Physical Sciences and Mathematics Commons^™

Elucidating The Pd Active Sites Of Bimetallic Gold-Palladium Catalysts Using Chemisorption And Titration Techniques, Andrew T. Boucher

Electronic Theses and Dissertations

A bimetallic nanoparticle catalyst combines two different metals on an oxide support, which can increase the selectivity towards useful products that may be too tightly bound to a monometallic catalyst. To explore the surface properties of such a system, we made a group of four PdAu bimetallic catalysts with varying gold mass loadings to compare with a parent Pd catalyst. The parent catalyst was synthesized using ion exchange, and gold was added to this parent Pd catalyst using incipient wetness impregnation (IWI) to create four bimetallic catalysts. All catalysts were characterized using H₂ and CO chemisorption in tandem with …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

The Investigation Of Singlet Fission From The Perspective Of Hierarchy Of Pure States (Hops), Tao (James) Chen

Chemistry Theses and Dissertations

This thesis provides a preliminary investigation of singlet fission from the perspective of Hierarchy of pure states (HOPS), which provides a numerical exact solution for the investigation of a series of open quantum systems. Since the inception of the concept of singlet fission about half a century ago, this photo-physical process has attracted the attention of a multitude of researchers and has been extensively studied theoretically and experimentally. However, these previous methods for the investigation of singlet fission focus more or less on tackling the underlying mechanisms of singlet fission from the perspective of perturbation. So far, the HOPS method …

Modeling Excited State Processes In Molecular Aggregates By Constructing An Adaptive Basis For The Hierarchy Of Pure States, Leonel Varvelo

Chemistry Theses and Dissertations

Simulating excitation energy transfer (EET) in molecular materials is of crucial importance for the development of and understanding of materials such as organic photovoltaics and photosynthetic systems and further development of novel materials. The Hierarchy of Pure States (HOPS) is an exact framework for the time evolution of an open quantum system in which a hierarchy of stochastic wave functions are propagated in time. The adaptive HOPS (adHOPS) method achieves size-invariant scaling with the number of simulated molecules for sufficiently large aggregates by using an adaptive basis that moves with the excitation through the material. To demonstrate the power of …

Acetylacetone Oxidation At Room Temperature: A Multiplexed Photoionization Mass Spectrometric Investigation, Study Of The Russell Intermediates In Gas Phase Reactions, And The Investigation Of Oxidation Reaction Products Of Ethanol At Room Temperature, Sara Gallarati

Master's Theses

This thesis presents the combustion study of acetyl acetone using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at 298 K. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The reaction of acetyl acetone with chlorine (Cl) radicals was analyzed based on their photoionization spectra and reaction kinetic profiles.

Additionally, a study of the Russell intermediate has been performed. Previous to experimentation at the Advanced Light Source, computational analysis has been investigated to evaluate compounds that could possibly lead to the formation of a stable species. The …

Unraveling Molecular Mechanisms Of Antibiotic Resistance Through Multiscale Simulations And Explainable Machine Learning, Zilin Song

Chemistry Theses and Dissertations

Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation …

Gas-Phase Acid-Base Properties And Conformations Of Oligopeptides Through Mass Spectrometry And Computational Studies, Yuntao Zhang

University of the Pacific Theses and Dissertations

This dissertation presents a comprehensive study of the peptides of interest to deeper understand the gas-phase acid-base properties in relation to their conformations and chirality. In the first part of the study, two pairs of alanine (A)-based isomeric peptides consisting of a basic probe, lysine (Lys) or 2,3-diaminopropionic acid (Dap), were investigated to understand the nature of the enhanced basicity when the basic probe was moved from the N-terminus to the C-terminus. In the second part of the study, alanine-based peptides containing a cysteine (C) as the acidic probe were investigated to understand the chirality effects on the gas-phase acidity …

From Small Molecules To Infinite Crystals: Probing Noncovalent Interactions Through Vibrational Spectroscopy, Sadisha Nanayakkara

Chemistry Theses and Dissertations

During my four years in the CATCO group supervised by Dr. Kraka, I have been exposed to various topics targeted to address a multitude of chemical problems, broadening our knowledge of modern chemistry research as we know it. In undertaking the age-old problem of understanding the nature of chemical bonding, I could modestly contribute with my work, using in-house tools based on vibrational spectroscopy.

First part of my dissertation is focused on inventing new methods and tools to efficiently investigate chemical bonding, followed by the study of some non-covalent interactions, imperative in catalysis and solid-state chemistry. This includes analysis of …

Quantum Chemical Investigation Of Novel Noncovalent Interactions Utilizing Vibrational Spectroscopy, Seth Francis Yannacone

Chemistry Theses and Dissertations

Theoretical/computational methods have been utilized to investigate a diverse array of questions currently at the forefront of modern chemistry research. The focus of this work is Local Vibrational Mode (LVM) Theory, originally formulated by Konkoli and Cremer, and under continuous development by the CaTcO research group. Derived from LVM theory, local stretching force constants (ka) represent physically meaningful measurements of chem- ical bond strength. Decomposition of normal vibrational modes into LVM contributions, also called characterization of normal modes (CNM), is another powerful manifestation of LVM theory; most notably when applied to the analysis of theoretical/experimental IR/Ra- man spectra. Recent developments …

Small Molecule Activation By Transition Metal Complexes: Studies With Quantum Mechanical And Machine Learning Methodologies, Justin Kyle Kirkland

Doctoral Dissertations

One of the largest areas of study in the fields of chemistry and engineering is that of activation of small molecules such as nitrogen, oxygen and methane. Herein we study the activation of such molecules by transition metal compounds using quantum mechanical methods in order to understand the complex chemistry behind these processes. By understanding these processes, we can design and propose novel catalytic species, and through the use of data-driven machine learning methods, we are able to accelerate materials discovery.

Indolizine Donor-Based Dyes For Applications In Fluorescence Biological Imaging, William Meador

Honors Theses

NIR emissive fluorophores are intensely researched due to their potential to replace modern imaging procedures. Many molecular strategies have been employed in the literature to optimize fluorophores for deeper NIR absorption and emission, biocompatibility, and higher fluorescence quantum yields. Amongst the fluorophores studied to date, proaromatic indolizine donors are attractive alternatives to traditional alkyl amine and indoline based donors due to their 1) lower energy absorption and emission facilitated by proaromaticity, 2) large Stokes shifts due to increased dihedral angles about the π-system, 3) ease of functionalization and capacity for bioconjugation at the phenyl ring, and 4) potential for further …

Breakthroughs In Obtaining Qm/Mm Free Energies, Phillip S. Hudson

USF Tampa Graduate Theses and Dissertations

The computation of free energy is pivotal to understanding the fundamental nature of chemical phenomena. That is, whether a specific molecular outcome occurs spontaneously or is inherently unfavorable. The need to do this with consistent accuracy begs for the use of quantum mechanical (QM) methods. However, techniques for directly computing free energy differences with QM or mixed QM/MM methods are untenable, as the computational expense is quite exorbitant. At present, the most feasible approach for obtaining QM/MM free energies is employing the so-called indirect cycle, which relies on accurately computing free energy differences between low (e.g., molecular mechanical, MM) and …

Evaluation Of The Mechanisms And Effectiveness Of Nano-Hydroxides, Wood And Dairy Manure-Derived Biochars To Remove Fluoride And Heavy Metals From Water, Anna Rose Wallace, Wenjie Sun Dr, Chunming Su Dr

Civil and Environmental Engineering Theses and Dissertations

The development of effective treatment processes for the removal contaminants, such as fluoride and heavy metals, from polluted water have been urgently needed due to serious environmental health and safety concerns. In this dissertation, a variety of materials including various (hydro)oxide nanomaterials, biochars and surface modified biochar were studied to evaluate their effectiveness and mechanism on removing fluoride or mixed heavy metals from water.

In the Chapter 2, this study investigated the adsorptive removal of fluoride from water using various (hydro)oxide nanomaterials, focusing on ferrihydrite, hydroxyapatite (HAP) and brucite, which have the potential to be used as sorbents for surface …

Roaming Transition States And Highly Accurate Thermochemistry: A Pepico Study Of Two Small Combustion Systems, Kyle John Covert

University of the Pacific Theses and Dissertations

Two small combustion systems, methyl hydroperoxide (CH₃OOH) and 2-propanol ((CH₃)₂CHOH), were studied using imaging photoelectron photoion coincidence spectroscopy (iPEPICO), which combines photoelectron spectroscopy and photoionization mass spectrometry to detect coincident photoelectron-photoion pairs. In the photon energy range of 11.4–14.0 eV, energy selected CH₃OOH⁺ ions dissociate into CH₂OOH⁺, HCO⁺, CH₃⁺, and H₃O⁺ ions. The lowest-energy dissociation channel is the formation of the cation of the smallest “QOOH” radical, CH₂OOH⁺. A statistical rate model fitted to the …

Steric Effects Of Alkyl Ammonium Salts On The Combustion Of Exchanged Smectite Clays, Celeste A. Keith

Electronic Theses and Dissertations

Bomb calorimetry was explored as a new method for determining the cation exchange capacity (CEC) of clays. Smectite clays were modified with several alkyl ammonium salts varying in number of carbons and the spatial orientation of the carbons about the central nitrogen atom. The clays used, standards purchased from the Source Clay Repository, have CECs of 44, 80, 88, and 120 meq/100 g. Theoretically, the combustion energy of the organo-clays should be approximately the same for each salt. Any differences in energy would be due to the different structures of the salts and how they are oriented in the interlamellar …

Advances In Local Vibrational Mode Theory And Unified Reaction Valley Approach (Urva), Yunwen Tao

Chemistry Theses and Dissertations

Since the establishment of the Local Vibrational Mode Theory and the Unified Reaction Valley Approach (URVA), these two research pillars have been pushed forward in the CATCO group and played an important role in (i) characterizing the chemical bonds in molecules and (ii) molecular chemical reactions. This dissertation elaborates my contributions to the Local Vibrational Mode Theory and the Unified Reaction Valley Approach (URVA).

We have applied the Local Vibrational Mode Theory to hydrogen bonding in liquid water and proposed an explanation for the Mpemba effect. We explored and discovered new directions of applying local vibrational modes majorly in characterizing …

Multi-Reference Systems In Chemistry; Unconventional Bonding In Organic Chemistry; Covalent Bonding In Transition Metal Clusters, Alan Wilfred Humason

Chemistry Theses and Dissertations

The geometries, chemical properties, and reactivities of molecules are determined by their electronic structure. The field of ab initio computational chemistry works to calculate the kinetic and potential energies between the nuclei and electrons of a molecule. These calculations usually begin with the determination the electronic ground state.

Molecules that cannot be adequately described with a single, ground state configuration are called \textit{multi-reference systems}, which require the calculation of a linear combination of all pertinent electronic configurations, with a corresponding increase in computational cost. This is not `black box' methodology, because solving these systems requires a good understanding of the …

From Flasks To Applications: Design And Optimization Of Giant Quantum Dots Using Traditional And Automated Synthetic Methods, Christina J. Hanson

Nanoscience and Microsystems ETDs

Semiconducting nanocrystals, also known as quantum dots (QDs), that emit light with near-unity quantum yield and are extremely photostable are attractive options as down-conversion and direct electricity-to-light materials for a variety of applications including solid-state lighting, display technologies, bio-imaging and optical tracking. Standard QDs with a core/thin shell structure display fluorescence intermittency (blinking) and photobleaching when exposed to prolonged room temperature excitation for single dot measurements, as well as significant reabsorption and energy transfer when densely packed into polymers or at high solution concentrations.

We have developed thick shell “giant” QDs (gQDs), ultra-stable photon sources both at the ensemble and …

Quantum Chemical Studies Of Noncovalent Interactions And Multicenter Bonds Utilizing Local Vibrational Modes, Vytor Oliveira

Chemistry Theses and Dissertations

Noncovalent interactions play an important role for the design of novel drugs, better catalysts, synthesis of complex supramolecular structures, and so on. To develop new materials, a well-founded knowledge of how to control the strength of these interactions is desirable. Despite the many investigations done so far, a quantitative assessment of the intrinsic strength of most types of noncovalent interactions is still missing. Recently and for the first time, the Konkoli-Cremer local modes analysis was successfully used to probe the intrinsic strength of hydrogen and pnicogen bonds. We extended these investigations to more than 300 halogen and chalcogen bonds. A …

Interactions Of The Naphthalene Radical Cation With Polar And Unsaturated Molecules In The Gas Phase, Sean P. Platt

Theses and Dissertations

Characterizing the interactions of solvent molecules with ions is fundamental in understanding the thermodynamics of solution chemistry. These interactions are difficult to observe directly in solution because the number of solvent molecules far exceed that of ions. This lend the gas phase to be the ideal medium in the study ion-solvent interactions on a molecular level. Ionized polycyclic aromatic hydrocarbon (PAH) molecules can readily form hydrogen bonds with neutral solvent molecules in aqueous and interstellar medium. Previous research has been done for stepwise solvation of small molecules such as benzene⁺, pyridine, and phenylacetylene. The similarity in these results …

The Role Of Organic Matter In The Surface Chemistry Of Arsenic Compounds On Iron−(Oxyhydr)Oxides Studied By Atr-Ftir, Arthur Situm

Theses and Dissertations (Comprehensive)

The interaction of organic matter with the interfaces of active soil components such as iron oxides is ubiquitous within soil environments. The presence of organics at these interfaces may have implications for other soil constituents whose mobility is controlled by their ability to bind to active soil components. Most of the studies performed to date which look at these interactions are bulk/batch studies performed ex-situ. Attenuated total internal reflectance Fourier transform infrared spectroscopy (ATR-FTIR) was utilized within this work to study interactions between select model organics (citrate, oxalate and pyrocatechol) and iron−(oxyhydr)oxides, as well as their effect on the surface …

Kinetic Decay Of A Polymer/Ink Complex As An O2 Indicator, Becca Hoene

All Master's Theses

Indicator inks are an important part of the continued consumption of packaged goods. This thesis is focused on understanding the kinetics and reaction mechanism for a unique indicator ink that is based upon the oxidation of indigotetrasulfonate (ITS) encapsulated in the polyelectrolyte poly(diallyldimethylammonium chloride) (polyDADMAC). Sodium bisulfite (NaHSO₃) was used as the initial oxygen scavenger and to drive the reduction of the ITS. Studies were predominantly done in solution phase through the dilution of the ink systems. Fluorescence spectroscopy was the primary method used to determine the kinetic decay rates and interaction between the ITS dye molecules and …

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 …

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 …

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 …

Hindered Rotation Of Dihydrogen On Synthesized Metal Oxides, George Houston Rouvelas

Masters Theses

A MATLAB program was written to calculate the hindered rotational energies of the hydrogen and deuterium molecules interacting with an anisotropic potential, which may be thought of as a potential energy surface of a metal oxide substrate. It was found that an increase in the hindering potential of the rotation about the azimuthal angle lifted the degeneracy of the j = 1,mj [magnetic quantum number] = plus or minus 1 states. A better understanding of how the rotational states of these systems change as a function of the hindering potential can help to explain features in rotational inelastic neutron scattering …

Exploration Of Aqueous Interfaces And Their Effect On Ion Behavior, Oneka T. Cummings

Doctoral Dissertations

An in-depth understanding of a wide range of physical, chemical, atmospheric and biological processes can only be achieved after the structure and dynamics of interfaces and the interfacial behavior of aqueous species, such as ions, are thoroughly studied and understood. This dissertation describes computational studies conducted to gain a more comprehensive understanding of such interfaces and the behavior of ions in the bulk and interfacial regions of the (1) air/water interface, and (2) alkane/water interfaces.

At the air/water interface the effect of counterion (sodium cations) charge and the influence of ion pairing on anion (chloride) propensity for the air/water interface …

Controlling Nanoparticle Dispersion For Nanoscopic Self-Assembly, Nathan S. Starkweather

Master's Theses

Nanotechnology is the manipulation of matter and devices on the nanometer scale. Below the critical dimension length of 100nm, materials begin to display vastly different properties than their macro- or micro- scale counterparts. The exotic properties of nanomaterials may trigger the start of a new technological revolution, similar to the electronics revolution of the late 20^th century. Current applications of nanotechnology primarily make use of nanoparticles in bulk, often being made into composites or mixtures. While these materials have fantastic properties, organization of nano and microstructures of nanoparticles may allow the development of novel devices with many unique properties. …

Multi-Configurational Investigation Of Thermolytic Pathways Of Highly Strained Ring Systems, Jeffrey Dwayne Veals

Electronic Theses and Dissertations

The isomerization pathways of model high energy structures are of interest because of their relation to high energy density fuels. Electron resonance has been found to greatly affect the relative activation barriers for several isomerization pathways, and the major goal of this research is to accurately describe its role in determining the relative barriers for strain energy release pathways. This research is centered around the potential energy surfaces (PES's) for ? bond breaking and ? bond rotation in these highly strained structures. Of particular interest was how would resonance and or electronegativity affect the allowed/disallonature of the activation barriers in …

A Kinetic Analysis Of The Iodination Of Pyruvic Acid And Pyruvate Esters, Mohamed M. Fahmi Hegazi

All Master's Theses

In the present work the relative rates of iodination of pyruvic acid and ethyl and methyl pyruvate have been compared at 25.0° C. These studies allow the determination of the respective free energies of activation for these processes. Measurements have also been carried out at various temperatures to determine the enthalpies and entropies of activation for the spontaneous and base catalysed iodinations of these pyruvate systems. The present thesis also includes a comparison of the solvent deuterium isotope effects associated with the spontaneous rate of iodination of pyruvic acid and the alkyl pyruvates. Also, the catalytic rate coefficients associated with …