Chemistry Commons^™

Rational Design Of The Metabolite Mimics As Novel Antibiotics Targeting Sam-I/Ii Riboswitches, Dr. Young Wan Ham

Journal of Undergraduate Research

In our 2009 MEG application, we have proposed structure-based rational design of metabolite mimics based on S-adenosylmethionine (SAM) as novel antibiotics targeting SAM-I/II riboswitches and subsequent development of fluorescence assay to evaluate binding of the designed mimics to SAM-I/II riboswitches.

A Computational Study Of The Vibrational Spectra Of Mono-Nitrated Fluoranthenes, Jorge Ojeda

Undergraduate Research Conference

No abstract provided.

A Determination Of The Aspartame Content In Select Diet Beverages, Jorge Ojeda

Undergraduate Research Conference

Millions of dollars are spent every year on diet beverages and there has been much controversy on the contents in these beverages, mainly the artificial sweetener aspartame. It is known that aspartame is included in many diet beverages, but the actual amount of aspartame used is not listed in the nutritional facts or provided by the beverage manufacturers. For this reason, the aspartame content of various soft drinks, Coke Zero, Pepsi Max, Diet Pepsi, and Pepsi Next, was analyzed and compared to a calibration plot utilizing Diet Coke as a standard. Diet Coke was used due to the unavailablity of …

Incorporating Catalysis In Inorganic Chemistry 1 Lecture And Laboratory At Onu, Bradley M. Wile

Chemistry and Biochemistry Faculty Scholarship

No abstract provided.

Energetics And Dynamics In Quantum Confined Semiconductor Nanostructures, Jessica Hoy

All Theses and Dissertations (ETDs)

The ability to tune the band-gap energies of semiconductor quantum dots, nanoplatelets, and quantum wires, their significant absorption cross sections, and high photoluminescence quantum yields make these nanostructures promising moieties for use in optoelectronic devices, solar concentrators, chemical sensors, and biological labels. The variable dynamics of the electron-hole pairs that occur within semiconductor nanostructures, however, can complicate the utility of these devices. The variability of the dynamics is born from the different paths accessible for the charge carriers to undergo. In this work, three pathways are proposed to be of primary consequence, namely, electronic intraband relaxation, coupling to surface-mediated processes, …

Side Chain Requirements For Affinity And Specificity In D5, An Hiv-1 Antibody Derived From The Vh1-69 Germline Segment, Alex Stewart, Joseph S. Harrison, Lauren K. Regula, Jonathan R. Lai

College of the Pacific Faculty Articles

BACKGROUND: Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the …

Nutrient Recycling Potential Of Algal Biomass Grown In Eutrophic Water, Kristin Hampel

Research and Creative Activities Poster Day

No abstract provided.

Graphene Oxide/Zinc Oxide Nanocomposites As Dissolved Oxygen Sensors, Jameel A. Hasan

Research and Creative Activities Poster Day

No abstract provided.

Molecularly Woven Materials From Metal-Organic Precursors, Gellert Mezei, Jaafar Hachem, Isurika R. Fernando, Natasha R. Wadhwa, Neil C. Hughes

Faculty Research and Creative Activities Award (FRACAA)

No abstract provided.

Electron Transfer In Electrophilic Aromatic Nitration And Nitrosation, Yirong Mo, Zhenhua Chen

Faculty Research and Creative Activities Award (FRACAA)

No abstract provided.

Exploration Of Non-Specific Peptide Inhibitors Of Amylin Aggregation In Type-2 Diabetes, Hector Figueroa

Senior Honors Theses and Projects - Chemistry

Polypeptide aggregation is seen in a variety of diseases (termed amyloidoses) but remains poorly understood. This study uses the polypeptide amylin to investigate how nonspecific interactions between peptides can inhibit aggregation. A set of 5 heptapeptides was assessed for its ability to impact amylin-induced membrane damage and aggregation. Solvent effects precluded accurate assessment of the impact on membrane damage; however a method of subtracting out the solvent effect is offered. The two most hydrophobic compounds showed the ability to substantially slow amylin aggregation, while those compounds carrying charged side chains tended to increase the rate of aggregation. Only one compound …

Patent: Dual Function Proteins For Treating Metabolic Disorders, Brian R. Boettcher, Shari L. Caplan, Susan E. Cellitti, Douglas S. Daniels, Norio Hamamatsu, Bernhard Hubert Geierstanger, Stuart Licht, Andreas Loew, Stephen Craig Weldon

Chemistry Faculty Publications

The present invention relates to new proteins comprising fibroblast growth factor 2 1 (FGF21 ) and other metabolic regulators known to improve metabolic profiles in subjects to whom they are administered.

Facile Synthesis Of Silver Nanoparticles Stabilized By Cationic Polynorbornenes And Their Catalytic Activity In 4-Nitrophenol Reduction, Bharat Baruah, Gregory J. Gabriel, Michelle J. Akbashev, Matthew E. Booher

Faculty Articles

We report the facile one-pot single-phase syntheses of silver nanoparticles stabilized by norbornene type cationic polymers. Silver nanoparticles (AgNPs) stabilized by polyguanidino oxanorbornenes (PG) at 5 and 25 kDa and polyamino oxanorbornenes (PA) at 3 and 15 kDa have been synthesized by the reduction of silver ions with NaBH4 in aqueous solutions at ambient temperature. The four different silver nanoparticles have been characterized by UV-vis spectroscopy, Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and transmission electron microscopy (TEM) for their particle size distributions. Interestingly, PG stabilizes the silver nanoparticles better than PA as evident from our spectroscopic data. …

Chemistry & Biochemistry Newsletter, Department Of Chemistry & Biochemistry, South Dakota State University

Chemistry & Biochemistry Newsletter: 2002-2015

Inside:

Page 2 SDSU scientists help retrieve ice core from West Antarctica

Page 3 Pat Tille granted tenure, promoted ; Alumni updates; Ron Hirko featured author; Undergrads present posters

Page 4 Biochemist earns prestigious NIH research fellowship

Page 5 GAANN Chemistry Doctoral Fellowship reaches capacity

Page 6 National group honors SDSU’s Medical Laboratory Science

Page 7 Graduate Student Council aims for community voice; Graduating Seniors; Grad students win awards at Sigma Xi Banquet; Grad students attend Pittcon Conference

Page 8 Recent publications

The Low-Resolution Structure Of Nascent High Density Lipoprotein Reconstituted With Dmpc With And Without Cholesterol Reveals A Mechanism For Particle Expansion, Valentin Gogonea, Gary S. Gerstenecker, Zhiping Wu, Xavier Lee, Celalettin Topbas, Matthew A. Wagner, Thomas C. Tallant, Jonathan D. Smith, Phil Callow, Vitaliy Pipich, Helen Malet, Guy Schoehn, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

High density lipoproteins (HDL) are athero-protective particles under investigation as potential therapeutic agents for cardiovascular disease. We applied small angle neutron scattering (SANS) with contrast variation to obtain the low resolution structure of nascent HDL (nHDL) reconstituted with dimyristoyl phosphatidyl choline (DMPC), apoA1:DMPC (1:80, mol:mol). The overall shape of the entire particle is discoidal, with low resolution architecture of apoA1 visualized as an open, contorted, and slightly out of plane structure with three arms, while the low resolution shape of the lipid phase is an oblate ellipsoid that fits well within the protein shape. Modeling studies incorporating the SANS data …

Multiscale Modeling Of Enzyme-Catalyzed Methanol Production By Particulate Methane Monooxygenase, Katherine K. Bearden

Doctoral Dissertations

In this work, the conversion of methane to methanol by the particulate Methane Monooxygenase (pMMO) enzyme is investigated using a multi-scale modeling approach. This enzyme participates in carbon cycling and aids in the removal of harmful atmospheric methane, converting it to methanol. The interaction between pMMO and a neighboring enzyme that is present in the same organism is studied, and the unknown pMMO active site is elucidated and tested for methane oxidation towards the production of methanol.

Fundamental knowledge of pMMO's mechanism is not fully understood. Understanding how this enzyme works in nature will provide information towards designing efficient synthetic …

Ipads In The Science Laboratory: Experience In Designing And Implementing A Paperless Chemistry Laboratory Course, Tiffany Hesser, Pauline Schwartz

Chemistry and Chemical Engineering Faculty Publications

In the fall of 2012, 20 General Chemistry Honors students at the University of New Haven were issued the new iPad 3 to incorporate these devices both in the classroom and the laboratory. This paper will focus on the integration of the iPad into the laboratory curriculum while creating a paperless experience, an environment where no paper would enter or be used for the laboratory over the course of the year. Specific apps were chosen that would allow for an easy transition of course materials into an electronic format. After a transition period for the students and instructor, the overall …

Human Papillomavirus Episome Stability Is Reduced By Aphidicolin And Controlled By Dna Damage Response Pathways, Terri G. Edwards, Michael J. Helmus, Kevin Koeller, James K. Bashkin, Chris Fisher

Educator Preparation & Leadership Faculty Works

A highly reproducible quantitative PCR (Q-PCR) assay was used to study the stability of human papillomavirus (HPV) in undifferentiated keratinocytes that maintain viral episomes. The term “stability” refers to the ability of episomes to persist with little copy number variation in cells. In investigating the mechanism of action of PA25, a previously published compound that destabilizes HPV episomes, aphidicolin was also found to markedly decrease episome levels, but via a different pathway from that of PA25. Since aphidicolin is known to activate DNA damage response (DDR) pathways, effects of inhibitors and small interfering RNAs (siRNAs) acting within DDR pathways were …

Multiphoton Fluorescence Spectroscopy To Monitor The Unfolding Of The Green Fluorescent Protein, Ibtesam Y. Alja'afreh, Ramakrishna Guda, David Huffman

Research and Creative Activities Poster Day

Green fluorescent protein (GFP), from Aequorea coerulescens, has been expressed as a His-tag fusion protein in E. coli cells and purified using metal chelate affinity and gel filtration chromatography. The protein fluoresces at 510 nm due to its natural chromophore that is spontaneously formed after properly folding and remains stable and intact after protein unfolding. The chromophore is buried in a beta barrel and has a permanent dipole moment in both the ground state and the excited state. The difference between permanent dipole moments Δμ_ge is highly proportional to the electrostatic environment around the chromophore. Since Δμ_{ge …}

Study And Identification Of Environmental Nanoparticles In Governors State University (Gsu's) Agricultural Fields, Ekta Desai

All Capstone Projects

Main purpose of this project is to study nanoparticles in Governors State University’s agricultural field and design experimental protocol for the same. Nanoparticles have one dimension that measures between 1 - 100 nanometers or less. Nanoparticles are widely used in day to day life such as in medicines, textiles, manufacturing and cosmetics. Due to their wide use, they can enter environment through many ways such as accidental spills during handling. Waste water treatment plant disposal serves as a main source of their entrance into the environment. Analysis of nanoparticles in environmental samples presents a number of challenges, including separation and …

Folic Acid And Its Receptors, Jacqueline Spreadbury

All Capstone Projects

Folic acid, also known as folate or vitamin B9, is essential for various functions in the human body and life as we know it. Folate is the compound that occurs naturally in food, and folic acid is the synthetic form of this vitamin. Chemically speaking, folic acid has the hydrogen (H+) attached to the compound whereas folate is the conjugate, having lost the hydrogen (H+). Structure, Functions of Folate, Folic Acid in Bacteria, Folate Receptors, and Folic Acid Receptor in Macrophages are discussed in this literature review project. (abstract by OPUS staff)

Synthesis Of A Folate Conjugated Fluorescent Imaging Dye, Daniel Bonner

All Capstone Projects

In recent years methods of selective targeting of pathologic cells have become increasingly important for both detection and treatment of various cancers. The use of folic acid as a selective therapeutic and targeting agent for cancer cells is becoming ever more significant. This is due to the well characterized up regulation of folate receptors for cancer cells.

In this experiment we focus on the development of a new folate conjugate dye by using a small fluorescent molecule known as Oregon Green 514 for fluorescent imaging of cancer cells. To obtain this objective we I inked folate with Oregon green 514 …

Uhplc In The Analysis Of Drug Components, Rana Chandra Sekhar Reddy Pulagam

All Capstone Projects

The main objective of this article is to highlight the new trends that have emerged in the enhancement of the HPLC which have given rise to the use of UHPLC. This innovative tool is much more reliable and effective as compared to HPLC, in the investigation of many chemical compounds. In this article, special insight is given on the changes that have been made with regards to both instruments. In this article focus is also placed on the implementation of UPLC in various fields of interest, in order to enhance the processes for which it is utilized. The pros and …

Novel Algorithms And Instrumentation For Vibrational Spectroscopic Methods Of Analysis, Mohamed F. Abdelkader

Chemistry & Biochemistry Theses & Dissertations

Raman spectroscopy is a form of vibrational spectroscopy that has been increasingly applied to qualitative analysis of chemicals, explosives, pharmaceuticals, and fuels due to its non-invasive and non-destructive nature; its ease of sampling; and its high molecular specificity. These characteristics of Raman spectroscopy also facilitate its use for both in-line and at-line analysis. The principle limitation of Raman spectroscopy is optical interference arising from both analyte and non-analyte fluorescence. In this dissertation, a solution to this problem is presented in the form of a novel spectrometer design which operates in a sequentially shifted excitation mode to eliminate fluorescence backgrounds, fixed …

Metal-Organic And Supramolecular Architectures Based On Mechanically Interlocked Molecules, Isurika Rosini Fernando

Dissertations

The focus of this work is on mechanically interlocked molecules (MIMs), which have unusual physicochemical and mechanical properties with potential applications in nano-scale/molecular devices and high strength materials.

Rotaxanes, for example, consist of an axle-like molecule threaded through a wheel-like molecule, with bulky groups at the two ends of the axle preventing the wheel from dissociating. The position of the wheel along the axle can be switched in a controllable and reversible manner by applying external stimuli, a feature that might lead to the next generation of computers. Molecularly woven materials (MWMs), another example of molecules with mechanically interlocked features, …

A Density Functional Theory Study Of The Formation Of Environmentally Persistent Free Radicals On Zinc Oxide Clusters, Charles Halliburton

Honors Capstones

No abstract provided.

Development Of Method For Detection Of Lead In Samples Collected From Keweenaw Peninsula Mines, Michigan In Collaboration With Environmental Biology Research Students, Sindhu Reddy Aaireddy

All Capstone Projects

Mining is one of the most important industries and a main cause of global pollution due to release of heavy metals into air, water, and soil. Some of these elements are persistent in the environment for years and bioaccumulation in living organisms causing toxic effects. Such elements are known as PBTs (persistent, bioaccumulate and toxic). The nature of toxicity depends on the properties, size of population exposed to it and period of exposure. For this reason, we are interested in developing a method to detect heavy metals in soil samples, mine tailings, plant and animal samples collected from surroundings of …

Comparison Of Two Methods Of Monitoring Corn Mash At Corn Plus Ethanol Plant, Lanay Walker

Undergraduate Research Symposium 2013

In the ethanol industry, several variables affect the amount and grade of ethanol that is produced which affects a plant’s ability to make a profit. This research is focused on one of those variables, ‘corn mash solid content’, which must be closely monitored before the fermentation step. If the mash out of the mix tank is the wrong consistency, the alpha-amylase and gluco-amylase enzymes will not efficiently break the starch into simple sugars that yeast can consume which will decrease the amount of ethanol produced. The mash solid and moisture content is measured daily in order to ensure that the …

Study Of The Insulin Mimetic Sodium Orthovanadate In Glucosamine Induced Insulin Resistnace In Primary Rat Hepatocytes, Kalan Mcpherson

Masters Theses

Insulin resistance and type II diabetes is a disease state characterized by a lack of sensitivity of insulin to provoke a proper response in insulin sensitive tissues. Currently, we utilize glucosamine to increase flux through the Hexosamine Biosynthetic Pathway (HBP) to induce an insulin resistance like state in primary rat hepatocytes. We tested the effectiveness of the insulin mimetic sodium orthovanadate to determine if it could elicit an insulin-like response under these conditions. Mixed results were obtained on the effectiveness of vanadate as an insulin mimetic in this insulin resistant model.

One-Pot Reactions Of Ethyl Propiolate, Ana Maria Neferu

Honors Theses

Through an efficient one-pot reaction sequence, ethyl propiolate can be transformed into a complex, usefully functionalized bicyclic product. Thioconjugate addition yielding Z-selective enoates has been developed for both aromatic thiols (trialkylamine-catalyzed) and aliphatic thiols (KOt-Bu-catalyzed). The oxidation of the thioenoates thus generated is followed by Li-catalyzed oxidation to sulfones using mCPBA, and Li-catalyzed Diels–Alder addition of cyclopentadiene. These subsequent steps are performed in situ, without any purification of intermediates. The yields obtained using the described synthesis are acceptable for a one-pot three-step sequence. Preliminary conjugate addition results with alcohols and amines as nucleophiles are also presented.