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Articles 31 - 60 of 564
Full-Text Articles in Physical Sciences and Mathematics
Identification Of A Putative Caspase Protein In S.Commune, Emma Ester Bendaña Flores
Identification Of A Putative Caspase Protein In S.Commune, Emma Ester Bendaña Flores
Honors Theses
Caspases are the proteins responsible for apoptosis in cells. Others have recently identified a caspase in Saccharomyces cerevisiae, a unicellular fungus.2, 3, 4 Isolation of a caspase protein from Schizophyllum commune will allow for the examination of a caspase in a simple multicellular organism.4 The S.cerevisiae caspase sequence was used to search the genomes of several fungi and identify similar sequences. Regions with high sequence identity in the aligned sequences were used to design degenerate PCR primers. The sequence of the resultant PCR product was then used to prepare primers for 3'RACE and determine the 3'end of the sequence. Through …
Binding Studies Of 2-Acetylnaphthalene With Native And Methylated Cyclodextrins Using Fluorescence Spectroscopy : The Use Of Gas Chromatography/Mass Spectrophotometry To Analyze Organic Contaminants In Local Waters, Amy L. Payeur
Honors Theses
The main goal of this work: was to explore complexes formed between 2-acetylnaphthalene (2-AN) and unsubstituted α, β, and y-cyclodextrins as well as 2-An and methylated α, β and y-cyclodextrins. The substituted cyclodextrins used were trimethyl-α-cyclodextrin (TM-α-CD), trimethyl-β-cyclodextrin (TM-β-CD), trimethyl-y-cyclodextrin (TM-y-CD), and dimethyl-β-cyclodextrin (DM-β-CD). For the trimethylated cyclodextrins, all three of the -OH groups on the cyclodextrin ring are replaced by -OCH3 groups. The dimethylated cycloextrin on the other hand only has 18 of the 21 -OH groups replaces by -OCH3 groups. Binding constants were determined for complexes using fluorescence quenching experiments at varying temperatures. Thermodynamic parameters of complex formation …
The Use Of Fluorescence To Investigate The Factors Leading To Complex Formation Between Naphthalenes And ├Ƒ-Cyclodextrins, Jamie M. Iannacone
The Use Of Fluorescence To Investigate The Factors Leading To Complex Formation Between Naphthalenes And ├Ƒ-Cyclodextrins, Jamie M. Iannacone
Honors Theses
Fraiji et al. determined a binding constant (K) of 581 = 6 M-1 for the 1:1 complex between 2-acetylnaphthalene (2-AN) and β-cyclodextrin (β-CD) in H20 using fluorescence quenching experiments (Appl. Spectrosc. 1994, 48, 79). Molecular modeling experiments indicate the possibility of complex stabilization resulting from hydrogen bonds between the C=O group of 2-AN and the -OH groups on the rim of β-CD. To check this possibility, we measured the K of the 2-AN:trimethyl-β-CD (TM-β- CD) complex, where all rim -OH groups are converted to –OCH3. In this case, K decreases to 134 M-1. To show that this is due to …
Sol-Gel-Platform Optical Sensors For Oxygen Gas : Sensor Development And Investigation Of Probe Partitioning In Sol-Gel Matrices, Desiree L. Plata
Sol-Gel-Platform Optical Sensors For Oxygen Gas : Sensor Development And Investigation Of Probe Partitioning In Sol-Gel Matrices, Desiree L. Plata
Honors Theses
I have developed gas sensors that respond rapidly and noticeably to changes in oxygen concentration by doping fluorescent complexes into gas-permeable sol-gel materials. Ruthenium (II) 4,7-diphenyl-1,10- phenanthroline, Ru(dpp)32+, responds to variations in ambient oxygen concentrations through marked changes in its fluorescence intensity. I investigated the response of Ru(dpp)32+ to oxygen in solution, in aerogels (sol gels dried under ambient conditions) and in aerogels (sol gels dried using supercritical conditions). Aerogels have particularly high porosity and low density, which allows for rapid diffusion of gases into the material. The aerogel sensor responds reversibly to changes in ambient oxygen concentration within 10 …
Investigation Of Indicators In Aerogels And Xerogels, Rebecca L. Wolfe
Investigation Of Indicators In Aerogels And Xerogels, Rebecca L. Wolfe
Honors Theses
A sol-gel is a silicon-oxygen matrix that is suitable for the entrapment of chemical species, including biological species, indicators, dyes, and sensors. Aerogels are sol-gels prepared by supercritical extraction, whereas aerogels are allowed to dry under ambient conditions. The resulting materials differ considerably in their physical properties. We are investigating a series of luminescent species for use as probes of the microenvironment in different sol-gel materials. Sol gels containing each probe are prepared as both aerogels and aerogels; aerogels are formed using a novel contained mold process. Spectral properties, including absorption or excitation spectra, emission spectra, time-based fluorescence scans, and …
Solution Structure Refinement Comparing Reference Model Noe Volumes, Maura Mahar
Solution Structure Refinement Comparing Reference Model Noe Volumes, Maura Mahar
Honors Theses
NMR is a powerful experimental technique which can be used to determine protein structures. Central to this process is conversion of peak volumes in the NOE data sets into distance constraints and then structural refinement against those constraints. In general, each solution structural analysis is initiated de novo. We are interested in the structural analysis of a series of hybrids derived from two parental proteins (rubredoxins from mesophilic bacterium Clostridium pasteurianum (Cp) and the hyperthermophilic archaeon Pyrococcus furiosus (Pf)). Near 1 A resolution X-ray structures of Cp and Pf rubredoxins are available to provide a basis for quantitative comparison of …
Weinreb Amides : Novel Titanium Enolate Reagents, Andrew J. Leyhane
Weinreb Amides : Novel Titanium Enolate Reagents, Andrew J. Leyhane
Honors Theses
The amides of N-methoxy-N-methylamine or "Weinreb amide" have earned an important role in synthetic chemistry as both a protective group and as synthetic intermediates. We have discovered that the Weinreb amide of acetic acid, N-methoxy-N-methylacetamide adds to aldehydes to afford classic aldol products in good to excellent yields. The scope of this novel aldol reaction will be discussed.
Inclusion Chemistry Of Neutral Nonlinear Optical Dyes Within Organically Modified Silicates, Ian Saratovsky
Inclusion Chemistry Of Neutral Nonlinear Optical Dyes Within Organically Modified Silicates, Ian Saratovsky
Honors Theses
The field of photonics involves the use of light to acquire, store, process, and transmit information. Nonlinear optical (NLO) materials are crucial for success in the advancement of photonic devices. Laponite and hectorite host assemblies have been shown previously by our group to induce I -aggregation of nonlinear optical (NLO) dyes and offer facile routes to film fabrication. Head-to-tail alignment (J-aggregation) of the NLO chromophores is a required condition for photonic applications. In this study, tetrabutylammonium, triethylhexylammonium, trimethyldodecylammonium, and trimetylcetylarunonium surfactants were utilized to render the smectic intergallery region organophilic thus facilitating chromophore intercalation and an increased J-aggregated dye fraction. …
A Stereoselective Multi-Component Synthesis Of Alpha-Oxy-Beta-Substituted-Beta-Amino Esters, Avrum L. Joffe
A Stereoselective Multi-Component Synthesis Of Alpha-Oxy-Beta-Substituted-Beta-Amino Esters, Avrum L. Joffe
Honors Theses
Previous work has shown that chlorotitanium enolates of methylmethoxy acetate add to aryl aldimines in a stereoselective fashion. Aryl aldimines are non-enolizable, which contributes to their ability to add to the enolates. Previous attempts to add the enolates to enolizable alkyl aldimines were unsuccessful. By using a multi-component process in which the aldimine is synthesized in-situ, we have expanded the scope of this chemistry to the enolizable alkyl aldimines. Furthermore, the multi-component process has proven to be stereoselective for the anti-adduct.
The Use Of Substituted Cyclodextrins In Capillary Electrophoresis For The Separation And Identification Of Methorphan Enantiomers, Colleen Strait
The Use Of Substituted Cyclodextrins In Capillary Electrophoresis For The Separation And Identification Of Methorphan Enantiomers, Colleen Strait
Honors Theses
The goal of this project was to separate the enantiomers levo and dextromethorphan using capillary electrophoresis (CE). Levomethorphan is a controlled substance, and dextromethorphan is an active ingredient in many cough syrups. Methylated-β-cyclodextrins (CDs) are used as additives because the CDs have chiral centers, allowing them to bind differently to the two enantiomers and thereby changing the enantiomer migration times in CE. Dimethyl- β-CD did not separate the levo and dextromethorphans; however the trimethyl-β-CD was successful at producing baseline separation with migration times of roughly 6 minutes. We are optimizing it by changing variables such as type of buffer, buffer …
The Optimization Of Sol-Gels As Sensing Arrays And The Testing Of Sol-Gel Precursors Through The Use Of Fluorescence Measurements Of Eosin-Y, Rachel M. Bukowski
The Optimization Of Sol-Gels As Sensing Arrays And The Testing Of Sol-Gel Precursors Through The Use Of Fluorescence Measurements Of Eosin-Y, Rachel M. Bukowski
Honors Theses
The purpose of the first project, performed in collaboration with Professor Frank Bright of SUNY at Buffalo, was to optimize the conditions and variables for a Cartesian Technologies Pinprinter to print reproducible spots of sol-gels doped with Ruthenium Diphenylphenathrene (Ru(dpp)32+), an oxygen-sensing complex, on microscope slides. We attempted to optimize these variables by l) the alteration of the printing speed of the sol-gel microarrays, 2) variation of the drying temperature of the gels after they had been printed, 3) controlling the reaction rate of the sol-gel, and 4) various methods of slide pre-treatment. We found that a print speed of …
The Optimization Of Sol-Gels As Sensing Arrays And The Testing Of Sol-Gel Precursors Through The Use Of Fluorescence Measurements Of Eosin-Y, Rachel M. Bukowski
The Optimization Of Sol-Gels As Sensing Arrays And The Testing Of Sol-Gel Precursors Through The Use Of Fluorescence Measurements Of Eosin-Y, Rachel M. Bukowski
Honors Theses
The purpose of the first project, performed in collaboration with Professor Frank Bright of SUNY at Buffalo, was to optimize the conditions and variables for a Cartesian Technologies Pinprinter to print reproducible spots of sol-gels doped with Ruthenium Diphenylphenathrene (Ru(dpp)32+), an oxygen-sensing complex, on microscope slides. We attempted to optimize these variables by l) the alteration of the printing speed of the sol-gel microarrays, 2) variation of the drying temperature of the gels after they had been printed, 3) controlling the reaction rate of the sol-gel, and 4) various methods of slide pre-treatment. We found that a print speed of …
Structural And Functional Analysis Of Mutant Matal Homeodomains By Multidimensional Nmr Spectroscopy, David F. Ott
Structural And Functional Analysis Of Mutant Matal Homeodomains By Multidimensional Nmr Spectroscopy, David F. Ott
Honors Theses
Homeodomain proteins are transcription factors that contain a conserved 60- residue sequence, beginning with an N-terminal unstructured arm, followed by an alpha helix, a loop, and a helix-tum-helix. The yeast protein MATa1 is unusual among homeodomains in that, as a monomer, it binds very poorly to its DNA operator. However, the a1- α2 heterodimer binds to the hsg operator with 3000 times the affinity it has for nonspecific DNA. Studies have shown that most of the heterodimer's binding specificity is due to a1 rather than α2 (1,2). To identify the structural changes that transform al into a strong, sequence-specific DNA …
Self-Assembled Aggregates Of Neutral Nonlinear Optical Dyes In Smectite Clay Films, Mark Kostuk
Self-Assembled Aggregates Of Neutral Nonlinear Optical Dyes In Smectite Clay Films, Mark Kostuk
Honors Theses
The field of photonics relies on nonlinear optical (NLO) materials and their unique light interacting properties to guide and manipulate light for such uses as optical switches and optical data storage. Hybrid organic-inorganic composites offer excellent routes to such materials synthesis. We report herein the first study of neutral organic NLO chromophores adsorbed onto hectorite and laponite clay films. Seven different dyes (disperse red 1; disperse red 13; disperse red 19; disperse orange 3; disperse orange 13; disperse orange 25, and DANS, [4-dimethylamino-4' -nitrostilbene]), and two exchangeable cations (sodium and zinc), are used to create the hybrid films. The nature …
Separation Of Chiral Controlled Substances Using Capillary Electrophoresis, Tania Magoon
Separation Of Chiral Controlled Substances Using Capillary Electrophoresis, Tania Magoon
Honors Theses
The separation of the chiral narcotic propoxyphene by capillary electrophoresis (CE) is the goal of this work. A three-way collaboration between our research group, Professor lsiah Warner (LSU) and the New York State Forensic Investigation Center is underway to separate propoxyphene enantiomers and to develop a protocol for the Forensic Center. We are investigating the application of both polymer surfactants and cyclodextrins as CE additives for the separation of enantiomeric propoxyphene. We have synthesized or obtained several polymerized N-undecylenyl-L-amino acid and N-undecylenyl-L-dipeptide derivatives as a pseudo-stationary phase in capillary zone electrophoresis for the separation of chiral compounds. Though no separation …
Interactions Between Oxazine Dyes And Sodium Dodecyl Sulfate Studied By Molecular Spectroscopy, Michael R. Webb
Interactions Between Oxazine Dyes And Sodium Dodecyl Sulfate Studied By Molecular Spectroscopy, Michael R. Webb
Honors Theses
We present the results of a fundamental investigation of how the presence of surfactant affects the self-interaction of cationic laser dyes in aqueous solution. Oxazine 1 and oxazine 170 are known to form non-fluorescent H-aggregates (n-stacked dimers). The interactions of each of these laser dyes with sodium dodecyl sulfate (SDS), a micelle forming, anionic surfactant, have been examined using UV-visible absorption and fluorescence spectroscopy, fluorescence anisotropy, and Rayleigh scattering. The colors of oxazine 170 solutions are visually distinguishable into three stages: solutions with no SDS, solutions with SDS below the erne (8mM), and solutions with SDS concentrations above the erne. …
Forensic Applications Of Capillary Electrophoresis, Jennifer A. Jakubowski
Forensic Applications Of Capillary Electrophoresis, Jennifer A. Jakubowski
Honors Theses
The separation by capillary zone electrophoresis (CZE) of the chiral narcotic propoxyphene is the goal of this work. A three-way collaboration between our research group, Professor lsiah Warner (LSU), and the New York State Forensic Investigation Center is underway, with the goal of separating controlled substances and developing techniques that the Forensic Center can apply in it& investigations. Earlier studies by Warner's group have shown that using polymerized N-undecylenyl-L-amino acid and peptide derivatives as pseudo-stationary phases in CZE has resulted in the separation of chiral molecules. Our separations were attempted by combining the drug samples with polymerized N-undecylenyl-L-amino acid and …
Stereoselection In The Preparation Of Alpha-Oxy-Beta-Amino Esters : Revealing The Mechanism, Richard James Fox
Stereoselection In The Preparation Of Alpha-Oxy-Beta-Amino Esters : Revealing The Mechanism, Richard James Fox
Honors Theses
Due to their significant pharmaceutical applications, the development of efficient, stereoselective synthetic routes for the preparation of α-substituted-β-amino esters has become increasingly important. We demonstrated that the titanium enolates (47) of a.alkoxy acetate esters (48) add cleanly to imines (49), and predominately afford the anti diastereomer of the a.-oxy-f3-amino ester product (50). Furthermore, by altering the electronic properties of the ether oxygen, sterics of the ester and temperature conditions, we changed the anti:syn product ratio. We rationalized the origin of these effects, and proposed a mechanism of imine addition.
Diastereoselection In Titanium Enolate Addition To Aldmines, Julia Leigh Barkin
Diastereoselection In Titanium Enolate Addition To Aldmines, Julia Leigh Barkin
Honors Theses
A mild and versatile synthesis of a-oxy-6-amino esters has been performed by condensation of the chlorotitanium enolates of methyl methoxyacetate with aldimines. The imine-aldol addition occurs in excellent yields without Lewis acid activation of the imine. All aryl imines examined show good to excellent diastereoselection for the anti isomers.
Fluorescence Studies Of Tris (2,2'-Bipyridine) Ruthenium (Ii) In Thin Clay Films, Samuel James Salamone
Fluorescence Studies Of Tris (2,2'-Bipyridine) Ruthenium (Ii) In Thin Clay Films, Samuel James Salamone
Honors Theses
Because of their rich intercalation chemistry and ability to enhance the thermal stability of the included guest, layered silicate clays are excellent hosts for the fabrication of organic/inorganic nanocomposites. Composites of hectorite and tris(2, 2' -bipyridine) ruthenium(U), Ru(bpy), 3 2+, have attracted attention owing to their potential applications as glucose and oxygen based chemical sensors. Previous studies on the fluorescence behavior of Ru(bpy)3 2+ complexes in aqueous colloidal clay suspensions have shown enhanced emission traces. We report here the first study of the fluorescence responses of Ru(bpy) 3 2+ exchanged thin clay films. Variation of guest concentration and exposure time …
The Binding Of Fluorophores To Beta-Cyclodextrin Derivatives, Kellie J. Forrestall
The Binding Of Fluorophores To Beta-Cyclodextrin Derivatives, Kellie J. Forrestall
Honors Theses
β-cyclodextrin (β-CD) is a seven-unit cyclic sugar molecule with a toroidal shape, a hydrophilic exterior and a hydrophobic cavity. It has been suggested that pyrene (P) forms a 2:1 (P(β-CD)2) complex with β-CD, where pyrene lies in-between the two wider rims of the β-CD. We examined this hypothesis by comparing the spectral properties of pyrene in the presence of substituted β-CDs. These properties include the shape and lifetime of pyrene fluorescence and the effect on pyrene fluorescence of added iodide quencher and alcohol. The derivatives studied included those with substituents only on the narrow rim, and those with substitution on …
The Characterization Of Methylene-Blue-Doped Sol Gels And The Development Of A Fluorenscence-Based Fiber-Optic Sensor For Sulfite, Tara K. Morcone
The Characterization Of Methylene-Blue-Doped Sol Gels And The Development Of A Fluorenscence-Based Fiber-Optic Sensor For Sulfite, Tara K. Morcone
Honors Theses
The purpose of this research was to develop a fiber-optic sensor for sulfite via immobilizing Methylene Blue (MB) within a sol-gel matrix. MB is a redox-indicating dye. In the oxidized form, the dye is a blue color, but reduction causes a change to the colorless, leuco form. This property is advantageous for the detection of reducing agents, such as sulfite. In solution, leuco-MB reverts to its blue form in the presence of an oxidizing agent. The method of MB immobilization is through the use of sol gels. The environment of a sol gel is chemically inert and small analytes can …
The Dynamic Interactions Of Actin Stress Fibers And Microtubutes, Daniel Jason Kelmanovich
The Dynamic Interactions Of Actin Stress Fibers And Microtubutes, Daniel Jason Kelmanovich
Honors Theses
The regulation of actin stress fibers (SF) are linked to the stability of microtubule (M1) structures. The exact method of interaction is not understood. To study the interaction, live cells containing fluorescent α-actinin were observed and treated with MT perturbing drugs as well as ATP-depletion. These treatments affect the stability of the microtubules and stress fibers respectively. A plasmid coding for fluorescent tubulin was also inserted into these cells to aid in observing both the MTs and SFs simultaneously. The observation relies on fluorescent microscopy and digital imaging. By observing the changes in the MTs and SFs in live cells, …
The Polymerization Of Aniline On Transition-Metal Cation Exchanged Hectorite Films, Charity Mcmanaman
The Polymerization Of Aniline On Transition-Metal Cation Exchanged Hectorite Films, Charity Mcmanaman
Honors Theses
Inorganic-organic materials often exhibit enhanced flexibility and thermal stability over their individual inorganic and organic precursors. We are studying the polymerization of organic aniline monomers on inorganic hectorite clay thin film supports. Previous research has shown that aniline polymerizes on the surface and intergallery regions of Cu(II)-exchanged hectorite films. We have synthesized a library of first row transition-metal exchanged hectorite thin film hosts and are probing the effects of the different transition metal cations on aniline polymerization. We have used infrared spectroscopy, X-ray diffraction and digital photography to characterize the extent of aniline polymerization on the films. Utilizing the transition …
Studies Directed Toward The Enantioselective Addition Of Reformatsky Reagents To Aldimines, Lamyaa Hassib
Studies Directed Toward The Enantioselective Addition Of Reformatsky Reagents To Aldimines, Lamyaa Hassib
Honors Theses
Interest in β-amino esters and β-lactams has grown significantly due to their applications in the synthesis of compounds of pharmaceutical interest. Examples include β-lactam antibiotics such as the penicillin and carbapenem families. Because β-lactams and β-amino esters share a common pathway, methods to prepare either are often contaminated and thus complicated by the formation of the other. We have developed convenient and highly controllable method which can afford either product cleanly.
Dinetic And Mechanistic Investigations Of Photocatalysis : Photoreactions Of Cr(Co)6 With Alkenes, Aaron E. Dietrich
Dinetic And Mechanistic Investigations Of Photocatalysis : Photoreactions Of Cr(Co)6 With Alkenes, Aaron E. Dietrich
Honors Theses
Flash photolysis has proven to be an effective technique for determining reaction mechanisms. Upon photolysis, a CO ligand is removed from Cr(CO)6 forming the reactive molecular fragment Cr(C0)5. In the presence of alkene, L, Cr(CO)s can react to form the meta-stable intermediate Cr(C0)5L. At high L concentrations, Cr(CO)5L decays by pseudo-first-order kinetics with an observed rate constant, kobs, which is dependent on the concentration of both L and added CO. The exar.t nature of the dependence provides insight into the mechanism of the decay of Cr(C0)5L and a plot of 1/kobs vs. [L] will give the rate constants for both …
Studies Directed Toward The Enantioselective Addition Of Reformatsky Reagents To Aldimines, Lamyaa Hassib
Studies Directed Toward The Enantioselective Addition Of Reformatsky Reagents To Aldimines, Lamyaa Hassib
Honors Theses
Interest in β-amino esters and β-lactams has grown significantly due to their applications in the synthesis of compounds of pharmaceutical interest. Examples include β-lactam antibiotics such as the penicillin and carbapenem families. Because β-lactams and β-amino esters share a common pathway, methods to prepare either are often contaminated and thus complicated by the formation of the other. We have developed convenient and highly controllable method which can afford either product cleanly.
The Effect Of Protein Environment And Ring Substitution On The Electrostatic Charges, Dipole Moment, And Ultraviolet Spectra Of Flavin, Jared Berger
Honors Theses
Old Yellow Enzyme is an interesting protein clue to its involvement in many biochemical systems, such as bioluminescence and degradation of variety of substrates. The flavin mononucleotide (FMN) is the active site of the protein. The FMN is an isoalloxazine ring with a phospholipid tail, which attaches to the protein through a phosphate group and hydrogen bonding in the hydrophilic section of the ring system. My research is a theoretical, computational calculation, which uses Spartan, a quantum mechanical calculation program, to determine how the dipole moment and electrostatic charges change upon the substitution of the FMN and within the protein …
Molecular Recognition Of Blunt-Ended Dna, Michael D. Farwell
Molecular Recognition Of Blunt-Ended Dna, Michael D. Farwell
Honors Theses
Many important enzymatic and physical processes occur specifically at the ends of DNA molecules. The goal of this project was to develop a molecule that would be an effective probe of the chemistry a. the ends of DNA. To do this, ethidium bromide, a well-known intercalation (a molecule that binds between DNA base pairs), was blocked to intercalation with bulky t-butyl groups. We proposed that this new molecule would preferentially bind to blunt-ended DNA, where there is much less steric hindrance. The synthesized molecule was characterized by NMR, Fluorescence, UV/Vis, and Mass Spectroscopy. Supporting data were acquired through fluorescence lifetime …
Methylene Blue Doped Sol-Gels Preparation And Application As Fiber-Optic Fluorescence Sensors, Dawn M. Landry
Methylene Blue Doped Sol-Gels Preparation And Application As Fiber-Optic Fluorescence Sensors, Dawn M. Landry
Honors Theses
The goal of this thesis project was to create a Methylene Blue (MB) doped sol-gel fiber-optic fluorescence sensor. Ideally this sensor would be capable of detecting changes in sulfite concentration in solution continuously and reversibly. In aqueous solution, MB, a redox indicator, is converted from a bright blue color to the colorless leuco-MB species upon exposure to sulfite or other reducing agents. This reaction is reversible in the presence of an oxidizing agent Therefore, if MB can be immobilized properly, it would make a suitable reversible indicator for the sulfite anion in solution. The method of MB immobilization employed in …