Chemistry Commons^™

Studies Of The Reaction Of Rongalite With Epoxides, Anuj Aryal

Theses, Dissertations and Culminating Projects

Reactions between Rongalite (Na⁺O^-SOCH₂OH) and epoxides were studied with the aim of developing new synthetic routes for the procurement of sulfone diols. This class of compounds contains essential building blocks in the construction of sulfur heterocycles, which have been implied in the development of several medicinal compounds. Thus far, the desired diols have not been isolated. During control experiments with bromo alcohols, an unknown product was isolated but remains to be identified.

Design Of Block Copolymer With Tunable Hydrophobic/Hydrophilic/Fluorophilic Interactions, Tatiane De Fatima Dutra

Theses, Dissertations and Culminating Projects

Block copolymers (BCP) with balanced interactions and their resultant bulk-phase self-assembly have become increasingly important in advancing nanotechnology, separation, and energy applications. However, a few reports have addressed the synthesis challenge and bulk-phase self-assembly of such triblock copolymers. This thesis presents a facile route for preparing triblock copolymer via controlled radical and organocatalytic ring-opening polymerization that allows precise control over the incorporation of individual moieties in resultant polymer, responsible for balanced hydrophilic, hydrophobic/lipophilic, and fluorophilic interactions. Synthesized polymer with suggested self-assembled 2D lamellar nanostructure exhibits high-temperature stability. The long-term goal of this work is to selectively use this polymer class …

A Computational Study Of The Copper-Catalyzed Trifluoromethylation Of Boronic Acids, Kevin Nyhuis

Theses, Dissertations and Culminating Projects

This work is a computational study of a reaction mechanism for the trifluoromethylation of boronic acids. Three steps of the proposed reaction mechanism are studied, •CF₃ addition to a copper catalyst center, base promoted transmetalation between copper and aryl boronic acid, and bond forming reductive elimination in which the CF₃ and aryl substituent form a bond. Limited information is known about this mechanism. This study uses computational methods to attempt to elucidate the mechanism and provide the groundwork for potential improvement. Quantum chemical methods in conjunction with tight-binding based conformational sampling methods are used to investigate the possible …

Advances Of Biowaste-Derived Porous Carbon And Carbon–Manganese Dioxide Composite In Supercapacitors: A Review, A. Zekenova, M. Nazhipkyzy, Wanlu Li, A. Kalybayeva, G. Zhumanova, O. Zubova

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

One of the global problems is environmental pollution by different biowaste. To solve the problem, biowaste must be recycled. Waste-free technology is also a way of saving exhaustible raw materials. Research on electrochemical energy sources is currently the most dynamically developing area of off-grid energy. Electrochemical capacitors can operate for a long time without changing performance, they have smaller dimensions, high mechanical strength, and a wide operating temperature range. These properties are effective energy-saving devices. Therefore, supercapacitors are widely used in various industries. This review discussed the methods of obtaining and the characteristics of biowaste-derived activated carbon and carbon–manganese oxide …

An Investigation Towards The Synthesis Of A Novel Conformationally Restricted Ethylenediamine Scaffold, Fanny Mai

Theses, Dissertations and Culminating Projects

This study reports the synthesis of a novel conformationally restricted ethylenediamine scaffold that can be explored for drug discovery. There was significant progress in synthesizing the target scaffolds, but future studies are needed to finish this synthesis. This potential ethylenediamine compound may offer new scaffolds for exploration in drug design and orexin receptor antagonists with improved selectivity for OX1R and OX2R.

Role Of E168d In M. Tuberculosis Igps Catalysis, Hedda Booter

Theses, Dissertations and Culminating Projects

Mycobacterium tuberculosis is a bacterium that affects the lungs and causes tuberculosis, infecting over 10 million people worldwide each year. Owing to the organism’s evolving drug resistance, existing antibiotics no longer combat the disease. The need to discover new drug targets has never been greater. Previous findings suggest that the protein IGPS (indole-3-glycerol phosphate synthase) in M. tuberculosis (MtIGPS) may be a target in the treatment of the disease. MtIGPS catalyzes the fourth step in the tryptophan biosynthetic process. The ability to create their own tryptophan is a major advantage that many bacteria have. The role of E168, in the …

Cyclic Sulfones From Double Conjugate Addition Of Rongalite, Hao Zong

Theses, Dissertations and Culminating Projects

We report a cyclic sulfone synthesis method from the addition of sodium hydroxymethanesulfinate to doubly electrophilic dienone substrates. The novel synthesis of the cyclic sulfone thus avoided the using the toxic and odorous sulfides, and also oxidizing reagents. We prepared both the symmetrical and unsymmetrical substrates, and then used the substrate for the synthesis of cyclic sulfone.

Vertical Metal Distributions In Brownfield Soils Drive Enzyme Activities And Plant Success, Eshariah N. Dyson

Theses, Dissertations and Culminating Projects

The distribution of contaminants in polluted soils can vary through depth. We measured the vertical distributions of heavy metals and enzyme activities in the top 10 cm of side-by-side, vegetated and barren brownfield soils. The data showed metals significantly accumulated in the top 2 cm of barren soil and uniformly distributed through vegetated soil. When planted, germination rate was significantly lower in the previously barren soil, with the metal layer intact, compared to mixed barren soil. These data suggest a feedback loop in which plant roots redistribute metals, diluting metal-rich regions, yet germination remains initially limited by a metal cap. …

Investigating The Effects Of Catalytic Activity In Mycobacterium Tuberculosis Indole-3-Glycerol Phosphate Synthase In Wildtype, N189l, And E57d Variants, Sarah S. Cho

Theses, Dissertations and Culminating Projects

Indole-3-glycerol phosphate synthesis (IGPS) is an enzyme that catalyzes the ring closure in 1-(o-carboxylphenylamino)-1-deoxyribulose 5-phosphate (CdRP). Multiple steps are expected to be involved in formation of the pyrrole ring including dehydration, decarboxylation, cyclization, and condensation. IGPS is an essential protein in the pathogen Mycobacterium tuberculosis and a potential target in the treatment of drug-resistant tuberculosis. In order to better understand the function of Mycobacterium tuberculosis IGPS (mtIGPS), we introduced single-point mutations into active site residues. This was based on the hypothesis that introducing mutations would affect the catalysis in a way where we would be able to obtain more information …

Determining The Relative Activities Of Wild-Type Mycobacterium Tuberculosis Indole-3-Glycerol Phosphate Synthase And Mutants E57a And E219a With An Investigation Into The Relationship Between Wild-Type Mycobacterium Tuberculosis Igps Activity And Ph, Thomas Emmanuel Candela

Theses, Dissertations and Culminating Projects

The relationship between wild-type protein indole-3-glycerol phosphate synthase (IGPS) activity and pH was investigated through the formation of pH activity profiles, and the relative catalytic activities of wild-type Mycobacterium tuberculosis and mutants E57A and E219A were also deduced in this work. The activity of each enzyme variant was determined by reacting native substrate 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate with enzyme buffered at pH 7.5 in a cuvette and using a fluorometer to detect the increase in fluorescent signal produced by the formation of fluorescent product indole-3 glycerol phosphate. Work with wild-type IGPS showed the enzyme to have a kcat of 1.26 ± 1.75 (s …

Characterizing Functions Of Two Regulatory Proteins In The Parasitic Nematode Brugia Malayi And Their Potential As Drug Targets In Treating Lymphatic Filariasis, Brittany Amber Hart

Theses, Dissertations and Culminating Projects

Lymphatic filariasis (LF) is a debilitating disease caused by parasitic nematodes that affect millions of people in largely tropical environments. While drugs are available for treating LF, they suffer from a lack of efficacy against adult parasites, toxicity, and emergence of resistance. Here, we describe two novel potential drug targets within the filarial parasite, Brugia malayi (B. malayi). These two proteins, bm9350, a predictive MAPK stress response protein, and bm2032, a potential histone modifying enzyme, have little or no annotation or experimental evidence of function. Using predictive analysis and tools, we examined potential functions of these proteins and their potential …

Studies Toward The Synthesis Of A Novel Diamine Scaffold, Joseph Edward Quinlan Iii

Theses, Dissertations and Culminating Projects

The orexin system in humans contains receptors Orexin 1 (OX1) and Orexin 2 (OX2). These receptors are involved in numerous physiological processes including wake/sleep cycling, energy homeostasis, and motivation/reward. In scientific literature, it is known that antagonism of these receptors exhibits therapeutic effects in the realm of cocaine and alcohol addiction, as well as sleep disorders. On the market today exist drugs for treatment of sleep disorders through orexin receptor antagonization. Here we report a synthesis toward novel conformationally rigid antagonists of the orexin receptor system that may provide improved affinity and/or selectivity compared to known compounds. We report the …

Discovery Of Single-Stranded Dna Aptamers For The Detection Of Ranavirus, Allyssa Angel

Theses, Dissertations and Culminating Projects

A key problem when developing molecular diagnostic techniques is procuring target detection probes. The need of a stable and selective probe is necessary for accurate target identification in disease detection. Antibodies are widely used but they are unstable at ambient temperatures and are expensive and time consuming to develop. The use of aptamers (short singlestranded DNA) as molecular probes provides several advantages over protein-based methods because they are more stable, easily selected and modifiable. The need of a reliable and stable probe is necessary for accurate detection tests in the field for disease monitoring. Currently, field methods are limited in …

Synthesis Of Amide And Sulfonamides As Pde11 Inhibitors, Noor Abouchakra

Theses, Dissertations and Culminating Projects

With increasing age, individuals begin to experience cognitive decline, especially memory deficits. Given the lack of effective treatments for memory loss, a new promising approach includes targeting second messenger systems that play a critical role in cognitive processes by inhibiting phosphodiesterases (PDEs), specifically PDE11A since its expression is restricted to the brain. PDE11A is responsible for regulating levels of second messengers, such as cyclic AMP and cyclic GMP, which participate in several biochemical processes relating to long term memory function. Since these signaling cascades are controlled by PDEs that result in turning off the signaling pathway, inhibiting phosphodiesterases will lead …

Temperature Dependence On Enzymatic Activity Of A82f F87a Mutant And Wild-Type Cytochrome P450 Bm-3, Sally Seder

Undergraduate Theses

Cytochrome P450 is an enzyme mainly found in liver cells. It plays a key role in the breakdown of drugs and toxins by hydroxylating substrates making the substrates more water soluble. P450s are also involved in cholesterol and hormone synthesis. The third P450 from bacterium Bacillus Megaterium (BM3) is used as a model P450 enzyme due to its structural similarity to human P450s and due to its efficiency in the hydroxylation of fatty acids. Within the enzyme’s active site, substrates can occupy a distal or proximal conformation monitored by UV-vis spectroscopy. The proximal conformation is more effective when it comes …

A Study And Synthesis : Bronze Compounds, Patricia Rose Olsen

Theses, Dissertations and Culminating Projects

The focus of this thesis is the investigation of ternary and quaternary reduced metal oxide compounds termed “bronzes.” The name bronze originally arose from the metallic-like luster of these compounds. Examples of these compounds range from sodium tungsten oxides to the more complex potassium cesium molybdenum oxides. These compounds are crystalline solids at room temperature.

The “bronzes” are compounds that have been studied since their initial synthesis by Wohler in 1824. These compounds belong to a class of compounds that are known as “nonstoichiometric” compounds. The general formula for reduced ternary transition metal oxides is AxMyOz. In this general formula, …

A Comparative Study Of Drug Affinities Determined By Thermofluor And Kinetic Analysis, Oruba Shatnawi

Theses, Dissertations and Culminating Projects

Determining the binding affinity and potency in vitro is one of the significant steps that can give a clue for a new candidate drug during the drug discovery process. Thermofluor is a method used in measuring binding affinity (Kd) of protein-ligands interaction through determining the change in thermal denaturation temperature of protein using real time PCR (RT-PCR). Kinetic analysis assay is used to screen a library of compounds to calculate their potencies (IC50) and inhibition constants (Ki) and it can be performed by spectrophotometer technique. In this study, we used bovine carbonic anhydrase II (BCA II) enzyme, and four of …

Preparation And Crystal Structures Of Racemic And Quasiracemic Imidazole Or N-Methyl Imidazole Copper Complexes Containing Substituted N-Benzoylalanines, Emily Catherine Chong

Theses, Dissertations and Culminating Projects

A quasiracemate is the cocrystallization of two similarly shaped but chemically distinct molecules of opposite handedness. There has been limited to no work regarding quasiracemates in the field of inorganic chemistry. The goal of this study was to prepare various metal based enantiomers, racemates, and quasiracemates using N-benzoylalanines with imidazole or N-methylimidazole as ligands bound to copper to form a metal complex. In this study, we developed a method to prepare substituted N-benzoylalanines and its copper complexes. We also prepared one co-crystal between two differently substituted N-benzoylalanines.

This work reports the successful synthesis and crystal structure analysis of an organic …

Characterization Of Coal Particles In The Soil Of A Former Rail Yard And Urban Brownfield: Liberty State Park, Jersey City (Nj), Usa, Diane F. Hagmann, Michael A. Kruge, Nina M. Goodey, Jennifer Adams Krumins

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

From the 1850's until the 1960's, the Central Railroad of New Jersey was among several major railways shipping anthracite and bituminous coal to the New York City area, transferring coal from railcar to barge at its extensive rail yard and port facility in Jersey City. The 490 ha Liberty State Park was developed on the site after the rail yard closed, but a ca. 100 ha brownfield zone within the park remains off limits to visitors pending future remediation. As part of an environmental forensic and industrial archeological investigation of this zone, the present study characterizes anthracite and bituminous coal …

Environmental Forensics Of Complexly Contaminated Sites: A Complimentary Fingerprinting Approach, Michael A. Kruge, Azucena Lara-Gonzalo, José Luis Gallego

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The environmental forensics approach is most often applied in petroleum and fuel spill incidents, for which sophisticated chemical fingerprinting procedures have evolved. In cases in which pollutant discharges occur in settings with prior contamination, more care must be taken in source discrimination, requiring further advances in methodology. Additional obstacles can arise if the spill is an atypical industrial discharge. This would necessitate painstaking characterization of unfamiliar substances lying outside of existing regulatory regimes and thus overlooked by mandated analytical protocols (i.e., contaminants of emerging concern). Towards these ends, this paper presents a systematic, multi-faceted GC-MS approach using the saturated, aromatic, …

High Functional Diversity Of Contaminated Soils From Liberty State Park, Nina M. Goodey

Sustainability Seminar Series

Urban brownfields present an opportunity to study the functioning of degraded ecosystems. We investigated the soils of Liberty State Park in Jersey City, New Jersey, which once supported a major rail yard and port facility with docks for shipping cargo to New York City. ICP-MS and pyrolysis-GC-MS studies were used to show that our study site is contaminated with heavy metals and organic contaminants, including polycyclic aromatic hydrocarbons. We used fluorescence spectroscopy to measure soil enzymatic function at multiple locations within the brownfield and found the following types of sites: 1.) hotspots with high heavy metal concentrations and high extracellular …

Soil Microbial Response To Metal Contamination In A Vegetated And Urban Brownfield, Jay Prakash Singh, Bhagyashree P. Vaidya, Nina Goodey, Jennifer Krumins

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The ubiquity of urban brownfields presents not only a challenge for environmental managers but also an opportunity to study the functional aspects of degraded ecosystems that are in close contact with human habitation. In this study, we investigate the soil microbial community response to heavy metal contamination at Liberty State Park (LSP), an urban brownfield in Jersey City, NJ, USA. Heavy metal contamination of the soils at LSP is heterogeneous, varying widely across site and among metals. We collected soils along a previously mapped gradient of metal contamination at LSP and sampled soil from a local and uncontaminated reference site …

The Effects Of Active Site And Allosteric Residues On Catalysis And Inhibitor Selectivity In The Bacillus Stearothennophilus Dihydrofolate Reductase, Tyler Eck

Theses, Dissertations and Culminating Projects

In drug discovery, building a comprehensive picture of the binding events between a drug and its enzyme target can be useful, especially in the development of new drugs or predicting the effect of a drug on a similar target from the same protein family. It is well known that a drug's selectivity is influenced by its interactions with amino acid residues within the active site, but contributions from residues situated away from (distal to) the active site are less well understood. Using a novel predictive approach PAnPredictor that employs sequence alignments, we have previously predicted residue positions in the dihydrofolate …

Indole-3-Glycerol Phosphate Synthase Ligand Binding Interactions, Oshane Thomas

Theses, Dissertations and Culminating Projects

Indole-3-glycerol phosphate synthase (IGPS) catalyzes the irreversible ring closure of 1-(ocarboxyphenylamino)- 1-deoxyribulose 5- phosphate (CdRP) into indole-3-glycerol phosphate (IGP) during the fourth step in tryptophan biosynthesis. Analysis of the crystal structure of IGPS from Mycobacterium tuberculosis (MtIGPS) hinted the importance of Lys119 for binding or catalysis. Lys110 from sulfolobus sulfataricus IGPS (ssIGPS) that aligns with Lys119 from MtIGPS, was proposed to be a general acid for the proton transfer that initiates the ring closure and decarboxylation of CdRP. To study the importance of Lys119 in the chemical mechanism for MtIGPS, an amino acid change was made at this position to …

Light Addressable Electrode For Neurotransmitter Sensing, Irina Michelle Terrero Rodríguez

Theses, Dissertations and Culminating Projects

Electrochemical sensors are important for a variety of applications. However, they suffer from physical constraints, as each electrode requires a dedicated wire. Although arrays of 500 electrodes have been reported, achieving high-density electrochemical measurements is still difficult.

In a light-addressable electrode, electrochemical processes occur only when the electrode is illuminated. Light-addressable electrodes could potentially solve many of the drawbacks of traditional electrode arrays, as light is used to spatially confine the redox process to only a small part of the electrode and only one connection is needed. It could also allow for new imaging techniques.

Light-addressable electrodes require a semiconductor …

Inhibition Of Hsv-1 Binding By Egcg-Stearate, Valerie Paschalis

Theses, Dissertations and Culminating Projects

Herpes simplex virus type 1 (HSV-1) is the causative agent of oral herpes, and is able to establish lifelong latent infection along with painful, recurring symptoms. Epigallocatechin-3- gallate (EGCG) is the most abundant polyphenol derived from green tea (Camellia sinensis), whose anti-inflammatory, antioxidant, anti-cancer, and antiviral properties have been widely studied. Although EGCG is not chemically stable and has poor hydrophobicity, lipophilic derivatives of EGCG have shown increased stability as well as increased antiviral efficacy against HSV. Previous studies have demonstrated that EGCG stearate (EGCG-S), a derivative of EGCG esterified at the 4’ position with stearic acid, is able to …

Environmental Forensic Characterization Of Former Rail Yard Soils Located Adjacent To The Statue Of Liberty In The New York/New Jersey Harbor, Diane Hagmann, Michael A. Kruge, Matthew Chi-Hymn Cheung, Maria Mastalerz, José Luis Gallego, Jay Prakash Singh, Jennifer Krumins, Xiaona N. Li, Nina M. Goodey

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Identifying inorganic and organic soil contaminants in urban brownfields can give insights into the adverse effects of industrial activities on soil function, ecological health, and environmental quality. Liberty State Park in Jersey City (N.J., USA) once supported a major rail yard that had dock facilities for both cargo and passenger service; a portion remains closed to the public, and a forest developed and spread in this area. The objectives of this study were to: 1) characterize the organic and inorganic compounds in Liberty State Park soils and compare the findings to an uncontaminated reference site (Hutcheson Memorial Forest); and 2) …

Reactive Iron Mineral Coatings In Redox Transition Zones And Their Impact On Natural Attenuation, Lisa Axe

Sustainability Seminar Series

Reactive Fe mineral coatings play an important role in contaminant attenuation in redox transition zones at sites with subsurface contamination. An anaerobic 60 foot core was collected from the Chambers Works Site in Deepwater, NJ. Working in a glovebox, two-inch subsamples were used to evaluate redox transition zones using bulk composition, redox potential, pH, VOCs in the headspace, as well as abundant bacteria. A number of redox transition zones were identified and further studied with a suite of complementary analyses to characterize the surface chemistry. Analyses have included sequential extraction (phases and speciation), x-ray diffraction (mineralogy), x-ray fluorescence (composition), fieldemission …

Elucidation Of Substrate Binding To Photolyase From Sulfolobus Solfataricus Using Isothermal Titration Calorimetry, Amanda Rose Kuerzi

Theses, Dissertations and Culminating Projects

DNA photolyase is a DNA repair enzyme commonly found across the kingdom of life. Binding studies for the hyperthermophilic photolyase derived from Sulfolobus solfataricus (SsPL) may serve to illuminate how DNA photolyase can adapt over a large temperature range. In the first section of this study, the thermodynamics of substrate binding for SsPL in a choline chloride buffer were determined using isothermal titration calorimetry. Using the Counter-Ion Condensation Concept as a model, ionic strength studies were performed to separate the binding interactions into electrostatic, and nonelectrostatic components. The electrostatic interactions do not appear to make a significant contribution to the …

Using Natural Resources To Control The Fate Of Contaminants In The Environment, Lucia Rodriguez Freire

Sustainability Seminar Series

Environmental contamination poses an increased health risk to those communities living nearby impacted sites, and it is imperative to find sustainable remediation strategies to restore the natural systems. My research investigates natural biogeochemical processes and the use of ubiquitous materials to the design remediation solutions that are site-specific and take into consideration the needs of the affected communities. The first example is the investigation of uranium (U) accumulation in plants growing along the Rio Paguate, which flows through the Jackpile Mine, and open-pit U mine listed on the National Priority List as a Superfund site. Two villages of the Laguna …