Chemistry Commons^™

Structure Evolution Of Gold Cluster Anions Between The Planar And Cage Structures By Isoelectronic Substitution: AuN− (N = 13–15) And MauN− (N = 12–14; M = Ag, Cu), Rhitankar Pal, Lei-Ming Wang, Wei Huang, Lai-Sheng Wang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

The structural and electronic effects of isoelectronic substitution by Ag and Cu atoms on gold cluster anions in the size range between 13 and 15 atoms are studied using a combination of photoelectron spectroscopy and first-principles density functional calculations. The most stable structures of the doped clusters are compared with those of the undoped Au clusters in the same size range. The joint experimental and theoretical study reveals a new C_3v symmetric isomer for Au₁₃ ⁻, which is present in the experiment, but has hitherto not been recognized. The global minima of Au₁₄ ⁻ and Au …

Human Fatty Acid Transport Protein 2a/Very Long Chain Acyl-Coa Synthetase 1 (Fatp2a/Acsvl1) Has A Preference In Mediating The Channeling Of Exogenous N-3 Fatty Acids Into Phosphatidylinositol, Elaina M. Melton, Ronald Cerny, Paul A. Watkins, Concetta C. Dirusso, Paul N. Black

Ronald Cerny Publications

The trafficking of fatty acids across the membrane and into downstream metabolic pathways requires their activation to CoA thioesters. Members of the fatty acid transport protein/ very long chain acyl-CoA synthetase (FATP/Acsvl) family are emerging as key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis.We have expressed two naturally occurring splice variants of human FATP2 (Acsvl1) in yeast and 293T-REx cells and addressed their roles in fatty acid transport, activation, and intracellular trafficking. Although both forms (FATP2a (Mr 70,000) and FATP2b (Mr 65,000 and lacking exon3, which encodes part of the …

Overexpression Of Galnac-Transferase Galnac-T3 Promotes Pancreatic Cancer Cell Growth, Keisuke Taniuchi, Ronald Cerny, Aki Tanouchi, Kimitoshi Kohno, Norihiro Kotani, Koichi Honke, Toshiji Saibara, Michael A. Hollingsworth

Ronald Cerny Publications

O-linked glycans of secreted and membrane bound proteins play an important role in the pathogenesis of pancreatic cancer by modulating immune responses, inflammation, and tumorigenesis. A critical aspect of O-glycosylation, the position at which proteins are glycosylated with N-acetyl-galactosamine on serine and threonine residues, is regulated by the substrate specificity of UDP-GalNAc: polypeptide N-acetylgalactosaminyl-transferases (GalNAc-Ts). Thus, GalNAc-Ts regulate the first committed step in O-glycosylated protein biosynthesis, determine sites of O-glycosylation on proteins, and are important for understanding normal and carcinoma-associated O-glycosylation. We have found that one of these enzymes, GalNAc-T3, is overexpressed in …

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.

Ultrasonic Activation Of Triacetone Triperoxide, Latravia R. Dobson

Department of Chemistry: Dissertations, Theses, and Student Research

Triacetone triperoxide (TATP) is an organic peroxide that has received widespread attention in recent years. TATP is a ketone peroxide with a high active oxygen content. It is relatively shock sensitive, with explosive decomposition easily initiated, and is therefore considered a primary explosive. However, TATP is also a powerful explosive possessing about 83 % of the power of TNT. TATP can be prepared quickly and easily from inexpensive household chemicals in the absence of any specialized facilities, making it the explosive of choice for modern day terrorists. TATP poses a major challenge for security and law enforcement services around the …

Synthesis And Catalytic Activity Of Nanostructured Cerium Oxide, Neil J. Lawrence

Department of Chemistry: Dissertations, Theses, and Student Research

Cerium oxide (ceria, CeO_2-x where x is 0 to 0.5) has been one of the most widely used heterogeneous catalysts particularly in three way catalytic converters. Most of the catalytic traits can be attributed to two properties of ceria: first, the high mobility and storage capacity of oxygen within the lattice; second, the ease with which cerium changes between Ce³⁺ and Ce⁴⁺ states. These properties, combined with the abundance of cerium on earth, make ceria a low-cost highly effective alternative to noble metal catalysts. Recent research has been focused on the nanoscale properties of ceria.

The effect …

Characteristics And Stability Of Oxide Films On Plutonium Surfaces, Harry Guillermo García Flores

Department of Chemistry: Dissertations, Theses, and Student Research

The oxidation of plutonium (Pu) metal continues to be an area of considerable activity. The reaction characteristics have significant implications for production use, storage, and disposition of this radiological material. Developing an accurate physical model of the structures, oxidation states, and oxygen concentration gradients present during oxidation are essential to understanding this process. Traditionally, the stable oxides of Pu have been thought to be plutonium sesquioxide (Pu₂O₃, O/Pu = 1.5, Pu³⁺) and plutonium dioxide (PuO₂, O/Pu = 2.0, Pu⁴⁺), existing in a layered structure on Pu metal. Many of the …

I, A New Synthetic Approach To The Synthesis Of N-(Phosphonoacetyl)-L-Ornithine. Ii, The Influence Of Pyridine On The Ozonolysis Of Alkenes, Bradley M. Johnson

Department of Chemistry: Dissertations, Theses, and Student Research

Part I. The use of chemical inhibitors to manipulate the level of amino acids in cells has proven to be invaluable in the mechanistic study of gene expression in bacteria and fungi. Here we present a new approach to the synthesis of δ‐N‐ (phosphonoacetyl)‐L‐ornithine (PALO), a potent ornithine transcarbamylase inhibitor, using a new amino acid protecting group, 9‐borabicyclononane (9‐BBN). Starting from commercially available reagents and utilizing mild reaction conditions, we were able to form PALO in fewer synthetic steps and in greater yields than previous attempts.

Part II. Ozonolysis is widely used to transform alkenes into oxygen‐rich functional groups (e.g.– …

A Concise Synthesis Of Β-Sitosterol And Other Phytosterols, Jiliang Hang, Patrick Dussault

Patrick Dussault Publications

A convenient synthesis of sidechain-modified phytosterols 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. The approach is applied to the syntheses of β-sitosterol and campesterol acetate, and suggests a facile route to the (Z)-isomers of Δ^22–23 phytosterols.

Includes Supplementary Data.

Nuclear Magnetic Resonance Affinity Screening Methods For Functional Annotation Of Proteins And Drug Discovery, Matthew D. Shortridge

Department of Chemistry: Dissertations, Theses, and Student Research

With nearly 1,350 complete genome sequences available our understanding of biology at the molecular level has never been more complete. A consequence of these sequencing projects was the discovery of large functionally unannotated segments of each genome. The genes (and proteins they encode) found in these unannotated regions are considered “hypothetical proteins”. Current estimates suggest between 12%-50% of the known gene sequences are functionally unannotated. Incomplete functional annotation of the various genomes significantly limits our understanding of biology. Pragmatically, identifying the functions of these proteins could lead to new therapeutics; making functional annotation of paramount importance.

This dissertation describes the …

Fluoride-Promoted Ligand Exchange In Diaryliodonium Salts, Bijia Wang, Ronald Cerny, Shriharsha Uppaluri, Jayson J. Kempinger, Stephen G. Dimagno

Stephen DiMagno Papers

Diaryliodonium salts are shown to undergo rapid, fluoride-promoted aryl exchange reactions at room temperature in acetonitrile. Aryl exchange is shown to be exquisitely sensitive to the concentration of fluoride ion in solution; fast exchange is observed as the fluoride concentration approaches a stoichiometric amount at 50 mM substrate concentration. The reaction is slowed, but not halted if benzene is the solvent, indicating that free fluoride ion or a four-coordinate anionic I(III) species may be responsible for the exchange. The fluoride-promoted aryl exchange reaction is general and allows direct measurement of the relative stabilities of diaryliodonium salts featuring different aryl substituents. …

Nanopod Formation Through Gold Nanoparticle Templated And Catalyzed Cross-Linking Of Polymers Bearing Pendant Propargyl Ethers, Ke Zhang, Joshua I. Cutler, Jian Zhang, Dan Zheng, Evelyn Auyeung, Chad A. Mirkin

Department of Chemistry: Faculty Publications

A novel method for synthesizing polymer nanopods from a linear polymer bearing pendant propargyl ether groups, using gold nanoparticles as both the template and the catalyst for the crosslinking reaction, is reported. The transformations involved in the cross-linking process are unprecedented on the surface of a gold particle. A tentative cross-linking mechanism is proposed.

Includes Supporting Information.

Efficient Synthesis And Conformational Investigations Of Cis-Pentacenediols, Jinyue Jiang, Charles E. Schiaffo, Chris P. Schwartz, Yong Pei, Joseph J. Dumais, Xiao Cheng Zeng, Patrick Dussault, Li Tan

Patrick Dussault Publications

Diisobutylaluminum hydride is utilized to reduce pentacene-6,13-diones to the corresponding diols, useful precursors to functionalized pentacenes. This pathway is mild and efficient, and produces the cis-diols as major products. Further, we found the cis-diols adopt endo conformation, which cannot flip to the exo conformation under ambient conditions. Due to the cis and endo orientation, the cis-diols can be potential bidentates in catalysis, molecular propellers, and optoelectronic devices.

Dna-Nanoparticle Superlattices Formed From Anisotropic Building Blocks, Matthew R. Jones, Robert J. Macfarlane, Byeongdu Lee, Jian Zhang, Kaylie L. Young, Andrew J. Senesi, Chad A. Mirkin

Department of Chemistry: Faculty Publications

Directional bonding interactions in solid-state atomic lattices dictate the unique symmetries of atomic crystals, resulting in a diverse and complex assortment of three-dimensional structures that exhibit a wide variety of material properties. Methods to create analogous nanoparticle superlattices are beginning to be realized, but the concept of anisotropy is still largely underdeveloped in most particle assembly schemes. Some examples provide interesting methods to take advantage of anisotropic effects, but most are able to make only small clusters or lattices that are limited in crystallinity and especially in lattice parameter programmability. Anisotropic nanoparticles can be used to impart directional bonding interactions …

Fragmentation Of Chloroperoxides: Hypochlorite-Mediated Dehydration Of Hydroperoxyacetals To Esters, Thomas J. Fisher, Patrick Dussault

Patrick Dussault Publications

Hypochlorites efficiently dehydrate hydroperoxyacetals to furnish the corresponding esters. The reaction, which can be accomplished with stoichometric Ca(OCl)₂ or with catalytic amounts of t-BuOCl, appears to involve formation and heterolytic fragmentation of secondary chloroperoxides, species not previously described in solution chemistry.

Includes Supporting Information (52 pp).

I, Development Of The In Situ Reductive Ozonolysis Of Alkenes With Tertiary Amine N-Oxides. Ii, Progress Toward The Asymmetric Synthesis Of Peroxyplakoric Acid A3, Christopher P. Schwartz

Department of Chemistry: Dissertations, Theses, and Student Research

Ozone, first discovered in the mid 1800’s, is a triatomic allotrope of oxygen that is a powerful oxidant. For over a century, research has been conducted into the synthetic application and mechanism of reactions of ozone with organic compounds. One of the major areas of interest has been the ozonolysis of alkenes. The production of carbonyl compounds is the most common synthetic application of ozonolysis. The generally accepted mechanism developed by Rudolf Criegee for this reaction involves the 1,3-electrocyclic addition of ozone to the π bond of the alkene to form a 1,2,3-trioxolane or primary ozonide. The primary ozonide is …

Photomediated Synthesis Of Silver Triangular Bipyramids And Prisms: The Effect Of Ph And Bspp, Jian Zhang, Mark R. Langille, Chad A. Mirkin

Department of Chemistry: Faculty Publications

The photomediated synthesis of silver right triangular bipyramids and prisms has been studied, and we have determined that pH and [BSPP]/[Ag⁺] ratio (bis(p-sulfonatophenyl)phenylphosphine, BSPP) finely control the reaction rate and, consequently, the crystal growth pathway and morphology of final products. A fast reaction rate, realized at a high pH such as 10 or 11 and a [BSPP]/[Ag⁺] ratio close to 1.0, is necessary to synthesize (100)-faceted right triangular bipyramids in high yield by preferential deposition on (111) facets of planar-twinned seeds. A slower reaction rate, which occurs at lower pH or higher [BSPP]/[Ag^{+ …}

Plant Sterol And Stanol Substrate Specificity Of Pancreatic Cholesterol Esterase, Andrew W. Brown, Jiliang Hang, Patrick H. Dussault, Timothy P. Carr

Patrick Dussault Publications

Consumption of plant sterols or stanols (collectively referred to as phytosterols) and their esters results in decreased lowdensity lipoprotein cholesterol, which is associated with decreased atherosclerotic risk. The mechanisms by which phytosterols impart their effects, however, are incompletely characterized. The objective of the present study is to determine if pancreatic cholesterol esterase (PCE; EC 3.1.1.13), the enzyme primarily responsible for cholesterol ester hydrolysis in the digestive tract, is capable of hydrolyzing various phytosterol esters and to compare the rates of sterol ester hydrolysis in vitro. We found that PCE hydrolyzes palmitate, oleate and stearate esters of cholesterol, stigmasterol, stigmastanol and …

High Temperature Rare Earth Compounds: Synthesis, Characterization And Applications In Device Fabrication, Joseph R. Brewer

Department of Chemistry: Dissertations, Theses, and Student Research

As the area of nanotechnology continues to grow, the development of new nanomaterials with interesting physical and electronic properties and improved characterization techniques are several areas of research that will be remain vital for continued improvement of devices and the understanding in nanoscale phenomenon. In this dissertation, the chemical vapor deposition synthesis of rare earth (RE) compounds is described in detail. In general, the procedure involves the vaporization of a REClx (RE = Y, La, Ce, Pr, Nd, Sm, Gd, Tb, Dy, Ho) in the presence of hydride phase precursors such as decaborane and ammonia at high temperatures and low …

Controlling Reductive Elimination From Novel I(Iii) Salts Using A Secure Method, Joseph W. Graskemper

Department of Chemistry: Dissertations, Theses, and Student Research

Positron Emission Tomography (PET) is a valuable clinical, research, and diagnostic technique for human and animal organ imaging. The current market for PET in the United States is $500 million per year and is projected to be $5.4 billion per year globally by 2015. To synthesize labeled radiotracers, we are most interested in using ¹⁸F as the isotope of choice because it is a nearly ideal positron emitting radionuclide.

Electron-rich aromatic substrates can be particularly difficult to fluorinate. We show that reductive elimination of I(III) diaryliodonium salts provide increased fluorination of electron-rich aromatic substrates. Modest yields of fluorinated product …

Theoretical And Experimental Studies In Nuclear Magnetic Resonance, Adrienne M. Roehrich

Department of Chemistry: Dissertations, Theses, and Student Research

Nuclear magnetic resonance (NMR) is a tool used to probe the physical and chemical environments of specific atoms in molecules. This research explored small molecule analogues to biological materials to determine NMR parameters using ab initio computations, comparing the results with solid-state NMR measurements. Models, such as dimethyl phosphate (DMP) for oligonucleotides or CuCl for the active site of the protein azurin, represented computationally unwieldy macromolecules. ³¹P chemical shielding tensors were calculated for DMP as a function of torsion angles, as well as for the phosphate salts, ammonium dihydrogen phosphate (ADHP), diammonium hydrogen phosphate, and magnesium dihydrogen phosphate. The …

Rhodium-Catalyzed Hydroboration: Directed Asymmetric Desymmetrization, Judy L. Miska

Department of Chemistry: Dissertations, Theses, and Student Research

Rhodium-catalyzed asymmetric hydroboration in conjunction with directing groups can be used control relative and absolute stereochemistry. Hydroboration has the potential to create new C–C, C–O, and C–N bonds from an intermediate C–B bond with retention of stereochemistry. Desymmetrization resulting in the loss of one or more symmetry elements can give rise to molecular chirality, i.e., the conversion of a prochiral molecule to one that is chiral. Unsaturated amides and esters hold the potential for two-point binding to the rhodium catalyst and have been shown to direct the regiochemistry and impact stereochemistry in asymmetric hydroborations of acyclic β,γ-unsaturated substrates. In …

Excited State Geometry Of Photoactive Yellow Protein Chromophore: A Combined Conductorlike Polarizable Continuum Model And Time-Dependent Density Functional Study, Yali Wang, Hui Li

Hui Li Publications

Analytic gradient of the combined conductorlike polarizable continuum model (CPCM) and time-dependent density functional theory method is derived and implemented. Due to the use of the fixed points with variable areas tessellation scheme, the excited state potential energy surfaces (PESs) are rigorously continuous and smooth. The CPCM/TD-B3LYP method is used to study an analog of the photoactive yellow protein chromophore, anionic thiomethyl p-coumaric acid (TMpCA⁻). Although CPCM/TD-B3LYP method may not be accurate in predicting solvent effect on vertical excitation of TMpCA⁻, it may be used to predict redshiftings of emission maxima relative to absorption maxima with …

Use Of A Robust Dehydrogenase From An Archael Hyperthermophile In Asymmetric Catalysis–Dynamic Reductive Kinetic Resolution Entry Into (S)-Profens, Jacob A. Friest, Yukari Maezato, Sylvain Broussy, Paul H. Blum, David B. Berkowitz

David Berkowitz Publications

Hyperthermophilic archaea are of great interest in evolutionary microbiology, owing to their ability to withstand high temperatures, and often extremes of pressure, pH and salinity. Enzymes from these organisms¹ may offer particular opportunities for asymmetric synthesis, complementary to approaches with mesophilic enzymes,² or those involving enzyme³ and pathway⁴ reengineering. However, perhaps due to a bias that hyperthermophilic enzymes have “narrow substrate specificities,”⁵ archaeal extremophiles remain a largely untapped resource in asymmetric synthesis.⁶

Herein, we disclose a remarkably general Dynamic Reductive Kinetic Resolution (DYRKR) entry into (S)-profens, including several important NSAIDs. The enzyme employed is …

Chromatographic Studies Of Drug-Protein Binding In Diabetes, Kathryn (Krina) S. Joseph

Department of Chemistry: Dissertations, Theses, and Student Research

Drug-protein binding can have a dramatic impact on the distribution and metabolism of a drug. This manuscript describes the use of high-performance affinity chromatography to examine the binding of various compounds to human serum albumin (HSA) in normal and diabetic disease states. The first study examined the use of four coumarin compounds as possible alternatives to warfarin as a probe for Sudlow site I on HSA. High-performance affinity chromatography and immobilized HSA columns were used to compare and evaluate the binding properties of these probe candidates. It was found from this group that 4-hydroxycoumarin was the best alternative to warfarin …

Classification, Synthesis And Characterization Of Pyridyl Porphyrin Frameworks, Lucas D. Devries

Department of Chemistry: Dissertations, Theses, and Student Research

Structural analysis of a solid-state material is vital because the structure often determines the physical (or chemical) properties of the material. An understanding of the relationship between structural components and bulk properties can be used to design materials with specific properties. To achieve such understanding, two things are required: a rigorous structural analysis method and a study of the properties of materials with noteworthy structural features. In this thesis, the author reviews 44 pyridyl porphyrin frameworks in an effort to determine how these framework structures are formed, and if any overreaching trends can be observed. The observed trends are used …

Functionalization Of Aromatic Organic Molecules By Anhydrous Fluorides And By Reductive Elimination Of Iodine(Iii), Bijia Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Solution phase reactivity of nucleophilic fluoride reagents is attenuated by ion-pairing interactions. ¹H-¹⁹F HOESY competition experiments permit generation of a fluoride ion affinity scale in the weak-binding regime. Direct DFT calculations of ion pair interaction energies as well as calculated cation electrostatic potential maps can be used to predict solution phase ion pairing tendencies for closely related ammonium cations. It was found by studying the decomposition of tetra-substituted ammonium cations by fluoride that: 1) rates of E2 decomposition is faster than the S_N2 pathway; 2) aryl substituents destabilize the cations; 3) steric strain tends to …

Characterization Of Glycation Sites On Human Serum Albumin Using Mass Spectrometry, Omar S. Barnaby

Department of Chemistry: Dissertations, Theses, and Student Research

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that  explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation …