Physical Sciences and Mathematics Commons^™

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

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

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

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 …

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 …

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 …