Chemistry Commons^™

Miniature Mass Spectrometry: Rf Amplitude Control System Design, Matthew Allen Kirleis

Purdue Polytechnic Masters Theses

This thesis covers the methods used to construct and characterize a custom digital RF amplitude control system. Many types of mass spectrometers exist, but few have been miniaturized as much as the Mini instruments developed at Purdue University. The goal of this research was to improve upon an earlier amplitude control system consisting of analog circuits first implemented in the Mini 11.5 mass spectrometer developed at Purdue University.

A custom set of control and data acquisition electronics were developed for testing the digital and analog control systems in a Mini 11.5 mass spectrometer chassis. A MATLAB Simulink simulation was done …

53rd Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 53rd annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Society for Applied Spectroscopy. Held in Snowmass, Colorado, July 24-28, 2011.

Do Wind Turbines Affect Weather Conditions?: A Case Study In Indiana, Meghan F. Henschen, Brittany Herrholtz, Lacey Rhudy, Kathryn Demchak, Brian Doogs, Joshua Holland, Erik Larson, Johnny Martin, Matthew Rudkin

The Journal of Purdue Undergraduate Research

Wind turbines are becoming increasingly widespread in the United States as the world looks for cleaner sources of energy. Scientists, policymakers, and citizens have strong opinions regarding the positive and negative effects of wind energy projects, and there is a great deal of misinformation about wind energy circulating on the Web and other media sources. The purpose of this study is to gain a better understanding of how the rotation of hundreds of turbines can influence local weather conditions within a wind farm and in the surrounding areas. This experiment measures temperature, atmospheric pressure, wind speed, wind direction, relative humidity, …

Hiv-1 Matrix Protein Binding To Rna, Ayna Alfadhli, Henry Mcnett, Seyram Tsagli, Hans Peter Bachinger, David H. Peyton

Chemistry Faculty Publications and Presentations

The matrix (MA) domain of the HIV-1 precursor Gag (PrGag) protein plays multiple roles in the viral replication cycle. One essential role is to target PrGag proteins to their lipid raft-associated phosphatidylinositol-(4,5)-bisphosphate (PI[4,5]P2) assembly sites at the plasma membranes (PMs) of infected cells. In addition to this role, several reports have implicated nucleic acid binding properties to retroviral MAs. Evidence indicates that RNA binding enhances the binding specificity of MA to PI(4,5)P2-containing membranes, and supports a hypothesis in which RNA binding to MA acts as a chaperone that protects MA from associating with inappropriate cellular membranes prior to PrGag delivery …

The Role Of Amyloid-Beta Assembly State In Monocyte Maturation And Smooth Muscle Cell Degeneration, Nikkilina Renee Crouse

Dissertations

Alzheimer's Disease (AD) is a progressive, neurodegenerative disorder which is ranked as a leading cause of death among Americans. AD is characterized by the presence of intracellular neurofibrillary tangles and extracellular plaques made of amyloid ß (Aß). Together these pathologies lead to severe memory impairment in patients, but research has implicated the presence of the Aß deposits as likely causes for AD progression. Aß is produced through the proteolytic cleavage of the integral membrane amyloid precursor protein, which occurs through the action of beta- and gamma-secretases and produces 39-43 amino acid Aß peptides. In AD, the Aß plaques are comprised …

Efficient Quantum Trajectory Representation Of Wavefunctions Evolving In Imaginary Time, Sophya V. Garashchuk, James Mazzuca, Tijo Vazhappilly

Faculty Publications

The Boltzmann evolution of a wavefunction can be recast as imaginary-time dynamics of the quantum trajectory ensemble. The quantum effects arise from the momentum-dependent quantum potential – computed approximately to be practical in high-dimensional systems – influencing the trajectories in addition to the external classical potential [S. Garashchuk, J. Chem. Phys.132, 014112 (2010)]. For a nodelesswavefunction represented as ψ(x, t) = exp ( − S(x, t)/ℏ) with the trajectory momenta defined by ∇S(x, t), analysis of the Lagrangian and Eulerian evolution shows that for bound potentials the former …

Zirconium Mediated One-Pot Synthesis Of Γ-Amino Acids From Carbon Dioxide, Diego A. Pedroza ^, Shizue Mito *

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Fullerene-Based Organized Self-Assembled Photoactive Layer, Marcelo A. Yates ^, Danisha M. Rivera, Luis Echegoyen *

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Endohedral Derivatives For Bulk Heterojunction Organic Photovoltaic Devices, Gustavo Hernandez^, Michael D. Irwin*

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Octaethyl-Nickel-Porphyrin Functionalized Silica For Fullerene Separation, Adriana Rodríguez^, Danisha M. Rivera, Luis Echegoyen*

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Triphenylamine-Fullerene Dyads As Photoactive Layers In Photovoltaic Cells, Luis F. Gardea^, Mahsa Hosseini, Luis A. Echegoyen*

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Synthesis Of The Precursors For A New Covalent Organic Framework With Triangular Shaped Pores, Fernando J. Correa ^, Venkata P. Neti, Luis A. Echegoyen *

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Electronic States In Layered Si/Sio2/Mos2 Nanostructures, Luis Edgardo Luciano^, Domingo Ferrer, Russell R. Chianelli, Manuel Ramos*

COURI Symposium Abstracts, Summer 2011

No abstract provided.

Thermal-Initiated Hydroxyethyl Methacrylate Functionalization Of Multiwalled Carbon Nanotubes, Greg Curtzwiler, Philip Costanzo, Ray Fernando, Jeffrey E. Danes, Keith Vorst

Chemistry and Biochemistry

Multiwalled-carbon nanotubes (MWCNTs) were functionalized via thermoinitiated free radical polymerization of 2-hydroxyethyl methacrylate (HEMA) using benzoyl peroxide. Tip sonication was used during the polymerization reaction to separate agglomerated nanotubes. The functionalization was confirmed by control experiments and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). Differential scanning calorimetry indicated that the addition of poly(HEMA)-MWCNTs to a two-component polyurethane coating will have little effect on the glass transition temperature of the coating. The poly(HEMA)-functionalized MWCNTs formed large colloidal structures of highly dispersed nanotubes in both the nonsheared and sheared coatings as determined by atomic force microscopy. This study determined a quick …

Green Decarbonylation Of Aldehydes Using Palladium (Ii) Acetate, Jessica Konopka

Pell Scholars and Senior Theses

Decarbonylation reactions are important reactions in the chemical industry with typical methods being costly and wasteful. It is important to determine an effective catalyst and to see how general the reaction is with varying aldehydes, as well as to reduce the waste and make the reaction more cost effective. Several different aldehydes were studied using palladium (II) acetate as a catalyst. The samples were analyzed using Gas Chromatography Mass Spectroscopy (GC-MS) to determine if a product was formed based on the percent report obtained. Palladium (II) acetate was found to be an effective catalyst, yielding 100% product for several aldehydes …

Utilizing Service-Learning In The Analytical Chemistry Laboratory: Soil And Water Analysis In Rochester, New York, Kimberly D. Chichester, Irene Kimaru, Lynn Donahue, Maryann Herman

Chemistry Faculty/Staff Publications

For an analytical chemistry course at St. John Fisher College, instructors designed a servicelearning project on soil and water analysis to achieve the following two goals: 1) to introduce analytical chemistry students to soil- and water-testing methods by working in collaboration with surrounding neighborhoods residents and government agencies and 2) to prepare written reports of the results for the designated community partners. Service-learning students conducted soil testing for lead on homes and perspective community garden sites around Rochester, NY with plans to establish planting methods to revitalize polluted soil. Four different communities contributed soil samples. The entire project was performed …

Direct Patterning Of A Cyclotriveratrylene Derivative For Directed Self-Assembly Of C60, Zachary R. Osner, Dorjderem Nyamjav, Richard C. Holz, Daniel P. Becker

Chemistry: Faculty Publications and Other Works

A novel apex-modified cyclotriveratrylene (CTV) derivative with an attached thiolane-containing lipoic acid linker was directly patterned onto gold substrates via dip-pen nanolithography (DPN). The addition of a dithiolane-containing linker to the apex of CTV provides a molecule that can adhere to a gold surface with its bowl-shaped cavity directed away from the surface, thereby providing a surface-bound CTV host that can be used for the directed assembly of guest molecules. Subsequent exposure of these CTV microarrays to C60 in toluene resulted in the directed assembly of predesigned, spatially controlled, high-density microarrays of C60. The molecular recognition capabilities of this CTV …

Solid-State Synthesis Of Imide Ligands For The Self-Assembly Of Metal-Organic Materials, Jason Alexander Perman

USF Tampa Graduate Theses and Dissertations

In this research project, reduction or complete elimination of organic solvents is explored in the synthesis of cyclic imides using a technique that brings reagents into favorable position to react. Cocrystal Controlled Solid-State Synthesis (C³S^y3), takes advantage of supramolecular interactions such as hydrogen bonding and π-π stacking to form a cocrystal which can sequential be heated to complete the condensation reaction and produce a desirable product. Twenty-five successful condensation reactions result in high and clean yield.

C³S^y3 of cyclic imides with auxiliary hydrogen bonding moieties like carboxylic acid, carboxylate or pyridyl groups are …

The Molecular Mechanism Of Migraine, Kristin Dawn Watson

Theses and Dissertations

Migraine is a common, episodic neurological disorder that includes headache, nausea and hypersensitivity to sensory stimuli. During the headache phase of migraine, migraine patients can be especially hypersensitive to thermal stimuli. The unpredictable and episodic nature of migraine makes it difficult to treat and much of the mechanism of migraine has yet to be elucidated. A T44A substitution in casein kinase 1δ is inherited with migraine with aura. A transgenic mouse model suggests that animals with this mutation exhibit increased sensitivity to thermal stimuli after injection with nitroglycerin (NTG). We performed behavior assays that measure animal responses to thermal stimuli, …

Structures Of Poliovirus And Antibody Complexes Reveal Movements Of The Capsid Protein Vp1 During Cell Entry, Jun Lin

Theses and Dissertations

In the infection process, native poliovirus (160S) first converts to a cell-entry intermediate (135S) particle, which causes the externalization of capsid proteins VP4 and the N-terminus of VP1 (residues 1-53). The externalization of these entities is followed by release of the RNA genome, leaving an empty (80S) particle. Three antibodies were utilized to track the location of VP1 residues in different states of poliovirus by cryogenic electron microscopy (cryo-EM). "P1" antibody binds to N-terminal residues 24-40 of VP1. Three-dimensional reconstruction of 135S-P1 showed that P1 binds to a prominent capsid peak known as the "propeller tip". In contrast, our initial …

Probing Morphology-Dependent Aggregation And Photocurrent Generation In Polymer/Fullerene Photovoltaic Devices, Yongqian Gao

Chemistry and Chemical Biology ETDs

In this dissertation, new spectroscopic and electrical imaging approaches were developed to map morphology-dependent aggregation properties of polymer chains in model solar cell devices. These techniques reveal new correlations between local structure and material performance on sub-micron size scales which are not accessible by other techniques. Resonance Raman spectroscopic imaging was developed as a physical probe to identify and spatially map morphology-dependent variations of intra- and interchain interactions and order in poly-3-hexylthiophene (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) photovoltaic blend thin films. The C=C band of P3HT backbone was decomposed into aggregated and unaggregated component contribution at ~1450 cm …

Quantitative Structure-Property Relationships For Predicting Chlorine Demand And Disinfection Byproducts Formation In Drinking Water, Gebhard Balthazar Luilo

Chemistry and Chemical Biology ETDs

Models are important tools for designing or redesigning water treatment processes and technologies to minimize disinfection byproducts (DBPs) formation without compromising disinfection efficiency. Empirical models, which are the most common, are based on bulk water quality parameters that vary with time and space. These parameters may not always have linear relationships with chlorine demand and DBPs formation which make structure-based models more attractive to study. In this dissertation, Quantitative Structure-Property Relationship (QSPR) models which make use of structural properties of individual molecules were developed using experimental data obtained from the literature. The amounts are reported in moles of chlorine (HOCl) …

Spectroscopic And Electronic Structure Studies Of Metalloenzyme Active Sites, Joseph Sempombe

Chemistry and Chemical Biology ETDs

This work reports on the electronic and geometric structural studies of xanthine oxidoreductase (XO), S-ribosylhomocysteinase (LuxS) and inducible nitric oxide synthase (iNOS) active sites resulting from the joint applications of electronic absorption, electron paramagnetic resonance and magnetic circular dichroism spectroscopic methods. XO catalyzes formal oxygen atom insertion into a substrate C-H bond, but differs from monooxygenase enzymes in that the inserted oxygen atom derives from metal activated water and reducing equivalents are generated rather than consumed. Studies on aldehyde inhibited' XO (a paramagnetic form observed during XO catalysis), analyzed in terms of the relationships between the g-, ^95,97Mo hyperfine, …

Spectroscopic And Electronic Structure Studies Of Bis-Metallodithiolenes, Regina Peter Mtei

Chemistry and Chemical Biology ETDs

Dimethylsulfoxide reductase (DMSOR) enzyme family members catalyze oxygen atom transfer to or from organic or inorganic substrate and play important roles in the global cycles of sulfur and nitrogen, as well as the detoxification of arsenite. This enzyme has recently been subject of investigation due to its catalytic nature of oxygen atom transfer. This work reports on the electronic structure and reactivity properties of dimethylsulfoxide reductase enzyme studied using spectroscopic and computational methods. The spectroscopic methods included electronic absorption (EA), electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD) and resonance Raman rRaman). Here, we report full characterization of the DMSOR …

Emerging Solar Cell Technology: Advances In Solid-State Polymer Hybrid Dye-Sensitized Solar Cells, Andrew De Jong

Environmental Analysis Program Mellon Student Summer Research Reports

Mr. de Jong worked at Oxford University to extend solid-state solar cells’ photoresponse by taking advantage of a favorable energy-transfer mechanism.

Quantifying The Flux Of Caco3 And Organic Carbon From The Surface Ocean Using In Situ Measurements Of O-2, N-2, Pco(2), And Ph, Steven Emerson, Christopher Sabine, Meghan F. Cronin, Richard Feely, Sarah E. Cullison Gray, Michael Degrandpre

Chemistry and Biochemistry Faculty Publications

Ocean acidification from anthropogenic CO2 has focused our attention on the importance of understanding the rates and mechanisms of CaCO3 formation so that changes can be monitored and feedbacks predicted. We present a method for determining the rate of CaCO3 production using in situ measureme nts of fCO(2) and pH in surface waters of the eastern subarctic Pacific Ocean. These quantities were determined on a surface mooring every 3 h for a period of about 9 months in 2007 at Ocean Station Papa (50 degrees N, 145 degrees W). We use the data in a simple surface ocean, mass balance …

A Systems Approach To Understanding The Role Of Glycans In Cancer, John F. Rakus, Kaneolani T. Pilobello, Laura K. Mahal

Chemistry Faculty Research

Glycosylation involves the post-translational addition of carbohydrates to protein molecules and is an intricate and indispensable biochemical process. Study of this complicated network of interactions is hindered by the lack of a coding template analogous to the genetic code, and by the vast structural complexity inherent to carbohydrate polymers. We use lectins (non-enzymatic carbohydrate-binding proteins of non-immunological origin) as microarray probes to identify carbohydrate features expressed on cellular surfaces. Specifically, we utilized lectin microarray technology to investigate the differences in carbohydrates expressed by the cell lines of the Nation Cancer Institute’s NCI-60 panel. Our investigation identified tissue-specific expression differences in …

Comparative Analysis Of Peak-Detection Techniques For Comprehensive Two-Dimensional Chromatography, Indu Latha, Stephen E. Reichenbach, Qingping Tao

School of Computing: Faculty Publications

Comprehensive two-dimensional gas chromatography (GC×GC) is a powerful technology for separating complex samples. The typical goal of GC×GC peak detection is to aggregate data points of analyte peaks based on their retention times and intensities. Two techniques commonly used for two-dimensional peak detection are the two-step algorithm and the watershed algorithm. A recent study [4] compared the performance of the two-step and watershed algorithms for GC×GC data with retention-time shifts in the second-column separations.In that analysis,the peak retention-time shifts were corrected while applying the two-step algorithm but the watershed algorithm was applied without shift correction. The results indicated that the …

Webfr3d-A Server For Finding, Aligning And Analyzing Recurrent Rna 3d Motifs, Craig L. Zirbel, Neocles B. Leontis, Anton I. Petrov

Chemistry Faculty Publications

WebFR3D is the on-line version of 'Find RNA 3D' (FR3D), a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions. In both modes, users can specify sequence, sequence-continuity, base pairing, base-stacking and other …

Negative Polaron And Triplet Exciton Diffusion In Organometallic "Molecular Wires", Julia M. Keller, Ksenija D. Glusac, Evgeny O. Danilov, Sean Mcilroy, Paiboon Sreearuothai, Andrew R. Cook, Hui Jiang, John R. Miller, Kirk S. Schanze

Chemistry Faculty Publications

The dynamics of negative polaron and triplet exciton transport within a series of monodisperse platinum (Pt) acetylide oligomers is reported. The oligomers consist of Pt-acetylide repeats, [PtL(2)-C C-ph-C C-](n) (where L = PBu(3) and Ph = 1,4-phenylene, n = 2, 3, 6, and 10), capped with naphthalene diimide (NDI) end groups. The Pt acetylide segments are electro- and photoactive, and they serve as conduits for transport of electrons (negative polaron) and triplet excitons. The NDI end groups are relatively strong acceptors, serving as traps for the carriers. Negative polaron transport is studied by using pulse radiolysis/transient absorption at the Brookhaven …