Physical Chemistry Commons^™

A Spectroscopic And Quantum Chemical Investigation Into The Noncovalent Interactions And Charge Accommodation Of Biomolecules And Their Building Blocks In Various Environments, Ashley Elizabeth Williams

Electronic Theses and Dissertations

As optical measurements have grown increasingly more precise with the rage of the technological revolution, the computer’s ability has matched in computing speed to produce accurate quantum chemical predictions of systems ranging from the atomic to multi-molecular levels. Application of spectroscopy in the investigation of the structure and function of biomolecules and their building blocks has a rich literature background, with applications among cancer research, charge transfer and energy storage, and drug design and delivery. The focus of this dissertation is thus a quantum chemical and/or spectroscopic investigation of a series of biomolecules which include the vibrational band positions of …

Carbon Dioxide And Particulate Matter Concentration On Hampton Roads Air Quality, Gregory Hubbard

OUR Journal: ODU Undergraduate Research Journal

Hampton Roads has been a maritime crossroads for the last 400 years. Industrialization has impacted the coastal region for the last 250 years. The expansion of the Port of Virginia in 2019 has created dense traffic in the region resulting in impacts to air quality. Two waste products that affect humans are particulate matter and carbon dioxide. Both respective emissions can cause adverse effects on humans, such as asthma, some lung cancers, and other respiratory distress. Scientists and health practitioners are studying the effects of particulate matter on human health. Hampton Roads, in particular, because of its unique location on …

Fluid Model Of Plasma-Liquid Interaction: The Effect Of Interfacial Boundary Conditions And Henry's Law Constants, Yifan Liu, Dingxin Liu, Jishen Zhang, Bowen Sun, Santu Luo, Hao Zhang, Li Guo, Mingzhe Rong, Michael G. Kong

Bioelectrics Publications

Plasma–liquid interaction is a critical area of plasma science, mainly because much remains unknown about the physicochemical processes occurring at the plasma–liquid interface. Besides a lot of experimental studies toward the interaction, a few fluid models have also been reported in recent years. However, the interfacial boundary conditions in the models are different and the Henry's law constants therein are uncertain; hence, the accuracy and robustness of the simulation results are doubtable. In view of this, three 1D fluid models are developed for the interaction between a plasma jet and deionized water, each of which has a unique interfacial boundary …

The Quantitative Assessment Of Pond Scum: An Examination Of The Biogeochemistry Of Phosphorus Cycling In The Belgrade Lakes, Abbey M. Sykes

Honors Theses

The internal recycling phosphorus in freshwater lake bottom sediments represents a significant source of hypolimnetic phosphorus (P) release for many of Maine’s lakes. In summer months, Maine lakes often thermally stratify and the lake hypolimnion develops anoxia, leading to a reduction in redox potential at the sediment-water interface. These reducing conditions facilitate the reductive dissolution of ferric iron, and, since phosphorus is often present in freshwater lake sediments as solid FeOOH-PO₄ complexes, results in release of soluble phosphorus into the water column. Our current study presents field and laboratory data from sediment fractionation extractions designed to quantify concentrations of …

Energy Renewal: Isothermal Utilization Of Environmental Heat Energy With Asymmetric Structures, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

Through the research presented herein, it is quite clear that there are two thermodynamically distinct types (A and B) of energetic processes naturally occurring on Earth. Type A, such as glycolysis and the tricarboxylic acid cycle, apparently follows the second law well; Type B, as exemplified by the thermotrophic function with transmembrane electrostatically localized protons presented here, does not necessarily have to be constrained by the second law, owing to its special asymmetric function. This study now, for the first time, numerically shows that transmembrane electrostatic proton localization (Type-B process) represents a negative entropy event with a local protonic entropy …

Computational Study Of Radical Cation Rearrangements, Mi'kayla D. Word

Theses and Dissertations

A radical cation is a molecule that has one unpaired electron that holds a positive charge. The unpaired electron within a radical cation causes the molecule to be reactive. The high reactivity of these species allows for radical cations to be commonly studied experimentally using mass spectrometry and other multi-mass imaging techniques. However, these methods often cannot resolve the reaction mechanisms for these fast reactions. Specifically, radical cation rearrangement mechanisms are particularly unresolved within experiments. For this reason, radical cation rearrangements are computationally investigated to explain complex reaction pathways for processes to understand reactions leading to the initiation of detonation …

Gas Phase Reactions Of Cyclopentadiene With Ch And Oh Radicals, Kacee Lynn Caster

Graduate Theses, Dissertations, and Problem Reports (ETD)

The formation of polycyclic aromatic hydrocarbons (PAHs) and carbon-based nanoparticles in combustion environments is driven by the pyrolysis and oxidation of abundant fuel molecules. The subsequent growth of these pyrolytic byproducts is then propagated by reactions with small free radical species like OH, CH, O atoms, and C₂H. Cyclopentadiene (C₅H₆) is a significant five-member combustion intermediate that has been detected in many high temperature reactions, such as in the pyrolysis of jet fuels like JP-10. Experimental and theoretical investigations in the reactions of cyclopentadiene with these small free radical species are necessary towards understanding …

Proto-Rna Synthesis Using Glycerol And Phosphate Anion, Noah Parker

Williams Honors College, Honors Research Projects

Nucleic acids are important molecules for all life, serving as the primary molecules for information storage and reproduction. RNA has long been thought to be the molecule that initiated protein synthesis. However, RNA has recently been thought to be too complex to synthesize prebiotically. Through a 1:1 mole ratio condensation of glycerol and phosphoric acid, I generated glycerol-phosphate oligomers that resemble a primitive form of the carbon-phosphate backbone of RNA. 75 mmol MgCl2 was added to some samples to see if the Mg cation could stabilize the reaction intermediates and further promote longer proto-RNA oligomers. These samples were all heated …

Environmental Modifications Of Atomic Properties: The Ground And 1s2p Excited States Of Compressed Helium, N. C. Pyper, T. C. Naginey, Colm T. Whelan

Physics Faculty Publications

Atoms remaining as recognizably distinct constituents of bulk condensed phases can have properties modified from those of the isolated species. Dense helium bubbles at high pressures are a common form of radiation damage degrading the mechanical and electrical properties of host materials. Detailed knowledge is critical for predicting their long term performance. Modifications of the ground and first singlet excited states of confined compressed helium are investigated using an entirely non-empirical theory based on the results of ab initio self-consistent field calculations with corrections for the effects of electron correlation. For finite sized portions representing bulk condensed fcc and bcc …

Synthesis Of Novel Porphyrin Derived Molecules For The Study Of Self Assembly And Photophysical Properties, Alex Nguyen

Williams Honors College, Honors Research Projects

The photochemical capabilities of self-assembling porphyrins holds the potential to eliminate the use of fossil fuels. Porphyrins have the ability to absorb solar energy to excite its electrons within the highly conjugated π system of the porphyrin ring. The excited electron can then be donated thus creating a charge separated state between the porphyrin donor and the electron acceptor. With self-assembly of porphyrin monomers into a supramolecular structure, this charge separated state can be emphasized and prolonged so the energy potential generated can be harvested. Here, the synthesis of porphyrin derivatives substituted with biologically found molecules is described. The lysine …

Solubility Critical Effects In Binary Liquid Mixture, Rosa Mauro

Summer Community of Scholars Posters (RCEU and HCR Combined Programs)

No abstract provided.

Multiple Wetting−Dewetting States Of A Water Droplet On Dual-Scale Hierarchical Structured Surfaces, Yurui Gao, Yuan Liu, Jian Jiang, Chongqin Zhu, Craig Zuhlke, Dennis Alexander, Joseph S. Francisco, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Surfaces with microscale roughness can entail dualscale hierarchical structures such as the recently reported nano/ microstructured surfaces produced in the laboratory (Wang et al. Nature 2020, 582, 55−57). However, how the dual-scale hierarchical structured surface affects the apparent wetting/ dewetting states of a water droplet, and the transitions between the states are still largely unexplored. Here, we report a systematic large-scale molecular dynamics (MD) simulation study on the wetting/dewetting states of water droplets on various dual-scale nano/near-submicrometer structured surfaces. To this end, we devise slab-water/slab-substrate model systems with a variety of dual-scale surface structures and with different degrees of intrinsic …

Comparison Of Calculated Normal Mode Molecular Vibrations With Experimental Gas-Phase Infrared Spectroscopy, Anila Renis Sutar

Dissertations and Theses

Computational vibrational spectroscopy serves as an important tool in the interpretation of experimental infrared (IR) spectra. Analysis of computational results provides a perspective over broader wavelength ranges and at higher precision. Although there are issues regarding accuracy, this can be approximated by using a scaling factor. High-resolution gas-phase FTIR spectroscopy at a resolution of 0.125 cm^-1 can partially resolve rovibrational transitions in the P, Q, and R bands and therefore identify fundamental frequencies with approximately 1 cm^-1 precision.

This research has compared high-resolution gas-phase FTIR absorption peaks to calculated vibrational frequencies. In the calculation of normal mode frequencies, …

Activity Of Saccharomyces Cerevisiae By Single Entity Electrochemistry, John Lutkenhaus

Graduate Research Posters

According to the Centers of Disease Control and Prevention, antibiotics decrease in effectiveness as bacteria gain resistance for previously treatable illnesses. Currently, antibiotic susceptibility is typically carried out via the Kirby-Bauer method. Even with automation, this process requires two incubation periods so a less time-consuming technique is desirable. Single entity electrochemistry (SEE) detects changes in current when collisions of individual particles at an ultramicroelectrode (UME) are linked with an electrochemical event. Our group has obtained step-like and spike-like responses of Saccharomyces cerevisiae at the UME surface as a result of adsorption and desorption, respectively. This response is due to the …

Using Molecular Dynamics To Characterize The Relationship Between Membrane Components And Dynamics And Supramolecular Organization Of Membrane Proteins, Eric Sefah

Graduate Theses, Dissertations, and Problem Reports (ETD)

Molecular dynamics (MD) simulations have gained impetus as a technique for elucidating structural and dynamical information about membrane proteins (MP). In particular, coarse-grained (CG) MD simulations have provided valuable information about the relationship between membrane components and supramolecular organization of MPs. In this work MD simulations are used to characterize the effects of hopanoids on bacterial membrane dynamics and association in a model protein proteorhodopsin (PR), as well as the role of the extended C-terminus of the human adenosine receptor (A_2AR) on its dimerization. PR is found to dimerize in a manner that is dependent on both the …

Huntingtin Aggregation At Interfaces Associated With Membranes And Organelles, Adewale Vincent Adegbuyiro

Graduate Theses, Dissertations, and Problem Reports (ETD)

Huntington’s Disease (HD) is a genetic neurodegenerative disease caused by the expansion of polyglutamine (polyQ) domain within the first exon (exon1) of the huntingtin (htt) protein. Due to this mutation within the polyQ domain, htt aggregates into various toxic species such as oligomers, fibrils, and other amorphous aggregates. While the aggregation of htt strongly correlates with polyQ length, other factors, e.g. interaction with membranes or organelles and posttranslational modifications (PTMs), modulate aggregation. The first 17 N-terminal amino acids (Nt17) that precede the polyQ in htt-exon1 enhances aggregation and facilitated binding of htt to membranous organelles, promoting morphological changes and disfunction. …

Photochemical Motion Control Of Belousov-Zhabotinsky Droplets And Turbulence-Like Patterns In The Aluminum Hydroxide Precipitation System, Syed Jazli Syed Jamaluddin

Graduate Theses, Dissertations, and Problem Reports (ETD)

A Belousov-Zhabotinsky (BZ) droplet that is immersed in an oil-phase can self-propel due to a surface tension gradient that exists on the droplet surface. The surface tension gradient is created as a result of the reactions that occur within and on the surface of the BZ droplet. By affecting the rates of these reactions, the BZ droplet direction can be controlled. In our experiments, we tune the reactions that occur within and on the BZ droplet surface by imposing a light intensity gradient on the droplet. We analyzed the BZ droplet motion and demonstrated that we can control the droplet …

Nanopore Detection Of Long Time-Scale Single Metallic Cluster Conformational Changes And Surface Ligand Exchange, Bobby D. Cox

Theses and Dissertations

Single molecule nanopore spectroscopy serves as an emerging tool for studying small molecules in aqueous environments without the need for additional chemical labels. Recently it has been seeing increased use as a tool for investigating small metallic nanoparticles and clusters. These clusters consist of a handful of metallic atoms (e.g. Au18) and are regularly ‘passivated’ with organic ligands to provide functionality and protect against aggregation. There has been a widening gap in research studying the surface kinetics of these passivating ligands at the single molecule level as well as during the exchange process. In this work we investigated these surface …

Determining Material Structures And Surface Chemistry By Genetic Algorithms And Quantum Chemical Simulations, Josiah Jesse Roberts

Theses and Dissertations--Chemistry

With the advent of modern computing, the use of simulation in chemistry has become just as important as experiment. Simulations were originally only applicable to small molecules, but modern techniques, such as density functional theory (DFT) allow extension to materials science. While there are many valuable techniques for synthesis and characterization in chemistry laboratories, there are far more materials possible than can be synthesized, each with an entire host of surfaces. This wealth of chemical space to explore begs the use of computational chemistry to mimic synthesis and experimental characterization. In this work, genetic algorithms (GA), for the former, and …

Plasmon Enhanced Single Molecule Fluorescence In Zero Mode Waveguides (Zmws), Abdullah Masud

Theses and Dissertations--Chemistry

Plasmonic nanostructures are an extensive research focus due to their ability to modify the photophysical properties of nearby fluorophores. Surface plasmons (SP), defined as the collective oscillation of delocalized electrons, are the fundamental characteristic primarily responsible for altering those photophysical properties. Studying fluorophores at the single-molecule level has received significant attention since more specific information can be extracted from single molecule-based studies, which otherwise could be obscured in ensemble studies. However, single-molecule studies are inherently challenging because the signal from a single molecule is usually dim, making it difficult to detect. The situation is even worse in a crowded environment …