Chemistry Commons^™

Computational Study About Noncovalent Bonding Systems Involving Halogen, Chalcogen And Pnicogen Bonds, Jia Lu

All Graduate Theses and Dissertations, Fall 2023 to Present

First terms used in this thesis are introduced and defined as follows. In the periodic table, the elements in the 17^th column are named halogen including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I). The elements in the 16^th column are named chalcogen including oxygen (O), sulfur (S), selenium (Se) and tellurium (Te). The elements in the 15^th column are named pnicogen including nitrogen (N), phosphorus (P), arsenic (As) and antimony (Sb).

After hydrogen bonds (B-H⋅⋅⋅B) are well studied and understood by scientists and researchers, halogen bonds (R-X⋅⋅⋅B) have drawn attention due to the similarities in …

Scandium Triflate-Catalyzed Aromatic Aldehydic C-H Activation, Nicholas Griffin

Honors Projects

Herein described is a scandium triflate-catalyzed C-H activation of commercially available aromatic aldehydes achieved in low yields. The reaction occured in a one-pot synthesis over a two-hour duration and required minimal purification. Inclusion of a fluorine-tagged phenol allowed for reaction monitoring via ¹⁹FNMR.

Elucidating The Structure And Regulatory Interactions Of The Hotair Non-Coding Rna And The Bacterial Rnase P. Holoenzyme, Ainur Abzhanova

Dissertations (1934 -)

RNA structures and RNA-protein interactions are studied as potential drug targets, biomarkers in cancer, and can be administered as vaccines. The cancer associated HOTAIR (HOX transcript antisense RNA) exists in higher vertebrates and interacts with chromatin remodeling enzymes. We examined the thermodynamic folding properties and structural propensity of the exonic regions of HOTAIR using biophysical methods and NMR spectroscopy. Different exons of HOTAIR contain variable degrees of structural heterogeneity. We identify one exonic region, exon 4, that adopts a stable and compact fold under low magnesium concentrations. Close agreement of NMR spectroscopy and chemical probing confirm conserved base pair interactions …

Advances In Structure Elucidation Of Small Molecules And Peptides By Nuclear Magnetic Resonance Spectroscopy And Mass Spectrometry, Ryan D. Cohen

Seton Hall University Dissertations and Theses (ETDs)

This dissertation reports on improvements in nuclear magnetic resonance (NMR) and mass spectrometry (MS) structure determination methods of organic compounds, with particular focus on challenging cyclic peptides. A recent and important innovation in NMR spectroscopy is the combination of theoretical property predictions, such as chemical shifts, using density functional theory (DFT) to aid in challenging NMR structure assignments, such as determination of regio- and stereo-configurations. In the first part of this thesis, a comprehensive benchmark study of DFT chemical shift prediction methods was performed using experimental NMR data collected from 50 well curated compounds, which was referred to as the …

Modeling Accuracy Matters: Aligning Molecular Dynamics With 2d Nmr Derived Noe Restraints, Milan Patel

Honors Scholar Theses

Among structural biology techniques, Nuclear Magnetic Resonance (NMR) provides a holistic view of structure that is close to protein structure in situ. Namely, NMR imaging allows for the solution state of the protein to be observed, derived from Nuclear Overhauser Effect restraints (NOEs). NOEs are a distance range in which hydrogen pairs are observed to stay within range of, and therefore experimental data which computational models can be compared against. To that end, we investigated the effects of adding the NOE restraints as distance restraints in Molecular Dynamics (MD) simulations on the 24 residue HP24stab derived villin headpiece subdomain to …

Extracellular Poly(Hydroxybutyrate) Bioplastic Production Using Surface Display Techniques, Kevin Beaver, Ashwini Dantanarayana, Willisa Liou, Markus Babst, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Poly(hydroxybutyrate) is a biocompatible, biodegradable polyester synthesized naturally in a variety of microbial species. A greener alternative to petroleum-based plastics and sought after for biomedical applications, poly(hydroxybutyrate) has failed to break through as a leading material in the plastic industry due to its high cost of production. Specifically, the extraction of this material from within bacterial cells requires lysis of cells, which takes time, uses harsh chemicals, and starts the process again with growing new living cells. Recently, surface display of enzymes on bacterial membranes has become an emerging technique for extracellular biocatalysis. In this work, a fusion protein lpp-ompA-phaC …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …

Enhancing The Conformational Stability Of The Cl-Par-4 Tumor Suppressor Via Site-Directed Mutagenesis, Samjhana Pandey, Krishna K. Raut, Andrea M. Clark, Antoine Baudin, Lamya Djemri, David S. Libich, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40 kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered protein whose downregulation has been observed in various cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) is active and plays a role in tumor suppression by inhibiting cell survival pathways. Here, we employed site-directed mutagenesis to create a cl-Par-4 point mutant (D313K). The expressed and purified D313K protein was characterized using biophysical techniques, and the results were compared to that of the wild-type (WT). We have …

Tenvr: Matlab-Based Toolbox For Environmental Research, Aleksandar I. Goranov, Rachel L. Sleighter, Dobromir A. Yordanov, Patrick G. Hatcher

Chemistry & Biochemistry Faculty Publications

With the advancements in science and technology, datasets become larger and more multivariate, which warrants the need for programming tools for fast data processing and multivariate statistical analysis. Here, the MATLAB-based Toolbox for Environmental Research "TEnvR" (pronounced "ten-ver") is introduced. This novel toolbox includes 44 open-source codes for automated data analysis from a multitude of techniques, such as ultraviolet-visible, fluorescence, and nuclear magnetic resonance spectroscopies, as well as from ultrahigh resolution mass spectrometry. Provided are codes for processing data (e.g., spectral corrections, formula assignment), visualization of figures, calculation of metrics, multivariate statistics, and automated work-up of large datasets. TEnvR allows …

Conformation Of The U12-U6atac Snrna Complex Of The Minor Spliceosome And Binding By Ntc-Related Protein Rbm22, Joanna Ciavarella

Dissertations, Theses, and Capstone Projects

Splicing of precursor messenger (pre-m)RNA is a critical process in eukaryotes in which the non-coding regions, called introns, are removed and coding regions, or exons, are ligated to form a mature mRNA. This process is catalyzed by the spliceosome, a multi-mega Dalton ribonucleoprotein complex assembled from five small nuclear ribonucleoproteins (snRNP) in the form of small nuclear (sn)RNA-protein complexes (U1, U2, U4, U5 and U6) and >100 proteins. snRNA components catalyze the two transesterification reactions while proteins perform critical roles in assembly and rearrangement. U2 and U6 snRNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA. …

Meta-Analysis Reveals Both The Promises And The Challenges Of Clinical Metabolomics, Heidi E. Roth, Robert Powers

Chemistry Department: Faculty Publications

Clinical metabolomics is a rapidly expanding field focused on identifying molecular biomarkers to aid in the efficient diagnosis and treatment of human diseases. Variations in study design, metabolomics methodologies, and investigator protocols raise serious concerns about the accuracy and reproducibility of these potential biomarkers. The explosive growth of the field has led to the recent availability of numerous replicate clinical studies, which permits an evaluation of the consistency of biomarkers identified across multiple metabolomics projects. Pancreatic ductal adenocarcinoma (PDAC) is the third-leading cause of cancer-related death and has the lowest five-year survival rate primarily due to the lack of an …

Optimization Of The Synthesis Parameters Of Sapo-34, Adam Honchar

Undergraduate Student Research Internships Conference

A microporous material known as SAPO-34 is a very efficient catalyst in methanol-to-olefins reactions. My project aimed to optimize synthesis parameters of SAPO-34 to reduce crystallization time in order to study the formation mechanism using In-situ NMR spectroscopy. Understanding the crystallization mechanism would allow us to make it more efficient and tailor-made to fit for other applications.

The Synthesis Of Deuterated Isohumulones For Use As Internal Standards In Lc-Ms Stable Isotope Dilution Assays, Patrick Gleason, Bruce Hamper Dr.

Undergraduate Research Symposium

Humulones are compounds that are prevalent in the hops flowers (Humulus Lupulus) used in beer brewing. These compounds undergo isomerization during the brewing process, and the resulting isohumulones are considered to be the primary contributors to the bitter flavors present in beer. As such, quantifying their presence, and the relative presence of their homologs(n-, co-, ad-), is of great importance in the characterization of beer. In this effort, one of the homologs of humulone (co) was isolated before being subsequently isomerized and deuterated for the purpose of analyzing beer by stable isotope dilution assay mass spectrometry(SIDA-MS). The addition of this …

Sortase-Mediated Ligation To Investigate Large Idr-Containing Cytoskeletal Regulators, Melissa Oueld Es Cheikh

WWU Graduate School Collection

About 43% of eukaryotic proteins contain intrinsically disordered regions (IDRs) of 40 residues or longer. These proteins modulate key cellular functions such as transcription, translation, and signal transduction. Despite their vital roles, little is known about the properties of large disordered proteins due to the difficulties encountered studying them. Solution nuclear magnetic resonance (NMR) spectroscopy is a unique tool allowing for their analysis but traditionally requires uniform protein labeling with 15N and 13C isotopesresulting in convoluted spectra which obscure any meaningful information on their structures and interactions. To remedy this issue, we aim at developing a procedure to segmentally label …

In Situ Study Of Geological Fluid Inclusions Using 23na Nuclear Magnetic Resonance Spectroscopy, Stephen Pilar

Electronic Thesis and Dissertation Repository

²³Na Magic Angle Spinning Solid State Nuclear Magnetic Resonance (MAS SS NMR) spectroscopy has been used to study natural geological samples of halite, fluorite, and quartz to evaluate the efficacy of NMR spectroscopy for in situ fluid inclusion analysis. NaCl calibration standards yielded a strong linear correlation (R²=0.9919) for salinity, albeit only over a ~1 ppm breadth of chemical shift. Fluid inclusions were successfully identified in all three types of minerals studied using MAS NMR. Chemical analysis with Inductively Coupled Plasma -- Mass Spectrometry (ICP-MS) was employed to quantify elemental contaminants in halite samples. Powder X-Ray Diffraction …

Characterization Techniques And Cation Exchange Membrane For Non-Aqueous Redox Flow Battery, Kun Lou

Doctoral Dissertations

The motivation of this work comes from one of the major problems of emerging non-aqueous flow battery (NAFB) that a separator or membrane which facilitates conductivity and blocks redox species crossover does not exist. Although many aspects of principles can be mirrored from mature fuel cell and aqueous flow battery, it is found that some well-defined membrane properties in aqueous systems such as swelling, transport and interactions are different in non-aqueous solvents to some extent. However, the approach of this work does follow the way perfluorosulfonate ion exchange membrane (PFSA) facilitated development of fuel cell and aqueous flow battery in …

Chemical Shift Assignments Of The N-Terminal Domain Of Psd95 (Psd95-Nt), Yonghong Zhang, Johannes W. Hell, James B. Ames

Chemistry Faculty Publications and Presentations

Postsynaptic density protein-95 (PSD95) contributes to the postsynaptic architecture of neuronal synapses and plays an important role in controlling synaptic plasticity. The N-terminal domain of PSD95 (residues 1–71, called PSD95-NT) interacts with target proteins (calmodulin, α-actinin-1 and CDKL5), which regulate the Ca2+-dependent degradation of glutamate receptors. We report complete backbone NMR chemical shift assignments of PSD95-NT (BMRB No. 50752).

Biochemical Analysis Of Dual T-Loop Rna Motifs That Perform Shape Recognition Of The Trna Elbow, John Aparicio Aguirre

Master's Theses (2009 -)

T-loops are highly abundant, structurally conserved five nucleotide motifs that facilitate long range intra- and intermolecular interactions and function to stabilize the tertiary fold of RNA. Interlocked or dual T-loop motifs provide additional thermodynamic stability and perform long-range docking of other RNA molecules. Dual T-loop RNA structures are present within the multi-turnover ribonuclease P-based ribozyme, the ribosome, and the bacterial tRNA-sensing riboswitch genetic element. In all three systems, a dual T-loop structure recognizes TYC/D-loop region of tRNA. Interestingly, sequence conservation at specific positions in the T-loops suggest a conserved interlocked RNA architecture. While X-ray crystallography provides insight into the putative …

Investigations Of The Structure And Protein-Protein Interactions Of Chlamydia Trachomatis Scc4, Thilini Oshadhi Senarath Ukwaththage

LSU Doctoral Dissertations

Chlamydia trachomatis (CT) is the most common, sexually transmitted bacterial disease (STD) in the world. In the developmental cycle of CT, specific chlamydia chaperone 4 (Scc4) is a unique protein with essential and multiple roles. Hence, Scc4 is significant as a virulence target for therapeutic approaches to treat chlamydial infections. A novel approach was discovered to purify tag free Scc4 by utilizing a 6X-histidine-tag on Scc1 in the co-expressed Scc4:Scc1 complex by capturing the complex on nickel-charged immobilized metal affinity chromatography resin, followed by dissociation of Scc4 with sarkosyl. Using triple resonance NMR experiments, backbone and sidechain resonances …

Comparison Of Bifurcated Halogen With Hydrogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way …

Synthetic Pathways For Potential Platinum 1,10-Phenanthroline Compounds, Jacob Young

Mahurin Honors College Capstone Experience/Thesis Projects

There are extremely important uses for platinum when it comes to the treatment of cancers and dementias. One potential therapeutic combines platinum with a structure known as phenanthroline. This platinum phenanthroline structure is normally extremely water-insoluble, rendering it difficult to study and use in biological systems. The Williams’ Biochemistry Laboratory endeavored to find a simpler synthetic pathway for a water-soluble phenanthroline product. While unsuccessful in identifying a product as of yet, many synthetic pathways have been ruled out, and more hypothetical pathways are being formulated for testing.

Among the strategies analyzed are varying solvent, reagents, apparatus, methodology, and temperature in …

Direct Determination Of Absolute Stereochemistry Of Α-Methylselenocysteine Using The Mosher Method, Robert J. Wehrle, Douglas R. Powell, Douglas S. Masterson

Faculty Publications

Mosher amides of α-methylselenocysteine were synthesized to determine the absolute stereochemistry of the sterically hindered α-carbon utilizing ¹H, ¹³C, ¹⁹F, and ⁷⁷Se NMR spectroscopies. After analysis of these spectra using the established Mosher method, the stereochemistry of the α-carbon was determined to be (R), which was subsequently confirmed using x-ray crystallography.

The Application Of Machine Learning In Analyzing Organic Compounds From Nmr Spectral Data, Nicole Maia Powell

Senior Independent Study Theses

Nuclear magnetic resonance (NMR) is used in organic chemistry to identify unknown organic compounds. The data obtained from an NMR spectrometer are typically shown in the form of a spectrum, which is then analyzed by an analytical chemist. The action of analyzing a spectrum, especially one of a large and complex molecule, is a long and tedious process. In this project, Python is used to implement hierarchical clustering on NMR data obtained from an NMR spectrometer at the College of Wooster to explore its application in NMR analysis. MATLAB is used to build a decision tree from the same data, …

Functionalized Materials From Atom Transfer Radical Processes, Sean Fischer

Electronic Theses and Dissertations

This work is focused on the synthesis, characterization, and application of functionalized materials prepared from atom transfer radical processes. Atom transfer radical processes encompass both atom transfer radical addition (ATRA) and polymerization (ATRP) reactions, both of which are catalyzed by ppm amounts of copper complexes. The synthetic efforts of ATRA include increasing adduct selectivity through optimization of reaction conditions to generate small molecules in high to moderate yields. ATRA provides retention of the halogen moiety, which is an attractive functional group that can be further modified with other transformations. Specifically, the copper-catalyzed azide-alkyne [3+2] cycloaddition (CuAAC) allows for the realization …

Characterization Of Dna Interstrand Cross-Linking Agents By Liquid Chromatograhy-Mass Spectrometry, Anahit Marina Campbell

Theses and Dissertations

This study is to characterize novel reactive oxygen species (ROS)-activated nitrogen mustard analogues and UV-activated alkylating agents by Liquid Chromatography-Mass Spectrometry (LC-MS). First, we optimized the instrument conditions to successfully ionize a few novel binapthalene analogues and methoxybenzene analogues by MS. The highest signal intensity for compounds 3-10 was observed when atmospheric pressure chemical ionization (APCI) with an optimized corona needle position of 5mm or 10 mm was used, which led to successful analysis of compounds 3-10 by MS. Second, we determined pharmacokinetic properties of a drug compound (FAN-NM-CH3), including animal study, assay development, optimization of MS/MS instrumental parameter and …

Electrochemical Reduction Of Carbon Dioxide And Carbon Monoxide For The Production Of Green Fuels And Chemicals., Jacob M. Strain

Electronic Theses and Dissertations

It has become apparent that closing the carbon cycle on this planet in order to mitigate disastrous consequences of runaway global warming has become one of the most pressing issues of our civilization. One of the ways we need to accomplish this goal is by finding news methods to generate fuels that will be carbon neutral. Renewable fuels and green chemicals will be a major component of closing the carbon cycle and restoring our planet’s ecosystem into a sense of balance. A method that can help achieve this goal is the reduction of CO₂. If CO₂ can …

Phosphorus Nmr And Its Application To Metabolomics, Paula Evans, Fatema Bhinderwala, Robert Powers, Martha Morton, Thomas Smith

UCARE Research Products

Stable isotopes are routinely employed by NMR metabolomics to highlight specific metabolic processes and to monitor pathway flux. 13C-carbon and 15N-nitrogen labeled nutrients are convenient sources of isotope tracers and are commonly added as supplements to a variety of biological systems ranging from cell cultures to animal models. Unlike 13C and 15N, 31P-phosphourous is a naturally abundant and NMR active isotope that doesn’t require an external supplemental source. To date, 31P NMR has seen limited usage in metabolomics because of a lack of reference spectra, difficulties in sample preparation, and an absence of two-dimensional (2D) NMR experiments. But, 31P NMR …

Nucleophilic Substitution Reactions Of Monofunctional Nucleophilic Reagents Withcyclotriphosphazenes Containing 2,2-Dioxybiphenyl Units, Esra Tanriverdi̇ Eçi̇k, Hani̇fe İbi̇şoğlu, Gönül Yeni̇lmez Çi̇ftçi̇, Gi̇zem Demi̇r, Eda Erdemi̇r, Fatma Yüksel

Turkish Journal of Chemistry

The nucleophilic substitution reactions of mono- and bis-spiro-2,2' -dioxybiphenyl cyclotriphosphazenes (3 and 4) with cyclopropanemethylamine (5) and aniline (6) were performed in the presence of trimethylamine in THF. Five novel cyclopropanemethylamino- and anilino-substituted spiro-2,2' -dioxybiphenyl cyclotriphosphazene derivatives (7-11) were obtained from these reactions. The molecular structures of the new cyclotriphosphazene derivatives (7- 11) were characterized by elemental analysis, MALDI-TOF MS, FT-IR, and NMR ( $^{31}$P and $^{1}$H) spectroscopies. The structure of the spiro-(2,2' -dioxybiphenyl)-bis-(anilino)-cyclotriphosphazene (11) was also determined by single-crystal X-ray crystallography.

Ribbon Α-Conotoxin Ktm Exhibits Potent Inhibition Of Nicotinic Acetylcholine Receptors, Leanna A. Marquart, Matthew W. Turner, Lisa R. Warner, Matthew D. King, James R. Groome, Owen M. Mcdougal

Chemistry and Biochemistry Faculty Publications and Presentations

KTM is a 16 amino acid peptide with the sequence WCCSYPGCYWSSSKWC. Here, we present the nuclear magnetic resonance (NMR) structure and bioactivity of this rationally designed α-conotoxin (α-CTx) that demonstrates potent inhibition of rat α3β2-nicotinic acetylcholine receptors (rα3β2-nAChRs). Two bioassays were used to test the efficacy of KTM. First, a qualitative PC12 cell-based assay confirmed that KTM acts as a nAChR antagonist. Second, bioactivity evaluation by two-electrode voltage clamp electrophysiology was used to measure the inhibition of rα3β2-nAChRs by KTM (IC₅₀ = 0.19 ± 0.02 nM), and inhibition of the same nAChR isoform by α-CTx MII (IC₅₀ = …

Synthesis Of Novel Reiii And Rev Metallointercalator Complexes For Use As Dna Damage Probes, Eli Schwartz

Honors Program Theses and Projects

Cancer is a disease that affects millions around the globe. Treatments such as radiation and chemotherapy are often used to treat cancerous tumors, but are not 100% effective in curing the patient. Alternatively, some research groups have proposed the use of metallointercalators, metal complexes consisting of a rhodium, ruthenium, or iridium metal center with bidentate supporting ligands such as bipyridine and phenanthroline, or tridentate ligands such as terpyridine. The complexes also contain a bidentate intercalating group such as dipyridophenazine. These complexes possess the ability to directly bind to DNA through intercalation between the stacks of DNA base pairs, giving them …