While investigating strategies to prepare precursors to highly strained buckybowls, we focused our attention on the Lewis acid aldol cyclization of 1-acenaphthenone derivatives which has been shown to produce a cyclic tetramer as a byproduct. Surprisingly, despite the interesting structural and electronic properties that have recently been observed as a result of the incorporation of eight-membered rings into polycyclic aromatic hydrocarbons, this cyclic tetramer has largely been ignored. As a result of this, we set our sights on the isolation and characterization of this cyclic tetramer. The initial approach employed subjecting 1-acenaphthenone to the most common conditions used in trimerization—TiCl4 in boiling o-dichlorobenzene. Surprisingly, this resulted in exclusive formation of the cyclic tetramer, which we have named tridecacyclene. The results of these studies were promising, establishing structural characterization and supramolecular assemblies with C60 in the solid-state. The optoelectronic properties revealed a significantly lower reduction potential (~0.4 eV) than the trimeric species of 1-acenaphthenone. This is attributed to the central eight-membered ring of tridecacyclene. Reduction proceeded through two single-electron processes. Further examining the electrochemical properties, we were able to gain new insight into the relation of structure and aromaticity. Reduction of tridecacyclene with potassium metal allowed us to characterize the radical anion and dianion through NMR and UV-Vis spectroscopy. Solid-state analysis of the dipotassium adduct revealed that despite the propensity of the reduced form of cyclooctatetraene derivatives to flatten as the molecule adopts a Hückel aromatic core, tridecacyclene maintains its tub shape. Significant bond equalization was observed in the center eight-membered ring—a strong indication of a delocalized π-system. This was supported by harmonic oscillator model of aromaticity calculations of the central ring with the value increasing from 0.09 to 0.48 where a value of 1 indicates a fully aromatic ring. Tridecacyclene represents the precursor to a fragment of the fullerene C240. A broad variety of reactions to facilitate the necessary strain inducing C–C bonds to formthe fragment have been attempted. To date, we have not been able to synthesize the fragment. However, the parent molecule tridecacyclene shows great promise in the development of non-aqueous redox flow batteries and is currently being explored for this purpose in our laboratory.

abstract: Aromatic compounds have traditionally been generated via petroleum feedstocks and have wide ranging applications in a variety of fields such as cosmetics, food, plastics, and pharmaceuticals. Substantial improvements have been made to sustainably produce many aromatic chemicals from renewable sources utilizing microbes as bio-factories. By assembling and optimizing native and non-native pathways to produce natural and non-natural bioproducts, the diversity of biochemical aromatics which can be produced is constantly being improved upon. One such compound, 2-Phenylethanol (2PE), is a key molecule used in the fragrance and food industries, as well as a potential biofuel. Here, a novel, non-natural pathway was engineered in Escherichia coli and subsequently evaluated. Following strain and bioprocess optimization, accumulation of inhibitory acetate byproduct was reduced and 2PE titers approached 2 g/L – a ~2-fold increase over previously implemented pathways in E. coli. Furthermore, a recently developed mechanism to allow E. coli to consume xylose and glucose, two ubiquitous and industrially relevant microbial feedstocks, simultaneously was implemented and systematically evaluated for its effects on L-phenylalanine (Phe; a precursor to many microbially-derived aromatics such as 2PE) production. Ultimately, by incorporating this mutation into a Phe overproducing strain of E. coli, improvements in overall Phe titers, yields and sugar consumption in glucose-xylose mixed feeds could be obtained. While upstream efforts to improve precursor availability are necessary to ultimately reach economically-viable production, the effect of end-product toxicity on production metrics for many aromatics is severe. By utilizing a transcriptional profiling technique (i.e., RNA sequencing), key insights into the mechanisms behind styrene-induced toxicity in E. coli and the cellular response systems that are activated to maintain cell viability were obtained. By investigating variances in the transcriptional response between styrene-producing cells and cells where styrene was added exogenously, better understanding on how mechanisms such as the phage shock, heat-shock and membrane-altering responses react in different scenarios. Ultimately, these efforts to diversify the collection of microbially-produced aromatics, improve intracellular precursor pools and further the understanding of cellular response to toxic aromatic compounds, give insight into methods for improved future metabolic engineering endeavors. / Dissertation/Thesis / Doctoral Dissertation Chemical Engineering 2019

Due to its low cost and large availability lignocellulosic biomass is being studied worldwide as a feedstock for renewable liquid biofuels. Currently there are several routes being studied to convert solid biomass to a liquid fuel, which involve multiple steps at long residence times thus greatly increasing the cost of biomass processing. Catalytic fast pyrolysis (CFP) is a new promising technology to convert directly solid biomass to gasoline-range aromatics that fit into the current infrastructure. CFP involves the rapid heating of biomass (~500˚C sec-1) in an inert atmosphere to intermediate temperatures (400 to 600 ˚C) in the presence of zeolite catalysts. During CFP, biomass is converted in a single step to produce gasoline-range aromatics which are compatible with the gasoline of the current market. CFP has many advantages over other conversion processes including short residence times (2-10 s) and inexpensive catalysts. The major impediment to the further development of CFP is the lack of fundamental understanding of the underlying chemistry of the process. The first goal of this thesis is to study the underlying chemistry of the CFP process using model compounds in a small pyroprobe micro reactor. For this part of the study the homogeneous thermal decomposition routes of glucose were identified along with the key intermediates. Through isotopic labeling studies the heterogeneous C-C bond forming reactions were determined. Lastly, the relative rates of the homogeneous and heterogeneous reactions were estimated. Since CFP in the small pyroprobe reactor is not scalable the second part of the study focused on designing and building a bench scale fluidized bed reactor to demonstrate CFP on a larger scale. This fluidized bed reactor was used to optimize the CFP of pine wood with ZSM-5 catalyst. The effect of reaction conditions such as temperature and biomass space velocity on the aromatic yield and selectivity was determined. The long term stability of the catalyst was also studied.

Diminishing petroleum resources combined with concerns about global warming and dependence on fossil fuels are leading our society to search for renewable sources of energy. In this respect, lignocellulosic biomass has a tremendous potential as a renewable energy source, once we develop the economical processes converting biomass into useful fuels and chemicals. Catalytic fast pyrolysis (CFP) is a promising technology for production of gasoline range aromatics, including benzene, toluene, and xylenes (BTX), directly from raw solid biomass. In this single step process, solid biomass is fed into a catalytic reactor in which the biomass first thermally decomposes to form pyrolysis vapors. These pyrolysis vapors then enter the zeolite catalysts and are converted into the desired aromatics and olefins along with CO, CO2, H2O, and coke. The major challenge with the CFP process is controlling the complicated homogeneous and heterogeneous reaction chemistry. The focus of this thesis is to study the reaction chemistry, catalyst design, and process development for CFP to advance the CFP technology. To gain a fundamental understanding of the underlying chemistry of the process, we studied the reaction chemistry for CFP of glucose (i.e. biomass model compound). Glucose is thermally decomposed in a few seconds and produce dehydrated products, including anhydrosugars and furans. The dehydrated products then enter into the zeolite catalyst pore where they are converted into aromatics, CO, CO2, H2O and coke. The zeolite catalyzed step is far slower than the initial decomposition step (>2 min). Isotopic labeling studies revealed that the aromatics are formed from random hydrocarbon fragments composed of the dehydrated products. The major competing reaction to aromatic production is the formation of coke. The main coking reaction is the polymerization of the furan intermediates on the catalyst surface. CFP is a shape selective reaction where the product selectivity is related to the zeolite pore size and structure. The shape selectivity of the zeolite catalysts in the CFP of glucose was systematically studied with different zeolites. The aromatic yield is a function of the pore size and internal pore space of the zeolite catalyst. Medium pore zeolites with pore sizes in the range of 5.2 to 5.9 Å and moderate pore intersection size, such as ZSM-5 and ZSM-11 produced the highest aromatic yield and least amount of coke. The kinetic diameter estimation of the aromatic products and the reactants revealed that the majority of these molecules can fit inside the zeolite pores of the medium pore zeolites. The ZSM-5 catalyst, the best catalyst for aromatic production, was modified further to improve its catalytic performance. These modifications include: (1) adjusting the concentration of acid sites inside the zeolites catalyst; (2) incorporation of mesoporosity into the ZSM-5 framework to enhance its diffusion characteristics, and (3) addition of Ga to the ZSM-5. Mesoporous ZSM-5 showed high selectivity for heavier alkylated monoaromatics. Ga promoted ZSM-5 increased the aromatic yield over 40%. A process development unit was designed and built for continuous operation of the CFP process in a pilot scale. The effects of process variables such as temperature, biomass weight hourly space velocity, catalyst to biomass ratio, catalyst static bed height, and fluidization gas velocity were studied to optimize the reactor performance. It was demonstrated that CFP could produce liter quantities of aromatic products directly from solid biomass.

A exaustão de um veículo de motor a diesel é uma importante fonte de poluentes atmosféricos, pois forma uma matriz complexa composta de poluentes regulados e não regulados pelos órgãos governamentais. Dentre os poluentes regulados podemos citar óxidos de nitrogênio (NOx) e material particulado. Os poluentes não regulados são pouco estudados até hoje e dentre estes encontra-se a classe dos hidrocarbonetos policíclicos aromáticos e seus derivados nitrados (nitro-HPA). Estes são encontrados na exaustão do diesel na forma gasosa ou agregados ao material particulado. Hoje, o interesse em estudos destes compostos vem aumentando, devido às suas atividades carcinogênicas e mutagênicas às quais estão sujeitas as populações dos centros urbanos. O impacto causado pelos nitro-HPA emitidos por motores a ciclo diesel ao ambiente não está ainda completamente estabelecido. Este estudo consiste na modelagem e simulação do processo de combustão de hidrocarbonetos na faixa de C1 a C4 com o objetivo de descrever a formação de compostos aromáticos, principalmente HPA, e óxidos de nitrogênio a partir de modelos cinéticos de combustão propostos na literatura como referência e fazendo uso do software de simulação Kintecus. Este projeto tem como objetivo em longo prazo propor um modelo cinético para combustão do óleo Diesel. Foi iniciada a construção de um modelo cinético de combustão a partir de modelos de hidrocarbonetos simples de C1 a C4, com formação de aromáticos, HPA e óxidos de nitrogênio. Os modelos originais foram avaliados e modificados a fim de estudar como parâmetros do modelo afetam a concentração das espécies de interesse. Foi observado a tendência de formação de benzeno e fulveno em baixas temperaturas e a tendência de formação de antraceno, pireno, fenantreno a temperaturas mais altas. Foi avaliado que a conversão NO-NO2 ocorre em maiores proporções em reações iniciadas a baixas temperaturas, 600 K. Os resultados indicam que propano é o maior responsável por esta conversão. O modelo final obtido resultou da união dos modelos de combustão Hori e Marinov mais inclusão do GRI-Mech 3.0 e reações adicionais de NOx retiradas da base de dados NIST / The diesel engine exhaust is an important source of air pollutants, which comprises a complex matrix of regulated and unregulated pollutants. The nitrogen oxides (NOx) and the particulate material are examples of regulated pollutants found in the engine exhaust. The unregulated pollutants are poorly studied until today, being the polycyclic aromatic hydrocarbons and its nitrated derivatives (nitro-PAH) a class of unregulated pollutant observed in diesel exhaust. The nitro-PAHs are observed in gas phase or aggregated to the particulate material. At the present, the interest in those compounds raised due to their carcinogenic and mutagenic properties, which the population of urban centers are subject. The environmental impact caused by nitro-PAH is not fully established. This study consists in the modeling and simulation of the hydrocarbons combustion process comprising the C1 to C4 hydrocarbons using kinetic models proposed in the literature as reference models and the Kintecus software. The purpose of the present study is to describe the formation of aromatic compounds, mainly PAH, and nitrogen oxides. The long term goal is to build a combustion model to Diesel oil. The kinetic model was constructed based on known combustion models of C1 to C4 hydrocarbons, which includes the formation of aromatics, PAH and nitrogen oxides. The original models were evaluated and modified to analyze how the model parameters affects the species concentration. There is a trend to the formation of benzene and fulvene at low temperatures, and a tendency to formation of antracene, pyrene and antracene at high temperatures. The NO-NO2 conversion was evaluated and the high rates of conversion was obtained in simulations started at temperature. The results indicates that propene is the major hydrocarbon that promotes the NO-NO2 conversion. The final model proposed is based in the combination of Marinov and Hori models with the inclusion of GRI-Mech 3.0 plus additional reactions extracted from NIST database

A exaustão de um veículo de motor a diesel é uma importante fonte de poluentes atmosféricos, pois forma uma matriz complexa composta de poluentes regulados e não regulados pelos órgãos governamentais. Dentre os poluentes regulados podemos citar óxidos de nitrogênio (NOx) e material particulado. Os poluentes não regulados são pouco estudados até hoje e dentre estes encontra-se a classe dos hidrocarbonetos policíclicos aromáticos e seus derivados nitrados (nitro-HPA). Estes são encontrados na exaustão do diesel na forma gasosa ou agregados ao material particulado. Hoje, o interesse em estudos destes compostos vem aumentando, devido às suas atividades carcinogênicas e mutagênicas às quais estão sujeitas as populações dos centros urbanos. O impacto causado pelos nitro-HPA emitidos por motores a ciclo diesel ao ambiente não está ainda completamente estabelecido. Este estudo consiste na modelagem e simulação do processo de combustão de hidrocarbonetos na faixa de C1 a C4 com o objetivo de descrever a formação de compostos aromáticos, principalmente HPA, e óxidos de nitrogênio a partir de modelos cinéticos de combustão propostos na literatura como referência e fazendo uso do software de simulação Kintecus. Este projeto tem como objetivo em longo prazo propor um modelo cinético para combustão do óleo Diesel. Foi iniciada a construção de um modelo cinético de combustão a partir de modelos de hidrocarbonetos simples de C1 a C4, com formação de aromáticos, HPA e óxidos de nitrogênio. Os modelos originais foram avaliados e modificados a fim de estudar como parâmetros do modelo afetam a concentração das espécies de interesse. Foi observado a tendência de formação de benzeno e fulveno em baixas temperaturas e a tendência de formação de antraceno, pireno, fenantreno a temperaturas mais altas. Foi avaliado que a conversão NO-NO2 ocorre em maiores proporções em reações iniciadas a baixas temperaturas, 600 K. Os resultados indicam que propano é o maior responsável por esta conversão. O modelo final obtido resultou da união dos modelos de combustão Hori e Marinov mais inclusão do GRI-Mech 3.0 e reações adicionais de NOx retiradas da base de dados NIST / The diesel engine exhaust is an important source of air pollutants, which comprises a complex matrix of regulated and unregulated pollutants. The nitrogen oxides (NOx) and the particulate material are examples of regulated pollutants found in the engine exhaust. The unregulated pollutants are poorly studied until today, being the polycyclic aromatic hydrocarbons and its nitrated derivatives (nitro-PAH) a class of unregulated pollutant observed in diesel exhaust. The nitro-PAHs are observed in gas phase or aggregated to the particulate material. At the present, the interest in those compounds raised due to their carcinogenic and mutagenic properties, which the population of urban centers are subject. The environmental impact caused by nitro-PAH is not fully established. This study consists in the modeling and simulation of the hydrocarbons combustion process comprising the C1 to C4 hydrocarbons using kinetic models proposed in the literature as reference models and the Kintecus software. The purpose of the present study is to describe the formation of aromatic compounds, mainly PAH, and nitrogen oxides. The long term goal is to build a combustion model to Diesel oil. The kinetic model was constructed based on known combustion models of C1 to C4 hydrocarbons, which includes the formation of aromatics, PAH and nitrogen oxides. The original models were evaluated and modified to analyze how the model parameters affects the species concentration. There is a trend to the formation of benzene and fulvene at low temperatures, and a tendency to formation of antracene, pyrene and antracene at high temperatures. The NO-NO2 conversion was evaluated and the high rates of conversion was obtained in simulations started at temperature. The results indicates that propene is the major hydrocarbon that promotes the NO-NO2 conversion. The final model proposed is based in the combination of Marinov and Hori models with the inclusion of GRI-Mech 3.0 plus additional reactions extracted from NIST database

This thesis focuses on the structural and functional characterization of two integral membrane proteins; CfrA, an outer membrane TonB-dependent transporter (TBDT) from Campylobacter jejuni, and ELIC, a pentameric ligand-gated ion channel (pLGIC) from Erwinia Chrysanthemi. The spectroscopic characterization of CfrA revealed a fold consistent with the structural and biophysical properties observed for other TBDT. Both a homology model of CfrA and sequence alignments of CfrA with other ferric-enterobactin transporters suggested a unique mode of ligand binding, thus raising the possibility that C. jejuni can be specifically inhibited. To investigate the molecular determinates of binding to CfrA, I set out to crystallize CfrA. Hundreds of crystal trials led to crystals diffracting to 3.6 Å resolution, with a complete data set acquired at 5 Å resolution that led to a structural model of the CfrA β-barrel. In the second part of this thesis, I reconstituted ELIC into model membranes in order to test the role of intramembrane aromatic interactions in ELIC gating and lipid sensing. ELIC was reconstituted into both asolectin (aso-ELIC) and 1-palmitoyl-2-oleoyl phosphatidylcholine (PC-ELIC), membranes that stabilize the homologous nicotinic acetylcholine receptor (nAChR) in functional coupled versus non-functional uncoupled conformations, respectively. In both membrane environments, ELIC exhibits a mixed α-helical and β-sheet secondary structure, with a thermal denaturation intermediate between those of the nAChR and the close prokaryotic homolog, GLIC, in similar membranes. The data suggest that although ELIC has a decreased propensity to adopt an uncoupled conformation relative to the nAChR, its ability to undergo cysteamine-induced channel gating is sensitive to its lipid environment. The decreased propensity to uncouple may reflect an increased level of aromatics at the interface between the transmembrane α-helices, M1, M3, and M4. To test this hypothesis further, the level or aromatic residues at the M1, M3, and M4 interface in both GLIC and ELIC were varied, and in both cases the levels of intramembrane aromatic interactions correlated with the efficiency of coupling binding to gating. The data provide further evidence for a role of intramembrane aromatics in channel gating and in dictating the propensity of pentameric ligand-gated ion channels to adopt an uncoupled conformation.

Master of Science / Department of Biochemistry / Paul E. Smith / We are developing a force field (FF) for molecular dynamics (MD) simulations of peptides and small proteins that is grounded in the Kirkwood-Buff theory of solutions. Here we present the Kirkwood-Buff Force Field (KBFF) parameters for the aromatic amino acids, based upon simulations of binary mixtures of small molecules representative of these amino acids over their entire composition ranges (excluding Histidine). Many aromatics are not fully soluble in water, so they have instead been studied in solvents of methanol or toluene. The parameters were developed by studying the following binary solutions: Phenylalanine − benzene + methanol, toluene + methanol, and toluene + benzene; Tyrosine − toluene + phenol and toluene + p-Cresol; Tryptophan − pyrrole + methanol and indole + methanol; Histidine − pyrrole + methanol, pyridine + methanol, pyridine + water, histidine + water (at 0.25 molal), and histidine monohydrochloride + water (at 0.3 molal and 0.6 molal). Our simulations reproduce the Kirkwood-Buff integrals, which guarantees that the KBFF provides an adequate balance of solute-solvent, solute-solute, and solvent-solvent interactions. Additionally, we show that the KBFF does not sacrifice reproduction of other solution properties in order to achieve this improved description of intermolecular interactions. We present these results as validating evidence for the future use of the KBFF in simulations of peptides and small proteins.

Over the past decades, functional group manipulation of aromatic precursors has been a common strategy to access new aromatic compounds. However, these classical methods, such as Friedel-Crafts alkylations and electrophilic/nucleophilic aromatic substitutions, have shown lack of regioselectivity besides the use of activators in excess amounts. To this end, numerous benzannulations to form benzo-fused substrates via Diels-Alder (DA), ring-closing metathesis (RCM), cycloaddition, and transition-metal-promoted processes have been reported. Appending a benzene ring directly onto a pre-existing ring is preferable to many classical methods due to the likely reduction of reaction steps and superior regiocontrol. However, many of these benzannulation reactions require air- and/or moisture- sensitive reaction conditions, a last oxidation step, or the use of highly functionalized precursors. Here we disclose three ‘complementary’ intramolecular ring-opening benzannulations to access a large array of functionalized (hetero)aromatic scaffolds utilizing cyclopropenes-3,3-dicarbonyls, alkylidene cyclopropanes-1,1-diesters, and 2,3-dihydrofuran O,O- and N,O- acetals as building blocks. More than 70 benzo-fused aromatic compounds were synthesized using this complementary approach with yields up to 98% and low catalyst loadings. With these benzannulation reactions in hand, we aim to open the synthetic door to a handful of bioactive natural products.

No description available.