Chemistry Commons^™

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 …

Investigations Of Inter- And Intramolecular C-O Bond Forming Reactions Of Peroxide Electrophiles, Benjamin W. Puffer

Department of Chemistry: Dissertations, Theses, and Student Research

A common reaction to yield ethers relies on an alkoxide nucleophile and a carbon electrophile (Williamson ether formation). Ethers can also be formed by reactions with carbon nucleophiles and oxygen electrophiles by way of the peroxide functional group. We screened a number of carbon nucleophiles suitable for attack on dialkyl peroxides to form new C-O bonds. Also a novel approach using a peroxyketal electrophile is shown to increase the efficiency of this intermolecular reaction. This method of C-O bond formation can also be implemented intramolecularly, not seen before in the literature, to yield cyclic ethers. This approach requires the generation …

The Use Of Rhenium (Vii) Oxide As A Catalyst For The Substution Of Hemiacetals, Michael W. Richardson

Department of Chemistry: Dissertations, Theses, and Student Research

Rhenium (VII) oxides have proven to be mild and versatile catalysts in organic chemistry. They have previously been utilized to catalyze the transposition of allylic aclohols, Prins reaction, and reductive amination to name a few examples. This thesis reports the application of Re(VII) oxide in the substitution of hemi-acetals with a wide array of nucleophiles including oxo-, thio-, and peroxy-nucleophiles. These reactions proceed efficiently with rapid reaction times and high yields.

Adviser: Patrick H. Dussault

Using Slow-Release Permanganate Candles To Remove Tce From A Low Permeable Aquifer At A Former Landfill, Mark D. Christenson, Ann Kambhu, Steve D. Comfort

School of Natural Resources: Faculty Publications

Past disposal of industrial solvents into unregulated landfills is a significant source of groundwater contamination. In 2009, we began investigating a former unregulated landfill with known trichloroethene (TCE) contamination. Our objective was to pinpoint the location of the plume and treat the TCE using in situ chemical oxidation (ISCO). We accomplished this by using electrical resistivity imaging (ERI) to survey the landfill and map the subsurface lithology. We then used the ERI survey maps to guide direct push groundwater sampling. A TCE plume (100-600 µg L^-1) was identified in a low permeable silty-clay aquifer (K_h = 0.5 …

Restricted Access Media And Methods For Making Restricted Access Media, David S. Hage, Chunling Wa, Abby Jackson, Hai Xuan

David Hage Publications

The present invention is directed to restricted access media (RAM), methods for preparing restricted access media, and kits for preparing restricted access media that contain protected ligand binding agents or protected enzymes. Certain RAM provided contain a plurality of protected regions of the Support that contain ligand binding agents that are protected by blocking agents. Certain RAM provided contain a plurality of protected regions of the support that contain unbound ligand binding agents or enzymes that are retained in the protected regions by a capping agent. Methods of making the RAM of the invention and associated kits are also provided.

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 …

Experimental And Theoretical Studies In Nuclear Magnetic Resonance, John D. Persons

Department of Chemistry: Dissertations, Theses, and Student Research

Nuclear Magnetic Resonance (NMR) has proven to be an excellent tool to probe the structure of molecules by gaining insight into nuclear interactions. Used in conjunction with theoretical calculations, NMR has the potential to elucidate these nuclear interactions and how they affect structure, bonding and dynamics on a molecular scale. The first two projects presented herein study the peroxide explosive hexamethylene triperoxide diamine (HMTD). In the first project, we use the characteristics of the solid-state NMR lineshape to determine the ¹⁴N quadrupole coupling constant (C_Q). The second project uses multi-dimensional solution-state NMR and chiral shift reagents …

Experimental And Theoretical Studies In Solid-State Nuclear Magnetic Resonance, Monica N. Kinde

Department of Chemistry: Dissertations, Theses, and Student Research

Solid-state nuclear magnetic resonance (SSNMR) has proven to be a powerful tool for probing molecular structure and dynamics. Deuterium SSNMR is particularly useful due to the presence of anisotropic interactions whose motional averaging contributes structural and dynamical insight. The magnitude and type of molecular motion can be determined from analysis of solid echo deuterium lineshapes and/or relaxation studies. This work uses various applications of solid-state NMR as well as ab initio and density functional computational methods to study three different areas of physical chemistry: biophysical chemistry, materials science and fundamental concepts of physical chemistry. The first project addressed the dynamics …

Data Mining Of Protein Databases, Christopher Assi

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Data mining of protein databases poses special challenges because many protein databases are non-relational whereas most data mining and machine learning algorithms assume the input data to be a relational database. Protein databases are non-relational mainly because they often contain set data types. We developed new data mining algorithms that can restructure non-relational protein databases so that they become relational and amenable for various data mining and machine learning tools. We applied the new restructuring algorithms to a pancreatic protein database. After the restructuring, we also applied two classification methods, such as decision tree and SVM classifiers and compared their …

Directed Catalytic Asymmetric Hydroboration Of 1,1-Disubstituted Alkenes, Mohammad Odeh Bani Khaled

Department of Chemistry: Dissertations, Theses, and Student Research

Since the beginning of catalytic asymmetric hydroboration (CAHB) in 1989, many new approaches have been developed. Developing an efficient method of catalytic asymmetric hydroboration to produce useful chiral organoboranes is still a challenge due to limited success with a small range of substrates. Typically, effective CAHB requires the presence of vinylarene moiety or a particular substitution pattern around the alkene. One area of research in the Takacs group has been to expand this substrate scope by incorporating two-point binding to direct the reaction to one regioisomer selectively. CAHB of two-point binding substrates in the presence of simple chiral monophosphite and …

Unleashing A “True” Pser-Mimic In The Cell, Kaushik Panigrahi, David L. Nelson, David B. Berkowitz

David Berkowitz Publications

In this issue of Chemistry & Biology, Arrendale and coworkers demonstrate a new prodrug strategy for intracellular delivery of an α, α-(difluoromethylene)phosphonate phosphoserine mimic. The deprotected pseudo-phosphopeptide releases the pro-apoptotic FOXO3a-transcription factor from its 14-3-3-adaptor protein complex, resulting in leukemic cell death.

Regioselective Synthesis Of Tetraalkynylarenes By Consecutive Dual Sonogashira Coupling Reactions Of The Bis(Triflate) Of 4,5-Diiodobenzene-1,2-Diol, Thomas J. Fisher, Patrick H. Dussault

Patrick Dussault Publications

Abstract The regioselective synthesis of nonsymmetric tetraalkynylarenes has been readily achieved through consecutive sets of Sonagashira cross-coupling reactions of the bis(triflate) derivative of 4,5-diiodobenzene-1,2-diol. The initial coupling reactions proceeded with nearly complete selectivity for the reaction at the Ar–I linkages. Subsequent coupling reactions at the Ar–OTf linkages were efficiently conducted. The tetraalkynylarene products are of interest as components of organic molecular materials.

I. Synthesis Of Β-Sitosterol And Phytosterol Esters; Ii. New Methodology For Singlet Oxygen Generation From 1,1-Dihydroperoxides, Jiliang Hang

Department of Chemistry: Dissertations, Theses, and Student Research

Phytosterols are steroid compounds structurally similar with cholesterol and vary in the nature of carbon side chain. β-Sitosterol is commercially available in preparative amount only as mixtures with other phytosterols. New semipreparative synthesis of pure β-sitosterol and sidechain-modified phytosterols is discussed in this dissertation. This new synthesis is achieved via a temporary masking of the stigmasterol 5,6-alkene as an epoxide. Following performance of the desired modification, the alkene is regenerated through a mild deoxygenation. Preparation of phytosterol esters for cholesterol metabolism study is also discussed in this dissertation.

Singlet oxygen (¹O₂) is the lowest excited state …

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

Chemistry Department: 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 …

Rhodium-Catalyzed Hydroboration Of 1,1-Disubstituted Alkenes, Scott A. Pettibone

Department of Chemistry: Dissertations, Theses, and Student Research

Enantioselective rhodium-catalyzed hydroboration is becoming an increasingly important asymmetric transformation of alkenes based upon the utility of the organo boranate ester intermediate. The newly acquired asymmetric C-B bond can be converted to C-O, C-N, C-C bonds and the organo borante can be coupled to SP2 hybridized halogen bonds, all with retention of configuration. Catalyzed hydroboration of 1,1-disubstituted alkenes are an especially challenging substrate class for this enantioselective transformation. The difficulty for catalysts to distinguish between the two enantiotopic faces of the olefin is one of the major issues that have to be overcome to achieve a desirable level of enantioselectivity. …

Halocarbocyclization Entry Into The Oxabicyclo[4.3.1]Decyl Exomethylene-Δ-Lactone Cores Of Linearifolin And Zaluzanin A - Exploiting Combinatorial Catalysis, Sandeep K. Ginotra, Jacob A. Friest, David B. Berkowitz

David Berkowitz Publications

A streamlined entry into the sesquiterpene lactones (SQL) cores of linearifolin and zaluzanin A is described. Stereochemistry is controlled through transformations uncovered by ISES (In-Situ- Enzymatic-Screening). Absolute stereochemistry derives from kinetic resolution of 5- benzyloxypentene-1,2-oxide, utilizing a β-pinene-derived-Co(III)-salen. Relative stereochemistry (1,3-cis-fusion)is set via formal halometalation/carbocyclization, mediated by [Rh(O₂CC₃F₇)₂]₂/ LiBr. Subsequent ring-closing metathesis (RCM-Grubbs II) yields the title exomethylene-δ- lactone SQL-cores. In complementary fashion, RCM with Grubbs-I catalyst provides the oxabicyclo[3.3.1]nonyl-core of xerophilusin R and zinagrandinolide.

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.

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

Chemistry Department: 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, …

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

Chemistry Department: 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.

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

Chemistry Department: 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 …

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).

Accessibility And Selective Stabilization Of The Principal Spin States Of Iron By Pyridyl Versus Phenolic Ketimines: Modulation Of The 6A1 ↔ 2T2 Ground-State Transformation Of The [Fen4O2]+ Chromophore, Musa S. Shongwe, Usama A. Al-Zaabi, Faizah Al-Mjeni, Carla S. Eribal, Imaddin A. Al-Omari, Hussein H. Hamdeh, Dariusz Matoga, Harry Adams, Michael J. Morris, Arnold L. Rheingold, Eckhard Bill, David J. Sellmyer

David Sellmyer Publications

Several potentially tridentate pyridyl and phenolic Schiff bases (apRen and HhapRen, respectively) were derived from the condensation reactions of 2-acetylpyridine (ap) and 2′-hydroxyacetophenone (Hhap), respectively, with N-R-ethylenediamine (RNHCH₂CH₂NH₂, Ren; R = H, Me or Et) and com-plexed in situ with iron(II) or iron(III), as dictated by the nature of the ligand donor set, to generate the six-coordinate iron compounds [Fe^II(apRen)₂]X₂ (R = H, Me; X– = ClO4–, BPh4–, PF6–) and [Fe^III(hapRen)₂]X (R = Me, Et; X– = ClO_4–, BPh_4–). Single-crystal X-ray …

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 …