Other Chemistry Commons^™

An Expanded Genetic Code In Mammalian Cells With A Functional Quadruplet Codon, Wei Niu, Peter G. Schultz, Jiantao Guo

Department of Chemistry: Faculty Publications

We have utilized in vitro evolution to identify tRNA variants with significantly enhanced activity for the incorporation of unnatural amino acids into proteins in response to a quadruplet codon in both bacterial and mammalian cells. This approach will facilitate the creation of an optimized and standardized system for the genetic incorporation of unnatural amino acids using quadruplet codons, which will allow the biosynthesis of biopolymers that contain multiple unnatural building blocks.

Probing The Bifunctional Catalytic Activity Of Ceria Nanorods Towards The Cyanosilylation Reaction, Gonghua Wang, Lu Wang, Xiang Fei, Yunyun Zhou, Renat F. Sabirianov, Wai-Ning Mei, Chin Li Cheung

Department of Chemistry: Faculty Publications

Ceria nanorods were demonstrated to be an active, bifunctional catalyst for the cyanosilylation of aldehydes. The catalytic activity of ceria was shown to be positively correlated with a decrease in the coordination numbers of neighbouring oxygen atoms around cerium atoms in the catalyst. Chemisorption and density functional theory studies suggested that the coordinatively unsaturated cerium sites exposed by the surface oxygen vacancy defects functioned as Lewis acid sites and the neighbouring oxygen atoms behaved as Lewis base sites in the catalytic cycle.

Porous Polymer Coatings As Substrates For The Formation Of High-Fidelity Micropatterns By Quill-Like Pens, Michael Hirtz, Marcus Lyon, Wenqian Feng, Andrea E. Holmes, Harald Fuchs, Pavel A. Levkin

Department of Chemistry: Faculty Publications

We explored the potentials of microarray printing using quill-like microcantilevers onto solid supports that are typically used in microspot printing, including paper, polymeric nitrocellulose and nylon membranes. We compared these membranes with a novel porous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) support (HEMA) with narrow pore size distribution in the 150 nm range, which demonstrated advantages in pattern definition, spot homogeneity, and consistent spot delivery of different dyes (phloxine B and bromophenol blue) with diameters of several micrometres. The bromophenol blue arrays on HEMA support were used to detect the presence of bovine serum albumin (BSA). In the presence of BSA, …

Single Transcriptional And Translational Preq1 Riboswitches Adopt Similar Pre-Folded Ensembles That Follow Distinct Folding Pathways Into The Same Ligand-Bound Structure, Krishna C. Suddala, Arlie J. Rinaldi, Jun Feng, Anthony M. Mustoe, Catherine D. Eichhorn, Joseph A. Liberman, Joseph E. Wedekind, Hashim M. Al-Hashimi, Charles L. Brooks Iii, Nils G. Walter

Department of Chemistry: Faculty Publications

Riboswitches are structural elements in the 50 untranslated regions of many bacterial messenger RNAs that regulate gene expression in response to changing metabolite concentrations by inhibition of either transcription or translation initiation. The preQ₁ (7-aminomethyl-7-deazaguanine) riboswitch family comprises some of the smallest metabolite sensing RNAs found in nature. Once ligand-bound, the transcriptional Bacillus subtilis and translational Thermoanaerobacter tengcongensis preQ₁ riboswitch aptamers are structurally similar RNA pseudoknots; yet, prior structural studies have characterized their ligand-free conformations as largely unfolded and folded, respectively. In contrast, through single molecule observation, we now show that, at nearphysiological Mg²⁺ concentration and pH, …

Iodonium Cyclophanes For Secure Arene Functionalization, Stephen Dimagno

Department of Chemistry: Faculty Publications

This disclosure relates to compounds, reagents, and methods useful in the synthesis of aryl fluorides, for example, in the preparation of 18F labeled radiotracers. For example, this disclosure provides universal “locked” aryl substituents that result in StereoElectronic Control of Unidirectional Reductive Elimination (SECURE) from diaryliodonium salts. The reagents and methods provided herein may be used to access a broad range of compounds, including aromatic compounds, heteroaromatic compounds, amino acids, nucleotides, and synthetic compounds.

Identification And Analysis Of Stereoselective Drug Interactions With Low Density Lipoprotein By High-Performance Affinity Chromatography, Matt Sobansky, David S. Hage

Department of Chemistry: Faculty Publications

Columns containing immobilized low density lipoprotein (LDL) were prepared for the analysis of drug interactions with this agent by high-performance affinity chromatography (HPAC). R/SPropranolol was used as a model drug for this study. The LDL columns gave reproducible binding to propranolol over 60 h of continuous use in the presence of pH 7.4, 0.067 M potassium phosphate buffer. Experiments conducted with this type of column through frontal analysis indicated that two types of interactions were occurring between R-propranolol and LDL, while only a single type of interaction was observed between S-propranolol and LDL. The first type …

Ccpa Regulates Arginine Biosynthesis In Staphylococcus Aureus Through Repression Of Proline Catabolism, Austin S. Nuxoll, Steven M. Halouska, Marat R. Sadykov, Mark L. Hanke, Kenneth W. Bayles, Tammy Kielian, Robert Powers, Paul D. Fey

Department of Chemistry: Faculty Publications

Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, …

Unraveling The Structural Complexity In A Single-Stranded Rna Tail: Implications For Efficient Ligand Binding In The Prequeuosine Riboswitch, Catherine D. Eichhorn, Jun Feng, Krishna C. Suddala, Nils G. Walter, Charles L. Brooks Iii, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Single-stranded RNAs (ssRNAs) are ubiquitous RNA elements that serve diverse functional roles. Much of our understanding of ssRNA conformational behavior is limited to structures in which ssRNA directly engages in tertiary interactions or is recognized by proteins. Little is known about the structural and dynamic behavior of free ssRNAs at atomic resolution. Here, we report the collaborative application of nuclear magnetic resonance (NMR) and replica exchange molecular dynamics (REMD) simulations to characterize the 12 nt ssRNA tail derived from the prequeuosine riboswitch. NMR carbon spin relaxation data and residual dipolar coupling measurements reveal a flexible yet stacked core adopting an …

Crystalline Nano Structures, Barry Chin Li Cheung, Joseph Reese Brewer, Nirmalendu Deo

Department of Chemistry: Faculty Publications

The present invention comprises nano obelisks and nanostructures and methods and processes for same. The nano obelisks of the present invention are advantageous structures for use as electron source emitters. For example, the ultra sharp obelisks can be used as an emitter source to generate highly coherent and high energy electrons with high current.

Identification And Characterization Of The Anti-Methicillin-Resistant Staphylococcus Aureus Wap-8294a2 Biosynthetic Gene Cluster From Lysobacter Enzymogenes Oh11, Wei Zhang, Yaoyao Li, Guoliang Qian, Yan Wang, Haotong Chen, Yue-Zhong Li, Fengquan Liu, Yuemao Shen, Liangcheng Du

Department of Chemistry: Faculty Publications

Lysobactor enzymogenes strain OH11 is an emerging biological control agent of fungal and bacterial diseases. We recently completed its genome sequence and found it contains a large number of gene clusters putatively responsible for the biosynthesis of nonribosomal peptides and polyketides, including the previously identified antifungal dihydromaltophilin (HSAF). One of the gene clusters contains two huge open reading frames, together encoding 12 modules of nonribosomal peptide synthetases (NRPS). Gene disruption of one of the NRPS led to the disappearance of a metabolite produced in the wild type and the elimination of its antibacterial activity. The metabolite and antibacterial activity were …

Characterizing Rna Dynamics At Atomic Resolution Using Solution-State Nmr Spectroscopy, Jameson R. Bothe, Evgenia N. Nikolova, Catherine D. Eichhorn, Jeetender Chugh, Alexandar L. Hansen, Hashim M. Al-Hashimi

Department of Chemistry: Faculty Publications

Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering.

Corrosion Rate Trajectories Of Concreted Iron And Steel Shipwrecks And Structures In Seawater— The Weins Number, Donald L. Johnson, D. J. Medlin, L. E. Murphy, J. D. Carr, D. L. Conlin

Department of Chemistry: Faculty Publications

The Weins number (Wn) concept is proposed to predict the long-term corrosion rate of wrought iron and steel in seawater for variable marine environments. Plotted as a function of reciprocal absolute temperature, Weins numbers generate a linear plot from which the corrosion rates are calculated when temperature, oxygen concentration, and concretion thickness are known. Application of the theory of absolute reaction rates is described.

Transition States In Ei Reactions, Charles A. Kingsbury

Department of Chemistry: Faculty Publications

The pyrolysis of amine oxides, sulfoxides, selenoxides, and esters to form alkenes is believed to be a concerted reaction with a cyclic transition state. Phosphine oxides, sulfones, and nitro compounds are unreactive. This study seeks to identify reasons for the lack of reactivity of the latter. Transition states were located for all substrates progressing from RHF/3-21G* to the MP2/6-31+G(d,p) level (in certain cases). For sulfones and nitro compounds, two possible reasons for lack of reactivity were considered: (1) Atoms approaching one another in the transition state may be considered to participate in a local n_O→σ*_{CH …}

Process For Preparation Of Conducting Polymers, Reuben D. Rieke

Department of Chemistry: Faculty Publications

Methods of preparing conducting polymers and the conductive polymers prepared therefrom are provided. The method includes a) combining a monomer-metal complex together with a manganese (II) halide to provide a monomer-manga nese complex, and b) combining the monomer-manganese complex together with a metal catalyst to provide the conductive polymer. Electronic devices can be made using the polymers prepared as described herein.

Self-Assembled Heteroleptic Chiral Ligands, Asymmetric Catalyst Systems And Methods, James M. Takacs

Department of Chemistry: Faculty Publications

A method of synthesizing a heteroleptic, multiple metal containing metallocyclic catalyst, particularly Suited for asymmetric catalysis, comprising combining a plurality of plural functional group-containing, monodentate ligands of complementary chirality, said plural functional groups being tethered to each other by tethers in the presence of a scaffold structural metal Ms or derivative thereof, wherein at least one functional group on each ligand combines to ligate M to form a bidentate, M_s centered ligand scaffold containing the remaining functional groups and combining said bidentate ligand scaffold with a catalytic metal M_c or derivative thereof whereby the remaining functional groups combine …

Corrosion Of Steel Shipwreck In The Marine Environment: Uss Arizona—Part 1, Donald L. Johnson, Brent M. Wilson, James D. Carr, Matthew A. Russell, Larry E. Murphy, David L. Conlin

Department of Chemistry: Faculty Publications

The USS Arizona has remained submerged in Pearl Harbor, Hawaii, since the Japanese attack on December 7, 1941. The ship presents a potential hazard from fuel oil still present in the ship’s hull. As an important factor in management decisions, the effect of corrosion after nearly 65 years is being studied to determine the integrity of the ship’s structure. Coupon samples from the hull revealed decreasing corrosion rates from ~1 to 3 mpy (0.03 to 0.08 mm/y) from just below the water surface to the mudline. This is about one-third of that expected in the absence of biofouling or concretion. …

Corrosion Of Steel Shipwrecks In The Marine Environment: Uss Arizona—Part 2, Donald L. Johnson, Brent M. Wilson, James D. Carr, Matthew A. Russell, Larry E. Murphy, David L. Conlin

Department of Chemistry: Faculty Publications

This article is a continuation of Part 1 (October 2006 MP) on the USS Arizona hull. It discusses additional methods being investigated for use in determining corrosion rates with a minimal impact on the existing structure. Marine biofouling (concretion) has accumulated on the hull. Concretion samples have been studied using x-ray diffraction, environmental electron microscopy, and corrosion potential (E_corr) to characterize the relationship between concretion and the steel substrate. The data presented in this study confirm the viability of concretion analysis as a minimum-impact procedure to estimate the corrosion rate of mild steel in seawater.

Corrosion Of Civil War Era Sub Marine Explorer—Part 2, Donald L. Johnson, James D. Carr, Brent M. Wilson, Larry E. Murphy, James P. Delgado

Department of Chemistry: Faculty Publications

The Sub Marine Explorer was designed and built by Julius H. Kroehl, who was born in Prussia in 1820. After migrating to the United States in 1838 and becoming a citizen, he served in the Union Navy (United States Navy during the Civil War) as an underwater demolitions expert. He left the Navy in 1863 and began designing a “sub-marine” that would facilitate Union forces’ mine removal and obstruction clearance. At the end of the Civil War, he became an engineer for the Pacific Pearl Co., an organization interested in using the craft to recover pearls from deep sea oyster …

Corrosion Of Civil War Era Sub Marine Explorer—Part 1, Donald L. Johnson, James D. Carr, Brent M. Wilson, Larry E. Murphy, James P. Delgado

Department of Chemistry: Faculty Publications

The Sub Marine Explorer is one of five submersibles (submarines) constructed prior to 1870 that have survived either in museums or as in situ archaeological sites around the world. Since 1869, the wreck of Explorer has emerged at low tide on the beach of Isla San Telmo, Archipiélago de las Perlas, Panama, located ~75 km southwest of Panama City in the Bay of Panama. In 2001, James Delgado visited the site. Locals described the wreck as a World War II-era Japanese midget submarine. Delgado consulted with Richard Wills, an expert on American Civil War submarines, and confirmed that the well-preserved …

Method For Monitoring The Stereoselectivity And Relative Rate Of Organic Chemical Reactions, David R. Berkowitz, Sangeeta Dey, Kannan R. Karukurichi, Weijun Shen

Department of Chemistry: Faculty Publications

A method for monitoring the stereoselectivity of at least one organic chemical reaction and the relative rate of at least one organic chemical reaction, wherein the reaction produces a product that can exist as at least two stereoisomers, is provided herein. Also disclosed are methods for identifying and preparing catalysts for the above reactions.

Immobilization Method For Producing Active Α1-Acid Glycoprotein, David S. Hage, Hai Xuan

Department of Chemistry: Faculty Publications

A method and kit for immobilization of a glycoprotein. The method may include activating an affinity Support. The affinity Support may be activated by reacting the affinity Support with a compound that is reactive with one or more functional groups included within the glycoprotein. The method may also include oxidizing the glycoprotein in which oxidation conditions are selected to yield an oxidized glycoprotein that is biologically active and contains a Sufficient number of reactive aldehyde groups for coupling to a Support. For example, the oxidized glycoprotein may include five reactive aldehyde groups. In addition, the method may include reacting the …

A Multi-Step Nmr Screen For The Identification And Evaluation Of Chemical Leads For Drug Discovery, Kelly A. Mercier, Matthew D. Shortridge, Robert Powers

Department of Chemistry: Faculty Publications

A multi-step NMR based screening assay is described for identifying and evaluating chemical leads for their ability to bind a target protein. The multi-step NMR assay provides structure-related information while being an integral part of a structure based drug discovery and design program. The fundamental principle of the multi-step NMR assay is to combine distinct 1D and 2D NMR techniques, in such a manner, that the inherent strengths and weakness associated with each technique is complementary to each other in the screen. By taking advantage of the combined strengths of 1D and 2D NMR experiments, it is possible to minimize …

Anhydrous Fluoride Salts And Reagents And Methods For Their Production, Stephen G. Dimagno, Haoran Sun

Department of Chemistry: Faculty Publications

Anhydrous organic fluoride salts and reagents prepared by a method comprising the nucleophilic Substitution of a fluorinated aromatic or fluorinated unsaturated organic compound with a salt having the formula: [Q_nM]^x+A_x^- in an inert polar, aprotic solvent; wherein M is an atom capable of supporting a formal positive charge, the n groups Q are independently varied organic moieties, n is an integer such that the [Q_nM] carries at least one formal positive charge, x is an integer defining the number of formal positive charge(s), +, carried by the [Q_nM], A^{- …}

Structure And Biosynthesis Of Heat-Stable Antifungal Factor (Hsaf), A Broad-Spectrum Antimycotic With A Novel Mode Of Action, Fengan Yu, Kathia Zaleta-River, Xiangcheng Zhu, Justin Huffman, Jeffrey C. Millet, Steven D. Harris, Gary Y. Yuen, Xing-Cong Li, Liangcheng Du

Department of Chemistry: Faculty Publications

A screen for antifungal compounds from Lysobacter enzymogenes strain C3, a bacterial biological control agent of fungal diseases, has previously led to the isolation of heat-stable antifungal factor (HSAF). HSAF exhibits inhibitory activities against a wide range of fungal species and shows a novel mode of antifungal action by disrupting the biosynthesis of a distinct group of sphingolipids. We have now determined the chemical structure of HSAF, which is identical to that of dihydromaltophilin, an antifungal metabolite with a unique macrocyclic lactam system containing a tetramic acid moiety and a 5,5,6-tricyclic skeleton. We have also identified the genetic locus responsible …

Corrosion Studies On The Uss Arizona With Application To A Japanese Midget Submarine, Brent M. Wilson, Donald L. Johnson, Hans Vantilburg, Matthew A. Russell, Larry E. Murphy, James D. Carr, Robert J. De Angelis, David L. Conlin

Department of Chemistry: Faculty Publications

The assessment of corrosion on the USS Arizona included the pioneering development of a minimum-impact cost-effective technique to determine the corrosion rate of steel-hulled shipwrecks in seawater. The technique, with potential application worldwide, is illustrated in this paper with the application to a World War II Japanese midget submarine submerged in deep waters off the Oahu, Hawaii, coast.

A Minimum-Impact Method For Measuring Corrosion Rate Of Steel-Hulled Shipwrecks In Seawater, Matthew A. Russell, David L. Conlin, Larry E. Murphy, Donald L. Johnson, Brent M. Wilson, James D. Carr

Department of Chemistry: Faculty Publications

Current research on USS Arizona is focused on a minimum-impact technique for calculating corrosion rate of the battleship’s steel hull by analysing physical and chemical properties of marine encrustation covering the exposed hull. An equation is derived that allows concretion thickness, density, and total iron content to be used to calculate corrosion rate of steel hull plate.

Analysis Of Free Analyte Fractions By Rapid Affinity Chromatography, David S. Hage, William A. Clarke

Department of Chemistry: Faculty Publications

The invention is generally directed toward an analytical method to determine the concentration of the free analyte fraction in a sample. More particularly, the method encompasses applying a sample comprising a free and bound analyte fraction to an affinity column capable of selectively extracting the free fraction in the millisecond time domain. The signal generated by the free fraction is then quantified by standard analytical detection techniques. The concentration of the free fraction may then be determined by comparison of its signal with that of a calibration curve depicting the signal of known concentration of the same analyte.

Oligothiophenes And Synthesis Thereof, Andrzej Rajca

Department of Chemistry: Faculty Publications

Novel oligothiophenes and intermediates therefor are disclosed together with a process for synthesizing them. The oligothiophenes are in the form of a helix which contains five-membered rings unsaturated heterocycles that are cross-conjugated and annelated into a helix.

Preliminary X-Ray Diffraction Studies Of The Transcriptional Inhibitory Antibody Fab41.4, Johanna Mazlo, Robyn L. Stanfield, Ian A. Wilson, Steven H. Hinrichs, John J. Stezowski

Department of Chemistry: Faculty Publications

The binding of transcription factor ATF-1 to DNA contributes to gene expression and regulation of cell growth. Antibody Mab41.4, raised against ATF-1, and its derivatives Fab41.4 and scFv41.4 inhibit specific DNA binding in vitro and induce apoptotic death of tumor cells in vivo. Structural studies of Fab41.4 were performed to gain insight into the mechanism of action of this potentially therapeutic antibody. The optimal conditions for crystallization of Fab41.4 were determined. Crystals were needle-like in appearance, displayed C2 space-group symmetry and diffracted to a resolution of 1.6 Å. The unit-cell parameters were determined to be a = 186.64, b = …

Octafluoro-Meso Tetraarylporphyrins And Methods For Making These Compounds, Stephen G. Dimagno

Department of Chemistry: Faculty Publications

The novel compounds of the present invention are f-octafluoro-meso-tetraarylporphyrins of formula (I) and their metallic complexes of formula (II):

B-octafluoro-meso-tetraaryl porphyrins are Synthesized by reacting 3,4-difluoropyrrole with an aromatic aldehyde in the presence of boron trifluoride etherate, followed by oxidation. The difluoropyrrole used in this reaction is pro duced by reacting 3,3,4,4-tetrafluoropyrroline or its corre sponding Salt, 3,3,4,4-tetrafluoropyrrolidinium Salt, with a base Such as potassium tert-butoxide. The metalloporphyrins of the present invention are Synthesized by deprontonating B-octafluoro-meso-tetraarylporphyrin ligands and treating Said ligands with metal ions.