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Full-Text Articles in Physical Sciences and Mathematics
Use Of Molecular Logic Gates For The Tuning Of Chemosensor Dynamic Range, Orhan Acikgoz
Use Of Molecular Logic Gates For The Tuning Of Chemosensor Dynamic Range, Orhan Acikgoz
Undergraduate Honors Theses
The first molecular logic gates were created in the 1990s; integrating such logic gates into fluorescent chemosensors allowed for the detection of different types of ions in solution. In this study, we have developed a new use of molecular logic gates by having two of the same type of binding site. The two binding sites on a fluorophore that both detect Na+ ions led to an increase in the detection limit compared with the chemosensor with a single binding site. Since the two sodium binding sites create an AND logic gate, two sodium ions are needed to generate a …
Gas-Phase Proton Affinities For Twenty Of The Proline-Containing Dipeptides, Henry Cardwell
Gas-Phase Proton Affinities For Twenty Of The Proline-Containing Dipeptides, Henry Cardwell
Undergraduate Honors Theses
Peptide fragmentation plays a crucial role in the analysis of proteins through mass spectrometry-based proteomics. Most proteomics experiments take place in the low-energy regime and are governed by the mobile proton model which predicts random cleavages along the peptide backbone; however, there sometimes arise circumstances where the mobile proton model fails causing sequencing algorithms to misidentify peptides. One such example is noted in the “proline effect” wherein proline-containing peptides preferentially fragment N-terminal. While it has been established that the “proline effect” is due to the rigidity and basicity of the proline N-terminus, a further understanding of the factors influencing the …
Chemical Analysis Of Organic Compounds In Dew Water, Monica Dibley
Chemical Analysis Of Organic Compounds In Dew Water, Monica Dibley
Undergraduate Honors Theses
Water films on outdoor surfaces, such as dew, can act as a reservoir for organic molecules deposited from the atmosphere and they present a potential reactive medium for chemical transformations. To better understand the flux of volatile organic compounds from evaporating films, the composition and reactivity of the complex mixture of dissolved organic material (DOM) found in these films need to be characterized. Previous studies have measured the salts and the small organic molecules in dew collected on clean Teflon surfaces or condensers. Here, we expand on this by probing the organic chemicals found on natural outdoor surfaces covered in …
Differential Protein Expression In Bacteriophages Crimd And Larva, Daria Moody
Differential Protein Expression In Bacteriophages Crimd And Larva, Daria Moody
Undergraduate Honors Theses
Proteomics studies allow us to answer questions about differential protein expression across different systems. Mass spectrometry is a powerful tool in these studies due to the distinct masses of the amino acids that compose proteins. In our experiment, we used a bottom-up approach and focused on two bacteriophages found on the William & Mary campus, CrimD and Larva. The infection of Mycobacterium smegmatis, a nonpathogenic model for tuberculosis, by these two bacteriophages was frozen at five different timepoints, and our goal was to compare the differential protein expression across the samples in order to gain a greater understanding of …
Characterization Of Indoor Surface Films By High-Resolution Mass Spectrometry, Emily Nicole Legaard
Characterization Of Indoor Surface Films By High-Resolution Mass Spectrometry, Emily Nicole Legaard
Dissertations, Theses, and Masters Projects
Atmospheric chemistry has primarily focused on outdoor environments for many decades. Plenty of models based on the findings of outdoor atmospheric researchers have been built to deepen the understanding of outdoor environments and predict how certain changes in specific parameters may affect the overall atmosphere. The same cannot be said for indoor environments, which remain relatively unknown despite the fact that humans in developed countries spend the vast majority of their lives in indoor environments. This thesis seeks to provide an early look at the makeup of indoor surface films, specifically at their molecular compositions and thicknesses. These characteristics are …
Proteomic Analysis Of Mycobacteriophage Crimd, William Moeller
Proteomic Analysis Of Mycobacteriophage Crimd, William Moeller
Undergraduate Honors Theses
Bacteriophages represent a large portion of the biomatter on our planet, and many of them have yet to be fully characterized. Here we discuss the proteomic analysis of a particular Bacteriophage, Mycobacteriophage CrimD. This phage was discovered on the Campus of William & Mary and has had its genome characterized. We took the next logical step of proteomic analysis.
In our analyses we made use high pressure liquid chromatography paired with linear ion trap mass spectrometry to analyze the proteome of CrimD at specific time points after the infection of its host, Mycobacterium smegmatis. Additionally, we used nanospray ionization with …
Investigating Charge Transfer Complexes In Brown Carbon Aerosols, Brianna Peterson
Investigating Charge Transfer Complexes In Brown Carbon Aerosols, Brianna Peterson
Undergraduate Honors Theses
Aerosols are suspensions of particles in the air, commonly seen as dust or fog in the atmosphere. Brown carbon is a particular classification of carbonaceous atmospheric aerosol that increases in absorption from the visible to ultraviolet region, making it important for radiative forcing models. Elucidating the structures of brown carbon chromophores has been difficult as brown carbon is a broad category and the chromophore type can change depending on emission source, temperature, humidity, and season. Twisted intramolecular charge transfer (TICT) molecules have been identified as potential brown carbon chromophores. TICT molecules are those that allow charge transfer to occur between …
Complex Mixtures: Identifying And Characterizing Secondary Organic Aerosols, Emma Quinn Walhout
Complex Mixtures: Identifying And Characterizing Secondary Organic Aerosols, Emma Quinn Walhout
Dissertations, Theses, and Masters Projects
Complex organic mixtures in the environment can contain hundreds to thousands of different organic molecules, and their composition and reactivity can have important environmental implications. In addition to gases, the atmosphere is made of a variety of small liquids and solids called aerosols. These aerosols have large impacts on human health, climate, and atmospheric chemical reactions. Here, secondary organic aerosol (SOA) from the ozonolysis of α-pinene is characterized. The atmospheric lifetime of SOA is very uncertain, but recent laboratory and modeling studies have demonstrated that photolysis is potentially an important process for organic mass loss from aerosol particles.1-5 Photolysis modifies …
Computational Investigations Of The Structure And Spectroscopy Of Small Biomolecules In The Gas Phase, Zachary Michael Smith
Computational Investigations Of The Structure And Spectroscopy Of Small Biomolecules In The Gas Phase, Zachary Michael Smith
Dissertations, Theses, and Masters Projects
Small biomolecule systems were interrogated using infrared multiple photon dissociation (IRMPD) action spectroscopy and corresponding quantum chemical calculations with a particular focus on peptide fragmentation and protonation site preference. b2+ and b3+ fragment ions with a terminal lysine homolog residue were investigated using IRMPD in the fingerprint region (1000 cm-1 – 2000 cm-1) and a variety of computational methods. We present the first spectroscopic confirmation of b-ion formation with a lactam structure. Infrared spectra for b2+ fragment system indicate the presence of a mixture of structures, though final determination will require further investigation. The b3+ fragment ion infrared spectra show …
Monitoring Infection Of E. Coli By Bacteriophage T7 Through Mass Spectrometry-Based Proteomics, Amy Swayne Schienschang
Monitoring Infection Of E. Coli By Bacteriophage T7 Through Mass Spectrometry-Based Proteomics, Amy Swayne Schienschang
Dissertations, Theses, and Masters Projects
Mass spectrometry-based proteomics has become an important and versatile tool in analytical chemistry, making sense of complex biological samples and shedding light on the intricate proteomes of living organisms. Bottom-up proteomics studies are used to elucidate the changes in gene expression of bacteriophage T7 over the course of infection of Escherichia coli. E. coli cultures were infected with T7, sampled over time, and proteins were isolated and enzymatically digested. Nanoflow liquid chromatography combined with tandem mass spectrometry was used to detect proteolytic peptides and identify host and phage proteins. Generally, phage proteins were detected on a time scale fitting the …
Surface-Enhanced Raman And Single-Molecule Spectroscopy Studies Of Fugitive Artists' Pigments, Kristen A. Frano
Surface-Enhanced Raman And Single-Molecule Spectroscopy Studies Of Fugitive Artists' Pigments, Kristen A. Frano
Dissertations, Theses, and Masters Projects
No abstract provided.
Studies Of Molecular Dynamics Of Fmoc Amino Acids Using Solid State Deuteron Nuclear Magnetic Resonance Spectroscopy, Wei Xu
Dissertations, Theses, and Masters Projects
The purpose of devising and validating models for intramolecular motions for FMOC amino acids is to quantify side chain motion in proteins which plays an important role in understanding biological structure function relations of proteins. In this thesis, spin lattice relaxation times (Ti) of FMOC amino acids were m easured under both static and magic angle spinning (MAS) condition at variable tem peratures. Lower activation energies of the relaxation times than the normal amino acids observed indicate a less sterically crowded environment for the rotation methyl group. A three-site jump model for the methyl group w as developed to fit …
Electroless Gold Deposition With Self-Assembled Monolayers For Gas Chromatography Stationary Phases, Jessica Lynn Belton
Electroless Gold Deposition With Self-Assembled Monolayers For Gas Chromatography Stationary Phases, Jessica Lynn Belton
Dissertations, Theses, and Masters Projects
No abstract provided.
Surface Modifications For Gas Chromatography Micro Columns, Daniel Andre Hirtenstein
Surface Modifications For Gas Chromatography Micro Columns, Daniel Andre Hirtenstein
Dissertations, Theses, and Masters Projects
No abstract provided.
Thermochemistry Of Amino Acids And Constrained Diamines, Erica Jane Tullo
Thermochemistry Of Amino Acids And Constrained Diamines, Erica Jane Tullo
Dissertations, Theses, and Masters Projects
The gas-phase proton affinities of several highly basic amino acids and diamines were determined using the extended kinetic method in an ESI-quadrupole ion trap instrument. The non-protein amino acid L-canavanine is structurally related to L-arginine with an oxygen substituted for the terminal methylene group of L-arginine and is highly toxic to humans. The proton affinity of L-arginine, a protein amino acid, was determined to be 1036 kJ mol -1, whereas the proton affinity of L-canavanine was determined to be 1005 kJ mol-1. Thus, substitution of an oxyguanidino group for the guanidine group in L-arginine results in a large decrease in …
The Development And Application Of An Antibody-Based Biosensor For The Detection Of The Petroleum-Derived Compounds, Candace Rae Spier
The Development And Application Of An Antibody-Based Biosensor For The Detection Of The Petroleum-Derived Compounds, Candace Rae Spier
Dissertations, Theses, and Masters Projects
Petroleum is one of the most important natural resources, but can also be problematic to environmental and human health. Petroleum is comprised of thousands of compounds, including polycyclic aromatic hydrocarbons (PAHs) and heterocycles, some of which are toxic and/or carcinogenic. Traditional analytical methods for environmental monitoring of low-level PAHs are time-consuming labor-intensive, and often laboratory-bound. Efforts to achieve timely, sensitive, and accurate analysis of PAHs in the field have become a priority for environmental research and monitoring. Antibody-based biosensors are presently being developed for environmental analysis. Anti-PAH antibody molecules can be coupled with electronic transducers to provide new biosensor technology …
Bioavailability Of Biosolids- And Consumer Product-Associated Polybrominated Diphenyl Ether (Pbde) Flame Retardants To Terrestrial Invertebrates, Michael O. Gaylor
Bioavailability Of Biosolids- And Consumer Product-Associated Polybrominated Diphenyl Ether (Pbde) Flame Retardants To Terrestrial Invertebrates, Michael O. Gaylor
Dissertations, Theses, and Masters Projects
The primary objectives of this research were therefore to evaluate polybrominated diphenyl ether (PBDE) bioavailability to ecologically distinct soil invertebrates exposed to Penta-BDE-treated consumer polyurethane foam (PUF) products and biosolid products with incurred PBDEs. In laboratory bioassays, earthworms (Eisenia fetida) bioaccumulated SigmaPBDEs (47+99+100+183) up to 11,000 mug/kg lipid after 28 days from a mixture of artificial soil and anaerobically-digested sludge biosolid (ADB). Earthworms also bioaccumulated SigmaPBDEs (47+99+100+153+154+183) up to 13,500 and 838,000 mug/kg lipid after 28 d from a mixture of artificial soil and composted sludge biosolid (CB) and Penta-BDE-spiked artificial soil (SAS), respectively. No previous lab studies on bioaccumulation …
Environmental Analysis Of Selected Estrogens And Androgens: Applying Ultra-Performance Liquid Chromatography And Combating Matrix Interference, Stacie L. Rice
Environmental Analysis Of Selected Estrogens And Androgens: Applying Ultra-Performance Liquid Chromatography And Combating Matrix Interference, Stacie L. Rice
Dissertations, Theses, and Masters Projects
Investigations of environmental hormone contamination commonly utilize solidphase extraction (SPE) followed by high-performance liquid chromatography / (electrospray ionization) tandem mass spectrometry (HPLC/(ESI)MS2) in the detection of estrogens. Matrix interference is widely reported. In this study, androgens were targeted alongside estrogens as environmentally co-introduced endocrine disrupting chemicals. Analytical methods were developed in parallel for detection of several hormones from each class, with comparison of protocols and instrumental parameters. Ultraperformance LC (UPLC®), an emerging technology advertised for reduced retention times, was used in place of HPLC for hormone separation. Applicability to diverse aqueous samples was tested. Matrix interference was combated with two …
Identification And Quantification Of Polycyclic Musks And Methyl-Triclosan In Unknown Freshwater Fish Tissue Samples, Elizabeth Mara Jacobs
Identification And Quantification Of Polycyclic Musks And Methyl-Triclosan In Unknown Freshwater Fish Tissue Samples, Elizabeth Mara Jacobs
Dissertations, Theses, and Masters Projects
No abstract provided.
Novel Derivatizing Agents For The Determination Of Methylmercury By Gas Chromatography Using Electron Capture Detection, Crystal Marie Irwin
Novel Derivatizing Agents For The Determination Of Methylmercury By Gas Chromatography Using Electron Capture Detection, Crystal Marie Irwin
Dissertations, Theses, and Masters Projects
No abstract provided.
Automated Peak Identification For Time -Of -Flight Mass Spectroscopy, Haijian Chen
Automated Peak Identification For Time -Of -Flight Mass Spectroscopy, Haijian Chen
Dissertations, Theses, and Masters Projects
The high throughput capabilities of protein mass fingerprints measurements have made mass spectrometry one of the standard tools for proteomic research, such as biomarker discovery. However, the analysis of large raw data sets produced by the time-of-flight (TOF) spectrometers creates a bottleneck in the discovery process. One specific challenge is the preprocessing and identification of mass peaks corresponding to important biological molecules. The accuracy of mass assignment is another limitation when comparing mass fingerprints with databases.;We have developed an automated peak picking algorithm based on a maximum likelihood approach that effectively and efficiently detects peaks in a time-of-flight secondary ion …
Heavy Metal Complexes Of Mixed S,N Donor Ligands: X-Ray Crystallography And Solution-State 1h Nmr, Wei Lai
Heavy Metal Complexes Of Mixed S,N Donor Ligands: X-Ray Crystallography And Solution-State 1h Nmr, Wei Lai
Dissertations, Theses, and Masters Projects
No abstract provided.
Characterization Of Ionic, Dipolar And Molecular Mobility In Polymer Systems, Zhenrong Guo
Characterization Of Ionic, Dipolar And Molecular Mobility In Polymer Systems, Zhenrong Guo
Dissertations, Theses, and Masters Projects
Changes in the ionic and dipolar molecular mobility in a polymer system are the basis for the changes in the dielectric mechanical properties of polymer materials. Frequency Dependent Dielectric Measurements (FDEMS) and Ion Time-of-Flight (ITOF) are two important techniques to investigate ionic and dipolar molecular mobility in polymer systems. The results can be related to the macro- and molecular dielectric, electrical and dynamic properties of polymeric materials. The combination of these two methods provides a full view of electric, dielectric and dynamic behavior for the systems as they undergo chemical and/or physical changes during polymerization crystallization, vitrification, and/or phase separation.;The …
Development Of A Technique To Isolate Measurement Of Ionic Mobility, Jie Guo
Development Of A Technique To Isolate Measurement Of Ionic Mobility, Jie Guo
Dissertations, Theses, and Masters Projects
No abstract provided.
Effects Of Humic Acids And Salinity On Pesticide Bioavailability And Toxicity As Estimated By Spme And Toxicity Tests, Laurent C. Mézin
Effects Of Humic Acids And Salinity On Pesticide Bioavailability And Toxicity As Estimated By Spme And Toxicity Tests, Laurent C. Mézin
Dissertations, Theses, and Masters Projects
The interactive effects of humic acids (HAs) and salinity on the bioavailability and toxicity of the pesticides chlorpyrifos and 4,4'-dichlorodiphenyltrichloroethane (DDT) were investigated. The effects of various HAs on the toxicity of chlorpyrifos were initially assessed with the chronic MicrotoxRTM test. Environmentally relevant concentrations of Aldrich, Peat, Leonardite and Suwannee River HAs had no significant effect on the toxicity of either chlorpyrifos or copper (Cu), the test's positive control. as reductions in contaminant toxicity had previously been reported for some contaminants by HAs, it appeared that salinity might be a mitigating factor. Thus salinity effects were further investigated with Aldrich …
Analysis Of Mercury Coordination Environments Of Tridentate And Tetradentate Imidazole Based Ligands By X-Ray Crystallography And Nmr Spectroscopy, Geoffrey Murphy
Analysis Of Mercury Coordination Environments Of Tridentate And Tetradentate Imidazole Based Ligands By X-Ray Crystallography And Nmr Spectroscopy, Geoffrey Murphy
Dissertations, Theses, and Masters Projects
No abstract provided.
Determination Of Trace Levels Of Lead In Whole Blood By Graphite Furnace Atomic Absorption Spectroscopy, Leslie A. Sombers
Determination Of Trace Levels Of Lead In Whole Blood By Graphite Furnace Atomic Absorption Spectroscopy, Leslie A. Sombers
Dissertations, Theses, and Masters Projects
No abstract provided.
Development Of A Quantitative Competetive Polymerase Chain Reaction Assay For The Detection And Quantitation Of Perkinsus Marinus In Oyster Tissues And Environmental Water Samples, Heather A. Yarnall
Development Of A Quantitative Competetive Polymerase Chain Reaction Assay For The Detection And Quantitation Of Perkinsus Marinus In Oyster Tissues And Environmental Water Samples, Heather A. Yarnall
Dissertations, Theses, and Masters Projects
No abstract provided.
The Analysis Of Plasmid Conformers Using Dynamic Size-Sieving Capillary Electrophoresis, Stacey Nevins
The Analysis Of Plasmid Conformers Using Dynamic Size-Sieving Capillary Electrophoresis, Stacey Nevins
Dissertations, Theses, and Masters Projects
No abstract provided.
Analysis Of Mercury Coordination Environments Of Tridentate And Tetradentate Nitrogen Based Ligands By Nmr Spectroscopy And X-Ray Crystallography, Rachel E. Freer
Analysis Of Mercury Coordination Environments Of Tridentate And Tetradentate Nitrogen Based Ligands By Nmr Spectroscopy And X-Ray Crystallography, Rachel E. Freer
Dissertations, Theses, and Masters Projects
No abstract provided.