Chemistry Commons^™

Synthetic Investigations In Chemical Probe Development Part 1: Design And Synthesis Of Novel Triton X-405 Adenosine Conjugates; Part 2: Synthesis Of 2,8-Dihydroxychrysene, Rachel Irene Hammond

Honors Theses

Although not drugs themselves, chemical probes are a necessary tool in biomedical research for the interrogation of biological systems. In the present synthetic investigation, two chemical probes were developed – a Triton X-405 adenosine conjugate (TX-405A) and 2,8-dihydroxychrysene. The designed TX-405A conjugate was generated in four steps through tosylation and amination of TX-405 such that EDC-coupling of TX-amine with 2’,3’-Isopropylidene adenosine-5’-carboxylic acid afforded TX-405A following acetonide deprotection. The development of TX-405A represents the first report of the synthesis and utilization of a detergent-linked dosimeter. The synthesis of 2,8-dihydroxychrysene provided an in-depth exploration on the unique reactivity of chrysene. The desired …

Dicyanobenzothiadiazole-Based Organic Dye As A Visible Light Absorbing Strong Photoinduced Oxidant With A 16 Microsecond Long-Lived Excited State, Ivy Li

Honors Theses

Strong photoinduced oxidants are important to organic synthesis and solar energy conversion to chemical fuels or electric. For these applications, visible light absorption is important to solar energy conversion and long-lived excited states are needed to drive catalysis. With respect to these desirable qualities, a series of five 5,6-dicyano[2,1,3]benzothiadiazole ((CN)₂BTD) dyes are examined as organic chromophores that can serve as strong photooxidants in catalytic systems. The series utilizes a ((CN)₂BTD) core with aryl groups on the periphery varying electron donation strengths relative to the core. The dyes are studied via both steady-state and transient absorption and …

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.

The Design Of A Pcr-Based Assay To Detect And Isolate The Serine Palmitolytransferase Gene From Environmental Bacteria, Lana Taylor

Honors Theses

Sphingolipids are a natural class of lipids that function as structural elements of cell membranes and signaling molecules for important cellular activities such as cell growth, differentiation, apoptosis, recognition, and adhesion. These lipids can be found universally in eukaryotic cells as well as some species of bacteria, such as those found in the human gut microbiome and in the environment in soils. Though sphingolipid production is rare in bacteria, both eukaryotic and prokaryotic sphingolipid biosynthesis begin with the condensation of serine and palmitoyl CoA into 3-ketodihydrosphingosine catalyzed by the enzyme serine palmitoyltransferase (SPT). In recent years, several studies have shown …

Covalent Modification Of Recombinant Protein With Reactive Thiols, Sawyer Dulaney, Bailey Taylor

Honors Theses

Many diseases cause chronic and painful inflammation in different body systems. One of the front-line drug classes to treat such inflammation is Nonsteroidal Anti-Inflammatory Drugs (NSAIDs). Despite the benefits of oral administration of NSAIDs, there are drawbacks to their long-term usage because they can cause detrimental effects on off-target systems in the body such as the liver, kidney, or the lining of the intestinal tract. An alternative to NSAIDs is the usage of hydrogels for targeted drug delivery. Hydrogels can provide drug delivery in a specific portion of the site of inflammation, thus allowing higher doses of medication to be …

Spectral Signatures Of Hydrogen Thioperoxide (Hosh) And Hydrogen Persulfide (Hssh): Possible Molecular Sulfur Sinks In The Dense Ism, Charles Z. Palmer, Ryan C. Fortenberry, Joseph S. Francisco

Faculty and Student Publications

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use …

Collision-Induced Dissociation And Ion Mobility Mass Spectrometry Of Au30(S-Tbu)18 Nanoclusters, Christopher Hood

Honors Theses

Collision Induced Dissociation (CID) and Ion Mobility Mass Spectrometry (IM-MS) are methods used to understand the structural arrangement and stability of large molecules. In this study, the gold nanocluster Au₃₀(S-tBu)₁₈ was dissociated at varying Trap collision energies, and drift time vs mass spectrometry data was plotted to determine the order of cluster fragmentation. Comparing Au₃₀(S-tBu)₁₈ data to that of Au₂₅(SCH₂CH₂Ph)₁₈, the only current nanocluster published with IM-MS data, two distinctly different dissociation patterns were seen. Unlike the linear CID fragmentation of Au …

Targeting Platelets Using Ionic Liquid Coated Nanoparticles, Karen Mun Wong

Honors Theses

Platelets are key players in our body’s inflammatory processes upon activation, which can create physiological problems. Researchers are actively seeking solutions by targeting platelets with therapeutics. The objective of the research in this thesis was to investigate a new and potentially less invasive drug delivery platform using nanoparticles. The topic of the project was to explore the world of ionic liquids and their abilities, when coated on nanoparticles, to bind to platelets. A library of choline carboxylic acid-based ionic liquids (ILs) was first synthesized via salt metathesis while PLGA-based nanoparticles were simultaneously being synthesized via the nanoprecipitation method. The ionic …

Synthesis And Characterization Of Redox-Active Multidentate Ligands For Catalytic C-H Bond Oxidation And Carbon Dioxide Reduction, Caroline Hodge

Honors Theses

This thesis focuses on two research projects. The first project reported in Chapter 1 involves the synthesis and application of a tetradentate ligand (2-(1,1-di(pyridin-2-yl)ethyl)-1,10-phenanthroline, PhenPY2Me) that is metalated with iron to give a catalyst capable of carbon-hydrogen (C-H) bond oxidation. C-H bond oxidation provides a method that may allow some transformations in organic syntheses to be streamlined. The mononuclear iron complex supported by PhenPY2Me was found to dimerize in the presence of O₂ in a non-coordinating solvent. These iron complexes and a previously reported system were assessed and compared in C-H bond oxidation with model substrates using the sacrificial …

Fast Photochemical Oxidation And Footprinting Of Proteins Via Trifluoromethyl Radical Chemistry, Elaine Morrow

Honors Theses

Fast photochemical oxidation of proteins (FPOP) is a useful tool in proteomics because of the ability for modifications to occur on the scale of microseconds which reduces the modifications to tertiary and quaternary structure allowing for more accurate labeling of the protein. Labels for FPOP are generated from various radicals in our experiments which include hydroxyl radicals and trifluoromethyl radicals. Hydroxyl radicals are easily generated by using an excimer laser (KrF laser, 248 nm) or a UV flash lamp (as a part of the Fox™ System) by the photolysis of hydrogen peroxide. Trifluoromethyl radicals, however, need hydroxyl radicals to be …

Raman Spectroscopic And Quantum Chemical Investigation Of The Pyridine-Borane Complex And The Effects Of Dative Bonding On The Normal Modes Of Pyridine, Ethan C. Lambert, Benjamin W. Stratton, Nathan I. Hammer

Faculty and Student Publications

The pyridine-borane (PyBH3) complex was analyzed by Raman vibrational spectroscopy and density functional theory to elucidate its structural and vibrational properties and to compare these with those for neat pyridine (Py). The borane-nitrogen (BN) bond length, the BN dative bond stretching frequency, and the effects of dative-bonded complex formation on Py are presented. Rather than having a single isolated stretching motion, the complex exhibits multiple BN dative bond stretches that are coupled to Py's vibrations. These modes exhibit large shifts that are higher in energy relative to neat Py, similar to previous observations of Py/water mixtures. However, significantly higher charge …

Relative Energy Comparison For Various Water Clusters Using Mp2, Df-Mp2, And Ccsd(T):Mp2 Methods, Qihang Wang

Honors Theses

The study of water clusters is an important area of research in many disciplines, such as biology, physical chemistry, and environmental studies. However, due to the difficulty in studying larger water clusters, such as clathrate hydrates, it is beneficial to obtain accurate descriptions of smaller water clusters to use as models for larger systems via computational methods. By starting with small water clusters, such as (H2O)₆, and moving into larger systems it is possible to build up data on various water structures that can determine the energetics of the various geometries within a certain number of water molecules. …

Valence-, Dipole-And Quadropole-Bound Electronically Excited States Of Closed-Shell Anions Formed By Deprotonation Of Cyano-And Ethynyl-Disubstituted Polycyclic Aromatic Hydrocarbons, Marie E. Strauss, Taylor J. Santaloci, Ryan C. Fortenberry

Faculty and Student Publications

Dicyano-functionalized benzene and naphthalene anion derivatives exhibit a relatively rich population of electronically excited states in stark contrast to many assumptions regarding the photophysics of anions in general. The present work has quantum chemically analyzed the potential electronically excited states of closed-shell anions created by replacing hydrogen atoms with valence-bound lone pairs in benzene and naphthalene difunctionalized with combinations of-CN and-C2H. Dicyanobenzene anion derivatives can exhibit dipole-bound excited states as long as the cyano groups are not in para position to one another. This also extends to cyanoethynylbenzene anions as well as deprotonated dicyano-and cyanoethynylnaphthalene anion derivatives. Diethynyl functionalization is …

Near-Infrared Unsymmetrical Squaraine Core-Based Sensitizers For Co-Sensitized High-Photocurrent Dye-Sensitized Solar Cells, Jonathon Watson, Roberta R. Rodrigues, Jared H. Delcamp

Faculty and Student Publications

Increased conversion of near-infrared (NIR) photons to electricity is needed to improve dye-sensitized solar cells (DSCs). Here, we report two squaraine dyes (RR13 and RR14) with unsymmetrical cores as NIR dyes in DSCs. Both dyes feature a conjugated indolizine donor with an indoline donor on the opposite side of the squaraine core. The dyes are studied via absorption spectroscopy, computational interrogation, and electrochemical analysis. The use of the strongly donating indolizine donor results in NIR photon-to-current conversion extending beyond 800 nm on TiO2 in DSC devices. The DSC devices were characterized by current-voltage curves, incident photon-to-current conversion efficiency measurements, and …

Synthesis Of Methanediol [Ch2(Oh)2]: The Simplest Geminal Diol, Cheng Zhu, N. Fabian Kleimeier, Andrew M. Turner, Santosh K. Singh, Ryan C. Fortenberry, Ralf I. Kaiser

Faculty and Student Publications

Geminal diols—organic molecules carrying two hydroxyl groups at the same carbon atom—have been recognized as key reactive intermediates by the physical (organic) chemistry and atmospheric science communities as fundamental transients in the aerosol cycle and in the atmospheric ozonolysis reaction sequence. Anticipating short lifetimes and their tendency to fragment to water plus the aldehyde or ketone, free geminal diols represent one of the most elusive classes of organic reactive intermediates. Here, we afford an exceptional glance into the preparation of the previously elusive methanediol [CH2(OH)2] transient—the simplest geminal diol—via energetic processing of low-temperature methanol–oxygen ices. Methanediol was identified in the …

Anharmonic Vibrational Frequencies Of Water Borane And Associated Molecules, Brent R. Westbrook, Ryan C. Fortenberry

Faculty and Student Publications

Water borane (BH3 OH2 ) and borinic acid (BH2 OH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimen-tally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two poten-tially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for …

Are Rural And Small Community Aerated Wastewater Stabilization Ponds A Neglected Source Of Microplastic Pollution?, Zhiqiang Gao, James V. Cizdziel, Kendall Wontor, Haitao Lu

Faculty and Student Publications

Wastewater treatment systems collect and treat sewage that includes microplastics (MPs). However, we are not aware of any studies on the occurrence and distribution of MPs in wastewater stabilization ponds (WSPs), which serve small communities worldwide. Here, we characterized MPs (~45 µm–5 mm) in an aerated WSP serving ~500 houses and an adjacent lake. Putative MPs were most abundant in duckweed (Lemna minor) and sludge (75 ± 22 and 12.8 ± 3.1 particles/g, respectively: ±1 standard deviation (SD), n = 6, dry weight). In the water, average concentrations (particles/L ± 1 SD, n = 6) were highest in the pond …

Further Astrochemical Insights From Bond Strengths Of Small Molecules Containing Atoms From The First Three Rows Of The Periodic Table, Edmund S. Doerksen, Ryan C. Fortenberry

Faculty and Student Publications

The atoms contributing to the strongest “single bonds” on the periodic table do not continue to produce the strongest “double bonds” or “triple bonds.” In fact, the opposite appears to be the case. This quantum chemical examination of nominal X = Y and X ≡ Y bonds in model molecules of atoms from the first three rows of the periodic table shows that the strongest “double bond” is in formaldehyde once the astrophysically-depleted Be and B atoms are removed from consideration. The strongest “triple bond” is a close match between acetylene and N2. However, these results indicate that astrophysical regions …

Swir Emissive Rosindolizine Dyes With Nanoencapsulation In Water Soluble Dendrimers, Satadru Chatterjee, William E. Meador, Cameron Smith, Indika Chandrasiri, Mohammad Farid Zia, Jay Nguyen, Austin Dorris, Alex Flynt, Davita L. Watkins, Nathan I. Hammer, Jared H. Delcamp

Faculty and Student Publications

Shortwave infrared (SWIR) emission has great potential for deep-tissuein vivobiological imaging with high resolution. In this article, the synthesis and characterization of two new xanthene-based RosIndolizine dyes codedPhRosIndz andtolRosIndz is presented. The dyes are characterizedviafemtosecond transient absorption spectroscopy as well as steady-state absorption and emission spectroscopies. The emission of these dyes is shown in the SWIR region with peak emission at 1097 nm.TolRosIndz was encapsulated with an amphiphilic linear dendritic block co-polymer (LDBC) coded 10-PhPCL-G3 with high uptake yield. Further, cellular toxicity was examinedin vitrousing HEK (human embryonic kidney) cells where a >90% cell viability was observed at practical concentrations …

Tracking The Amide I And Αcoo− Terminal Ν(C=O) Raman Bands In A Family Of L-Glutamic Acid-Containing Peptide Fragments: A Raman And Dft Study, Ashley E. Williams, Nathan I. Hammer, Ryan C. Fortenberry, Dana N. Reinemann

Faculty and Student Publications

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length …

Linear Discriminant Analysis Based On Gas Chromatographic Measurements For Geographical Prediction Of Usa Medical Domestic Cannabis, Ramia Z. Al Bakain, Yahya S. Al-Degs, James V. Cizdziel, Mahmoud A. Elsohly

Faculty and Student Publications

Fifty four domestically produced cannabis samples obtained from different USA states were quantitatively assayed by GC-FID to detect 22 active components: 15 terpenoids and 7 cannabinoids. The profiles of the selected compounds were used as inputs for samples grouping to their geographical origins and for building a geographical prediction model using Linear Discriminant Analysis. The proposed sample extraction and chromatographic separation was satisfactory to select 22 active ingredients with a wide analytical range between 5.0 and 1,000 μg/mL. Analysis of GC-profiles by Principle Component Analysis retained three significant variables for grouping job (Δ9-THC, CBN, and CBC) and the modest discrimination …

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 …

One-Pot Synthesis Of Disubstituted Primary Amines From Nitriles Via Grignard Addition And Metal-Alcohol Reduction, Joshua Peltan

Honors Theses

The process of developing a working base case procedure for a novel one-pot-two-step synthesis of primary amines from Grignard reagents, nitriles, sodium metal or alkali metal loaded silica gel, and alcohol is described. Initial steps towards applying the process broadly are detailed. The process has the potential to be an affordable, convenient, safer, greener, and more accessible alternative to exiting methods of accomplishing the same transformation. The reaction scheme has been proven to provide yields and purity comparable to existing methods for certain pairs of substrates; however, its utility as a general-purpose method for transforming arbitrary pairs of Grignard reagent …

Determination Of Metals And Microplastics In Sediment From Oyster Reefs In The Mississippi Sound, Shelby Goza

Honors Theses

This research centers on the determination of metals (Cd, Pb, V, Cr, Mn, Fe, Co, Ni, Cu) and microplastics (MPs) in marine sediment from oyster reefs in the Mississippi Sound Estuary. Oysters (Crassostrea virginica) are a vital part of the Gulf Coast economy, but their population has dramatically declined in recent years due to multiple stressors, including oil spills and fluctuations in salinity from flooding. Increasingly frequent flooding events also introduce high loads of MPs and sediments containing heavy metals from the Mississippi River. These pollutants can have deleterious effects on oyster biology; however, they have not been adequately …

Effects Of Halogen Bonding On 13c Nmr Shifts Of Various Tolan Species, Anthony Lybrand

Honors Theses

Halogen bonding is slowly becoming a more and more useful part of the world of chemistry and is beginning to be incorporated into various aspects of the chemical industry. This study’s purpose is to determine whether or not halogen bonding can cause any effect in the 13C NMR shifts. The specific purpose of this study is to determine whether these chemical shifts change when a Lewis Base is added to the dissolved sample. In order to do this, the tolan species (4-iodotolan and 4-chlorotolan) had to be synthesized. Once synthesized, the tolan species were analyzed via NMR. NMR data indicated …

End Group Modification Of Linear Dendritic Block Copolymers (Ldbcs), Chinwe Udemgba

Honors Theses

Linear dendritic block copolymers are amphiphilic molecules that consist of a dendritic hydrophilic portion and a linear hydrophobic portion. Its unique ability to self-assemble into spherical nanoaggregates while having the potential to uptake and transport both hydrophilic and hydrophobic drugs makes these polymers an item of interest in regard to the drug delivery field. The synthesis of polyamidoamine-polylactide linear dendritic block copolymers was designed to address the common issues in drug delivery systems, including problems in permeability, solubility, stability, specificity, and retention. Though this linear dendritic block copolymer has previously been synthesized in our lab with cationic amine surface functionalities, …

Effects Of Crowding Agents On I-Motif Dna, Hayden Brines

Honors Theses

Deoxyribonucleic acid (DNA) is a well-known double stranded, helical, biological molecule. In addition to its more commonly known structure, DNA can also form more complicated structures like G-quadruplexes and i-motifs (iM). The iMs are formed by cytosine rich DNA and are a four stranded structure that is typically looped around itself. The iM formation is typically pH-dependent and is favored in more acidic conditions; the pKa value is approximately 6.5. This pKa value allows for potential in vivo formation, since the cells have a pH of approximately 7.3. Due to this, iMs are thought to be powerful, innovative molecules for …

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 …

Applications Of Sodium Azide In The Synthesis Of Tetrazines And Hydrolysis Reactions, My Le

Honors Theses

The inverse electron demand Diels−Alder cycloadditions of heterocyclic azadienes have provided a robust methodology for synthesizing highly substituted and functionalized heterocycles. It is widely used in organic synthesis and the pharmaceutical industry in the divergent construction of screening libraries and bioorthogonal conjugation. Each heterocyclic azadiene was found to possess a unique reactivity toward different classes of dienophiles, display predictable modes of cycloaddition, and exhibit substantial substituent electronic effects impacting their intrinsic reactivity and cycloaddition regioselectivity. Synthesis of 1,2,4,5-tetrazine has been reported in the literature since the late 19th century, showing scientists' tremendous interest in its application.

Herein we attempt to …

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 …