Chemistry Commons^™

Modifications On Translation Initiation, Sarah F. Mitchell

Chemistry and Biochemistry Faculty Works

Two studies by Meyer et al. and Wang et al. demonstrate a role for m6A modification of mRNA in stimulating translation initiation. These findings add to the growing number of diverse mechanisms for translation initiation in eukaryotes.

Dynamic Motions Of The Hiv-1 Frameshift Site Rna, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The HIV-1 frameshift site (FS) plays a critical role in viral replication. During translation, the HIV-1 FS transitions from a 3-helix to a 2-helix junction RNA secondary structure. The 2-helix junction structure contains a GGA bulge, and purine-rich bulges are common motifs in RNA secondary structure. Here, we investigate the dynamics of the HIV-1 FS 2-helix junction RNA. Interhelical motions were studied under different ionic conditions using NMR order tensor analysis of residual dipolar couplings. In 150 mM potassium, the RNA adopts a 43°(±4°) interhelical bend angle (β) and displays large amplitude, anisotropic interhelical motions characterized by a 0.52(±0.04) internal …

Global Shape Mimicry Of Trna Within A Viral Internal Ribosome Entry Site Mediates Translational Reading Frame Selection, Kathryn Mouzakis

Chemistry and Biochemistry Faculty Works

The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the threehelical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and …

Transition States And Modeling For Co9s8/Mos2 Catalysis, Gabriel Angel Gonzalez

Open Access Theses & Dissertations

Transition state computational studies of the sulfur removal from dibenzothiophene (DBT) molecule have herein been performed considering the Co9S8/MoS2 interface existing on unsupported Co/MoS2 catalysts. The linear synchronous transit (LST) and quadratic synchronous transit (QST) methods integrated in a density functional theory (DFT) program such as Dmol3 were used for the calculations of energy barriers of the transition states. Three different configurations present on the Co9S8/MoS2 interface have been envisaged as possible catalytic sites: sulfur-sulfur (S, S) sites, and molybdenum-sulfur (Mo, S) and molybdenum-molybdenum (Mo, Mo) edge sites. This study revealed that the (Mo, Mo) edge site is the most …

Total Synthesis Of Syringolides 1 And 2, Sudhakar Kalagara

Open Access Theses & Dissertations

The total synthesis of Syringolides is described. The synthetic pathway was designed in order to synthesize Syringolides in high yields using inexpensive starting materials. The synthesis strategy features a preparation of the linear tricarbonyl compound followed by intramolecular cyclization. The linear precursor is divided into two fragments, β-keto acid and protected D-xylulose, which are the key fragments and were synthesized from α,β-unsaturated compound followed by asymmetric dihydroxylation. The α,β-unsaturated compound was efficiently prepared by a Wittig reaction between aldehyde and ylide fragments. The butenolide derivative was also achieved by the Knoevenagel condensation of the tricarbonyl compound.

Transition Metal Carbide (Tmc) Novel Materials For Novel Catalytic Applications, Svetlana Lagoykina

Open Access Theses & Dissertations

Transition metal carbides (TMC) constitute a diverse class of materials and traditionally have many technological applications. TMC became a subject of extensive research since 1973, when their platinum -like properties were discovered. They demonstrated high catalytical activity and selectivity in a variety of chemical reaction and have potential for some novel catalytic application.

This research is an effort to design new high effective, selective and stable bimetal or alkali promoted TMC catalyst. After extensive theoretical research a wide range of TMC, including bimetal and alkali promoted carbides, were synthesized by different methods. All solids were characterized by XRD and microscopy. …

On The Path To Multi-Electron Redox Chemistry With Bimetallic Systems, Nathalie Metta

Open Access Theses & Dissertations

The following study is presented in two sections, in the first, a novel digold (II) complex with semi-bridging chlorides supported by two bulky formamidinates was synthesized for the purpose of studying late-transition metal multi-electron redox chemistry. Electrochemical analysis shows one non-reversible reduction. Although the electrochemistry of this complex is restricted, the compound shows interesting electronic properties. The crystal structure reveals a geometry distortion of the Au2ï?­-Cl2 core. The coupling of an unoccupied orbital and an occupied orbital through a vibrational mode, causes a distortion in the geometry of the molecule lowering the D2h symmetry to C2h. This is an example …

Mutagenic Studies Of A Unique Cysteine Ligase Enzyme, Emily David, Paul Cook

Student Summer Scholars Manuscripts

BshC is the final enzyme in a three step pathway for the synthesis of bacillithiol, a compound that enables resistance to fosfomycin in Gram-positive bacteria. BshC is unique from other enzymes of its kind because of an additional ADP binding site and inactivity when studied in the laboratory. To explore BshC function, several site-directed mutants have been selected within the ADP binding pocket. Fluorescence assays have been utilized on the wild-type BshC and one mutant, Y510Q. We determined that Y510Q does not bind ATP as effectively as wild-type BshC. These fluorescence assays will be utilized on W506L, E384A, and H386A …

The Subject Librarian Newsletter, Chemistry, Fall 2015, Patti Mccall

Libraries' Newsletters

No abstract provided.

Tuning The Physical Properties Of Poly(Arylene Ether)S Prepared From 3,5-Difluorobenzene Sulfonamides, Renata Mitton

Browse all Theses and Dissertations

A series of functionalized poly(arylene ether)s, PAEs, based on 3,5-difluorobenzene sulfonamides with varying groups on the sulfonamide moiety were investigated. The main goal of the project was to tune the physical properties of the PAEs by altering the organic groups present on the sulfonamide nitrogen atom, including combinations of aryl iodide, alkyl, allyl, 4-ethoxycarboxylphenyl and benzyl moieties.

Using 3,5-difluorobenzenesulfonyl chloride as a starting material, N-R1-N-R2-3,5-difluorobenzenesulfonamides were prepared, followed by conversion to the corresponding PAEs by reaction of 3,5-difluorobenzene sulfonamides with Bisphenol-A, via a typical NAS polycondensation. Copolymers with varying contents of the functional monomer ranging from 10 to 25 %, …

Work Function Modification Of Metal Electrodes Via Printing Of Pedot:Pss And Carbon Nanotubes, Carly A. Jordan

Browse all Theses and Dissertations

Work function tunability of metal electrodes provides a route to improving performance of organic electronic devices. Using an electrode with a different work function changes the potential barrier at the polymer/electrode interface, leading to altered device characteristics, such as turn-on voltage in light emitting diodes or series resistance photodiodes. In this work, we explore work function modification by employing solution-based conducting materials, poly(3,4-ethylenedioxythiophene) : poly(styrene sulfonate) (PEDOT:PSS) and carbon nanotubes (CNTs), printed as overcoatings on oxidized Ni. The capability of direct write technologies, namely inkjet and aerosol jet printing, to control thin film thickness is investigated. The correlation between film …

Polymerization Of Peek Ab Monomers With Oxyalkylene Linkages Via Nas And Friedel-Crafts Reactions, Shannon Theresa Hennelly

Browse all Theses and Dissertations

The synthesis of the NAS monomer, 4-fluoro-4'-(2-(4-benzyloxyphenoxy)ethoxy) benzophenone, was envisioned as a two-step process. Thus, the synthesis of 4-fluoro- 4'-(2-(4-benzyloxyphenoxy)ethoxy)benzophenone was accomplished by the reaction of 4-fluoro-4'-hydroxybenzophenone and 1-(benzyloxy)-4-(2bromoethoxy) benzene. Hydrogenation of 4-fluoro-4'-(2-(4-benzyloxyphenoxy)ethoxy) benzophenone with 10% Pd/C was used to successfully remove the benzylic ether protective group, however, the reaction also reduced the benzophenone carbonyl. The synthesis of the EAS monomer, 4-(2-(4-phenoxyphenoxy)ethoxy)benzoic acid, was also a two-step process. The reaction of ethyl p-(2-hydroxyethoxy)benzoate and 4-phenoxyphenol gave ethyl 4-(2-(4-phenoxyphenoxy)ethoxy)benzoate in good yield. This ester could be easily hydrolyzed to 4-(2-(4-pheonxyphenoxy)ethoxybenzoic acid. The polymerization of the EAS monomer, 4-(2-(4-pheonxyphenoxy)ethoxybenzoic acid, was carried …

Regional-Scale Simulations Of Fungal Spore Aerosols Using An Emission Parameterization Adapted To Local Measurements Of Fluorescent Biological Aerosol Particles, Matthias Hummel, Corinna Hoose, M. Gallagher, D. A. Healy, J. Alex Huffman, D. O'Connor, U. Pöschl, C. Pöhlker, N. H. Robinson, M. Schnaiter, J. R. Sodeau, M. Stengel, E. Toprak, H. Vogel

Chemistry and Biochemistry: Faculty Scholarship

Fungal spores as a prominent type of primary biological aerosol particles (PBAP) have been incorporated into the COSMO-ART (Consortium for Small-scale Modelling- Aerosols and Reactive Trace gases) regional atmospheric model. Two literature-based emission rates for fungal spores derived from fungal spore colony counts and chemical tracer measurements were used as a parameterization baseline for this study. A third, new emission parameterization for fluorescent biological aerosol particles (FBAP) was adapted to field measurements from four locations across Europe. FBAP concentrations can be regarded as a lower estimate of total PBAP concentrations. Size distributions of FBAP often show a distinct mode at …

The Micro-Orifice Uniform Deposit Impactor–Droplet Freezing Technique (Moudi-Dft) For Measuring Concentrations Of Ice Nucleating Particles As A Function Of Size: Improvements And Initial Validation, R. H. Mason, C. Chou, C. S. Mccluskey, E. J. T. Levin, C. L. Schiller, T. C. J. Hill, J. Alex Huffman, P. J. Demott, A. K. Bertram

Chemistry and Biochemistry: Faculty Scholarship

The micro-orifice uniform deposit impactor– droplet freezing technique (MOUDI-DFT) combines particle collection by inertial impaction (via the MOUDI) and a microscope-based immersion freezing apparatus (the DFT) to measure atmospheric concentrations of ice nucleating particles (INPs) as a function of size and temperature. In the first part of this study we improved upon this recently introduced technique. Using optical microscopy, we investigated the non-uniformity of MOUDI aerosol deposits at spatial resolutions of 1, 0.25 mm, and for some stages when necessary 0.10 mm. The results from these measurements show that at a spatial resolution of 1mm and less, the concentration of …

Fluorescence Imaging Of Analyte Profiles In An Inductively Coupled Plasma With Laser Ablation As A Sample Introduction Source, Lance Moses

Theses and Dissertations

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has risen to among the top tier techniques for the direct analysis of solid samples. However, significant problems remain that must be solved to achieve the full analytical potential of LA-ICP-MS. Inefficient conversion of aerosol to ions within the ICP or transmission through the MS interface may decrease precision, sensitivity, and/or accuracy. Although fundamental mechanisms that govern ion production and transmission have been studied extensively in solution-nebulization (SN) ICP-MS instruments, significant gaps in our understanding remain. Furthermore, it is unclear to what extent differences between the aerosols generated during SN and LA …

A Silylation-Based Kinetic Resolution Of Hydroxy Lactones And Lactams With Subsequent Mechanistic Investigations, Robert W. Clark

Theses and Dissertations

The work contained herein focuses on the methodology and design of new reactions for the production of stereoenriched compounds. The primary focus of research discussed is kinetic resolution, a classic and powerful methodology for the separation of a single enantiomer from a racemic mixture. In 2011, a silylation-based resolution catalyzed by a chiral isothiourea produced synthetically useful selectivity factors for mono-functional secondary alcohols. In chapter 2, this methodology was subsequently expanded to include α-hydroxy lactones with selectivity factors up to 100. This study resulted in the most selective reaction reported to date for the aforementioned silylation-based resolution. In addition to …

B27−: Appearance Of The Smallest Planar Boron Cluster Containing A Hexagonal Vacancy, Wei-Li Li, Rhitankar Pal, Zachary A. Piazza, Xiao Cheng Zeng, Lai-Sheng Wang

Xiao Cheng Zeng Publications

Photoelectron spectroscopy and ab initio calculations have been carried out to probe the structures and chemical bonding of the B₂₇⁻ cluster. Comparison between the experimental spectrum and the theoretical results reveals a two-dimensional (2D) global minimum with a triangular lattice containing a tetragonal defect (I) and two low-lying 2D isomers (II and III), each with a hexagonal vacancy. All three 2D isomers have 16 peripheral boron atoms and 11 inner boron atoms. Isomer I is shown to be mainly responsible for the observed photoelectron spectrum with isomers II and III as minor contributors. Chemical bonding analyses of these …

Electronic Structures And Electronic Spectra Of All-Boron Fullerene B40, Rongxing He, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

This study is motivated by the recent discovery of the first all-boron fullerene analogue, a B₄₀ cluster with D_2d point-group symmetry, dubbed borospherene (Nat. Chem., 2014, 6, 727). Insight into the electronic structures and spectral properties of B₄₀ is timely and important to understand the borospherene and the transition from open-ended plate or ribbon-like structures to a hollow-cage structure at B₄₀. Optimized geometries of borospherene B₄₀ for both the ground state and the first excited state allow us to compute spectral properties including UV-vis absorption, infrared (IR) and Raman spectra. Highly resolved absorption and …

Room-Temperature Distance Measurements Of Immobilized Spin-Labeled Protein By Deer/Peldor, Virginia Meyer, Michael A. Swanson, Laura J. Clouston, Przemysław J. Boratyński, Richard A. Stein, Hassane S. Mchaourab, Andrzej Rajca, Sandra S. Eaton, Gareth R. Eaton

Andrzej Rajca Publications

Nitroxide spin labels are used for double electron-electron

resonance (DEER) measurements of distances between sites in

biomolecules. Rotation of gem-dimethyls in commonly used

nitroxides causes spin echo dephasing times (T_m) to be too

short to perform DEER measurements at temperatures between

∼80 and 295 K, even in immobilized samples. A spirocyclohexyl

spin label has been prepared that has longer T_m between 80

and 295 K in immobilized samples than conventional labels. Two

of the spirocyclohexyl labels were attached to sites on T4 lysozyme introduced by site-directed spin labeling. Interspin

distances up to ∼4 nm were …

Exploiting Enzymatic Dynamic Reductive Kinetic Resolution (Dyrkr) In Stereocontrolled Synthesis, Gregory A. Applegate, David B. Berkowitz

David Berkowitz Publications

Over the past two decades, the domains of both frontline synthetic organic chemistry and process chemistry have seen an increase in crosstalk between asymmetric organic/organometallic approaches and enzymatic approaches to stereocontrolled synthesis. This review highlights the particularly auspicious role for dehydrogenase enzymes in this endeavor, with a focus on dynamic reductive kinetic resolutions (DYRKR) to “deracemize” building blocks, often setting two stereocenters in so doing. The scope and limitations of such dehydrogenase-mediated processes are overviewed, as are future possibilities for the evolution of enzymatic DYRKR.

Research-Based Implementation Of Peer Instruction: A Literature Review, Trisha Vickrey, Kaitlyn Rosploch, Reihaneh Rahmanian, Matthew Pilarz, Marilyne Stains

Department of Chemistry: Faculty Publications

Current instructional reforms in undergraduate science, technology, engineering, and mathematics (STEM) courses have focused on enhancing adoption of evidence-based instructional practices among STEM faculty members. These practices have been empirically demonstrated to enhance student learning and attitudes. However, research indicates that instructors often adapt rather than adopt practices, unknowingly compromising their effectiveness. Thus, there is a need to raise awareness of the research-based implementation of these practices, develop fidelity of implementation protocols to understand adaptations being made, and ultimately characterize the true impact of reform efforts based on these practices. Peer instruction (PI) is an example of an evidence-based instructional …

New Insight Into The Helium-Induced Damage In Max Phase Ti3Alc2 By First-Principles Studies, Yiguo Xu, Xiaojing Bai, Xianhu Zha, Qing Huang, Jian He, Kan Luo, Yuhong Zhou, Timothy C. Germann, Joseph S. Francisco, Shiyu Du

Department of Chemistry: Faculty Publications

In the present work, the behavior of He in the MAX phase Ti3AlC2 material is investigated using first-principle methods. It is found that, according to the predicted formation energies, a single He atom favors residing near the Al plane in Ti3AlC2. The results also show that Al vacancies are better able to trap He atoms than either Ti or C vacancies. The formation energies for the secondary vacancy defects near an Al vacancy or a C vacancy are strongly influenced by He impurity content. According to the present results, the existence of trapped He atoms in primary Al vacancy can …

Communication: Spectroscopic Consequences Of Proton Delocalization In Ochco+, Ryan C. Fortenberry, Qi Yu, John S. Mancini, Joel M. Bowman, Timothy J. Lee, T. Daniel Crawford, William F. Klemperer, Joseph S. Francisco

Department of Chemistry: Faculty Publications

Even though quartic force fields (QFFs) and highly accurate coupled cluster computations describe the OCHCO⁺ cation at equilibrium as a complex between carbon monoxide and the formyl cation, two notable and typical interstellar and atmospheric molecules, the prediction from the present study is that the equilibrium C_∞v structure is less relevant to observables than the saddle-point D_∞h structure. This is the conclusion from diffusion Monte Carlo and vibrational self-consistent field/virtual state configuration interaction calculations utilizing a semi-global potential energy surface. These calculations demonstrate that the proton “rattle” motion (ν₆) has centrosymmetric delocalization of the …

Structural And Optical Properties Of Cobalt Slanted Nanopillars Conformally Coated With Few-Layer Graphene, Peter M. Wilson, Alexey Lipatov, Daniel Schmidt, Eva Schubert, Mathias Schubert, Alexander Sinitskii, Tino Hofmann

Department of Chemistry: Faculty Publications

Optical characterization of anisotropic multicomponent nanostructures is generally not a trivial task, since the relation between a material’s structural properties and its permittivity tensor is nonlinear. In this regard, an array of slanted cobalt nanopillars that are conformally coated with few-layer graphene is a particularly challenging object for optical characterization, as it has a complex anisotropic geometry and comprises several materials with different topologies and filling fractions. Normally, a detailed characterization of such complex nanostructures would require a combination of several microscopic and spectroscopic techniques. In this letter, we demonstrate that the important structural parameters of these graphene-coated sculptured thin …

Few-Layer Titanium Trisulfide (Tis3) Field-Effect Transistors, Alexey Lipatov, Peter M. Wilson, Mikhail Shekhirev, Jacob D. Teeter, Ross Netusil, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Titanium trisulfide (TiS₃) is a promising layered semiconductor material. Several-mm-long TiS₃ whiskers can be conveniently grown by the direct reaction of titanium and sulfur. In this study, we exfoliated these whiskers using the adhesive tape approach and fabricated few-layer TiS₃ field-effect transistors (FETs). The TiS₃ FETs showed an n-type electronic transport with roomtemperature field-effect mobilities of 18-24 cm²V^-1s^-1 and ON/OFF ratios up to 300. We demonstrate that TiS₃ is compatible with the conventional atomic layer deposition (ALD) procedure for Al₂O₃. ALD of alumina on TiS3 …

Biotechnological Production Of 1,2,4-Butanetriol: An Efficient Process To Synthesize Energetic Material Precursor From Renewable Biomass, Yujin Cao, Wei Niu, Jiantao Guo, Mo Xian, Huizhou Liu

Department of Chemistry: Faculty Publications

1,2,4-Butanetriol (BT) is a valuable chemical with extensive applications in many different fields. The traditional chemical routes to synthesize BT suffer from many drawbacks, e.g., harsh reaction conditions, multiple steps and poor selectivity, limiting its industrial production. In this study, an engineered Escherichia coli strain was constructed to produce BT from xylose, which is a major component of the lignocellulosic biomass. Through the coexpression of a xylose dehydrogenase (CCxylB) and a xylonolactonase (xylC) from Caulobacter crescentus, native E. coli xylonate dehydratase (yjhG), a 2-keto acid decarboxylase from Pseudomonas putida (mdlC) and …

Fine-Tuning Interaction Between Aminoacyl-Trna Synthetase And Trna For Efficient Synthesis Of Proteins Containing Unnatural Amino Acids, Nanxi Wang, Tong Ju, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

By using a directed evolution approach, we have identified aminoacyl-tRNA synthetase variants with significantly enhanced activity for the incorporation of unnatural amino acids into proteins in response to the amber nonsense codon in bacteria. We demonstrated that the optimization of anticodon recognition of tRNA by aminoacyltRNA synthetase led to improved incorporation efficiency that is unnatural amino acid-specific. The findings will facilitate the creation of an optimized system for the genetic incorporation of unnatural amino acids in bacteria.

A Comparison Of Energy-Resolved Vibrational Activation/Dissociation Characteristics Of Protonated And Sodiated High Mannose N-Glycopeptides, Forouzan Aboufazeli, Venkata Kolli, Eric D. Dodds

Department of Chemistry: Faculty Publications

Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinction dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/ dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly …

Stretchable Conductive Composites For Use In Soft Devices, Joshua Aaron Lessing, Stephen A. Morin, George M. Whitesides

Department of Chemistry: Faculty Publications

An elastically-deformable, conductive composite using elastomers and conductive fibers and simple fabrication procedures is provided. Conductive elastomeric composites offer low resistance to electrical current and are elastic over large (>25%) extensional strains. They can be easily interfaced/built into structures fabricated from elastomeric polymers.

Apparatus, Systems, And Methods For Modular Soft Robots, Stephen A. Morin, Sen Wai Kwok, Robert F. Shepherd, George M. Whitesides

Department of Chemistry: Faculty Publications

Apparatus, Systems, and methods for providing modular soft robots are disclosed. In particular, the disclosed modular soft robot can include a flexible actuator having a plurality of molded flexible units. Each molded flexible unit can include a mechanical connector configured to provide a physical coupling to another molded flexible unit, and the plurality of molded flexible units are arranged to form an embedded fluidic channel. The modular soft robot can also include an inlet coupled to the embedded fluidic channel, where the inlet is configured to receive pressurized or depressurized fluid to inflate or deflate a portion of the flexible …