Physical Sciences and Mathematics Commons^™

Numerical Simulation And Graphical Analysis Of In Vitro Benign Tumor Growth: Application Of Single-Particle State Bosonic Matter Equation With Length Scaling, Pradip K. Biswas, Jiansen Niu, Tobias Frederico, Valentin Gogonea

Chemistry Faculty Publications

We describe the application of a non-linear single-particle state bosonic condensate equation to simulate multicellular tumor growth by treating it as a coupling of two classical wave equations with real components. With one component representing the amplitude of the cells in their volume growth phase and the other representing the amplitude of the cells in their proliferation or mitosis phase, the two components of the coupled equation feed each other during the time evolution and are coupled together through diffusion and other linear and non-linear terms. The features of quiescent and necrotic cells, which result from poor nutrient diffusion into …

The Synthesis Of Zinc Oxide By Direct And Indirect Methods, Grainne Duffy

Masters

The synthesis of zinc oxide through three routes was investigated; carboxylic acid chelation, polymer assisted synthesis in an alcoholic medium and slow thermolysis of precursor. In the case of carboxylic acid chelation, it was determined that the rate at which the precursor is formed has a significant effect on the quality of zinc oxide particles produced. Investigation of the effect of concentration, pH and species of chelating agent used on the purity and structure of product was undertaken. Examination of the composition and morphology of materials produced revealed the presence of single-crystalline spheres, the packing density and aggregation morphology of …

Coordination Environment: A New Approach To The Sensing Of Lead (Ii) Itself, Kristina Marie Nespechal

Masters Theses

Lead(II) is a silent poison that has plagued society since 3800 B. C. The average intake of lead in the United States alone is 50 μg per day, which is approximately 100-1000 times greater than that of prehistoric lead levels. Regardless of the banning of lead in paints and gasoline, lead poisoning prevails as a major environmental health risk. Science has the ability to address the concern with this environmental contaminant. The future production of an economical and reliable test kit for lead(II) relies on the luminescence of the heavy metal itself.

The absorption and emission spectra for a series …

Direct Experimental Evidence For The Atomic Tunneling Of Europium In Crystalline Eu₈Ga₁₆Ge₃₀, Raphäel P. Hermann, Veerle M. Keppens, Pierre Bonville, George S. Nolas, Fernande Grandjean, Gary J. Long, Hans Martin Christen, Bryan C. Chakoumakos, Brian C. Sales, David G. Mandrus

Chemistry Faculty Research & Creative Works

Mössbauer-effect and microwave absorption experimental evidence unambiguously demonstrates the presence of slow, ~450 MHz, tunneling of magnetic europium between four equivalent sites in Eu₈Ga₁₆Ge₃₀, a stoichiometric clathrate. Remarkably, six of the eight europium atoms, or 11% of the constituents in this solid, tunnel between these four sites separated by 0.55 Å. The off centering of the atoms or ions in crystalline clathrates appears to be a promising route for producing Rabi oscillators in solid-state materials.

Mechanism Of A Solid-State Formation Of La1-Xsrxmno3+Δ (0 < X < 0.5) And Magnetic Characterization Thereof, Vuk Uskoković, Miha Drofenik

Pharmacy Faculty Articles and Research

Rich diversity of potential, substantially different micro-structural arrangements - reflecting on the wide potential set of interesting properties, ranging from high electrical conductivity to giant, collossal and/or low-field magnetoresistance to low Curie point - of LaSr-manganite materials opens possibilities for numerous scientific investigations oriented towards revealing correlations on the influence line: procedure of synthesis → inherent properties → measured properties → application of the material. The investigations of the influence of synthesis procedures and LaSr-manganite stoichiometries on the Curie point (and other magnetic characteristics) of the material, being the topic of this work, are attractive since they present a necessary …

Investigation Of Ruthenium (Ii) Polypyridyl Dimers As Potential Chemotherapeutic Agents, Thamara K. Janaratne

Chemistry & Biochemistry Dissertations

The exploration of transition metal complexes as chemotherapeutic agents is still a relatively unexplored but promising area of research. Chapter 1 highlights the most successful anticancer drugs and potential drugs based on metal complexes, with an emphasis of platinum and ruthenium complexes. In Chapter 2, the biological activity of a series of novel ruthenium dimers is investigated with special attention given to evaluating their potential as anticancer chemotherapeutic agents. A partial list of the compound prepared includes: [Ru(bpy)(CO)2}2tpphz]4+ (74+), [Ru(bpy)(CH3CN)2}2tpphz]4+ (84+),[Ru(bpy)(C2O4)}2tpphz] (9), [Ru(bpy)(CO)(Cl)}2tpphz]2+ (102+), [(bpy)2Ru(tpphz)Ru(bpy)2]4+ (114+), [(phen)2Ru(tpphz)Ru(phen)2]4+ (124+), [(phen)2Ru(tatpp)Ru(phen)2]4+ (Pp4+), [(phen)2Ru(tatpq)Ru(phen)2]4+ (Qp4+), [(bpy)2Ru(tatpp)Ru(bpy)2]4+ (Pb4+) and [(bpy)2Ru(tatpq)Ru(bpy)2]4+ (Qb4+). Systematic changes in …

Model Studies Towards The Total Synthesis Of Lyconadin A Via An Acyl Radical Cascade Reaction, Koudi Zhu

Theses and Dissertations

Lyconadin A is an alkaloid possessing a unique structure and antitumor activity. The total synthesis of Lyconadin A was proposed via an acyl radical cascade reaction. To investigate the possibility and stereoselectivity of the cascade cyclization, phenyl selenoester 16 was chosen as a model substrate to study the 7-exo-5-exo radical cyclization. A synthetic route to phenyl selenoester 16 was developed. The 7-exo-5-exo radical cyclization was found to occur with a high yield and excellent stereoselectivty. Attempts were also tried to synthesize another radical precursor 14 albeit with less success. A synthetic pathway to the synthesis of 14 as well as …

Semiclassical Nonadiabatic Dynamics Based On Quantum Trajectories For The O(3P,1D)+H2 System, Sophya Garashchuk, Vitaly A. Rassolov, George C. Schatz

Faculty Publications

The O(³P,¹D)+H₂→OH+H reaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J = 0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions …

The Particle In A Box (And In A Circular Box), Carl W. David

Chemistry Education Materials

The particle in a box problem in 1 and 2 dimensions is treated both for the Cartesian problem (square, rectangle) but for circular boundary conditions.

The Importance Of The Strictly Conserved, C-Terminal Glycine Residue In Phosphoenolpyruvate Carboxylase For Overall Catalysis: Mutagenesis And Truncation Of Gly-961 In The Sorghum C4 Leaf Isoform, Wenxin Xu, Shaheen Ahmed, Hideaki Moriyama, Raymond Chollet

Hideaki Moriyama Publications

Phosphoenolpyruvate carboxylase (PEPC) is a “multifaceted,” allosteric enzyme involved in C4 acid metabolism in green plants/microalgae and prokaryotes. Before the elucidation of the three-dimensional structures of maize C4 leaf and Escherichia coli PEPC, our truncation analysis of the sorghum C4 homologue revealed important roles for the enzyme’s C-terminal α-helix and its appended QNTG⁹⁶¹ tetrapeptide in polypeptide stability and overall catalysis, respectively. Collectively, these functional and structural observations implicate the importance of the PEPC C-terminal tetrapeptide for both catalysis and negative allosteric regulation. We have now more finely dissected this element of PEPC structure-function by modification of the absolutely conserved …

The Hamiltonian And Schrodinger Equation For Helium's Electrons (Hylleraas), Carl W. David

Chemistry Education Materials

The Hylleraas forms for the kinetic energy operator for the two electrons of Helium in the ground singlet Sigma state are obtained explicitly.

The Mechanism Of Assembly Of The G-Protein Beta Gamma Subunit Dimer By Ck2 Phosphorylated Phosducin-Like Protein And The Chaperonin Containing Tcp-1, Christine M. Baker

Theses and Dissertations

Phosducin-like protein (PhLP) binds G-protein beta gamma subunits and is thought to assist in assembly of the G-protein beta gamma dimer. Phosphorylation of PhLP at serine residues 18-20 by the casein kinase 2 (CK2) appears to play an essential role in this process. PhLP has also been shown to interact with the chaperonin containing TCP-1 (CCT) atop its apical domain, not entering the substrate folding cavity. However, the physiological role of the PhLP-CCT interaction in G-protein beta gamma dimer formation remains unclear. This study addresses the mechanism of G-protein beta gamma assembly by exploring the specific roles of CCT and …

Crystallographic Analysis And Kinetic Studies Of Hiv-1 Protease And Drug-Resistant Mutants, Yunfeng Tie

Chemistry Dissertations

HIV-1 protease is the most effective target for drugs to treat AIDS, however, the long-term therapeutic efficiency is restricted by the rapid development of drug resistant variants. To better understand the molecular basis of drug resistance, crystallographic and kinetic studies were applied to wild-type HIV-1 protease (PR) and drug-resistant mutants, PRV82A, and PRI84V, in complex with substrate analogues, the current drug saquinavir and the new inhibitor UIC-94017 (TMC-114). UIC-94017 was also studied with mutants PRD30N and PRI50V. The drug-resistant mutations V82A, I84V, D30N and I50V participate in substrate binding. Eighteen crystal structures were refined at resolutions of 0.97-1.60A. The high …

On The Mechanistic Roles Of The Protein Positive Charge Close To The N(1)Flavin Locus In Choline Oxidase, Mahmoud Ghanem

Chemistry Dissertations

Choline oxidase catalyzes the oxidation of choline to glycine betaine. This reaction is of considerable medical and biotechnological applications, because the accumulation of glycine betaine in the cytoplasm of many plants and human pathogens enables them to counteract hyperosmotic environments. In this respect, the study of choline oxidase has potential for the development of a therapeutic agent that can specifically inhibit the formation of glycine betaine, and therefore render pathogens more susceptible to conventional treatment. The study of choline oxidase has also potential for the improvement of the stress resistance of plant by introducing an efficient biosynthetic pathway for glycine …

Energy Storage In Cold Non-Elastic Deformation Of Glassy Polymers, E.F. Oleinik, S.N. Rudnev, O.B. Salamatina, S.V. Shenogin, M.I. Kotelyanskii, T.V. Paramzina, S.I. Nazarenko

Faculty Publications

Experimental results on work W(epsilon), heat Q(epsilon) and stored energy U(epsilon) of deformation for glassy polymers such as linear PS, PC, PMMA, Polyimid, amorphous PET, thermotropic aromatic polyesters, Vectra T for example, crosslinked epoxy are presented. All the data was obtained by a deformation calorimetry technique. Loading and unloading of samples were performed at room temperature with strain rate epsilon = 10(-2) - 10(-4) sec(-1) under uniaxial compression up to engineering strains of epsilon(def) = 40-50%. During straining all polymers accumulate an excess of the latent energy U( e). Elastic fraction of the energy is released completely at sample unloading …

Characterizing The Potential Energy Surface Of The Water Dimer With Dft: Failures Of Some Popular Functionals For Hydrogen Bonding, Julie A. Anderson, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

Ten stationary points on the water dimer potential energy surface have been examined with ten density functional methods (X3LYP, B3LYP, B971, B98, MPWLYP, PBE1PBE, PBE, MPW1K, B3P86, and BHandHLYP). Geometry optimizations and vibrational frequency calculations were carried out with the TZ2P(f,d)+dif basis set. All'ten of the density functionals correctly describe the relative energies of the ten stationary points. However, correctly describing the curvature of the potential energy surface is far more difficult. Only one functional (BHandHLYP) reproduces the number of imaginary frequencies from CCSD(T) calculations. The other nine density functionals fail to correctly characterize the nature of at least one …

Fabrication Of Polymeric Microfluidic Devices For Protein Analysis, Jikun Liu

Theses and Dissertations

2-Bromoisobutyryl bromide was immobilized on poly(methyl methacrylate) (PMMA) substrates activated using an oxygen plasma. Atom-transfer radical polymerization was then performed to graft poly(ethylene glycol) (PEG) on the PMMA surface. PMMA micro capillary electrophoresis (µCE) devices made with the covalently modified surfaces exhibited substantially reduced electroosmotic flow and nonspecific adsorption of proteins. Both column efficiency and migration time reproducibility were one order of magnitude better with derivatized PMMA µCE devices compared to untreated versions. Fast, reproducible, and efficient separations of proteins and peptides were demonstrated using the PEG-grafted PMMA µCE chips. All analyses were completed in less than 60 seconds, and …

Chromatographic Analysis Of Carbamazepine Binding To Human Serum Albumin: Ii. Comparison Of The Schiff Base And N-Hydroxysuccinimide Immobilization Methods, Hee Seung Kim, Rangan Mallik, David S. Hage

David Hage Publications

Recent studies with carbamazepine on human serum albumin (HSA) columns have noted an appreciable degree of non-specific binding on supports prepared by the Schiff base immobilization method. This work examines an alternative immobilization method for HSA based on N-hydroxysuccinimide (NHS)-activated silica. This support was prepared by reacting HPLC-grade silica directly with disuccinimidyl carbonate. The resulting material was compared to an HSA support prepared by the Schiff base method in terms of its activity for carbamazepine and non-specific interactions with this drug. When examined by frontal analysis, both supports gave comparable association equilibrium constants for carbamazepine interactions with HSA ((0.53–0.55) …

(Review) Green Fluorescent Proteins, Marc Zimmer

Chemistry Faculty Publications

Reviews the book:Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain.Green Fluorescent Protein: Properties, Applications, and Protocols. Second Edition. Methods of Biochemical Analysis, Volume 47. Edited by Martin Chalfie and Steven R Kain. Hoboken (New Jersey): Wiley-Interscience. $89.95. xv + 443 p + 24 pl; ill.; index. ISBN: 0–471–73682–1. 2006.

Kinetics Of The Dna Polymerase Pyrococcus Kodakaraensis, Mark A. Griep, Casey A. Kotera, R.M. Nelson, Hendrik J. Viljoen

Mark Griep Publications

The polymerase chain reaction is one of the most important reactions in molecular biology. Single stranded DNA is copied in a complex series of steps, at the core of which lies the action of the DNA polymerase. At each nucleotide along the template, the polymerase screens the dNTP pool until it finds the complementary dNTP. The insertion of each dNMP is a balance between high fidelity and rapid elongation. In this study the kinetics of the β type polymerase pyrococcus kodakaraensis (KOD) is analyzed. The kinetics is influenced by reaction conditions such as the dNTP pool composition and temperature. In …

Dynamics Of Surface Catalyzed Reactions; The Roles Of Surface Defects, Surface Diffusion, And Hot Electrons, Gabor Somorjai, Kaitlin Bratlie, Max Montano, Jeong Park

Kaitlin M. Bratlie

The mechanism that controls bond breaking at transition metal surfaces has been studied with sum frequency generation (SFG), scanning tunneling microscopy (STM), and catalytic nanodiodes operating under the highpressure conditions. The combination of these techniques permits us to understand the role of surface defects, surface diffusion, and hot electrons in dynamics of surface catalyzed reactions. Sum frequency generation vibrational spectroscopy and kinetic measurements were performed under 1.5 Torr of cyclohexene hydrogenation/dehydrogenation in the presence and absence of H2 and over the temperature range 300-500 K on the Pt(100) and Pt(111) surfaces. The structure specificity of the Pt(100) and Pt(111) surfaces …

Molecular Simulations Of Solid-Liquid Interfacial Tension Of Silicon, Yuk Wai Tang, Jun Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Silicon is an important semiconductor for manufacturing of microelectronic chips used in computers and other electronic devices. During the manufacturing process, liquid silicon is being solidified to make high-grade solid semiconductors. Thus, improved data of the solid-liquid interfacial properties of silicon will be useful towards optimizing the experiment condition for making better quality electronics. Yet it is difficult to perform experiments of liquid silicon due to its high melting point. Thus far, most experimental measurements of the solid-liquid interfacial tension are based on the measurement of rate of homogeneous crystal nucleation at a given undercooling. The first measurement of solidliquid …

Α-Arylation Of Cyclopentanone : Palladium-Catalyzed Coupling Of Enamines And Aryliodides & N-Acyloxazines As Novel Bicyclic Weinreb Amides, Kristina M. Gehring

Honors Theses

The introduction of an aryl group a to a carbonyl is a useful step in the preparation of a variety of biologically interesting compounds. The palladium-catalyzed a-arylation of ketones and esters, through their enolates, has received a great deal of attention lately. Despite these efforts, cyclopentanones remain one of the most difficult classes ofketones to arylate. Many of these methods suffer from the limitation of the relatively basic reaction conditions needed in order to prepare the enolate nucleopbiles in­situ. The direct palladium-catalyzed α-arylation of enamines as an alternative route to α­aryl ketones bas received very little attention and might be …

Synthesis And Characterization Of Novel 1-Substituted Meta-Terphenyls For Platinum Complexes, Sarah Marie Sparks

Honors Theses

The unique luminescent properties of aryl, tridentate platinum complexes has led to an increased interest and investigation of various binding modes, with an emphasis on ligand design. These complexes are anticipaterl to be useful in chemical sensing, organic light emitting diodes, and solar energy converters.

Efficient Synthesis Of N9-Alkylguanines : & Evaluation Of A More Highly Conjugated Analog Of Guanidinium-Rich Molecular Transporters Using A Ph Dependent Fluorescence Assay, David E. Olson

Honors Theses

Synthesis of N9-(2-chloroethyl)guanine from 2-amino-6-chloropurine was accomplished in three steps with an overall yield of 83%. All products were purified via crystalli7.ation and no chromatography was required. Selective crystallization of the desired N9 isomer subsequent to the key alkylation step completely and efficiently removed the N7 isomer. This compound was shown to be a versatile reagent in the synthesis of various N9-substituted guanines.

The Synthesis And Characterization Of A Metal Complex Containing Chemically Non-Equivalent Axial Cyanide Ligands, Derek D. Wayman

Honors Theses

In order to analyze the magnitude and factors which effect 13C-13C NMR coupling through a metal center, we have synthesized an octahedral dicyano cobalt (III) complex in which two trans cyanides are chemically non-equivalent. Although similar complexes have been reported, their spectroscopic characterization with isotopically labeled cyanide (13CN) has yet to be studied in detail.

The Synthesis And Characterization Of A Metal Complex Containing Chemically Non-Equivalent Axial Cyanide Ligands, Derek D. Waymand

Honors Theses

In order to analyze the magnitude and factors which effect 13C-13C NMR coupling through a metal center, we have synthesized an octahedral dicyano cobalt (III) complex in which two trans cyanides are chemically non-equivalent. Although similar complexes have been reported, their spectroscopic characterization with isotopically labeled cyanide ( 13CN) has yet to be studied in detail.

Structure Determination Of A2m3+Tao6 And A2m3+Nbo6 Ordered Perovskites: Octahedral Tilting And Pseudosymmetry, Paris W. Barnes, Michael W. Lufaso, Patrick M. Woodward

Chemistry Faculty Research and Scholarship

The room-temperature crystal structures of six A₂M³⁺M⁵⁺O₆ ordered perovskites have been determined from neutron and X-ray powder diffraction data. Ba₂YNbO₆ adopts the aristotype high-symmetry cubic structure (space group Fm3̄m, Z = 4). The symmetries of the remaining five compounds were lowered by octahedral tilting distortions. Out-of-phase rotations of the octahedra about the c axis were observed in Sr₂CrTaO₆ and Sr₂GaTaO₆, which lowers the symmetry to tetragonal (space group = I4/m, Z = 2, Glazer tilt system = …

Structure Prediction Of Ordered And Disordered Multiple Octahedral Cation Perovskites Using Spuds, Michael W. Lufaso, Paris W. Barnes, Patrick M. Woodward

Chemistry Faculty Research and Scholarship

The software package SPuDS has previously been shown to accurately predict crystal structures of AMX₃ and A_{1 - x}A'_xMX₃ perovskites that have undergone octahedral tilting distortions. This paper describes the extension of this technique and its accuracy for A₂MM'X₆ ordered double perovskites with the aristotype Fm3̄m cubic structure, as well as those that have undergone octahedral tilting distortions. A survey of the literature shows that roughly 70% of all ordered double perovskites undergo octahedral tilting distortions. Of the 11 distinct types of octahedral tilting that can occur in …

Probing Synergism, Antagonism, And Additive Effects In Poly(Vinyl Ester) (Pve) Composites With Fire Retardants, Everson Kandare, Grace Chigwada, Dongyan Wang, Charles Wilkie, Jeanne Hossenlopp

Chemistry Faculty Research and Publications

Potential fire retardants, including copper hydroxy dodecyl sulfate (CHDS), organically-modified montmorillonite (Cloisite 15A), and resorcinol di-phosphate (RDP), were added to pure poly(vinyl ester) (PVE) individually or in combinations at low concentration formulations. Thermogravimetric analysis and cone calorimetry were used to study the thermal stability and fire performance of the composites. Synergistic, antagonistic, and additive effects were observed depending on the specific formulation. Time to self-sustained combustion is greatly reduced, but the flame extinguishes faster, for the composites containing CROS alone or in combination with either RDP or Cloisite 15A compared to the virgin polymer. The presence of copper in PVE …