Physical Sciences and Mathematics Commons^™

Photooxidation Reactions Of Small-Chain Methyl Esters, Aerosol Photoelectron Spectroscopy, And The Photodissociation Of Ethylenediamine, Giel Muller

Master's Theses

Research conducted at the University of San Francisco is presented within this masters thesis, including the Cl-initiated photooxidation reactions of methyl propanoate, methyl butanoate, and methyl valerate (pentanoate), the aerosol photoelectron spectroscopy of isoprene and gamma-valerolactone, and the TPEPICO investigation of ethylenediamine. Experiments were conducted at the Lawrence Berkeley National Lab Advanced Light Source (ALS), the National Synchrotron Radiation Research Center in Hsinchu City (NSRRC), and the University of Stockton in California, respectively.

Vibrational Imaging At The Nanoscale: Surpassing The Diffraction Limit Using Tip-Enhanced Raman Spectroscopy, Farshid Pashaee

Electronic Thesis and Dissertation Repository

A deep understanding of the chemical composition of surfaces, interfaces or nanoscale structure with a high spatial resolution is an important goal in nanoscience and nanotechnology. Structural information can be collected using a variety of high spatial resolution techniques such as atomic force microscopy (AFM), scanning tunneling microscopy (STM), scanning electron microscopy (SEM), or transmission electron microscopy (TEM). Nevertheless, these methods do not offer molecular information such as vibrational spectroscopy techniques that allow one to collect molecular or lattice vibrations yielding to a precise picture of the molecular interactions in bulk materials as well as in surfaces and interfaces. Unfortunately …

Understanding The Influence Of Non-Covalent Interactions And Nanoparticle Geometries In Carbon Based Polymer Nanocomposites, Bradley Carroll Miller

Doctoral Dissertations

Low-loading polymer nanocomposites (PNC) are an area of great interest in polymer science. As nanoparticles (NP) are typically expensive in comparison to matrix materials; the low loading regime makes the most efficient use of materials, and represents the optimum for realizing cost effective, high-performance PNCs. However, formulating effective low-loading composites is not without challenges. In addition to the typical requirement of good dispersion for efficient translation of NP properties to the bulk, low-loading composites can sometimes exhibit anomalous (non-classical) dynamics, and unpredictable properties. It is within this context that this thesis aims to examine the effects of NP geometry and …

Porphyrin As A Spectroscopic Probe Of Net Electric Fields In Heme Proteins, Hannah Elizabeth Wagie

Theses and Dissertations

Heme proteins have diverse functions as well as varied structures but share the same organic, conjugated cofactor. Similarly varied approaches have been taken to deduce how heme can take on different roles based on its protein environment. A unique approach is to view the protein matrix as a constellation of point charges that generates a defined, reproducible, net internal electric field that has influence over the electronic properties of the heme cofactor. This work considers how porphyrins, the basic chromophore building block of heme, can be used as a native spectroscopic sensor of internal electric field at the active site …

Bombardment Simulations And Intercalation Studies Of Carbon Materials, Charles Lowe

All Dissertations

Molecular bombardment experiments have led to the possibility of altering materials with properties not normally associated with those materials. Molecular bombardment leads to defect formation in the material, potentially creating a pore, depending on the material and bombarding molecule. Carbon allotropes, specifically graphite and graphene, make excellent candidates for molecular bombardment experimentation. Depending on the bombarding molecule and the kinetic energy associated with that molecule, the defects induced will be sufficient to create a pore in the graphene. The AIREBO potential is used to simulate a graphene bilayer being bombarded with a single Ar atom, or a fullerene molecule, to …

From Dye Sensitized Solar Cells To Organic Field Effect Transistors: A Computational Investigation Into The Structural And Electronic Properties Of Novel Phthalocyanines, Patrick J. Dwyer

Seton Hall University Dissertations and Theses (ETDs)

Phthalocyanines (Pc) have gained intense research attention in many diverse application areas due to their highly tunable electronic and structural properties through modification of the molecular periphery and metal center. Throughout this work a series of novel perfluoro-isopropyl substituted MPc have been investigated through theoretical methods. First, the synthetic mechanisms of these Pcs will be explored to gain insight into the experimentally observed Pc product distribution. By examining the electronic structure and formation energies of the various Pc precursors, we explain the product distribution as well as propose the formation of additional Pcs, which were not currently believed to form. …

Hydrogen Bond-Mediated Structural Order In Hydroxylated Bis-Mpa Dendritic Polymers: Experimental And Molecular Dynamics Simulation Study, Maliha N. Syed

Dissertations

Dendritic architectures are echoed throughout nature. While the significance of these pervasive patterns is not entirely clear, connections between their structures and physical properties are fascinating to contemplate. Particular interest has been paid to a family of synthetically manufactured and commercially available dendritic polymers based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) as a monomer. Composed of two hydroxyls and a carboxyl group, bis-MPA based structures hydrogen bond (H-bond) profusely. Given the high concentration and unique spatial orientation of end-groups, as well as the multitude of carbonyl, ester, and ether interior H-bond acceptors, a set of distinct H-bond organizations may be observed …

Photochemistry Of A Series Of Weakly Coupled Dinuclear Ruthenium(Ii) Complexes, Latisha Michelle Puckett

Graduate Theses and Dissertations

An improved synthetic method was developed for symmetric ruthenium(II) polypyridine complexes with the form L2Ru(diphen)RuL2. The scope of the reaction was investigated in regards to the ligands, bridging ligands, and starting materials. Several ligands were successful in the synthesis, including 2,2’-bipyridine (bpy), 4,4’-dimethyl-2,2’-dipyridyl (dmb), 1,10-phenanthroline (phen), 4,7-diphenyl-1,10-phenanthroline (dpphen), and 3,4,7,8-tetramethyl-1,10-phenanthroline (tmphen). Ligands that did not react to form symmetric dimeric complexes were 2,2’-bipyrazine, bpz, and 2,2’-bipyrimidine, bpm.

Dpp, 2,3-bis(2-pyridyl)-pyrazine, effectively replaced diphen as the bridging ligand to produce (phen)2Ru(dpp)Ru(phen)24+. However, replacing the [Ru(CO)2Cl2]n with Ru(DMSO)4Cl2 did not prove successful. The newly developed synthesis was also applied to the synthesis of …

Influence Of Shelling Temperature And Time On The Optical And Structural Properties Of Cuins2/Zns Quantum Dots, Colette Robinson

Graduate Theses and Dissertations

CIS/ZnS core/shell QDs are an important class of nanomaterials for optoelectronic, photovoltaic and photoluminescence applications. They consist of lower toxicity materials than the prototypical II-VI Cd-based QDs and show long fluorescence lifetimes, which generates prospective in biological imaging applications. It is vital to develop reproducible synthetic methods for this new class of nanomaterials in order to maintain small sizes with high QYs. CIS core QDs have been shelled with ZnS at various temperatures from 90-210°C for reaction times ranging from 20-140 minutes to examine the role of thermodynamics and kinetics on the shell growth. Using HR-TEM and ICP-MS, it was …

Mixed Valent Metal Pincer Complexes And Reactivity Of Metal Complexes Of Extended Pincer Ligands, Jeewantha Sampath Hewage

Dissertations (1934 -)

Historically, the study of mixed valence complexes has been critical for advancing our understanding of electron transfer processes in biological and abiological systems. The recent use of mixed valence complexes in electrochromic materials, and the promise of their use in future technological or molecular electronic applications, has spurred further interest in this class of compound. Previous studies by our research group have shown that gallium(III) or tricarbonylrhenium(I) complexes of pincer-type ligands with diarylamido anchors and either pyrazol-1-yl (pz) or diarylphosphino (PAr2) flanking donors are electroactive species with quasi reversible ligand-centered oxidations. Moreover, the one-electron oxidized derivative with pz flankers, [Ga(L)(L+)]2+ …

With Vibrationally Excited Thiophosgene Molecule And Double-Well Ion Traps, Dmytro Shyshlov

Dissertations (1934 -)

For practical realization of quantum information processing we need a quantum system that provides reliable preparation of the initial state, high-fidelity quantum gate operations, error tolerance, readout of the result of quantum computation and scalability of the system to increase the number of qubits. In this dissertation we show how these requirements can be addressed for molecular quantum computer. For computational study of quantum information processing with molecules we employ thiophosgene (SCCl2) molecule that has been used as a test system for quantum control experiments [Mol. Phys. 105, 1999 (2007)]. We investigate the gateway scheme of control in which transitions …

S-Nitrosothiols: Electronic Structure And Substituent Effects, Matthew Flister

Dissertations (1934 -)

S-nitrosothiols (RSNOs) are biologically important molecules involved in the storage and transport of nitric oxide (NO) and account for much of its signaling activity in living organisms. RSNOs have significant impact on NO signaling through, S-nitrosation, a major post-translational modification of proteins. These unstable thiol derivatives readily undergo homolytic dissociation of the S–N bond to release NO. RSNOs have potential therapeutic applications as NO donors, although the development of novel RSNOs has been slow due to the complex electronic structure of the –SNO group. A specific focus on the impact of the –R group on RSNO properties via substituent effect …

Density Functional Theory For The Investigation Of Transition Metal Complexes: Structure, Binding, And Spectroscopy Of Metal-Siderophores And The Catalase-Peroxidase Enzyme, Bonnie I. Kruft

Dissertations, Theses, and Capstone Projects

Since the development of quantum mechanics in the 1920's and with the introduction of the Schrödinger equation in 1926, various methods to solve the Schrödinger equation have evolved. With advances in these computational methods, we are now able to solve the Schrödinger equation for systems that did not seem possible less than a century ago. Density functional theory (DFT) is a valuable tool for the exploration of the molecular properties of biological systems, and is based upon the theory that the exact energy could be determined from the knowledge of the electron density. The purpose of this dissertation is to …

Dynamic Studies Of Guest Molecules In Metal-Organic Frameworks Using Solid-State Nmr, Yuanjun Lu

Electronic Thesis and Dissertation Repository

Metal-organic frameworks (MOFs) are a new class of porous materials that possess large three-dimensional voids in their structures. In this work, Solid-state NMR (SSNMR) is used to examine the dynamics of guest molecules at various temperatures in MOFs that possess different types of channels. Chapter 2 introduces the ¹³CO₂ adsorption behavior in α-Mg formate studied by ¹³C SSNMR in conjunction with molecular dynamic simulation. ¹H-¹³C cross polarization technique has successfully determined the adsorption sites of CO₂ in this type of MOF to be hydrogen atoms. The dynamic analysis detects that at low temperature, …

Case Studies Of The Hot Dog-Fold And Acyl-Adenylate-Forming Superfamilies: Characterizing The Importance Of Functional Divergence In Cellular Metabolism, Lucas Zimney

Chemistry and Chemical Biology ETDs

Some of the biggest contributors to cellular respiration (and cellular metabolism in general) are acyl-CoA derivatives, a subclass of biological thioesters. Known to function in a variety of pathways, the regulation of their formation and breakdown are critical, carried about by acyl-CoA synthetases and thioesterases, respectively. The work reported within this dissertation will focus on functional divergence within two enzyme superfamilies -- the hot dog-fold and acyl-adenylate-forming superfamilies — and can be broken down into two main parts. Part one will look at tracking the functional divergence within the hot dog-fold superfamily thioesterases. A highly evolved thioesterase, flK, has been …

Mining Public Databases For Discovery Of Structure And Function Within The Hotdog-Fold Thioesterase And Had Phosphatase Enzyme Families, Sarah Toews Keating

Chemistry and Chemical Biology ETDs

For my doctoral work, I have developed strategies to mine public databases for data that can be used to infer structural and functional information for the hotdog-fold and HADSF superfamilies. For the hotdog-fold superfamily, I used curated and automatically applied annotations of structure, taxonomic lineage, function, and subfamily membership from the UniProtKB, gene context and taxonomic information from the NCBI, and the results of several in-depth explorations of subfamily/function and structural class membership. Based on the distribution of the aforementioned annotations mapped onto a sequence similarity network (SSN), I applied structural assignments to sequences and/or specific function/subfamily assignments to ~143,000 …

Design, Synthesis And Evaluation Of Bivalent Inhibitors Of Trehalose-6-Phosphate Phosphatase, Chunliang Liu

Chemistry and Chemical Biology ETDs

The D-glucose disaccharide α, α-D-trehalose is synthesized by a variety of bacteria, fungi, plants and invertebrates to support cell survival by functioning as a fuel, a metabolic regulator or a protectant against environmental stress. Five different trehalose biosynthetic pathways are known to exist, one of which, the OtsA/OtsB pathway is common among pathogenic bacteria and fungi and is also found in parasitic nematodes. Previously reported otsA and otsB gene knockout (or knockdown) experiments have shown that both pathway enzymes are essential for M. tuberculosis cell growth and host colonization. RNAi gene silencing carried out in the nematode model system Caenohabditis …

Design And Fabrication Of Integrated Plasmonic Platforms For Ultra-Sensitive Molecular And Biomolecular Detections, Mohammadali Tabatabaei

Electronic Thesis and Dissertation Repository

One of the major challenges in analytical and biological sciences is to develop a device to obtain unambiguous chemical and structural properties of a material or a probe biomolecule with high reproducibility and ultra-high sensitivity. Moreover, in addition to such a high sensitivity, other cases such as minimum intrusiveness, small amounts of analyte, and short acquisition time and high reproducibility are key parameters that can be valued in any analytical measurements. Among the promising methods to achieve such endeavor, plasmon-mediated surface-enhanced spectroscopic techniques, such as surface-enhanced Raman spectroscopy (SERS), are considered as suitable options. Such techniques take advantage of the …

X-Ray Absorption Fine Structure Studies Of Calcium Silicate Hydrate Biomaterials In Drug Delivery, Xiaoxuan Guo

Electronic Thesis and Dissertation Repository

Calcium silicate hydrate (CSH), a new type of bioceramics, has gained significant attention in hard tissue restoration because of their impressive role in the stimulation of osteoblast proliferation and differentiation in vitro. The further development of mesoporous bioceramics opens up new opportunities for drug delivery in hard tissue therapies. In this thesis, interaction mechanisms of drug molecules with CSH of different morphologies and CSH/polymer composites, imaging of drug distributions in CSH carriers in nanoscale, and the biomineralization mechanisms of CSH in vitro during drug release are extensively investigated using X-ray absorption near edge structure (XANES) and scanning transmission X-ray …

In Situ High-Pressure Study Of Metal-Organic Frameworks And Their Performance For Co2 Storage Probed By Vibrational Spectroscopy, Yue Hu

Electronic Thesis and Dissertation Repository

Metal-organic frameworks (MOFs) are an important class of porous materials, owing to their potential applications in a variety of areas, including gas storage, molecular separations, catalysis, sensors and so on. Most importantly, their extraordinary surface areas, tunable pore properties and potential for industrial scale production have made MOFs a promising material for clean energy applications, such as CO₂ storage. The chemical and mechanical stabilities of MOFs play a crucial role in their CO₂ storage performance, which require extreme loading pressures that are far beyond ambient pressure at times. Application of high external pressure (e.g., in gigapascal range) on …

Computational Studies Of Compressed Diborane And Engineered Narrow-Gap Semiconductors, Amin Torabi

Electronic Thesis and Dissertation Repository

The research contained in this thesis is two-fold: understanding the behavior of diborane under pressure, and engineering wide-gap semiconductors in order to promote their optical eciency. Each of these themes are further explained below.

Diborane (B₂H₆), is a prototypical electron-deficient molecule and has received a great deal of attention in recent years due to its unique and peculiar structure, as well as its potential applications as a hydrogen-storage material. At high pressures, vibrational spectroscopy analysis have revealed several changes in the spectral profile that suggest occurrence of polymorphic transformations; however, the new crystal structures at high …

Correlating Morphology To Performance In Conjugated Polymer Nanocomposite Thin Films, Siddharth Pradhan

Masters Theses

The morphology and performance of thin films that consist of conjugated polymers and nanoparticles are investigated in this thesis. In the first system, the morphology of the nanocomposite that consists of low band gap alternating copolymers with a methano-fullerene are determined by neutron scattering and correlated to their photovoltaic performance as polymer solar cells. These results show that the conjugated alternating copolymers have high miscibility relative to other conjugated polymers. The analysis of the scattering data shows that the morphology of the conjugated polymer-fullerene bulk heterojunction can be described as the formation of aggregates on two length scales. Important parameters …

Morphology-Property Relationship For Binary Organic Thin Films, Alyssa Lynn Griffin

Master's Theses

Organic thin films can be readily mass-produced through solution-based fabrication methods including ink-printing and solution-casting because their light weight, flexibility, and inexpensive sources. Their applications range from organic field-effect transistors (OFET), organic solar cells (OSC), to organic light emitting diodes (OLEDs). Compared with pure component films, binary organic thin films (BOTF) allows for novel characteristics and specialized features to handle more demanding tasks. Due to the complex intermolecular interactions in BOTF, various microscopic phases with different morphological and electronic properties may be formed and this information is difficult to extract through conventional bulk measurements.

Organic thin films can be readily …

Complementary Mass Spectrometry Methods For Characterizing Protein Folding, Structure, And Dynamics, Siavash Vahidi

Electronic Thesis and Dissertation Repository

Proteins are involved in virtually every biochemical process. A comprehensive characterization of factors that govern protein function is essential for understanding the biomedical aspects of human health. This dissertation aims to develop complementary mass spectrometry-based methods and apply them to solve problems pertaining to the area of protein structure, folding and dynamics.

‎Chapter 1 uses fast photochemical oxidation of proteins (FPOP) to characterize partially disordered conformers populated under semi-denaturing conditions. In FPOP, ·OH generated by laser photolysis of H₂O₂ introduces oxidative modifications at solvent accessible side chains. By contrast, buried sites are protected from radical attack. Using …

Transition Metal-Olefin Bonding Interactions: A Density Functional Theory Study [ M ( Co ) X ( Æ? 2-C 2 H 3-C 6 H 4-Y) ], Michael John Berninger

Theses and Dissertations

Metal-olefin equilibrium geometries, bond formation energies (Î?E), enthalpies (Î?H), and free energies (Î?G) for a select series of transition (M = Ni, Fe, Cr, Mo and W) metal-olefin carbonyl complexes [M(CO)x(Æ?2-C2H3-C6H4-Y)] have been calculated and compared using density functional theory (DFT), with the BP86 functional under standard state conditions (1 atm, 298.15 K) for the general gas phase formation reaction:

M(CO)x + (C2H3-C6H4-Y) â?? [M(CO)x(Æ?2-C2H3-C6H4-Y)] (1)

Y = NO2, CN, COOH, H, OH, NH2, N(CH3)2

In regards to the electronic modification of the substituent (Y) on styrene at the para position, this study quantitatively investigated the effect of electron-withdrawing and …

From Solution Into The Gas Phase: Studying Protein Hydrogen Exchange And Electrospray Ionization Using Molecular Dynamics Simulation, Robert G. Mcallister

Electronic Thesis and Dissertation Repository

Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in …

The Quantum Efficiency Of Cdse Semiconducting Nanocrystals, Charles Bledsoe

Undergraduate Theses

CdSe molecules are semiconducting nanocrystals that absorb visible light and emit broad wavelengths of light in response. They utilize electromagnetic radiation not only for emitting broad wavelengths of visible light, but for fluorescence, conducting electricity, and vibrational relaxation. The Thermal Lensing technique (TL) can be used to study the lifetimes of the excited state transitions and the various nonradiative processes molecules can undergo in order to better understand the excited state dynamics of semiconducting nanocrystals, and in turn, better understand how these molecules may be applied in solar cells, lasers, and fluorescence labeling. Using known methods, four samples of CdSe …

Fundamental Studies Of Magnetoconvective Forces And Density Gradients In A Microfluidic Environment, Adam James Kreidermacher

Graduate Theses and Dissertations

Magnetoconvection is a promising phenomenon for developing new electrochemical-based microfluidic flow devices with unique capabilities, such as easily switching flow direction and adjusting flow speeds and flow patterns as well as avoiding bubble formation. In order to develop these devices it is necessary to study the underlying forces. Four contributions toward fluid flow were considered. The first and foremost is the magnetohydrodynamic force, which is the magnetic component of the Lorentz force and governed by the right hand rule. It generates the majority of the convention, and is the most well-known. The second is the gravitational force, which causes convection …

A Lego® Brewster Angle Microscope For Quantitative Monolayer Film Analysis, Nicholas Benz

Physics

In order to study single-molecule thick films and their phase behavior we built a Brewster Angle Microscope (BAM). BAM’s are inherently expensive due to their accuracy and precision. We built a fully functional BAM using Lego® Mindstorm® kits for the fraction of the price of a commercial BAM. And by utilizing the 10µm patented Lego® tolerance, comparable accuracy was attained. The BAM was mounted to a Langmuir-trough and will be used for laboratory experiments for optics and physical chemistry along with research on lung surfactant and on liquid crystals.

Surface Modification Of Noble Metal Nanostructures Toward Biomedical Applications, Samir V. Jenkins

Graduate Theses and Dissertations

Noble metal nanostructures have seen a steady increase in biomedical application over the last several decades; new diagnostic and therapeutic modalities are under intense investigation. Many of these applications are possible because of post-synthetic modifications to the particle surface. These modifications take a variety of forms and can significantly affect the pharmacokinetics of these particles. In this work, various surface modifications were investigated. Particle agglomeration, which occurs when particle surfaces remain in contact, can significantly affect the toxicity and efficacy of a nanomedicine. Darkfield microscopy and single-particle ICP-MS were developed as complementary methods to detect agglomeration in blood, with the …