-closing metathesis can be performed with a commercially available Mo-based complex and an easily accessible linear diene precursor. Accordingly, we can synthesize a skeletally diverse array of otherwise difficult-to-access macrocyclic alkenes, a critical set of compounds in drug discovery, in either isomeric form. The utility of the method is highlighted in two instances. The first is the near complete reversal of substrate-controlled selectivity in the generation of the macrolactam intermediate, in the total synthesis of the anti-fungal agent Fluvirucin B1. The second is an exceptionally stereoselective late-stage formation of a 24-membered macrocyclic E-trisubstituted alkene, enabling the completion of the total synthesis of a cytotoxic natural product dolabelide C, which is seven times more efficient than that reported previously. Chapter 4: Stereodefined Alkenes with a Fluoro-Chloro Terminus as a Uniquely Enabling Compound Class We have offered a practical solution for the synthesis of trisubstituted alkenyl fluorides by unveiling a widely applicable strategy for stereodivergent synthesis of olefins bearing a fluoro and chloro terminus. The core transformation is unprecedented: cross-metathesis between two trisubstituted olefins, one of which is a commercially available but scarcely utilized trihalo alkene. Alkenes bearing a fluoro,chloro-terminus are versatile substrates for the generation of otherwise difficult-to-access trisubstituted alkenyl fluorides, through stereospecific catalytic cross-coupling reactions. We also highlighted the utility of the method throguh synthesis of, among others, a fluoro-nematic liquid crystal component, peptide analogs bearing an E- or a Z-amide bond mimic, and all four stereoisomers of difluoro-rumenic ester (anti-cancer). / Thesis (PhD) — Boston College, 2021. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.

Langmuir-monolayer formation at the air/water interface (A/W) can be achieved by spreading amphiphilic molecules on a liquid subphase and compressing them into an ordered arrangement. The use of the Langmuir-Blodgett technique (LB) to prepare ultra thin films on solid surfaces from monolayers at A/W has considerable utility for studying surface interactions. In particular, the phase behavior of polyhedral oligomeric silsesquioxanes (POSS) was examined using a combination of LB and Brewster angle microscopy (BAM).Polymer fillers have been shown to reduce the cost and often improve the properties of high performance polymer composites. The utility of POSS as a potential nanofiller in blends with polymers such as poly(dimethylsiloxane) (PDMS) and poly(vinylacetate) (PVAc) was explored using surface pressure-area per monomer isotherms (P-A) and BAM. Substantial morphological differences are seen between polymer blends with heptasubstituted trisilanol-POSS and fully condensed octasubstituted-POSS due to differences in subphase affinity.Several poly(1-alkene-alt-maleic anhydride) (PXcMA) polymers were studied at both the gas/liquid interface as Langmuir films and at the gas/solid interface as Langmuir-Blodgett thin films on silicon substrates. A 0.01 M HCl solution (pH~2) was used during film deposition to ensure the carboxylic acids were fully protonated. The PXcMA polymers included X=1-hexene, 1-octene, 1-decene, and 1-octadecene (represented as PHcMA, POcMA, PDcMA, and PODcMA respectively). The P-A isotherms of these polymers were consistent with those obtained previously.1Tensiometry was used to determine the critical micelle concentrations (c.m.c.) of variable molar mass poly(dimethylsiloxane-b-(3-cyanopropyl)methylsiloxane-b-dimethylsiloxane) (PDMS-PCPMS-PDMS) triblock copolymers and a poly(dimethylsiloxane-b-2-ethyl-2-oxazoline) diblock copolymer. Dynamic light scattering (DLS) corroborated interfacial tension results. The polymers exhibited well-defined temperature-independent c.m.c.'s. These measurements ensured that the synthesis of cobalt nanoparticles for biocompatible magnetic fluids occurred above the c.m.c. / Master of Science

Site-selective protein modification has become an important tool to study protein functions in chemical biology. In the preliminary work, allyl sulfides were found to be reactive substrates in aqueous cross-metathesis (CM) enabling the first examples of protein modification via this approach. In order to access the enhanced CM reactivity of allyl sulfide on proteins, facile chemical methods to install S-allyl cysteine on protein surface were developed. In particular, a cysteine-specific allylating reagent – allyl selenocyanate was used on protein substrate for the first time. The substrate scope of allyl sulfide-tagged proteins and factors that affect the outcome of CM was also investigated. A range of metathesis substrates containing different olefin tether of various lengths were screened; allyl ethers were found to be most suitable as CM partners. By reducing the steric hindrance around the allyl sulfide on protein surface through a chemical spacer, the rate and conversion of metathesis reaction on proteins was greatly enhanced. Moreover, allyl selenides were found to be more reactive than allyl sulfides in CM and enabled reactions with substrates that were previously impossible for the corresponding sulfur-analogue. Through this work, substrate selection guidelines for successful metathesis reaction on proteins were established. Rapid Se-relayed CM was further investigated through biomimetic chemical access to Se-allyl selenocysteine (Seac) via dehydroalanine. On-protein reaction kinetics revealed rate constants of Seac-mediated CM to be comparable or superior to off-protein rates of many current bioconjugations. This CM strategy was applied to histone proteins to install a mimic of acetylated lysine (K9Ac, an epigenetic marker). The resulting synthetic H3 was successfully recognized by antibody that binds natural H3-K9Ac. A Cope-type selenoxide elimination subsequently allowed the removal of such modification to regenerate dehydroalanine. Finally, preliminary research efforts towards metabolic incorporation of allyl sulfide-containing amino acid into proteins, and CM on cell surfaces were discussed.

This thesis describes the catalytic asymmetric epoxidation of olefins mediated by chiral iminum salts. The first chapter introduces some of the most novel and effective catalytic asymmetric methods for preparing chiral oxiranes. The second chapter is divided into three sections. The first section of chapter two is dedicated to our efforts to develop new aqueous oxidative conditions using both hydrogen peroxide and sodium hypochlorite as efficient, green oxidants that remove the temperature boundaries observed with the use of Oxone® as the stoichiometric oxidant. A wider range of available temperatures was examined allowing optimization of both oxidative systems. Ethereal hydrogen peroxide was observed to mediate asymmetric epoxidation within an acetonitrile monophasic co-solvent system giving enantioselectivities of up to 56%. When sodium hypochlorite was used in a biphasic solvent system in conjunction with dichloromethane; it was observed to mediate oxidation of the substrate alkenes in up to 71% ee. The second and third sections of chapter two are dedicated to our efforts to synthesize chiral iminium salts as catalysts for asymmetric epoxidation based on a biphenyl azepinium salt catalyst structure. From previous work within the Page group, the asymmetric synthesis and subsequent defined stereochemistry of a chiral carbon atom α to the iminium nitrogen atom was shown to have significant effect on the enantiocontrol of epoxidation using the iminium salt catalyst. Work was completed on biphenyl azepinium salt catalysts, inserting an alkyl or aryl Grignard reagent into the iminium bond using a pre-defined dioxane unit as a chiral auxiliary. Oxidation of the subsequent azepine gave a single diastereoisomerically pure azepinium salt. The methyl analogue of this sub-family of azepinium catalysts has been shown to give up to 81% ee for epoxidation of 1-phenylcyclohexene, furthermore, the binaphthalene azepinium salt with an additional methyl group was also synthesized and was shown to give up to 93% for epoxidation of 1-phenylcyclohexene. Continuation of the substitution α to the nitrogen atom gave rise to an interesting tetracyclic (biphenyl) azepinum salt catalyst. Construction of an asymmetric oxazolidine ring unit encapsulating the azepinium nitrogen and one of the methylene carbon atoms was achieved. In doing so two chiral centres α to the nitrogen atom were generated. The azepinium chiral carbon atom was populated by an addition methyl group with variation in the substitution on the oxazolidine chiral carbon atom. The benzyl analogue of this sub-family of tetracyclic azepinium catalysts has shown to give up to 79% ee for epoxidation 1-phenylcyclohexene. The third chapter is the experimental section and is dedicated to the methods of synthesis and characterization of the compounds mentioned in the previous chapter. X-ray reports regarding the crystallographic analysis of the structures presented in chapter two are provided in appendix A. Appendix B contains the analytical spectra for the determination of enantiomeric excess of the epoxides.

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In der vorliegenden Arbeit wurden die Reaktionen elektrophiler und nucleophiler Schwefeldonoren mit cyclischen Alkenen und Alkinen untersucht, wobei ungewöhnliche und neuartige Schwefelchemie aufgedeckt wurde. Als elektrophile Schwefeldonoren wurden ein Sulten und ein Thiophenendoperoxid eingesetzt. Als Schwefelakzeptoren standen die cyclische Alkene, Enolether und Alkine zur Verfügung. Das Sulten überträgt unter Lewissäure-Katalyse das Schwefelatom auf verschiedene gespannte cyclische Olefine, wobei diastereoselektiv die entsprechenden Episulfide sowie ein Oxetan und/oder ein Aldehyd gebildet werden. Es kamen dabei verschiedene Lewissäuren wie z. B. Metallhalogenide (BF3•Et2O, ZnCl2 und SnCl4), Metallkomplexe [Mn(salen*)PF6] und Porphyrine zum Einsatz. Als beste Lewissäure erweist sich das Zinnporphyrin Sn(tpp)(ClO4)2, mit der die Olefine bei Raumtemperatur in 30 Prozent bis > 95 Prozent Ausbeute episulfidiert werden. Beim Schwefeltransfer vom Sulten auf 1-Methoxycycloocten entsteht das Produkt einer Insertion des Enolethers in die O-S-Bindung des Sultens in 69 Prozent Ausbeute. Wird das Sulten mit Cyclooctin und einem Äquivalent Trifluoressigsäure oder einer anderen starken Säure umgesetzt, wird ein Thiireniumion erhalten, das in stark saurer Lösung bis zu 24 h persistent ist und unter neutralen Bedingungen zu einem Dien umlagert. Die Bildung des Thiireniumions ist unter Einwirkung von Base reversibel. Mit Dithiacyclononin wird ein analoges Thiireniumion postuliert, das jedoch nicht direkt beobachtet werden kann. Persistentes Endprodukt dieser Reaktion ist ein Thioacetal. Das Thiophenendoperoxid wurde durch Tieftemperatur-Photooxygenierung des entsprechenden Thiophens in situ generiert. Bei der Thermolyse in Gegenwart von Cyclooctin bildet sich diastereoselektiv in 70 Prozent Ausbeute ein Episulfid. Bei der Reaktion des nucleophilen Schwefeldonors Thiotosylat mit Ninhydrin oder Indantrion in Gegenwart von trans-Cycloocten entsteht ein Cycloaddukt in bis zu 63 Prozent Ausbeute, während das Episulfid des trans-Cyclooctens nur in maximal 18 Prozent Ausbeute erhalten wird. Mit dem Schwefelnucleophil Diethylphosphorothioat und Indantrion wird neben dem Cycloaddukt das Diethylphosphat generiert. Wird Alloxanhydrat als Substrat verwendet, entsteht ein analoges Cycloaddukt in 33 Prozent Ausbeute. Indantrion geht mit 1 Methoxycycloocten eine Carbonyl-En-Reaktion ein, bei der ausschließlich ein Regioisomer in 51 Prozent Ausbeute entsteht. / In this dissertation, the reactions of electrophilic and nucleophilic sulfur donors with cyclic alkenes and alkynes were investigated, whereby unusual and novel sulfur chemistry was revealed. A sultene and a thiophene endoperoxide have been employed as electrophilic sulfur donors. Cyclic alkenes, enol ethers and alkynes have been made available through standard synthesis procedures. The sultene transfers its sulfur atom to various strained cyclic alkenes with Lewis-acid catalysis, through which the corresponding episulfides are formed diastereoselectively. An oxetane and/or an aldehyde are the desulfurized products. Various Lewis acids, e.g. metal halogenides (BF3•Et2O, ZnCl2 und SnCl4), metal complexes [Mn(salen*)PF6] and porphyrins, have been employed. The tin porphyrin Sn(tpp)(ClO4)2 proves to be the best Lewis acid, with which the olefins are episulfurized at room temperature (ca. 20 °C) in 30 per cent to > 95 per cent yields. The sulfur transfer from the sultene to 1-methoxycyclooctene gives an insertion product of the enol ether into the S-O-bond of the sultene in 69 per cent yield. When a mixture of the sultene and cyclooctyne is treated with one equivalent of trifluoroacetic acid or other strong acids, a thiirenium ion is generated. In strongly acidic medium, it persists for up to 24 h, whereas under neutral conditions it rearranges to a diene. The formation of the thiirenium ion is reversible under the action of a base (K2CO3). With dithiacyclononyne, an analogous thiirenium ion is postulated, but which cannot be observed directly. A spirocyclic compound is the final end product of this reaction sequence. The thiophene endoperoxide was generated in situ by low-temperature photooxygenation of the corresponding thiophene. On thermolysis in the presence of cyclooctyne, an episulfide is formed in 70 per cent yield. In the reaction of the nucleophilic sulfur donor thiotosylate with ninhydrin or indantrione in the presence of trans-cyclooctene, a cycloadduct is formed in up to 63 per cent yield, whereas the episulfide of trans-cyclooctene is formed maximally in only 18 per cent yield. With the sulfur nucleophile diethyl phosphorothioate and indantrione, cycloadduct and diethyl phosphate are generated. When alloxane hydrate is employed as substrate, the analogous cycloadduct is formed in 33 per cent yield. Indantrione undergoes a carbonyl ene reaction with 1-methoxycyclooctene, which produces exclusively one regioisomer in 51 per cent yield.

Free radicals play a critical role in the formation of tropospheric air pollution, but current condensed chemical mechanisms used in gridded photochemical models under-predict total radical concentrations. This dissertation evaluates three hypotheses regarding radical sources and sinks using environmental chamber data and ambient data from southeast Texas. The first hypothesis, that aromatics chemistry is under-represented as a radical source in condensed chemical mechanisms, was evaluated mainly by using environmental chamber simulations and in part by using ambient simulations. Results indicate that improved characterization of aromatics chemistry in condensed chemical mechanisms will lead to more rapid and extensive free radical formation. The second hypothesis, that alkene reactions are under-represented as a radical source in condensed chemical mechanisms, was also evaluated using chamber data and TexAQS-2000 data. Results indicate that the methods used in mechanism condensation lead to lower estimates of free radical production than detailed, compound specific models. The third hypothesis, chlorine emissions and chemistry as a radical source, was also evaluated in a series of sensitivity analyses with various levels of molecular chlorine emissions. Results imply that incorporating chlorine chemistry in condensed chemical mechanisms is expected to lead to more accurate modeling of OH, HO₂ and O₃, particularly for the southeast Texas region where relatively large chlorine emissions occur from various anthropogenic sources of molecular chlorine. The relative magnitudes of these radical sources (aromatics, alkenes, and molecular chlorine) in southeast Texas were also compared using box modeling with TexAQS-2000 data. Results indicate that the relative importance of these three types of radical sources depends on the strengths of their corresponding emissions. / text

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