Chemistry Commons^™

Novel Mass Spectrometric Approaches For Deciphering The Epitranscriptomic Code, William D. Mcintyre

Legacy Theses & Dissertations (2009 - 2024)

According to the results of the Human Genome Project, less than 5% of our genome consists of sequences that code for actual proteins. At the same time, however, ~90% of these non-coding sequences are transcribed into a myriad of classes of ribonucleic acids collectively known as ncRNAs, which have been recognized as essential regulatory factors. It has been recently shown that the activity of ncRNAs can be in turn modulated by post-transcriptional modifications (PTMs), covalent marks that can be established/removed by tightly regulated enzymatic pathways. Now, the race is on to understand the new set of controls of cellular functions …

Modeling Chaperone-Substrate Interactions Of Alpha Crystallin From The Ocular Lens, Lisa Marie S. Ramirez

Legacy Theses & Dissertations (2009 - 2024)

The α-crystallins (αA- and αB-crystallin isoforms) from the ocular lens are small heat shock proteins and molecular chaperones, widely believed to play a significant role in protecting the lens from cataract. Mutations and modifications on human αA- and αB-crystallin (HAA and HAB, respectively) are linked to a variety of diseases, including cataract formation, neuropathological protein folding disorders, and many others. It is believed that HAA and HAB prevent the aggregation of other lens proteins. However, the structural and thermodynamic details of the chaperone-substrate (aka “client”) interaction are sparse. Therefore, the main objective of this dissertation is to reveal structural and …

Characterizing Body Fluids With Raman Spectroscopy : Towards Real World Application, Marisia Ann Fikiet

Legacy Theses & Dissertations (2009 - 2024)

This project continues the research on a new method of body fluid identification and furthers its field capabilities. This method of identification uses Raman spectroscopy and advanced chemometrics to distinguish between body fluids. It is an improvement on current methods because it is confirmatory, non-destructive, and has simple sample preparation. The first objective of this research is to create a model for differentiating body fluids for a new desktop instrument. It was determined that due to resolution differences from a research grade instrument, a new model needed to be made for this the desktop instrument. This model will be able …

Permanently Heated Micro-Wire Electrodes For Electrochemistry Above The Boiling Point, Zhihua Chang

Legacy Theses & Dissertations (2009 - 2024)

Heated micro-wire electrodes offer lots of advantages, such as, accurate temperature control, enhanced diffusion and accelerated reaction kinetics through micro-stirring effect, easy cleaning, and low cost, etc. Its application in high temperature electrochemistry has gained lots of interests since its debut in the mid-1990s. A maximum of 250 °C has been reported using heating pulses in duration of 5 ms. For various applications, permanently heating would be more useful. In this study, two types of micro-wire electrodes were successfully developed for electrochemistry above the boiling point with acetaminophen as model compound and a continuous heating time of at least 2 …

Synthesis Of Cadmium Arsenide Semiconductor Nanoparticles, Superatomic Silver Clusters, And Silver Coordination Polymers, Sarthak Jashubhai Patel

Legacy Theses & Dissertations (2009 - 2024)

Nanomaterials have chemical, electronic, optical, and other properties distinct from their bulk counterparts. However, the atom-precise synthesis of these materials remains a challenge, leaving open many scientific questions regarding the size regime between nanoparticulate (quantum confined) and bulk character. In this work, efforts toward the synthesis of nanoparticulate and atom-precise metal and semimetal materials are described. The synthesis of II-V semiconductor Cd3As2 having a near-zero bandgap is discussed. Analysis by UV-Vis absorption spectroscopy and powder X-ray diffraction indicate the formation of material with unexpected crystallinity and absorption properties The interaction between the molecular source of As and the solvent was …

Protein Ligation : Selenocysteine, Komal Shah

Legacy Theses & Dissertations (2009 - 2024)

Selenium is present in human and animal body in the form of selenocysteine and

Chemical Enhancement Of Thrombin Binding Aptamer (Tba), Goh Woon Lee

Legacy Theses & Dissertations (2009 - 2024)

The Thrombin Binding Aptamer (TBA), a short DNA strand with G-quadruplex conformation, binds to Thrombin with high affinity and acts as an inhibitor in the blood clotting. The TBA folds into a G-quadruplex conformation and stabilize the binding toward Thrombin. With this specificity of TBA with Thrombin, our goal is to enhance the binding affinity between them to observe the possibility of developing a new anticoagulant. First modification that we studied was dendrimer linkers which are called Trebler (T) and Long Trebler (LT). Those linkers were incorporated at the 5’ end of TBA by using solid phase oligonucleotide synthesis. Second …

Evaluation Of Fingerprint Content For Forensic Crime Scene Analysis And Drug Metabolite Detection, Erica Kathryn Brunelle

Legacy Theses & Dissertations (2009 - 2024)

With respect to criminal investigations, one key piece of evidence that often gets overlooked are fingerprints. For years, fingerprint samples have been believed to be useful only for matching purposes using their unique ridges, shapes, and sizes. With the rapid growth of forensic science, it has become evident that the development of fingerprint analysis has been stagnant. The traditional approach has been advantageous for the identification of many individuals; however, many fingerprint samples have been labeled “unusable” due to smudging, smearing, or any one of a myriad of reasons that could cause inconclusive matches. These samples can, however, still be …

Characterization Of Ambient Aerosols And Their Evolution Under Various Atmospheric Conditions In The Northeast U.S, Jie Zhang

Legacy Theses & Dissertations (2009 - 2024)

The University at Albany Atmospheric Sciences Research Center (ASRC) mobile laboratory, which includes a High Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS), a Scanning Mobility Particle Sizer (SMPS), and several gas sensors, etc., has been used to characterize atmospheric aerosols and air quality at different locations in the Northeastern US (including urban, forest, and mountain areas) and the aerosol evolutions under a variety of atmospheric conditions (including extreme weather, fog, and cloud, etc.). In this dissertation, I present the findings of the several field measurements using the ASRC mobile lab, focusing on the influences of extreme events (including high O3, heatwave, …

Legislation To Reduce Microplastic Pollution : Understanding The Factors That Facilitated Passage Of The Federal Microbead-Free Waters Act Of 2015, Alyson Kelly Northrup

Legacy Theses & Dissertations (2009 - 2024)

The full environmental impacts of microplastic pollution in aquatic environments remain uncertain, but several detrimental effects have been documented, including adverse health effects in multiple species and the susceptibility of microplastics to adsorb toxins and leach plastic additives. Plastic microbeads from rinse-off personal care products are a source of microplastic pollution that is introduced directly into the environment through runoff, including wastewater treatment plant effluent. In December 2015, the federal Microbead-free Waters Act of 2015 banned the manufacture and sale of all rinse-off personal care products containing plastic microbeads in the United States.

Sers For Protein Detection At A Single Molecule Level For Developing A New Medical Diagnostics Platform, Lamyaa Almehmadi

Legacy Theses & Dissertations (2009 - 2024)

A two-step process of protein detection at a single molecule level using Surface Enhanced Raman Spectroscopy (SERS) was developed as a new platform for medical diagnostics in this proof-of-concept study. First, a protein molecule was bound to a linker in the bulk solution and then this adduct was chemically reacted with the SERS substrate. Traut’s Reagent (TR) was used to thiolate Bovine serum albumin (BSA) in solution followed by chemical cross linking to a gold surface through a sulfhydryl group. A Glycine-TR adduct was used as a control sample to identify the protein contribution to the SER spectra. Gold SERS …

Defining And Harnessing Nature's Selection Of Geranylation In Rna Modification, Phensinee Haruehanroengra

Legacy Theses & Dissertations (2009 - 2024)

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. Geranylated-2-thiouridine is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, namely E. coli, E. aerogenes, P. aeruginosa and S. typhimurium by Liu group. It has been found as a post-transcription modification on the wobble position of anticodon of tRNAs specific for glutamic acid, glutamine and lysine. Geranylated-tRNA was shown to correct the frameshifting during the translation of E. coli. However, the reason of the existing of the modification is still largely unclear. To understand why nature incorporates such a hydrophobic group in …

Quantification Of Hemoglobin In Human Blood To Differentiate Individuals From One Another, Audrey Jeanne Auleley

Legacy Theses & Dissertations (2009 - 2024)

Blood is one of the principal sources of evidence in crime scene investigations. The level of hemoglobin in human blood is known to hardly fluctuate over time in a healthy adult patient. Using a method like the sodium lauryl sulfate (SLS) method for hemoglobin level determination is beneficial because SLS converts any other derivates of hemoglobin into methemoglobin. The amount of hemoglobin would be determined using the linear correlation between the absorbance of methemoglobin and its amount in blood samples. Those curves differ significantly from sample to sample. Therefore, a differentiation can be observed between the blood samples of different …

Saliva As A Diagnostic Biological Fluid And The Human Salivary Proteome, Jessica Ghassan Emsies

Legacy Theses & Dissertations (2009 - 2024)

Saliva is a unique biologic fluid that contains a varying spectrum of proteins, nucleic acids, electrolytes, and hormones.31 It is an exocrine secretion of the salivary glands which is hypotonic in nature with a pH of 7.2-7.4.31 Saliva plays an important role in the oral cavity.33 It lubricates, hydrates, and bathes the oral cavity, therefore, aiding speech and mastication.33 Saliva forms a barrier on the teeth, protects against demineralization, and aids in remineralization.33 Saliva is required for chewing and food bolus preparation, it contains enzymes necessary for digestion, and mediates the sense of taste.33 It also helps wound healing and …

Synthesis And Adsorption Experiments With Metal-Organic Frameworks For High School And Undergraduate Laboratory Settings, Kate Holley

Legacy Theses & Dissertations (2009 - 2024)

Seven experiments are described and outlined here that introduce high school and undergraduate students to metal–organic frameworks (MOFs) and their applications. The experiments were designed to be completed with basic laboratory equipment and supplies and without the use of expensive characterization instruments, simulating typical high school chemistry laboratory conditions. Students synthesized two well-known MOFs, HKUST-1 and aluminum fumarate, using simple, safe, and rapid methods (fast enough to be performed within the time constrains of a typical high school class). Students then use their synthesized MOFs to explore their inherent sorption properties. In one set of experiments, the synthesized MOFs are …

Accumulation And Spatial Distribution Of Lead And Other Trace Elements In Keratinized Tissues : Investigations Based On Analytical Atomic Spectrometry, Mina W. Tehrani

Legacy Theses & Dissertations (2009 - 2024)

Human biomonitoring for toxic metals such as lead (Pb) provides information about absorbed dose from all exposure routes, and is critical for identifying exposed individuals and assessing health risks. Blood Pb and bone Pb are the primary validated biomarkers for assessing short-term and historical Pb exposures, respectively, while non-traditional matrices, including keratinized tissues, can provide complementary exposure information. Hard keratinized tissues – including hair, nails, hooves, and horns – grow incrementally, potentially preserving chemical exposure histories over a span of days to years. Analytical limitations and poor interlaboratory reproducibility, however, have led to debate around the use of human nails …

Study Of Small Molecules With Dna Monolayers On Gold Electrodes Using Electrochemical Quartz Crystal Microbalance On The Millisecond Timescale, Sarasi Kaushalya Kumari Galagedera

Legacy Theses & Dissertations (2009 - 2024)

Biosensors based on DNA self-assembled monolayers (SAMs) combined with electrochemical transducers have shown great potential to serve an important role in simple, accurate and inexpensive genetic analyses relevant to many fields. The most popularly adapted method in designing biosensing platforms is the self-assembly of 5’-alkylthiol-modified single stranded or double stranded DNA on gold surfaces followed by a passivation step using a diluent like mercaptohexanol (MCH). Since analytical performance (sensitivity, selectivity and stability) of such sensors is solely related to the probe surface architecture, methods to characterize and measure the surface density has gained a lot of interest among the scientific …

Computational Modeling As A Tool For Designing Ligands And Receptors, Waqas S. Awan

Legacy Theses & Dissertations (2009 - 2024)

Computational methods can be used for a wide range of applications, especially regarding DNA and RNA. Interactions such as sugar torsions, receptor-ligand interactions, ligand docking/drug docking, receptor modeling, and drug design are excellent candidates for computational analysis and in silico experiments. The use of molecular dynamics software (GROMACS) coupled with molecular design software (MOE) produce insights that may have been otherwise difficult to assess. All these problems are academic in nature but have practical uses outside of academia. Understanding alternate linkages can lead to antibiotic assays to address potential superbug epidemics. Modeling DNA superstructures can provide insight into how large …

Machine Learning Enabled Prediction Of Mechanical Properties Of Tungsten Disulfide Monolayer, Xinyu Wang, Dan Han, Yang Hong, Haiyi Sun, Jingzhi Zhang, Jingchao Zhang

Department of Chemistry: Faculty Publications

One of two-dimensional transition metal dichalcogenide materials, tungsten disulfide (WS₂), has aroused much research interest, and its mechanical properties play an important role in a practical application. Here the mechanical properties of h-WS₂ and t-WS₂ monolayers in the armchair and zigzag directions are evaluated by utilizing the molecular dynamics (MD) simulations and machine learning (ML) technique. We mainly focus on the effects of chirality, system size, temperature, strain rate, and random vacancy defect on mechanical properties, including fracture strain, fracture strength, and Young’s modulus. We find that the mechanical properties of h-WS₂ surpass those of …

Extreme Molecular Diversity In Biomass Burning Atmospheric Organic Aerosol Observed Through Ultrahigh Resolution Mass Spectrometry, Matthew Brege

Dissertations, Master's Theses and Master's Reports

Ambient atmospheric aerosol is ubiquitous in the atmosphere, originating from a variety of natural and man-made sources. These microscopic particles have profound impacts on the global climate system as well as human health. The organic fraction of atmospheric aerosol is an extremely complex mixture which is not yet fully characterized. These unknown organic aerosol species contribute to the uncertainty in the effect of aerosol on climate and uncertainty in overall ambient aerosol toxicity. Light absorbing organic aerosol can interact with incoming solar radiation and contribute to atmospheric heating; however, the source apportionment and overall fate of these absorbing organic aerosol …

Insights Into Gemcitabine Resistance And The Potential For Therapeutic Monitoring, Teklab Gebregiworgis, Fatema Bhinderwala, Vinee Purohit, Nina V. Chaika, Pankaj K. Singh, Robert Powers

Department of Chemistry: Faculty Publications

Introduction—Gemcitabine is an important component of pancreatic cancer clinical management. Unfortunately, acquired gemcitabine resistance is widespread and there are limitations to predicting and monitoring therapeutic outcomes.

Objective—To investigate the potential of metabolomics to differentiate pancreatic cancer cells that develops resistance or respond to gemcitabine treatment.

Results—We applied 1D ¹H and 2D ¹H-¹³C HSQC NMR methods to profile the metabolic signature of pancreatic cancer cells. ¹³C₆-glucose labeling identified thirty key metabolites uniquely altered between wild-type and gemcitabine-resistant cells upon gemcitabine treatment. Gemcitabine resistance was observed to reprogram glucose metabolism and to enhance the pyrimidine …

Detailed Characterization Of The Solution Kinetics And Thermodynamics Of Biotin, Biocytin And Haba Binding To Avidin And Streptavidin, Roberto F. Delgadillo, Timothy C. Mueser, Kathia Zaleta-Rivera, Katie A. Carnes, Jose Gonzalez-Valdez, Lawrence J. Parkhurst

Department of Chemistry: Faculty Publications

The high affinity (K_D ~ 10⁻¹⁵ M) of biotin for avidin and streptavidin is the essential component in a multitude of bioassays with many experiments using biotin modifications to invoke coupling. Equilibration times suggested for these assays assume that the association rate constant (kon) is approximately diffusion limited (10⁹ M^-1s^-1) but recent single molecule and surface binding studies indicate that they are slower than expected (10⁵ to 10⁷ M^-1s^-1). In this study, we asked whether these reactions in solution are diffusion controlled, which reaction model and thermodynamic …

Carl Bosch And The Haber-Bosch Process, Jacob Larkin

Natural Sciences Student Research Presentations

This poster for the Natural Sciences Poster Session at Parkland College features organic chemist Carl Bosch, winner of the Nobel Prize of Chemistry in 1931 for his contribution to the development of chemical high pressure methods, Bosch built on Fritz Haber's process of fixing nitrogen using high pressure chemistry to industrialize the process on a large scale to mass produce fertilizer, now known as the Haber-Bosch process, which takes nitrogen from the air, bonds it with hydrogen from natural gases and converts it to ammonia.

Robert J. Lefkowitz And Discovery Of The G-Protein-Coupled Receptor Family, Clarence Lee

Natural Sciences Student Research Presentations

This poster for the Natural Sciences Poster Session at Parkland College features Dr. Robert J. Lefkowitz, 2012 Nobel Prize in Chemistry winner (with Brian Kobilka) for their research on G-protein-coupled receptors, proteins in the plasma membrane that allow for the transmission of information through the membrane and into the cell. This research was to impact the development of medications that target these receptors, such as SSRIs.

Ligand Effect On Gold Nanomolecules Demonstrated Using Aliphatic, Aromatic And Bulky Thiolate Ligands, Milan Rambukwella

Electronic Theses and Dissertations

Atomically precise thiolate protected gold nanoparticles (AuNPs) known as gold nanomolecules (AuNMs) are intensely pursued owing to their feasibility to elucidate their structure by single crystal X-ray crystallography. They have distinct number of Au atoms (n) and thiolate (-SR, R-hydrocarbon chain) ligands (m) with molecular formula of the form [Aun(SR)m]. AuNMs are made of a gold core protected by a thiolate-monolayer and possess size-dependent properties conferred by quantum confinement. Atomic precision has been achieved in the 1-3 nm range and crystal structures of several AuNMs ranging from 18 to 279gold atoms have been studied. They provide significant insights into the …

Probing Atypical Noncovalent Interactions Using Electronic Structure Theory, Katelyn Mae Dreux

Electronic Theses and Dissertations

Some of the most important topics in modern chemistry involve noncovalent interactions in a variety of ways, from pharmacological processes to materials design. Due to the comparatively weak nature of these interactions, they can be difficult to investigate experimentally. Beyond what might be considered the ‘typical’ noncovalent interactions such as hydrogen bonding or London dispersion, there are less well known noncovalent interactions such as coordinate covalent, dihydrogen, and nonconventional hydrogen bonding, which have been the focus of much of this research. Through the use of electronic structure theory, fundamental information about the structure, energetics, and molecular properties of noncovalently bound …

Evaluating Green Solvents And Techniques In Extraction Methods, Shanmugapriya Dharmarajan

Electronic Theses and Dissertations

Of all analytical techniques, extraction is a huge solvent-consuming process that could adversely impact the environment. Use of petroleum-based solvents for extraction of oilseeds is still a common practice, despite the potential fire hazard and the toxic water pollution. The rising awareness of chemical activities created immense need for sustainable development schemes and strategies that should address the environmental impact without compromising the yield. In the course of developing green extraction techniques, automation, alternative solvents, and selective extractions are the growing trend. This dissertation aligns with that progress by surveying green solvents, comparing their performance during oil extraction, examining a …

Characterization Of Hydrogen Bonding, Halogen Bonding And Argyrophilic Interactions Using Computational Modeling, Sarah Nicole Arradondo

Electronic Theses and Dissertations

Non-covalent interactions govern multiple important chemical processes throughout nature from those within the human body to the complex environment of the atmosphere. Quantum mechanical electronic structure modeling of these relatively weak interactions can provide molecular level insight that can further our understanding of specific macroscopic properties. In the present work different non-covalent interactions are computationally evaluated within four systems. A small prototypical hydrogen bonded system and the various structural motifs that promoted proton transfer within concentrated acid and water clusters are characterized with sophisticated wavefunction based methods and large robust basis sets in order to accurately predict the structures energies …

Theranostics Based On Linear Dendritic Block Copolymers, Jon Williams

Electronic Theses and Dissertations

When combining imaging and therapeutic motifs, known as theranostics, amphiphilic diblock copolymers have a strong precedent of success. These polymers can self-assemble into a variety of morphologies that are known to concentrate in areas of inflammation such as tumors. However, prediction of size and morphology from polymer structure still remains an open challenge. Another system with promise of therapeutic efficacy are tree-like struc- tures known as dendrimers, such as poly(amidoamine) (PAMAM) and bis-(hydroxymethyl) propionic acid (bMPA), which can uptake drugs and dyes into their branches. It is desireable to combine these two motifs, using linear-dendritic block copolymers (LDBCs). These represent …

The Promoted Synthesis Of Minoxidil By Magnetic Nanoparticles Of Cobalt Ferrite (Cofe$_{2}$O$_4$) As A Heterogeneous Reusable Catalyst, Ronak Eisavi, Fateme Ahmadi, Behzad Zeynizadeh, Mehri Kouhkan

Turkish Journal of Chemistry

Minoxidil (2,4-diamino-6-piperidinopyrimidine 3-oxide) was primarily recognized as a drug for reducing vascular resistance to blood flow. It was later introduced as a more important medicine for topical stimulation of hair growth and baldness reverting as well as treatment of androgenic alopecia through increasing prostaglandin endoperoxide synthesis. In this study, magnetic nanoparticles (MNPs) of spinel ferrites (MFe$_{2}$O$_{4}$, M = Co, Ni, Fe, Cu, and Zn) via solid-state grinding procedure were prepared and then characterized using X-ray diffraction, scanning electron microscopy, transmission electron microscopy, vibrating sample magnetometer, and Fourier transform infrared techniques. The prepared nanoferrites were utilized as efficient and green heterogeneous …