Analytical Chemistry Commons^™

Bulk Properties Of Solution-Synthesized Chevron-Like Graphene Nanoribbons, Timothy H. Vo, Mikhail Shekhirev, Alexey Lipatov, Rafal A. Korlacki, Alexander Sinitskii

Department of Chemistry: Faculty Publications

Graphene nanoribbons (GNRs) have received a great deal of attention due to their promise for electronic and optoelectronic applications. Several recent studies have focused on the synthesis of GNRs by the bottom-up approaches that could yield very narrow GNRs with atomically precise edges. One type of GNRs that has received a considerable attention is the chevron-like GNR with a very distinct periodic structure. Surface-assisted and solution-based synthetic approaches for the chevron-like GNRs have been developed, but their electronic properties have not been reported yet. In this work, we synthesized chevron-like GNRs in bulk by a solution-based method, characterized them by …

Highly Selective Gas Sensor Arrays Based On Thermally Reduced Graphene Oxide, Alexey Lipatov, Alexey Varezhnikov, Peter Wilson, Victor Sysoev, Andrei Kolmakov, Alexander Sinitskii

Department of Chemistry: Faculty Publications

The electrical properties of reduced graphene oxide (rGO) have been previously shown to be very sensitive to surface adsorbates, thus making rGO a very promising platform for highly sensitive gas sensors. However, poor selectivity of rGO-based gas sensors remains a major problem for their practical use. In this paper, we address the selectivity problem by employing an array of rGO-based integrated sensors instead of focusing on the performance of a single sensing element. Each rGO-based device in such an array has a unique sensor response due to the irregular structure of rGO films at different levels of organization, ranging from …

Structure And Function Of Preq1 Riboswitches, Catherine D. Eichhorn, Mijeong Kang, Juli Feigon

Department of Chemistry: Faculty Publications

PreQ₁ riboswitches help regulate the biosynthesis and transport of PreQ₁ (7-aminomethyl-7- deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of PreQ₁ riboswitches have been identified (PreQ₁-I and PreQ₁-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon PreQ₁ binding, each of which has distinct unusual features and modes …

Metallurgical And Corrosion Assessment Of Submerged Tanker S.S. Montebello, Dana Medlin, James D. Carr, Donald L. Johnson, David L. Conlin

Department of Chemistry: Faculty Publications

The Union Oil Tanker S.S. Montebello was torpedoed and sunk six miles (9.7 km) off the coast of Cambria, California by a Japanese submarine on December 23, 1941, two weeks after the attack on Pearl Harbor. With close proximity to the National Monterey Bay Marine Sanctuary, concern about possible crude oil contamination led to the most recent expedition to the site in October 2011. Assessment of the shell plate found that the average corrosion rate was very low and the structure will remain stable for many decades.

Advances In Chemical And Structural Characterization Of Concretion With Implications For Modeling Marine Corrosion, Donald L. Johnson, Robert J. Deangelis, Dana J. Medlin, James D. Carr, David L. Conlin

Department of Chemistry: Faculty Publications

The Weinsnumber model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selectedarea EDS …

Analogues Of (-)-Picropodophyllin, Synthesis And Uses Thereof, David B. Berkowitz, Sylvain Broussy

Department of Chemistry: Faculty Publications

Analogs of (-)-Picropodophyllin, synthesis thereof, and uses in pharmaceuticals as inhibitors of IGF1RK.

Fluorination Of Aromatic Ring Systems, Stephen G. Dimagno

Department of Chemistry: Faculty Publications

This disclosure relates to reagents and methods useful in the synthesis of aryl fluorides, for example, in the preparation of ¹⁸F labeled radiotracers. 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.

The Development And Applications Of Nmr Metabolomics Analysis Of Bacterial Metabolomes, Steven M. Halouska

Department of Chemistry: Dissertations, Theses, and Student Research

Metabolomics is a relatively new field that involves the study of metabolic responses that are occurring within a biological system. Metabolite profiles of an organism, tissue extract, and biofluids are important indicators to determine the physiological state of a biological profile. Comparison of such profiles from different phenotypes can be used to identify specific metabolic changes leading to the understanding of metabolic pathways, disease progression, drug toxicity and efficacy, and cellular responses to different intracellular and extracellular conditions. Metabolomics investigations often use sophisticated analytical techniques such as NMR spectroscopy to provide an unbiased and comprehensive approach to evaluate metabolic perturbation …

Reliable Peak Selection For Multisample Analysis With Comprehensive Two-Dimensional Chromatography, Stephen E. Reichenbach, Xue Tian, Akwasi A. Boateng, Charles A. Mullen, Chiara Cordero, Qingping Tao

School of Computing: Faculty Publications

Comprehensive two-dimensional chromatography is a powerful technology for analyzing the patterns of constituent compounds in complex samples, but matching chromatographic features for comparative analysis across large sample sets is difficult. Various methods have been described for pairwise peak matching between two chromatograms, but the peaks indicated by these pairwise matches commonly are incomplete or inconsistent across many chromatograms. This paper describes a new, automated method for postprocessing the results of pairwise peak matching to address incomplete and inconsistent peak matches and thereby select chromatographic peaks that reliably correspond across many chromatograms. Reliably corresponding peaks can be used both for directly …

Utilizing Nmr Spectroscopy And Molecular Docking As Tools For The Structural Determination And Functional Annotation Of Proteins, Jaime Stark

Department of Chemistry: Dissertations, Theses, and Student Research

With the completion of the Human Genome Project in 2001 and the subsequent explosion of organisms with sequenced genomes, we are now aware of nearly 28 million proteins. Determining the role of each of these proteins is essential to our understanding of biology and the development of medical advances. Unfortunately, the experimental approaches to determine protein function are too slow to investigate every protein. Bioinformatics approaches, such as sequence and structure homology, have helped to annotate the functions of many similar proteins. However, despite these computational approaches, approximately 40% of proteins still have no known function. Alleviating this deficit will …

Overexpression Of Human Fatty Acid Transport Protein 2/Very Long Chain Acyl-Coa Synthetase 1 (Fatp2/Acsvl1) Reveals Distinct Patterns Of Trafficking Of Exogenous Fatty Acids, Elaina M. Melton, Ronald Cerny, Concetta C. Dirusso, Paul N. Black

Ronald Cerny Publications

In mammals, the fatty acid transport proteins (FATP1 through FATP6) are members of a highly conserved family of proteins, which function in fatty acid transport proceeding through vectorial acylation and in the activation of very long chain fatty acids, branched chain fatty acids and secondary bile acids. FATP1, 2 and 4, for example directly function in fatty acid transport and very long chain fatty acids activation while FATP5 does not function in fatty acid transport but activates secondary bile acids. In the present work, we have used stable isotopically labeled fatty acids differing in carbon length and saturation in cells …

A Facile, Low-Cost Route For The Preparation Of Calcined Porous Calcite And Dolomite And Their Application As Heterogeneous Catalysts In Biodiesel Production, Rui Wang, Hu Li, Fei Chang, Jiafeng Luo, Milford A. Hanna, Daoyang Tan, Deyu Hu, Yuping Zhang, Baoan Song, Song Yang

Department of Chemistry: Faculty Publications

Despite their potential for biodiesel synthesis, directly calcined minerals rich in magnesium/calcium carbonates are used at the expense of large amounts of the catalyst, high alcohol loading, long processing times, and severe conditions. We report a facile and low-cost route for preparing calcined porous calcite (CPC) and dolomite (CPD) via simple thermal decomposition of the reaction mixtures of natural calcite and dolomite with stearic acid. CPC and CPD, both of which have porous structures, were compared with previously reported catalysts and examined as promising heterogeneous base catalysts under mild conditions. A 40% increase in conversion through CPC and CDC was …

Re2o7-Catalyzed Reaction Of Hemiacetals And Aldehydes With O-, S-, And C-Nucleophiles, Wantanee Sittiwong, Michael W. Richardson, Charles E. Schiaffo, Thomas J. Fisher, Patrick H. Dussault

Department of Chemistry: Faculty Publications

Re(VII) oxides catalyze the acetalization, monoperoxyacetalization, monothioacetalization and allylation of hemiacetals. The reactions, which take place under mild conditions and at low catalyst loadings, can be conducted using hemiacetals, the corresponding O-silyl ethers, and, in some cases, the acetal dimers. Aldehydes react under similar conditions to furnish good yields of dithioacetals. Reactions of hemiacetals with nitrogen nucleophiles are unsuccessful. 1,2-Dioxolan-3-ols (peroxyhemiacetals) undergo Re(VII)-promoted etherification but not allylation. Hydroperoxyacetals (1-alkoxyhydroperoxides) undergo selective exchange of the alkoxide group in the presence of either Re₂O₇ or a Brønsted acid.

Stress Reduction For Pillar Filled Structures, Rebecca J. Nikolic, Adam Conway, Qinghui Shao, Lars Voss, Chin Li Cheung, Mushtaq A. Dar

Department of Chemistry: Faculty Publications

According to one embodiment, an apparatus for detecting neutrons includes an array of pillars, wherein each of the pillars comprises a rounded cross sectional shape where the cross section is taken perpendicular to a longitudinal axis of the respective pillar, a cavity region between each of the pillars, and a neutron sensitive material located in each cavity region.

High-Performance Flexible Solid-State Supercapacitors Based On Mno2-Decorated Nanocarbon Electrodes, Yang Gao, Yun Shen Zhou, Min Qian, Hao Ming Li, Jody G. Redepenning, Li Sha Fan, Xiang Nan He, Wei Xiong, Masoud Majhouri-Samani, Lan Jiang, Yongfeng Lu

Department of Chemistry: Faculty Publications

Flexible energy storage units are highly desired to meet the ever-increasing demands for flexible electronics. In this paper, highly flexible solid-state supercapacitors are fabricated using MnO₂-decorated nanocarbon electrodes and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide–poly(vinylidene fluoride)- hexafluoropropylene ([EMIM][NTf2]–PVdF(HFP)) gel electrolytes. The flexible electrodes are prepared by electrodepositing MnO₂ onto the carbon nanotube/carbon nanoonion (CNT/CNO) films. CNT/CNO films have a large surface area for MnO₂ deposition and work as mechanical supports with high flexibility and light weight. CNOs act as spacers to separate CNTs, introducing mesopores inside the CNT/CNO films for preventing pore blocking during MnO₂ deposition. The supercapacitor exhibits …

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.

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.

Homogeneous Connectivity Of Potential Energy Network In A Solidlike State Of Water Cluster, Takuma Akimoto, Toshihiro Kaneko, Kenji Yasuoka, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A novel route to the exponential trapping-time distribution within a solidlike state in water clusters is described. We propose a simple homogeneous network (SHN) model to investigate dynamics on the potential energy networks of water clusters. In this model, it is shown that the trappingtime distribution in a solidlike state follows the exponential distribution, whereas the trapping-time distribution in local potential minima within the solidlike state is not exponential. To confirm the exponential trapping-time distribution in a solidlike state, we investigate water clusters, (H₂O)₆ and (H₂O)12, by molecular dynamics simulations. These clusters change dynamically from …

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.

Polymorphism And Polyamorphism In Bilayer Water Confined To Slit Nanopore Under High Pressure, Jaeil Bai, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

A distinctive physical property of bulk water is its rich solid-state phase behavior, which includes 15 crystalline (ice I–ice XIV) and at least 3 glassy forms ofwater, namely, low-density amorphous, highdensity amorphous, and very-high-density amorphous (VHDA). Nanoscale confinement adds a new physical variable that can result in a wealth of new quasi-2D phases of ice and amorphous ice. Previous computer simulations have revealed that when water is confined between two flat hydrophobic plates about 7–9 Å apart, numerous bilayer (BL) ices (or polymorphs) can arise [e.g., BL-hexagonal ice (BL-ice I)]. Indeed, growth of the BL-ice I through vapor deposition on …

Long-Range Ordered Carbon Clusters: A Crystalline Material With Amorphous Building Blocks, Lin Wang, Bingbing Liu, Hui Li, Wenge Yang, Yang Ding, Stanislav V. Sinogeikin, Yue Meng, Zhenxian Liu, Xiao Cheng Zeng, Wendy L. Mao

Xiao Cheng Zeng Publications

Solid-state materials can be categorized by their structures into crystalline (having periodic translation symmetry), amorphous (no periodic and orientational symmetry), and quasi-crystalline (having orientational but not periodic translation symmetry) phases. Hybridization of crystalline and amorphous structures at the atomic level has not been experimentally observed. We report the discovery of a long-range ordered material constructed from units of amorphous carbon clusters that was synthesized by compressing solvated fullerenes. Using x-ray diffraction, Raman spectroscopy, and quantum molecular dynamics simulation, we observed that, although carbon-60 cages were crushed and became amorphous, the solvent molecules remained intact, playing a crucial role in maintaining …

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 …

Unusual Activities Of The Thioesterase Domain For The Biosynthesis Of The Polycyclic Tetramate Macrolactam Hsaf In Lysobacter Enzymogenes C3, Lili Lou, Haotong Chen, Ronald Cerny, Yaoyao Li, Yuemao Shen, Liangcheng Du

Ronald Cerny Publications

HSAF is an antifungal natural product with a new mode of action. A rare bacterial iterative PKSNRPS assembles the HSAF skeleton. The biochemical characterization of the NRPS revealed that the thioesterase (TE) domain possesses the activities of both a protease and a peptide ligase. Active site mutagenesis, circular dichroism spectra and homology modeling of the TE structure suggested that the TE may possess uncommon features that may lead to the unusual activities. The iterative PKS-NRPS is found in all polycyclic tetramate macrolactam gene clusters, and the unusual activities of the TE may be common to this type of hybrid PKS-NRPS.

Ƴ-Selective Directed Catalytic Asymmetric Hydroboration Of 1,1-Disubstituted Alkenes, Sean M Smith, Gia L. Hoang, Rhitankar Pal, Mohammad O. Bani Khaled, Liberty S. W. Pelter, Xiao Cheng Zeng, James M. Takacs

Xiao Cheng Zeng Publications

Directed catalytic asymmetric hydroborations of 1,1-disubstituted alkenes afford ƴ

-dioxaborato amides and esters in high enantiomeric purity (90–95% ee).

Features For Non-Targeted Cross-Sample Analysis With Comprehensive Two-Dimensional Chromatography, Stephen E. Reichenbach, Xue Tian, Chiara Cordero, Qingping Tao

School of Computing: Faculty Publications

This review surveys different approaches for generating features from comprehensive two-dimensional chromatography for non-targeted cross-sample analysis. The goal of non-targeted cross-sample analysis is to discover relevant chemical characteristics (such as compositional similarities or differences) from multiple samples. In non-targeted analysis, the relevant characteristics are unknown, so individual features for all chemical constituents should be analyzed, not just those for targeted or selected analytes. Cross-sample analysis requires matching the corresponding features that characterize each constituent across multiple samples so that relevant characteristics or patterns can be recognized. Non-targeted, cross-sample analysis requires generating and matching all features across all samples. Applications of …

Self-Assembling Subnanometer Pores With Unusual Mass-Transport Properties, Xibin Zhou, Guande Liu, Kazuhiro Yamato, Yi Shen, Ruixian Cheng, Xiaoxi Wei, Wanli Bai, Yi Gao, Hui Li, Yi Liu, Futao Liu, Daniel M. Czajkowsky, Jingfang Wang, Michael J. Dabney, Zhonghou Cai, Jun Hu, Frank V. Bright, Lan He, Xiao Cheng Zeng, Zhifeng Shao, Bing Gong

Xiao Cheng Zeng Publications

A long-standing aim in molecular self-assembly is the development of synthetic nanopores capable of mimicking the mass-transport characteristics of biological channels and pores. Here we report a strategy for enforcing the nanotubular assembly of rigid macrocycles in both the solid state and solution based on the interplay of multiple hydrogen-bonding and aromatic π − π stacking interactions. The resultant nanotubes have modifiable surfaces and inner pores of a uniform diameter defined by the constituent macrocycles. The self-assembling hydrophobic nanopores can mediate not only highly selective transmembrane ion transport, unprecedented for a synthetic nanopore, but also highly efficient transmembrane water permeability. …

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, …