Research and Publications - Department of Chemistry & Biochemistry
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Item Radical reactions involving cyclodextrins and model sugars(UMI Company, 1997) Lehmann, Marc N.Time-resolved EPR/laser flash photolysis studies of aqueous solutions of D-glucose, alpha-methyl-D-glucose, maltose and alpha-, beta- and gamma-cyclodextrin (CD) with acetone, pyruvic acid (PA), methylethylketone (MEK) and levulinic acid (LA) showed that the excited triplet state of these ketones could be used to selectively produce different polarized sugar radicals depending on the substrate used. For both D-glucose and maltose the C1 carbon centered radical was observed to be most intense and thought to be a consequence of the anomeric effect which favors binding of the ketone to the hydroxyl group situated on this carbon. For alpha-methyl-D-glucose the C7, C6 and C2 centered radicals were most intense and their selective formation is attributed to affinity effects. The following CD radicals were identified. From alpha-CD; C3 and C5 centered radicals. From beta-CD; C3, C5 and C1. From gamma-CD; C1 and C6. A C5 carbon centered radical formed from glucopyranoside ring-opening of the C1 radical was also observed for beta-CD and gamma-CD. Changes in the intensity of the spectra of the radicals observed between alpha-, beta- and gamma-CD were explained to arise from the extent ketone binding to the cyclodextrin cavity.Item Tryptophan operon read-through. Isolation and characterization of an abnormally long tryptophan synthetase alpha subunit from a frame-shift mutant of Escherichia coli(American Society for Biochemistry and Molecular Biology, 1975-06-25) Hardman, John K.; Berger, Hillard; Goodman, MyronA new mutant strain of Escherichia coli, strain ICR-47, contains a frame-shift mutation in the trpA gene, the gene most distal to the operator in the trp operon. Mapping experiments indicate that the lesion is located at a site within 10 to 15% of the end of this gene. The mutation results in "out-of-phase" translation of the distal portion of the trp mRNA; normal translational termination signal(s) are not encountered and a trpA gene product longer than the wild type protein is produced. As with the other enzymes produced from this operon, the in vivo level of the altered protein (the alpha subunit of the tryptophan synthetase enzyme complex) is controlled by exogenous L-tryptophan. The altered alpha subunit from the strain ICR-47 has been isolated and characterized. Molecular weight estimations indicate a molecular weight of approximately 37,000, an increase beyond the wild type enzyme corresponding to an additional 50 to 70 amino acid residues. The protein has a new COOH-terminal amino acid sequence. Results of preliminary hybridization experiments suggest that the ICR-47 mRNA, which is necessarily longer than that needed to code for wild type enzyme, is not detectably different in size from wild type mRNA. The enzymatic properties of the ICR-47 alpha subunit indicates a greatly reduced ability of the mutant subunit to combine functionally with wild type beta2 subunit, the second protein component in the tryptophan synthetase enzyme complex. In contrast, only 40 to 50% of the intrinsic enzymatic activity of the alpha subunit is lost.Item Constituents of the Blood of the Hibernating and Normal Rattlesnake, Crotalus Horridus(1945-12-01) Carmichael, Emmett B.; Petcher, Paul W.Item William Owen Baldwin(Paul B. Hoeber, 1942) Carmichael, Emmett B.Item La Fayette Guild(Paul B. Hoeber, 1935-03) Carmichael, Emmett B.Item Charles Alexander Pope(P.B. Hoeber, 1940-09-01) Carmichael, Emmett B.Item On Osmious Acid, and the Position of Osmium in the List of Elements(American Journal of Science, 1860) Mallet, John WilliamsItem Theory of electrical rectification in a molecular monolayer(American Physical Society, 2001) Krzeminski, C.; Delerue, C.; Allan, G.; Vuillaume, D.; Metzger, R.M.The current-voltage characteristics in Langmuir-Blodgett monolayers of γ-hexadecylquinolinium tricyanoquinodimethanide (C16H33Q-3CNQ) sandwiched between Al or Au electrodes is calculated, combining ab initio and self-consistent tight binding techniques. The rectification current depends on the position of the LUMO and HOMO relative to the Fermi levels of the electrodes as in the Aviram-Ratner mechanism, but also on the profile of the electrostatic potential which is extremely sensitive to where the electroactive part of the molecule lies in the monolayer. This second effect can produce rectification in the direction opposite to the Aviram-Ratner prediction.Item Evidence for two active branches for electron transfer in photosystem I(The National Academy of Sciences, 2001) Guergova-Kuras, Mariana; Boudreaux, Brent; Joliot, Anne; Joliot, Pierre; Redding, KevinAll photosynthetic reaction centers share a common structural theme. Two related, integral membrane polypeptides sequester electron transfer cofactors into two quasi-symmetrical branches, each of which incorporates a quinone. In type II reaction centers [photosystem (PS) II and proteobacterial reaction centers], electron transfer proceeds down only one of the branches, and the mobile quinone on the other branch is used as a terminal acceptor. PS I uses iron-sulfur clusters as terminal acceptors, and the quinone serves only as an intermediary in electron transfer. Much effort has been devoted to understanding the unidirectionality of electron transport in type II reaction centers, and it was widely thought that PS I would share this feature. We have tested this idea by examining in vivo kinetics of electron transfer from the quinone in mutant PS I reaction centers. This transfer is associated with two kinetic components, and we show that mutation of a residue near the quinone in one branch specifically affects the faster component, while the corresponding mutation in the other branch specifically affects the slower component. We conclude that both electron transfer branches in PS I are active.Item Synthesis and Characterization of Multifunctional Chitosan- MnFe2O4 Nanoparticles for Magnetic Hyperthermia and Drug Delivery(MDPI, 2010) Kim, Dong-Hyun; Nikles, David E.; Brazel, Christopher S.; University of Alabama TuscaloosaMultifunctional nanoparticles composed of MnFe2O4 were encapsulated in chitosan for investigation of system to combine magnetically-triggered drug delivery and localized hyperthermia for cancer treatment with the previously published capacity of MnFe2O4 to be used as an efficient MRI contrast agent for cancer diagnosis. This paper focuses on the synthesis and characterization of magnetic MnFe2O4 nanoparticles, their dispersion in water and their incorporation in chitosan, which serves as a drug carrier. The surface of the MnFe2O4 nanoparticles was modified with meso-2,3-di-mercaptosuccinic acid (DMSA) to develop stable aqueous dispersions. The nanoparticles were coated with chitosan, and the magnetic properties, heat generation and hydrodynamic size of chitosan-coated MnFe2O4 were evaluated for various linker concentrations and in a range of pH conditions.Item Biodegradable Orthopedic Magnesium-Calcium (MgCa) Alloys, Processing, and Corrosion Performance(MDPI, 2012) Salahshoor, Meisam; Guo, Yuebin; University of Alabama TuscaloosaMagnesium-Calcium (Mg-Ca) alloy has received considerable attention as an emerging biodegradable implant material in orthopedic fixation applications. The biodegradable Mg-Ca alloys avoid stress shielding and secondary surgery inherent with permanent metallic implant materials. They also provide sufficient mechanical strength in load carrying applications as opposed to biopolymers. However, the key issue facing a biodegradable Mg-Ca implant is the fast corrosion in the human body environment. The ability to adjust degradation rate of Mg-Ca alloys is critical for the successful development of biodegradable orthopedic implants. This paper focuses on the functions and requirements of bone implants and critical issues of current implant biomaterials. Microstructures and mechanical properties of Mg-Ca alloys, and the unique properties of novel magnesium-calcium implant materials have been reviewed. Various manufacturing techniques to process Mg-Ca based alloys have been analyzed regarding their impacts on implant performance. Corrosion performance of Mg-Ca alloys processed by different manufacturing techniques was compared. In addition, the societal and economical impacts of developing biodegradable orthopedic implants have been emphasized.Item Proteomic analysis of Staphylococcus aureus biofilm cells grown under physiologically relevant fluid shear stress conditions(BMC, 2014) Islam, Nazrul; Kim, Yonghyun; Ross, Julia M.; Marten, Mark R.; University of Maryland Baltimore County; University of Alabama TuscaloosaBackground: The biofilm forming bacterium Staphylococcus aureus is responsible for maladies ranging from severe skin infection to major diseases such as bacteremia, endocarditis and osteomyelitis. A flow displacement system was used to grow S. aureus biofilms in four physiologically relevant fluid shear rates (50, 100, 500 and 1000 s(-1)) to identify proteins that are associated with biofilm. Results: Global protein expressions from the membrane and cytosolic fractions of S. aureus biofilm cells grown under the above shear rate conditions are reported. Sixteen proteins in the membrane-enriched fraction and eight proteins in the cytosolic fraction showed significantly altered expression (p < 0.05) under increasing fluid shear. These 24 proteins were identified using nano-LC-ESI-MS/MS. They were found to be associated with various metabolic functions such as glycolysis / TCA pathways, protein synthesis and stress tolerance. Increased fluid shear stress did not influence the expression of two important surface binding proteins: fibronectin-binding and collagen-binding proteins. Conclusions: The reported data suggest that while the general metabolic function of the sessile bacteria is minimal under high fluid shear stress conditions, they seem to retain the binding capacity to initiate new infections.Item Mechanistic and Bioinformatic Investigation of a Conserved Active Site Helix in alpha-Isopropylmalate Synthase from Mycobacterium tuberculosis, a Member of the DRE-TIM Metallolyase Superfarnily(American Chemical Society, 2014) Casey, Ashley K.; Hicks, Michael A.; Johnson, Jordyn L.; Babbitt, Patricia C.; Frantom, Patrick A.; University of Alabama Tuscaloosa; University of California San FranciscoThe characterization of functionally diverse enzyme superfamilies provides the opportunity to identify evolutionarily conserved catalytic strategies, as well as amino acid substitutions responsible for the evolution of new functions or specificities. Isopropylmalate synthase (IPMS) belongs to the DRE-TIM metallolyase superfamily. Members of this superfamily share common active site elements, including a conserved active site helix and an HXH divalent metal binding motif, associated with stabilization of a common enolate anion intermediate. These common elements are overlaid by variations in active site architecture resulting in the evolution of a diverse set of reactions that include condensation, lyase/aldolase, and carboxyl transfer activities. Here, using IPMS, an integrated biochemical and bioinformatics approach has been utilized to investigate the catalytic role of residues on an active site helix that is conserved across the superfamily. The construction of a sequence similarity network for the DRE-TIM metallolyase superfamily allows for the biochemical results obtained with IPMS variants to be compared across superfamily members and within other condensation-catalyzing enzymes related to IPMS. A comparison of our results with previous biochemical data indicates an active site arginine residue (R80 in IPMS) is strictly required for activity across the superfamily, suggesting that it plays a key role in catalysis, most likely through enolate stabilization. In contrast, differential results obtained from substitution of the C-terminal residue of the helix (Q84 in IPMS) suggest that this residue plays a role in reaction specificity within the superfamily.Item Emergence of californium as the second transitional element in the actinide series(Nature Portfolio, 2015) Cary, Samantha K.; Vasiliu, Monica; Baumbach, Ryan E.; Stritzinger, Jared T.; Green, Thomas D.; Diefenbach, Kariem; Cross, Justin N.; Knappenberger, Kenneth L.; Liu, Guokui; Silver, Mark A.; DePrince, A. Eugene; Polinski, Matthew J.; Van Cleve, Shelley M.; House, Jane H.; Kikugawa, Naoki; Gallagher, Andrew; Arico, Alexandra A.; Dixon, David A.; Albrecht-Schmitt, Thomas E.; Florida State University; University of Alabama Tuscaloosa; United States Department of Energy (DOE); Argonne National Laboratory; Oak Ridge National Laboratory; National Institute for Materials ScienceA break in periodicity occurs in the actinide series between plutonium and americium as the result of the localization of 5f electrons. The subsequent chemistry of later actinides is thought to closely parallel lanthanides in that bonding is expected to be ionic and complexation should not substantially alter the electronic structure of the metal ions. Here we demonstrate that ligation of californium(III) by a pyridine derivative results in significant deviations in the properties of the resultant complex with respect to that predicted for the free ion. We expand on this by characterizing the americium and curium analogues for comparison, and show that these pronounced effects result from a second transition in periodicity in the actinide series that occurs, in part, because of the stabilization of the divalent oxidation state. The metastability of californium(II) is responsible for many of the unusual properties of californium including the green photoluminescence.Item Palladium-Catalyzed Modification of Unprotected Nucleosides, Nucleotides, and Oligonucleotides(MDPI, 2015) Shaughnessy, Kevin H.; University of Alabama TuscaloosaSynthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.Item Signatures of nonthermal melting(American Institute of Physics, 2015) Zier, Tobias; Zijlstra, Eeuwe S.; Kalitsov, Alan; Theodonis, Ioannis; Garcia, Martin E.; Universitat Kassel; University of Alabama Tuscaloosa; National Technical University of AthensIntense ultrashort laser pulses can melt crystals in less than a picosecond but, in spite of over thirty years of active research, for many materials it is not known to what extent thermal and nonthermal microscopic processes cause this ultrafast phenomenon. Here, we perform ab-initio molecular-dynamics simulations of silicon on a laser-excited potential-energy surface, exclusively revealing nonthermal signatures of laser-induced melting. From our simulated atomic trajectories, we compute the decay of five structure factors and the time-dependent structure function. We demonstrate how these quantities provide criteria to distinguish predominantly nonthermal from thermal melting. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.Item Achieving Excellence in Graduate Research: A Guide for New Graduate Students(Wiley-Blackwell, 2015) Parker, Charles B.; Amsden, Jason J.; Peng, Qing; Stoner, Brian R.; Glass, Jeffrey T.; Duke University; University of Alabama Tuscaloosa; Research Triangle InstituteItem Developmental and Reproductive Effects of Iron Oxide Nanoparticles in Arabidopsis thaliana(MDPI, 2015) Bombin, Sergey; LeFebvre, Mitchell; Sherwood, Jennifer; Xu, Yaolin; Bao, Yuping; Ramonell, Katrina M.; University of Alabama TuscaloosaIncreasing use of iron oxide nanoparticles in medicine and environmental remediation has led to concerns regarding exposure of these nanoparticles to the public. However, limited studies are available to evaluate their effects on the environment, in particular on plants and food crops. Here, we investigated the effects of positive (PC) and negative (NC) charged iron oxide (Fe2O3) nanoparticles (IONPs) on the physiology and reproductive capacity of Arabidopsis thaliana at concentrations of 3 and 25 mg/L. The 3 mg/L treated plants did not show evident effects on seeding and root length. However, the 25 mg/L treatment resulted in reduced seedling (positive-20% and negative-3.6%) and root (positive-48% and negative-negligible) length. Interestingly, treatment with polyethylenimine (PEI; IONP-PC coating) also resulted in reduced root length (39%) but no change was observed with polyacrylic acid (PAA; IONP-NC coating) treatment alone. However, treatment with IONPs at 3 mg/L did lead to an almost 5% increase in aborted pollen, a 2%-6% reduction in pollen viability and up to an 11% reduction in seed yield depending on the number of treatments. Interestingly, the treated plants did not show any observable phenotypic changes in overall size or general plant structure, indicating that environmental nanoparticle contamination could go dangerously unnoticed.Item Short- and Long-Term Effects of Prenatal Exposure to Iron Oxide Nanoparticles: Influence of Surface Charge and Dose on Developmental and Reproductive Toxicity(MDPI, 2015) Di Bona, Kristin R.; Xu, Yaolin; Gray, Marquita; Fair, Douglas; Hayles, Hunter; Milad, Luckie; Montes, Alex; Sherwood, Jennifer; Bao, Yuping; Rasco, Jane F.; University of Alabama TuscaloosaIron oxide nanoparticles (NPs) are commonly utilized for biomedical, industrial, and commercial applications due to their unique properties and potential biocompatibility. However, little is known about how exposure to iron oxide NPs may affect susceptible populations such as pregnant women and developing fetuses. To examine the influence of NP surface-charge and dose on the developmental toxicity of iron oxide NPs, Crl:CD1(ICR) (CD-1) mice were exposed to a single, low (10 mg/kg) or high (100 mg/kg) dose of positively-charged polyethyleneimine-Fe2O3-NPs (PEI-NPs), or negatively-charged poly(acrylic acid)-Fe2O3-NPs (PAA-NPs) during critical windows of organogenesis (gestation day (GD) 8, 9, or 10). A low dose of NPs, regardless of charge, did not induce toxicity. However, a high exposure led to charge-dependent fetal loss as well as morphological alterations of the uteri (both charges) and testes (positive only) of surviving offspring. Positively-charged PEI-NPs given later in organogenesis resulted in a combination of short-term fetal loss (42%) and long-term alterations in reproduction, including increased fetal loss for second generation matings (mice exposed in utero). Alternatively, negatively-charged PAA-NPs induced fetal loss (22%) earlier in organogenesis to a lesser degree than PEI-NPs with only mild alterations in offspring uterine histology observed in the long-term.Item The Synthesis, Characterization and Dehydrogenation of Sigma-Complexes of BN-Cyclohexanes(Wiley-VCH, 2016) Kumar, Amit; Ishibashi, Jacob S. A.; Hooper, Thomas N.; Mikulas, Tanya C.; Dixon, David A.; Liu, Shih-Yuan; Weller, Andrew S.; University of Oxford; Boston College; University of Alabama TuscaloosaThe coordination chemistry of the 1,2-BN-cyclohexanes 2,2-R-2-1,2-B,N-C4H10 (R-2=HH, MeH, Me-2) with Ir and Rh metal fragments has been studied. This led to the solution (NMR spectroscopy) and solid-state (X-ray diffraction) characterization of [Ir(PCy3)(2)(H)(2)(eta(2)eta(2)-H2BNR2C4H8)][BAr4F] (NR2=NH2, NMeH) and [Rh(iPr(2)PCH(2)CH(2)CH(2)PiPr(2))(eta(2)eta(2)-H2BNR2C4H8)][ BAr4F] (NR2=NH2, NMeH, NMe2). For NR2=NH2 subsequent metal-promoted, dehydrocoupling shows the eventual formation of the cyclic tricyclic borazine [BNC4H8](3), via amino-borane and, tentatively characterized using DFT/GIAO chemical shift calculations, cycloborazane intermediates. For NR2=NMeH the final product is the cyclic amino-borane HBNMeC4H8. The mechanism of dehydrogenation of 2,2-H,Me-1,2-B,N-C4H10 using the {Rh(iPr(2)PCH(2)CH(2)CH(2)PiPr(2))}+ catalyst has been probed. Catalytic experiments indicate the rapid formation of a dimeric species, [Rh-2(iPr(2)PCH(2)CH(2)CH(2)PiPr(2))(2)H-5][BAr4F]. Using the initial rate method starting from this dimer, a first-order relationship to [amine-borane], but half-order to [Rh] is established, which is suggested to be due to a rapid dimer-monomer equilibrium operating.