Chemistry Commons^™

Green Chemistry As A Tool For Understanding The Toxic Substances Control Act: A Lecture Module For Undergraduate Students, Molly R. Blessing

Honors Scholar Theses

The Toxic Substances Control Act (TSCA) is the central form of chemical regulation existent in the United States today, yet scientists are often unaware or uncertain of its provisions. Violations of TSCA by unknowing chemists set industry and government unnecessarily at odds. A lecture on TSCA was developed for undergraduate students that uses the concept of green chemistry to promote interest and incentivize learning. Green chemistry methods are cleaner and less wasteful than traditional chemical ones, and many companies using them are at the forefront of technological innovation. The lecture explains both green chemistry and TSCA, includes company case studies, …

Analysis Of Free Solute Fractions And Solute-Protein Interactions Using Ultrafast Affinity Extraction And Affinity Microcolumns, Xiwei Zheng

Department of Chemistry: Dissertations, Theses, and Student Research

This dissertation describes the use of a high-performance affinity chromatography method based on ultrafast affinity extraction and microcolumns to study biological interactions.

In the first project, a new method was created and based on ultrafast affinity extraction to determine both the dissociation rate constants (k_d) and association equilibrium constants (K_a) for drug-protein interactions in solution. Various conditions to optimize the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered.

The objective of the next portion of this dissertation was to develop a chromatographic approach to measure free drug fractions in more …

Chromatographic Analysis Of Drug-Protein Interactions During Diabetes And Characterization Of Human Serum Albumin Through Multidimensional Mass Spectrometry, Ryan E. Matsuda

Department of Chemistry: Dissertations, Theses, and Student Research

Diabetes is a metabolic disease that can lead to the non-enzymatic glycation of serum proteins such as human serum albumin (HSA). Previous studies have indicated that glycation can affect the structure and function of these proteins. This dissertation describes the development of tools and techniques based on high performance affinity chromatography (HPAC) and multidimensional mass spectrometry to analyze the effects of glycation on the function and structure of HSA.

A major portion of this research involved the utilization of HPAC to examine the effect of glycation on the binding of three second-generation sulfonylurea drugs and one third-generation sulfonylurea drug. These …

Optimized Acid/Base Extraction And Structural Characterization Of Β-Glucan From Saccharomyces Cerevisiae, Shardrack O. Asare

Electronic Theses and Dissertations

β-glucan is a major component of the fungal cell wall consisting of (1→3)-β linked glucose polymers with (1→6)-β linked side chains. The published classical isolation procedure of β-glucan from Saccharomyces cerevisiae is expensive and time-consuming. Thus, the aim of this research was to develop an effective procedure for the extraction of glucans. We have developed a new method for glucan extraction that will be cost effective and will maintain the native structure of the glucan. The method that we developed is 80% faster and utilizes ¹/₃ of the reagents compared to the published classical method. Further, the method …

Simulation In Algorithmic Self-Assembly, Jacob Hendricks

Graduate Theses and Dissertations

Winfree introduced a model of self-assembling systems called the abstract Tile Assembly Model (aTAM) where square tiles with glues on their edges attach spontaneously via matching glues to form complex structures. A generalization of the aTAM called the 2HAM (two-handed aTAM) not only allows for single tiles to bind, but also for "supertile" assemblies consisting of any number of tiles to attach. We consider a variety of models based on either the aTAM or the 2HAM. The underlying commonality of the work presented here is simulation. We introduce the polyTAM, where a tile system consists of a collection of polyomino …

Distinguishing Macrophage Activation States By Mass Spectrometry, Matthias Manfred Knust

Graduate Theses and Dissertations

Macrophages are versatile and highly adaptive cells that are involved in a wide range of physiological processes including host defense, homeostasis or regeneration, as well as pathogenesis. They react to their microenvironment, assuming various roles based on chemical and/or physical cues, and can reversibly shift between these so-called activation states. Concurrently, the technique of immunohistochemistry is used to gain spatial information on activated macrophages on tissue sections. The aim of this work was to find mass spectral biomarkers that allow the differentiation of activation states, and establish conditions that can be used in imaging mass spectrometry (IMS) experiments to investigate …

Unraveling Structures Of Protection Ligands On Gold Nanoparticle Au68(Sh)32, Wen Wu Xu, Yi Gao, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

New low-energy atomic structures of the thiolate-protected gold nanoparticle Au₆₈(SH)₃₂ are uncovered, where the atomic positions of the Au atoms are taken from the recent single-particle transmission electron microscopy measurement by Kornberg and co-workers, whereas the pattern of thiolate ligands on the gold core is attained on the basis of the generic formulation (or rule) of the “divide and protect” concept. Four distinct low-energy isomers, Iso1 to Iso4, whose structures all satisfy the generic formulation, are predicted. Density-functional theory optimization indicates that the four isomers are all lower in energy by 3 to 4 eV than the …

The 8-Silyloxyquinoline Scaffold As A Versatile Platform For The Sensitive Detection Of Aqueous Fluoride, Xinqi Zhou

Department of Chemistry: Dissertations, Theses, and Student Research

As one of the most essential elements in nature, fluoride has been well known and extensively studied since the 16^th century. Since then the two-edged nature of fluoride in biological systems has been well described. Specifically, moderate fluoride exposure can aid in tooth and bone development, while fluoride overexposure results in the depilating disease known as fluorosis. Because of the side effects upon overexposure of fluoride, there is a need to develop fast and straight forward methods to sensitively and selectively detect and quantify fluoride concentration in drinking water. With this goal in mind and by taking advantage of …

Urine Proteomics Identifies Preeclampsia Subphenotypes, Michelle R. Axe

Undergraduate Honors Thesis Projects

Preeclampsia is a perinatal complication of unknown etiology, resulting in 76,000 maternal deaths and 500,000 infant deaths annually₁. The Nationwide Children’s Center for Perinatal Research was the first cohort to propose that preeclampsia is rooted in protein misfolding. We aimed to characterize the misfolded protein components of maternal urine samples and to determine if distinct molecular profiles exist for clinical preeclampsia phenotypes. A total of 86 maternal urine samples from Yale-New Haven Hospital were analyzed for this study, from six clinical preeclampsia subphenotypes- pregnant control (n=10), idiopathic proteinuria (n=15), mild preeclampsia (n=14), superimposed preeclampsia (n=12), typical severe preeclampsia …

Laboratory Studies On The Production Of Alpha-Pinene-Derived Organic Nitrates And Their Atmospheric Fate, Joel David Rindelaub

Open Access Dissertations

Currently, the formation yields of organic nitrates from the oxidation of biogenic volatile organic compounds, such as α-pinene, is highly uncertain, negatively impacting our knowledge on tropospheric ozone production and the fate of atmospheric NO_x. To lower this uncertainty, we quantified the organic nitrate yield from the OH radical oxidation of α-pinene under high NO_x conditions. The α-pinene- derived nitrates created in chamber experiments readily partitioned to the aerosol phase and underwent particle phase hydrolysis, indicating that these processes are likely a sink for atmospheric NO_x. The hydrolysis of organic nitrates was found to be …

A Bracketing Method For Proton Affinity Measurements Of Dehydro-And Didehydropyridines, Guannan Li

Open Access Theses

Proton affinity (PA) is a fundamental property that is related to the structure and reactivity of a molecule. Currently, very few experimental PA values are available for organic radicals and none for biradicals. Equilibrium methods cannot be used for these measurements. The traditional bracketing method is based on monitoring reactions of different reference bases with known proton affinities with the protonated analyte for the occurrence of exothermic proton transfer to determine the upper and lower limits of proton affinity. However, the energy deposited into the precursor ions upon CAD when forming protonated radicals may cause endothermic proton transfer reactions occur …

Development Of Experimental And Instrumental Systems To Study Biological Systems, Amanda J Hemphill

Open Access Dissertations

Chapters 1-4 of this thesis describes the development of an experimental system to measure diffusion-limited reaction kinetics in a biological environment. About 100 years ago, the relationship between reaction rate and diffusion in homogenous solution, ie water or buffer, was described as a linear relationship by Smoluchowski. Applying this theory naively would suggest that since the diffusion coefficients drop by factors of 4-100 then the rates of reaction would drop by the same amount. However, recent theory and simulations suggest that this does not hold. Even though biological diffusion coefficients drop to 0.1-20% of that in buffer, these recent studies …

Molecular Diagnosis Of Cancer Using Ambient Ionization Mass Spectrometry, Kevin S Kerian

Open Access Dissertations

My dissertation focuses on advancing the development and application of ambient ionization mass spectrometry methodology and technology to the biomedical field. The primary ambient ionization method used in my studies is desorption electrospray ionization mass spectrometry (DESI-MS) imaging, which has been previously used to analyze and differentiate disease state (i.e. tumor and normal) and in some cases tumor subtype of human liver, kidney, bladder, testicular, prostate, and brain cancers. DESI-MS imaging is an ideal method for disease diagnosis, because it can be used to directly correlate disease state with histopathology to develop and validate MS libraries built using the molecular …

Polarization-Dependent Nonlinear Optical Microscopy Methods For The Analysis Of Crystals And Biological Tissues, Emma L. Kerian

Open Access Dissertations

The ability to solve a high-resolution protein structure is largely dependent on the successful generation and identification of protein crystals prior to X-ray diffraction (XRD). For novel protein targets, high-throughput crystallography often involves generation of multiple targets and thousands of crystallization trials per target to generate diffraction-quality crystals. Second harmonic generation (SHG) imaging has been developed as a fast, non-destructive and sensitive method for the selective identification of protein crystals, even in highly scattering environments. Polarization-dependent SHG microscopy methods were developed to assess the presence of multidomain crystals to provide a handle on crystal quality. In addition, polarization-dependent two-photon excited …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Studies Of Arctic Halogen Chemistry From The Snowpack To The Gas Phase, Kyle D Custard

Open Access Dissertations

The temporary depletion of both tropospheric ozone and gaseous mercury during the Arctic springtime has been a focus of active research over the past several decades. Both of these phenomena have been linked to chemical reactions with halogen radicals. In particular, bromine atoms have been shown to act as the primary driver for these chemical depletions, although both chlorine and iodine atoms also contribute. Molecular bromine, along with its oxidation products, have been well studied in the Arctic, yet chlorine has not. Chlorine is known to impact the local oxidation capacity via its high reactivity with volatile organic compounds. Despite …

Toward An Expanded Role For Collision-Induced Dissociation In Glycoproteomic Analysis, Venkata Kolli

Department of Chemistry: Dissertations, Theses, and Student Research

This thesis begins with an overview of the state-of-the-art in tandem mass spectrometry (MS/MS) analysis of glycopeptides. In this introduction, the primary focus is on utilization of different ion dissociation techniques for MS/MS to obtain structural information of N-glycopeptides. This includes a discussion of the importance of complementary MS/MS methods to attain complete structural characterization of N-glycopeptides. Emerging methods involving the use of a single ion dissociation technique for complete glycopeptide connectivity analysis were also presented. Next, the application of collision-induced dissociation (CID) to provide both amino acid sequence and monosaccharide connectivity for model N-glycopeptides was discussed in detail. Implementation …

Synthesis And Characterization Of Low Valent Metalloporphyrins, Nagabhushanam Kundakarla

Master's Theses (2009 -)

Metalloporphyrins and metalloporphinones have been seen in a number of enzymes and involved in nitrogen metabolism, photosynthesis, and methanogenesis. The reduction of metalloporphyrins and metalloporphinones are achievable, but the site of reduction in either, the metal center or porphyrin core is still debatable. This prompted us to investigate the position of reduction in order to generate low valent metalloporphyrins and porphinones. The reduced porphyrins were characterized by spectroscopic and X-ray crystallographic methods. Previous work in our laboratory has generated low valent metalloporphyrins and porphinones by electrochemical reduction. In this work cobalt, manganese, and iron low valent metalloporphyrins were generated via …

Phosphorus Measurements In Aqueous Media Using Inorganic Phosphorus Sources As Compared To Organic Sources And Resulting Complications, Robert Underhile

All Student Theses and Dissertations

The phosphorus moiety that exists in both inorganic and organic molecules has significant importance. Phosphorus serves as nutrient, a plant building block, a control agent for pests (both plant and insect), and can be an inadvertent cross contaminant in herbicide production, and is often seen as an environmental pollutant. As a cross contaminant, samples suspected of containing the phosphorus moiety are traced to the source of manufacture. Upon suspicion of the source, serious consequences for the manufacturer can develop including loss of relationships, heavy fines and legal matters. Quantitation of phosphorus is not straightforward. Phosphorus can be present in the …

Polycyclic Aromatic Hydrocarbon Determination In Liver Of Menhaden Exposed To The Deep Water Horizon Oil Spill, Rebecca Hawke

Seton Hall University Dissertations and Theses (ETDs)

The April 2010 BP® oil spill has caused great concern for ecological impacts in the Gulf of Mexico. Crude oil contains polycyclic aromatic hydrocarbon (PAHs) and oil spills increase the exposure of aquatic organisms to this class of chemicals. The overall detrimental health effects associated with PAH exposure depend on the exposure period, the concentration of PAHs, and the toxicity of the PAHs in the mixture. Brevoortia tyrannus and Brevoortia patronus are filter feeding fish commonly known as menhaden and account for over 40% of the commercial industry fisheries catch. As primary consumers, they are a major link in the …

Novel Dna Electrochemical Biosensor For K-Ras Point Mutation Detection Based On Dna Polymerase I, Li-Qing Lin, Cheng-Fei Zhao, Zhou-Qian Jiang, Shao-Huang Weng, Xiao-Lan Xie, Xin-Hua Lin

Journal of Electrochemistry

In this article, we developed a novel DNA electrochemical sensor for obtaining a current-time curve based on DNA polymerase I. The capture probes were fixed on the Au electrode by Au interacting with -SH, and then hybridized with the K-ras mutant target DNA as far as one base before the mutation site. After hybridizing the K-ras mutant or wild target DNA, the resulting assembly reacted with the dUTP-biotin in the presence of DNA polymerase I. Then avidin-HRP combined the dUTP-biotin on the electrode. The proposed electrode was applied for detection in TMB solution by electrochemical technology. The experimental results showed …

A Novel Nitrite Sensing Electrode Based On Au/Fe3O4/Chitosan Nanocomposite, Ying Dong, Yong Wang, Huan-Huan Xing, Jian-Ying Qu

Journal of Electrochemistry

A novel nitrite sensing electrode based on gold nanoparticles and iron oxides (Fe₃O₄) magnetic nanoparticles was fabricated with chitosan as the protective film on glassy carbon matrix. Experiment results showed that the sensing electrode exhibited good electrocatalytic activity toward oxidation of nitrite, and the oxidation peak current increased linearly with the concentration of nitrite varying from 5.0×10^-6 to 2.0×10^-3 mol·L^-1 (R=0.9996) with a detection limit of 7.1×10^-7 mol·L^-1 (S/N=3). The sensing electrode exhibited good sensitivity, selectivity and repeatability.

Electrochemiluminescence Assay Based On Bipolar Electrode For Bioanalysis, Mei-Sheng Wu, Jing-Juan Xu, Hong-Yuan Chen

Journal of Electrochemistry

Bipolar electrodes (BPEs) are electronic conductors which are usually embedded into microchannels. The potential difference at the BPE/solution interface is obtained by applying a voltage at the two ends of the microchannel. When it reaches a critical value, the redox reaction takes place at both poles of the BPE simultaneously. Compared with other detection methods, the electrochemiluminescence (ECL) platform based on BPE possesses the advantages of concentration enrichment, high sensitivity, low cost, portable sensor system, no need for a light source, which is quite suitable for bioanalysis. This paper reviews the ECL-BPE strategy for bioanalysis and proposes the future research …

Electrochemiluminescence Biosensors Based On The Signal Amplification Of Co-Reactants, Hai-Jun Wang, Li-Juan Xiao, Ying He, Xin-Ya Jiang, Ya-Li Yuan, Ying Zhuo, Ya-Qin Chai, Ruo Yuan

Journal of Electrochemistry

Using co-reactants to enhance the luminous efficiency of luminophores is a common, convenient and effective method in the construction of the electrochemiluminescence (ECL) biosensors. However, the different methods of introducing co-reactants in the construction of the ECL biosensors will bring different amplification effects. In this review, several signal amplification methods through co-reactants are summarized: 1) Adding the co-reactants directly into the detection solution; 2) Immobilizing the co-reactants onto the electrode surface; 3) Using enzymatic reaction to generate co-reactants in situ around the electrode surface. And then, the outlook of the ECL signal amplification strategy is proposed on those bases.

Sensitive Detection Of Hydroxyl Radical Based On Silver-Enhanced Gold Nanoparticle Label, Yan Yang, Peng Yu, Xiao-Hua Zhang, Jin-Hua Chen

Journal of Electrochemistry

A novel DNA-based electrochemical sensor has been successfully constructed for sensitive detection of hydroxyl radical (·OH) based on the silver-enhanced gold nanoparticle label. Thiolated DNA1 was firstly immobilized on the gold electrode through Au—S bonds. The ·OH generated from Fenton reaction could induce serious oxidative damage of the DNA1 layer on the electrode surface. Then DNA2-functionalized gold nanoparticles (DNA2-AuNPs) were linked on the electrode through the hybridization between DNA2 and undamaged DNA1. Based on the catalytic reduction of silver ion by AuNPs, a silver layer was formed on the surface of AuNPs. The quantitative assay of ·OH was carried out …

A Multi-Channel Electrochemical Immunosensing System With Polyhrp-Based Signal Amplification For The Detection Of Tumor Markers, Wang-Ping Deng, Yan-Zhi Dou, Jing Su, Lin Hao, Shi-Ping Song, Chun-Hai Fan

Journal of Electrochemistry

We have developed a multi-channel electrochemical immunosensing system for the detection of α-fetoprotein (AFP). The sensing system consisted of carbon screen-printed electrode (SPCE) arrays and polyHRP-based signal amplification probes. AFP antigens could bind to both capture antibodies immobilized on electrode arrays ant detection antibodies (anti-AFP IgG developed in rabbit). The anti-rabbit IgG conjugated to poly-horseradish peroxidase were used as a signaling probe to bind to the immuno-complex. The current signals were harvested by a home-made multi-channels electrochemical detector. AFP could be detected in the concentration ranges of 64 pg·mL^-1 ~ 250 ng·mL^-1. The detection limit was as …

Fabrication And Application Of Cytochrome P450 Electrochemcial Biosensor In Drug Metabolism, Xuan Xu, Ju-Sheng Lu, Song-Qin Liu

Journal of Electrochemistry

The process of drug metabolism plays an important role in drug efficacy and toxicity in vivo. Thus, the development of cheap, continent, rapid and high-throughput method for drug metabolism studies has great guiding significance for the design of new drugs, the determination of drug dosage and the detection of clinical drugs. Since the key role played by Cytochrome P450 (CYP450) in phase-I drug reaction, the constructed CYP450 enzyme biosensor can be used for the initial screening of drugs. It is found that the replacement of coenzyme NADPH with an electrode is to provide two electrons demanded in the catalytic reaction. …

Electrochemical Detection Of L-Cysteine Based On Iron Phthalocyanine/Nitrogen-Doped Graphene Modified Electrodes, Jing-Jing Xiao, Hui-Ying Xu, Li Xu, Bao-Hong Liu

Journal of Electrochemistry

In this study, we report a facile method to develop FePc/N-G hybrid modified electrode for the detection of L-cysteine. The electrochemical sensor was characterized by cyclic voltammetry and amperometric response. The sensor exhibited a wider linear range with rapid response which has outperformed pure FePc/GCE, highlighting the important role of nitrogen doped graphene as substrate for improving the electrochemical response property.

Sulfidic Spring In The Gypsum Karst System Of Monte Conca (Italy): Chemistry And Microbiological Evidences, Marianna Messina, Tiziana Grech, Fiorenzo Fiorenza, Alessandro Marlettta, Pietro Valenti, Salvatore Petralia

International Journal of Speleology

Monte Conca Cave is a karst system placed in Messinian evaporites, consisting of an active cave and a resurgence located on the massif of Monte Conca, Campofranco within the "Riserva Naturale Integrale di Monte Conca". A sulfidic spring is located in the terminal gallery of the cave. To characterize the physical and chemical parameters of the Monte Conca cave and of the sulfidic spring, air temperature, relative humidity, water pH, and concentrations of dissolved sulfides, nitrates and sulfates were monitored. The high sulfide consumption rate in the sulfidic spring, evaluated by a kinetic study, suggests that biotic consumption is dominant. …

Chloroamino Acids As A Chemical Explanation For Viking Labeled Release Soil Activity On Mars, John C. Hironimus

STAR Program Research Presentations

The Viking missions to Mars, which took place in the 1970’s, performed several experiments on martian soil in an attempt to discern if there was microbial life present. In one set of experiments, a nutrient solution containing amino acids and organic substrates tagged with carbon-14 was injected into sample cells containing martian soil, and the evolution of labeled CO2 was monitored. The evolution of labeled CO2 indicated that there was a process occurring that broke down the nutrients in solution and released CO2 as a byproduct. Cellular metabolism releases CO2, so this result supported the idea of microbial life on …