Other Chemistry Commons^™

A Library Of Coumarin-Enaminone Chemodosimeters For The Detection Of Analytes, Aaron Berrell Davis

Dissertations

Many anions and metal ions are of biological and environmental importance. This work describes our attempts to synthesize molecular probes to specifically target cyanide, zinc, cadmium and mercury as these species can often result in negative effects to the environment and the human body.

The work in this dissertation, describes the synthesis of a family of coumarin-enamine chemodosimeters, in a straightforward synthetic procedure, the reaction between 7-(diethylamino)-4-hydroxycoumarin and a primary amine. The work presented in this dissertation demonstrates that these molecules can play dual roles and therefore the work is split into two distinct parts: Part 1 describes one role …

Mida Boronates Are Hydrolysed Fast And Slow By Two Different Mechanisms, Jorge A. Gonzalez, O. Maduka Ogba, Gregory F. Morehouse, Nicholas Rosson, Kendall N. Houk, Andrew G. Leach, Paul H.-Y. Cheong, Martin D. Burke, Guy C. Lloyd-Jones

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

MIDA boronates (N-methylimidodiacetic boronic acid esters) serve as an increasingly general platform for building-block-based small molecule construction, largely due to the dramatic and general rate differences with which they are hydrolysed under various basic conditions. Yet the mechanistic underpinnings of these rate differences have remained unclear, hindering efforts to address current limitations of this chemistry. Here we show that there are two distinct mechanisms for this hydrolysis: one is base-mediated and the other neutral. The former can proceed more than three orders of magnitude faster, and involves rate-limiting attack at a MIDA carbonyl carbon by hydroxide. The alternative ‘neutral’ hydrolysis …

Predictive Coupled-Cluster Isomer Orderings For Some SiNCM (M, N ≤ 12) Clusters: A Pragmatic Comparison Between Dft And Complete Basis Limit Coupled-Cluster Benchmarks, Jason N. Byrd, Jesse J. Lutz, Duminda S. Ranasinghe, Yifan Jin, Ajith Perera, Xiaofeng F. Duan, Larry W. Burggraf, John A. Montgomery Jr.

Faculty Publications

The accurate determination of the preferred Si₁₂C₁₂ isomer is important to guide experimental efforts directed towards synthesizing SiC nano-wires and related polymer structures which are anticipated to be highly efficient exciton materials for opto-electronic devices. In order to definitively identify preferred isomeric structures for silicon carbon nano-clusters, highly accurate geometries, energies and harmonic zero point energies have been computed using coupled-cluster theory with systematic extrapolation to the complete basis limit for set of silicon carbon clusters ranging in size from SiC₃ to Si₁₂C₁₂. It is found that post-MBPT(2) correlation energy plays a …

Biological Information And Its Origins: The Curious Case Of Rna, Grace E. Andrews

Honors Projects

Information is an important pre-requisite for the onset of life, which means that any study of the origins of life must also address the origin of information. Biological information today is generally conceptualized in terms of the Central Dogma of Biology, with DNA as a digitized code within the cell. However, here I propose that biological information - particularly in prebiotic conditions, where information would have first arisen - is better understood in terms of the three-dimensional structure of a molecule. Evidence for information storage in RNA can be seen in a number of ways. One of these is that, …

Interaction Of Spliceosomal U2 Snrnp Protein P14 With Its Branch Site Rna Target, William Perea Vargas

Dissertations, Theses, and Capstone Projects

Newly transcribed precursor messenger RNA (pre-mRNA) molecules contain coding sequences (exons) interspersed with non-coding intervening sequences (introns). These introns must be removed in order to generate a continuous coding sequence prior to translation of the message into protein. The mechanism through which these introns are removed is known as pre-mRNA splicing, a two-step reaction catalyzed be a large macromolecular machine, the spliceosome, located in the nucleus of eukaryotic cells. The spliceosome is a protein-directed ribozyme composed of small nuclear RNAs (snRNA) and hundreds of proteins that assemble in a very dynamic process. One of these snRNAs, the U2 snRNA, is …

Cyclotron Production And Biomedical Imaging Applications Of The Pet Isotope Manganese-52, Andrew Lake Wooten

McKelvey School of Engineering Graduate Student Theses & Dissertations

Manganese is an important element for biomedical research because of its roles as an essential micronutrient and as a neurotoxin from chronic elevated exposure, as well as the role of manganese(II) as a paramagnetic core for contrast agents in T1-weighted magnetic resonance imaging (MRI). Using a radiotracer of manganese provides excellent sensitivity for studying these phenomena, but only 52Mn met the criteria for our experiments: (1) a half-life (t1/2=5.6 days) that was long enough to examine timepoints over several days, (2) a half-life that was short enough to emit sufficient counts for a realistic scan time, and (3) emitted radiation …

Direct Band Gap Gallium Antimonide Phosphide (Gasbxp1-X) For Solar Fuels., Harry Benjamin Russell

Electronic Theses and Dissertations

Photoelectrochemical water splitting has been identified as a promising route for achieving sustainable energy future. However, semiconductor materials with the appropriate optical, electrical and electrochemical properties have yet to be discovered. In search of an appropriate semiconductor to fill this gap, GaSbP, a semiconductor never tested for PEC performance is proposed here and investigated. Density functional theory (DFT+U) techniques were utilized to predict band gap and band edge energetics for GaSbP alloys with low amount of antimony. The overall objective of this dissertation is to understand the suitability of GaSb_xP_1-x alloys for photoelectrochemical water splitting application. Specifically, …

Staphylococcal Nuclease And Ubiquitin Local Folding Energies And Rates Using Peps-Hdx-Esi-Ms, Julie Rhee

Chemistry & Biochemistry Undergraduate Honors Theses

In this study, Protein Equilibrium Population Snapshot Hydrogen-Deuterium Exchange Electrospray Ionization Mass Spectrometry (PEPS-HDX-ESI-MS) was applied to study the local regions of model proteins, staphylococcal nuclease and ubiquitin. The hydrogen deuterium exchange (HDX) has become a key technique for studying the structural and dynamic aspects of proteins in solution. This technique creates a rapid exchange between all of the exchangeable hydrogen ions with deuterium when the protein is exposed to a solvent. The PEPS method is an equilibrium-based method used to determine the populations of the closed native and open denatured states of a protein. By combining the applications of …

Regulation Of The Reaction Between Cytochrome C And Cytochrome Oxidase, Jennifer Silva-Nash

Chemistry & Biochemistry Undergraduate Honors Theses

Irreversible brain damage is commonly seen in patients that have suffered strokes, cardiac arrest, or other brain ischemia events. The hypoxic conditions result in neuron death, and previous studies have shown that additional damage occurs when blood flow is restored. It is thought that the lack of energy production during post-ischemia events also causes severe brain damage, as the brain heavily depends on oxidative phosphorylation. Cytochrome c (Cyt c) plays a crucial role in this energy production by means of the electron transport chain (ETC), transferring electrons between complexes ΙΙΙ (cytochrome bc1) and ΙV (cytochrome c oxidase, CcO). Mitochondrial …

Facilitating Conceptual Learning In Quantitative Chemistry, Sarah R. Johnson

Electronic Theses and Dissertations

Traditional chemistry laboratory courses have a manual consisting of “step-by-step” experiments; instructions are given to complete experiments, requiring minimal information/concepts processing to be successful. This experience leaves students unprepared for the real-world, where critical thinking skills are needed to conduct research. This study focused on building analytical techniques, conceptual knowledge, and critical thinking skills used to solve research problems. A new quantitative chemistry laboratory manual was developed to transition students from traditional to inquiry-based experiments, requiring analytical method development. Data showed students having less difficulty using the new manual (0.8281 average difficulty) on method development exam questions and experiments, compared …

Atp Usage In The Dark-Operative Protochlorophyllide Oxidoreductase, Mark S. Soffe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chlorophylls are essential pigment molecules that function in photosynthesis, and serve to aid in utilizing energy from sunlight to power cellular processes in plants, and other organisms. To make chlorophyll, photosynthetic organisms devote an abundance of resources and energy to ensure their appropriate construction. This process of making chlorophylls is highlighted by the penultimate step in the pathway—the conversion of protochlorophyllide (Pchlide) to chlorophyllide a (Chlide).

This conversion can be mediated in two different ways, depending on the type of organism. The first method incorporates the use of a light-activated system called the light-dependent protochlorophyllide oxidoreductase (LPOR). This system, as …

Structural Insights Into The Regulation Of Electron Transfer In Nitrogenase, And Modulating The Reactivity Of The Isolated Iron Molybdenum Cofactor, Andrew J. Rasmussen

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

One of the most important scientific advances in the last century was the Haber-Bosch process, the industrial process of fixing nitrogen from the atmosphere to ammonia. This allowed for the commercial production and sale of nitrogen for important uses such as fertilizer for farming. The Haber-Bosch process is partially credited with the population boom that has been seen in the last century and has greatly increased the standard of living in the developed world today. While this was a great scientific breakthrough, the cost of producing the required ammonia is high, and roughly 2% of worldwide energy is used annually …

Titanium-Oxides As A Stabilizing Agent For Environmentally Persistent Free Radicals (Epfrs), Josef Baylis

Scholarly and Creative Works Conference (2015 - 2021)

The mechanism of formation for surface bound radicals were studied using ab initio quantum methods. The shift in electron density from transition metal surfaces to surface bound radical groups was studied to learn the mechanism for the binding. Results indicate an oxidation-reduction based mechanism of formation.

Ruthenium-Catalyzed Amination Of Secondary Alcohols Using Borrowing Hydrogen Methodology, Kostiantyn O. Marichev, James M. Takacs

Department of Chemistry: Faculty Publications

A new ruthenium complex catalyzes the amination of primary and secondary alcohols and the regioselective mono- and sequential diamination of diols via the borrowing hydrogen pathway. Several variations on new intra- and intermolecular cyclizations of aminoalcohols, diols and diamines lead to heterocyclic ring systems.

Αβ-Peptide Mimics Of Z-Domain Peptides, Samuel H. Gellman, James W. Checco

Department of Chemistry: Faculty Publications

Described are αβ-peptide mimics of Z-domain scaffold pep tides, methods of making them, and methods of using them. The αβ-peptide mimics include B-amino acid residues and, optionally, disulfide bonds to stabilize the conformation of the mimics. The compounds may be truncated as compared to conventional Z-domain scaffold peptides and are resistant to proteolytic degradation due to the presence off-amino acid residues. The mimics can be made so as to bind selectively to a desired target.

Theoretical Investigation Of Interaction Between The Set Of Ligands And Α7 Nicotinic Acetylcholine Receptor, O. E. Glukhova, Tatiana Prytkova, D. S. Shmygin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between …

Hlarp7 C-Terminal Domain Contains An Xrrm That Binds The 3' Hairpin Of 7sk Rna, Catherine D. Eichhorn, Rahul Chug, Juli Feigon

Department of Chemistry: Faculty Publications

The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal Lamodule binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear.We report the solution NMR structure of the hLARP7 CTD and …

Analytic Ab Initio-Based Molecular Interaction Potential For The Bro·H2O Complex, Ross D. Hoehn, Sachin D. Yeole, Sabre Kais, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrO·H₂O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrO·H₂O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES …

Ring Closures And The Hammond Postulate, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

This work reports an investigation of ring closure processes in relation to the Hammond postulate. Calculations favor the importance of thermodynamics, not kinetics, as the basis for the Hammond postulate. A kinetically rapid, but thermodynamically unfavorable reaction is shown to resemble product. The ease of ring closure to three-membered rings, compared to four-membered rings, is thought to be associated with conformational mobility and perhaps vibrations coupled to the reaction coordinate motion in the case of four-membered rings.

Live, Attenuated Vaccines And Methods Of Making And Using, Jiantao Guo, Qingsheng Li, Wei Niu, Yue Li, Nanxi Wang

Department of Chemistry: Faculty Publications

A live, attenuated HIV vaccine is provided, and methods of making a atenuated HIV vaccine are provided.