Digital Commons Network^™

Development Of A 3-Body:Many-Body Integrated Fragmentation Method For Weakly Bound Clusters And Application To Water Clusters (H2o) N=3-10, 16, 17, Desiree M. Bates, Joshua R. Smith, Tomasz Janowski, Gregory S. Tschumper

Chemistry Faculty Research & Creative Works

A 3-body:many-body integrated quantum mechanical (QM) fragmentation method for non-covalent clusters is introduced within the ONIOM formalism. The technique captures all 1-, 2-, and 3-body interactions with a high-level electronic structure method, while a less demanding low-level method is employed to recover 4-body and higher-order interactions. When systematically applied to 40 low-lying (H₂O)_n isomers ranging in size from n = 3 to 10, the CCSD(T):MP2 3-body:many-body fragmentation scheme deviates from the full CCSD(T) interaction energy by no more than 0.07 kcal mol-1 (or < 0.01 kcal mol-1 per water). The errors for this QM:QM method increase only slightly for various low-lying isomers of (H₂O)₁₆ and (H₂O)₁₇ (always within 0.13 kcal mol^{-1 …}

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.

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 …

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 …

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 …

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 …

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 …

Fliposomes: Ph-Sensitive Liposomes Containing A Trans-2-Morpholinocyclohexanol-Based Lipid That Performs A Conformational Flip And Triggers An Instant Cargo Release In Acidic Medium, Nataliya M. Samoshina, Xin Liu, Barbora Brazdova, Andreas H. Franz, Vyacheslav V. Samoshin, Xin Guo

College of the Pacific Faculty Articles

Incorporation of a pH-sensitive conformational switch into a lipid structure enables a drastic conformational flip upon protonation that disrupts the liposome membrane and causes rapid release of cargo specifically in areas of increased acidity. pH-sensitive liposomes containing the amphiphile (1) with trans-2-morpholinocyclohexanol conformational switch, a phospholipid, and a PEG-lipid conjugate were constructed and characterized. The optimized composition—1/POPC/PEG-ceramide (50/45/5)—could be stored at 4 °C and pH 7.4 for up to 1.5 years, and was stable in blood serum in vitro after 48 h at 37 °C. Liposomes loaded with ANTS/DPX or methotrexate demonstrated an unusually quick content release (in a few …

Novel Ion Trap Made Using Lithographically Patterned Plates, Ying Peng

Theses and Dissertations

A new approach of making ion trap mass analyzers was developed in which trapping fields are created in the space between two ceramic plates. Based on microfabrication technology, a series of independently-adjustable electrode rings is lithographically patterned on the facing surfaces of each ceramic plate. The trapping field can be modified or fine-tuned simply by changing the RF amplitude applied to each electrode ring. By adjusting the potential function applied to the plates, arbitrary trapping fields can be created using the same set of ceramic plates. Unlike conventional ion traps, the electrodes of planar ion traps have a non-equipotential surface, …

Assessing Secondary And College Students’ Implicit Assumptions About The Particulate Nature Of Matter: Development And Validation Of The Structure And Motion Of Matter Survey, Marilyne Stains, Marta Escriu-Sune, Myrna Lisseth Molina Alvarez De Santizo, Hannah Sevian

Department of Chemistry: Faculty Publications

Development of learning progressions has been at the forefront of science education for several years. While understanding students’ conceptual development toward “big ideas” in science is extremely valuable for researchers, science teachers can also benefit from assessment tools that diagnose their students’ trajectories along the learning progressions. In this paper, we describe the development and validation of a teacher-friendly survey, the Structure and Motion of Matter (SAMM) survey, designed to measure students’ trajectories along aspects of a research-based learning progression on the particulate nature of matter. Specifically, the survey assesses students’ implicit assumptions about four concepts: the structure of solute …

Nanoencapsulated Drug-Carrying System For Photodynamic Antimicrobial Chemotherapy (Pact), Gopala Krishna Murthy Kalapala

All Capstone Projects

The purpose of this study is to develop nanoparticulate drug-carrying systems that are capable of directly delivering photodynamic antimicrobial agents to treat patients with chronic wounds. Chronic wounds are considered as a pandemic health problem. Approximately 1% to 2% of the population in developing countries has experienced a chronic wound during their lifetime. In the United State States, according to the American Academy of Dermatology, the expense of treating chronic wounds constitutes over half of the total cost for all skin diseases, which exceeds $10 billion annually. For the last decade extensive basic science and clinical research in chronic wounds …

Novel Ruthenium Complexes As Photodynamic Therapeutic Agents, Sareen Kumar Kushangari

All Capstone Projects

This project reviews the literature of novel ruthenium c complexes in photodynamic drug therapy. (Abstract by OPUS staff)

The Nature, Origin And Preservation Of Amide Organic Nitrogen In Organic Matter, Georgina Anne Mckee

Chemistry & Biochemistry Theses & Dissertations

Past studies have found much of nonliving sedimentary/aqueous nitrogen-containing organic matter (NCOM) is composed of amides, assumed to be peptides/proteins. Their lability calls into question their survival, and several hypotheses have been suggested to explain this. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and nuclear magnetic resonance (NMR) spectroscopy I investigated the molecular amide composition in sedimentary/aqueous systems while reassessing their preservation and formation routes.

Development of a suitable methodology is essential for successful NCOM study due to electrospray ionisation source requirements: sediment samples need to be rendered into solution. Based on NMR and FT-ICR-MS analysis, I determined …

Using Nanotechnology To Detect Nerve Agents, Mark N. Goltz, Dong-Shik Kim, Leeann Racz

Faculty Publications

Nanotechnology has opened a wide range of opportunities having potential impacts in areas as diverse as medicine and consumer products. In collaboration with researchers at the University of Toledo UT, Air Force Institute of Technology AFIT scientists are exploring the possibility of using a nanoscale organic matrix to detect organophosphate OP nerve agents. Current techniques for detecting OP compounds are expensive and time consuming. Developing a nanoscale organic matrix sensor would allow for direct, real-time sensing under field conditions. This article describes the science behind such a sensor and its possible applications. High-performance sensors are needed to protect Soldiers and …

Development And Applications Of Ionic Liquids And Near-Infrared Multispectral Imaging Techniques, Irena Mejac

Dissertations (1934 -)

In this work, we explore novel analytical applications of Ionic Liquids and Near-infrared multispectral imaging microscopy.

Ionic liquids (ILs) belong to a group of organic salts that are liquid at room temperature and can be, due to their unique chemical and physical properties, successfully used for a variety of applications. The main goal of this study was to explore the synergistic use of ILs in chemical separations. Specifically, chiral ILs were used as novel chiral selectors for Capillary Electrophoresis and as solvents for stationary phase in Gas Chromatography. As chiral selectors IL provides baseline-separation as well as enantiomeric separation of …

Generation Of Diverse Molecular Complexity From Simple Hydrocarbons, Anobick Sar

Dissertations (1934 -)

In an effort to make diverse molecular complexity from simple hydrocarbons, tricarbonyl(cyclohexadienyl)iron(+1) cation was prepared in two steps from 1, 3-cycloxehadiene. Reactivity of the symmetric iron cation with heteroatom nucleophiles and stabilized carbon nucleophiles was studied. Nucleophilic attack of potassium phthalimide at the dienyl terminus of the cation followed by oxidative decomplexation with Ce4+ provided the ligand N-(2,4-cyclohexadiene-1-yl)phthalimide. A series of stereochemically diverse polyhydroxyl aminocyclohexane "aminocyclitols" derivatives and a number of racemic and optically active hydroxy-and polyhydroxy 1,3-diaminocyclohexane derivatives have been synthesized from N-(2,4-cyclohexadiene-1-yl)phthalimide. The relative stereochemistries of the compounds ware assigned on the basis of the 1H NMR data …

Spectroelectrochemistry And Voltammetry Of Metalloporphinones, Florentina Tutunea

Dissertations (1934 -)

Metalloporphinones have been found in a number of enzymes involved in nitrogen metabolism. The emphasis of this research project has been to develop spectroscopic markers in order to identify metal versus porphinone reduction. The carbonyl group in the porphinone has a very strong signal which is quite sensitive to the extent of reduction of the porphinone macrocycle.

The spectral change makes IR an important tool in the process of structure determination of metalloporphyrins because the carbonyl group shift can be correlated with the metal oxidation state. It was observed from previously published studies that a higher metal oxidation state moves …

The Preparation And Characterisation Of Silver Nanomaterials And Their Application In Sensing Techniques, Aoife Power

Doctoral

In this work the impact of nanomaterial, specifically silver nanostructures, on sensing techniques is investigated. The work can be divided in to three sections, preparation and characterisation of silver nanoparticles, their application as a nanocomposite based chemiresistor humidity sensing device and finally their application within the surface enhanced (resonance) Raman spectroscopy, SE(R)RS, technique. In the first study silver nanoparticles were prepared as aqueous colloidal dispersions. The colloids were of either a defined diameter (average diameter ~ 20 nm) with high silver loading or lower loaded colloids of tuneable morphology and hence optical properties. In a subsequent study the high load …

Effect Of Freshman Chemistry On Student Performance In Sophomore Engineering Courses, Michael A. Collura, Shannon Ciston, Nancy Ortins Savage

Chemistry and Chemical Engineering Faculty Publications

The role of first year chemistry courses in engineering programs varies somewhat across programs and disciplines. Clearly most engineering majors will encounter chemistry topics of a general nature in some of their upper-level course work. The purpose of requiring chemistry in the first year, however, goes well beyond learning chemical concepts. As a quantitative science, chemistry requires the use of math, principally algebra, on a regular basis in solving various problems. Students should gain an appreciation of the importance of units in solving problems should come to understand the difference between implicit and explicit properties and should develop other quantitative …

Vibrational Spectroscopy Of N-Methyliminodiacetic Acid (Mida)-Protected Boronate Ester: Examination Of The B-N Dative Bond, Dana N. Reinemann, Ashley M. Wright, Jonathan D. Wolfe, Gregory S. Tschumper, Nathan I. Hammer

Chemistry Faculty Research & Creative Works

N-Methyliminodiacetic acid (MIDA)-protected boronate esters are a new class of reagents that offer great promise in iterative Suzuki-Miyaura cross-coupling reactions. Compared to earlier reagents, MIDA esters are easily handled and are benchtop stable under air indefinitely. The success of this new species is tied to its unique molecular architecture. Compared to the simpler B-N containing molecules ammonia borane and trimethylamine borane, MIDA esters are much larger, and the sp3 hybridized boron atom is secured by two five membered rings, making this molecular class stable for spectroscopic study. Here, we present infrared, Raman, and surface enhanced Raman (SERS) spectra of methylboronic …