Chemistry Commons^™

Effects Of Carbon Chain Substituent On The P∙∙∙N Noncovalent Bond, U. Adhikari, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The effects of carbon chains placed on the electron-accepting P atom of a P⋯N bond are examined via ab initio calculations. Saturated alkyl groups have a mild weakening effect, regardless of chain length. In contrast, incorporation of double bonds into the chain strengthens the interaction, Ctriple bond; length of mdashC triple bonds even more so. These effects are only slightly enhanced by additional conjugated double bonds or an aromatic ring. Placing F atoms onto the carbon chains strengthens the P⋯N bond, but only by a small amount, which wanes as the F atom is displaced further from the P along …

Ligand And Metal Effects On The Co-Release Reactivity Of Metal Acireductone And Flavonolate Complexes, Katarzyna Grubel

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research reported herein involves synthetic metal complexes of relevance to dioxygenase enzymes (Ni(II)-containing acireductone dioxygenase (Ni(II)-ARD) and quercentinase (2,4-flavonol dioxygenase) that promote oxidative carbon-carbon bond cleavage and CO release. The experiments focus on the elucidation of structure-reactivity relationships and evaluation of the conditions under which CO is generated.

It had been proposed that hydrogen bond donors in the secondary environment of the active site metal center in Ni(II)-ARD influence the coordination of the acireductone substrate on the nickel center. To evaluate this proposal, we investigated the Ni(II) coordination chemistry of an acireductone-type enolate anion using a supporting chelate ligand …

A New Noncovalent Force: Comparison Of P∙∙∙N Interaction With Hydrogen And Halogen Bonds, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

When PH(3) is paired with NH(3), the two molecules are oriented such that the P and N atoms face one another directly, without the intermediacy of a H atom. Quantum calculations indicate that this attraction is due in part to the transfer of electron density from the lone pair of the N atom to the σ(∗) antibond of a P-H covalent bond. Unlike a H-bond, the pertinent hydrogen is oriented about 180° away from, instead of toward, the N, and the N lone pair overlaps with the lobe of the P-H σ(∗) orbital that is closest to the P. In …

Kinetic, Mechanistic, And Structural Investigation Of Features Controlling Stereoselectivity Of (R)- And (S)-Hydroxypropyl Com Dehydrogenases From Xanthobacter Autrophicus Strain Py2, Dariusz Adam Sliwa

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Enantiopure alcohols are valuable intermediates in fine organic synthesis, in particular for preparation of biologically active compounds. The necessity of preparing single enantiomer drugs in an optically pure form has triggered much research, especially in the pharmaceutical industry. The biocatalytical production of chiral alcohols by alcohol dehydrogenase enzymes is characterized by the asymmetric reduction of the corresponding ketones, usually with high degree of stereoselectivity. The commercial value of the enzymes as stereoselective biocatalysts has been a significant driving force in understanding features that control their mechanism of catalysis and stereoselectivity. This work focuses on two enantiocomplementary dehydrogenase enzymes ((R …

Ab Initio Search For Novel Bxhy Building Blocks With Potential For Hydrogen Storage, Jared K. Olson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

On-board hydrogen storage presents a challenging barrier to the use of hydrogen as an energy source because the performance of current storage materials falls short of platform requirements. Because boron is one of the lightest chemical elements that can form strong covalent bonds with hydrogen, it provides an excellent opportunity to design new lightweight materials on the basis of novel boron hydride building blocks. Realizing this potential requires an understanding of the electronic structure, chemical bonding, and stability of neutral and anionic B_xH_y clusters with variable stoichiometry. While a large number of boron hydride compounds are known, …

Analysis Of Ammonia And Volatile Organic Amine Emissions In A Confined Poultry Facility, Hanh Hong Thi Dinh

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The National Air Emission Monitoring Study (NAEMS) project was funded by the Agricultural Air Research Council (AARC) to evaluate agricultural emissions nationwide. Utah State University (USU) is conducting a parallel study on agricultural emissions at a Cache Valley poultry facility. As part of this parallel study, samples of animal feed, eggs and animal waste were collected weekly from three manure barns (designated: manure barn, barn 4 - manure belt and barn 5 - high rise) from May 2008 to November 2009.

These samples were analyzed to determine ammonia content, total Kjeldahl nitrogen content and ammonia emission. The yearly average calculated …

Diffusion Monte Carlo Studies Of Quantum Solvation: Finding Nodal Functions Of Wavefunctions Using A Genetic Algorithm, Christina Hansen Howell

Undergraduate Honors Capstone Projects

Solvation is important in many chemical reactions since most reactions occur in solution. Recently, progress has been made using helium-4 nanodroplets as the solvent at temperatures close to absolute zero. Because helium-4 is a superfluid it solvates dissolved molecules much differently that does a conventional solvent. This opens up the possibility of performing new types of chemistry in the superfluid environment. However, the nature of the interaction of the dissolved species with the solvent remains poorly understood. The basic question to be answered in this project is: how does the quantum solvent perturb the rotational dynamics of the solute particles? …

Field And Smog Chamber Studies Of Agricultural Emissions And Reaction Products, Derek J. Price

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Agricultural emissions are an important contributor to atmospheric aerosol. These emissions include nitrogen containing organic compounds, primarily as amines, which have not been well investigated to date. Although there have been several studies that have looked at the emission of gas phase amines, there are only a few studies that have focused on ambient amine-based aerosol. There have also only been a handful of smog chamber studies that have investigated amine aerosol chemistry. Kinetic studies have looked at the reactions of amines with OH and ozone. However, amine reactions with nitrate radical (NO₃) are not well understood. Several …

A Synthetic Biological Engineering Approach To Secretion- Based Recovery Of Polyhydroxyalkanoates And Other Cellular Products, Elisabeth Linton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The costs associated with cellular product recovery commonly account for as much as 80% of the total production expense. As a specific example, significant recovery costs limit commercial use of polyhydroxyalkanoates (PHA), which comprise a class of microbially-accumulated polyesters. PHAs are biodegradable compounds that are of interest as a sustainable alternative to petrochemically-derived plastics. Secretion-based recovery of PHAs was studied to decrease PHA production costs. Type I and II secretory pathways are commonly used for the translocation of recombinant proteins out of the cytoplasm of E. coli. Proteins were targeted for translocation using four signal peptides (HlyA, TorA, GeneIII, …

Pulsed-Laser Excited Photothermal Study Of Glasses And Nanoliter Cylindrical Sample Cell Based On Thermal Lens Spectroscopy, Prakash Raj Joshi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research in this dissertation presents Pulsed-Laser Excited photothermal studies of optical glasses and cylindrical sample cell.

First, a study of a photothermal lens experiment and the finite element analysis modeling for commercial colored glass filters is done. The ideal situation of a semiinfinite cylinder approximate model used to describe the photothermal lens experiment requires the boundary condition that there is no transfer of heat from the glass to surrounding when the glass is excited with a laser. The finite element analysis modeling for photothermal signal with coupling heat with surrounding shows the thermal heat transfer between the glass surface …

Library Synthesis Of Anticancer And Antibacterial Agents Via Azide Chemistry, Jianjun Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Various anticancer and antibacterial agents have been synthesized via azide chemistry by taking advantage of carbohydrate. Starting from the synthesis of 14 glycosyl azides, a library of carbohydrate-oxazolidinone conjugates and a library of carbohydrate-cyclopamine conjugates with biological interests were synthesized based on a highly efficient "click reaction" assisted by sonication. Some of the conjugates have improved solubility and enhanced anticancer activity.

A library of neomycin B derivatives with various modifications at the 5" position has been synthesized. Two leads exhibit prominent activity against both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Antibacterial activities were measured when combined with other …

Dynamics Of Van Der Waals Clusters: Theoretical And Computational Studies, Jordan Aleksander Ramilowski

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The marriage of two very powerful techniques – cryogenic matrix isolation spectroscopy and seeded supersonic molecular beams – has led to the development of a novel type of cryogenic matrix isolation spectroscopy in ultracold, near 0 K, He droplets. The technique known as helium nanodroplet isolation (HENDI) has seen tremendeous experimental interest over the past 20 years; this in turn has resulted in the availability of spectroscopic data for many molecules and clusters embedded in He clusters. The experimental findings have motivated a large number of theoretical calculations. This dissertation focuses on theoretical and computational studies of the rotational dynamics …

An Entrepreneurial Approach To Librarianship, Flora Shrode, Jennifer Duncan, Wendy Holliday

Library Faculty & Staff Publications

Librarians from Utah State University explain recent efforts to encourage subject librarians to take a more holistic view of their roles. We are shifting from a traditional emphasis primarily on collection development and refocusing on natural connections between collections, instruction, liaison, and reference service. The poster provides background about Utah State University’s situation and explains our approach to analyzing local needs and culture to inform development of a new organizational structure. We describe our vision of subject librarianship, the process by which we assessed librarians’ ideas and goals for performing as subject librarians, and the actions we are taking to …

Neuraminidase Activity Of Influenza Virus Strains That Differ In The Ability To Cause Disease, Benjamin Hanks Brown, Bart Tarbet

Browse All Undergraduate research

Influenza viruses are classified based on their surface glycoproteins: hemagglutinin and neuraminidase.  Hemagglutinin (HA) is responsible for binding to the host cell, while neuraminidase (NA) facilitates escape of newly formed virus particles. These studies determined the NA activity of three subtypes of influenza A virus that differ in their ability to cause disease in mice:  influenza A/NWS/33 (H1N1), influenza A/Victoria/3/75 (H3N2), and influenza A/Duck/MN/1525/81 (H5N1).  Chemiluminescent quantitation of NA activity in equal amounts of each virus was determined in three replicate experiments.  Results indicate that N1 virus subtypes have higher NA activity than do N2 subtypes.  In addition, the NA …

Geometry And Electronic Structure Of Doped Clusters Via The Coalescence Kick Method, Boris Averkiev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Developing chemical bonding models in clusters is one of the most challenging tasks of modern theoretical chemistry. There are two reasons for this. The first one is that clusters are relatively new objects in chemistry and have been extensively studied since the middle of the 20th century. The second reason is that clusters require high-level quantum-chemical calculations; while for many classical molecules their geometry and properties can be reasonably predicted by simpler methods.

The aim of this dissertation was to study doped clusters and explain their chemical bonding. The research was focused on three classes of compounds: aluminum clusters doped …

Subcutaneous Administration Of Tc007 Reduces Disease Severity In An Animal Model Of Sma, Virginia B. Mattis, Marina Y. Fosso, Cheng-Wei Tom Chang, Christian L. Lorson

Chemistry and Biochemistry Faculty Publications

Background Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the …

Detecting Organic Molecules On The Surface Of Inorganic Dust Particles Using Aerosol Mass Spectrometry, Sileola B. Akinsiku

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Detection of organic molecules present on the surface of dust particles is important in homeland security, agriculture, and several other applications. The research presented reports the ability of the aerosol mass spectrometer (AMS) to detect molecules on the surface of dust particles without detecting the particle core.

Experiments were carried out to detect semi-volatile organic compounds adsorbed onto the surface of particulates without interference from the dust particle core. Methyl salicylate, oleic acid, and organophosphorus pesticides such as Malathion were detected on the surface of particles representative of dust-type materials. Zeolite powders were used as aerosol support, representative of a …

Carbohydrate Derivatives In Antibiotics Research, Yi Liang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In this study, we investigated the potential applications of carbohydrates in the development of new antibiotics. To tackle the problem of multidrug-resistant variants of M. tuberculosis (MDR-TB), we investigated the biosynthesis pathways of trehalose, which has contributed to significant drug resistance. Some new methods were developed for the synthesis of potential inhibitors (6-azido-trehalose and 6,6'-diazido-trehalose) that have been designed to imitate the intermediate molecule (trehalose 6-phosphate, TPP) of OtsA-OtsB pathway. At the same time, some new antibacterial agents based on trehalose have been synthesized. Members of the 1,2,3-triazole family have shown interesting biological properties. Steroid derivatives have been developed in …

Synthetic Studies Of Laulimalide Analogues, Ian Addison Mcalexander

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Chapter 1 provides some background information on the disease area of cancer and current modes of treatment. Chemotherapy treatment is discussed with a focus on the major cellular targets for these drugs: DNA and microtubules. For each target, classes of active compounds are described along with their mode of action. The microtubule stabilizing agent laulimalide is introduced and a case is made for analogue synthesis.

Chapter 2 describes our first generation efforts toward synthesis of des-methyl laulimalide. The target compound is divided into a northern and southern fragment with the synthesis of each fragment described. The preparation of landmark intermediates …

A Comparative Study Of The Structural Features And Kinetic Properties Of The Mofe And Vfe Proteins From Azotobacter Vinelandii, Miguel Alejandro Pabon Sanclemente

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Biological nitrogen fixation is accomplished in the bacterium Azotobacter vinelandii by means of three metalloenzymes: The molybdenum, vanadium, and iron-only nitrogenase. The knowledge regarding biological nitrogen fixation has come from studies on the Mo-dependent reaction. However, the V- and Fe-only-dependent reduction of nitrogen remains largely unknown.

By using homology modeling techniques, the protein folds that contain the metal cluster active sites for the V- and Fe-only nitrogenases were constructed. The models uncovered similarities and differences existing among the nitrogenases regarding the identity of the amino acid residues lining pivotal structural features for the correct functioning of the proteins. These differences, …

Sonication Assisted Synthesis Of Oligomannosides, Christabel Tomla Tanifum

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Oligomannosides prevalently exist as cell surface antigens. They play important roles in diseases such as viral infection and cancer, and they have been shown to be useful as candidates for vaccines. HIV, one of the most devastating modern diseases, has a high content of mannose sugars on its envelope glycoprotein gp120. Oligomannosides of the HIV virus, also called Man9, which are found on the glycoprotein gp120, have been shown to play a protective role for the HIV virus, shielding highly conserved protein domains of gp120 from proteolytic attacks. Thus gp120 plays an important role in HIV infection of cells, being …

Liposomes Recruit Ipac To The Shigella Flexneri Type Iii Secretion Apparatus Needle As A Final Step In Secretion Induction, C. R. Epler, Nicholas E. Dickenson, A. J. Olive, W. L. Picking, W. D. Picking

Chemistry and Biochemistry Faculty Publications

Shigella flexneri contact with enterocytes induces a burst of protein secretion via its type III secretion apparatus (TTSA) as an initial step in cellular invasion. We have previously reported that IpaD is positioned at the TTSA needle tip (M. Espina et al., Infect. Immuno. 74:4391-4400, 2006). From this position, IpaD senses small molecules in the environment to control the presentation of IpaB to the needle tip. This step occurs without type III secretion induction or IpaC recruitment to the S. flexneri surface. IpaC is then transported to the S. flexneri surface when target cell lipids are added, and this event …

Analysis Of Chemical Bonding In Clusters By Means Of The Adaptive Natural Density Partitioning, Dmitry Yu Zubarev

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Models of chemical bonding are essential for contemporary chemistry. Even the explosive development of the computational resources including, both hardware and software, cannot eliminate necessity of compact, intuitive, and efficient methods of representing chemically relevant information. The Lewis model of chemical bonding, which was proposed eleven years before the formulation of quantum theory and preserves its pivotal role in chemical education and research for more than ninety years, is a vivid example of such a tool. As chemistry shifts to the nanoscale, it is becoming obvious that a certain shift of the paradigms of chemical bonding is inescapable. For example, …

Pulse-Laser Infrared Photothermal Spectrometry Of Condensed-Phase Aerosols Based On Photothermal Deflection Spectroscopy, Oluwatosin Olubunmi Dada

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research reported in this dissertation is aimed at development of photothermal deflection detector that is consistent with constraints imposed by aerosols sampling and analysis. The main objectives of this project are: 1) the design and evaluation of initial apparatus prototypes and 2) a test of the prototype apparatus with surrogate substances using conventional mid-infrared gas lasers.

Experimental evaluation of reduced size photothermal apparatus is first performed with gaseous samples. Analysis of trichlorofluoromethane (CFC-11) and ethanol vapors is performed with both conventional large apparatus and the prototype small apparatus. Comparison studies in terms of photothermal signal from both apparatuses are …

Synthetic Complexes Of Relevance To Ni(Ii)-Containing Enzymes, Katarzyna Rudzka

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The work outlined herein presents an investigation of synthetic model complexes of relevance to the active sites of Ni(II)-containing enzymes, particularly urease, glyoxalase I, and acireductone dioxygenase. The research focuses on studying the structural and reactivity features of nickel complexes with biologically relevant substrates. The anion of acetohydroxamic acid is a well-known inhibitor of urease enzymes, including those isolated from Klebsiella aerogenes and Bacillus pasteurii. A precursor to the acetohydroxamate coordination in ureases is proposed to be an interaction between Ni(II) and acetohydroxamic acid. By using a novel supporting chelate ligand capable of secondary hydrogen bonding interactions a novel …

Sources And Source Processes Of Organic Nitrogen Aerosols In The Atmosphere, Mark E. Erupe

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The research in this dissertation explored the sources and chemistry of organic nitrogen aerosols in the atmosphere. Two approaches were employed: field measurements and laboratory experiments. In order to characterize atmospheric aerosol, two ambient studies were conducted in Cache Valley in Northern Utah during strong winter inversions of 2004 and 2005. The economy of this region is heavily dependent on agriculture. There is also a fast growing urban population. Urban and agricultural emissions, aided by the valley geography and meteorology, led to high concentrations of fine particles that often exceeded the national ambient air quality standards. Aerosol composition was dominated …

Characterization Of Power Induced Heating And Damage In Fiber Optic Probes For Near-Field Scanning Optical Microscopy, Nicholas E. Dickenson, E. S. Erickson, O. L. Mooren, R. C. Dunn

Chemistry and Biochemistry Faculty Publications

Tip-induced sample heating in near-field scanning optical microscopy (NSOM) is studied for fiber optic probes fabricated using the chemical etching technique. To characterize sample heating from etched NSOM probes, the spectra of a thermochromic polymer sample are measured as a function of probe output power, as was previously reported for pulled NSOM probes. The results reveal that sample heating increases rapidly to ~55–60°C as output powers reach ~50 nW. At higher output powers, the sample heating remains approximately constant up to the maximum power studied of ~450 nW. The sample heating profiles measured for etched NSOM probes are consistent with …

Oxidative Damage Caused By Iron Loading Into Ferritin, Talina Christensen Watts

Undergraduate Honors Capstone Projects

Ferritin is the iron storage protein found in humans, animals, plants, fungi and bacteria. We are interested in how iron is loaded and stored in mammalian ferritin. Ferrous iron must be oxidized to ferric iron in order to be stored in ferritin. It is generally believed that ferritin does the loading itself, dependant upon a "ferroxidase activity." Oxidation of iron can result in the production of the hydroxyl radical which can cause oxidative damage to surrounding proteins and other biomolecules. An indicator of oxidative damage to proteins is the formation of carbonyl groups. Using only the H subunit of human …

Aldol Reactions: E-Enolates And Anti-Selectivity, Matthew Grant Anderson

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

A common structural motif in complicated natural product molecules is an alkyl group at an alpha position to a carbonyl and an alcohol at the beta position anti to each other. This arrangement occurs in bioactive molecules that are important for medical research such as spongistatin A at the C15-C16 position and in (-)-baconipyrone C at C12-C13. Bioactive molecules such as these generally occur in such a low concentration in the organism in which they originate that deriving them from the natural source for research is not practical so efficient syntheses are sought. Reactions that produce 1,2 syn aldol products …

Genetic Analysis Of Acetone Carboxylase In Azotobacter Vinelandii, Jessica Gardner

Undergraduate Honors Capstone Projects

Acetone carboxylase, an inducible multimeric enzyme found in several bacteria, catalyzes the carboxylation of acetone to produce acetoacetate. This is an important reaction for the bacteria because, upon addition of coenzyme A, the acetoacetate can be converted to acetyl-CoA, a common metabolic intermediate. Azotobacter vinelandii, one of the bacteria that produces acetone carboxylase, has two different genes encoding this enzyme. We knocked out the first of these by disrupting it with a kanamycin cassette to help us understand the function of the second gene. Knocking out the gene will also make possible the use of site-directed mutagenesis to further study …