Physical Sciences and Mathematics 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 …

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 …

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. …

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 …

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 …

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 …

Obscurin Is A Semi-Flexible Molecule In Solution, Jacob Whitley

Senior Honors Projects, 2010-2019

Obscurin, a giant modular cytoskeletal protein, is comprised mostly of tandem immunoglobulin-like (Ig-like) domains. This architecture allows obscurin to connect distal targets within the cell. The linkers connecting the Ig domains are usually short (3-4 residues). The physical effect arising from these short linkers is not known; such linkers may lead to a stiff elongated molecule or, conversely, may lead to a more compact and dynamic structure. In an effort to better understand how linkers affect obscurin flexibility, and to better understand the physical underpinnings of this flexibility, here we study the structure and dynamics of four representative sets of …

The Benefit Of Precise Chemical Shift And Concentration Referencing In Nmr Applications, Ming Huang

Doctoral Dissertations

“In Nuclear Magnetic Resonance (NMR) spectroscopy, the chemical shift and intensity of NMR signals provide critical information about a sample's molecular structure, reaction conditions, and material properties. For the precise determination of structures and properties, it is critical to know sample or reaction conditions such as temperature, pH, concentration, or absolute amount of material. Chemical-shift and signal-intensity calibrations play a key role for extracting the maximum amount of information from NMR experiments. In this dissertation, internal and external reference standards are used to calibrate NMR spectra with respect to chemical shift and signal intensity. Sealed capillary tubes filled with specific …

Modeling Chaperone-Substrate Interactions Of Alpha Crystallin From The Ocular Lens, Lisa Marie S. Ramirez

Legacy Theses & Dissertations (2009 - 2024)

The α-crystallins (αA- and αB-crystallin isoforms) from the ocular lens are small heat shock proteins and molecular chaperones, widely believed to play a significant role in protecting the lens from cataract. Mutations and modifications on human αA- and αB-crystallin (HAA and HAB, respectively) are linked to a variety of diseases, including cataract formation, neuropathological protein folding disorders, and many others. It is believed that HAA and HAB prevent the aggregation of other lens proteins. However, the structural and thermodynamic details of the chaperone-substrate (aka “client”) interaction are sparse. Therefore, the main objective of this dissertation is to reveal structural and …

Nmr Spectroscopic Properties Of Nucleotides, And A New Method Of Numeric Calculation Of Raman Intensities For Organic Molecules, William R. Ehrhardt

MSU Graduate Theses

General and accurate computational methodologies are currently lacking for large chemical systems. This is primarily due to the computational expense required to perform calculations on systems with one hundred or more atoms. Calculated spectroscopic properties could aid in the process of elucidating structural features of large biologically relevant molecules if accurate and inexpensive methods are developed. Towards this end the first steps were taken to design a general methodology for predicting NMR chemical shifts of large nucleic acid systems. It was found that HF and semi-empirical methods were not sufficient for optimization of nucleobases, and therefore larger nucleotide or nucleic …

Investigation Of Novel Electrolytes For Use In Lithium-Ion Batteries And Direct Methanol Fuel Cells, Kartik Pilar

Dissertations, Theses, and Capstone Projects

Energy storage and conversion plays a critical role in the efficient use of available energy and is crucial for the utilization of renewable energy sources. To achieve maximum efficiency of renewable energy sources, improvements to energy storage materials must be developed. In this work, novel electrolytes for secondary batteries and fuel cells have been studied using nuclear magnetic resonance and high pressure x-ray scattering techniques to form a better understanding of dynamic and structural properties of these materials. Ionic liquids have been studied due to their potential as a safer alternative to organic solvent-based electrolytes in lithium-ion batteries and composite …

Bimetallic Complexes: The Fundamental Aspects Of Metal-Metal Interactions, Ligand Sterics And Application, Michael Bernard Pastor

University of the Pacific Theses and Dissertations

Metal containing complexes have been used to catalyze various organic transformations for the past few decades. The success of several mononuclear catalysts led to transition metal catalysts used in pharmaceuticals, environmental, and industrial processes. While mononuclear complexes have been used extensively, bimetallic systems have received far less attention. Bimetallic or polynuclear sites are commonly found in metalloenzymes that perform elegant transformation in biological systems, underlying their significance. Inorganic chemists take inspiration from nature and design model bimetallic complexes to further study this cooperativity effect. A bimetallic platform offers many structural and functional differences such as the identity of the metal …

Structure Of The Picornavirus Replication Platform: A Potential Drug Target For Inhibiting Virus Replication, Meghan Suzanne Warden

Chemistry & Biochemistry Theses & Dissertations

Picornaviruses are small, positive-stranded RNA viruses, divided into twelve different genera. Members of the Picornaviridae family cause a wide range of human and animal diseases including the common cold, poliomyelitis, foot and mouth disease, and dilated cardiomyopathy. The picornavirus genome is replicated via a highly conserved mechanism involving a presumed cloverleaf structure located at the 5’ noncoding region of the virus genome. The 5’ cloverleaf consists of three stem loops (B, C, and D) and one stem (A), which interact with a variety of virus and host cell proteins during replication. In this dissertation, human rhinovirus serotype 14 (HRV-14) SLB …

Hydroformylation And Aldehyde-Water Shift Catalysis By Dirhodium Tetraphosphine Complexes, Marshall Douglas Moulis

LSU Doctoral Dissertations

The use of a unique tetraphosphine ligand (et,ph-P4) allows for the chelating of two rhodium centers to perform bimetallic coopertivity in hydroformylation reactions to better the yields the linear aldehyde product. The proposed catalyst is [Rh₂(μ-H)₂(CO)₄(rac-et,ph-P4)]²⁺ and has been studied by in situ FT-IR and NMR. When tested in a polar phasic acetone/water (30 % by vol.), the catalyst forms a monocationic system [Rh₂(μ-H)₂(CO)₄(rac-et,ph-P4)]⁺ that has an initial TOF of 26 min^-1, selectivity of 27:1 L:B, and low byproducts of …

Alicyclic And Aromatic Carboxylic Acids In Soil Organic Matter: An Investigation Of Potential Origin And Association With Plutonium Using Advanced Analytical Techniques, Nicole Didonato

Chemistry & Biochemistry Theses & Dissertations

Carboxylic acids are a defining component of soil organic matter, responsible for many of the physical and chemical properties, including metal-organic matter interactions, which govern its role as an important constituent of soils. However, there is a shortage of detailed molecular level information regarding orientation and structural arrangement of carboxylic acids within soil organic matter. This dissertation utilizes electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) as well as solid-state and multi-dimensional nuclear magnetic resonance (NMR) to investigate the molecular formula composition within several organic matter sources and the primary structures that feature carboxylic acids. Soil organic matter …

Structural Characterization Of The Interactions Of Nicotinamide And Analogs With Human Sirt6 By Saturation Transfer Difference (Std) Nmr And Site Directed Mutagenesis, Beatriz Elena Bolivar-Vega

Legacy Theses & Dissertations (2009 - 2024)

The allosteric regulation of SIRT6 by nicotinamide (NAM), along with the growing evidence of this enzyme's key role in the immune response, prompted the mechanistic study of SIRT6 inhibition by pyrazinamide (PZA) and analogs. In our current study, PZA, an analog of NAM, was revealed to have a modest modulatory effect on SIRT6, an enzyme that regulates the NF-κB signaling pathway at the transcriptional level (a relevant pathway to inflammation). Similarly, the analogs of PZA, 5-Cl PZA, 5-MeO PZA, and POA exhibited a modulatory effect against SIRT6 in our in vitro studies, enabling identification of a potential new target for …

Synthesis, Reactivity, And Nmr Trends Of Early Transition Metal Compounds, Tabitha Marie Cook

Doctoral Dissertations

This dissertation focuses of three different subjects. The first is the synthesis and characterization of heptacoordinate amidinate compounds. Heptacoordinate compounds are not common, but their structures have been studied. Group 4 amidinate compounds have been used as precursors in the CVD/ ALD processes. Ancillary ligands, such as amidinates, have been used to reduce air-sensitivity of complexes. Reactions of these complexes with water have been used to make metal oxide thin films.

In the first study, the complexes Zr[MeC(NⁱPr)₂]₃Cl [zirconium trisamidinate chloride], Hf[MeC(NⁱPr)₂]₃Cl [hafnium trisamidinate chloride], Zr[MeC(NⁱPr) …

Modeling The 3-Dimensional Structure Of D(Cgcgaattcgcg) And Its 8-Oxo-Da5 Adduct With 1h Nmr Noesy Refinements, Christopher Miles Reynolds

MSU Graduate Theses

Since the characterization of the oligomer d(CGCGAATTCGCG) has been published by Dickerson et al., computational studies have been carried out to produce an accurate 3D model. These models are important for visualizing how certain DNA repair enzymes, such as the glycosylases, recognize sites of damage by signatures of local 3D distortion. Using 1H NOESY-generated internuclear distances to replicate the model of this oligomer and a derivative with an 8-oxo-dA5 lesion, we propose characteristics of helical distortion that DNA glycosylases might use for identifying this form of damage. In addition, this method of comparison can be used to study the repair …

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 …

Evaluating The Role That A Putative Fxiii Binding Site Plays In The Reactivity Of Three Glutamines Within The Coagulation Substrate Fibrinogen Aα (233-425)., Chad A. Stephens

College of Arts & Sciences Senior Honors Theses

Formation of a stable thrombus in vivo depends on the interaction between fibrinogen and the transglutaminase factor XIII (FXIII). Characteristics of blood plasma, such as concentration of Ca2+, are well known to regulate the activation and subsequent reactivity of FXIII. Despite this knowledge, the role fibrin(ogen) plays in modulating FXIII activation and reactivity is not entirely delineated. Currently, the coagulation substrate fibrinogen Aα is proposed to contain a binding site for the active factor XIII with fibrinogen Aα E396 serving a major role. A series of mass spectrometry and NMR spectroscopy studies was conducted to assess whether putative interactions between …

Optimizing Protocols For Carbohydrate Nmr Chemical Shift Computations, Michael Trent Kemp

USF Tampa Graduate Theses and Dissertations

The spectroscopic analysis of cellulose is experimentally challenging while computationally accessible with recent developments in NMR code. However, prior to using density functional theory to calculate the NMR chemical shifts of cellulose, smaller, sugar-like molecule systems need to be benchmarked against experimental values. The quantum mechanical / molecular mechanical (QM/MM) calculations presented herein utilize six test systems: ethanol, pyridine, pyrrolidine, pyrrole, myo-inositol and scyllo-inositol in conjunction with the reference tetramethylsilane used to scale the calculated isotropic shielding tensors to relative chemical shifts. The effect of solvent on calculated NMR chemical shifts has also been investigated with regard to quantity of …

Fundamental Studies Of Humic Acid's Influence On Pollutant Toxicity To Aquatic Organisms, Rachel Dawn Deese

LSU Doctoral Dissertations

The main purpose of the research presented in this dissertation was to further understand the intricate and convoluted interactions between natural organic material, biological entities, and pollutants. This was achieved by utilizing humic acids (HAs) from differing sources, chemically modified humic acid, two biological entities (model biomembranes and Artemia Franciscana), and three types of pollutants (cations, surfactants, and carbon nanotubes). Fluorescence spectroscopy and model biomembranes were used to measure the change in HA’s ability to interact with the biomembranes in the presence of cations. Three differently sourced HAs, chemical modified HAs, and a range of cations were studied to elucidate …

Investigating The Structure Of The Papain-Inhibitor Complex Using Spr And Nmr, Margaret Sara Thomasson

LSU Doctoral Dissertations

Cysteine proteases (CPs) are enzymes with a nucleophilic thiol in their active sites. Inhibitors of cysteine proteases (ICPs) occur naturally in bacterial pathogens and some protozoa. In parasites, ICPs are often virulence factors, contributing to the formation and survival of amastigotes within host cells. These amastigotes have higher CP activity, therefore making both ICPs and CPs potential drug targets. Despite great genetic variability, ICPs contain highly conserved structural features, including a series of defined loops that play a significant role in binding CPs. Papain, a CP from Carica papaya, complexes with ICP from Leishmania mexicana. Although the individual 3-D structures …