Physical Sciences and Mathematics Commons^™

Development And Application Of Explicitly Correlated Wave Function Based Methods For The Investigation Of Optical Properties Of Semiconductor Nanomaterials, Jennifer Mary Elward

Dissertations - ALL

Semiconductor nanoparticles, or quantum dots (QDs), are well known to have very unique optical and electronic properties. These properties can be controlled and tailored as a function of several influential factors, including but not limited to the particle size and shape, effect of composition and heterojunction as well as the effect of ligand on the particle surface. This customizable nature leads to extensive experimental and theoretical research on the capabilities of these quantum dots for many application purposes.

However, in order to be able to understand and thus further the development of these materials, one must first understand the fundamental …

Covalent Modification That Enhances Protein Properties And Functions And Folds Random Coil Into Alpha-Helix, Deepali Prashar

Chemistry - Dissertations

Understanding the fundamental science of aggregation and surface adsorption of proteins is critical for developing protein-based drugs, understanding aggregation-induced diseases and for preventing biofouling that impacts a wide range of industries. In spite of the advances in sensitive and high-throughput analytical methods, the commercialization of protein drugs has been impeded by poor solubility, inevitable aggregation, and difficulty in purification. The primary aim of this dissertation is to modify proteins covalently to induce folding in random coil sequences, prevent aggregation, surface adsorption and for increasing the thermal stability against aggregation of proteins.

The first chapter describes the chemistry for modifying the …

Cytotoxicity Of Cu(Ii) And Zn(Ii) 2,2′-Bipyridyl Complexes: Dependence Of Ic_50 On Recovery Time, Yi Shi, Bonnie B. Toms, Namrata Dixit, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

We measure the cytotoxicity of three metal complexes containing the 2,2′-bypyridine ligand, Cu(bpy)(NCS)2, 1, [Cu(bpy)2(H2O)](PF6)2, 2, and Zn(bpy)2(NCS)2, 3, toward neuroblastoma cells (SKN- SH) and ovarian cancer cells (OVCAR-3) using two different cell assays. The cells were exposed to various concentrations of the compounds for 1 h and the percent inhibition of cell growth, I, measured for various times after exposure, i.e., as a function of the recovery time t. After developing the theory showing the relationship between I and t, the cytotoxicity data were analyzed to reveal that the two copper complexes, 1 and 2, cause the cells to …

Mesoporosity And Functional Group Dependent Endocytosis And Cytotoxicity Of Silica Nanomaterials, Zhimin Tao, Jerry Goodisman, Tewodros Asefa, Bonnie B. Toms

Chemistry - All Scholarship

We report different mesoporosity-dependent and functional group-dependent cytotoxicity and endocytosis of various silica nanomaterials on suspended and adherent cells. This dependency further varied with incubation time and particle dosage, and appeared to be associated with the particles’ endocytotic efficiency and their chemical and physical properties. We studied two common mesoporous nanomaterials (MSNs), MCM-41 and SBA-15, and one type of solid-cored silica microsphere, paralleled by their quaternary amine functionalized counterparts. Compared to SBA-15, MCM-41 has a larger surface area but smaller pore size, whereas SMS exhibits low surface area and poor porosity. In Jurkat cells, SBA-15 and MCM- 41 exhibited different …

Modification Of Carboplatin By Jurkat Cells, Anthony J. Di Pasqua, Jerry Goodisman, Deborah J. Kerwood, James C. Dabrowiak, Bonnie B. Toms

Chemistry - All Scholarship

Using [¹H,¹⁵N] heteronuclear single quantum coherance (HSQC) NMR and ¹⁵N-labeled carboplatin, 1, we show that Jurkat cells affect the rate of disappearance of the HSQC NMR peak in culture medium for this Pt²⁺ anticancer drug. The decay or disappearance rate constant for 1 in culture medium containing cells is k1=kc[CO32-]+km+kuN, where k_c is the rate constant for reaction of 1 with carbonate in the medium, k_m is the rate constant for reaction of 1 with all other components of the medium, and k_u is the rate constant for reaction of …

Inhibition Of Cellular Respiration By Doxorubicin, Zhimin Tao, Henry G. Withers, Harvey S. Penefsky, Jerry Goodisman, Abdul Kader Souid

Chemistry - All Scholarship

Doxorubicin executes apoptosis, a process known to produce leakage of cytochrome c and opening of the mitochondrial permeability transition pores. To define the loss of mitochondrial function by apoptosis, we monitored cellular respiration during continuous exposure to doxorubicin. A phosphorescence analyzer capable of stable measurements over at least 5 h was used to measure [O(2)]. In solutions containing glucose and cells, [O(2)] declined linearly with time, showing that the kinetics of oxygen consumption was zero order. Complete inhibition of oxygen consumption by cyanide indicated that oxidations occurred in the respiratory chain. A decline in the rate of respiration was evident …

Activation Of Carboplatin By Carbonate, Anthony J. Di Pasqua, Jerry Goodisman, Deborah J. Kerwood, Bonnie B. Toms, James C. Dabrowiak

Chemistry - All Scholarship

Carboplatin, [Pt(NH3)2(CBDCA-O,O')], 1, where CBDCA is cyclobutane-1,1-dicarboxylate, is in wide clinical use for the treatment of ovarian, lung, and other types of cancer. Because carboplatin is relatively unreactive toward nucleophiles, an important question concerning the drug is the mechanism by which it is activated in vivo. Using [1H,15N] heteronuclear single quantum coherance spectroscopy (HSQC) NMR and 15N-labeled carboplatin, we show that carboplatin reacts with carbonate ion in carbonate buffer to produce ring-opened products, the nature of which depends on the pH of the medium. The assignment of HSQC NMR resonances was facilitated by studying the reaction of carboplatin in strong …

Cisplatin Carbonato Complexes. Implications For Uptake, Antitumor Properties, And Toxicity, Corey R. Centerwall, Jerry Goodisman, Deborah J. Kerwood, James C. Dabrowiak

Chemistry - All Scholarship

The reaction of aquated cisplatin with carbonate which is present in culture media and blood is described. The first formed complex is a monochloro monocarbonato species, which upon continued exposure to carbonate slowly forms a biscarbonato complex. The formation of carbonato species under conditions that simulate therapy may have important implications for uptake, antitumor properties, and toxicity of cisplatin.

Experimental And Theoretical Studies On The Pharmacodynamics Of Cisplatin In Jurkat Cells, Kirk A. Tacka, Dava Szalda, Abdul-Kader Souid, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

For Jurkat cells in culture exposed to cisplatin (1), we measured the number of platinum adducts on DNA and showed that it is proportional to the AUC, the area under the concentration vs time curve, for cisplatin. The number of platinum-DNA adducts is measured immediately following exposure to drug. The AUC is calculated either as the product of the initial cisplatin concentration and the exposure time or as the integral under the concentration vs time curve for the unreacted dichloro species, which decreases exponentially. We also show that the number of adducts correlates with decreases in respiration, with the amount …

Effects Of Cisplatin On Mitochondrial Function In Jurkat Cells, Kirk Tacka, James C. Dabrowiak, Jerry Goodisman, Harvey S. Penefsky, Abdul Kader Souid

Chemistry - All Scholarship

In this work, we measured the effects of pharmacological concentrations of cisplatin (cis-diaminedichloroplatinum II) on mitochondrial function, cell viability, and DNA fragmentation in Jurkat cells. The exposure of cells to 0-25 microM cisplatin for 3 h had no immediate effect on cellular mitochondrial oxygen consumption, measured using a palladium-porphyrin oxygen sensing phosphor. Similarly, the cell viability as measured by trypan blue staining was unchanged immediately following exposure to the drug, and no small DNA fragments, characteristic of drug-induced apoptosis, appeared. At 24 h after exposure to cisplatin, cellular respiration and viability decreased relative to controls and the amount of small …

Footprinting And Circular Dichroism Studies On Paromomycin Binding To The Packaging Region Of Human Immunodeficiency Virus Type-1, Mark P. Mcpike, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

We have studied the interaction of the aminoglycoside drug, paromomycin, with a 171-mer from the packaging region of HIV-1 (ψ-RNA), using quantitative footprinting and circular dichroism spectroscopy. The footprinting autoradiographic data were obtained by cutting end-labeled RNA with RNase I or RNase T1 in the presence of varying paromomycin concentrations. Scanning the autoradiograms produced footprinting plots showing cleavage intensities for specific sites on the ψ-RNA as functions of drug concentration. Footprinting plots showing binding were analyzed using a two-state model to give apparent binding constants for specific sites of the ψ-RNA. These plots show that the highest-affinity paromomycin binding site …

Conductivity Of Irradiated Pure Water, Jerry Goodisman, Rick Blades

Chemistry - All Scholarship

The conductivity of water having parts per billion concentrations of oxygen, hydrogen, and bicarbonate was measured while the water was irradiated by a low-pressure mercury vapor lamp, which was turned on and off periodically. A cell normally used for measurement of dissolved oxidizable carbon was modified for use in these measurements. When the lamp is turned on, the conductivity increases (sometimes decreases) with a time constant of about 50 ms; when the lamp is turned off, the conductivity changes in the opposite direction with a time constant of about 275 ms, but does not return to its value before the …

Monomer-Dimer Equilibrium Constants Of Rna In The Dimer Initiation Site Of Human Immunodeficiency Virus Type 1, Michael F. Shubsda, Mark P. Mcpike, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

The genome of the human immunodeficiency virus (HIV) exists as a dimer of two identical RNA molecules hydrogen bonded to each other near their 5' ends. The dimer, known to be important for viral infectivity, is formed by two monomers interacting through a stem-loop structure called the dimer initiation site (DIS). An initially formed intermediate, the "kissing" dimer, is unstable and rearranges to the stable, duplex form. In this report we use nondenaturing polyacrylamide gel electrophoresis to measure the monomer-dimer equilibrium constant of three RNA sequences, 41-, 27-, and 19-mers, located in the DIS of the MAL isolate of HIV-1. …

Quadratic Electro-Optic Effects In Bacteriorhodopsin: Measurement Of Γ(-Ω;0,0,Ω) In Dried Gelatin Thin Films, Mikio Yamazaki, Jerry Goodisman, Robert R. Birge

Chemistry - All Scholarship

Quadratic electro-optic effects (dc or low frequency Kerr effect) of bacteriorhodopsin dispersed in dried gelatin thin films are examined in the near resonance region at three wavelengths: 633, 647, and 676 nm. The films show relatively large quadratic electro-optic effects compared to other molecular dispersed systems. The purple membrane is fixed within the polymerized gelatin matrix, and we show that the electronic contribution to γ dominates over possible orientational contributions. At 676 nm. the quadratic electro-optic coefficient s₁₁₃₃( - ω;0,0,ω) is 6.7 × 10^-20 m²/V² and the third order nonlinear susceptibility X₁₁₃₃^{(3) …}

Quantitation Of Ethidium-Stained Closed Circular Dna In Agarose Gels, Michael F. Shubsda, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

The fluorescence of ethidium bromide (EB) bound to equimolar amounts of supercoiled form I and unstrained linear form III pBR322, SV40 and PM2 DNA in agarose gels has been measured by scanning a photographic negative of the gel with a microdensitometer. For SV40 and PM2 DNA, commonly used staining conditions cause both forms, i.e. linear and supercoiled, to fluoresce to the same extent. This obviates the need to use a correction factor for the fluorescence of form I DNA when measuring the amount of this form relative to the amounts of unstrained forms in agarose gels. In the case of …

Kinetics Of Cleavage Of Intra- And Extracellular Simian Virus 40 Dna With The Enediyne Anticancer Drug C- 1027, Jerry Goodisman, James C. Dabrowiak, Christopher A. Kirk, Terry A. Beerman, Loretta S. Gawron

Chemistry - All Scholarship

A kinetic analysis of cleavage of simian virus DNA (SV40 DNA) inside and outside green monkey BSC-I cells by the enediyne-protein antibiotic C-1027 and its free chromophore is described. Information on rate constants was obtained by fitting populations of forms I (closed circular DNA), II (nicked circular DNA) and III (linear DNA) of SV4f.J DNA as a function of drug concentration to a kinetic model which includes: cutting of form I to give form II with rate constant k1. cutting of form I to give form III with rate constant k4, and cutting of form II to give form III …

Cleavage Of Dna By The Insulin-Mimetic Compound, Nh4[Vo(O2)2(Phen)], Catharina Hiort, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

The kinetics and mechanism of cleavage of DNA by the insulin-mimetic peroxo-vanadate NH4[VO(O2)2(phen)], pV, are described. In the presence of low energy UV radiation or biologically common reducing agents, pV decomposes into the monomer, dimer, and tetramer of vanadate and an uncharacterized compound of V4+ as shown by 51V NMR, ESR, and absorption spectra. The rate of photodecomposition of pV is reduced in the presence of calf thymus DNA, indicating that a decomposition product of the peroxo-vanadate, that is important in the destruction pathway of the complex, is interacting with DNA. This species, probably a short-lived complex of V4+, may …

Interaction Of Cationic Porphyrins With Dna, Ulrica Sehlstedt, Pamela Carter, Jerry Goodisman, James C. Dabrowiak, Seog K. Kim

Chemistry - All Scholarship

Utilizing linear dichroism (LD), circular dichroism (CD), and fluorescence energy transfer, the binding geometries of a series of Co3+-porphyrins and their free ligands were examined. The compounds studied were Co-meso-tetrakis(N-methylpyridinium-4-yl)porphyi(nC oTMPyP) and its free ligand (H2- TMPyP), Co-meso-tetrakis(N-n-butylpyridinium-4-yl)porphyrin( CoTBPyP) and its free ligand (H2TBPyP), and Co-meso-tetrakis(N-n-octylpyridinium-4-yl)porphyrin (CoTOPyP). The two non-metalloporphyrins exhibit negative LD, having angles of roughly 75' relative to the DNA helix axis. They also display negative CD and a significant contact energy transfer from the DNA bases. On the other hand, the three metalloporphyrins display orientation angles of roughly 45' between the porphyrin plane and the helix axis …

Quantitative Footprinting Analysis Of The Chromomycin A 3 - D N A Interaction, Allison Stankus, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

Chromomycin A3 (CHR) binding to the duplex d(CAAGTCTGGCCATCAGTC)- d(GACTGATGGCCAGACTTG) has been studied using quantitative footprinting methods. Previous NMR studies indicated CHR binds as a dimer in the minor groove. Analysis of autoradiographic spot intensities derived from DNase I cleavage of the 18-mer in the presence of various amounts of CHR revealed that the drug binds as a dimer to the sequence 5’-TGGCCA-3’, 3’-ACCGGT-5’ in the 18-mer with a binding constant of (2.7 f 1.4) X lo7 M-l. Footprinting and fluorescence data indicate that the dimerization constant for the drug in solution is -lo5 M-l. Since it has been suggested that …

Structural Changes And Enhancements In Dnase I Footprinting Experiments?, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

In footprinting experiments, an increase in DNA cleavage with addition of ligand to a system may be due to a ligand-induced structural change. Ligand binding also enhances cleavage by displacing the cleavage agent from ligand-binding sites, thus increasing its concentration elsewhere. The theory and characteristics of this mass-action enhancement are given, and it is shown how it may be recognized. Results of DNase I footprinting of small oligomers, with actinomycin D as ligand, are analyzed to reveal which enhancements are due to mass action, and which can reasonably be ascribed to structural changes. Patterns in the footprinting plots from our …

Site-Specific Binding Constants For Actinomycin D On Dna Determined From Footprinting Studies, Jerry Goodisman, Robert Rehfuss, Brian Ward, James C. Dabrowiak

Chemistry - All Scholarship

We report site-specific binding constants for the intercalating anticancer drug actinomycin D (Act-D), binding to a 139-base-pair restriction fragment from pBR 322 DNA. The binding constants are derived from analysis of footprinting experiments, in which the radiolabeled 139-mer is cleaved using DNase I, the cleavage products undergo gel electrophoresis, and, from the gel autoradiogram, spot intensities, proportional to amounts of cleaved fragments, are measured. A bound drug prevents DNase I from cleaving at -7 bonds, leading to decreased amounts of corresponding fragments. With the radiolabel on the 3’ end of the noncoding strand (A-label), we measured relative amounts of 54 …

Surface Tension Of A Charged And Polarized System, Jerry Goodisman

Chemistry - All Scholarship

Usually, the formula for the surface tension of a planar charged and polarized interface is obtained from that for a system involving only short-range forces, y = - dz [p - px(z)] by replacing the tangential pressure p , by p , + E2/8u. Problems with this include (a) p, is no longer explicitly defined, (b) the electrostatic stress term E2/8 pi is not correct in general but only if polarization is proportional to density of polarizable species, (c) the derivation of the formula in terms of p and p, involves calculating the work to expand a volume containing the …

Coupled Kinetic Analysis Of Cleavage Of Dna By Esperamicin And Calicheamicin, Hiroko Kishlkawa, Ying-Ping Jiang, Jerry Goodisman

Chemistry - All Scholarship

A coupled kinetic analysis of esperamicin, calicheamicin, and DNase I cleavage of covalently closed circular PM2 DNA has been carried out. Analysis of the optical density data derived from agarose gel electrophoresis experiments shows that esperamicin A,, like the hydrolytic enzyme DNase I, produces mainly single-strand breaks in DNA. These agents cause covalently closed circular form I DNA to be initially converted to nicked circular form I1 DNA. However, the ratio of the rate constant for this process (k,') to that associated with conversion of form I1 to linear form I11 DNA ( k i ) is not consistent with …

Thermodynamic Data From Drug-Dna Footprinting Experiments, James C. Dabrowiak, Jerry Goodisman, Koren Kissinger

Chemistry - All Scholarship

Sequence-dependent thermodynamic quantities for the antiviral agent netropsin and a related bis(N-methylimidazole) dipeptide, lexitropsin, have been determined by DNase I footprinting techniques. The primary data are autoradiographic spot intensities derived from 10 footprinting experiments carried out in the temperature range 0-45 OC. After exclusion effects due to overlapped drug sites on DNA and redistribution phenomena associated with the enzyme were accounted for, sequence-dependent binding constants for the two ligands were calculated. Our approach does not require an independent determination of the free drug concentration, which is calculated, with individual site binding constants, by using only footprinting data. The temperature dependence …

Quantitative Footprinting Analysis. Binding To A Single Site, Robert Rehfuss, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

The theory for measuring ligand binding constants from footprinting autoradiographic data associated with a single binding site is derived. If the ligand and DNA cleavage agent compete for a common site, the spot intensities are not proportional to the amount of DNA not blocked by ligand. The analysis of a single site is experimentally illustrated by using results for the anticancer drug actinomycin D interacting with the duplex d(TAGCGCTA)2 as probed with the hydrolytic enzyme DNase I.

Quantitative Footprinting Analysis Using A Dna-Cleaving Metalloporphyrin Complex+, James C. Dabrowiak, Brian Ward, Jerry Goodisman

Chemistry - All Scholarship

The results of quantitative footprinting studies involving the antiviral agent netropsin and a DNA-cleaving cationic metalloporphyrin complex are presented. An analysis of the footprinting autoradiographic spot intensities using a model previously applied to footprinting studies involving the enzyme DNase I [Ward, B., Rehfuss, R., Goodisman, J., & Dabrowiak, J. C. (1988) Biochemistry 27, 1198-12051 led to very low values for netropsin binding constants on a restriction fragment from pBR-322 DNA. In this work, we show that, because the porphyrin binds with high specificity to DNA, it does not report site loading information in the same manner as does DNase I. …

Determination Of Netropsin-Dna Binding Constants From Footprinting Data, Brian Ward, Robert Rehfuss, Jerry Goodisman, James C. Dabrowiak

Chemistry - All Scholarship

A theory for deriving drug-DNA site binding constants from footprinting data is presented. Plots of oligonucleotide concentration, as a function of drug concentration, for various cutting positions on DNA are required. It is assumed that the rate of cleavage at each nucleotide position is proportional to the concentration of enzyme at that nucleotide and to the probability that the nucleotide is not blocked by drug. The probability of a nucleotide position not being blocked is calculated by assuming a conventional binding equilibrium for each binding site with exclusions for overlapping sites. The theory has been used to evaluate individual site …

Calculated Electronic Profiles For Liquid-Metal Surfaces, Jerry Goodisman

Chemistry - All Scholarship

The electronic density profile for a liquid-metal surface can be calculated by solving the self-consistent Lang-Kohn equations for the electronic wave functions. One requires a surface density profile for the ion cores, which enters the electrostatic and pseudopotential parts of the electronic Hamiltonian. We use oscillatory profiles, suggested by those found by molecular-dynamics simulations on a pseudoatom model. Calculating surface potentials and work functions, we obtain excellent agreement with experiment (within 0.2 eV). It is shown that use of either step-function ion profiles or a simple variational method leads to serious errors (12 eV) for these quantities.

The Metal In The Polarisable Interface Coupling With The Solvent Phase, Jerry Goodisman, Jean Paul Badiali, Martin Luc Rosinberg

Chemistry - All Scholarship

A quantum mechanical treatment of the conduction electrons of a metal in a polarisable interface shows that they can make an appreciable contribution to the electrical capacitance. Results for six metals are given, showing how differences in metal properties account qualitatively for experimentally observed differences in interfacial capacities, when the solvent is replaced by a dielectric film. To justify the neglect of solvent structure when metal properties are treated, the coupling between metal and solvent is discussed for orientable point solvent dipoles, and for a representation of the solvent polarisation by a pair of charged planes. The electron profile affects …

Density Functional Calculations For Liquid Metal Surfaces, Jerry Goodisman, M-L Rosinberg

Chemistry - All Scholarship

Various forms for the ion density profiles of Cs and Na have been tested in the density functional formalism. The large oscillations expected for Coulombic systems are largely suppressed by the pseudopotential. While oscillatory profiles give some improvement in surface tension, the values obtained are still about twice the experimental ones. It is concluded that the treatment of the pseudopotential or the gradient expansion of the functional is responsible for the unsatisfactory results obtained.