Chemistry Commons^™

Investigations Into The Fluorescent Covalent Labeling Of Biomolecules Utilizing Rhodamine Dyes, Electrophilic Leaving Groups And Mrna Display., Susan D. Selaya

Theses and Dissertations

The discovery of a method by which proteins of interest can selectively be labeled with a probe of choice intracellularly is a longstanding goal in chemical biology research. Conventional labeling techniques have utilized large domain tags but despite the development of small labeling molecules there have been no short peptide sequences known to covalently label a small molecule without the aid of an enzymatic process or metal chelation. We aimed to find a sequence of nucleophilic peptides that reacted covalently and specifically with electrophilic small labeling molecules using mRNA display. Our goal was to show that an electrophilic small labeling …

Platinum Complexes And Zinc Finger Proteins: From Target Recognition To Fixation, Samantha Tsotsoros

Theses and Dissertations

Bioinorganic chemistry strives to understand the roles of metals in biological systems, whether in the form of naturally occurring or addition of non-essential metals to natural systems. Metal ions play vital roles in many cellular functions such as gene expression/regulation and DNA transcription and repair. The study of metal-protein-DNA/RNA interactions has been relatively unexplored. It is important to understand the role of metalloprotein interactions with DNA/RNA as this enhanced knowledge may lead to better understanding of diseases and therefore more effective treatments. A major milestone in the development of this field was the discovery of the cytotoxic properties of cisplatin …

Fabrication Of Nanoporous Gold And Biological Applications, Badharinadh Uppalapati

Theses and Dissertations

FABRICATION OF NANOPOROUS GOLD AND BIOLOGICAL APPLICATIONS By Badharinadh Uppalapati A Dissertation submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. Virginia Commonwealth University, 2014 Major Director: Maryanne M. Collinson, Professor, Department of Chemistry Fabrication of nanoporous gold electrodes by dealloying Au:Ag alloys has attracted much attention in sensing applications. In the first part of this work, the electrochemical response of the redox active molecule, potassium ferricyanide, in a solution of bovine serum albumin in buffer, serum or blood was studied using nanoporous gold and comparisons made to planar gold. Nanoporous …

Affinity Enrichment And Mass Spectrometric Quantitation Of Protein Carbonyls, Suresh Narayanasamy

Theses and Dissertations

The importance of the role of oxidative stress in aging and numerous age-related diseases has become undeniable due to enormous weight of supporting evidence from the field of free radical biology. One of the most prominent oxidative modifications of proteins is the introduction of carbonyl groups. As with oxidative stress, protein carbonylation has been correlated with various disease states and natural aging. While protein carbonyls are relatively stable, reproducible detection and modification site localization are still challenging. This thesis details attempts to improve the analytical methodology used for the identification and quantitation of carbonylated proteins. We have studied the impact …

Light Mediated Drug Delivery Using Photocaged Molecules And Photoswitchable Peptides, Deboleena Mitra

Theses and Dissertations

There are many different types of targeted therapy for cancer treatment. The method of light mediated targeted therapy that we have developed uses photocaged molecules and photoswitchable peptides.

In photocaging, a biologically active molecule is made inactive by the attachment of a photocleavable blocking group. On exposure to UV radiation the photocleavable entity is removed and the biologically active molecule is released. Using this concept we have designed a prodrug that consists of a cell impermeable hydrophilic molecule attached to a photocaged doxorubicin. Upon irradiation with UV light the photosensitive group is removed and cytotoxic doxorubicin is released at the …

Real Time Monitoring Of Surface Chemical Events By Streaming Potentials In Microfluidic Channels, Kenji Nokura

Theses and Dissertations

Zeta potential is one of the tools to measure the surface charge of materials, and Alvarez et al. have developed a microchannel device to measure zeta potentials in real time for label-free sensing using immobilized receptors on microchannel surfaces. However, the challenge has been the charge interference of surface modifiers on analyte detection. Therefore, it was necessary to find the best strategy to regenerate minimal surface charge after modifying the channel with polymer films that would anchor the affinity groups for the analyte. It was demonstrated that adsorption of positively and negatively charged analytes were monitored via real time zeta …

Synthesis, Characterization, And Functionalization Of Magnetic Iron Nanoparticles For Enhanced Biological Applications, Christopher Warren

Theses and Dissertations

The transition metal ferrites of composition MFe2O4 where M is Fe, Co, or Ni are well established materials for various biological applications due to their interesting magnetic properties. Their elemental and stochiometric composition can be easily manipulated which allows further tuning of their ferrimagnetic properties. By changing the identity of M and by changing the crystallite size of the ferrites, nanocrystals with diverse magnetic properties can be systematically produced. Furthermore, ferrites are more stable in diverse chemical environments, as compared to metallic nanoparticles, which make ferrites particularly useful for a broad range of biomedical applications, especially in the field of …

The Design And Synthesis Of Magnetic Nanocomposites, Daniel Hudgins

Theses and Dissertations

Magnetism lies at the core of modern technology and can be found in industries such as oil refining, automotive, telecommunications, personal electronics, and power generation that are integral to our day to day lives. This permeation into everyday life has been enhanced in the past several decades with improvements in material design based upon the principles of nanotechnology leading to smaller, faster, and more efficient devices. The presented research will discuss the synthesis and processing of multiple magnetic nanoparticle structures designed for the enhancement of various, application specific, properties. In the first experiments a tunable core/shell structure was developed with …

Zinc Environment In Proteins: The Flexible And Reactive Core Of Hiv-1 Ncp7 And The Inhibitory Site Of Caspase-3, A. Gerard Daniel

Theses and Dissertations

Zinc is an essential cofactor of several proteins. The roles of zinc in these proteins are classified as catalytic, structural or regulatory. Zinc present in structural sites is considered to be a chemically inert, static structural element. On the contrary, previous studies on a C2H2 type zinc finger model compound and the C3H type HIV-1 NCp7 C-terminal zinc knuckle have shown that zinc at these sites can undergo coordination sphere expansion under the influence of a Pt based electrophile. The pentacoordination observed around zinc in these experiments raises an important question: are the structural zinc motifs found in the proteins …

Laser Vaporization Methods For The Synthesis Of Metal And Semiconductor Nanoparticles; Graphene, Doped Graphene And Nanoparticles Supported On Graphene, Parichehr Afshani

Theses and Dissertations

The major objective of the research described in this dissertation is the development of new laser vaporization methods for the synthesis of metal and semiconductor nanoparticles, graphene, B- and N-doped graphene, and metal and semiconductor nanoparticles supported on graphene. These methods include the Laser Vaporization Controlled Condensation (LVCC) approach, which has been used in this work for the synthesis of: (1) gold nanoparticles supported on ceria and zirconia nanoparticles for the low temperature oxidation of carbon monoxide, and (2) graphene, boron- and nitrogen-doped graphene, hydrogen-terminated graphene (HTG), metal nanoparticles supported on graphene, and graphene quantum dots. The gold nanoparticles supported …

Fabrication Of Surface Amine Gradients By Controlled-Rate Infusion For Chromatographic Applications, Balamurali Kannan

Theses and Dissertations

Surface gradients are materials that exhibit a variation in properties such as chemical composition, topography etc., in a continuous and/or discrete fashion. They are broadly classified as chemical and physical gradients depending upon the properties that gradient exhibits. Among those, chemical gradients on various surfaces have been a great interest in materials research for the last two decades. This is due to the applications of gradients in various fields such as biological sciences, separation science, etc. There have been several different approaches developed for the preparation of chemical gradients. Silane-based approaches are among those that are widely used because of …

Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah

Theses and Dissertations

In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and …

Formation Mechanisms And Photocatalytic Properties Of Zno-Based Nanomaterials, Natalie Herring

Theses and Dissertations

Zinc Oxide (ZnO) is one of the most extensively studied semiconductors because of its unique properties, namely, its wide band gap (3.37 eV) and high excitation binding energy (60 meV). These properties make ZnO a promising material for uses in a broad range of applications including sensors, catalysis and optoelectronic devices. The presented research covers a broad spectrum of these interesting nanomaterials, from their synthesis and characterization to their use as photocatalyts. A new synthetic approach for producing morphology controlled ZnO nanostructures was developed using microwave irradiation (MWI). The rapid decomposition of zinc acetate in the presence of a mixture …

Graphene-Based Semiconductor And Metallic Nanostructured Materials, Abdallah Zedan

Theses and Dissertations

Exciting periods of scientific research are often associated with discoveries of novel materials. Such period was brought about by the successful preparation of graphene which is a 2D allotrope of carbon with remarkable electronic, optical and mechanical properties. Functional graphene-based nanocomposites have great promise for applications in various fields such as energy conversion, opteoelectronics, solar cells, sensing, catalysis and biomedicine. Herein, microwave and laser-assisted synthetic approaches were developed for decorating graphene with various semiconductor, metallic or magnetic nanostructures of controlled size and shape. We developed a scalable microwave irradiation method for the synthesis of graphene decorated with CdSe nanocrystals of …

Hydration Of The Pyrimidine Radical Cation And Stepwise Solvation Of Protonated Pyrimidine With Water, Methanol, And Acetonitrile, Ahmed M. Hamid, Pramod Sharma, M. Samy El-Shall, Rifaat Hilal, Shaaban Elroby, Saadullah G. Aziz, Abdulrahman O. Alyoubi

Chemistry Publications

Equilibrium thermochemical measurements using an ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes associated with the stepwise hydration of the biologically significant ions pyrimidine radical cation and protonated pyrimidine. The binding energy of the hydrated pyrimidine radical cation is weaker than that of the proton-bound dimer pyrimidineH+(H2O) consistent with the formation of a weak carbon-based CHδ+··OH2 hydrogen bond (11.9 kcal/mol) and a stronger NH+··OH2 hydrogen bond (15.6 kcal/mol), respectively. Other proton-bound dimers such as pyrimidineH+(CH3OH) and pyrimidineH+(CH3CN) exhibit higher binding energies (18.2 kcal/mol and 22.8 kcal/mol, respectively) due to the higher proton …

Dynamics At A Janus Interface, M. Von Domaros, D. Bratko, B. Kirchner, A. Luzar

Chemistry Publications

Electric field effects on water interfacial properties abound, ranging from electrochemical cells to nanofluidic devices to membrane ion channels. On the nanoscale, spontaneous orientational polarization of water couples with field alignment, resulting in an asymmetric wetting behavior of opposing surfacesa field-induced analogue of a chemically generated Janus interface. Using atomistic simulations, we uncover a new and significant field polarity (sign) dependence of the dipolar- orientation polarization dynamics in the hydration layer. Applying electric fields across a nanoparticle, or a nanopore, can lead to close to 2 orders of magnitude difference in response times of water polarization at opposite surfaces. Typical …

Impact Of Post-Synthesis Modification Of Nanoporous Organic Frameworks On Selective Carbon Dioxide Capture, Timur İslamoğlu

Theses and Dissertations

Porous organic polymers containing nitrogen-rich building units are among the most promising materials for selective CO2 capture and separation applications that impact the environment and the quality of methane and hydrogen fuels. The work described herein describes post-synthesis modification of Nanoporous Organic Frameworks (NPOFs) and its impact on gas storage and selective CO2 capture. The synthesis of NPOF-4 was accomplished via a catalysed cyclotrimerization reaction of 1,3,5,7-tetrakis(4-acetylphenyl)adamantane in Ethanol/Xylenes mixture using SiCl4 as a catalyst. NPOF-4 is microporous and has high surface area (SABET = 1249 m2 g-1). Post-synthesis modification of NPOF-4 by nitration afforded (NPOF-4-NO2) and subsequent reduction resulted …

Acid-Base Catalysis In Proton-Coupled Electron Transfer Reactions (Pcet): The Effects Of Brönsted Bases On The Oxidation Of Glutathione And Hydroquinone, Ramos Jonnathan Medina

Theses and Dissertations

This thesis presents the results and discussion of the investigation of the effects of Brönsted bases on the kinetics and thermodynamics of two proton-coupled electron transfer processes: the mediated oxidation of glutathione and the electrochemical oxidation of hydroquinone. Proton-coupled electron transfer (PCET) is the name given to reactions that involve the transfer of electron(s) accompanied by the exchange of proton(s). PCETs are found in many chemical and biological processes, some of current technological relevance such as the oxygen reduction reaction in fuel cells, which involves the transfer of four electrons and four protons (4e-, 4H+); or the splitting of water …

Investigations Into Background Correction And Retention Time Alignment To Enhance Quantitative Chemometric Analysis Of Comprehensive Two-Dimensional Liquid Chromatography-Diode Array Detection Data, Robert Allen

Theses and Dissertations

The focus of the projects presented here was to develop possible solutions to three issues commonly encountered during chemometric analysis of comprehensive two-dimensional liquid chromatography diode array detector (LCxLC-DAD) data. The focus of the first project was to determine a means of performing background correction that removed two background ridges. The methods of simply subtracting out a mean blank sample, singular value decomposition based background correction (SVD-BC) and asymmetrically weighted least squares (AWLS) were compared. AWLS was found to be the only background correction technique to fully remove the ridges. However, AWLS was also found to attenuate the peak intensity …

Chemometric Analysis Of Comprehensive Two-Dimensional Liquid Chromatographic-Diode Array Detection Data: Peak Resolution, Quantification And Rapid Screening, Hope P. Bailey

Theses and Dissertations

This research project sought to explore, compare and develop chemometric methods with the goal of resolving chromatographically overlapped peaks though the use of spectral information gained from the four-way data sets associated with comprehensive two-dimensional liquid chromatography with diode array detection (LC ´ LC-DAD). A chemometric method combining iterative key set factor analysis (IKSFA) and multivariate curve resolution-alternating least squares (MCR-ALS) was developed. In the section of urine data analyzed, over 50 peaks were found, with 18 visually observable and 32 additional compounds found only after application of the chemometric method. Upon successful chemometric resolution of chromatographically overlapped peaks, accurate …

Mass Spectroscopic Identification And Quantification Of Protein Carbonyls, Zafer Ugur

Theses and Dissertations

It is well established that free radical mediated oxidative stress plays a critical role in aging and age-related diseases. Among the post-translational protein modifications, carbonylation has attracted a great deal of attention due to its irreversible and irreparable nature. Despite the fact that protein carbonylation is associated with a series of physiological and pathological processes, there are still issues to be clarified such as why certain proteins are more vulnerable to modification, what are the locations of the protein modifications, and how does the nature of the oxidant affect the preferred site of modification. In this study, we will seek …

Accurate Methodology For Monitoring Biomembrane Events, Christine A. Winschel

Theses and Dissertations

Abstract ACCURATE METHODOLOGY FOR MONITORING BIOMEMBRANE EVENTS By Christine A. Winschel, Ph.D. A Dissertation submitted in partial fulfillment of the requirements for the degree of Doctorate of Philosophy in Chemistry at Virginia Commonwealth University. Virginia Commonwealth University, 2012 Major Director: Dr. Vladimir A. Sidorov ASSOCIATE PROFESSOR, DEPARTMENT OF CHEMISTRY This study describes the synthesis and characterization of a new receptor (cyclen 1) capable of strong selective binding of pyrene-based anionic dyes under near-physiological conditions. This receptor comprises four naphthylthiourea groups tethered to a cyclen core via an ester linkage. The most important finding was the ability of cyclen 1 to …

Development Of Nano-Scale Featured Materials For Electrode Modification And Solid Supports., Amy Rue

Theses and Dissertations

This work utilized the sol-gel process in two ways. First, macroporous silica thin films were developed using a combination of casting techniques and templating. Macroporsity was introduced to the silica thin films by either doping the silica sol before casting or by ordering the template on a substrate and then casting a sol over it. These techniques were first used to create silica thin films with long microchannel pores (200 nm x 60 µm) from a doped sol with the bacteria, B. Megaterium, as the template for nanomaterial formation. To enable the formation long microchannels, the flexible bacteria chains were …

Unconventional Superhalogens: Design And Applications, Devleena Samanta

Theses and Dissertations

Electron affinity is one of the most important parameters that guide chemical reactivity. Halogens have the highest electron affinities among all elements. A class of molecules called superhalogens has electron affinities even greater than that of Cl, the element with the largest electron affinity (3.62 eV). Traditionally, these are metal-halogen complexes which need one electron to close their electronic shell. Superhalogens have been known to chemistry for the past 30 years and all superhalogens investigated in this period are either based on the 8-electron rule or the 18-electron rule. In this work, we have studied two classes of unconventional superhalogens: …

Solvation Of Organic Cations In The Gas Phase And Within Molecular Clusters, Ahmed Hamid

Theses and Dissertations

The role of the solvent in ionic and ion-molecule interactions is of fundamental importance in kinetics and thermodynamics of solution chemistry. However, the study of the ionic interactions in the presence of a large number of solvent molecules is very challenging. Therefore, the gas-phase is the appropriate medium to study such reactions on a molecular level where the ion-solvent interaction can be examined by studying ions surrounded with a cluster of solvent molecules in the complete absence of the any interference caused by the bulk of the solvent. In nature, organic ions can form hydrogen bonds with solvents. An insight …

Drug Delivery Strategies Using Light Sensitive Molecules, Martin Dcona

Theses and Dissertations

Cancer remains one of the most dreaded diseases due to inevitable suffering and possible fatality. Only cardiac disease has caused more deaths than cancer. Present day cancer treatment involves radiation, surgery or chemotherapy. In chemotherapy, an anti-tumoral drug is used to treat the tumor either by killing or stalling the growth of the tumor cells. In certain types of cancer, for e.g. metastatic breast cancer, the first line of therapy is often chemotherapy. But the inability of current clinically approved drugs to selectively target tumor cells, ultimately results in side effects. To reduce these side effects, prodrug therapies have been …

Hierarchical Templates And Their Application To Multimodal Porous Materials Fabrication, Bo Zhao

Theses and Dissertations

Hierarchical materials offer great promise for high-performance sensors and catalysis carriers. Well-defined hierarchically porous materials are promising candidates for a wide range of applications relating to biosensors, separations, drug delivery, surface-enhanced Raman scattering (SERS), etc. Research on synthetic methodologies is expanding. However, fabrication of hierarchical porous structures with tunable pore dimension and shape, controllable pore distribution and interconnectivity is still a challenging task in materials science. One of the main tasks of this work is to establish a facile and reliable approach of making well-defined hierarchically porous materials. Then, based on those multimodal porous structures, different functions and applications can …

Identification And Quantification Of Protein Carbonylation By Mass Spectrometry, Qingyuan Liu

Theses and Dissertations

Accumulated evidence indicates oxidative stress plays important roles in disease and aging. Under oxidative stress, lipid peroxidation (LPO) leads to reactive carbonyl species (RCS) that can modify a wide range of biomolecules including protein, DNA and carbohydrate. In this dissertation, we investigate the modification of two model proteins, human serum albumin (HSA) and aconitase (ACO), by the LPO-relevant a, b-unsaturated aldehydes, acrolein (ACR) and 4-hydroxy-2-nonenal (HNE). The investigation is focused on the characterization and quantification ACR and HNE addition to the model proteins. A correlation between HNE modification and ACO activity is also determined. These results provide insights into the …

Magnetic Properties Of Co2c And Co3c Nanoparticles And Their Assemblies, Kyler J. Carroll, Zachary J. Huba, Steven R. Spurgeon, Meichun Qian, Shiv N. Khanna, Daniel M. Hudgins, Mitra L. Taheri, Everett E. Carpenter

Chemistry Publications

Nano-composite material consisting of Co₂C and Co₃C nanoparticles has recently been shown to exhibit unusually large coercivities and energy products. Experimental studies that can delineate the properties of individual phases have been undertaken and provide information on how the coercivities and the energy product change with the size and composition of the nanoparticles. The studies indicate that while both phases are magnetic, the Co₃C has higher magnetization and coercivity compared to Co₂C. Through first principles electronic structure studies using a GGA+U functional, we provide insight on the role of C intercalation on …

Controlled Synthesis Of Superparamagnetic Iron-Oxide Nanoparticles By Phase Transformation, Mark A. Laurenzi, Everett E. Carpenter

Chemistry Publications

A synthesis procedure for generating a uniform distribution of iron-oxide nanoparticles from an amorphous precursor is reported. The investigation suggests no evidence of the formation of unwanted surface oxide layers, internal stress, and multiple phases. This is likely because the physical properties of the diffusion fields surrounding the nanoparticles are self-limiting by Fe(II) depletion. Inside the diffusion field surrounding the nucleation site, decreasing Fe(II) concentration results in a decrease in the diffusion rate that continues to decrease until self-limiting kinetic arrest occurs. The initial Fe(II) concentration is established by reducing a system abundant in Fe(III) by means of exposure to …