Chemistry Commons^™

Rational Design Of Memory-Based Sensors: The Case Of Molecular Calorimeters, Obianuju Augusta Nwokolo

Graduate Research Theses & Dissertations

Thermodynamic characterization is crucial for understanding molecular interactions. However, methodologies for measuring heat changes in small open systems are extremely limited. We document a new approach for designing molecular sensors that function as calorimeters: sensors based on memory. To design a memory-based sensor, we take advantage of the unique kinetic properties of nucleic acid scaffolds. Particularly, we elaborate on the differences in folding and unfolding rates in nucleic acid quadruplexes. DNA-based i-motifs unfold fast in response to small heats but do not fold back when the system is equilibrated with surroundings. We translated this behaviour into a molecular memory function …

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 …

Applications Of Drones In Atmospheric Chemistry, Travis J. Schuyler

Theses and Dissertations--Chemistry

The emission of greenhouse gases (GHGs) has changed the composition of the atmosphere during the Anthropocene. A major technical and scientific challenge is quantifying the resulting fugitive trace gas fluxes under variable meteorological conditions. Accurately documenting the sources and magnitude of GHGs emission is an important undertaking for discriminating contributions of different processes to radiative forcing. Therefore, the adverse environmental and health effects of undetected gas leaks motivates new methods of detecting, characterizing, and quantifying plumes of fugitive trace gases. Currently, there is no mobile platform able to quantify trace gases at altitudes(UASs), or drones, can be deployed on-site in …

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 …

Flavodoxin, The Hydrogen Atom Of Flavoproteins: A 19f Nmr Study Of Dynamics And Conformational Changes Utilizing Flavodoxin From Rhodopseudomonas Palustris, Taylor Varner

Theses and Dissertations--Chemistry

Flavodoxin is a small, highly stable protein that contain a single FMN cofactor used to transfer single electrons at low potentials. The organism Rhodopseudomonas palustris contains a long-chain flavodoxin. Long-chain flavodoxins are characterized by a 20 amino acid loop that is proposed to allow interactions with partner proteins. We plan to utilize this protein as a model to build our repertoire with protein fluorination and fluorine NMR in flavoproteins. This tool kit will then be applied to the study of a partner protein of interest that is capable of performing electron bifurcation. We have incorporated m-fluoro tyrosine into flavodoxin and …

Synthesis Of Metal Oxide Surface And Interface Arrays By A Combined Solid-Liquid- Vapor/Vapor-Liquid-Solid Approach, Alexandra J. Riddle

Theses and Dissertations--Chemistry

This project was motivated by an in situ heating experiment in the transmission electron microscope (TEM) in which gold (Au) nanoparticles were observed to dissolve tin dioxide (SnO2) nanowires (NWs) under vacuum. The explanation for this observation was that the high-temperature and low-pressure environment of the TEM caused the reverse reaction of the well-known vapor-liquid-solid (VLS) method commonly used to grow NWs. In the VLS process, a metal catalyst absorbs reactant vapor until it becomes supersaturated. The precipitation of the NW occurs at the liquid-solid interface, which ceases when there is no longer reactant vapor, and the diameter of the …

Threshold Ionization Spectroscopy And Spin-Orbit Coupling Of Lanthanide Complexes, Yuchen Zhang

Theses and Dissertations--Chemistry

The C-C and C-H bonds have high bond strength and low polarization, which make many small hydrocarbons too inert to react with other molecules under ambient pressure and temperature conditions. Therefore, activation of these bonds is required to convert such small molecules into other value-added chemicals. Among various bond activation methods, metal activation is widely used and reported in the literature, because of its relatively mild reaction conditions and high selectivity.

In this work, Ce atom reactions with several small hydrocarbons are carried out in a pulsed laser vaporization supersonic molecular beam source, and Ce -hydrocarbon species are observed with …

Interfaces In Lead-Free Tin Perovskite Photovoltaics: An Investigation Of Energetics, Ion Mobility, Surface Modification, And Performance, Alex Boehm

Theses and Dissertations--Chemistry

Halide perovskites have generated tremendous interest as low-cost semiconductors for optoelectronics, such as photovoltaics, lasers, and light emitting diodes due to their extraordinary optical and transport properties. Perovskite photovoltaics in particular have demonstrated a meteoric rise in power conversion efficiencies and drawn considerable interest as a next-generation solar energy technology. The rapid development has centered around lead-based derivatives, and concerns regarding the toxicity of lead has sparked interest in low toxicity and more environmentally friendly perovskite derivatives. In this regime tin (Sn) is regarded as a prominent alternative owing to the ideal bandgap and reduced toxicity exhibited by Sn-halide perovskites. …

Towards The Rational Design Of Organic Semiconductors Through Computational Approaches, Qianxiang Ai

Theses and Dissertations--Chemistry

Though organic semiconductors have illustrated potential as industry-relevant materials for electronics applications, there are few guidelines that can take one from molecular design to functional materials. This limitation is, in part, due to incomplete understanding as to how the atomic-scale construction of the π-conjugated molecules that comprise the organic semiconductors determines the nature and strength of both the noncovalent intramolecular interactions that govern molecular conformation and noncovalent intermolecular interactions that regulate the energetic preference for solid-state packing. Hence, there remain several fundamental questions that need to be resolved in order to design organic semiconductors from a priori knowledge, including: What …

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 …

Identification Of Adsorbate Ft-Ir Bands Using In-Situ Techniques: Pd Speciation And Adsorption Chemistry Of Pd-Zeolites For Passive Nox Adsorption, Robert Bruce Pace Iii

Theses and Dissertations--Chemistry

To meet increasingly stringent automotive emissions standards, further improvements in catalytic converter design are necessary. Current automotive catalyst systems are effective at eliminating emission of nitrogen oxides (NO_x) once the catalyst reaches operational temperature (~200 °C). NO_x emitted at lower catalyst temperatures now comprises most of the NO_x released during a typical test cycle. Referred to as “the cold start problem” this issue has come to the forefront of automotive catalyst development, as mitigating these emissions is necessary to further reduce automotive emissions. Passive NO_x adsorbers present an appealing solution to the cold start problem, …

Spatial Defects Nanoengineering For Bipolar Conductivity In Mos2, Xiaorui Zheng, Annalisa Calò, Tengfei Cao, Xiangyu Liu, Zhujun Huang, Paul Masih Das, Marija Drndic, Edoardo Albisetti, Francesco Lavini, Tai-De Li, Vishal Narang, William P. King, Michele Vittadello, Carmela Aruta, Davood Shahrjerdi, Elisa Riedo

Advanced Science Research Center

Understanding the atomistic origin of defects in two-dimensional transition metal dichalcogenides, their impact on the electronic properties, and how to control them is critical for future electronics and optoelectronics. Here, we demonstrate the integration of thermochemical scanning probe lithography (tc-SPL) with a flow-through reactive gas cell to achieve nanoscale control of defects in monolayer MoS₂. The tc-SPL produced defects can present either p- or n-type doping on demand, depending on the used gasses, allowing the realization of field effect transistors, and p-n junctions with precise sub-μm spatial control, and a rectification ratio of over 10⁴. Doping …

Hijacking The Fusion Complex Of Human Parainfluenza Virus As An Antiviral Strategy, T. C. Marcink, E. Yariv, K. Rybkina, V. Más, F. T. Bovier, A. Des Georges, A. L. Greninger, C. A. Alabi, M. Porotto, N. Ben-Tal, A. Moscona

Advanced Science Research Center

The receptor binding protein of parainfluenza virus, hemagglutinin- neuraminidase (HN), is responsible for actively triggering the viral fusion protein (F) to undergo a conformational change leading to insertion into the target cell and fusion of the virus with the target cell membrane. For proper viral entry to occur, this process must occur when HN is engaged with host cell receptors at the cell surface. It is possible to interfere with this process through premature activation of the F protein, distant from the target cell receptor. Conformational changes in the F protein and adoption of the postfusion form of the protein …

Correction: Visible-Light Photooxidation In Water By 1o2-Generating Supramolecular Hydrogels, Sankarsan Biswas, Mohit Kumar, Andrew Levine, Ian Jimenez, Rein V. Ulijn, Adam Braunschweig

Advanced Science Research Center

Correction for ‘Visible-light photooxidation in water by ¹O₂-generating supramolecular hydrogels’ by Sankarsan Biswas et al., Chem. Sci., 2020, 11, 4239–4245, DOI: 10.1039/C9SC06481H.

Polymer Brush Hypersurface Photolithography, Carlos Carbonell, Daniel J. Valles, Alexa M. Wong, Andrea S. Carlini, Mollie A. Touve, Joanna Korpanty, Nathan C. Gianneschi, Adam B. Braunschweig

Advanced Science Research Center

Polymer brush patterns have a central role in established and emerging research disciplines, from microarrays and smart surfaces to tissue engineering. The properties of these patterned surfaces are dependent on monomer composition, polymer height, and brush distribution across the surface. No current lithographic method, however, is capable of adjusting each of these variables independently and with micrometer-scale resolution. Here we report a technique termed Polymer Brush Hypersurface Photolithography, which produces polymeric pixels by combining a digital micromirror device (DMD), an air-free reaction chamber, and microfluidics to independently control monomer composition and polymer height of each pixel. The printer capabilities are …

Cu(Ii) Phenanthroline-Phenazine Complexes Dysregulate Mitochondrial Function And Stimulate Apoptosis, Garret Rochford, Zara Molphy, Kevin Kavanagh, Malachy Mccann, Michael Devereux, Andrew Kellett, Orla L. Howe

Articles

Herein we report an in-depth study on the cytotoxic mechanism of action of four developmental cytotoxic copper(II) complexes: [Cu(phen)2]2+ (Cu-Phen); [Cu(DPQ)(Phen)]2+ (Cu-DPQ-Phen); [Cu(DPPZ)(Phen)]2+; and [Cu(DPPN)(Phen)]2+ (where Phen = 1,10-phenanthroline, DPQ = dipyrido[3,2-f:20,30-h]quinoxaline, DPPZ = dipyrido[3,2-a:20,30-c]phenazine, and DPPN = benzo[i]dipyrido[3,2-a:20,30-c]phenazine). This complex class is known for its DNA intercalative properties and recent evidence—derived from an in vivo proteomic study—supports the potential targeting of mitochondrial function. Therefore, we focused on mitochondrial-mediated apoptosis related to cytotoxic activity and the potential impact these agents have on mitochondrial function. The Cu(II) complexes demonstrated superior activity regardless of aromatic extension within the phenazine ligand to the …

Sorption Of U(Vi) Onto Manganese Oxides In The Presence Of Siderophore Desferrioxamine-B, Morgan Snyder

Electronic Theses and Dissertations, 2020-2023

Anthropogenic activities, such as uranium mining and the production of nuclear energy and nuclear weapons, have led to significant uranium contamination of the environment, leaving populations vulnerable to negative health effects. In order to effectively remediate uranium contamination, the mobility of uranium in the environment and its natural attenuation through sorption with active mineral phases, needs to be studied in depth first. This study aims to determine how U(VI) mobility is affected by manganese oxides in the presence and absence of siderophore Desferrioxamine-B (DFOB). Experiments focused on two common manganese minerals, pyrolusite (ß-MnO2) and manganite (γ-MnOOH). Adsorption experiments with U(VI)-DFOB …

Quantum Biology? From Dna Point Mutations To Fibril Formation In Alzheimer Disease, Eduardo Romero Camacho

Electronic Theses and Dissertations, 2020-2023

In the '60s, Löwdin explored the realm of Quantum Biology. Löwdin defined Quantum Biology as the use of quantum mechanics to study the activity and molecular properties of biologically active molecules such as DNA, RNA, and proteins. This dissertation aims to describe molecules of biological interest such as DNA base pairs and amyloid-beta peptides and treat them using a quantum mechanical approach. We used electronic structure methods to achieve the quantum biological nature of these molecules under our computational power, tools, and techniques. In chapter 2, we present the quantum mechanical description of the spontaneous mutations in DNA base pairs …

2-(Di­Phenyl­Methyl­Idene)-2,3-Di­Hydro-1h-Inden-1-One, Tao Zhang, Vilmar Bandero, Tom Mccabe, Neil Frankish, Helen Sheridan

Articles

In the title mol­ecule, C₂₂H₁₆O, the indanone ring system is approximately planar with a dihedral angle between the fused rings of 5.13 (14)°. Two benzene rings are linked together at one side of a double bond, sitting on either side of the indanone ring system and making dihedral angles of 70.30 (12) and 44.74 (13)° with it. In the crystal, hydrogen bonding is not present, but weak C—H⋯π or π–π inter­actions occur and mol­ecules form a sheet-like structure in the bc plane.

Elephant And Anchors ‒ Photoelectron Photoion Coincidence Spectroscopy Of Small Oxygenated Molecules, Apeter Weidner

University of the Pacific Theses and Dissertations

The dissociative photoionization reactions of two small, oxygenated organics, namely 1,3-dioxolane and methyl vinyl ketone, were studied by photoelectron photoion coincidence (PEPICO) spectroscopy. Experiments involving 1,3-dioxolane were carried out in the photon energy range of 9.5‒13.5 eV. The statistical thermodynamics model shows that a total of six dissociation channels are involved in the formation of three fragment ions, namely C3H5O2+ (m/z 73), C2H5O+ (m/z 45) and C2H4O+ (m/z 44), with two channels contributing to the formation of each. By comparing the results of ab initio quantum chemical calculations to the experimentally derived appearance energies of the fragment ions, the most …

Studies On The Size And Non-Planarity Of Aromatic Stacking Moiety On Conformation Selectivity And Thermal Stabilization Of G-Quadruplexes, Mandeep Singh

University of the Pacific Theses and Dissertations

Targeting DNA has the advantage over proteins for cancer remediation because of the fewer copies of the ligands required for the desired therapeutic effect. Traditionally, covalent DNA binders like alkylating agents have been used to induce genetic instability through the formation of DNA lesions and strand breaks, leading to cellular apoptosis. The primary drawback of this treatment is the non-specific binding that affects both cancerous and non-cancerous cells. G-quadruplexes are the DNA secondary structures that are present in abundance near the promoter regions of the oncogenes and are involved in the regulation of their activities. A ligand-mediated stabilization of G-quadruplexes …

Synthesis And Thermodynamic Characterization Of Free And Surface Water Of Colloidal Unimolecular Polymer (Cup) Particles Utilizing Dsc And Tga, Peng Geng

Doctoral Dissertations

“Colloidal Unimolecular Polymer (CUP) is spheroidal nanoscale polymer particle (3-9 nm) with charged hydrophilic gruops on the surface and a hydrophobic core. The formation of CUPs involves a simple free radical polymerization and a water reduction process. CUPs are thermodynamically stable in water, molecular weight, particle size and charge density can be designed and controlled. CUPs have a layer of surface associated water, due to the small particle size, the surface water/CUP volume ratio is ultra-high. Therefore, CUP is a very promising candidate to investigate the thermodynamic of surface water characteristics. In addition, CUP solution is free of surfactant and …

Tools To Evaluate Nanodiamond-Mediated Delivery Of Tiopronin For Cataract Prevention, Justin Beltz

Doctoral Dissertations

”There is a growing demand for non-surgical means of cataract treatment. This dissertation presents three bodies of work that reflect the early-stage development of eye drop formulations aimed at delaying cataract progression. These formulations consist of the antioxidant 2-mercaptopropionylglycine (MPG) loaded onto nanodiamond particles.

Cataractogenesis is linked to oxidative damage to lens proteins. To investigate the potential of MPG for protection against oxidative damage, A549 cells were incubated in 0.6 mM tert-butylhydroperoxide (tBHP). Cells exposed to tBHP without MPG exhibited elevated levels of reactive oxygen species, which led to the depletion of the vital antioxidant glutathione and, ultimately, apoptosis. Co-administration …

Continuous-Flow Synthesis Of Fine Chemicals And Pharmaceutical Compounds Over Intelligent Organocatalysts With Bifunctional Reactivity, Abdo-Alslam Alwakwak

Doctoral Dissertations

“Many biological systems that utilize organic active sites to catalyze reactions under mild conditions invoke cooperative catalytic pathways, whereby two or more active sites work together to activate the reactant(s). The use of cooperative (bifunctional) catalysts and continuous flow chemistry (a reaction within the narrow channels of a micro‐ or microfluidic reactor) are commonplace in sustainable chemical transformation and attract a great deal of interest with respect to economic and environmentally-sustainable production of fine chemicals, pharmaceuticals, and agrochemicals, water treatment, as well as upgrading of biomass feedstocks. Although, some methods have been developed for immobilization of bifunctional catalysts for cooperative …

Structurally And Electronically Diverse Polyanion-Based Cathode Materials For Alkali-Ion Batteries, Prashanth Sandineni

Doctoral Dissertations

”Through this investigation polyanion-based cathode materials including sulfates, phosphates, and phosphites of transition metal have been synthesized for lithium and sodium-ion batteries and their electrochemical performances were evaluated. The emphasis was on soft chemical routes to discover metastable phases which are often missed in high temperature synthesis. Iron-based compounds were the main focus of this investigation, however, concurrently a few vanadium-analogues of iron compounds were investigated to evaluate the effect of multi-electron process on achievable voltage and capacity.

This investigation resulted in the discovery of several compounds with unique crystal structures, namely AFe₃(SO₄)₂(OH)_{6 …}

Transition Metal Chalcogenide Hybrid Systems As Catalysts For Energy Conversion And Biosensing, Siddesh Umapathi

Doctoral Dissertations

"Generation of hydrogen and oxygen through catalyst-aided water splitting which has immense applications in metal air batteries, PEM fuel cells and solar to fuel energy production, has been one of the critical topics in recent times. The state of art oxygen evolution reaction (OER), oxygen reduction reaction (ORR), hydrogen evolution reaction (HER) catalysts are mostly comprised of precious metals. The current challenge lies in replacing these precious metal-based catalysts with non-precious earth-abundant materials without compromising catalytic efficiency.

This research explores mixed metal selenides containing Fe-Ni, Fe-Co and RhSe which were hydrothermally synthesized and/or electrodeposited and tested for OER and ORR …

Intra- And Intermolecular Self-Assembly Of A 20-Nm-Wide Supramolecular Hexagonal Grid, Zhe Zhang, Yiming Li, Bo Song, Yuan Zhang, Xin Jiang, Ming Wang, Ryan Tumbleson, Changlin Liu, Pingshan Wang, Xin-Qi Hao, Tomas Rojas, Anh T. Ngo, Jonathan L. Sessler, George R. Newkome, Saw Wai Hla, Xiaopeng Li

Physics Faculty Publications

For the past three decades, the coordination-driven self-assembly of three-dimensional structures has undergone rapid progress; however, parallel efforts to create large discrete two-dimensional architectures—as opposed to polymers—have met with limited success. The synthesis of metallo-supramolecular systems with well-defined shapes and sizes in the range of 10–100 nm remains challenging. Here we report the construction of a series of giant supramolecular hexagonal grids, with diameters on the order of 20 nm and molecular weights greater than 65 kDa, through a combination of intra- and intermolecular metal-mediated self-assembly steps. The hexagonal intermediates and the resulting self-assembled grid architectures were imaged at submolecular …

Structural Characterization Of Emerging Synthetic Drugs, Jay Tyler Davidson

Graduate Theses, Dissertations, and Problem Reports (ETD)

The identification of well-characterized seized drugs is performed thousands of times a day in the United States; however, the expanding use of emerging synthetic drugs is creating a growing problem for both toxicological and seized drug analyses. Two of the most rapidly growing areas of emerging synthetic drugs are synthetic cathinones and fentanyl-related compounds (FRCs). In this work we demonstrate the combination of multi-stage mass spectrometry (MSⁿ), accurate mass measurements with high-resolution mass spectrometry (HRMS), and isotopic labeling for the structural characterization of synthetic cathinones and fentanyl analogs. The deliverables of this research include the identification of conserved …

Factors Influencing Huntingtin Aggregation At Surfaces: Implications For Huntington’S Disease, Sharon E. Groover

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a genetic, neurodegenerative disease characterized by an abnormal polyglutamine (polyQ) expansion in the first exon of the huntingtin protein (htt). The polyQ domain facilitates aggregation and initiates the formation of a diverse collection of aggregate species, including fibrils, oligomers and annular aggregates. The first 17 amino acids of htt (Nt17) directly flank the polyQ domain and is a key factor in htt’s association to membranous structures. In addition to Nt17 being an amphipathic αhelix, it also promotes aggregation through self-association and contains numerous posttranslational modifications (PTMs) that can modulate toxicity and subcellular localization. For in depth …