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- Genre: Doctoral Dissertation
Description
In this work, secretion of free fatty acids (FFAs) and ω-hydroxy FFAs wasachieved in the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), and
FFAs were detected by a novel fluorescence assay. Current methods of detecting FFA
concentrations, including HPLC-based and GC-based methods or enzyme-based kits,
have hindered research advancement due to their laborious and/or expensive nature. The
work herein establishes a novel, rapid, fluorescence-based assay for detecting total FFA
concentrations secreted by Synechocystis FFA secretion strains. The novel FFA-detection
assay demonstrates the efficacy of using Nile Red as a fluorescent reporter for laurate or
palmitate at concentrations up to 500 µM in the presence of cationic surfactants. Total
FFA concentrations in Synechocystis supernatants quantified by the novel, Nile Red fluorescence-based assay are demonstrated herein to be highly correlative to total FFA
concentrations quantified by LC-MS; this correlation was seen in supernatant samples of
wild type Synechocystis and Synechocystis FFA secretion strains, both in 96-well plates
and 30-mL, aerated culture tubes.
This work also establishes the expression of a cytochrome P450 fusion enzyme,
CYP153A-CPRmut, or a monooxygenase system from Pseudomonas putida GPo1,
AlkBGT, in FFA secretion strains of Synechocystis for the generation of ω-hydroxy
laurate from laurate. After finding greatly increased ω-hydroxylation activity of
CYP153A-CPRmut with concurrent superoxide dismutase and catalase overexpression, 55
or 1.5 µM of ω-hydroxy laurate were produced over five days by Synechocystis strains
expressing CYP153A-CPRmut or AlkBGT, respectively. As further indication of the
presence of reactive oxygen species affecting ω-hydroxy laurate production with
Synechocystis strains expressing CYP153A-CPRmut, concentrations of ω-hydroxy laurate
in the supernatant increased over two-fold in the presence of 250 µM of the anti-oxidant,
methionine, in bench-scale cultures and in 96-well plate cultures. Additionally, a
mutation at the 55th amino acid position in AlkB (tryptophan to cysteine; AlkBW55C),
resulted in a more than two-fold shift in AlkB’s substrate preference from decanoate
towards the desired substrate, laurate. As a result, Synechocystis expressing AlkBW55C
could produce 5.9 µM ω-hydroxy laurate and 2.0 µM dodecanedioic acid over five days
of growth.
ContributorsAshe, Christopher (Author) / Vermaas, Willem Fj (Thesis advisor, Committee member) / Wang, Xuan (Committee member) / Nielsen, David R (Committee member) / Misra, Rajeev (Committee member) / Arizona State University (Publisher)
Created2023
Description
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami technology enables the fabrication of nearly arbitrary DNA architectures with nanoscale precision, which can serve as excellent building blocks for the construction of tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, a general design and assembly method are described for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. A critical design parameter, interhelical distance (D), was identified, which determined the conformation of monomer tiles and the outcome of tessellation. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability. To demonstrate the generality of the design method, 9 tile geometries and 15 unique tile designs were generated. The designed tiles were assembled into single-crystalline lattices ranging from tens to hundreds of square micrometers with micrometer-scale, nearly defect-free areas readily visualized by atomic force microscopy. Two strategies were applied to further increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and co-assembling tiles of various geometries. The designed 6 complex tilings that includes 5 Archimedean tilings and a 12-fold quasicrystal tiling yielded various tiling patterns that great in size and quality, indicating the robustness of the optimized tessellation system. The described design and assembly approach can also be employed to create square DNA origami units for algorithmic self-assembly. As the square units assembled and expanded, they executed the binary function XOR, which generated the Sierpinski triangular pattern according to the predetermined instructions. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
ContributorsTang, Yue (Author) / Yan, Hao (Thesis advisor) / Guo, Jia (Committee member) / Stephanopoulos, Nicholas (Committee member) / Arizona State University (Publisher)
Created2023
Description
Perovskite solar cells are one of the rising stars in the solar cell industry. This thesis explores several approaches to enhance the properties of the perovskite layer and the solar cell devices in which they operate. They include studies of different antisolvent additives during spin coating of triple cation perovskites, the use of surfactants to improve the quality of perovskite film microstructures, the applicability of a new fabrication process, and the value of post-deposition thermal and chemical annealing processes.This thesis experimentally analyzes different antisolvents, viz., ethyl acetate, isopropyl alcohol, toluene, and chlorobenzene. It focuses on the antisolvent-assisted crystallization method to achieve homogenous nucleation of the perovskite film. Of all the antisolvents, ethyl acetate-treated films gave the best-performing device, achieving a power conversion efficiency of 15.5%.
This thesis also analyzes the effects of mixed antisolvents on the qualities of triple-cation perovskites. Different solution concentrations of chlorobenzene in ethyl acetate and isopropyl alcohol in ethyl acetate are optimized for optimal supersaturation to achieve enlarged perovskite grains. Evaluations are discussed in the context of solution polarity and boiling point of the antisolvents, where 25% chlorobenzene in ethyl acetate antisolvent mixture shows the best film properties.
Another study discusses a new fabrication process called electrical field-assisted direct ink deposition for large-scale printing of perovskite solar cells. This process involves the formation of nanodroplets under an electrical field deposited onto ITO/glass substrates. As a result, smooth Poly (3,4-ethylene dioxythiophene) polystyrene sulfonate layers are
ii
produced with an average effective electrical resistivity of 4.15104 0.26 -m compared to that of spin-coated films.
A successive chapter discusses the studies of the electrical field-assisted direct ink deposition of the photoactive CH3NH3PbI2 (MAPbI3) layer. Its focus is on the post-deposition chemical annealing of the MAPbI3 films in methylamine gas, termed as methylamine gas-assisted healing and growth of perovskite films. This treatment improved the smoothness, reduced porosity, increased density, and generated more uniform grain sizes. Moreover, it improved the inter-grain boundary contacts by eliminating secondary, fine-grained boundary structures. Mechanisms behind the initial liquefaction of the MAPbI3 film's subsequent re-solidification are discussed.
ContributorsGogoi, Banashree (Author) / Alford, Terry (Thesis advisor) / Petuskey, William (Thesis advisor) / Gould, Ian (Committee member) / Li, Jian (Committee member) / Arizona State University (Publisher)
Created2023
Description
Transition metal oxides are used for numerous applications, includingsemiconductors, batteries, solar cells, catalysis, magnetic devices, and are commonly
observed in interstellar media. However, the atomic-scale properties which dictate the
overall bulk material activity is still lacking fundamental details. Most importantly, how
the electron shells of metals and O atoms mix is inherently significant to reactivity. This
thesis compares the binding and excited state properties of highly correlated first-row
transition metal oxides using four separate transition metal systems of Ti, Cr, Fe and Ni.
Laser ablation coupled with femtosecond pump-probe spectroscopy is utilized to resolve
the time-dependent excited state relaxation dynamics of atomically precise neutral
clusters following 400 nm (3.1 eV) photoexcitation. All transition metal oxides form
unique stable stoichiometries with excited state dynamics that evolve due to oxidation,
size, or geometry. Theoretical calculations assist in experimental analysis, showing
correlations between charge transfer characteristics, electron and hole localization, and
magnetic properties to the experimentally determined excited state lifetimes.
This thesis finds that neutral Ti and Cr form stable stoichiometries of MO2 (M =
Ti, Cr) which easily lose up to two O atoms, while neutral Fe and Ni primarily form MO
(M = Fe, Ni) geometries with suboxides also produced. TiO2 clusters possess excited
state lifetimes that increase with additional cluster units to ~600 fs, owing to a larger
delocalization of excited charge carriers with cluster size. CrO2 clusters show a unique
inversed metallic behavior with O content, where the fast (~30 fs) metallic relaxation
component associated with electron scattering increases with higher O content, connected
to the percent of ligand-to-metal charge transfer (LMCT) character and higher density of
states. FeO clusters show a decreased lifetime with size, reaching a plateau of ~150 fs at
the size of (FeO)5 related to the density of states as clusters form 3D geometries. Finally,
neutral (NiO)n clusters all have similar fast lifetimes (~110 fs), with suboxides possessing
unexpected electronic transitions involving s-orbitals, increasing excited state lifetimes
up to 80% and causing long-lived states lasting over 2.5 ps. Similarities are drawn
between each cluster system, providing valuable information about each metal oxide
species and the evolution of excited state dynamics as a result of the occupied d-shell.
The work presented within this thesis will lead to novel materials of increased reactivity
while facilitating a deeper fundamental understanding on the effect of electron
interactions on chemical properties.
ContributorsGarcia, Jacob M. (Author) / Sayres, Scott G (Thesis advisor) / Yarger, Jeffery (Committee member) / Steimle, Timothy (Committee member) / Arizona State University (Publisher)
Created2021
Description
The development of sustainable catalysts that exhibit exceptional activity has become a major goal of organometallic chemists. Considering their low cost and environmentally benign nature, the use of base metals in catalysis has recently been explored. This dissertation is focused on the development of manganese catalysts for organic transformations and inorganic polymerizations. Previous advances in Mn-based hydrosilylation and hydroboration catalysis are reviewed in Chapter 1 and set the stage for the experimental work described herein.In Chapter 2, the electronic structure of [(2,6-iPr2PhBDI)Mn(μ-H)]2 is explored. This compound was evaluated by density functional theory calculations, SQUID magnetometry and EPR spectroscopy at low temperature. Single crystal X-ray diffraction data was collected for related compounds that feature bridging X-type ligands. The data revealed how bridging ligands impact the Mayer bond order between the two Mn atoms and explained why [(2,6-iPr2PhBDI)Mn(μ-H)]2 is an active catalyst for organic transformations.
Chapter 3 spotlights the first study to systematically demonstrate commercial aminosilane CVD precursor synthesis by way of SiH4 and amine dehydrocoupling using [(2,6-iPr2PhBDI)Mn(μ-H)]2. In addition, the study provided an efficient and halogen-free preparation of highly cross-linked polycarbosilazanes under ambient conditions. Furthermore, exceptionally pure perhydropolysilazane was directly prepared from ammonia and silane at room temperature through dehydrogenative coupling. These are also the first reported examples of Mn-catalyzed Si–N dehydrocoupling.
This research was then extended to the Mn-catalyzed dehydrogenative coupling of NH3 and diamines to organic silanes. Organic polysilazanes and polycarbosilazanes were synthesized and the structures were characterized by NMR, FT-IR, and MALDI-TOF spectroscopy. The thermal properties and coating applications of the products were evaluated by TGA, DSC, X-ray powder diffraction, SEM and EDX. A turnover frequency (TOF) experiment using 0.01 mol% of [(2,6-iPr2PhBDI)Mn(μ-H)]2 revealed a maximum TOF of 300 s-1, which is the highest activity ever reported for this transformation.
The last chapter highlights the first examples of nitrile dihydroboration mediated by a manganese catalyst. Using 0.5 mol% of [(2,6-iPr2PhBDI)Mn(μ-H)]2, 14 nitriles were reduced with HBPin at 80 ℃ to afford N,N-diborylamines after 24 h. A mechanism was proposed based on the isolation of [(2,6-iPr2PhBDI)Mn(NCHPh)]2 as an intermediate and further substantiated by DFT.
ContributorsNguyen, Thu Thao (Author) / Trovitch, Ryan (Thesis advisor) / Jones, Anne (Committee member) / Ackerman, Laura (Committee member) / Arizona State University (Publisher)
Created2022
Description
N-nitrosodimethylamine (NDMA) is a probable human carcinogen that has been detected in various environments including the atmosphere, clouds, surface waters, and drinking water. NDMA can form through natural reactions in the aqueous phase of the atmosphere and it can form as a disinfection byproduct in water treatment. Due to its carcinogenic nature, it is important to understand the mechanism of formation of NDMA in both engineered processes such as water treatment and in natural processes in fogs and clouds. NDMA might form through the reaction of chloramines with amines in both cases. This work analyzes polydiallyldimethyl ammonium chloride (PolyDADMAC), which is the most commonly used polymer at drinking water treatment plants and has the potential to form NDMA if free polymer is present during the chloramination (disinfection) process. The composition of industrial polyDADMAC solutions is not well understood and is difficult to analyze. This work uses 1H and 13C nuclear magnetic resonance (NMR) to analyze the polymer solution composition. Both 1H and 13C NMR allow investigation of the presence of trace impurities in the solution, gather structural information such as chain length, and inform on reaction mechanisms. The primary impurities of concern for NDMA formation were identified as dimethylamine (DMA) and short-chain oligomers of the polyDADMAC. 13C NMR was further used to confirm that NDMA likely forms from polyDADMAC via a Hofmann elimination.
Chloramines might also form in fogs and clouds although to date the potential for chloramines to form NDMA in atmospheric fog and cloud droplets has not been investigated. This work uses computational modeling to determine that at reported atmospheric conditions, the chloramine pathway contributes to less than 0.01% NDMA formation. The numerical modeling identified a need for more atmospheric HOCl measurements. This work proposes a concept of using HOCl to react to form chloramine, which can react to form NDMA as a way to quantify atmospheric HOCl.
ContributorsDonovan, Samantha Jo (Author) / Herckes, Pierre (Thesis advisor) / Westerhoff, Paul (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2022
Description
Acrylate polymers are a versatile class of polymers that have found extensive applications in diverse fields, including adhesive, coatings, packaging, cosmetics, textile, food, electronics, and automotive industries. Incorporating crosslinking elements such as supramolecular chemistry or photoreactive group imparts unique and desirable properties to the resulting acrylate polymers. In the first project, regioselective Michael addition allowed the efficient installation of the nucleobase, guanine and cytosine, on acrylate-containing monomers, which enabled the preparation of a series of nucleobase functionalized acrylate and n-butyl acrylate copolymers using conventional free radical copolymerization. Guanine-containing copolymers exhibited superior thermal, thermomechanical, and morphological properties than cytosine-containing copolymer analogs due to the relatively strong guanine self-association. Further understanding of rheological, mechanical, and adhesive properties revealed the influence of guanine content and provided valuable information for designing and optimizing guanine-containing copolymers for elastomers and adhesives. Controlled radical polymerization enabled the synthesis of guanine and cytosine-containing triblock copolymers. Blending these two triblock copolymers formed supramolecular networks through molecular recognitions between guanine and cytosine and enhanced polymer self-assembly. Next, incorporating spiropyran photoisomerization functional groups in the acrylate copolymer enabled the formation of zwitterionic polymers upon ultraviolet (UV) radiation, which facilitated the Cu ion removal from aqueous solutions. The final project aimed to synthesize a family of macro-crosslinkers bearing an acrylate pendant group, which demonstrated compatibility with versatile reactive diluents, such as poly(dimethyl siloxane) and epoxy. The designed macro-crosslinkers showed promise in developing UV adhesives with desirable properties, such as low shrinkage, fast curing, and high thermal stability. These projects offered valuable insights into the fundamental structure-property-morphology relationships in crosslinked acrylic polymers that incorporate supramolecular chemistry or photoreactive functional groups, paving the way for new advances in the design of acrylate polymer with enhanced mechanical and morphological properties.
ContributorsLiu, Boer (Author) / Long, Timothy TEL (Thesis advisor) / Moore, Robert RBM (Committee member) / Jin, Kailong KJ (Committee member) / Biegasiewicz, Kyle KFB (Committee member) / Arizona State University (Publisher)
Created2023
Description
Surface modification of (semi)conducting materials with polymers provides a strategy for interfacing electrodes with electrocatalysts for reactions of industrial importance. The resulting constructs create opportunities to capture, convert and store solar energy in the form of chemical bonds, generating solar fuels. This thesis describes III-V semiconductors, modified with molecular catalysts embedded in thin-film polymeric coatings. Overarching goals of this work include building protein-like, soft-material environments on solid-state electrode surfaces. This approach enables coordination of earth-abundant metal centers within the three-dimensional molecular coatings to modulate the electronic and catalytic properties of the overall assembly and provide assemblies for studying the effects of polymeric-encapsulation on electrocatalytic as well as photoelectrosynthetic performance. In summary, this work provides 1) new approaches to designing, interfacing, and characterizing (semi)conducting and catalytic materials to effectively power chemical transformations (including hydrogen evolution and carbon dioxide reduction), and 2) kinetic models for better understanding the structure-function relationships governing the performance of these assemblies.
ContributorsNguyen, Nghi Do Phuong (Author) / Moore, Gary F. (Thesis advisor) / Seo, Dong-Kyun (Committee member) / Sayres, Scott G. (Committee member) / Arizona State University (Publisher)
Created2023
Description
Exploration of long-range conductance in non-redox-active proteins at the single molecule scale is aided by the development of innovative, tailor-made quantitative data analysis techniques. This thesis details the rationale behind the proposed approaches, the steps taken to design and implement every method, and the validation of the methodologies using appropriate experiments, benchmarks, and rigorous statistical data analysis. The first chapter conducts a thorough literature review, sets the stage for the subsequent investigation, and underscores the importance of the research questions addressed in this thesis. The second chapter describes the solvent effects on the electronic conductance of a series of Consensus Tetratricopeptide Repeat proteins (CTPR) measured with Scanning Tunneling Microscopy (STM). The study reveals a reversible reduction in electronic conductance when water (H2O) is replaced with heavy water (D2O) due to a ~6-fold decrease in the carrier diffusion constant as proteins become solvated by D2O. Similar observations are made in a ~7 nm long tryptophan zipper protein, while a phenylalanine zipper protein of comparable length remains unchanged in D2O, highlighting the critical role of aromatic residues in proteins lacking redox cofactors. As an extension to this finding, the third chapter describes the development of a machine-learning model to detect the presence of a protein and identify essential features helping in the detection. For this purpose, a solid-state device was engineered to measure the conductance of CTPR-16 protein wires. This approach addresses the limitations in characterizing the STM gap, enables the collection of stable current vs. time data, and provides a statistical understanding of the electronic transport through a protein. The final chapter investigates real-time changes in conductance in response to protein conformation alterations. A deoxyribonucleic acid (DNA) polymerase Φ29 was chosen for its potential utility as a single-molecule DNA sequencing device. The modified enzyme was bound to electrodes functionalized with streptavidin. Φ29 connected by one biotinylated contact and a second nonspecific contact showed rapid small fluctuations in current when activated. Signals were greatly enhanced with two specific contacts. Features in the distributions of conductance increased by a factor of 2 or more over the open-to-closed conformational transition of the polymerase.
ContributorsMukherjee, Sohini (Author) / Lindsay, Stuart (Thesis advisor) / Moore, Thomas (Committee member) / Qing, Quan (Committee member) / Arizona State University (Publisher)
Created2023
Description
Without a doubt, protein is the most crucial biomolecule performing life and biological functions of any living cell. Profiling various protein expression in individual cells has raised a great interest for scientist and researchers over decades in attempts to reveal cell-to-cell variation, which used to be masked in many previous population average measurement methods. Immunofluorescence (IF) has been a well-established single cell protein analysis technique as for its fast and high-resolution detection and localization, simple and adaptable workflows, and affordable instrumentation. However, inadequate detection sensitivity and multiplexing capability are the two limitation of this platform that remain incompletely addressed in many decades. In this work, several improvements have been proposed and demonstrated to improve existing drawbacks of conventional immunofluorescence. An azide-based linker featured in the novel fluorescent probes synthesis has enable iterative protein staining on the same tissue sample, which subsequently increase the multiplex capacity of IF. Additionally, the multiple fluorophore introduction to the proteins target via either layer by layer biotin-cleavable fluorescent streptavidin or tyramide signal amplification (TSA) have significantly increase the detection sensitivity of the platform. With these advances, IF has the potential to detect, image and quantify up to 100 protein targets in single cell in the tissue sample. In addition of desirable features of IF, these improvements have further turned the technique into a powerful proteomic study platform for not only research setting but also clinical study setting. It is anticipated this highly sensitive and multiplexed, renovated IF method will soon be translated into biomedical studies.
ContributorsPham, Thai Huy (Author) / Guo, Jia (Thesis advisor) / Stephanopoulos, Nicholas (Committee member) / Chiu, Po-Lin (Committee member) / Arizona State University (Publisher)
Created2023