Chemistry Commons^™

Analysis Of Beverages By Total Reflection X-Ray Fluorescence, Martina Schmeling

Chemistry: Faculty Publications and Other Works

In advance of the Denver X-Ray Conference, we asked leading scientists who will be speaking at the conference about current trends and advances in X-ray fluorescence and X-ray diffraction. Here, these investigators discuss their work to advance these techniques and the sample preparation for such analyses, in areas such as photonics for telecommunications, steel structures, metals in pharmaceuticals, and imaging.

Generating Enzyme And Radical‐Mediated Bisubstrates As Tools For Investigating Gcn5‐Related N‐Acetyltransferases, Cory T. Reidl, Karolina A. Majorek, Joseph Dang, David Tran, Kristen Jew, Melissa Law, Yasmine Payne, Wladek Minor, Daniel P. Becker, Misty L. Kuhn

Chemistry: Faculty Publications and Other Works

Gcn5‐related N‐acetyltransferases (GNATs) are found in all kingdoms of life and catalyze important acyl transfer reactions in diverse cellular processes. While many 3D structures of GNATs have been determined, most do not contain acceptor substrates in their active sites. To expand upon existing crystallographic strategies for improving acceptor‐bound GNAT structures, we synthesized peptide substrate analogs and reacted them with CoA in PA4794 protein crystals. We found two separate mechanisms for bisubstrate formation: (a) a novel X‐ray induced radical‐mediated alkylation of CoA with an alkene peptide and (b) direct alkylation of CoA with a halogenated peptide. Our approach is widely …

Allosteric Control Of Substrate Specificity Of The Escherichia Coli Adp-Glucose Pyrophosphorylase, Ana C. Ebrecht, Ligin Solamen, Benhamin L. Hill, Alberto A. Iglesias, Ken W. Olsen, Miguel A. Ballicora

Chemistry: Faculty Publications and Other Works

The substrate specificity of enzymes is crucial to control the fate of metabolites to different pathways. However, there is growing evidence that many enzymes can catalyze alternative reactions. This promiscuous behavior has important implications in protein evolution and the acquisition of new functions. The question is how the undesirable outcomes of in vivo promiscuity can be prevented. ADP-glucose pyrophosphorylase from Escherichia coli is an example of an enzyme that needs to select the correct substrate from a broad spectrum of alternatives. This selection will guide the flow of carbohydrate metabolism toward the synthesis of reserve polysaccharides. Here, we show that …

Plp And Gaba Trigger Gabr-Mediated Transcription Regulation In Bacillus Subtilis Via External Aldimine Formation, Rui Wu, Ruslan Sanishvili, Boris R. Belitsky, Jose I. Juncosa, Hoang V. Le, Helaina J. S. Lehrer, Michael Farley, Richard B. Silverman, Gregory A. Petsko, Dagmar Ringe, Dali Liu

Chemistry: Faculty Publications and Other Works

The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5′-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the “active site” in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, ( …

Monofluorophosphate Blocks Internal Polysaccharide Synthesis In Streptococcus Mutans, Miguel Ballicora, Ana M. Demonte, Conrad Naleway, Matias D. Asencion Diez, Alberto A. Iglesias

Chemistry: Faculty Publications and Other Works

Streptococcus mutans is the leading cause of dental caries worldwide by accumulating a glycogen-like internal polysaccharide (IPS) that contributes to cariogenicity when sugars are in excess. Sodium monofluorophosphate (MFP) is an active anticariogenic compound in toothpastes. Herein, we show that MFP inhibits (with an I_0.5 of 1.5 mM) the S. mutans ADP-glucose pyrophosphorylase (EC 2.7.7.27), which catalyzes the key step in IPS biosynthesis. Enzyme inhibition by MFP is similar to orthophosphate (Pi), except that the effect caused by MFP is not reverted by fructose-1,6-bisP, as occurs with Pi. Inhibition was correlated with a decrease in acidogenesis and IPS …

Heterocycles Via The Pd-Catalyzed Heterofunctionalization Of Alkylidenecyclopropanes, Phillip Roman Lazzara

Dissertations

Natural compounds are often used as inspiration for novel chemical structures that provide medicinal benefits to human health. The unique 3-dimentional structures of these molecules make the majority of them synthetic challenges for organic chemists. While there is great diversity among these molecules, many of these carbon-based compounds exhibit similar key structural features. One of the most common features amongst biologically active molecules is a rigid carbon ring bearing nitrogen or oxygen atoms, which are known as heterocycles. The structural rigidity of heterocycles helps properly align key interactions of the molecule with those of a specific protein, which causes the …

Mild Hydrofunctionalizations Of Olefins Using More Cost-Effective Metal Catalysts, Alexander James Villani-Gale

Dissertations

The focus of this dissertation is the study of alkene hydroaylation reactions. In the first chapter, a review of the relevant literature concerning zinc- and iron-catalyzed hydroarylation of unsaturated bonds is presented. In chapter two, the development of a zinc-catalyzed hydroarylation of alkenes is presented, which is quickly followed by a detailed investigation into the probable mechanism. Chapter three discusses the development of an iron/silver-catalyzed arene prenylation reaction, followed by the development of an iron/zinc-catalyzed arene prenylation reaction. The final section of chapter three discusses the adaptation of the iron/zinc-catalyzed arene prenylation into an undergraduate organic teaching laboratory.

Detection Of Unknown Emerging Contaminants In Natural Water Using Tandem Mass Spectrometry, Qian Wang

Dissertations

Recently, a great deal of concern has been given to the quality of drinking water. Lake Michigan is the drinking water source of Chicago area. It is very important that the quality of drinking water meets the standard setup by the EPA. However, there is a group of chemicals that are not being monitored regularly or are unknown to researchers and are the so-called emerging contaminants.

So the objective of this study is to using tandem-mass spectrometry to detect and identify emerging contaminants. Water samples were obtained along a few locations along the Chicago River and Lake Michigan. By using …

Chemically Accurate Simulation Of A Polyatomic Molecule-Metal Surface Reaction, Francesco Nattino, Davide Migliorini, Geert-Jan Kroes, Eric Dombrowski, Eric A. High High, Daniel Killelea, Arthur Utz

Chemistry: Faculty Publications and Other Works

Although important to heterogeneous catalysis, the ability to accurately model reactions of polyatomic molecules with metal surfaces has not kept pace with developments in gas phase dynamics. Partnering the specific reaction parameter (SRP) approach to density functional theory with ab initio molecular dynamics (AIMD) extends our ability to model reactions with metals with quantitative accuracy from only the lightest reactant, H2, to essentially all molecules. This is demonstrated with AIMD calculations on CHD3 + Ni(111) in which the SRP functional is fitted to supersonic beam experiments, and validated by showing that AIMD with the resulting functional reproduces initial-state selected sticking …

Thermally Selective Formation Of Subsurface Oxygen In Ag(111) And Consequent Surface Structure, Jonathan Derouin, Rachael G. Farber, Marie E. Turano, Erin V. Iski, Daniel Killelea

Chemistry: Faculty Publications and Other Works

A long-standing challenge in the study of heterogeneously catalyzed reactions on silver surfaces has been the determination of what oxygen species are of greatest chemical importance. This is due to the coexistence of several different surface phases on oxidized silver surfaces. A further complication is subsurface oxygen (Osub). Osub are O atoms absorbed into the near surface of a metal, and are expected to alter the surface in terms of chemistry and structure, but these effects have yet to be well characterized. We studied oxidized Ag(111) surfaces after exposure to gas-phase O atoms to determine how Osub is formed and …

Double-Stranded Water On Stepped Platinum Surfaces, Manuel J. Kolb, Rachael G. Farber, Jonathan Derouin, Cansin Badan, Federico Calle-Vallejo, Ludo B. F. Juurlink, Daniel Killelea, Marc T. M. Koper

Chemistry: Faculty Publications and Other Works

The interaction of platinum with water plays a key role in (electro)catalysis. Herein, we describe a combined theoretical and experimental study that resolves the preferred adsorption structure of water wetting the Pt(111)-step type with adjacent (111) terraces. Double stranded lines wet the step edge forming water tetragons with dissimilar hydrogen bonds within and between the lines. Our results qualitatively explain experimental observations of water desorption and impact our thinking of solvation at the Pt electrochemical interface.

Binding Of Transcription Factor Gabr To Dna Requires Recognition Of Dna Shape At A Location Distinct From Its Cognate Binding Site, Dali Liu, Walid A. Al-Zyoud, Robert Mg. Hynson, Lorraine A. Ganuelas, Adelle Cf. Coster, Anthony P. Duff, Matthew Ab. Baker, Alastair G. Stewart, Eleni Giannoulatou, Joshua Wk> Ho, Katharina Gaus, Lawrence K. Lee, Till Böcking

Chemistry: Faculty Publications and Other Works

Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one …

The Utilization Of Liquid Chromatography Tandem Mass Spectrometry And Related Techniques For The Analysis And Identification Of Emerging Contaminants In Aqueous Matrices, Matthew Reichert

Dissertations

Environmental pollutants can be found in many ecosystems and cover many different compound classes. The Environmental Protection Agency is responsible for monitoring and regulating several of these classes of compounds which daily enter the environment. However, there are still hundreds, if not thousands, of compounds present in the environment which have yet to be regulated or even identified. The discovery and identification of these unknown emerging pollutants is crucial for the prevention of potential human health risks and irreversible ecological damage.

The research presented is divided into two projects. The first part of this research investigates the disinfectant 3-Bromo-1-chloro-5,5-dimethylhydantoin, which …

Investigation Of Heavy Metals In Zebrafish Tissue By Total Reflection X-Ray Fluorescence, Martina Schmeling, E. Jamka, J. Arroyo, K. Niaz, T. Trinh

Chemistry: Faculty Publications and Other Works

Heavy metals are present in the environment, in many consumer products and can be found in food. Some heavy metals like zinc and copper are essential for enzymatic and metabolic function while others like lead and mercury are toxic and interfere with biological pathways. Zebrafish are a very popular model organism for monitoring toxicity of heavy metals and investigating vertebrate development. In this study we explore the possibility of using total reflection X-ray fluorescence spectrometry to analyze histological sections of zebrafish embryos after exposure to nickel and lead. A methacrylate resin embedding protocol and a paraffin embedding protocol were evaluated …

Atomic Oxygen Adsorption And Absorption On Rh(111) And Ag(111), Jonathan Derouin

Dissertations

A central question in the field of heterogeneous catalysis is how surface structure and subsurface species influence catalytic behavior. One key to answering that question is determining which surface structures and subsurface species are present under catalytically relevant conditions. This dissertation presents results of Auger electron spectroscopy, low energy electron diffraction, temperature programmed desorption, and scanning tunneling microscopy experiments on oxidized Rh(111) and Ag(111) crystals. Exposing Rh(111) to O2 produced a predominately (2 × 1) adlayer, but even after extended dosing, (2 × 2) domains were also present. Exposing Rh(111) to atomic oxygen yielded O coverages greater than 0.5 ML …

Development Of Folate Directed, Protein Based Photodynamic Therapy Agents, Rojenia Jones

Dissertations

To attack cancer cells in a specific manner, we have developed a folate-targeted, photodynamic therapy (PDT) agent. The folate (FA) and the chlorin e6 (Ce6) photosensitizer were attached to bovine serum albumin (BSA) using carbodiimide chemistry. Since over 50% of cancers overexpress folate receptors, FA-BSA-Ce6 can be taken up by them and is an effective PDT agent. Hela cells exposed to FA-BSA-Ce6 in the dark showed no cytotoxicity. Upon exposure to light, the conjugate was dose (time and concentration) dependent. Concentrations less than or equal to 2 µM were not effective at killing Hela cells but concentrations of at 5 …

Exploring Conditions For The Enhancement Of Acene Semiconductors Through The Use Of The Diels-Alder Reaction, Brittni Qualizza Qualizza

Dissertations

This dissertation demonstrates the application of SAMs to the surface of acene crystals, specifically of tetracene and rubrene, using the Diels-Alder reaction. The second chapter details preliminary reaction results and two analytical methods which were employed to confirm adsorption of the dienophile on the surface of single crystals, tetracene and rubrene. These were mass spectrometry and X-ray photoelectron spectroscopy (XPS). Mass spectrometry experiments distinguish the chemical identity of adduct on the crystals and also it discerned chemi- and physisorbed molecules from one another. XPS was used to prove face selectivity of the reaction by the detection of dichloromaleic anhydride. From …

Building And Optimizing A Spectroelectrochemical System For The Study Of Shewanella Putrefaciens, Jonathan Muscolino

Master's Theses

Shewanellaceae are among the most widely studied electroactive microorganisms. This study reports on Shewanella putrefaciens under anaerobic conditions during applied potential while monitored by spectroscopy. The attachment of the microbe Shewanella putrefaciens onto an indium tin oxide electrode was found to occur after 2 hr of +0.2 V applied potential. Microbial detachment occurred with a 5 mV/s scan rate cyclic voltammogram from +0.2 V to -0.5 V to +0.2 V. This was confirmed through use of a spectroelectrochemical apparatus utilizing a standard 3 electrode setup with evanescent wave spectroscopy.

An Analytical Method For Detecting Toxic Metal Cations Using Cyclotriveratrylene Derivative Capped Gold Nanoparticles, Zachary R. Osner, Richard C. Holz, Daniel P. Becker Ph.D.

Chemistry: Faculty Publications and Other Works

Cyclotriveratrylene-oxime (CTV-oxime) derivatives that terminate with a dithiolate linker were synthesized enabling the supramolecular scaffold to adhere to gold nanoparticles (AuNPs) with the bowl-shaped cavity of the CTV scaffold exposed for utilization in host–guest chemistry. Exposure of these CTV functionalized AuNPs to varying concentrations of di- and trivalent metal cations resulted in the formation of large CTV-AuNP polymeric clusters and an accompanying a shift in the plasmon resonance. These interactions between the CTV-AuNPs and the metal cations in solution provides proof-of-concept that supramolecular functionalized AuNPs can be used as a simple and straightforward, on-site detection system for toxic metal cations …

Metal-Free Tandem Beckmann–Electrophilic Aromatic Substitution Cascade Affording Diaryl Imines, Ketones, Amines, And Quinazolines, Samuel Sarsah, Marlon R. Lutz Jr., Kailyn Chichi Bobb, Daniel Becker

Chemistry: Faculty Publications and Other Works

A cascade reaction sequence involving a Beckmann rearrangement on benzophenone oxime followed by an electrophilic aromatic substitution (EAS) on the intermediate nitrilium ion affords N-phenyl diaryl imines that may then be hydrolyzed to ketones, or reduced to the corresponding amines. Reaction with benzonitrile afforded 2,4-diphenylquinazoline through a Beckmann–Ritter–EAS cascade.

The Crystal Structure Of Nitrosomonas Europaea Sucrose Synthase Reveals Critical Conformational Changes And Insights Into The Sucrose Metabolism In Prokaryotes, Rui Wu, Matías D. Asención Diez, Carlos M. Figueroa, Matías Machtey, Alberto A. Iglesias, Miguel Ballicora, Dali Liu

Chemistry: Faculty Publications and Other Works

In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the non-photosynthetic bacterium Nitrosomonas europaea. The obtained structure was in an open form, whereas the only other available structure from the plant Arabidopsis thaliana was in a closed conformation. Comparative structural analysis revealed a “hinge-latch” combination, which is critical to transition between the open and closed forms of the enzyme. The N. europaea sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family showed to be functionally critical …

Effects Of Mutations On The Molecular Dynamics Of Oxygen Escape From The Dimeric Hemoglobin Of Scapharca Inaequivalvis, Kevin Trujillo, Tasso Papagiannopoulos, Kenneth W. Olsen

Chemistry: Faculty Publications and Other Works

Like many hemoglobins, the structure of the dimeric hemoglobin from the clam Scapharca inaequivalvis is a “closed bottle” since there is no direct tunnel from the oxygen binding site on the heme to the solvent. The proximal histidine faces the dimer interface, which consists of the E and F helicies. This is significantly different from tetrameric vertebrate hemoglobins and brings the heme groups near the subunit interface. The subunit interface is also characterized by an immobile, hydrogen-bonded network of water molecules. Although there is data which is consistent with the histidine gate pathway for ligand escape, these aspects of the …

Design, Synthesis, And Biological Evaluation Of Folate Targeted Photosensitizers For Photodynamic Therapy, Laura Jean Donahue

Dissertations

Photodynamic therapy (PDT) is used to treat cancer, and involves a highly conjugated molecule, called a photosensitizer (PS), which is excited by wavelengths of light from visible to infrared. Photosensitizers that are highly conjugated will absorb longer wavelengths (600 – 900 nm), and have the potential to destroy cells of deeper tissue cancers. In PDT, a PS is administered to the patient, and after an appropriate time delay, the tissue is then exposed to light of a specific wavelength necessary for excitation of the PS. A transfer of energy can take place between the excited PS and oxygen that is …

Grazing Incidence X-Ray Fluorescence Measurements Of Genesis Sample 30580 For Determination Of Manganese And Nickel Fluences, Martina Schmeling, J. Davidson, P.J. Eng, J.E. Stubbs, A.J.G. Jurewicz, D.S. Burnett

Chemistry: Faculty Publications and Other Works

Genesis flight sample 30580 was analyzed by grazing incidence X-ray fluorescence spectrometry for subsequent calculation of Mn and Ni fluences.

Preparation Of Scanning Tunneling Microscopy Tips Using Pulsed Alternating Current Etching, Victor A. Valencia, Avesh A. Thaker, Johnathan Derouin, Damian N. Valencia, Rachael G. Farber, Dana A. Gebel, Daniel Killelea

Chemistry: Faculty Publications and Other Works

An electrochemical method using pulsed alternating current etching (PACE) to produce atomically sharp scanning tunneling microscopy (STM) tips is presented. An Arduino Uno microcontroller was used to control the number and duration of the alternating current (AC) pulses, allowing for ready optimization of the procedures for both Pt:lr and W tips using a single apparatus. W tips prepared using constant and pulsed AC power were compared. Tips fashioned using PACE were sharper than those etched with continuous AC power alone. Pt:lr tips were prepared with an initial coarse etching stage using continuous AC power followed by fine etching using PACE. …

Synthesis And Testing Of Photosensitizer-Folate Conjugates And Potential Photosensitizers For Photodynamic Therapy, Jeffrey A. Trautmann

Dissertations

Dissertation Proposal for Jeffrey Trautmann

Photodynamic Therapy (PDT) is a technique that destroys oncogenic (cancerous) cells. It has been used in several countries since the 1980’s. Molecules that contain chromophores can function as photosensitizers, and will absorb light at various wavelengths (that being dependent upon the extent of their conjugation). Certain functional groups, upon absorption of light, can be used to convert O2 to singlet oxygens which are destructive to the cellular environment. Once an in-vitro cell contains a high enough concentration of photosensitizer material and light is able to reach the photosensitizer material, PDT can be used effectively to …

Molecular Interactions With Ice: Molecular Embedding, Adsorption, Detection, And Release, K D. Gibson, Grant G. Langlois, Wenxin Li, Daniel Killelea, S J. Sibener

Chemistry: Faculty Publications and Other Works

The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion.We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF4 molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is …

A Novel Dual Allosteric Activation Mechanism Of Escherichia Coli Adp-Glucose Pyrophosphorylase: The Role Of Pyruvate, Matías D. Asención Diez, Mabel C. Aleanzi, Alberto A. Iglesias, Miguel Ballicora

Chemistry: Faculty Publications and Other Works

Fructose-1,6-bisphosphate activates ADP-glucose pyrophosphorylase and the synthesis of glycogen in Escherichia coli. Here, we show that although pyruvate is a weak activator by itself, it synergically enhances the fructose-1,6-bisphosphate activation. They increase the enzyme affinity for each other, and the combination increases Vmax, substrate apparent affinity, and decreases AMP inhibition. Our results indicate that there are two distinct interacting allosteric sites for activation. Hence, pyruvate modulates E. coli glycogen metabolism by orchestrating a functional network of allosteric regulators. We postulate that this novel dual activator mechanism increases the evolvability of ADP-glucose pyrophosphorylase and its related metabolic control.

Heavy Metal Analysis In Lens And Aqueous Humor Of Cataract Patients By Total Reflection X-Ray Fluorescence Spectrometry, Martina Schmeling, Bruce I. Gaines, Susanne Tidow-Kebritchi

Chemistry: Faculty Publications and Other Works

The human eye is continuously exposed to the environment yet little is known about how much of toxins, specifically heavy metals are present in its different parts and how they influence vision and acuity. To shed light into this subject, aqueous humor and lens samples were collected from 14 cataract patients to study the presence and concentration of selected metals in the eye. Subjects undergoing routine cataract surgery were consecutively enrolled for study by simple random sampling. Prior to surgery, subject demographic were compiled. The surgical procedure involved small incision cataract removal using phacoemulsification. During the procedure, a small aliquot …

Catalytic Kinetic Resolution Of A Dynamic Racemate: Highly Stereoselective Β-Lactone Formation By N-Heterocyclic Carbene Catalysis, Ryne C. Johnston, Daniel T. Cohen, Chad C. Eichman, Karl A. Scheidt, Paul Ha-Yeon Cheong

Chemistry: Faculty Publications and Other Works

This study describes the combined experimental and computational elucidation of the mechanism and origins of stereoselectivities in the NHC-catalyzed dynamic kinetic resolution (DKR) of α-substituted-β-ketoesters. Density functional theory computations reveal that the NHC-catalyzed DKR proceeds by two mechanisms, depending on the stereochemistry around the forming bond: 1) a concerted, asynchronous formal (2+2) aldol-lactonization process, or 2) a stepwise spiro-lactonization mechanism where the alkoxide is trapped by the NHC-catalyst. These mechanisms contrast significantly from mechanisms found and postulated in other related transformations. Conjugative stabilization of the electrophile and non-classical hydrogen bonds are key in controlling the stereoselectivity. This reaction constitutes an …