Physical Sciences and Mathematics Commons^™

Gene Vectors With Fluorescence Tracking Capabilities, Sophia Despina Angelopoulos

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This project focuses on the optimization of benzothiazole-based chromophores to utilize them as fluorescent tags functionalized onto stimuli-responsive, or “smart,” polymers as non-viral gene delivery vectors for gene therapy applications. Blue-fluorescent emissive chromophores will allow tracking capabilities for the transfection pathway of the vector to be monitored as it delivers the DNA payload within intercellular space. The most appropriate chromophore must be covalently bound to a free amine within the vector, which is accomplished through NAS chemistry from fluorophenyl-benzothiazoles (F-BTZ-CBz) derivatives to amidated hyperbranched poly(ethyleneimine)(HPEI-IBAm0.61). HPEI is considered to be a synthetic polycation, which promotes tunable solubility through characteristics of …

Conversation Among Physical Chemists: Strategies And Resources For Remote Teaching And Learning Catalyzed By A Global Pandemic, Andrea N. Giordano, David Gardner, William W. Kennedy, Chrystal D. Bruce

2021 Faculty Bibliography

In the midst of a global pandemic in spring 2020, physical chemistry faculty gathered to share strategies and resources for teaching remotely. During this conversation, instructors created a shared document compiling the challenges they faced in spring 2020 and ways to improve teaching and learning in the physical chemistry classroom and laboratory when institutions reopened in the fall. We present a content analysis of the shared document that provides a snapshot of physical chemists’ thoughts at that moment in June 2020. The themes that emerged from our analysis are assessment, choice of learning objectives, course management, opportunities, resources, student motivation, …

Raman Spectroscopic And Quantum Chemical Investigation Of The Effects Of Tri-Methylamine N-Oxide (Tmao) On Hydrated Urea, Hydrated Guanidinium, And Hydrogen Bonded Networks, Genevieve Verville

Honors Theses

Trimethylamine N-Oxide (TMAO), guanidinium, and urea are three important

osmolytes with their main significance to the biophysical field being in how they

uniquely interact with proteins. TMAO is known to stabilize and counteract the

destabilizing effects of both urea and guanidinium. The exact mechanisms by which

TMAO stabilizes and both guanidinium and urea destabilize folded proteins continue

to be debated in the literature. Some studies suggest that solvent interactions do not

play a large role in TMAO’s stabilizing effects and therefore advocate direct

stabilization, whereas others suggest that TMAO counteracts denaturation primarily

through an indirect effect of strong solvent interactions. …

An Investigation Into The Molecular Dynamics Of The Laser Induced Dissociation Of 2-Bromoethanol, Kirk French

Senior Honors Theses

The unimolecular dissociation of 2-bromoethanol is investigated using computational chemistry methods both to test the reliability of the theories and methods of computational chemistry and to explore the internal mechanism of the dissociation. The dissociation of the bromine ion from 2-bromoethanol was experimentally observed in a previous publication by Ratliff et. al. These experimental results were compared in this thesis to computational calculations of their research. The method of TD-B3LYP proved to be inadequate in this venture except for the lowest energies of the most stable conformer of 2-bromoethanol. However, interesting mechanisms were found such as the formation of HBr …

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 …

Quantum Chemical Pka Estimation Of Carbon Acids, Saturated Alcohols, And Ketones Via Quantitative Structure-Activity Relationships, Corey Adam Baldasare

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Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final …

The Analysis Of Trifluoromethylbenzimidazole (Tfmbi) Crystals Using Physical Chemistry Techniques To Explain Ferroelectric And Anti-Ferroelectric Properties Of The Compound, Kanwar Bhullar

Honors College Theses

Ferroelectrics are a group of materials possessing the unique chemical property of being able to switch their electrical polarity when exposed to an electric field. This property makes ferroelectrics a promising field of study with the potential to impact various future technologies in information and energy storage, as well as quantum mechanics. Understanding molecular structures of ferroelectric (and opposite anti-ferroelectric) materials, and how they relate to the compound’s properties is essential to harnessing the potential these materials carry. The report discusses analysis of anti-ferroelectric material trifluoromethylbenzimidazole (TFMBI), by subjecting the compound to various physical and computational chemistry techniques at varying …

Using Forensics To Introduce Ir Spectroscopy & Molecular Modeling, Joseph T. Golab

Faculty Publications & Research

A student activity is reported that analyzes “medical evidence” with experimental and computational methods. The lesson demonstrates benefits of solving practical problems with integrated tools.

Using In Situ Liquid Single Photon Ionization Mass Spectrometry (Spi-Ms) To Probe Lithium Polysulfide Electrolyte In Motion, Aala M. Al Hasan, Jiachao Yu, Juan Yao, Vijayakumar Murugesan, Manjula Nandasiri, Xiao-Ying Yu

STAR Program Research Presentations

The solid-liquid (s-l) interface is the most common interface encountered in electrochemical systems. The s-l interface has wide applications in energy storage, catalysis, and material sciences. In situ studies of chemical reactions taking place on the s-l interfaces can further our understanding of electron transfer and link to real-world device functions under challenging conditions. Direct probing of the solid electrode and liquid electrolyte interface has been realized using a vacuum compatible electrochemical microfluidic reactor, system for analysis at the liquid vacuum interface (SALVI) with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Most recently, the electrochemical version of SALVI was integrated to …

Mining Uranium From Seawater: A Coordination Chemistry Approach, Nada Mehio

Doctoral Dissertations

Poly(acrylamidoxime) fibers are the current state-of-the-art adsorbent for mining uranium from seawater. However, the amidoxime group is not perfectly selective towards the uranyl cation, in particular, competition with transition metal cations remains a major challenge. In order for subsequent generations of chelating polymer adsorbents to be improved, the coordination chemistry of amidoxime-uranyl and -transition metal cation complexes needs to be better understood. While the coordination mode of amidoxime-uranyl complexes has been established in the literature, a number of amidoxime-transition metal cation complex binding motifs can be observed on the Cambridge Structrural Database. Likewise, the formation constants, or log K values, …

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 …

Excited State Proton Transfer In 9-Aminoacridine Carboxamides In Water And In Dna , Charles Andrew Smith

Charles Kay Smith

The 9-aminoacridine molecule is important in several different fields of chemistry. The absorption and fluorescence spectra of this compound are pH sensitive and it is this property that allowed it to be used as a pH probe in different chemical environments. The compound exhibits proton transfer reactions which are among the most fundamental of chemical reactions. The planarity of 9-aminoacridine allows it to intercalate into DNA. Intercalation is a process in which the aromatic flat surface of the intercalator inserts between adjacent base pairs of DNA The large surface area of 9-aminoacridine's fused tricyclic ring system allows strong intercalative binding …

Work Function Modification Of Metal Electrodes Via Printing Of Pedot:Pss And Carbon Nanotubes, Carly A. Jordan

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Work function tunability of metal electrodes provides a route to improving performance of organic electronic devices. Using an electrode with a different work function changes the potential barrier at the polymer/electrode interface, leading to altered device characteristics, such as turn-on voltage in light emitting diodes or series resistance photodiodes. In this work, we explore work function modification by employing solution-based conducting materials, poly(3,4-ethylenedioxythiophene) : poly(styrene sulfonate) (PEDOT:PSS) and carbon nanotubes (CNTs), printed as overcoatings on oxidized Ni. The capability of direct write technologies, namely inkjet and aerosol jet printing, to control thin film thickness is investigated. The correlation between film …

Computational Estimation Of The Pka's Of Purines And Related Compounds, Kara L. Geremia

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The acid dissociation value pKa of a compound provides important information regarding the neutral and ionic forms of the compound present under different conditions. However, for many compounds experimental pKa values are not available, and for others the measured values are sometimes uncertain. Consequently, having a computational means for estimating pKa values can be of benefit for biochemical, pharmaceutical, polymer, and many other studies. Purines form a key group of bioactive compounds whose acid/base activities are of considerable interest. The purine class includes such diverse compounds as the nucleic acid bases adenine and guanine, the gout-related compound uric acid, the …

Using A Spreadsheet To Solve The SchröDinger Equations For The Energies Of The Ground Electronic State And The Two Lowest Excited States Of H2, Yingbin Ge, Robert C. Rittenhouse, Jacob C. Buchanan, Benjamin Livingston

All Faculty Scholarship for the College of the Sciences

We have designed an exercise suitable for a lab or project in an undergraduate physical chemistry course that creates a Microsoft Excel spreadsheet to calculate the energy of the S₀ ground electronic state and the S₁ and T₁ excited states of H₂. The spreadsheet calculations circumvent the construction and diagonalization of the Fock matrix and thus can be accomplished by any undergraduate chemistry student with basic calculus skills. The wave functions of the S₀, S₁, and T₁ states of H₂ are constructed from the symmetry-adapted bonding and antibonding molecular …

Near Single-Molecule Sers-Based Detection Using Ultrafiltered, Unfunctionalized Silver Nanoparticles, Joshua Dale Baker

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Silver nanoparticles (AgNPs) are currently widely-used in consumer products, therapeutics, biomedical devices, and electronics. Yet, one application for which AgNPs have been used extensively is surface-enhanced Raman spectroscopy (SERS)-based sensing. However, AgNP size and aggregation state are known to greatly influence these applications. This works aimed 1) to synthesize a large volume of unfunctionalized, Creighton AgNPs, to characterize their chemical and physical properties, 2) then to size-select AgNPs of 1-50 nm and 50-100 nm in diameter and to concentrate them using a three-step, "green" tangential flow ultrafiltration (TFU) process. 3) Finally, to determine and compare the SERS-based sensing capabilities of …

Particulate Pictures And Kinetic-Molecular Theory Concepts: Seizing An Opportunity, Mark Waner

Mark J. Waner

This work examines commonly used particulate-level pictures meant to illustrate gases. These pictures are found throughout textbooks in the middle grades through the college level, as well as in questions frequently used to assess conceptual learning in students. This work uses the kinetic-molecular theory of gases to demonstrate the inaccuracies often present in these figures, which offers the opportunity to address model limitations to students and to develop better pictures. A basis for using these pictures to discuss models and ideas for ways these pictures can be used for inquiry activities based on analysis of scales is also discussed.

Kinetic And Mechanistic Studies Of The Deuterium Exchange In Classical Keto−Enol Tautomeric Equilibrium Reactions, Michael Nichols, Mark Waner

Mark J. Waner

An extension of the classic keto−enol tautomerization of β-dicarbonyl compounds into a kinetic analysis of deuterium exchange is presented. It is shown that acetylacetone and ethyl acetoacetate undergo nearly complete deuterium exchange of the α-methylene carbon when dissolved in methanol-d4. The extent of deuteration may be monitored via NMR spectroscopy as a function of time. A mechanism for deuterium exchange is presented and shown to be consistent with a consecutive first-order process. The data for acetylacetone are consistent with steady-state kinetics, whereas those of ethyl acetoacetate illustrate nonsteady-state behavior, offering an accessible example where students might collect and analyze real …

'Partial Derivatives: Are You Kidding?': Teaching Thermodynamics Using Virtual Substance, Chrystal Bruce, Carribeth Bliem, John Papanikolas

Chrystal D. Bruce

No abstract provided.

Metal Binding Studies With Macrocyclic Hexathioethers: Transition Metal Complexes Of 22s6 And 20s6”,, Gregory Grant, Christopher Brandow, Chrystal Bruce, Mark Brandt, Rebecca Kirk, Sabrina Lee, Kerry Robinson, Larry Mehne

Chrystal D. Bruce

No abstract provided.

The Correlation Of Physical Properties Of Organic Molecules With Computed Molecular Surface Areas., Robert Mebane, Shannon Schanley, Thomas Rybolt, Chrystal Bruce

Chrystal D. Bruce

The objective of this paper is to show that a student's understanding of molecular properties can be enhanced with the study of molecular surface areas obtained from readily available molecular modeling software.

Dynamics Of Chain Molecules, Walter H. Stockmayer

DSLS 1988-1989

(Abstract taken from the Distinguished Scientist Lecture Series Program 1988-1989).

The recording of lecture not available.

Dr. Stockmayer is the Albert W. Smith Professor Emeritus at Dartmouth College, a position he has held since 1979. In 1935, Dr. Stockrnayer graduated from Massachusetts Institute of Technology. After two years at Oxford University, he returned to M.1.T. and earned his Ph.D. degree in 1940. His thesis, directed by James A. Beattie, was on the equation of state of gas mixtures. Dr. Stockrnayer became an Instructor in Chemistry at M.I.T. in 1939. Except for a two-year stint at Columbia University, he taught at …