Chemistry Commons^™

Novel Spectroscopic Tools To Differentiate Molecule-Dna Binding Interactions, Sense Dna And Track Dna Melting, Saad Hmoud Alotaibi

Dissertations

The discovery of DNA as a genetic material and its double helical structure led to numerous studies directed at understanding molecule-DNA interactions. These studies have played an integral role in medical diagnostics, forensics, imaging and therapeutics. Typically, molecule-DNA interactions have two prominent modes: intercalation and minor groove binding. Several optical techniques are available that can monitor molecule-DNA binding interactions, but they cannot differentiate between intercalation and minor-groove binding. The major goals of the research are to develop novel optical spectroscopic tools that can differentiate molecule-DNA binding interactions, selectively and sensitively detect one form of DNA over another, and track DNA …

Phenanthroline Derivatives As Potential Sensors, David L. Sellers

Research and Creative Activities Poster Day

Derivatives of 1,10-phenanthroline have great potential as functional sensor molecules for detection of nerve agents by colorimetric assays. In this study we prepared aminoalcohol deriviatives of 1,10-phenanthroline. Deriviatives were obtained in moderate to high yields. Metal complexes of 1,10-phenanthroline were also prepared. The metal complexes allow for greater stability of the sensors and greater possibilities for embedding in inert materials. Some aminoalcohol derivatives acted as turn-on sensors, fluorescing in the presence of DCP.

Improving The Analysis Of Proteins By Desorption Electrospray Lonization (Desi) By The Addition Of Ammonium Bicarbonate, Elahe Honarvar

Research and Creative Activities Poster Day

The analysis of proteins by Desorption Electrospray Ionization (DESI) is challenged by a mass depend loss in signal response. We show that this loss in sensitivity originates primarily from the incomplete dissolution of proteins into desorptiopn spray solvent. The addition of ammonium bicarbonate is used to improve protein dissolution and we demonstrate beneficial effects this has on protein detection by DESI-MS. We demonstrate improved signal to noise ratio's for all proteins investigated, up to 66kDa. In addition to improvements in signal to noise ratio, changes in charge states were also observed and are described.

Physicochemical Characterization Of Novel 1,1 0-Phenanthrolines, Dominic Millheim

Masters Theses

1,10-Phenanthroline is a well-known and often-used ligand with a variety of interesting properties and applications to both organic and inorganic chemistry. Interest in novel 1,10-phenanthrolines substituted at the 5- and 6- position has grown recently due to their interesting fluorometric and spectroscopic properties. They have been evaluated recently for applications including chemical sensors, chemical indicators, pharmacological targets and bioactive reagents.

1,10-Phenanthroline, an epoxidated synthetic intermediate, and a novel 5,6- disubstituted aminoalcohol derivative were studied to determine the degree of influence that iterative physical and chemical transformations have on the donor properties of the N-C-C-N pocket. Multiple analytical techniques including potentiometry …

Probing The Unfolding And The Stability Of The Last Four Metal Binding Domains Of Wilson Disease Protein Using Circular Dichroism And Novel Spectroscopic Techniques, Ibtesam Yaseen Alja’Afreh

Dissertations

Wilson disease protein is a copper-transporting P_1B type ATPase. It has large N-terminal copper binding domain which is composed of six homologous sub-domains. Each of these six domains is ~72 residues and connected to one another by linking regions of various lengths. They all possess similar ferrodoxin fold, and metal-binding motif, MXCXXC.

The need of having six metal binding domains and the manner in which they are communicating with each other is not well understood. To better understand how the last four metal binding domains function, I pursued a detailed biophysical characterization of these domains. Using molecular biology I …

Ultrafast Interfacial Electron Transfer Across Molecule-Tio2 Nanocomposites: Towards Solar Cells And Two Photon Absorption, Edwin Mghanga

Dissertations

Interfacial charge transfer (ICT) across the molecule-TiO2 nanoparticle interface has gained enormous research attention for applications in dye sensitized solar cells (DSSC), photo-catalysis, water splitting and nonlinear optics. DSSCs are promising clean alternative energy sources. However, current DSSCs suffer from lower efficiencies and higher cost. Better understanding of the ICT processes in DSSCs can help solve these problems. We have used two strategies to understand ICT in the context of DSSCs. Firstly, we used a computationally validated anchor group, acetylacetonate (acac) to bind molecules to the semiconductor surface and facilitate charge separation. Secondly, we used natural dye sensitizers, …

Magnetic Nickel Nanoparticles: Synthesis, Environmental Lmplications And Potential Role As Drug Carriers, Setare Tahmasebi Nick

Dissertations

The design and synthesis of well-defined magnetic particles with nanoscale dimensions is opening new avenues in understanding their fundamental chemical and physical properties. Our work describes a novel facile procedure for the synthesis of homogenous isotropic and anisotropic magnetic nickel nanoparticles. These nanoparticles were produced using a wet-chemical process and characterized by transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), selected-area electron diffraction (SAED), powder x-ray diffraction (XRD), energy dispersive spectroscopy (EDS) and thermogravimetric analysis (TGA). Magnetic measurements were acquired using a superconducting quantum interference device (SQUID) magnetometer. While there is significant interest in using magnetic nanoparticles for biological …

The Nucleic Acid Binding Properties Of The Pwi Motif, Hamideh Keshavarz-Mohammadian

Masters Theses

The PWI motif is a highly conserved domain that contains a Proline-Tryptophan-Isoleucine (PWI) tripeptide sequence, for which it is named. Proteins that contain a PWI motif are known to be involved in the constitutive and alternative splicing and the 3'-end processing of messenger RNA transcripts. The hypothesized role of the PWI motif is to nonspecifically interact with nucleic acids. The PWI motif is capable of binding both doublestranded and single stranded forms of DNA and RNA. The structure of the highly conserved core of the PWI motif reveals that it adopts a four-helix bundle fold. The structured core domain, however, …

Electron Transfer In Pnicogen Bond, Liangyu Guan

Masters Theses

Abstract is available for download as a separate file.

Chemistry Graduate Teaching Assistants: A Comparison Of The Classroom Discourse Within Expository And Problem-Based Learning Laboratories, Kelley M. Current

Masters Theses

Graduate Teaching Assistants (GTAs) commonly function as instructors within undergraduate chemistry laboratories. This study sought to explore and describe GTA classroom discourse within two distinct instructional modes, using discourse analysis as the theoretical framework. Theclassroom discourse within a series of verification style labs was comparedto the classroom discourse produced within a set of Problem-Based Learning (PBL) labs. The results suggest three primary findings: (1) the apparent relationship between the instructional mode and form of GTA classroom discourse, (2) the patterns in classroom discourse observed within a given instructional mode repeat, irrespective of content, and (3) the classroom discourse observed within …

Biophysical Characterization Of The First Four Metal-Binding Domains Of Human Wilson Disease Protein, Alia V.H. Hinz

Dissertations

Wilson disease protein (WLNP) is a P_1b-type ATPase crucial for maintaining copper homeostasis in humans. Mutations in this protein result in the autosomal recessive disorder Wilson disease, a condition characterized by copper accumulation in the liver and brain. WLNP provides copper for incorporation into cuproproteins and exports excess copper into the bile for excretion. There are six metal-binding domains (MBDs) in WLNP, found within the first 650 amino acids of this 1,465 amino acid protein. Though each MBD has a different amino acid sequence, all MBDs possess a similar ferredoxin fold with a conserved hydrophobic core and a …

Asymmetric Reactions Of N-Heterocyclic Carbenes Using Green Chemistry Principles, James J. J. Kiddle

Faculty Research and Creative Activities Award (FRACAA)

No abstract provided.

Probing Stability And Unfolding Of The N-Terminal Domains 5-6 Of Wilson Protein, Ibtesam Y. Alja'afreh, Ramakrishna Guda, David L. Huffman

Research and Creative Activities Poster Day

The Wilson protein (ATP7B) is a copper transporting P1b type ATPase found in the liver, brain, and other organs. The N-terminal end consists of six copper binding domains which have a ferrodoxin βαββαβ fold with a CxxC motif. Despite similarities in copper binding affinities they interact differently with the HAH1 metallochaperone. Studying the stability of these domains will help understanding the differences in their functions. The stability of WLN5-6 was probed using several different methods: Dynamic light scattering (DLS), Circular dichroism (CD) and Fluorescence spectroscopy methods.

Previous studies show that WLN5-6 has a spherical shape and CD chemical unfolding studies …

Two-Photon Absorption Spectroscopy To Differentiate Chromophore-Dna Binding Interactions, Saad H. Alotaibi, Kelly M. Usakoski, Mohammad Hatshan, Ramakrishna Guda

Research and Creative Activities Poster Day

The study of molecule-DNA binding interactions are vital as they are the principle components behind drug action, transcription and replication. Optical spectroscopic techniques are often used to study these interactions. However, the existing techniques cannot differentiate different binding motifs of intercalation and minor-grove binding. In the present study, we present a novel approach based on the two-photon absorption (2PA) cross-sections of chromophores to differentiate the intercalation and minor-grove binding interactions. The investigations are carried out using three cyanine derivatives Diethylthiacyanine iodide (DTI), 3,3′-Diethylthiacarbocyanine iodide (DTCI) and 3,3′- Diethylthiadicarbocyanine iodide (DTDCI). The chromophores were chosen as they are similar series of …

Multi-Electron Transfer From Charged Semiconductor Surfaces To Quantized Bimetallic Nanoparticles, Ali Bolandi, Sherine O. Obare

Research and Creative Activities Poster Day

Palladium-platinum bimetallic nanoparticles were prepared using a novel method of hydrothermal co-reduction of precursors. Elemental analysis, x-ray diffraction and electron microscopy indicated the formation of spherical bimetallic nanoparticles with a size distribution of 2.5 ± 0.5 nm. When the Pd/Pt bimetallic nanoparticles were brought in close contact with an electron-rich surface, the particles accepted and stored the electrons. Multiple electrons were found to be stored in the Pd/Pt bimetallic NPs.

Crystal And Molecular Structures Of New Metallocarboranes, Au25 Gold Cluster And Metal Sensor Molecules, Agozie N. Oyeamalu, Rathnayaka Madawala, Viraj Thanthirige, Ekkehard Sinn

Research and Creative Activities Poster Day

Introduction

Bragg’s equation has become one of the most trusted model used to calculate crystal structures.

2014 marks the 100th anniversary of Max von Laue’s Nobel Prize for discovering that X-Rays fired into a crystal of copper sulfate produced a characteristic diffraction pattern.

2015 will be the 100th anniversary of the Nobel Prize to Bragg and Bragg for their equation that ultimately led to X-ray crystallography.

Optical Properties Of Bi-Icosahedral Au25 And Au24 Clusters: Influence Of Central Gold Atom, Viraj Dhanushka Thanthirige, Ekkehard Sinn, Rongchao Jin, Guda Ramakrishna

Research and Creative Activities Poster Day

Temperature-dependent absorption and ultrafast luminescence measurements of [Au₂₄(PPh₃)₁₀(SC₂H₄Ph)₅Cl₂]+(bi-Au₂₄) were studied and compared with [Au₂₅(PPh₃)₁₀(C₆S)₅Cl₂]₂+ (bi-Au₂₅). The investigations are carried out on these two clusters as they are structurally similar except for the absence of central Au atom for bi-Au24. The objective of the work is to probe the influence of the central gold atom on the optical transitions and electron-phonon interactions in bi-icosahedral nanoclusters. The investigations are focused …

Synthesis, Characterization And Potential Applications Of Palladium And Ruthenium Nanostructures, Clara Patrice Adams

Dissertations

Controlling the size and shape of metal nanostructures is important for tuning the intrinsic chemical and physical properties of materials, and consequently their potential technological applications. Modulating the morphology of metal nanostructures is essential to understanding the structure-function relationship (for example, optical, magnetic, catalytic, and electronic properties) under various environmental conditions. Our work describes the development of new procedures for the synthesis of well-defined isotropic and anisotropic nanoparticles consisting of palladium (Pd) and ruthenium (Ru). Characterization of the nanostructures was carried out using transmission electron microscopy (TEM), high resolution-TEM (HRTEM), powder x-ray diffraction (XRD), selected area electron diffraction (SAED) and …

Size-Dependent Interactions Of Metal Nanoparticles With Fluorophores And Semiconductors, Liyana A. Wajira Ariyadasa

Dissertations

In recent years, nanoscale metallic particles have gained considerable interest due to their potential applications in advanced technology. Despite such interest, synthetic procedures that produce gram-scale, well-defined metallic nanoparticles with controlled size and shape, especially with diameters less than 5 nm remains a challenge. Our work has focused on developing synthetic procedures that produce well-defined platinum and palladium metal nanoparticles in the 1-5 nm size range. Thioether ligands were used as stabilizers and resulted in metal nanoparticles with controlled size. The nanoparticles were characterized using transmission electron microscopy (TEM), x-ray diffraction (XRD), selected area electron diffraction (SAED), x-ray photoelectron spectroscopy …

Fundamental Studies Of Protein Ionization For Improved Analysis By Electrospray Ionization Mass Spectrometry And Related Methods, Kevin A. Douglass

Dissertations

Mass spectrometry (MS) is an analytical technique in which a sample is converted to gas-phase ions that are subsequently separated and detected. It offers great speed, selectivity, and sensitivity during analysis, characteristics which have enabled it to become a leading method for the study of proteins. The applications of MS for these biologically significant macromolecules range from accurately determining identity and sequence to shedding light on post-translational modifications and protein-molecule interactions. As a first step towards analysis by MS, gas-phase protein ions must be formed. A common method for ionization is electrospray ionization (ESI), where a liquid sample including the …

Functional Variants Of Metal-Binding Domains 5 And 6 Of The Human Wilson Protein, Sandra Weitzner

Honors Theses

Wilson's disease is caused by mutations in atp7b, a gene that encodes a copper-transporting P_1B-type ATPase, otherwise known as the Wilson protein. Over 300 different mutations cause Wilson's disease, and we focused on missense mutations occurring in the 650 amino acid N-terminus of the Wilson protein. This portion of the protein includes six metal-binding domains that function to azquire Cu(I) from the cytosol, prior to passing it through the ATP-driven membrane-spanning pump. Of particular interest are metal-binding domains 5 and 6 (WLN5-6) since we know that they are absolutely required for function of the enzyme. Several missense mutations …

When All Seems Lost: A Discussion On The Implications Of Using Medicine For Scientific Advances, Rebecca Monterusso

Honors Theses

When All is Lost is a creative non-fiction piece following the lives of two fictional characters living during World War" and the Holocaust. It is meant to discuss the moral quandary when human experimentation is used for the purpose of scientific advancement. The two main characters lives' are depicted in a series of modified scenes that describe what happens to them throughout the war. Leo Weinstock is a Jewish man who is chosen for the high-altitude experiments at Dachau after he is imprisoned during Kristallnacht. Erich, on the other hand, is a young, successful Luftwaffe pilot defending his country. Both …

Using Soil Organic Matter As An Iron Chelate To Enhance The Efficiency Of Modified Fenton Oxidition Of Diesel Fuel In Arctic Soils, Mary K. Sherwood

Masters Theses

Laboratory experiments were conducted to investigate the use of modified fenton chemistry on the treatment of three soils from the Canadian arctic, all with abundant soil organic matter, iron and manganese oxides, and diesel fuel contamination. The purpose of these studies was to (I) to assess modified fenton chemistry as a treatment option for petroleum-contaminated arctic soils, and (2) to evaluate the impact of soil organic matter on the modified fenton treatment of soils. Modified fenton treatment was compared for reactions in which ethylenediaminetetraacetate was added as a chelate vs. reactions in which the native soil organic matter was the …

Ultrafast Dynamics And Two-Photon Absorption Properties Of Chromophores At Interfaces, Semere Ghebru Bairu

Dissertations

Materials with large two-photon absorption (2PA) cross-sections found applications in several areas such as sensor protection, 3D micro/nano fabrication, photodynamic therapy, optical data-storage, multi-photon sensing, multi-photon microscopy and imaging. Several successful research strategies were developed in literature to achieve 2PA materials with enhanced cross-sections. However, the obtained cross-sections are far from adequate and there is a need to develop new strategies. In a parallel development, numerous research efforts were focused on studying the dynamics of interfacial charge-transfer (ICT) across chromophoresemiconductor interfaces, especially in the context of dye-sensitized solar cells. While investigating the fundamentals of ICT, it was found that these …

Nutrient Recycling Potential Of Algal Biomass Grown In Eutrophic Water, Kristin Hampel

Research and Creative Activities Poster Day

No abstract provided.

Graphene Oxide/Zinc Oxide Nanocomposites As Dissolved Oxygen Sensors, Jameel A. Hasan

Research and Creative Activities Poster Day

No abstract provided.

Molecularly Woven Materials From Metal-Organic Precursors, Gellert Mezei, Jaafar Hachem, Isurika R. Fernando, Natasha R. Wadhwa, Neil C. Hughes

Faculty Research and Creative Activities Award (FRACAA)

No abstract provided.

Electron Transfer In Electrophilic Aromatic Nitration And Nitrosation, Yirong Mo, Zhenhua Chen

Faculty Research and Creative Activities Award (FRACAA)

No abstract provided.

Multiphoton Fluorescence Spectroscopy To Monitor The Unfolding Of The Green Fluorescent Protein, Ibtesam Y. Alja'afreh, Ramakrishna Guda, David Huffman

Research and Creative Activities Poster Day

Green fluorescent protein (GFP), from Aequorea coerulescens, has been expressed as a His-tag fusion protein in E. coli cells and purified using metal chelate affinity and gel filtration chromatography. The protein fluoresces at 510 nm due to its natural chromophore that is spontaneously formed after properly folding and remains stable and intact after protein unfolding. The chromophore is buried in a beta barrel and has a permanent dipole moment in both the ground state and the excited state. The difference between permanent dipole moments Δμ_ge is highly proportional to the electrostatic environment around the chromophore. Since Δμ_{ge …}

Study Of The Insulin Mimetic Sodium Orthovanadate In Glucosamine Induced Insulin Resistnace In Primary Rat Hepatocytes, Kalan Mcpherson

Masters Theses

Insulin resistance and type II diabetes is a disease state characterized by a lack of sensitivity of insulin to provoke a proper response in insulin sensitive tissues. Currently, we utilize glucosamine to increase flux through the Hexosamine Biosynthetic Pathway (HBP) to induce an insulin resistance like state in primary rat hepatocytes. We tested the effectiveness of the insulin mimetic sodium orthovanadate to determine if it could elicit an insulin-like response under these conditions. Mixed results were obtained on the effectiveness of vanadate as an insulin mimetic in this insulin resistant model.