Chemistry Commons^™

A Td-Dft Study Of The Absorption Spectra Of Mono-Nitrated Fluoranthenes [Abstract], Kefa Karimu Onchoke

Faculty Publications

No abstract provided.

Synthesis Of Fluorescent Molecules And Their Applications As Viscosity Sensors, Metal Ion Indicators, And Near-Infrared Probes, Mengyuan Wang

Electronic Theses and Dissertations

The primary focus of this dissertation is the development of novel fluorescent near-infrared molecules for various applications. In Chapter 1, a compound dU-BZ synthesized via Sonogashira coupling reaction methodology is described. A deoxyuridine building block was introduced to enhance hydrophilic properties and reduce toxicity, while an alkynylated benzothiazolium dye was incorporated for near-IR emission and reduce photodamage and phototoxicity that is characteristic of common fluorphores that are excited by UV or visible light. A 30-fold enhancement of fluorescence intensity of dU-BZ was achieved in a viscous environment. Values of fluorescence quantum yields in 99% glycerol/1% methanol (v/v) of varying temperature …

Analysis Of A Chemical Model System Leading To Chiral Symmetry Breaking: Implications For The Evolution Of Homochirality, Brandy N. Morneau, Jaclyn M. Kubala, Carl Barratt, Pauline Schwartz

Chemistry and Chemical Engineering Faculty Publications

Explaining the evolution of a predominantly homochiral environment on the early Earth remains an outstanding challenge in chemistry. We explore here the mathematical features of a simple chemical model system that simulates chiral symmetry breaking and amplification towards homochirality. The model simulates the reaction of a prochiral molecule to yield enantiomers via interaction with an achiral surface. Kinetically, the reactions and rate constants are chosen so as to treat the two enantiomeric forms symmetrically. The system, however, incorporates a mechanism whereby a random event might trigger chiral symmetry breaking and the formation of a dominant enantiomer; the non-linear dynamics of …

Complexation Of N So2 Molecules (N=1,2,3) With Formaldehyde And Thioformaldehyde, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Ab initio and density functional theory calculations are used to examine complexes formed between H2CO and H2CS with 1, 2, and 3 molecules of SO2. The nature of the interactions is probed by a variety of means, including electrostatic potentials, natural bond orbital, atoms in molecules, energy decomposition, and electron density redistribution maps. The dimers are relatively strongly bound, with interaction energies exceeding 5 kcal/mol. The structures are cyclic, containing both a O/S⋯S chalcogen bond and a CH⋯O H-bond. Addition of a second SO2 molecule leads to a variety of heterotrimer structures, most of which resemble the original dimer, where …

Complexes Containing Co2 And So2. Mixed Dimers, Trimers And Tetramers, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Mixed dimers, trimers and tetramers composed of SO2 and CO2 molecules are examined by ab initio calculations to identify all minimum energy structures. While AIM formalism leads to the idea of a pair of C···O bonds in the most stable heterodimer, bound by some 2 kcal mol(-1), NBO analysis describes the bonding in terms of charge transfer from O lone pairs of SO2 to the CO π* antibonding orbitals. The second minimum on the surface, just slightly less stable, is described by AIM as containing a single O···O chalcogen bond. The NBO picture is that of two transfers in opposite …

Interaction Between Temozolomide And Water: Preferred Binding Sites, O. E. Kasende, A. Matondo, M. Muzomwe, J. T. Muya, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Computational methods are used to predict the most favorable site of temozolomide towards attack by a water molecule. The energetics of the various complexes are presented as well as their geometries, including perturbations of each subunit caused by the presence of the other. Molecular electrostatic potential and Natural Bond Orbital (NBO) data are used to understand the interactions which conclude the terminal amide group is the preferred attack site where water can act as simultaneous proton donor and acceptor. Other potential proton acceptor N atoms within the aromatic ring structure represent weaker binding sites. Some of the less strongly bound …

Substituent Effects In The Noncovalent Bonding Of So2 To Molecules Containing A Carbonyl Group. The Dominating Role Of The Chalcogen Bond, L. M. Azofra, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The SO2 molecule is paired with a number of carbonyl-containing molecules, and the properties of the resulting complexes are calculated by high-level ab initio theory. The global minimum of each pair is held together primarily by a S···O chalcogen bond wherein the lone pairs of the carbonyl O transfer charge to the π* antibonding SO orbital, supplemented by smaller contributions from weak CH···O H-bonds. The binding energies vary between 4.2 and 8.6 kcal/mol, competitive with even some of the stronger noncovalent forces such as H-bonds and halogen bonds. The geometrical arrangement places the carbonyl O atom above the plane of …

An Exploration Of The Ozone Dimer Potential Energy Surface, L. M. Azofra, I. Alkorta, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

The (O3)2 dimer potential energy surface is thoroughly explored at the ab initio CCSD(T) computational level. Five minima are characterized with binding energies between 0.35 and 2.24 kcal/mol. The most stable may be characterized as slipped parallel, with the two O3 monomers situated in parallel planes. Partitioning of the interaction energy points to dispersion and exchange as the prime contributors to the stability, with varying contributions from electrostatic energy, which is repulsive in one case. Atoms in Molecules analysis of the wavefunction presents specific O⋯O bonding interactions, whose number is related to the overall stability of each dimer. All internal …

Intrinsic Delocalization During The Decay Of Excitons In Polymeric Solar Cells, Thomas George, W. Chen, D. Jiang, R. Chen, S. Li

Chemistry & Biochemistry Faculty Works

In bulk heterojunction polymer solar cells, external photoexcitation results in localized excitons in the polymer chain. After hot exciton formation and subsequent relaxation, the dipole moment drives the electron to partially transfer to extended orbitals from the original localized ones, leading to self-delocalization. Based on the dynamic fluorescence spectra, the delocalization of excitons is revealed to be an intrinsic property dominated by exciton decay, acting as a bridge for the exciton to diffuse in the polymeric solar cell. The modification of the dipole moment enhances the efficiency of polymer solar cells.

Constructing Tailored Isoprenoid Products By Structure-Guided Modification Of Geranylgeranyl Reductase, Yan Kung, Ryan P. Mcandrew, Xinkai Xie, Charlie C. Liu, Jose H. Pereira, Paul D. Adams, Jay D. Keasling

Chemistry Faculty Research and Scholarship

The archaeal enzyme geranylgeranyl reductase (GGR) catalyzes hydrogenation of carbon-carbon double bonds to produce the saturated alkyl chains of the organism's unusual isoprenoid-derived cell membrane. Enzymatic reduction of isoprenoid double bonds is of considerable interest both to natural products researchers and to synthetic biologists interested in the microbial production of isoprenoid drug or biofuel molecules. Here we present crystal structures of GGR from Sulfolobus acidocaldarius, including the structure of GGR bound to geranylgeranyl pyrophosphate (GGPP). The structures are presented alongside activity data that depict the sequential reduction of GGPP to H(6)GGPP via the intermediates H(2)GGPP and H(4)GGPP. We then modified …

Nanoconfined Water Under Electric Field At Constant Chemical Potential Undergoes Electrostriction, Davide Vanzo, D. Bratko, Alenka Luzar

Chemistry Publications

Electric control of nanopore permeation by water and solutions enables gating in membrane ion channels and can be exploited for transient surface tuning of rugged substrates, to regulate capillary permeability in nanofluidics, and to facilitate energy absorption in porous hydrophobic media. Studies of capillary effects, enhanced by miniaturization, present experimental challenges in the nanoscale regime thus making molecular simulations an important complement to direct measurement. In a molecular dynamics (MD) simulation, exchange ofwater between the pores and environment requires modeling of coexisting confined and bulk phases, with confined water under the field maintaining equilibrium with the unperturbed environment. In the …

Proton-Bound Dimers Of Nitrogen Heterocyclic Molecules: Substituent Effects On The Structures And Binding Energies Of Homodimers Of Diazine, Triazine, And Fluoropyridine, Isaac K. Attah, Sean P. Platt, Michael Mautner, M. S. El-Shall, Saadullah G. Aziz, Abdulrahman O. Alyoubi

Chemistry Publications

The bonding energies of proton-bound homodimers BH⁺B were measured by ion mobilityequilibrium studies and calculated at the DFT B3LYP/6-311++G^{* *} level, for a series of nitrogen heterocyclic molecules (B) with electron-withdrawing in-ring N and on-ring F substituents. The binding energies (ΔH°dissoc) of the proton-bound dimers (BH⁺B) vary significantly, from 29.7 to 18.1 kcal/mol, decreasing linearly with decreasing the proton affinity of the monomer (B). This trend differs significantly from the constant binding energies of most homodimers of other organic nitrogen and oxygen bases. The experimentally measured ΔH°dissoc for (1,3-diazine)2H⁺, i.e., (pyrimidine)2H⁺ and …

Unconventional Hydrogen Bonding To Organic Ions In The Gas Phase: Stepwise Association Of Hydrogen Cyanide With The Pyridine And Pyrimidine Radical Cations And Protonated Pyridine, Ahmed M. Hamid, M. Samy El-Shall, Rifaat Hilal, Shaaban Elroby, Saadullah G. Aziz

Chemistry Publications

Equilibrium thermochemical measurements using the ion mobility drift cell technique have been utilized to investigate the binding energies and entropy changes for the stepwise association of HCN molecules with the pyridine and pyrimidine radical cations forming the C5H5N^+· (HCN)nand C4H4N2 ^+· (HCN)n clusters, respectively, with n = 1–4. For comparison, the binding of 1–4 HCN molecules to the protonated pyridine C5H5NH⁺(HCN)n has also been investigated. The binding energies of HCN to the pyridine and pyrimidine radical cations are nearly equal (11.4 and 12.0 kcal/mol, respectively) but weaker than the HCN binding to the protonated pyridine (14.0 kcal/mol). …

Structural Dynamics Of A Single-Stranded Rna–Helix Junction Using Nmr, Catherine D. Eichhorn, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for …

Combining Experiment And Theory To Elucidate The Role Of Supercritical Water In Sulfide Decomposition, Yuko Kida, Caleb A. Class, Anthony J. Concepcion, Michael T. Timko, William H Green

Scholarship and Professional Work – COPHS

The cleavage of C–S linkages plays a key role in fuel processing and organic geochemistry. Water is known to affect these processes, and several hypotheses have been proposed, but the mechanism has been elusive. Here we use both experiment and theory to demonstrate that supercritical water reacts with intermediates formed during alkyl sulfide decomposition. During hexyl sulfide decomposition in supercritical water, pentane and CO + CO2 were detected in addition to the expected six carbon products. A multi-step reaction sequence for hexyl sulfide reacting with supercritical water is proposed which explains the surprising products, and quantum chemical calculations provide quantitative …

Applying Green Chemistry Principles In The Electrophilic Bromination Of Indole-3-Acetic Acid, Kyle Murphy

Undergraduate Review

The goals of green chemistry are to reduce or eliminate the use of hazardous reagents, prevent the synthesis of toxic products and byproducts, and improve the overall efficiency of chemical reactions. Green chemistry is incredibly important today as chemical products are produced and used around the world, resulting in the use and generation of hazardous chemicals, and unintended consequences to human health and the environment. Figure 1 shows the 12 Principles of Green Chemistry1, developed by Paul Anastas and John Warner, which provide the framework for a sustainable future in the design of more efficient technologies to produce consumer products …

Research Brief: Applying Green Chemistry Principles Towards The Sustainable Synthesis Of Biodiesel From Waste Vegetable Oil, Brandon Ackley

Undergraduate Review

In 2011, the U.S. consumed over 18 million barrels per day of refined petroleum products and biofuels; almost 22% of global petroleum consumption. This includes oil used for transportation, electricity, and production of consumer products. More than half of this oil was imported from foreign countries, and in his 2006 State of the Union Address President Bush warned that, “We have a serious problem, America is addicted to oil, which is often imported from unstable parts of the world”. With the need for new energy sources more apparent than ever, serious research is needed to further the advancement of alternative …

Field Measurements Of Trace Gases Emitted By Prescribed Fires In Southeastern Us Pine Forests Using An Open-Path Ftir System, S. K. Akagi, I. R. Burling, A. Mendoza, T. J. Johnson, M. Cameron, David W. T. Griffith, C. Paton-Walsh, D. R. Weise, J. Reardon, Robert Yokelson

Chemistry and Biochemistry Faculty Publications

We report trace-gas emission factors from three pine-understory prescribed fires in South Carolina, US measured during the fall of 2011. The fires were more intense than many prescribed burns because the fuels included mature pine stands not subjected to prescribed fire in decades that were lit following an extended drought. Emission factors were measured with a fixed open-path Fourier transform infrared (OP-FTIR) system that was deployed on the fire control lines. We compare these emission factors to those measured with a roving, point sampling, land-based FTIR and an airborne FTIR deployed on the same fires. We also compare to emission …

Aerosol Single Scattering Albedo Dependence On Biomass Combustion Efficiency: Laboratory And Field Studies, Shang Liu, Allison C. Aiken, Caleb Arata, Manvendra K. Dubey, C. Stockwell, Robert Yokelson, Elizabeth A. Stone, Thilina Jayarathne, Allen L. Robinson, Paul J. Demott, Sonia M. Kreidenweis

Chemistry and Biochemistry Faculty Publications

Single scattering albedo (ω) of fresh biomass burning (BB) aerosols produced from 92 controlled laboratory combustion experiments of 20 different woods and grasses was analyzed to determine the factors that control the variability in ω. Results show that ω varies strongly with fire-integrated modified combustion efficiency (MCE_FI)—higher MCE_FI results in lower ω values and greater spectral dependence of ω. A parameterization of ω as a function of MCE_FI for fresh BB aerosols is derived from the laboratory data and is evaluated by field observations from two wildfires. The parameterization suggests that MCE_FI explains 60% of …

The Periodical Winter 2014, Southern Adventist University

the Periodical – Chemistry Department Newsletter

Volume 1, issue 1 of the Periodical includes articles about Rhonda Scott's time as chair of the department, faculty news, a pictorial directory of 2014 graduates, an alumni spotlight, and Chemistry Club news.

The Role Of Platelets In Hyaluronan Degradation, Sami Albeiroti

ETD Archive

Following tissue injury, platelets rapidly interact with the exposed extracellular matrix (ECM) of blood vessel wall and the surrounding tissues. Hyaluronan (HA) is a major polysaccharide component of the ECM and plays a significant role in regulating inflammation. Human platelets can degrade HA from the surfaces of activated endothelial cells into fragments capable of inducing immune responses by monocytes. In addition, platelets contain the enzyme hyaluronidse-2 (HYAL2), one of two major hyaluronidases that digest HA in somatic tissues. The deposition of HA increases in the inflamed tissues in several inflammatory diseases, including Inflammatory Bowel Disease (IBD). This study provides evidence …

Hyaluronan Rafts On Airway Epithelial Cells, Amineh M. Abbadi

ETD Archive

Many cells, including murine airway epithelial cells, respond to a variety of inflammatory stimuli by synthesizing leukocyte-adhesive hyaluronan cables that remain attached to their cell surfaces. This study shows that air-liquid interface cultures of murine airway epithelial cells (AECs) also actively synthesize and release a majority of their HA onto their ciliated apical surfaces to form a heavy chain-hyaluronan (HC-HA) matrix in the absence of inflammatory stimuli. These matrices do not resemble the rope-like HA cables, but occur in distinct sheets, or rafts, that can capture and embed leukocytes from cell suspensions. The HC-HA modification involves the transfer of heavy …

Enzyme-Based Nitric Oxide Releasing Thin Films And Scaffolds, Mutha Merenna Nuwan Bhagya Gunasekera

ETD Archive

Nitric oxide synthase enzyme (NOS) embedded in thin films and scaffolds, when exposed to a solution of its substrate arginine, a source of reducing equivalents, and other required ingredients of the NOS reaction, can release fluxes of nitric oxide (NO). The latter is a molecule known to counteract platelet aggregation, and thus can prevent the thrombosis cascade on the surfaces of implantable medical devices. Therefore NO antithrombogenic regimens such as active coatings and embedded scaffolds have the potential to increase the lifespan of implantable biomaterials. Layer-by-layer electrostatic adsorption allows for assembly of multi-component protein/polyelectrolytes nanostructured films. Electrospun fiber matrices may …

Magnesium As A Regulator Of Hepatic Nadph In The Hepatocyte :;Prospective Roles Of Magnesium In Diabetes And Obesity Onset, Chesinta B. Voma

ETD Archive

No abstract provided.

The Role Of Rnase L In Thymic Homeostasis And Humoral Responses, Lin Zhang

ETD Archive

RNase L is highly expressed in the spleen, thymus, and multiple immune cells, suggesting that it may play an important role in the immune system against microbes. Previous studies in the lab have shown that deficiency of RNase L results in enlarged thymuses in mice at young age. However, relatively little is known about its influence on the thymic development and adaptive immunogenicity. The present Ph.D. study focuses on investigating the role of RNase L in the thymic homeostasis and humoral immune responses, thereby gaining new insights into the molecular aspects in thymocyte development, maturation and adaptive immunity.By using RNase …

Effects Of Shear Stress On The Distribution Of Kindlins In Endothelial Cells, Sidney V. Jones

ETD Archive

Endothelial cells (ECs) are exposed to changes in shear stress under a variety of physiological and pathological circumstances and respond by changing their shape, gene expression and cytoskeletal arrangement. Integrins are central mediators of these mechanotransduction responses of ECs and integrin function is in turn controlled by interaction of their short cytoplasmic tails with cytoplasmic binding partners. Recent studies have demonstrated the importance of the kindlin family members, known cytoplasmic tail binding proteins, as regulators of integrin function. Our lab has previously shown that kindlin-2 (K2) and kindlin-3 (K3) are both expressed and functionally significant for integrin mediated cellular events …

Precursors And Processes For The Growth Of Metallic First Row Transition Metal Films By Atomic Layer Deposition, Lakmal Charidu Kalutarage

Wayne State University Dissertations

As a result of the continuous miniaturization of microelectronics devices, atomic layer deposition (ALD) has gained much attention in the recent years. ALD allows the deposition of ultra-thin conformal films with accurate thickness control due to the self-limiting growth mechanism. The microelectronics industry requires the growth of metallic first row transition metal films by ALD. Due to the positive electrochemical potentials, the ALD growth of noble metal thin films has been well developed in the past. By contrast, the ALD growth of first row transition metal films remains poorly documented. The reasons for this scarcity include the lack of suitable …

Modulation Of Water-Exchange Rates Of Lanthanide(Iii)-Containing Complexes Using Polyethylene Glycol, Buddhima Nirodhi Siriwardena-Mahanama

Wayne State University Dissertations

MODULATION OF WATER-EXCHANGE RATES OF LANTHANIDE(III)-CONTAINING COMPLEXES USING POLYETHYLENE GLYCOL

by

BUDDHIMA N. SIRIWARDENA-MAHANAMA

May 2014

Advisor: Dr. Matthew J. Allen

Major: Chemistry

Degree: Doctor of Philosophy

A modular system of lanthanide(III)-containing polyethylene glycol (PEG) conjugates was synthesized and characterized to investigate the influence of length and density of PEG on water-exchange rates of lanthanide(III)-containing complexes. The water-exchange rates of lanthanide(III)-containing complexes contribute to the efficiency of these complexes as T₁-shortening and paramagnetic chemical exchange saturation transfer (PARACEST) contrast agents for magnetic resonance imaging (MRI). Because the mechanism of these two MRI methods is vastly different, there is …

Assembly And Function Of Macromolecular Complexes For Accurate Trna Aminoacylation In Helicobacter Pylori, Gayathri Niroshani Silva

Wayne State University Dissertations

ABSTRACT

ASSEMBLY AND FUNCTION OF MACROMOLECULAR COMPLEXES FOR ACCURATE TRNA AMINOACYLATION IN HELICOBACTER PYLORI

by

GAYATHRI SILVA

January 2014

Advisor: Dr. Tamara L. Hendrickson

Major: Chemistry (Biochemistry)

Degree: Doctor of Philosophy

Abstract

The aminoacylation of tRNA is a critical step in maintaining the accuracy of the genetic code. Many microorganisms are missing one or more aminoacyl tRNA synthetases (aaRSs) and rely on indirect pathways to produce certain aa–tRNAs. In Helicobacter pylori (H. pylori), the genes encoding both asparaginyl tRNA synthetase (AsnRS) and glutaminyl tRNA synthetase (GlnRS) are missing and the organism consequently relies on the indirect pathway for …

Evaluation Of Presynaptic Dopamine Dynamics After: Toluene Inhalation Or Trkb Receptor Activation, Aaron Kwaku Apawu

Wayne State University Dissertations

Dopamine (DA) neurons in the striatum mediate several functions of the brain and have been linked to a host of neurological disorders including Parkinson's disease and addiction, both of which occur as a result of dysfunction in the DA system. In the present study, our first objective was to understand how the striatal DA system adapts to acute and repeated administration of inhalant toluene. The use of toluene as inhalant, like other drugs of abuse, is known to perturb DA neurotransmission in the brain reward pathway. However, the exact mechanism underling toluene's influence on striatal DA neurotransmission is unknown. The …