Chemistry Commons^™

Corrosion Behavior Of Copper Thin Films In Organic Hf-Containing Cleaning Solution For Semiconductor Applications, Nabil George Mistkawi, Makarem A. Hussein, Malgorzata Ziomek-Moroz, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

The corrosion behavior of electrochemically deposited copper thin films in deaerated and non-deaerated commercial cleaning solutions containing HF was investigated. Potentiodynamic polarization experiments were carried out to determine active, active–passive, passive, and transpassive regions. Corrosion rates were calculated from Tafel slopes. The addition of hydrogen peroxide to the solution and its influence on corrosion was also investigated by employing inductively coupled plasma-mass spectroscopy (ICP-MS) and X-ray photoelectron spectroscopy (XPS). The ICP-MS and potentiodynamic methods yielded comparable Cu dissolution rates. Surface analysis using atomic force microscopy and scanning electron microscopy, performed before and after the cleaning solution treatment, did not reveal …

S-Nitrosothiols: Formation, Decomposition, Reactivity And Possible Physiological Effects, Moshood Kayode Morakinyo

Dissertations and Theses

Three biologically-active aminothiols cysteamine (CA), DL-cysteine (CYSH) and DL-homocysteine, were studied in this thesis. These aminothiols react with nitrous acid (HNO₂), prepared in situ, to produce S-nitrosothiols (RSNOs): S-nitrosocyteamine (CANO), S-nitrosocysteine (CYSNO) and S-nitrosohomocysteine (HCYSNO). They also react with S-nitrosoglutathione (GSNO) and S-nitroso-N-acetylpenicillamine (SNAP) through a transnitrosation reaction to produce their corresponding RSNOs. A detailed kinetics and mechanistic study on the formation of these RSNOs and their subsequent decomposition to release nitric oxide (NO) were studied.

For all three aminothiols the stoichiometry of their reaction with nitrous acid is strictly 1:1 with the formation of one mole …

Selective Fluorescence Detection Of Cysteine And N-Terminal Cysteine Peptide Residues, Soojin Lim, Jorge O. Escobedo, Mark Lowry, Xiangyang Xu, Robert M. Strongin

Chemistry Faculty Publications and Presentations

A new fluorogenic fluorescein derivative containing an α,β-unsaturated aldehyde moiety produces a selective fluorescent signal enhancement in the presence of cysteine or peptides containing N-terminal cysteine residues. The mechanism is based on synergistic covalent and supramolecular interactions.

Copper Thin-Film Dissolution/Precipitation Kinetics In Organic Hf Containing Cleaning Solution, Nabil George Mistkawi, Makarem A. Hussein, Malgorzata Ziomek-Moroz, Shankar B. Rananavare

Chemistry Faculty Publications and Presentations

The corrosion behavior of electrochemically deposited copper thin films in deaerated and non-deaerated commercial cleaning solution containing HF has been investigated. Thin-film copper dissolution and reaction kinetics were investigated by monitoring Cu²⁺ , employing inductively coupled plasma–mass spectroscopy, and the oxidation states of copper on Si wafer surface, employing X-ray photoelectron spectroscopy. It was determined that the reaction kinetics is first order with respect to both HF and oxygen concentrations. A kinetic scheme involving reduction of oxygen and oxidation of Cu⁰ and Cu¹⁺ is proposed, which is consistent with the experimentally determined reaction kinetic orders and the …

The Population Of Sap And Tsap Isomers In Cyclen-Based Lanthanide(Iii) Chelates Is Substantially Affected By Solvent, Kyle J. Miller, Ali A. Saherwala, Benjamin C. Webber, Yunkou Wu, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

The square antiprism/twisted square antiprism ratio in LnDOTA-tetraamide chelates is a critical parameter in governing water-exchange kinetics and ultimately the utility of a chelate as a PARACEST MRI contrast agent. In LnDOTA-tetraamide chelates with tertiary amides, this ratio and the rate of interconversion between these two structural isomers are found to be dramatically dependent upon the solvent and possibly other local environmental factors.

Solid State And Solution Dynamics Of Pyridine Based Tetraaza- Macrocyclic Lanthanide Chelates Possessing Phosphonate Ligating Functionality (Ln-Pctmb): Effect On Relaxometry And Optical Properties, Garry Kiefer, Mark Woods

Chemistry Faculty Publications and Presentations

The macrocyclic ligand 3,6,9-tris(methylenebutyl phosphonic acid)-3,6,9−15-tetraazabicyclo [9.3.1]pentadeca-1(15),11,13-triene (PCTMB) was synthesized and complexes of Eu³⁺, Tb³⁺, and Gd³⁺ studied by X-ray crystallography, luminescence, and relaxometry. In the crystal these complexes are dimeric and possess 8-coordinate Ln³⁺ centers that are linked by bridging phosphonates. The rigidity introduced by the pyridyl nucleus forces the EuPCTMB and TbPCTMB to adopt a twisted snub disphenoid (TSD) coordination geometry. Examination of the ⁵D₀ → ⁷F₀ luminescent transition of EuPCTMB in the solid state confirmed the existence of a single distinct Eu³⁺ coordination environment, whereas two …

Lipid-Protein Interactions Probed By Electron Crystallography, Steve L. Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Electron crystallography is arguably the only electron cryomicroscopy (cryoEM) technique able to deliver an atomic-resolution structure of membrane proteins embedded in the lipid-bilayer. In the electron crystallographic structures of the light driven ion pump, bacteriorhodopsin, and the water channel, aquaporin-0, sufficiently high resolution was obtained and both lipid and protein were visualized, modeled and described in detail. An extensive network of lipid-protein interactions mimicking native membranes is established and maintained in two-dimensional (2D) crystalline vesicles used for structural analysis by electron crystallography. Lipids are tightly integrated into the protein's architecture where they can affect the function, structure, quaternary assembly and …

Apoptotic And Chemotherapeutic Properties Of Iron (Iii)-Salophene In An Ovarian Cancer Animal Model, Thilo S. Lange, Carolyn Mccourt, Rakesh K. Singh, Kyu Kwang Kim, Ajay P. Singh, Brian S. Luisi, Onur Alptürk, Robert M. Strongin, Laurent Brard

Chemistry Faculty Publications and Presentations

The cytotoxicity of organometallic compounds iron(III)-, cobalt(III)-, manganese(II)-, and copper(II)-salophene (-SP) on platinum-resistant ovarian cancer cell lines was compared. Fe-SP displayed selective cytotoxicity (IC(50) at ~1 muM) against SKOV-3 and OVCAR-3 cell lines while Co-SP caused cytotoxic effects only at higher concentrations (IC(50) at 60 muM) and Cu-SP effects were negligible. High cytotoxicity of Mn-SP (30-60 muM) appeared to be nonspecific because the Mn-chloride salt reduced cell viability similarly. The effect of Fe-SP at 1 muM proved to be ovarian cancer cell selective when compared to a panel of cell lines derived from different tumors. The first irreversible step in …

Electron Transport And Sensor Characteristics Of Tin Dioxide Based Nanocrystalline Materials, Allen Chaparadza

Dissertations and Theses

Wide band gap, transparent semiconductor Sn0₂ is an n-type conductor and is widely used as a sensor material as well as transparent electrode material e.g. in solar cells and flat panel displays. Recent discovery of p-type doping with Li has opened exciting possibilities in new classes of sensors and transparent nanoelectronic devices. Li-doping in SnO₂ nanoparticles was explored through a gel-sol method of synthesis to examine the influence of reaction conditions such as pH, dopant concentration, and calcination temperature. The Li doping in nanoparticles was characterized using nuclear reaction analysis and the nanostructure with high-resolution electron transmission microscopy …

Synthesis And Evaluation Of Lanthanide Ion Dota-Tetraamide Complexes Bearing Peripheral Hydroxyl Groups, Azhar Pasha, Mai Lin, Gyula Tircso, Cynthia L. Rostollan, Mark Woods, Garry Kiefer, A. Dean Sherry, Xiankai Sun

Chemistry Faculty Publications and Presentations

The use of lanthanide-based contrast agents for magnetic resonance imaging has become an integral component of this important diagnostic modality. These inert chelates typically possess high thermodynamic stability constants that serve as a predictor for in vivo stability and low toxicity. Recently, a new class of contrast agents was reported having a significantly lower degree of thermodynamic stability while exhibiting biodistribution profiles indicative of high stability under biological conditions. These observations are suggestive that the nature of contrast agent stability is also dependent upon the kinetics of complex dissociation, a feature of potential importance when contemplating the design of new …

Characterization Of Putative Self-Resistance Genes In The Biosynthetic Gene Cluster Of Hygromycin A From Streptomyces Hygroscopicus Nrrl 2388, Vidya Dhote

Dissertations and Theses

Streptomyces hygroscopicus NRRL 2388 produces an aminocyclitol antibiotic called hygromycin A (HA), which targets bacterial protein synthesis by inhibiting the peptidyl transferase reaction. The hyg6, hygl9, hyg21, hyg28, and hyg29 genes in the biosynthetic gene cluster of HA are predicted to confer self-resistance to the producer strain by different mechanisms. Targeted gene disruptions and in vitro characterization of recombinant proteins were carried out to elucidate the functions of these genes. The hyg21 gene encodes an O-phosphotransferase with a proposed role in HA inactivation by phosphorylation. Disruption of hyg21 led to a significant decrease in HA production but did not …

Synthesis Of Aptamer-Porphyrin Conjugate For Photodynamic Therapy & Synthesis And Stability Of Mixed Thiol/Lipid Coated Gold Nanoparticles, Sarita Sitaula

Dissertations and Theses

An underlying problem in Photodynamic Therapy (PDT) is low selectivity of photosensitizers currently being used for the treatment of tumors. This thesis is focused on developing new PDT drugs and is divided into two parts. The first chapter describes a method for selective delivery of the photosensitizers to the tumor site by conjugating porphyrins to an aptamer for the targeted PDT. To achieve this, a novel synthesis of 2'-porphyrin-modified uridine was developed. The 3'-H-phosphonate derivatives of both 2'-porphyrin and 2'-dithiaporphyrin modified uridine were also synthesized. The 3'41-phosphonate derivative of 2'-porphyrin-modified uridine was conjugated to a 19-mer DNA and to a …

One Rna Plays Three Roles To Provide Catalytic Activity To A Group I Intron Lacking An Endogenous Internal Guide Sequence, Nilesh Vaidya, Niles Lehman

Chemistry Faculty Publications and Presentations

Catalytic RNA molecules possess simultaneously a genotype and a phenotype. However, a single RNA genotype has the potential to adopt two or perhaps more distinct phenotypes as a result of differential folding and/or catalytic activity. Such multifunctionality would be particularly significant if the phenotypes were functionally inter-related in a common biochemical pathway. Here, this phenomenon is demonstrated by the ability of the Azoarcus group I ribozyme to function when its canonical internal guide sequence (GUG) has been removed from the 5? end of the molecule, and added back exogenously in trans. The presence of GUG triplets in noncovalent fragments of …

Exploring The Ph Dependence Of Viologen Reduction By Alpha-Carbon Radicals Derived From Hcy And Cys, Dong Wang, William E. Crowe, Robert M. Strongin, Martha Sibrian-Vazquez

Chemistry Faculty Publications and Presentations

The colorimetric reaction of homocysteine (HCy) with a series of viologen salts suggests a linear correlation between the mid-point reduction potential of Hcy-derived α-carbon radicals and pH.

Structural Basis For Binding Specificity Between Subclasses Of Modular Polyketide Synthase Docking Domains, Tonia Buchholz, Todd W. Geders, Frank E. Bartley Iii, Kevin A. Reynolds, Janet L. Smith, David H. Sherman

Chemistry Faculty Publications and Presentations

Bacterial type I polyketide synthases (PKSs) assemble structurally diverse natural products of significant clinical value from simple metabolic building blocks. The synthesis of these compounds occurs in a processive fashion along a large multiprotein complex. Transfer of the acyl intermediate across interpolypeptide junctions is mediated, at least in large part, by N- and C-terminal docking domains. We report here a comprehensive analysis of the binding affinity and selectivity for the complete set of discrete docking domain pairs in the pikromycin and erythromycin PKS systems. Despite disconnection from their parent module, each cognate pair of docking domains retained exquisite binding selectivity. …

Optimising The Synthesis And Red–Green–Blue Emission Of A Simple Organic Dye, Martha Sibrian-Vazquez, Robert M. Strongin

Chemistry Faculty Publications and Presentations

Synthetic dyes have been widely used in supramolecular chemistry not only to probe fundamental chemical interactions but also as components of functional materials. Most current efforts in this regard are directed at designing new host systems for the dyes. Herein we report on the study of a versatile new organic fluorophore. We describe a synthesis which affords improved yields in a convenient one pot procedure. Moreover, a simple method for predicting and controlling the dye’s responses to external stimuli affords a potentially practical method for achieving red–green–blue and concomitant white light generation.

Effect Of The Regiochemistry Of Butyl Amide Substituents On The Solution-State Structures Of Lanthanide(Iii) Dota-Tetraamide Complexes, Tomoyasu Mani, Gyula Tircsó, Piyu Zhao, A. Dean Sherry, Mark Woods

Chemistry Faculty Publications and Presentations

The coordination geometry adopted by the lanthanide complexes of DOTA-tetraamides is a critical factor in determining their water exchange kinetics. Controlling the water exchange kinetics of DOTA-tetraamide complexes, and by extension their coordination geometry, is of particular interest because of the potential application of this class of complex as PARACEST MRI contrast agents. To facilitate the maximum CEST effect at the lowest pre-saturation powers much slower exchange kinetics are required than are commonly observed with these types of chelates. Complexes that adopt the more slowly exchanging square antiprismatic coordination geometry are therefore preferred; however, the factors that govern which coordination …

Generation Of Novel Pikromycin Antibiotic Products Through Mutasynthesis, Shuchi Gupta, Venkatraman Lakshmanan, Beom Seok Kim, Robert Fecik, Kevin A. Reynolds

Chemistry Faculty Publications and Presentations

Mutasynthesis in pikromycin PKS: The amenability of pikromycin polyketide synthase to mutational biosynthesis has been demonstrated. A natural triketide and its analogues, activated as N-acetyl-cysteamine thioesters, were synthesized and fed to a pikAI-deleted strain; this led to the production of new antibiotics. A vinyl analogue was found to have better antibacterial activity than pikromycin.

A Photochemically Initiated Chemistry For Coupling Underivatized Carbohydrates To Gold Nanoparticles, Xin Wang, Olof Ramström, Mingdi Yan

Chemistry Faculty Publications and Presentations

The sensitive optoelectronic properties of metal nanoparticles make nanoparticle-based materials a powerful tool to study fundamental biorecognition processes. Here we present a new and versatile method for coupling underivatized carbohydrates to gold nanoparticles (Au NPs) via the photochemically induced reaction of perfluorophenylazide (PFPA). A one-pot procedure was developed where Au NPs were synthesized and functionalized with PFPA by a ligand-exchange reaction. Carbohydrates were subsequently immobilized on the NPs by a fast light activation. The coupling reaction was efficient, resulting in high coupling yield as well as high ligand surface coverage. A colorimetric system based on the carbohydrate-modified Au NPs was …

The Effect Of The Amide Substituent On The Biodistribution And Tolerance Of Lanthanide(Iii) Dota-Tetraamide Derivatives, Mark Woods, Peter Caravan, Carlos F.G.C. Geraldes, Matthew T. Greenfield, Garry Kiefer, Mai Lin, Kenneth Mcmillan, M. Isabel M. Prata, Ana C. Santos, Xiankai Sun, Jufeng Wang, Shanrong Zhang, Piyu Zhao, A. Dean Sherry

Chemistry Faculty Publications and Presentations

Objectives—Recent advances in the design of MRI contrast agents have rendered the lanthanide complexes of DOTA-tetraamide ligands of considerable interest, both as responsive MR agents and paramagnetic chemical exchange saturation transfer agents. The potential utility of these complexes for in vivo applications is contingent upon them being well tolerated by the body. The purpose of this study was to examine how the nature of the amide substituent, and in particular its charge, affected the fate of these chelates postinjection.

Materials and Methods—Complexes of 6 DOTA-tetraamide ligands were prepared in which the nature of the amide substituent was systematically …

Polymeric Paracest Agents For Enhancing Mri Contrast Sensitivity, Yunkou Wu, Youfu Zhou, Olivier Quari, Mark Woods, Piyu Zhao, Todd B. Soesbe, Garry Kiefer, A. Dean Sherry

Chemistry Faculty Publications and Presentations

Linear polymers of PARACEST agents were prepared by using classical free radical chain polymerization conditions. The Eu³⁺-polymers exhibited similar intermediate-to-slow water exchange and CEST characteristics as the Eu³⁺-monomers. This provided an avenue to lower the detection limit of these imaging agents substantially and makes them potentially useful as MRI sensors for molecular imaging.

The Original Build Up Of Genetic Information By Rna Recombination, Eric John Hayden

Dissertations and Theses

This research demonstrates chemical reactions of RNA molecules that allow them to increase in length, from non-catalytic oligomers to complex RNA enzymes. The purpose of this research was to explain the origin of large RNA polymers required for life to begin in the proposed "RNA World". To do this, the Azoarcus group I ribozyme was engineered to catalyze phosphodiester exchange reactions that result in the recombination of short oligomer substrates marked by ^5'CAU^3' recognition tags.

To demonstrate the ability to produce catalytic RNA sequences through recombination, substrate oligomers were synthesized that could produce ribozymes if large portions of …

Non-Canonical Binding Of Calmodulin To Aquaporin-0: Implications For Channel Regulation, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins (AQPs) are a family of ubiquitous membrane channels that conduct water across cell membranes. AQPs form homo-tetramers containing four functional and independent water pores. Aquaporin-0 (AQP0) is expressed in the eye lens where its water permeability is regulated by calmodulin (CaM). Here we use a combination of biochemical methods and NMR spectroscopy to probe the interaction between AQP0 and CaM. We show CaM binds the AQP0 C-terminal domain in a calcium dependent manner. We demonstrate that only two CaM molecules bind a single AQP0 tetramer in a non-canonical fashion, suggesting a form of co-operativity between AQP0 monomers. Based on …

Synthesis And Relaxometric Studies Of A Dendrimer‐Based Ph‐Responsive Mri Contrast Agent, M. Meser Ali, Mark Woods, Peter Caravan, Ana C.L. Opina, Marga Spiller, James C. Fettinger, A. Dean Sherry

Chemistry Faculty Publications and Presentations

The design of effective pH responsive MRI contrast agents is a key goal in the development of new diagnostic methods for conditions such as kidney disease and cancer. A key factor determining the effectiveness of an agent is the difference between the relaxivity of the “on” state compared to that of the “off” state. In this paper, we demonstrate that it is possible to improve the pH-responsive action of a low molecular weight agent by conjugating it to a macromolecular construct. The synthesis of a bifunctional pH responsive agent is reported. As part of that synthetic pathway we examine the …

Nanostructered Aminophenylporphyrin Films For Use In Bulk Heterojunction And Inverse Dye-Sensitized Tio₂ Solar Cells, Michael George Walter

Dissertations and Theses

Conductive nanostructured films of poly-tetrakis-5,10,15,20-(4-aminophenyl)porphyrin (TAPP) can be grown electrochemically or through interfacial oxidative polymerization. The poly-TAPP nanomorphology is sensitive to the electrochemical solvent, potentiometric method, and the aminophenyl porphyrin monomer utilized. To elucidate the molecular structure of poly-TAPP and to correlate structures with proposed polymerization and conductivity mechanisms, reflectance FT-IR and spectroelectrochemistry were used to detect the presence and electroactivity of dihydrophenazine and phenazine polymer linkages formed during the polymerization.

Poly-TAPP nanofiber films were evaluated for use in a bulk heterojunction solar cell (with PCBM) and in an inverse dye-sensitized TiO2 solar cell using the poly-TAPP nanoporous scaffold to …

Design And Synthesis Of Antimalarial Drugs Based On A Chloroquine Scaffold, Steven James Burgess

Dissertations and Theses

There are between 350 and 500 million clinical cases of malaria each year, and over 1 million deaths, with pregnant women and children under the age of 5 being most at risk. Chloroquine (CQ) became the preferred drug to treat malaria in the late 1940s, but is now rendered mostly ineffective in many parts of the world, due to widespread CQ resistance by the malaria parasite. All other malaria treatments suffer from some drawbacks, which include development of resistance, side effects including toxicity, risk for pregnant women and young children, and high cost. Some existing, non-antimalarial, drugs have been found …

A Novel Approach To The Synthesis Of Silicon Nanowires, Joo Chick Chan

Dissertations and Theses

Contemporary VLS-SiNW synthetic methods employ CVD and laser ablation methods that produce single crystalline SiNW; which can be doped by co-flowing appropriate dopants, such as diborane (p-type) and phosphine (n-type). Not only are these gases toxic (non-green), but also the synthetic methods used are costly requiring elaborate instrumental assembly. This thesis presents a low-cost and "green" method in synthesizing and doping of SiNW in a glass tube. It was found that by selecting the appropriate metal catalyst, precursor reactants, and the reaction conditions both SiNW and carbon nanotube (CNT) can be synthesized on metallic (aluminum and copper), semiconducting (silicon) and …

Seminaphthofluorones Are A Family Of Water-Soluble, Low Molecular Weight, Nir-Emitting Fluorophores, Youjun Yang, Mark Lowry, Xiangyang Xu, Jorge O. Escobedo, Martha Sibrian-Vazquez, Lisa Wong, Corin M. Schowalter, Timothy J. Jensen, Frank R. Fronczek, Isiah M. Warner, Robert M. Strongin

Chemistry Faculty Publications and Presentations

A readily accessible new class of near infrared (NIR) molecular probes has been synthesized and evaluated. Specific fluorophores in this unique xanthene based regioisomeric seminaphthofluorone dye series exhibit a combination of desirable characteristics including (i) low molecular weight (339 amu), (ii) aqueous solubility, and (iii) dual excitation and emission from their fluorescent neutral and anionic forms. Importantly, systematic changes in the regiochemistry of benzannulation and the ionizable moieties afford (iv) tunable deep-red to NIR emission from anionic species and (v) enhanced Stokes shifts. Anionic SNAFR-6, exhibiting an unusually large Stokes …

Electron Crystallography Of Aquaporins, Simeon Andrews, Steve Reichow, Tamir Gonen

Chemistry Faculty Publications and Presentations

Aquaporins are a family of ubiquitous membrane proteins that form a pore for the permeation of water. Both electron and X-ray crystallography played major roles in determining the atomic structures of a number of aquaporins. This review focuses on electron crystallography, and its contribution to the field of aquaporin biology. We briefly discuss electron crystallography and the two-dimensional crystallization process. We describe features of aquaporins common to both electron and X-ray crystallographic structures; as well as some structural insights unique to electron crystallography, including aquaporin junction formation and lipid-protein interactions.

Development And Investigation Of Unique Organic Materials To Detect Disease Biomarkers, George Kiplimo Samoei

Dissertations and Theses

Chemomechanical polymer gels with the capability of recognizing specific biological molecules are promising materials for many biomedical applications. Glucose-selective hydrogels have potential utility in the continuous monitoring of glucose and glucose-triggered insulin delivery for the management of diabetes. Herein, the development and study of the first material which detects glucose via significant volume changes in the challenging matrix human blood plasma is described. The material was created via the modification of PMMA with supramolecular binding sites. The polymer exhibits excellent selectivity and reversibility including continuous expansion-contraction cycles.