Physical Sciences and Mathematics Commons^™

Probing Of Carbohydrate-Protein Interactions Using Galactonoamidine Inhibitors, Jessica B. Pickens

Graduate Theses and Dissertations

Glycoside hydrolases are ubiquitous and one of the most catalytically proficient enzymes known, and thus understanding their mechanisms are crucial. Most research has focused on the interaction of the glycon of substrates and their inhibitors within the active site of glycoside hydrolases. The inhibitors employed to probe these interactions generally had small aglycons (i.e. a hydrogen atom, amidines, small aliphatic groups, or benzyl groups). Here, the interactions of the aglycon with glycoside hydrolases are examined by probing the active sites with a library of 25 galactonoamidines. The studies described in this dissertation aim to increase the understanding of stabilization of …

The Curious Case Of Nad-Cleaving Nudix Hydrolases, Atreyei Ray

Theses and Dissertations

Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds (x). These enzymes have catalytic activity on a wide range of substrates such as dNTPs (both canonical and their oxidized forms), nucleotide sugars, alcohols, dinucleoside polyphosphates, dinucleotide cofactors, and nucleoside diphosphates linked to RNA. The bacterial genome encodes around 13, while the human genome encodes for 22 such nudix proteins.

The E. coli genome encodes for a mutT mutator gene, the progenitor of the family expressing the MutT pyrophosphohydrolase (NudA) protein (Treffers et al., 1954; Bhatnagar et al., 1988). The enzyme …

Synthesis And Study Of Hydroxytyrosol Derivatives, Ebenezer Ametsetor

Electronic Theses and Dissertations

Hydroxytyrosol is one of the most powerful known antioxidants. It is a naturally occurring polyphenol, most commonly produced in olive trees, (Olea europaea). The remarkable antioxidant and pharmacological properties of hydroxytyrosol has made it an outstanding compound in the polyphenol family and of great interest to many researchers. Hydroxytyrosol can scavenge free radicals produced during cellular oxidative stress and helps to protect the integrity of cells in living systems. Despite its numerous biological and pharmacological uses, it is found in very low concentration in olive oil, this limits its availability for biomedical applications. This work reports a novel and effective …

Structure Elucidation Of A Pyrrolobenzodiazepine Alkaloid And A Biologically Active Polyketide Produced By Rhodococcus Sp. Mtm3w5.2 Via Two-Dimensional Nmr Spectroscopy, Garrett Johnson

Electronic Theses and Dissertations

As the battle against ever-increasing drug resistence bacteria rages on, novel and sometimes more complex natural products can be used to combat this. In this study, two-dimensional NMR techniques were utilized to collect a complete spectral data set for two natural products. The first structure, a synthesized Pyrrolobenzodiazepine alkaloid natural product was confirmed through these methods. The second, a strain of Rhodococcus, MTM3W5.2, produces a novel antibacterial molecule in broth cultures and the active compound was fractionated using a Sephedex LH-20 column. Chromatographic purification yielded a pure sample at 58.90 minutes, RT.58. HRMS data deduced an exact mass of …

Reactivity Of Photogenerated Amine Radical Cations, Qile Wang

Graduate Theses and Dissertations

Recently photoredox catalysis has emerged as a powerful tool in organic synthesis led by Professor McMillan, Stephenson, Yoon. Upon absorption of visible light, photocatalyst can be excited to its singlet state followed by intersystem crossing to form a long lived excited triplet state. While amine serves as electron donor, single electron transfer (SET) can happen between excited triplet photocatalyst and nitrogen atom on amine to give a reduced photocatalyst and amine radical cation.

Cyclopropylamines or cyclobutylamines can be oxidized by excited photocatalyst to generate amine radical cations and due to the ring strain, subsequent C-C bond cleavages can lead to …

Preparation Of Folic Acid-Carbon Dots-Doxorubicin Nanoparticles As Targeting Tumor Theranostics, Samson Dada

Electronic Theses and Dissertations

Carbon dots (CDs) have attracted much attention as an excellent gene/drug delivery and biological imaging agent for early cancer theranostics. In this study, we prepared two series of nanoparticles (NPs), which are composed of (CDs) with a targeting agent, folic acid (FA), and a chemotherapeutic agent Doxorubicin (Dox). All the NPs and their intermediates were characterized using ultraviolet-visible spectroscopy (UV-vis), fluorescence spectroscopy, and Fourier transform-infrared spectroscopy (FT-IR). The drug loading capacity (DLC) and drug loading efficiency (DLE) of two series of FA-CDs-Dox were assessed using UV-vis absorption spectroscopy at the wavelength of 485 nm. Both showed good DLE and DLC …

Study Of Amorphous Boron Carbide And Hydrogenated Boron Carbide Materials Using Molecular Dynamics And Hybrid Reverse Monte Carlo, Rajan Khadka

MSU Graduate Theses

We present a computational study of amorphous boron carbide (a-B_xC) models using Molecular Dynamics (MD) studied with Stillinger-Weber (SW) and ReaxFF potential. The atomic structure factor (S(Q)), radial distribution function (RDF) and bond lengths comparison with other experimental and ab initio models shows that a random arrangement of icosahedra (B₁₂, B₁₁C) interconnected by chains (CCC, CBC) are present in a-B_xC. Afterward, Hybrid Reverse Monte Carlo (HRMC) technique is used to recreate a-B_xC structures. The existing SW potential parameters of Boron are optimized for the α-rhombohedral (Icosahedral B_{12 …}

Probing The Early Steps In The Catalytic Reduction Of Nitrite To Ammonia, Catalyzed By Cytochrome C Nitrite Reductase, Md Mahbbat Ali

Theses and Dissertations

Cytochrome c Nitrite Reductase (ccNiR) is a periplasmic, decaheme homodimeric enzyme that catalyzes the six-electron reduction of nitrite to ammonia. Under standard assay conditions catalysis proceeds without detected intermediates, and it’s been assumed that this is also true in vivo. However, this report demonstrates that in vitro it’s possible to trap putative intermediates by controlling the electrochemical potential at which reduction takes place. Such experiments provide valuable insights regarding ccNiR-catalyzed nitrite ammonification.

UV/Vis spectropotentiometry showed that nitrite-loaded Shewanella oneidensis ccNiR is reduced in a concerted 2-electron step to generate an {FeNO}7 moiety at the active site, with an associated midpoint …

Optimizing Hydrogen Sulfide Removal And Biogas Production Using The Water Wash Method, Brian Leightner

Theses and Dissertations

Biogas forms from decomposing organic material in agricultural digesters, landfills, and wastewater treatment plant digesters. Biogas is mostly composed of methane, and can be used as a carbon-based fuel. Microorganisms that consume organics in these waste streams also produce hydrogen sulfide (H2S) as part of the biogas, in varying trace amounts. H2S is corrosive to engines and pipes for machinery, a human health hazard when inhaled, and an aquatic hazard when dissolved in water. Water washing is an absorption process that dissolves hydrogen sulfide and other water soluble compounds in this process and carries it away from the gas, thereby …

Part I: A Concise Asymmetric Synthesis Of Microtubule Inhibitor Tryprostatin B Part Ii: Synthesis And Biological Assessment Of Histone Deacetylase (Hdac) Inhibitors Part Iii: Acid Catalyzed Reactions Of Aromatic Ketones With Ethyl Diazoacetate, Md Mizzanoor Rahaman

Theses and Dissertations

PART I: A CONCISE ASYMMETRIC SYNTHESIS OF MICROTUBULE INHIBITOR TRYPROSTATIN B

Tryprostatin (TPS) A and B, microtubule inhibitor, are the members of a family of prenylated Trp-Pro diketopiperzine alkaloids. These two natural products were isolated in 1995 from the fermentation broth of Aspergillus fumigatus BM939 by Osada and coworkers. TPS and related diketopiperazine containing compounds such as phenylahistins, spirotryprostatins, and cyclotryprostatins are inhibitors of the mammalian cell cycle. They prevent cell cycle progression at the G2/M phase through a unique mechanism consisting of inhibiting the interaction between microtubule assisted proteins (MAP-2) and the C-terminal end of tubulin. TPS A and …

Controlling And Manipulating Microscopic Particles In Solution By Using Various Electric Field Geometries, Xavier Sacro Udad

Theses and Dissertations

Progress in micro- and nanotechnologies depends on our capability of manipulating and interacting with microscopic particles and nanosize material. A promising approach towards this goal is the use of electric fields, which are the dominant forces at the molecular length scale. One technique for trapping nanoparticles in solution uses an externally controlled electric field, generated by two electrode pairs, to counteract the Brownian motion of a single, selected particle. Unlike other trapping tools, such as optical tweezers or magnetic tweezers, this approach scales favorably with particle size, down to the level of a single molecule. However, it depends on real-time …

Effects Of The Dihydrouracil Lesion On Dna Using 1h/31p 1d And 2d Solution Nmr, Benjamin M. Boyd

MSU Graduate Theses

The effects of the dihydrouracil lesion in DNA were studied using two dimensional NMR spectroscopy. The sequence used was based off of the Drew-Dickerson Dodecamer, with the cytosine in the three position replaced by a dihydrouracil. All of the nonexchangeable proton chemical shifts, with the exception of the H2, H5’, and H5’’, of the lesioned DNA were identified using NOESY spectra and then compared to the chemical shift values of the Drew Dickerson Dodecamer. The largest differences in chemical shifts were observed in the nucleotides neighboring the lesion, both within the strand and on the opposite strand. The imino exchangeable …

Towards The Synthesis Of An Artificial Fluorescent Siderophore, Ashley Burns

Honors Theses

Siderophores are molecules capable of binding ferric ions with high affinity (Ka = 1052). This thesis outlines our attempts to synthesize an artificial siderophore, which incorporates a signaling group to help monitor the uptake of ferric ions. The artificial siderophore is a tripodal molecular receptor synthesized in a five-step procedure with a proposed final sixth step. Rhodamine 6G azide (95.0% yield) was formed from rhodamine 6G and the synthesis of 2-azidoethanamine was modified from the literature. The tripodal arm portion of the sensor was successfully synthesized by protecting the catechol of 2,3-dihydroxybenzaldehyde to form 3-formyl-1,2-phenylene dimethanesulfonate (98.8% yield). The reduction …

Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. Mckay

Graduate Theses and Dissertations

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal averaging of NMR observables caused by …

Ultrafast Relaxation Dynamics In Graphene Oxide-Dye And Perovskites Nanocomposites, Abubkr A. Arzaq Abuhagr

Dissertations

Novel materials such as graphene oxide (GO), reduced graphene oxide (RGO), and Perovskites nanocomposites nanosheets have shown interesting electrical and optical properties. These materials have shown prominence in research regarding optical sensing applications. The interaction of different fluorescent molecules like dye molecules with GO, and RGO have been studied recently to develop novel optical sensors, photo-catalysts, and light-harvesting agents. In this study, we have monitored the excited state interactions of dyes covalently attached to GO and RGO nanosheets. Three amine derivatives of anthracene, pyrene, and coumarin were covalently bound to different systems via amide bonds and diazotization. Characterization of different …

Understanding And Controlling Lithium Microstructure During Electroplating For Energy Applications, Yang Tian

Graduate Theses and Dissertations

Lithium-ion batteries are reaching the specific theoretical capacity limit, while lithium metal batteries are regarded as the ideal energy storage system for the next generation “beyond lithium-ion” battery systems. The lithium metal anode is considered as the “Holy grail” of anodes due to its relatively low electrochemical potential (-3.04 V vs SHE) and high theoretical capacity (3860 mAh g-1). However, the application of lithium metal anodes is hindered because of significant reaction between metallic lithium and electrolytes, as well as uneven electro-plating, which leads to dendrite formation, causing safety problems.

The kinetic parameters of Li ions such as diffusion coefficient …

Asymmetric Synthesis Of The C29-C34 Moiety Of Fragment A Of The Antascomicin B & Thermal Azole Based Claisen Rearrangements, Dharma Theja Nannapaneni

Graduate Theses and Dissertations

The dissertation describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B and Thermal azole based Claisen rearrangements. In chapter 1, we describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B. The non-immunosuppressant Rapamycin, Ascomycin, and Tacrolimus (FK506), strongly binds with FKBP12, the ligand FKBP12 complexes responsible for immunosuppressive activity. Antascomicin B structurally related to Rapamycin, Ascomycin, and Tacrolimus (FK506), binds strongly to FKBP12, yet does not shown immunosuppressive activity. The ligand FKBP12 binding complexes shown to have potent neuroprotective and neurogenerative properties in mouse models of Parkinson’s disease. The linear synthesis of …

A Synthesis And Analysis Of Anhydrous Hydroxide Ion Conducting Polymer Electrolytes, Stanton Heydinger

Honors Theses

This project investigates the synthesis and physical properties of polyethylene glycol monomethyl ether (MePEGn where n=3 or 7) based polymer electrolytes. The two polymer electrolytes explored in the experiments were designed from two different MePEG chains that varied in their overall length and degree of polymerization. The first MePEG backbone contained three polymerized ethoxy groups and the second contained seven. Both MePEGn polymers were modified by substituting an imidazolium group in place of the alcohol functional group at the end of the PEG chain. This modification was made to create a polymer electrolyte with an attached positive charge that could …

Adsorption Of Polyisobutylene-Based Dispersants Onto Carbon Black, Travis Paul Holbrook

Dissertations

The formation of carbonaceous by-products (e.g. soot) during the operation of an internal combustion engine is unavoidable and the aggregation of this soot leads to deleterious effects including abrasive wear of the engine, increased oil viscosities, and sludge deposition. Dispersants, which are composed of a hydrophobic tail and a polar headgroup, are used as oil additives to aid in the suspension and stabilization of the soot particles. Polyisobutylene succinimide (PIBSI) is the most well-studied class of dispersants and is characterized by a linear architecture and polyamine headgroup that interacts with soot by acid-base and dipole-dipole interactions. As such, there remains …

The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi

Dissertations

Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …

Photocatalytic Degradation Of Simazine Under Visible Light Using Zinc Oxide/Molybdenum Disulfide Heterostructures, Alexandria Castillo

Theses and Dissertations

The photocatalytic degradation of simazine under visible light by using ZnO/MoS2 heterostructures was investigated. Reaction parameters studied to optimize simazine degradation included pH, loading mass of the photocatalyst, and percentage of MoS2 in the heterostructure. pH 2 was the optimal environment for the degradation reaction of all catalysts. A loading mass of 20 mg for each of the ZnO/MoS2 photocatalysts was determined to be the most effective for in the degradation process. The degradation reactions were observed to follow 2nd order kinetics for all photocatalysts at all temperatures. Band gap studies confirmed a lower energy than that of pure ZnO …

An Electrochemical Instrument For The Analysis Of Heavy Metals In Water Via Anodic Stripping Coulometry For Applications In Remote Sensing., Kelsey Lynn Kaht

Electronic Theses and Dissertations

From the high levels of arsenic in groundwater in Bangladesh to the lead contamination of drinking water in Flint, Michigan, there are incidents across the globe that highlight the need for a reliable instrument capable of monitoring heavy metals remotely and continuously in a variety of geographical locations. Typical instrumentation for water analysis, such as ICP and AAS, must be housed in a central lab and relies on an operator traveling to the collection site, obtaining a sample, and transporting it back to the lab. This analysis provides a snapshot of the water quality that is limited to the specific …

Synthesis, Characterization, And Drug Delivery Applications Of Carbohydrate Based Low Molecular Weight Gelators, Kristen Elizabeth Bashaw

Chemistry & Biochemistry Theses & Dissertations

The main aim of the research focuses on the study of self-assembly and gelation by several classes of simple sugar derivatives and the potential applications of them as drug delivery vehicles. Since carbohydrates are naturally abundant renewable resources and are therefore readily available and many of them are inexpensive compared to other raw materials. They are also biocompatible which makes them suitable for a wide variety of applications. Combining the use of carbohydrates with low molecular weight gelators (LMWGs) we can introduce a new class of soft materials that are able to self-assemble into spheres, fibers, sheets, and micelles in …

Smart Sensors With Dual Modes Of Signal Transduction For Monitoring Molecules Pertinent To Health And The Environment, Jared T. Wabeke

Dissertations

The dissertation focuses on the design and synthesis of smart materials for the detection of molecules pertinent to environmental protection and healthcare. The use of computational simulations is pivotal toward advancing molecular design for targeted applications. Research was conducted to investigate the use of simulations to develop novel sensors with dual modes of signal transduction. The molecular properties were determined using computational modelling, and then used to elucidate the binding mechanism of the corresponding sensor complexes. Several molecules were produced that respond to important organic analytes, such as glucose and fenthion, an organophosphorus pesticide. Glucose is an exceedingly important biological …

Characterization Of The Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor, Tyler Degener

Theses/Capstones/Creative Projects

The mannose-6-phosphate/insulin-like growth factor II (M6P/IGF2) receptor is a transmembrane protein known to sequester growth factors from the extracellular matrix. This behavior suggests a mechanism of tumor suppression. Structurally, the receptor’s extracellular region is segmented into 15 homologous repeats, which are divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. What is notable about the triplets is their propensity to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose of this experiment is to characterize these domain interactions. Using a urea …

Electrochemical Determination Of Surface Area-To-Volume Ratio For Metal Nanoparticle Analysis., Jay Narayan Sharma

Electronic Theses and Dissertations

This dissertation describes an electrochemical approach for measuring the surface area-to-volume ratio (SA/V) of electrode-attached metal nanoparticles (NPs), which was used to analyze their size, aggregation state, and porosity. This dissertation further describes the effect of the metal NP electrode assembly method on the SA/V, which is related to metal NP catalytic activity and stability. Cyclic voltammetry (CV) in acid electrolyte followed by anodic stripping voltammetry (ASV) in KBr electrolyte allows the electrochemical measurement of the SA/V of electrode-attached Au nanospheres (NSs). In CV, the forward scan produces a thin surface Au₂O₃ layer on the Au NSs. …

Gc×Gc-Ms And Parallel 2dlc-Ms Based Untargeted Metabolomics., Md Aminul Islam Prodhan

Electronic Theses and Dissertations

Untargeted metabolomics aims to analyze as many metabolites as possible in a biological system. Due to the vast complexity of the metabolome, bioanalytical platforms have been developed for untargeted metabolomics. While comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) has been used in different scientific fields, its use in untargeted metabolomics is limited due to several challenges, such as complicated data analysis and limited accuracy of metabolite identification. Two-dimensional liquid chromatography mass spectrometry (2DLC-MS) has also been employed in untargeted metabolomics, but with limited metabolite coverage. This dissertation describes the efforts in developing new data analysis algorithms to improve the accuracy …

Laser Spectroscopy Investigations Of Jet-Cooled Metal-Containing Free Radicals., Anam Chandra Paul

Electronic Theses and Dissertations

Metal-containing free radicals are important intermediates in metal-surface reactions and the interactions between metals and organic molecules. Among metal-containing free radicals, monovalent derivatives of alkaline earth metals have been extensively investigated by using spectroscopic techniques in a gas phase, mainly in Broida ovens or under supersonic-jet-cooled conditions. In the present study, the results of performed spectroscopic investigations of both metal-containing monoalkoxides (CaOR) and metal oxides (MO) radicals have been reported. Laser-induced fluorescence (LIF) and dispersed fluorescence (DF) spectra of the electronic transition of the calcium CaOR radicals have been obtained under jet-cooled conditions. Complete active space self-consistent field (CASSCF) and …

Laser Spectroscopy Investigations On Molecular And Free Radicals Dynamics., Hamzeh Telfah

Electronic Theses and Dissertations

Studying molecular dynamics and chemical kinetics is important to understand the chemical behavior of renewable energy sources. Laser spectroscopy techniques are powerful tools for the identification and diagnosis of such processes. In this dissertation, using our laser spectroscopy techniques, biofuels and solar energy were targeted as renewable energy sources study. We have studied the ultrafast exciton dynamics for a series of methylammonium lead bromide (CH3NH3PbBr3) nanostructures, nanocrystals (NCs, 0D), nanowires (NWs, 1D), and nanoplatelets (NPs, 2D) as a promising solar energy materials.1-2 Aided by analysis of UV−visible absorption and photoluminescence spectra, features in the transient absorption (TA) spectra are assigned …

Laser Spectroscopic Investigations Of Organic Alkoxy And Peroxy Radicals., Md Asmaul Reza

Electronic Theses and Dissertations

Understanding the mechanism of combustion reactions is key for advancing internal combustion engine design, improving the efficiency of ignition chemical reactions, and reducing pollutant formation. In order to model the extremely complicated chemical kinetics of combustion processes, it is critical to detect and identify transient reactive chemical intermediates, particularly free radicals. Hence, it needs to be fully understood the gas-phase chemistry of organic compounds in the lower atmosphere. Over the past fifty years, parallel advancement in observational, experimental, and theoretical techniques, tremendous strides have been made in our understanding of the role of organic compounds in the atmosphere. Combustion chemistry …