Organic Chemistry Commons^™

Modeling The Condensed-Phase Behavior Of Π-Conjugated Polymers, Walker Mask

Theses and Dissertations--Chemistry

It is well established that the morphology and physical properties of an organic semiconducting (OSC) material regulate its electronic properties. However, structure-function relationships remain difficult to describe in polymer-based OSC, which are of particular interest due to their robust mechanical properties. If relationships among the molecular and bulk levels of structure can be found, they can aid in the design of improved materials. To explore and detail important structure-function relationships in polymer-based OSC, this work employs molecular dynamics (MD) simulations to study various π-conjugated polymers in different environments. Two independent investigations are discussed in this work. One investigation examines how …

Development Of Synthetic Methodologies Of Nucleophile-Electrophile Chemistry, Michael R. Stentzel

Graduate Research Theses & Dissertations

The work outlined in this dissertation describes the development of synthetic methodologies utilizing a wide electrophilicity range of substrates towards the synthesis of new compounds. Substitution, addition, and superelectrophilic chemistry are powerful tools to afford potentially important compounds. These concepts are summarized in chapter 1.

Chapter 2 describes the capture of superacid catalyzed fluorenyl cations with nitriles (Ritter reaction) and alcohols. Optimization of reaction conditions and extensive scope studies were performed.

In chapter 3, the Michael addition of organometallic reagents with N-heterocyclic substituted olefins is explored. The nucleophilic carbanion intermediate species is shown to have reactivity towards strong electrophiles. With …

The Design, Synthesis, And Evaluation Of Inhibitors Of The Ispf Enzyme In The Mep Pathway, Christopher G. Stewart

Graduate Research Theses & Dissertations

Isoprenoids are a class of over 50,000 compounds that serve as key precursors for many compounds in plants and animals. These compounds play critical roles in many biological functions such as cellular growth, respiration, and go on to form critical compounds such as steroids and vitamins. Despite their overall necessity to life their biosynthesis only follows two synthetic pathways. These pathways are the Mevalonic Acid (MVA) Pathway and the 2-C-Methyl-D-Erythritol-4-Phosphate (MEP) Pathway also known as the non-mevalonate pathway. The MVA pathway is found primarily in humans and some higher plants while the MEP pathway is found in bacteria and some …

Ibuprofen As A Probe Of Lipid Metabolism, Jose Antonio Rosales

Open Access Theses & Dissertations

The hypothesis that deracemization of racemic ibuprofen (IBU) occurs via the enolization of a Candida rugosa lipase (CRL)-ibuprofen ester (Scheme 1.6.2) was disproven by reacting racemic IBU under the conditions that were used to deracemize ibuprofen methyl ester (IME), namely pH 7.6. At pH 7.6, IME through IBU butyl esters were not formed in-situ and racemic IBU was not deracemized by reacting the corresponding primary alcohol with racemic IBU in the presence of CRL.

At pH 7.6, hexyl through dodecyl IBU esters were formed in-situ by reacting the corresponding primary alcohol with racemic IBU in the presence of CRL. The …

Metaproteomics Reveal That Rapid Perturbations In Organic Matter Prioritize Functional Restructuring Over Taxonomy In Western Arctic Ocean Microbiomes, Molly P. Mikan, H. Rodger Harvey, Emma Timmins-Schiffman, Michael Riffle, Damon H. May, Ian Salter, William S. Noble, Brook L. Nunn

OES Faculty Publications

We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value < 0.01) in biological and molecular functions associated with carbon and nitrogen recycling were observed. Within the first day under both organic matter conditions, Bering Strait surface microbiomes increased protein synthesis, carbohydrate degradation, and cellular redox processes while decreasing C1 metabolism. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level. The dynamic responses of these two oceanic microbial communities have important implications for timing and magnitude of responses to organic perturbations within the Arctic Ocean and how community-level functions may forecast biogeochemical gradients in oceans.

Nucleophilic Phosphine Addition: Exploration Of Novel Alkyne Transformations, Brett Pierce

Murray State Theses and Dissertations

Nucleophilic phosphine catalysis has demonstrated its value in synthetic chemistry by allowing for mild carbon-carbon bond formation. Many phosphine-catalyzed reactions with electron-deficient alkynes have been reported in recent years, leading to an array of valuable products. Stemming from this field of study, phosphines can also be utilized as mild chemoselective reductants for alkynes, resulting in the corresponding alkenes. Herein, a mild, stereoselective, phosphine-mediated partial reduction of alkynes to (E)- and (Z)-alkenes is described. Specifically, a general method for the partial reduction of ynoates to the corresponding (E)- and (Z)-enoate, …

One-Pot Enol Silane Formation-Mukaiyama Aldol Reactions: Crossed Aldehyde-Aldehyde Coupling, Thioester Substrates, And Reactions In Ester Solvents, C. Wade Downey, Grant J. Dixon, Jared A. Ingersoll, Claire A. Fuller, Kenneth W. Maccormac, Anna Takashima, Rohina Sediqui

Chemistry Faculty Publications

Trimethylsilyl trifluoromethanesulfonate (TMSOTf) and a trialkylamine base promote both in situ enol silane/silyl ketene acetal formation and Mukaiyama aldol addition reactions between a variety of reaction partners in a single reaction flask. Isolation of the required enol silane or silyl ketene acetal is not necessary. For example, crossed aldol reactions between α-disubstituted aldehydes and non-enolizable aldehydes yield b- hydroxy aldehydes in good yield. In a related reaction, the common laboratory solvent ethyl acetate functions as both an enolate precursor and a green reaction solvent. When thioesters are employed as enolate precursors, high yields for additions to non-enolizable aldehydes are routinely …

Avoiding Adverse Effects: New Ideas In Drug Discovery For Targeting Pparγ, Trey M. Patton

Graduate Student Theses, Dissertations, & Professional Papers

Peroxisome proliferator-activated receptor gamma (PPARγ) has been a drug target to treat type 2 diabetes for the last 20 years when rosiglitazone and pioglitazone were approved by the FDA in 1999. While effective at increasing insulin sensitivity, these drugs cause serious adverse effects due to their full agonist characteristics. For that reason, drug discovery efforts have attempted to reduce or prevent the amount of agonist character of new PPARγ targeting ligands. Unfortunately, there have been no new FDA approved drugs for the receptor. There is a need for new ideas to produce better quality pharmaceuticals that lessen the impact of …

Method Considerations For Compound Identification In Complex Mixtures Using Electrospray Ionization Ultrahigh Resolution Mass Spectrometry, Tyler Leverton

Dissertations, Master's Theses and Master's Reports

Biomass burning aerosols are highly complex organic mixtures of thousands of components with consequences for global climate. Complex mixture component identification requires accurate mass measurement capability to separate components on a milli-Dalton scale, frequently using ultrahigh resolution mass spectrometry with electrospray ionization. Certain sample preparations and the ionization process may introduce artifacts that obscure the composition of the sample. Two method considerations were explored using isotopically labeled ¹⁵NH₄OH and MeOH-d₃ to track artifact formation in biomass burning samples. Informatics techniques and a custom molecular formula assignment software were used to identify the isotopic atoms in artifact …

Towards The Discovery Of Oligonucleotide Cross-Linking Agents, Bhaskar Halami

Dissertations, Master's Theses and Master's Reports

Oligonucleotide cross-linking agents are expected to become a new class of antisense drugs. They function by first hybridizing with a complementary mRNA and then form a covalent bond to permanently link the mRNA to the oligonucleotide agent. Because of covalent cross-linking, this new class of antisense drugs are expected to have much higher potency than existing ones.

Some oligonucleotide cross-linking agents have appeared in the literature, but they have various drawbacks, which include slow cross-linking rate and reversible cross-linking. To address these problems, we designed a series of new cross-linking oligonucleotides with a range of different reactivities. These oligonucleotides were …

Near-Infrared Fluorescent Probes For Sensitive Determination Of Lysosomal & Mitochondrial Ph In Live Cells, Wafa Mazi

Dissertations, Master's Theses and Master's Reports

Varied intracellular pH levels are critical for various physiological processes such as enzymatic activity, cell proliferation and apoptosis, ion transport, and muscle contraction. Cellular compartments, like lysosomes, must retain an acidic environment (pH ~ 4.5) to activate hydrolytic enzymes necessary for the breakdown of large biomolecules. Another cellular organelle, the mitochondria, provides the cell with energy and must retain an alkalis environment (pH ~ 8.0) for proper function. Substantial lysosomal and mitochondrial pH deviation is associated with cellular dysfunction and disease. Therefore, the precise detection of lysosomal and mitochondrial pH is essential to provide a better understanding of cellular physiological …

Synthesis Of Oligodeoxynucleotides Containing Sensitive Electrophiles, Shahien Shahsavari

Dissertations, Master's Theses and Master's Reports

Oligodeoxynucleotides (ODNs) containing electrophilic groups are useful in many studies including antisense drug development and DNA/protein interaction. Due to the use of strong nucleophiles for cleavage and deprotection, traditional ODN synthesis methods are not suitable for their preparation. To solve this problem, a new ODN synthesis technology using the 1,3- dithiane-2-yl-methoxycarbonyl (Dmoc) function as protecting groups and linker has been developed. Furthermore, Dmoc-derivatives were developed to demonstrate the feasibility of the technology. The Dmoc and Dmoc derivative functions are stable under all ODN synthesis conditions using the phosphoramidite chemistry. Upon oxidation of the sulfides in them, because of the drastically …

Vibrational Analysis Of A Rate-Slowing Conformational Kinetic Isotope Effect, O. Maduka Ogba, Zichen Liu, Daniel J. O'Leary

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

An enthalpy-entropy approach to analyzing a rate-slowing conformational kinetic isotope effect (CKIE) in a deuterated doubly-bridged biaryl system is described. The computed isotope effect (kH/kD = 1.075, 368 K) agrees well with the measured value (kH/kD = 1.06, 368 K). The rateslowing (normal isotope effect) nature of the computed CKIE is shown to originate from a vibrational entropy contribution defined by the twenty lowest frequency normal modes in the ground state and transition state structures. This normal entropy contribution is offset by an inverse vibrational enthalpy contribution, which also arises from the twenty lowest frequency normal modes. Zero point vibrational …

Atom-Specific Activation In Co Oxidation, Simon Schreck, Elias Diesen, Jerry Larue, Hirohito Ogasawara, Kess Marks, Dennis Nordlund, Matthew Weston, Martin Beye, Filippo Cavalca, Fivos Perakis, Jonas Sellberg, André Eilert, Kyung Hwan Kim, Giacomo Coslovich, Ryan Coffee, Jacek Krzywinski, Alex Reid, Stefan Moeller, Alberto Lutman, Henrik Öström, Lars G. M. Pettersson, Anders Nilsson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We report on atom-specific activation of CO oxidation on Ru(0001) via resonant X-ray excitation. We show that resonant 1s core-level excitation of atomically adsorbed oxygen in the co-adsorbed phase of CO and oxygen directly drives CO oxidation. We separate this direct resonant channel from indirectly driven oxidation via X-ray induced substrate heating. Based on density functional theory calculations, we identify the valence-excited state created by the Auger decay as the driving electronic state for direct CO oxidation. We utilized the fresh-slice multi-pulse mode at the Linac Coherent Light Source that provided time-overlapped and 30 fs delayed pairs of soft …

Development And Thermodynamic Analysis Of An Integrated Mild/Partial Gasification Combined Cycle (Impgc) Under Green And Brown Field Conditions With And Without Carbon Capture, Henry A. Long Iii

LSU New Orleans Theses and Dissertations

Coal is a very prominent energy source in the world, but it is environmentally unattractive due to its high sulfur and ash content as well as its alleged contribution towards climate change, but it is affordable, abundant, and has high energy content. Thus, utilizing coal in a cleaner and more efficient way has become necessary. One promising clean coal technology involves fully gasifying coal into synthesis gas, cleaning it, and feeding it into a high-efficiency combined cycle, such as an Integrated Gasification Combined Cycle (IGCC). Inspired by the recent success of warn gas cleanup (WGCU), mild and partial gasification are …

Stabilized, Hybrid Solid-State Photocatalysts For Water Purification: Preparation, Properties And Performance Under Visible Light Irradiation, Karpagavalli Ramji

Seton Hall University Dissertations and Theses (ETDs)

Stabilized heterogeneous photocatalysts that use only solar light and air have been prepared and successfully employed to decontaminate water from organic pollutants. Organic dye pollutants present, for example in textile effluents, are one of the major sources of water pollution owing to their limited biodegradability, toxicity and potential carcinogenic risks. Before certifying water for public consumption, reuse in industries or for discharge in surface water the organic pollutants must be degraded, an effort that is energy intensive and currently requires complex methodologies. We report solid-state photocatalysts that use only visible light and air to treat wastewater. Perfluoroalkyl perfluoro-substituted zinc phthalocyanine …

Syntheses Of A Tin (Iv) Meso-Tetra(4-Pyridyl) Porphyrin Dichloride-Tetrachlorobis (Bipy)2 Ruthenium (Ii) Complex And Studies Of Photophysical Properties Of 1-Nitropyrene, Phillip Sharp

Electronic Theses and Dissertations

Development of a photosensitizer that can work in both aerobic and anaerobic environments would increase the robustness of the cancer treatment known as photodynamic therapy. The development of a photosensitizer was first attempted by synthesizing a tin (IV) meso-tetra (4-pyridyl) porphyrin dichloride-tetrachlorobis (Bipy)₂ ruthenium (II) complex. The synthesize of the tin porphyrin was done by a method from literature and had a percent error of 31.58 and 37.31 when comparing the theoretical percentages of carbon (55.39) and nitrogen (12.92) meaning that photosensitizer was not synthesized.

The second type of chromophore that was studied was 1-nitropyrene do determine if it …

Inequality, Rubber, And Thermodynamics In Indonesia, Ernest M. Oleksy

The Downtown Review: An Interdisciplinary Journal Written and Peer-Reviewed by Mandel Honors College Students at Cleveland State University

Intersectionality has led the charge in ensuring that workplace justice is assured to all people, irrespective of their identities. While intersectionality is a useful theory for explaining inequality, what must not be understated is the contributions that postcolonialism and the blue-collar working identity can have on harsh working conditions. Particularly, miners in Indonesia have had to work in very hostile environments where they are at-risk for sulfur poisoning as they mine for materials to vulcanize rubber. This article serves two purposes. The first is to call attention to how place can help explain the differential experiences of miners in the …

Extraction And Purification Of Biologically Active Metabolites From Rhodococcus Sp. Mtm3w5.2, Mohrah Alenazi

Electronic Theses and Dissertations

Rhodococcushas been recognized as a potential antibiotic producer. Recently, a strain of Rhodococcussp. MTM3W5.2 was isolated from a soil sample collected in Morristown, Tennessee and was found to produce an inhibitory compound which is active against other related species. The purpose of this research is to extract, purify and analyze the active metabolite. The compound was extracted from RM broth cultures and purified by preliminary fractionation of crude extract through a Sephadex LH-20 column. Further purification was completed using semi-preparative reversed phase column chromatography. Final purification was obtained using multiple rounds of an analytical C18 HPLC column. Based …

Synthesis Of Dicamba Glucosides For The Study Of Environmental Dicamba Drift Effects On Soybeans, Holly Wallace

Graduate Theses and Dissertations

The most popular herbicide used for weed control has been glyphosate for many years in the Midwestern United States. Plants have begun to develop a resistance to glyphosate due to over use of the herbicide. This herbicide resistance has pushed farmers to turn to alternative herbicides such as dicamba and 2,4-D. Recently agrochemical companies have developed genetically modified crops that are resistant to herbicides such as dicamba. These modified crops allow farmers to spray their fields with dicamba without fear of crop damage. Farmers of non-genetically modified crops, however, suffer damage and loss of yield from herbicide drift effects of …