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Chemistry paper abstracts.

Binding of All-trans Retenoic Acid to Retinoic Acid Receptor. Alexander E. Vaughn, Tracy P. Hamilton, Department of Chemistry, Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294.

Members of the retinoid family interact with nuclear receptors(NR). NRs, which are regulated by small molecule signals, regulate transcription. All-trans retinoic acid (RA) and 9-cis-retinoic acid (9cRA) are activators of Retinoic Acid Receptors (RARs). UAB-30, an analog of 9cRA, is a drug targeted to prevent prevent cancer by targeting human RXR-gamma. This study will investigate the binding of RA to the human RAR ligand binding domain (RAR-LBD). The x-ray diffraction structure for the ligand binding domain of human RAR-gamma bound to RA was downloaded from the PDB data bank (Renaud, J.-P.; Rochel, N. R. Nature 1995, 378, 681-689). Waters were removed from this experimental structure and 25 RA molecules were added at random positions. The system was then minimized via molecular dynamics for 7.5ps (all molecular dynamics runs had a timestep of 1 fs). This structure was then solvated using a water box padded with 1.5nm of water molecules, and again minimized for 10ps. Afterwards the protein was brought to a temperature of 310K from 0K by 5K increments every picosecond. This work was made possible in part by a grant of high performance computing resources from the Department of Computer and Information Sciences at the University of Alabama at Birmingham, the School of Natural Sciences and Mathematics at the University of Alabama at Birmingham, and the National Science Foundation Award CNS-0420614.

BUFFERING CAPACITIES OF SOME COMMON FOODS. Stantafferta McPhee, Keri Reeves, and Brian Burnes, Department, of Biology, Judson College, Marion, AL 36756.

Common foods from a simple grocery list can be used as an alternate to commercially available antacids. Mashed potatoes, cream cheese, tomatoes, and jalapeno peppers, and sweet tea, orange juice, Gatorade, Coca-Cola, and milk, were compared for their pH buffering capacities by titration. Each food (10g) was mixed with water (20mL) to create a solution. Each solution was acidified and then titrated with 1M sodium hydroxide to slowly increase the pH from two to eleven. The pH was monitored and recorded, along with volume of base added, to create a titration curve for each substance. Foods with the strongest buffering capacities displayed a curve with a steady slope followed by a plateau and another slope. For both foods and beverages, dairy products required the most sodium hydroxide (8.7mL for cream cheese and 6.1mL for milk), in contrast to Coca-Cola or jalapenos (approximately 2.5mL for both). In conclusion, dairy products displayed the most buffering capacity and may be a good alternative to commercial antacids.

C-Terminal Endgroup Effects on Fragmentation of Peptides by Mass Spectrometry. Samantha S. Bokatzian-Johnson and Carolyn J. Cassady, Department of Chemistry, University of Alabama, Tuscaloosa, AL 35487.

Mass spectrometry has become an indispensable tool for the sequencing of peptides. The predictable fragmentation patterns gave way to nomenclature that is recognizable throughout the discipline. A peptide is a short polymeric compound based on a-amino acids connected by peptide bonds. The general structure has an amine group on one end (N-terminus) and a carboxylic acid group on the other end (C-terminus). If the C-terminus carboxylic acid group, (C=O)OH, is replaced with an amide group, (C=O)N[H.sub.2], the mass spectral fragmentation pattern of the peptide changes slightly.

Using peptides commercially available as both acid and amide forms at the C-terminus, fragmentation studies have been conducted using collision-induced dissociation (CID) and electron transfer dissociation (ETD) mass spectrometry methods with electrospray ionization/quadrupole ion trap (ESI/QIT). The results show that the differences between the fragmentation patterns of the analogs can be traced to a few characteristic peaks. The mechanisms responsible for the formation of these particular peaks can provide valuable insight to the effect of end groups on peptide fragmentation.

FABRICATION OF MICROFLUIDIC DEVICES UTILIZING CONSUMER PRODUCTS. Emanuel A. Waddell, Jeriel Johnson, Emily Haanschoten, and Arik Schwartz, University of Alabama in Huntsville, Huntsville, AL 35899.

The use of microfluidic devices has greatly increased over the past several years. Historically, the majority of microfluidic devices have been fabricated in silica substrates because of their well-understood silane-based chemistry, desirable optical properties, and easily transferable techniques from capillary electrophoresis in glass capillaries. Recently, there has been increased interest in utilizing polymer substrates as the basis for microfluidic devices. Advantages over silica devices include low cost, reduced weight, and ability to withstand shock. In addition, a number of methods for the rapid and low-cost fabrication of polymer based microfluidic devices have been published. Briefly, fabrication has been demonstrated by wire imprinting, hot-embossing, laser ablation, laser transparency methods, and x-ray lithography. An ideal rapid, inexpensive, and simple microfabrication process must meet several criteria. These criteria include (1) the ability to apply the fabrication process to different polymers without a modification in the fabrication process, (2) the ability to perform the fabrication in a desk-top setting; i.e., in environments where access to laboratory safety apparatus is limited, (3) the ability to fabricate multiple devices from a single mode, and (4) reduce total cost to dollars per device (on a manufacturing scale of tens of devices). The methods described here are based upon the use of off-the-shelf consumer products which are low cost and environmentally friendly. The research presented will provide a brief overview of several techniques.

Mass Spectrometry Investigations of Chromium(III) Complexed with Acidic Peptides Heather Watson and Carolyn J. Cassady, The University of Alabama, Tuscaloosa, AL 35487.

A chromium bound peptide has been reported to be involved in removing excess chromium from the body and in insulin signaling. Little is known about the structure of this chromium(III) bound peptide. Matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI/TOF MS) and electrospray ionization quadruple ion trap mass spectrometry (ESI/QIT MS) were used to study complexes formed between chromium(III) and synthetic acidic peptides. Similar spectra were obtained by using post source decay (PSD) in MALDI/TOF and by collision induced dissociation (CID) in ESI/QIT/MS. Differences in peptide fragmentation are seen when comparing the spectra of samples with and without the addition of chromium. Chromium drastically reduces the extent of fragmentation in peptides making their sequences difficult to establish by tandem mass spectrometry. Funding provided by NIH.

NOVELAND ROBUST PHOTOLABILE PROTECTING GROUP TOOLBOX FOR CARBONYL COMPOUNDS. * Yun Wang, Huayou Hu and Pengfei Wang, Dept. of Chemistry, Univ. of Ala. at Birmingham, Birmingham, AL 35294.

Photolabile protecting groups (PPGs) are very useful tools in organic synthesis, biochemistry, and biomedical applications. However, practically useful PPGs for some important functional groups such as the carbonyls are still rare. Herein, we report our effort in developing a toolbox of novel and robust PPGs for carbonyl compounds. These PPGs are structurally simple and can be readily synthesized from commercially available and inexpensive materials. The installation of the PPGs upon carbonyl compounds were achieved in excellent yields. Carbonyl compounds in their protected forms have excellent dark stability and can be photochemically released in high efficiency. Besides, photochemically orthogonal deprotection of PPGs by choosing different irradiation wavelength is feasible.

Palladium catalyzed coupling reactions using water-soluble phosphine ligands: DTBPSP and DAPSP and their ability to promote Suzuki-Miryaura, Heck, Sonagashira, and Carbonylation reactions. William S. Brown, Kevin H. Shaugnessy, Sara E. McClendon, Marry E. Killian, D. Denise Boykin, and M. QuentinSonnier. Department of Chemistry and Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336.

The development of water-soluble phosphine ligands for coupling reaction has been an expanding area of research over the past several years. The goal in many of these new reaction conditions has been to improve overall yield, reduce reaction time, and allow for catalyst recyclability. The motivation of this research is to demonstrate the utility of the ligands di-tert-butylpropylsulfonlyphosphine (DTBPPS) and di-adamantyl-propylsulfonylphosphine (DAPPS) as alternatives to other water-soluble ligands (such as TXPTS, TMAPTS, t-BuAmphos etc) which offer an alternative to ammonium based water-soluble ligands (Buchwalds ligands or t-BuAmphos) previously used. Previous efforts suggest that increasing the steries by addition of sterically demanding groups and increasing the electron donation ability of the phosphine ligand leads to an increase in the reactivity of the phosphine palladium catalyst. This increase in reactivity results in lower catalyst loading and higher turnover frequency of the catalyst, thereby providing a reduction in reaction time. Additionally, an increase in water-solubility of the active catalyst should afford means for the coupling of substrates that previously have proven challenging due to low solubility in traditional organic solvents. Both DTBPSP and DAPSP have been investigated and shown to give isolated yields between 75-98% for Suzuki, 68-92% for Sonagashira, and 75-99% for carbonylation, which are comparable to or in certain cases better than other water-soluble phosphines previously investigated.

Phenol Formaldehyde Nanocomposite Preparation with Tetraethylorthosilicates Zachary Whitfield, Mary Rogers, and Adriane Ludwick, Tuskegee University. Tuskegee, AL 36088.

The objective of this project is to study what effect incorporating nanosilicates will have on prepared resol polymer resins. The method being used to incorporate the nanosilicates throughout the polymer's matrix is a sol-gel process. Previous studies have shown improvements in thermal stability with the use of this method on nonvalac polymer resins. A comparative study is being done between phenol formaldehyde polymer resins and 1:1 phenol/p-bromophenol formaldehyde polymer resins. Preliminary studies were conducted to obtain a procedure for producing void-free polymers, to monitor the swelling process, and to monitor silicate uptake levels. This project is possible because of NSF/IGERT funding.

PLANNING EXPERIMENTS USING SIX THINKING HATS. M. B. Moeller, Dept. of Chemistry and Industrial Hygiene, University of North Alabama, Florence, AL 35632.

"Six Thinking Hats" is a system developed by Edward De Bono for guiding decision making, particularly for decisions in the business arena. The six hats process has been adapted for the purpose of teaching experimental design. Each aspect of planning for an experimental project is considered separately in six deliberate steps. The steps are interconnected, so that in performing the sequent of steps, previous steps can be revisited. The blue hat (sky) considers the overarching questions of purpose and goals for the experiment. The green hat (harvest) involves gathering information already available. The white hat (spreadsheets) deals with the information sought and with developing experimental protocol. The red hat (danger) entails recognizing potential hazards in the experiment. The yellow hat (action) looks for preliminary experiments can provide information to refine the experimental design. The black hat (devil's advocate) attempts to find weaknesses in the experimental design. The six hats process is well suited for team efforts although the programmed, compartmentalized thinking can also be useful to an individual. The process has been used to plan for an experiment to determine the water content of recently discovered species of flatworms that apparently go through anhydrobiosis to survive desiccation.

Reaction of 1,4-dicyclopropyl-1,3-butadienes with 4-methyl-l,2,4-triazoline-3,5-dione (MTAD) Duk K. Kim(1), Kevin E. O'Shea(2), and Christopher Gomez(2). (1) Department of Physical Sciences, Auburn University Montgomery, Montgomery, AL 36124 (2) Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199.

The reaction mechanisms of MTAD with isomeric 1,4-dicyclopropyl-1, 3-butadienes (DCPBD) were tried to be explained. The E,E and E, Z isomers of DCPBD react with MTAD to produce only the corresponding stereospecific 4+2 adducts and two 2+2 adducts. According to the Woodward-Hoffmann orbital symmetry rule, the [2+2] cycloaddition reactions are thermally forbidden. So the experimental results from the [2+2] cycloaddition reactions of DCPBD with MTAD seem to contradict the Woodward-Hoffmann rules if the reactions were working with concerted way. While the E,E and E,Z isomers show no trappable intermediates, the Z,Z isomer showed numerous methanol adducts. The nonstereospecificity and methanol adducts observed during the reaction of MTAD with the Z,Z isomer suggest the involvement of an open zwitterion. Low temperature NMR experiments reveal the presence of an aziridinium imide (A1) intermediate. We propose a concerted mechanism for the E,E and E,Z isomers and a non-concerted mechanism involving both open and closed (A1) zwitterionic species in the reaction of MTAD with the Z,Z isomer. Acknowledgment: This work was partially supported by AUM New Faculty Research Grant-In Aid.

RECOLLECTIONS OF A HYDROGEN CYANIDE CHEMIST. Richard C. Sheridan, Tennessee Valley Authority (Retired), Sheffield, AL 35660.

This paper reviews the experiences of a shift chemist in a hydrogen cyanide and acrylonitrile chemical plant in the 1950s. Then it discusses research done at Muscle Shoals, Alabama, in the 1960s on the synthesis of oxamide, a potential slow-release nitrogen fertilizer, from hydrogen cyanide (HCN). HCN was oxidized to cyanogen which was hydrolyzed to oxamide in concentrated hydrochloric acid. The oxidizing agents were regenerated for recycle. After studying the individual steps, including the synthesis of HCN from methane and ammonia or formamide, the four-step procedure using nitrogen dioxide was combined and operated in the laboratory. The use of a plasma torch to make HCN and the formation of oxamide from HCN and hydrogen peroxide were also investigated. No economical method was found for the production of oxamide as a fertilizer and the project was discontinued.

STUDIES OF ISOMERIC GEOMETRY AND PROPERTIES OF ENERGY-RICH NITROGEN CLUSTERS. Oluwaseyi Ogebule, Essence Brice, Geanee Quinney, Jong Hwa Kim, Jamiu A. Odutola, Department of Chemistry, Alabama A. & M. University, Normal, AL 35762.

Poly-nitrogen clusters have potential as an alternative source of fuel. Nitrogen clusters, ranging from N12 to N60 sizes, their isomers and geometries are built and their energetics studied using quantum mechanical methods in order to understand how much energy these molecules can store or release. The most stable conformation for each of the structures is obtained by geometry optimization and confirmed by frequency calculations using ab initio and DFT [B3LYP] methods with the 6-31+G(d) basis sets. Single point energy for each optimized structure is calculated by using larger basis sets, such as 6-311+G(3df). Nitrogen cluster molecules with the molecular formula N2n are found to be most stable than N2n+1. Based on our calculations, it appears that the geometry favors formation of stable single-bonded nitrogen cluster molecules. This work was made possible in part by a grant of high performance computing resources and technical support from the Alabama Supercomputer Center.

PALLADIUM CATALYZED SUZUKI COUPLING WITH WATER-SOLUBLE PHOSPHINE LIGANDS TO PROMOTE ACTIVATION OF ARYL HALIDES. M. Quentin Sonnier, William S. Brown, Kevin H. Shaughnessy, Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336

The development of new reaction conditions for Suzuki a coupling reactions has become an area of interest over the past several years. Previous studies have been undertaken with moderate to good yields under relatively benign reaction conditions. Our motivation is to utilize water-soluble phosphine derivatives to improve on these reaction conditions, improve yields, reaction time, allow for reactions to be carried out at ambient temperature, and lower catalyst loading. It is thought that increasing electronic donation into the palladium metal center from the phosphine will aide in oxidative addition into the aryl halide bond. Additionally it is thought that sterically demanding groups on the phosphine ligand increase subsequent reductive elimination or migratory insertion steps. Water-soluble phosphines have been developed to be electronic releasing and sterically demanding, while offering potential for recyclability due to water solubility. Moreover, the water-soluble ligands we have developed are phosphonium salts, which are easily deprotonated, that offer greater stability when shipping or in open atmosphere. The use of the water-soluble ligand, 3-(ditert-butylphosphino) propanesulfonate (DTBPSP) has demonstrated good activity towards Suzuki coupling of electron rich and deficient aryl bromides with 73-84% yields at room temperature. The water-soluble ligand 3-(diadamantylphosphino) propanesulfonate (DAPSP) has demonstrated activitation of electron rich and deficient aryl bromides with 64-92% yield at room temperature. Future work will include expanding these ligands to aryl chlorides. We also will be to expand these ligands to other coupling reactions and into generating palladium-ligand complexes.

Donald D. Muccio, *Bryan D. Cox*, Kenny F. Nguyen, Department of Chemistry, University of Alabama-Birmingham, Birmingham, AL 35294.

9-cis-UAB30 is a novel retinoid that is approaching clinical trials for cancer prevention. The stable conformations of 9-cis-UAB30 have been examined using a calculated torsion potential curve along the C8-C9 torsion. The energy, E, was calculated after a constrained geometry optimization as a function of the torsion angle, ?, at the B3LYP/6-3JG* level of theory. It was found that the most energetically favorable torsion angle was [+ or -]50[degrees] ([+ or -] s-gauche) and is dependant on the conformation of the ring system. Another favorable conformation was found at 180[degrees] (s-trans) which is 1.3 kcal/mol greater in energy than the global minimum at s-gauche. A barrier of 3.0 keal/mol separates the global minimum at s-gauche from s-trans, and a much larger barrier at 0[degree] separates the (+)-gauche from the (-)-gauche conformations. Populations of 9-cis-UAB30 were calculated using a normalized Boltzmann distribution. The populations for s-gauche and s-trans were found to be 82% and 18%, respectively. Using the methods described by Guo and Karplus, a series of diene models were used to analyze the steric effects that contribute to the torsion potential curve of 9-cis-UAB30.
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Publication:Journal of the Alabama Academy of Science
Article Type:Author abstract
Geographic Code:1U6AL
Date:Apr 1, 2008
Words:2852
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