Organic Chemistry Commons^™

Flavin Modification And Redox Tuning In The Bifurcating Electron Transfer Flavoprotein From Rhodopseudomonas Palustris: Two Arginines With Different Roles, Nishya Mohamed-Raseek

Theses and Dissertations--Chemistry

Electron bifurcation is considered as a third fundamental mode of energy conservation mechanism in addition to two well-known mechanisms, substrate level phosphorylation and Oxidative phosphorylation, in electron bifurcation endergonic and exergonic redox reactions are coupled. The newly discovered flavin based electron bifurcation in electron transfer flavoproteins (ETFs) helps to reduce low potential ferredoxin, which provides electrons to drive biologically demanding reactions such as atmospheric dinitrogen fixation in diazotroph and methane production in methanogens.

Current research demonstrates the capacity for electron bifurcation in the Rhodopseudomonas palustris ETF (RpalETF) system. RpalETF contains two chemically identical but functionally different FADs: …

Derivatization Of Stable, Soluble Redox-Active Organic Materials For Non-Aqueous Redox Flow Batteries, Thilini Malsha Suduwella

Theses and Dissertations--Chemistry

In screening active materials for redox flow batteries (RFBs) – in which solubility is important to raise the volumetric energy density – scientists are slave to trial and error, modifying organic molecules in an attempt to optimize (increase) solubility without compromising other important properties such as stability and redox potential. A trained chemist can often predict the trends of solubility with the structural modifications in the neutral state of the materials, but when it’s come to the charged state of the materials, it doesn’t follow the same trend as the neutral species and relative values are hard to predict. The …

Effects Of Hole Transporting Layers And Surface Ligands On Interface Energetics And Photovoltaic Performance Of Methylammonium Lead Iodide Perovskites, So Min Park

Theses and Dissertations--Chemical and Materials Engineering

Organic metal halide perovskites are promising materials for various optoelectronic device applications such as light emitting diodes (LED) and photovoltaic (PV) cells. Perovskite solar cells (PSCs) have shown dramatic increases in power conversion efficiency over the previous ten years, far exceeding the rate of improvement of all other PV technologies. PSCs have attracted significant attention due to their strong absorbance throughout the visible region, high charge carrier mobilities, color tunability, and ability to make ultralight weight devices. However, organic metal halide perovskites still face several challenges. For example, their environmental stability issue must be overcome to enable widespread commercialization. Meeting …

Multiscale Modeling Of Structure-Function Relationships Of Organic Semiconductors, Shi Li

Theses and Dissertations--Chemistry

While optoelectronic devices built from organic semiconductors (OSC) continue to find their way into the commercial landscape, there remain numerous challenges to overcome to supplant traditional semiconductors in many technologies. Chief among these are low performance metrics relative to devices with conventional semiconductors and device stability. In order to overcome these challenges, a wide range of new OSC and processing technologies have been developed. However, there remains limited fundamental understanding of the relationship between molecular structure, packing in the solid state, and the resulting materials properties. Here, we make use of multiscale molecular models and utilize classical all-atom molecular dynamic …

Designing Metal-Halide Perovskites With Enhanced Optical Properties And Stability Using Surface Ligands, Md Aslam Uddin

Theses and Dissertations--Chemistry

Metal-halide perovskites (MHPs), with formula ABX₃ (A = methylammonium, formamidinium, or Cs⁺; B = Sn²⁺ or Pb²⁺; and X = Cl^-, Br^-, or I^-) are versatile and attractive materials because of their tunable optical and electronic properties. These optical and electronic properties include tunable direct band gaps, high absorption coefficients, low exciton binding energies, relatively high electron and hole mobilities, narrow emission line-widths, and high photoluminescence (PL) quantum yields (Φ_PL). Much of the initial excitement around organic metal-halide perovskites focused on their application in photovoltaics (PVs) …

Developing And Testing Redox Active Organic Molecules For Nonaqueous Redox Flow Battery Applications, Nuwan Harsha Attanayake

Theses and Dissertations--Chemistry

Non-emissive, sustainable energy sources such as solar, wind, and geothermal power have continued to provide an increasing amount of electricity to support electrical grids. Due to the intermittent nature of renewable energy sources like wind and solar, grid energy storage systems must adjust for variations in and mismatches between electricity production and consumption. Among the available energy storage technologies, redox flow batteries (RFBs) are expected to play a critical role in the grid energy storage due to their decoupled energy and power, long service life, and simple manufacturing. However, the worldwide market penetration of RFB systems is still limited due …

A Theoretical And Experimental Study Of Charge Transport In Organic Thermoelectric Materials And Charge Transfer States In Organic Photovoltaics, Ashkan Abtahi

Theses and Dissertations--Physics and Astronomy

Applications of organic electronics have increased significantly over the past two decades. Organic semiconductors (OSC) can be used in mechanically flexible devices with potentially lower cost of fabrication than their inorganic counterparts, yet in many cases organic semiconductor-based devices suffer from lower performance and stability. Investigating the doping mechanism, charge transport, and charge transfer in such materials will allow us to address the parameters that limit performance and potentially resolve them. In this dissertation, organic materials are used in three different device structures to investigate charge transport and charge transfer. Chemically doped π-conjugated polymers are promising materials to be used …

Production Of Singlet Oxygen (1O2) During The Photochemistry Of Aqueous Pyruvic Acid: The Effects Of Ph And Photon Flux Under Steady-State O2(Aq) Concentration, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The photochemistry of pyruvic acid (PA) in aqueous atmospheric particles contributes to the production of secondary organic aerosols. This work investigates the fate of ketyl and acetyl radicals produced during the photolysis (λ ≥ 305 nm) of 5-100 mM PA under steady state [O₂(aq)] = 260 μM (1.0 ≤ pH ≤ 4.5) for photon fluxes between 1 and 10 suns. The radicals diffuse quickly into the water/air interface of microbubbles and react with dissolved O₂ to produce singlet oxygen (¹O₂^*). Furfuryl alcohol is used to trap and bracket the steady-state production of …

Crystal Structure Of Zymonic Acid And A Redetermination Of Its Precursor, Pyruvic Acid, Dominik Heger, Alexis J. Eugene, Sean R. Parkin, Marcelo I. Guzman

Chemistry Faculty Publications

The structure of zymonic acid (systematic name: 4-hy­droxy-2-methyl-5-oxo-2,5-di­hydro­furan-2-carb­oxy­lic acid), C₆H₆O₅, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra­molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo­propanoic acid), C₃H₄O₃, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977). Acta Cryst. B33, 210–212]. In zymonic acid, the hy­droxy­lactone ring …

The Effects Of Reactant Concentration And Air Flow Rate In The Consumption Of Dissolved O2 During The Photochemistry Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The sunlight photochemistry of the organic chromophore pyruvic acid (PA) in water generates ketyl and acetyl radicals that contribute to the production and processing of atmospheric aerosols. The photochemical mechanism is highly sensitive to dissolved oxygen content, [O₂(aq)], among other environmental conditions. Thus, herein we investigate the photolysis (λ ≥ 305 nm) of 10–200 mM PA at pH 1.0 in water covering the relevant range 0 ≤ [O₂(aq)] ≤ 1.3 mM. The rapid consumption of dissolved oxygen by the intermediate photolytic radicals is monitored in real time with a dissolved oxygen electrode. …

Toward An Enzyme-Coupled, Bioorthogonal Platform For Methyltransferases: Probing The Specificity Of Methionine Adenosyltransferases, Tyler D. Huber

Theses and Dissertations--Pharmacy

Methyl group transfer from S-adenosyl-l-methionine (AdoMet) to various substrates including DNA, proteins, and natural products (NPs), is accomplished by methyltransferases (MTs). Analogs of AdoMet, bearing an alternative S-alkyl group can be exploited, in the context of an array of wild-type MT-catalyzed reactions, to differentially alkylate DNA, proteins, and NPs. This technology provides a means to elucidate MT targets by the MT-mediated installation of chemoselective handles from AdoMet analogs to biologically relevant molecules and affords researchers a fresh route to diversify NP scaffolds by permitting the differential alkylation of chemical sites vulnerable to NP MTs that are unreactive to …

Oxidative Degradation Of Lignin And Investigation Of Utilization Of Lignin-Derived Materials As Building Blocks For Epoxy Resins, Zhen Fang

Theses and Dissertations--Chemistry

Lignin, the second most abundant biopolymer on earth, is potentially a replaceable source for bulky fuels and chemical feedstocks. There have been numerous reports on methods for the oxidative cleavage of β-O-4 linkages but relatively few reports of how those methods affect other linkages that are present in lignin. We investigated how the β-1 and β-5 linkages respond under oxidative conditions proposed for lignin deconstruction based on their effect on β-O-4 linkages. Mechanochemical treatment of lignin can greatly improve the yield of monomer products and we applied a mechanochemical approach, using powerful ring-and-puck milling to promote lignin degradation. Along with …

Oxidative Depolymerization Of Lignin To Low Molecular Weight Aromatics, Yang Song

Theses and Dissertations--Chemistry

To date, most lignocellulosic biorefinery strategies have focused on optimizing conversion of cellulose to ethanol, leaving lignin as an underutilized biomass constituent. Lignin is engineered by nature with the intent to protect plants from chemical and biological attack; this leaves lignin with high structural irregularity and recalcitrance, rendering conversion of the lignin macromolecule to valuable products particularly challenging. Nevertheless, given that the economics of cellulosic ethanol production are strongly dependent on the value that can be obtained for the lignin co-product, the successful valorization of lignin is a crucial step in the transition towards a bio-based economy.

This thesis focuses …

Modeling The Condensed-Phase Behavior Of Π-Conjugated Polymers, Walker Mask

Theses and Dissertations--Chemistry

It is well established that the morphology and physical properties of an organic semiconducting (OSC) material regulate its electronic properties. However, structure-function relationships remain difficult to describe in polymer-based OSC, which are of particular interest due to their robust mechanical properties. If relationships among the molecular and bulk levels of structure can be found, they can aid in the design of improved materials. To explore and detail important structure-function relationships in polymer-based OSC, this work employs molecular dynamics (MD) simulations to study various π-conjugated polymers in different environments. Two independent investigations are discussed in this work. One investigation examines how …

An Overview Of Dynamic Heterogeneous Oxidations In The Troposphere, Elizabeth A. Pillar-Little, Marcelo I. Guzman

Chemistry Faculty Publications

Due to the adverse effect of atmospheric aerosols on public health and their ability to affect climate, extensive research has been undertaken in recent decades to understand their sources and sinks, as well as to study their physical and chemical properties. Atmospheric aerosols are important players in the Earth’s radiative budget, affecting incoming and outgoing solar radiation through absorption and scattering by direct and indirect means. While the cooling properties of pure inorganic aerosols are relatively well understood, the impact of organic aerosols on the radiative budget is unclear. Additionally, organic aerosols are transformed through chemical reactions during atmospheric transport. …

Oxidation Of N-Doped Multiwalled Carbon Nanotubes And Formation Of Discontinuous Spiraled Carbon Nanoribbons, Aman Preet Kaur, Mark S. Meier, Rodney Andrews, Dali Qian

Chemistry Faculty Publications

The effects of five commonly used wet chemical oxidations were studied for the extent of oxidation of graphitized nitrogen-doped multiwalled carbon nanotubes (N-MWCNTs). KMnO₄/ H₂SO₄ was the most potent oxidant, as it produced the highest fraction of oxygen-containing functional groups. Electron microscopy studies showed that the treatment of annealed N-MWCNTs (G-N-MWCNTs) with H₂SO₄/HNO₃ and H₂SO₄/KMnO₄ mixtures leads to interesting spiraled ribbon textures. A structural model, involving the stacking of coiled subunits to form a discontinuous carbon nanoribbon rather than a continuous ribbon is proposed to …

Investigation Of Volatile Organic Compounds (Vocs) Detected At Vapor Intrusion Sites, Mohammadyousef Roghani

Theses and Dissertations--Civil Engineering

This dissertation investigates unexplained vapor intrusion field data sets that have been observed at hazardous waste sites, including: 1) non-linear soil gas concentration trends between the VOC source (i.e. contaminated groundwater plume) and the ground surface; and, 2) alternative pathways that serve as entry points for vapors to infiltrate into buildings and serve to increase VOC exposure risks as compared to the classic vapor intrusion model, which primarily considered foundation cracks as the route for vapor entry. The overall hypothesis of this research is that theoretical knowledge of fate and transport processes can be systematically applied to vapor intrusion field …

Oxidation Of Β-O-4 Lignin Model Compounds And Application To Lignin Linkage Degradation Facilitated By Mechanochemical Treatment And Two-Step Oxidative Depolymerization, Soledad G. Yao

Theses and Dissertations--Chemistry

The oxidation of lignin model compounds was studied in conventional solvents in parallel with oxidations in ionic liquid solvents. Catalyst systems were investigated in ionic liquid solvents to determine how reaction rates and the selectivity for benzylic carbon oxidation were affected. Oxidation rates were often lower in ionic liquids than in conventional solvents ‒ as indicated by lower conversion in a standard reaction time ‒ likely due, at least in part, to the higher viscosity of ionic liquids. Mechano chemical treatment of Indulin AT kraft lignin by ball milling with KOH and toluene produced significant carbonyl functionality, among other changes. …

Study Of The Effect Of Steric Bulk Of Side Chains On The Properties Of Conjugated Polymers, Bei Zhang

Theses and Dissertations--Chemistry

Donor-acceptor conjugated polymers opened a new era for conjugated polymer research due to the abundant selection and combination of different conjugated units. This class of polymers function as semiconductor materials with potential application in plastic consumer electronics. The frontier molecular orbital energies of the polymers are generally determined by the selection of donor and acceptor units in the backbone structure, and their substituents. The side chains attached to the backbone not only affect the solubility of the materials, but also their self-assembly and morphological characteristics, which indirectly govern optoelectronic properties. It is important therefore to consider backbone architectures and the …

Catalytic Conversion Of Monosaccharides Into 5-(Hydroxymethyl)Furfural In Ionic Liquids Using Aluminum Complexes Bearing Bidentate (Aminomethyl)Phenolate Ligands, Daudi Sayialel Saang'onyo

Theses and Dissertations--Chemistry

Currently, the major sources of fuel, energy, and chemicals are nonrenewable fossil resources such as petroleum, natural gas, and coal. Additionally, petroleum is used for the production of most transportation fuels and for the production of about 95% of organic chemicals. However, the production and use of non-renewable fossil fuels are unsustainable. For economic and environmental sustainability, there is a need to search for new and/or renewable resources and technologies for energy, fuels, and chemicals production that have the potential of effectively substituting fossil resources. In this context, lignocellulosic biomass is one of the candidates that meet these requirements due …

Design And Synthesis Of Functional Organic Materials, Anthony Joseph Petty Ii

Theses and Dissertations--Chemistry

Control of solid state ordering in conjugated small molecules is paramount to the continued development and implementation of organic materials in electronic devices. However, there exists no reliable method on which to predicatively determine how a change to the molecular structure will impact the solid-state packing. As such, the molecule must be synthesized before its solid-state packing can be definitively evaluated. However, once the packing structure of a material is known there exist both qualitative structure- function relationships derived from the literature, as well as quantitative computational methods that can be employed to suggest if a material will perform well …

Aqueous Photochemistry Of 2-Oxocarboxylic Acids, Alexis Eugene

Theses and Dissertations--Chemistry

Atmospheric aerosols affect climate change by altering the energy balance of the atmosphere, and public health due to their variable chemical composition, size, and shape. While the formation of secondary organic aerosol (SOA) from gas phase precursors is relatively well understood, it does not account for the abundance of SOA observed during field measurements. Recently it has become apparent that in-aerosol aqueous chemical reactions likely provide some of the missing sources of SOA production, and many studies of aqueous phase processes are underway.

This work explores the fates of the simplest 2-oxocarboxylic acids, glyoxylic acid (GA) and pyruvic acid (PA), …

The Role Of Catalytic Residue PKA On The Hydrolysis/Transglycosylation Partition In Family 3 Β-Glucosidases, Inacrist Geronimo, Christina M. Payne, Mats Sandgren

Chemical and Materials Engineering Faculty Publications

β-Glucosidases (βgls) primarily catalyze the hydrolysis of the terminal glycosidic bond at the non-reducing end of β-glucosides, although glycosidic bond synthesis (called transglycosylation) can also occur in the presence of another acceptor. In the final reaction step, the glucose product or another substrate competes with water for transfer to the glycosyl-enzyme intermediate. The factors governing the balance between the two pathways are not fully known; however, the involvement of ionizable residues in binding and catalysis suggests that their pK_a may play a role. Through constant pH molecular dynamics simulations of a glycoside hydrolase Family 3 (GH3) βgl, we …

Layer-By-Layer Assembled Membranes With Immobilized Porins, Sebastián Hernández, Cassandra Porter, Xinyi Zhang, Yinan Wei, Dibakar Bhattacharyya

Chemical and Materials Engineering Faculty Publications

New and advanced opportunities are arising for the synthesis and functionalization of membranes with selective separation, reactivity, and stimuli-responsive behavior. One such advancement is the integration of bio-based channels in membrane technologies. By a layer-by-layer (LbL) assembly of polyelectrolytes, outer membrane protein F trimers (OmpF) or “porins” from Escherichia coli with central pores ∼2 nm in diameter at their opening and ∼0.7 × 1.1 nm at their constricted region are immobilized within the pores of poly(vinylidene fluoride) microfiltration membranes, in contrast to traditional ruptured lipid bilayer or vesicle processes. These OmpF-membranes demonstrate selective rejection of non-charged organics over ionic solutes, …

Oxidation Of Substituted Catechols At The Air-Water Interface: Production Of Carboxylic Acids, Quinones, And Polyphenols, Elizabeth A. Pillar, Marcelo I. Guzman

Chemistry Faculty Publications

Anthropogenic activities contribute benzene, toluene, and anisole to the environment, which in the atmosphere are converted into the respective phenols, cresols, and methoxyphenols by fast gas-phase reaction with hydroxyl radicals (HO(•)). Further processing of the latter species by HO(•) decreases their vapor pressure as a second hydroxyl group is incorporated to accelerate their oxidative aging at interfaces and in aqueous particles. This work shows how catechol, pyrogallol, 3-methylcatechol, 4-methylcatechol, and 3-methoxycatechol (all proxies for oxygenated aromatics derived from benzene, toluene, and anisole) react at the air-water interface with increasing O3(g) during τc ≈ 1 μs contact time and contrasts their …

Reactivity Of Ketyl And Acetyl Radicals From Direct Solar Actinic Photolysis Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The variable composition of secondary organic aerosols (SOA) contributes to the large uncertainty for predicting radiative forcing. A better understanding of the reaction mechanisms leading to aerosol formation such as for the photochemical reaction of aqueous pyruvic acid (PA) at λ ≥ 305 nm can contribute to constrain these uncertainties. Herein, the photochemistry of aqueous PA (5-300 mM) continuously sparged with air is re-examined in the laboratory under comparable irradiance at 38° N at noon on a summer day. Several analytical methods are employed to monitor the time series of the reaction, including (1) the derivatization of carbonyl (C═O) functional …

Mechanisms Of Heterogeneous Oxidations At Model Aerosol Interfaces By Ozone And Hydroxyl Radicals, Elizabeth A. Pillar-Little

Theses and Dissertations--Chemistry

Atmospheric aerosols play an important role in climate by scattering and absorbing radiation and by serving as cloud condensation nuclei. An aerosol’s optical or nucleation properties are driven by its chemical composition. Chemical aging of aerosols by atmospheric oxidants, such as ozone, alters the physiochemical properties of aerosol to become more hygroscopic, light absorbing, and viscous during transport. However the mechanism of these transformations is poorly understood. While ozone is a protective and beneficial atmospheric gas in the stratosphere, it is a potent greenhouse gas in the troposphere that traps heat near the Earth’s surface. It also impacts human heath …

Heterogeneous Base Metal Catalyzed Oxidative Depolymerization Of Lignin And Lignin Model Compounds, John Adam Jennings

Theses and Dissertations--Chemistry

With the dwindling availability of petroleum, focus has shifted to renewable energy sources such as lignocellulosic biomass. Lignocellulosic biomass is composed of three main constituents, lignin, cellulose and hemicellulose. Due to the low value of cellulosic ethanol, utilization of the lignin component is necessary for the realization of an economically sustainable biorefinery model. Once depolymerized, lignin has the potential to replace petroleum-derived molecules used as bulk and specialty aromatic chemicals. Numerous lignin depolymerization strategies focus on cleavage of β-aryl ether linkages, usually at high temperatures and under reductive conditions.

Alternatively, selective benzylic oxidation strategies have recently been explored for …

Formation Of The Ether Bridge In The Loline Alkaloid Biosynthetic Pathway, Minakshi Bhardwaj

Theses and Dissertations--Chemistry

Lolines are specialized metabolites produced by endophytic fungi, such as Neotyphodium and Epichloë species, that are in symbiotic relationships with cool-season grasses. Lolines are vital for the survival of the grasses because their insecticidal and antifeedant properties protect the plant from insect herbivory. Although lolines have various bioactivities, they do not have any concomitant antimammalian activities.

Lolines have complex structures that are unique among naturally occurring pyrrolizidine alkaloids. Lolines have four contiguous stereocenters, and they contain an ether bridge connecting C(2) and C(7) of the pyrrolizidine ring. An ether bridge connecting bridgehead C atoms is unusual in natural products and …

Acenes, Heteroacenes And Analogous Molecules For Organic Photovoltaic And Field Effect Transistor Applications, Devin B. Granger

Theses and Dissertations--Chemistry

Polycyclic aromatic hydrocarbons composed of benzenoid rings fused in a linear fashion comprise the class of compounds known as acenes. The structures containing three to six ring fusions are brightly colored and possess band gaps and charge transport efficiencies sufficient for semiconductor applications. These molecules have been investigated throughout the past several decades to assess their optoelectronic properties. The absorption, emission and charge transport properties of this series of molecules has been studied extensively to elucidate structure-property relationships. A wide variety of analogous molecules, incorporating heterocycles in place of benzenoid rings, demonstrate similar properties to the parent compounds and have …