Physical Chemistry 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 …

Contributions Of Tunneling In 8Π-6Π Electrocyclic Cascade Reactions Of Bicyclo[4.2.0]Octa-2,4-Diene Moieties, Ishika Jain, Claire Castro, William L. Karney

Featured Student Work

Six-electron electrocyclic reactions usually require relatively high temperatures; however recent research has shown that such reactions can occur at significantly lower temperatures in biosynthetic and biomimetic pathways. Pathways resulting in bicyclo[4.2.0]octa-2,4-diene moieties arise from thermally allowed 8π-6π electrocyclization cascade reactions of 1,3,5,7-octatetraenes, as in the biosynthesis of endiandric acids, elysiapyrones, and numerous other natural products. We report multidimensional tunneling calculations to explore the possible contribution of heavy-atom tunneling (e.g. by carbon) to biosynthetic pathways and biomimetic syntheses, and thus to provide a more complete picture of biochemical kinetics. M06-2X/cc-pVDZ calculations on the 8π-6π cascade cyclizations of methylated octatetraene model systems …

Phosphorus And Its Role In Chemical Evolution, Asbel Gonzalez

PANDION: The Osprey Journal of Research and Ideas

Phosphorus is a minor element with a cosmic abundance of about 105.5 atoms per 1012 H atoms (Boudreaux, n.d.). Phosphorus was depleted as a volatile throughout the developing solar system, and as a result, volatile forms of phosphorus would have been minimal, even in the colder regions of the solar nebula. Despite its low abundance, phosphorus minerals play key roles in planetary petrology, including through the formation of phosphate minerals that trapped volatiles and rare Earth elements, and in the formation of metal phosphides that may have served as nucleation sites for kamacite and taenite crystal growth in minor planet …

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 …

Physical And Chemical Changes Lesson Plan, Admin Stem For Success

STEM for Success Showcase

Lesson plan and video for an activity on the difference between physical and chemical changes.

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 …

Novel Technique In Production Of Pb (Ii)- Imprinted Polymers, Ehab Mohammed, Mostafa M. Elsheikh, Adham A. El-Zomrawy, Farag A. Ahmed

Al-Azhar Bulletin of Science

Ion imprinting techniques were used to produce ion imprinted polymer (IIP) particles for the selective removal of Pb2+ from aqueous environments. As the Templating monomers, acrylic acid, acrylic amine ligand, and Methylene Bisacrylamide crosslinker were chosen. The imprinted polymer was prepared by free radical polymerization. By leaching with 0.1 M HCl, the (Pb2+) ion was removed from the template. The polymer particles were characterized by IR spectroscopy, Thermal analysis and potentiometric analysis. The produced polymer was mechanically crushed into fine particles, assembled into a sensor probe, and linked to a bare HB graphite pencil electrode (GPE). The sensor has a …

Enhanced Adsorption Of Anionic Dyes Using Sr-Doped Zno Nanoparticles: Nonlinear Kinetics And Isotherm Studies, Mostafa H. Mohamed, Taha M. Elmorsi, H. M. Abdelbary

Al-Azhar Bulletin of Science

Using a co-precipitation process, sr-doped ZnO was prepared and demonstrated to be effective in the removal of anionic congo red dye, since its surface positive charge was increased to 17.3 mV. To investigate the surface morphology and physicochemical characteristics of Sr-doped ZnO, FTIR spectroscopy, scanning electron microscopy (SEM), elemental analysis, and point of zero charges (pHPZC) were employed. We conducted batch adsorption experiments to investigate the effects of contact time (180 minutes), pH (3.5–11), adsorbent dosage (0.5–3.0 g L−1), and temperature (288–328 K). The kinetic study was modeled using several equations, including pseudo-firstorder (PFO), pseudo-second-order (PSO), Elovich, and intra-particle diffusion …

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 …

Physical Chemistry, Ruth E. Stark

Open Educational Resources

This is a provisional syllabus for Physical Chemistry I (Thermodynamics), to be taught using an OER Textmap in Fall, 2021.

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 …

The Statue Of Liberty Laboratory Activity: The Chemistry Of Copper, Jihyun Kim, Marcus D. Allen

Open Educational Resources

In this lab activity we observe chemical changes of copper in acidic conditions, salt water, and a mixture of lemon juice and vinegar and salt, and we discuss whether the Statue of Liberty would hold as much cultural icon today had the Lady Statue remain the original shiny brown color.

Visualization Without Vision – How Blind And Visually Impaired Students And Researchers Engage With Molecular Structures, Croix J. Laconsay, Henry B. Wedler, Dean J. Tantillo

Journal of Science Education for Students with Disabilities

This article examines the tools and techniques currently available that enable blind and visually impaired (BVI) individuals to visualize three-dimensional objects used in learning chemistry concepts. How BVI individuals engage with and visualize molecular structure is discussed and recent tactile (or haptic) and auditory methods for visualization of various chemistry concepts are summarized. Remaining challenges for chemistry education researchers are described with the aim of highlighting the potential value of educational research in further enabling BVI students to pursue careers in science, technology, engineering, and mathematics (STEM) fields.

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 …

Stimuli-Responsive Gelators From Carbamoyl Sugar Derivatives And Their Responses To Metal Ions And Tetrabutylammonium Salts, Dan Wang, Anji Chen, Joedian Morris, Guijun Wang

Chemistry & Biochemistry Faculty Publications

Carbohydrate-based low molecular weight gelators (LMWGs) are interesting compounds with a variety of applications. In this research, a library of nineteen carbamate derivatives of N-acetyl-D-glucosamine were synthesized and characterized, and several derivatives were found to be effective LMWGs. They formed gels in pump oils as well as mixtures of water with ethanol or water with DMSO. The structures of the carbamoyl chains played an important role in the gelation properties, short chain aliphatic derivatives and phenyl carbamates formed gels in more solvents than certain aromatic and dimeric carbamates. The phenyl carbamate gelator was also selected for the encapsulation of …

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 …

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

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 …