Chemistry Commons^™

Structural Integrity And Stability Of Dna In Ionic Liquid And Near-Infrared Indolizine Squaraine Dye, Ember Yeji Suh

Honors Theses

Luminol, the most common presumptive test for blood at a crime scene, has multiple issues, such as false positive results with chemical agents, no luminescence due to “active oxygen” cleaning agents on bloodstains, and inability to penetrate textile materials. A combination of indolizine squaraine dye and ionic liquid (IL), or Dye Enhanced Textile Emission for Crime Tracking (DETECT), have shown potential to address these issues. The purpose of this study was to assess the binding mechanism of CG (1:1) and SO₃SQ dye to HSA and how the mechanism can explain the W214 fluorescence quenching effect and to determine …

Photophysical And Photochemical Processes In Small Molecules And Materials For Solar Energy Conversion, Ethan Lambert

Honors Theses

The work covered in this thesis all falls under the theme of photophysical processes after light and matter interact. Those of primary interest are Raman scattering induced vibrations and excited state dynamics probed by transient absorption spectroscopy. Small molecules are studied with Raman spectroscopy and computational chemistry. These studies unearth the shifts in vibrational frequency as a function of charge transfer or receipt and how a quantitative assay of natural orbital populations and delocalization can offer both the nature and magnitude of this charge transfer. Further, a method is presented that builds upon previous work within the academic family tree; …

A Study Of Cannabigerolic Acid And Its Derivatives Via Raman Spectroscopy And Density Functional Theory, Trevor Wolfe

Honors Theses

The cannabinoids are a class of molecules endogenous to the cannabis plant. Their scientific relevance has increased in recent years due to the mercurial legal status of marijuana across the United States. Some of the most known are cannabidiol (CBD), δ9-tetrahydrocannabinol (δ9-THC), and δ8-THC due in large part to their widespread use, especially in states where marijuana and related products are legal. However, cannabigerolic acid (CBGA) is arguably the most important cannabinoid; it is enzymatically converted into other acidic cannabinoids, which subsequently undergo non-enzymatic processes (isomerization, thermal decarboxylation, oxidation, etc.) to synthesize further cannabinoids. Although there is a wealth of …

Lc-Ms Identification Of Serum Proteins Adsorbed Onto Ionic Liquid-Coated Nanoparticles, Anh M. Hoang

Honors Theses

Nanocarriers are promising candidates for drug delivery due to their size and tunable surface characteristics. However, when they are intravenously injected, few particles make it to their designated location. This is because upon entering the bloodstream, the serum in the blood, which is rich with a diversity of proteins, adsorbs onto the particles’ surfaces forming a protein corona. Many of the attached proteins trigger the mobile immune system and are removed by macrophages, and many particles are then filtered out by the liver and kidneys. Ionic Liquids (ILs), which consist of asymmetric, bulky components that are liquid

Computational Investigations Into Astrochemical Inorganic Oxides, Ammonia Borane, And Genetic Algorithms, E. Michael Valencia

Honors Theses

The formulations of quantum mechanics in the early 1900s were exciting theoretical discoveries, but were not practical to apply until the advent of computers and the subsequent computational methods in 1951. With the introduction of tractable simplifications, procedures such as Hartree-Fock allowed for determination of properties of non-trivial systems. Presently, huge leads of computational power have allowed for extremely precise, quantitative work that can be applied to the human body, synthesis, or even astrochemical processes. This thesis presents works concerning 1) the history of quantum mechanics; 2) a brief primer on computational chemistry and its methods; 3) inorganic oxides in …

Computational And Spectroscopic Studies Of New Sulfur-Containing Dipole-Bound Anions, Nicholas Allen Kruse

Honors Theses

Sulfur and Nitrogen are essential ingredients in both life-supporting and light-harvesting molecules. Their presence also usually leads to the delocalization of electrons and large dipole and quadrupole moments. Such molecules are sometimes able to form negative ions through the electrostatic binding of an excess electron. These so-called multipole-bound (dipole-bound, quadrupole-bound, etc.) anions have been shown to be important in radiation damage in biology and electron transport processes. Here, we present our recent computational and experimental results studying the creation of new multipole-bound anions.

A Theoretical Study Of Synchronous Proton Transfer In (Hf)N, (H2O) N, And (Hcl) N Where N = 3, 4, 5, Johnny Yang

Honors Theses

For (HF)_n, (H₂O)_n, and (HCl)_n (n = 3 − 5), we have rigorously characterized the structures for the minima and transition states for synchronous proton transfer (SPT) with the CCSD(T) method and aug-cc-pVTZ basis set. The electronic barrier heights (∆E^†) associated with these transition states have also been computed with the explicitly correlated CCSD(T)-F12 method and the aug-cc-pVQZ-F12 basis set (abbreviated aQZ-F12). (HCl)_n (n = 3 − 5) SPT transition states have not been previously identified to the best of our knowledge, and they have been found …

Computational Investigation Of Stellar Cooling, Noble Gas Nucleation, And Organic Molecular Spectra, Jax Dallas

Honors Theses

Since the advent and optimization of the Hartree-Fock method, quantum chemistry has been utilized to investigate systems operating on timeframes and environments traditionally unavailable to bench-top chemistry. As computational methods have grown more robust and less time consuming, quantum chemistry has been utilized to investigate a range of fields, including the steadily growing discipline of computational astrochemistry. Through the lens of computational astrochemistry, chemistry that occurred billions of years ago can be explored with equal clarity to that which is currently happening in the cosmos. The work presented throughout this thesis is a series of investigations into different timeframes of …

Spectroscopic Analysis Of Potential Astromolecules Via Quantum Chemical Quartic Force Fields, Mason Gardner

Honors Theses

Astrochemistry has been substantially aided by computational techniques, particularly through the use of Quartic Force Field (QFF) analysis. Several methods have proven useful at correlating computed spectroscopic data with experimental observations. The F12-TZ QFF correlated well with experimental data for silicon oxide compounds, particularly those potentially involved in development from rocky bodies to planetary masses [27]. Compared to argon matrix experimental data, the vibrational frequencies for the molecules SiO2, SiO3, Si2O3, and Si2O4 become less accurate as the complexity of the molecules increases but should still be predictive of infrared characteristics of silicon oxides as they form clusters in space …

A Spectroscopic And Computational Study Of Diacetyl And Water Clusters, Margaret Baldwin

Honors Theses

Diacetyl, otherwise known as 1,2-butadione or biacetyl, is a flavor additive used in microwave popcorn, and more importantly as of late, e-cigarettes. The compound is known to cause lung disease for those who have been exposed to a large quantity of the buttery smelling molecule. As such, the characterization of diacetyl’s vibrational modes when it interacts with water are pivotal to understanding the effects it has on human lung tissue. In this research, the intermolecular interactions between water and diacetyl and the effects they have on one another’s vibrational modes are explored. While some experimental data is presented, the spectra …

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 …

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 …

Comparison Of The Vibrational Modes Of Thiolated Gold Nanoparticles Undergoing Core-Conversions Via Raman Spectroscopy, William Gregory Cannella Jr.

Honors Theses

In this project, the vibrational characteristics/vibrational modes are explored via Raman Spectroscopy for thiolated-gold nanoparticles. This class of compounds is also known as gold nanoparticles (AuNPs). They remain of great interest in research areas such as catalysis, gold dependent nanoelectronics, drug delivery, and sensing, due to their unique size-dependent optical, chiroptical, and electronic properties. Vibrational spectroscopy of thiolated gold nanoparticles are oftentimes considered nontrivial as the compounds strongly absorb light in the visible region of the electromagnetic spectrum, are generally considered weak scatterers, and give off large amounts of fluorescence. This combined with their black appearance, susceptibility to localized heating, …

Study Of Pharmaceutical Tablets Using Raman Mapping, Kyle Joseph Pauly

Honors Theses

Covalent bonds are the strongest type of bonds holding molecules together. Based on the pattern of bonding of the molecule, the atoms associated with the bond will vibrate at a specific frequency. Utilizing vibrational spectroscopy, such as Raman spectroscopy, these unique vibrational frequencies can be used to detect the presence of analytes over a selected area. Furthermore, the intensities of the vibrational modes can be tracked to comparatively quantify the concentration of analytes at various locations. This is a method of great importance due to its ability to compare pharmaceutical tablets synthesized with different techniques. Here, the presence and concentration …

Raman Spectroscopy Study Of Delta-9-Tetrahydrocannabinol And Cannabidiol And Their Hydrogen-Bonding Activities, Kalee Sigworth

Honors Theses

Cannabis and products containing its cannabinoids have grown rapidly in acceptance and use in recent years with legalization of cannabis in many countries and US states. Cannabidiol and Delta-9-Tetrahydrocannabinol are two primary cannabinoids in Cannabis that have been shown to produce analgesic effects along with many other positive side effects for the user. These two cannabinoids interact with receptors in the Central and Peripheral Nervous Systems. No spectroscopic study to our knowledge has been performed to analyze the hydrogen bonding effects of interactions between these two cannabinoids and solvents. Here, we employ theoretical Raman spectra through computational methods to study …

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. …

Spectroscopic And Computational Studies Of The Agricultural Active Ingredient Dicamba, James Johnson

Honors Theses

3,6-dichloro-2-methoxy benzoic acid, more commonly known as Dicamba, is the active ingredient in an array of pesticides used on farmlands across the globe. Dicamba’s mode of action works by mimicking the plant hormone auxin, which is synonymous to growth hormones in mammals. The mimicking of auxin results in excessive elongation and growing, which is eventually fatal for plants when the rate of growth can no longer be sustained. Dicamba has risen in prominence in recent years due to drift damage as a result of Dicamba’s high volatility. Having the ability to identify Dicamba is crucial for the agricultural industry. The …

Characterization Of Hydrogen Bonding, Halogen Bonding And Argyrophilic Interactions Using Computational Modeling, Sarah Nicole Arradondo

Electronic Theses and Dissertations

Non-covalent interactions govern multiple important chemical processes throughout nature from those within the human body to the complex environment of the atmosphere. Quantum mechanical electronic structure modeling of these relatively weak interactions can provide molecular level insight that can further our understanding of specific macroscopic properties. In the present work different non-covalent interactions are computationally evaluated within four systems. A small prototypical hydrogen bonded system and the various structural motifs that promoted proton transfer within concentrated acid and water clusters are characterized with sophisticated wavefunction based methods and large robust basis sets in order to accurately predict the structures energies …

Characterization Of Charge Accommodation In Biologically Important Hydrogen-Bonded Clusters, John Thomas Kelly

Electronic Theses and Dissertations

The underlying motivation of chemical physics and physical chemistry is to understand naturally occurring chemical and physical processes from the nanoscopic molecular level to the macroscopic condensed phase. Over the past half-century, experimentalists have developed a number of laser-based analytical techniques to bridge the gap between the bulk phase and the single molecule. Here, we look at bulk phase and gas phase clusters to compare the local hydrogen-bonded network. To better understand the role noncovalent interactions have on biologically relevant building blocks in a natural environment, we compare the microhydration of gas phase cluster ions to condensed phase spectra. The …

The Spectroscopic Characterization Of Newly Developed Emissive Materials And The Effects Of Environment On Their Photophysical Properties, Louis Edward Mcnamara

Electronic Theses and Dissertations

The development of new materials capable of efficient charge transfer and energy storage has become increasingly important in many areas of modern chemical research. This is especially true for the development of emissive optoelectronic devices and in the field of solar to electric energy conversion. The characterization of the photophysical properties of new molecular systems for these applications has become critical in the design and development of these materials. Many molecular building blocks have been developed and understanding the properties of these molecules at a fundamental level is essential for their successful implementation and future engineering. This dissertation focuses on …

Noncovalent Interactions Involving Microsolvated Networks Of Trimethylamine N-Oxide, Kristina Andrea Cuellar

Electronic Theses and Dissertations

This thesis research focuses on the effects of the formation of hydrogen-bonded networks with the important osmolyte trimethylamine N-oxide (TMAO). Vibrational spectroscopy, in this case Raman spectroscopy, is used to interpret the effects of noncovalent interactions by solvation with select hydrogen bond donors such as water, methanol, ethanol and ethylene glycol in the form of slight changes in vibrational frequencies. Spectral shifts in the experimental Raman spectra of interacting molecules are compared to the results of electronic structure calculations on explicit hydrogen bonded molecular clusters. The similarities in the Raman spectra of microsolvated TMAO using a variety of hydrogen bond …

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 …

On The Nature Of Weak Intermolecular Forces: A First Principles Approach To Hydrogen Bonding And Pi-Type Interactions, Kari Lorene Copeland

Electronic Theses and Dissertations

Computational quantum chemistry is a branch of chemistry that is based on quantum mechanics. In this field, chemical phenomena is represented in mathematical form and computers are used to provide numerical solutions to rigorous mathematical equations. Through this medium, the properties of atoms and molecules are calculated with high accuracy. Chapter 1 opens with a general discussion of science, the development of atomic theory and computational chemistry. Electronic structure theory is more extensively reviein Chapter 2. Hydrogen bonding and dispersion forces are defined in Chapter 3, and the procedures used to computationally study these type interactions are considered. Chapter 4 …

Investigations Of Noncovalent Interactions Using Raman Spectroscopy And Electronic Structure Computations, Ashley Wright

Electronic Theses and Dissertations

This dissertation research focuses on the effects of noncovalent interactions on vibrational energy levels. Vibrational spectroscopy is a powerful tool for the study of the effects of weak intermolecular interactions such as hydrogen bonding and interactions with the environment, including solvation effects. Changes in the vibrational spectra of interacting molecules allow us to ascertain exactly which atoms and bonds are affected and to what extent they are affected. Quantum mechanical methods, ab initio theory and density functional theory, are employed to model molecular geometries, properties, and subtle interactions between molecules. Much of this research centers on the comparison of these …

Characterization Of Intermolecular Pi-Type Interactions Using Sophisticated Quantum Mechanical, Electronic Structure Computations, Emily Joy Carrell

Electronic Theses and Dissertations

Much like the instrumentation in an experimental lab, computational chemists use computers to solve the mathematical equations that describe the physics of electrons to understand the chemistry involved. The combination of the two main components of computational chemistry, the basis set and method, determines the ``cost'' (disk, memory, and CPU time) of a computation. A variety of basis sets and methods have been developed in the past century. The focus of this report is to accurately describe non-covalent interactions with the use of various quantum computational techniques. In Chapter 1 a brief discussion on the theory behind computational chemistry is …

Theoretical Characterization Of Non-Covalent Weakly Bound Clusters Through The Application Of Sophisticated Computational Quantum Chemistry Methodologies And The Development Of Integrated Fragmentation Techniques, Desiree Bates

Electronic Theses and Dissertations

Non-covalent, weakly bound clusters have been and remain of significant interest to many researchers. However, with computational studies, accurate description of these interactions requires sophisticated electronic structure methods employing large basis sets. This methodology becomes extremely computationally demanding as the size of the system increases. This work presents benchmark data and explores methods for obtaining highly accurate ab initio results for larger systems at greatly reduced computational costs. CCSD(T) complete basis set limit interaction energies are presented for a variety of parallel-slipped π...π dimers and low-lying isomers of (h₂o)₆. The calibration of a 2-body:Many-body fragmentation method …