Scientific Publications 2007
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
K
2007. "Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation." Journal of the American Society for Mass Spectrometry 18(7):1332-1343. doi:doi:10.1016/j.jasms.2007.04.011 Abstract ABSTRACT-Targeted tandem mass spectrometry (MS/MS) is an attractive proteomic approach that allows selective identification of peptides exhibiting abundance differences between culture conditions and/or diseased states. Herein, we report on a targeted LC-MS/MS capability realized with a 7 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer equipped with a quadrupole interface that provides data-dependent ion selection, accumulation, and dissociation externally to the ICR trap. Identification of a subset of differentially abundant proteins from Shewanella oneidensis grown under suboxic vs. aerobic conditions demonstrates the feasibility of such approach. High mass resolution offered by FTICR and effective on-the-fly elution time correction facilitated accurate selection of targets, while high mass measurement accuracy MS/MS data resulted in unambiguous peptide identifications.
2007. "Folding of a DNA Hairpin Loop Structure in Explicit Solvent UsingReplica-Exchange Molecular Dynamics Simulations." Biophysical Journal 93:3218-3228. doi:10.1529/biophysj.107.108019 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Hairpin loop structures are common motifs in folded nucleic acids. The 59-GCGCAGC sequence in DNA forms a characteristic and stable trinucleotide hairpin loop flanked by a two basepair stem helix. To better understand the structure formation of this hairpin loop motif in atomic detail, we employed replica-exchange molecular dynamics (RexMD) simulations starting from a single-stranded DNA conformation. In two independent 36 ns RexMD simulations, conformations in very close agreement with the experimental hairpin structure were sampled as dominant conformations (lowest free energy state) during the final phase of the RexMDs (;35% at the lowest temperature replica). Simultaneous compaction and accumulation of folded structures were observed. Comparison of the GCA trinucleotides from early stages of the simulations with the folded topology indicated a variety of central loop conformations, but arrangements close to experiment that are sampled before the fully folded structure also appeared. Most of these intermediates included a stacking of the C2 and G3 bases, which was further stabilized by hydrogen bonding to the A5 base and a strongly bound water molecule bridging the C2 and A5 in the DNA minor groove. The simulations suggest a folding mechanism where these intermediates can rapidly proceed toward the fully folded hairpin and emphasize the importance of loop and stem nucleotide interactions for hairpin folding. In one simulation, a loop motif with G3 in syn conformation (dihedral flip at N-glycosidic bond) accumulated, resulting in a misfolded hairpin. Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of nucleic acid hairpins that are slower than expected for a semiflexible polymer of the same size.
2007. "Direct Synthesis of Nanoceria in Aqueous Polyhydroxyl Solutions." Journal of Physical Chemistry C 111(46):17232-17240. doi:10.1021/jp076164k Abstract Nanoceria has been shown to possess biomedical properties which have potential use in treatment of diseases caused by reactive oxygen species (ROS) like cancer. In the present work, stability and redox changes in nanoceria in the presence of polyhydroxyl groups such as glucose and dextran is reported. The effect of both acidic and basic medium on stability of nanoceria in the absence of buffer had been examined using UV-Visible spectroscopy and transmission electron microscopy. Experimental results showed that both dextran and glucose can extend the stability of nanoceria in basic medium without interfering with the redox chemistry. A comparison of aqueous and saccharides suspension in acid/base media undergoing redox transformation has been reported.
2007. "Quantum Mechanical Calculations of Charge Effectson gating the KcsA channel." Biochimica et Biophysica Acta--General Subjects 1218-1229. Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A series of ab initio (density functional) calculations were carried out on side chains of a set of amino acids, plus water, from the (intracellular) gating region of the KcsA K+ channel. Their atomic coordinates, except hydrogen, are known from X-ray structures [D.A. Doyle, J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, R. MacKinnon, The structure of the potassium channel: molecular basis of K+ conduction and selectivity, Science 280 (1998) 69–77; R. MacKinnon, S.L. Cohen, A. Kuo, A. Lee, B.T. Chait, Structural conservation in prokaryotic and eukaryotic potassium channels, Science 280 (1998) 106–109; Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, R. MacKinnon, The open pore conformation of potassium channels. Nature 417 (2001) 523–526], as are the coordinates of some water oxygen atoms. The 1k4c structure is used for the starting coordinates. Quantum mechanical optimization, in spite of the starting configuration, places the atoms in positions much closer to the 1j95, more tightly closed, configuration. This state shows four water molecules forming a “basket” under the Q119 side chains, blocking the channel. When a hydrated K+ approaches this “basket”, the optimized system shows a strong set of hydrogen bonds with the K+ at defined positions, preventing further approach of the K+ to the basket. This optimized structure with hydrated K+ added shows an ice-like 12 molecule nanocrystal of water. If the water molecules exchange, unless they do it as a group, the channel will remain blocked. The “basket” itself appears to be very stable, although it is possible that the K+ with its hydrating water molecules may be more mobile, capable of withdrawing from the gate. It is also not surprising that water essentially freezes, or forms a kind of glue, in a nanometer space; this agrees with experimental results on a rather different, but similarly sized (nm dimensions) system [K.B. Jinesh, J.W.M. Frenken, Capillary condensation in atomic scale friction: how water acts like a glue, Phys. Rev. Lett. 96 (2006) 166103/1–4].
2007. "Kinetic Monte Carlo Model of Charge Transport in Hematite (α-Fe2O3)." Journal of Chemical Physics 127(12):Art. No. 124706. doi:10.1063/1.2768522 Abstract The mobility of electrons injected into iron oxide minerals via abiotic and biotic electron-transfer processes is one of the key factors that control the reductive dissolution of such minerals. Building upon our previous work on the computational modeling of elementary electron transfer reactions in iron oxide minerals using ab initio electronic structure calculations and parameterized molecular dynamics simulations, we have developed and implemented a kinetic Monte Carlo model of charge transport in hematite that integrates previous findings. The model aims to simulate the interplay between electron transfer processes for extended periods of time in lattices of increasing complexity. The electron transfer reactions considered here involve the II/III valence interchange between nearest-neighbor iron atoms via a small polaron hopping mechanism. The temperature dependence and anisotropic behavior of the electrical conductivity as predicted by our model are in good agreement with experimental data on hematite single crystals. In addition, we characterize the effect of electron polaron concentration and that of a range of defects on the electron mobility. Interaction potentials between electron polarons and fixed defects (iron substitution by divalent, tetravalent, and isovalent ions and iron and oxygen vacancies) are determined from atomistic simulations, based on the same model used to derive the electron transfer parameters, and show little deviation from the Coulombic interaction energy. Integration of the interaction potentials in the kinetic Monte Carlo simulations allows the electron polaron diffusion coefficient and density and residence time around defect sites to be determined as a function of polaron concentration in the presence of repulsive and attractive defects. The decrease in diffusion coefficient with polaron concentration follows a logarithmic function up to the highest concentration considered, i.e., ~2% of iron(III) sites, whereas the presence of repulsive defects has a linear effect on the electron polaron diffusion. Attractive defects are found to significantly affect electron polaron diffusion at low polaron to defect ratios due to trapping on nanosecond to microsecond time scales. This work indicates that electrons can diffuse away from the initial site of interfacial electron transfer at a rate that is consistent with measured electrical conductivities but that the presence of certain kinds of defects will severely limit the mobility of donated electrons.
2007. "Molecular Computational Investigation of Electron Transfer Kinetics across Cytochrome-Iron Oxide Interfaces." Journal of Physical Chemistry C 111(30):11363-11375. Abstract The interface between electron transfer proteins such as cytochromes and solid phase mineral oxides is central to the activity of dissimilatory-metal reducing bacteria. A combination of potential-based molecular dynamics simulations and ab initio electronic structure calculations are used in the framework of Marcus’ electron transfer theory to compute elementary electron transfer rates from a well-defined cytochrome model, namely the small tetraheme cytochrome (STC) from Shewanella oneidensis, to surfaces of the iron oxide mineral hematite (α-Fe2O3). Room temperature molecular dynamics simulations show that an isolated STC molecule favors surface attachment via direct contact of hemes I and IV at the poles of the elongated axis, with electron transfer distances as small as 9 Å. The cytochrome remains attached to the mineral surface in the presence of water and shows limited surface diffusion at the interface. Ab initio electronic coupling matrix element (VAB) calculations of configurations excised from the molecular dynamics simulations reveal VAB values ranging from 1 to 20 cm-1, consistent with nonadiabaticity. Using these results, together with experimental data on the redox potential of hematite and hemes in relevant cytochromes and calculations of the reorganization energy from cluster models, we estimate the rate of electron transfer across this model interface to range from 1 to 1000 s-1 for the most exothermic driving force considered in this work, and from 0.01 to 20 s-1 for the most endothermic. This fairly large range of electron transfer rates highlights the sensitivity of the rate upon the electronic coupling matrix element, which is in turn dependent on the fluctuations of the heme configuration at the interface. We characterize this dependence using an idealized bis-imidazole heme to compute from first principles the VAB variation due to porphyrin ring orientation, electron transfer distance, and mineral surface termination. The electronic matrix element and consequently the rate of electron transfer are found to be sensitive to all parameters considered. This work indicates that biomolecularly similar solvent-exposed bis-histidine hemes in outer-membrane cytochromes such as MtrC or OmcA are likely to have an affinity for the oxide surface in water governing the approach and interfacial conformation and, if allowed sufficient conformational freedom, will achieve distances and configurations required for direct interfacial electron transfer.
2007. "Water-induced Bulk Ba(NO3)2 Formation From NO2 Exposed Thermally Aged BaO/Al2O3." Applied Catalysis. B, Environmental 72(3-4):233-239. Abstract Phase changes in high temperature treated (> 900 °C) 8 or 20 wt% BaO supported on Al2O3 model lean NOx trap (LNT) catalysts, induced by NO2 and/or H2O adsorption, were investigated with powder X-ray Diffraction (XRD), solid state 27Al Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) spectroscopy, and NO2 Temperature Programmed Desorption (TPD) experiments. After calcination in dry air at 1000 °C, the XRD and solid state 27Al MAS NMR results confirm that stable surface BaO and bulk BaAl2O4 phases are formed for 8 and 20 wt% BaO/Al2O3, respectively. Following NO2 adsorption over these thermally treated samples, no additional phase changes are observed based on XRD results. However, when water was added to the thermally aged samples after NO2 exposure, the formation of crystalline Ba(NO3)2 particles was observed in both samples. Solid state 27Al MAS NMR is shown to be a good technique for identifying the various Al species present in the materials during the processes studied here. NO2 TPD results demonstrate a significant loss of uptake for the 20 wt% model catalysts upon thermal treatment. However, the described phase transformations upon subsequent water treatment gave rise to the partial recovery of NOx uptake, demonstrating that such a water treatment of thermally aged catalysts can provide a potential method to regenerate LNT materials.
2007. "Design of a reaction protocol for decoupling sulfur removal and thermal aging effects during desulfation of Pt-BaO/Al2O3 lean NOx trap catalysts." Industrial and Engineering Chemistry Research 46(9):2735-2740. doi:10.1021/ie061542d Abstract A novel reaction protocol was designed to decouple the effects of thermal deactivation from those due to, for example, incomplete de-sulfation during regeneration steps of Ba-based lean NOx trap catalysts. The protocol was applied to two samples: a Pt-BaO/Al2O3 model catalyst, and an enhanced model sample doped with promoter species. The results obtained from the reaction protocol demonstrate that regeneration (desulfation) temperatures need to be maintained below those that lead to significant Pt sintering in order to prevent permanent deactivation. In addition, the modified reaction protocol allows us to compare the regeneration behavior of samples with varying degrees of sulfation, while other approaches have difficulty differentiating the effects of thermal aging from those of sulfation. We believe that this approach provides a convenient way both to assess the relative sensitivities of various catalysts to regeneration conditions, and to develop regeneration strategies that minimize the separate but often linked deactivation effects of sulfation and high temperatures.
2007. "Phosphopeptide elution times in reversed-phase liquid chromatography." Journal of Chromatography A 1172(1):9-18. doi:doi:10.1016/j.chroma.2007.09.032 Abstract Elution time shifts between 33 different peptides and their corresponding phosphopeptides ranging from 4 amino acid residues to 35 amino acids in length were systematically investigated utilizing a high resolution reversed-phase liquid chromatography (RPLC) system. Observed peptide elution time shifts for a single phosphorylation ranged from -5.28 min (for pYVPML) to +0.59 min (for HRDpSGLLDSLGR). Peptides containing a phosphotyrosine residue displayed a significant decrease in elution time following phosphorylation compared to their similar-sized peptides with phosphoserine or phosphothreonine residues. While the observed elution time generally decreased due to phosphorylation, five peptides displayed increased elution time as a result of phosphorylation. For large peptides (≥ 18 amino acids), the elution time shifts due to single phosphorylation were limited (ranging between -0.48 min and +0.03 min), while the elution time shifts for small peptides (< 18 amino acids) were characterized by a larger deviation (ranging between -5.28 min and +0.59 min). The predictive capability for the observed RPLC elution time change due to phosphorylation has been suggested, which will aid in assigning confident phosphopeptide identifications and their subsequent confirmation.
2007. "Preparation and Characterization of Monodispersed WO3 Nanoclusters on TiO2(110)." Catalysis Today 120(2):186-195. doi:10.1016/j.cattod.2006.07.050 Abstract A procedure is described for preparing a novel model early transition metal oxide system for catalysis studies—direct sublimation of tungsten trioxide on TiO2(110). Isolated monodispersed cyclic trimers, i.e., (WO3)3, can be formed on TiO2(110) that are thermally stable up to at least 750 K. Although not readily generalizable to monodispersed (WO3)x clusters other than cyclic trimers, this protocol provides an ideal nanocluster platform for carrying out model system catalysis studies over a wide temperature range.
2007. "Crosslinked Enzyme Aggregates in Hierarchically-Ordered Mesoporous Silica: A Simple and Effective Method for Enzyme Stabilization." Biotechnology and Bioenegineering 96(2):210-218. doi:10.1002/bit.21107 Abstract alpha-chymotrypsin (CT) and lipase (LP) were immobilized in hierarchically-ordered mesocellular mesoporous silica (HMMS) in a simple but effective way for the enzyme stabilization, which was achieved by the enzyme adsorption followed by glutaraldehyde (GA) crosslinking. This resulted in the formation of nanometer scale crosslinked enzyme aggregates (CLEAs) entrapped in the mesocellular pores of HMMS (37 nm), which did not leach out of HMMS through narrow mesoporous channels (13 nm). CLEA of alpha-chymotrypsin (CLEA-CT) in HMMS showed a high enzyme loading capacity and significantly increased enzyme stability. No activity decrease of CLEA-CT was observed for two weeks under even rigorously shaking condition, while adsorbed CT in HMMS and free CT showed a rapid inactivation due to the enzyme leaching and presumably autolysis, respectively. With the CLEA-CT in HMMS, however, there was no tryptic digestion observed suggesting that the CLEA-CT is not susceptible to autolysis. Moreover, CLEA of lipase (CLEA-LP) in HMMS retained 30% specific activity of free lipase with greatly enhanced stability. This work demonstrates that HMMS can be efficiently employed as host materials for enzyme immobilization leading to highly enhanced stability of the immobilized enzymes with high enzyme loading and activity.
2007. "Alcohol Chemistry on Rutile TiO2(110): The Influence of Alkyl Substituents on Reactivity and Selectivity." Journal of Physical Chemistry C 111(49):18236-18242. doi:10.1021/jp075608+ Abstract Product yields and selectivities, based on ultra high vacuum temperature programmed desorption, are compared for ten C2 to C8 aliphatic alcohols dosed at 100 K on highly-ordered TiO2(110) with a 3.5 % concentration of surface oxygen vacancies. Dehydration to form an alkene and water typically dominates while two other channels, dehydrogenation to form aldehydes, and reformation of alcohol, make detectable contributions for primary alcohols. Depending on the alcohol there are two distinct dehydration pathways, one operative at low temperature (LT, 300 to 425 K) and the other at high temperature (HT, 480 to 650 K). The HT dehydration pathway is common, while the LT channel is not observed for tertiary butanol and 3- and 4-octanol. The observed trends are accounted for in terms of the inductive and steric effects of the alkyl substituents.
2007. "Inductive Effect of Alkyl Chains on Alcohol Dehydration at Bridge-Bonded Oxygen Vacancies of TiO2(110)." Catalysis Letters 119(1-2):1-4. doi:10.1007/s10562-007-9199-1 Abstract Reactivity of adsorbates with titania is typically influenced by the presence of surface oxygen vacancy defects. For alcohols, it is well-established that their dissociation on bridge-bonded oxygen vacancies (BBOV’s) of a prototypical TiO2(110) surface proceeds via heterolytic cleavage of the RO—H bond. The resulting intermediates are alkoxide (RO) that fills the vacancy and a proton that binds to a neighboring oxygen anion. Except for methoxide, these alkoxides dehydrate at elevated temperatures (well above 300 K) via β–hydride elimination to form alkenes.In some cases, the dehydration is accompanied by a minority dehydrogenation channel yielding aldehydes.
2007. "Crystalline Ice Growth on Pt(111) and Pd(111): Nonwetting Growth on a Hydrophobic Water Monolayer." Journal of Chemical Physics 126(11):Art. No. 114702. Abstract The growth of crystalline water films on Pt(111) and Pd(111) is investigated using temperature programmed desorption of the water films and of rare gases adsorbed on the water films. The water monolayer wets both Pt(111) and Pd(111) at all temperatures investigated (e.g. 20-155 K, for Pt(111)). However, crystalline ice films grown at higher temperatures (e.g. T>135 K) do not wet the monolayer. Similar results are obtained for crystalline ice films of D2O and H2O. Amorphous water films, which initially wet the surface, crystallize and dewet exposing the water monlayer when they are annealed at higher temperatures. Thinner films crystallize and dewet at lower temperatures than thicker films. For samples sputtered with energetic Xe atoms to prepare ice crystallites surrounded by bare Pt(111), subsequent annealing of the films causes water molecules to diffuse off the ice crystallites to reform the water monolayer. A simple model suggests that, for crystalline films grown at high temperatures, the ice crystallites are initially widely separated with typical distances between crystallites of ~14 nm or more. The experimental results are consistent with recent theory and experiments suggesting that the molecules in the water monolayer form a surface with no dangling OH bonds or lone pair electrons, giving rise to a hydrophobic water monolayer on both Pt(111) and Pd(111).
2007. "A Cu/Pt Near-Surface Alloy for Water-Gas Shift Catalysis." Journal of the American Chemical Society 129(20):6485-6490. doi:10.1021/ja0700855 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. The primary route to hydrogen production from fossil fuels involves the water-gas shift (WGS) reaction, and an improvement in the efficiency of WGS catalysts could therefore lead to a major leap forward in the realization of hydrogen economy. On the basis of a combination of high-resolution scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory (DFT) calculations, we suggest the existence of a new thermodynamically stable Cu/Pt near-surface alloy (NSA). Temperature-programmed desorption and DFT reveal that this Cu/Pt NSA binds CO significantly more weakly than does Pt alone, thereby implying a considerable reduction in the potential for CO poisoning of the Cu/Pt NSA surface as compared to that of pure Pt. In addition, DFT calculations show that this Cu/Pt NSA is able to activate H2O easily, which is the rate-determining step for the WGS on several metal surfaces, and, at the same time, to bind the products of that reaction and formate intermediates rather weakly, thus avoiding possible poisoning of the catalyst surface. The Cu/Pt NSA is thus a promising candidate for an improved WGS catalyst.
2007. "Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies." Journal of the American Chemical Society 111(19):5233-5242. doi:10.1021/jp067659x Abstract We performed molecular dynamics simulations of urea solutions at different concentrations with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodynamic solution properties. Our simulation results showed that hydrogen-bonding properties such as the average number of hydrogen bonds and their lifetime distributions were nearly constant at all concentrations between infinite dilution and the solubility limit. This implies that the characterization of urea-water solutions in the molarity concentration scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concentration does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. We found that the KBFF urea model in TIP3P water better reproduced the experimental density and diffusion constant data. Preferential solvation analysis showed that there were weak urea-urea and water-water associations in OPLS solution at short distances, but there were no strong associations. We divided urea molecules into large, medium, and small clusters to examine fluctuation properties and found that any particular urea molecule did not stay in the same cluster for a long time. We found neither persistent nor large clusters.
2007. "Preferential Solvation in Urea Solutions at Different Concentrations: Properties fromSimulation Studies." Journal of Physical Chemistry B 111(19):5233-5242. doi:10.1021/jp067659x Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We performed molecular dynamics simulations of urea solutions at different concentrations with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodynamic solution properties. Our simulation results showed that hydrogen-bonding properties such as the average number of hydrogen bonds and their lifetime distributions were nearly constant at all concentrations between infinite dilution and the solubility limit. This implies that the characterization of urea-water solutions in the molarity concentration scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concentration does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. We found that the KBFF urea model in TIP3P water better reproduced the experimental density and diffusion constant data. Preferential solvation analysis showed that there were weak urea-urea and water-water associations in OPLS solution at short distances, but there were no strong associations. We divided urea molecules into large, medium, and small clusters to examine fluctuation properties and found that any particular urea molecule did not stay in the same cluster for a long time. We found neither persistent nor large clusters.
2007. "Molecular Basis of the Apparent Near Ideality of Urea Solutions." Biophysical Journal 93(10):3392-3407. doi:10.1529/biophysj.107.114181 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Activity coefficients of urea solutions are calculated to explore the mechanism of its solution properties, which form the basis for its well-known use as a strong protein denaturant. We perform free energy simulations of urea solutions in different urea concentrations using two urea models (OPLS and KBFF models) to calculate and decompose the activity coefficients. For the case of urea, we clarify the concept of the ideal solution in different concentration scales and standard states and its effect on our subsequent analysis. The analytical form of activity coefficients depends on the concentration units and standard states. For both models studied, urea displays a weak concentration dependence for excess chemical potential. However, for the OPLS force-field model, this results from contributions that are independent of concentration to the van der Waals and electrostatic components whereas for the KBFF model those components are nontrivial but oppose each other. The strong ideality of urea solutions in some concentration scales (incidentally implying a lack of water perturbation) is discussed in terms of recent data and ideas on the mechanism of urea denaturation of proteins.
2007. "Biostimulation of Iron Reduction and Subsequent Oxidation of Sediment Containing Fe-silicates and Fe-oxides: Effect of Redox Cycling on Fe(III) Bioreduction." Water Research 41(13):2996-3004. doi:10.1016/j.watres.2007.03.019 Abstract Microbial reduction of iron has been shown to be important in the transformation and remediation of contaminated sediments. Re-oxidation of microbially reduced iron may occur in sediments that experience oxidation-reduction cycling and can thus impact the extent of contaminant remediation. The purpose of this research was to quantify iron oxidation in a flow-through column filled with biologically-reduced sediment and to compare the iron phases in the re-oxidized sediment to both the pristine and biologically-reduced sediment. The sediment contained both Fe(III)-oxides (primarily goethite) and silicate Fe (illite/vermiculite) and was biologically reduced in phosphate buffered (PB) medium during a 497 day column experiment with acetate supplied as the electron donor. Long-term iron reduction resulted in partial reduction of silicate Fe(III) without any goethite reduction, based on Mössbauer spectroscopy measurements. This reduced sediment was treated with an oxygenated PB solution in a flow-through column resulting in the oxidation of 38% of the biogenic Fe(II). Additional batch experiments showed that the Fe(III) in the oxidized sediment was more quickly reduced compared to the pristine sediment, indicating that oxidation of the sediment not only regenerated Fe(III) but also enhanced iron reduction compared to the pristine sediment. Oxidation-reduction cycling may be a viable method to extend iron-reducing conditions during in-situ bioremediation.
2007. "The Structure of the Iron Binding Protein, FutA1, from Synechocystis 6803*." Journal of Biological Chemistry 282(37):27468-27477. doi:10.1074/jbc.M704136200 Abstract Cyanobacteria account for a significant percentage of aquatic primary productivity even in areas where the concentrations of essential micronutrients are extremely low. To better understand the mechanism of iron selectivity and transport, the structure of the solute-binding domain of an ABC iron transporter, FutA1, was determined in the presence and absence of iron. The iron ion is bound within the ‘C-clamp’ structure via four tyrosine and one histidine residues. There are extensive interactions between these ligating residues and the rest of the protein such that the conformations of the side chains remain relatively unchanged as the iron is released by the opening of the metal binding cleft. This is in stark contrast to the zinc binding protein, ZnuA, where the domains of the metal binding protein remain relatively fixed while the ligating residues rotate out of the binding pocket upon metal release. The rotation of the domains in FutA1 is facilitated by two flexible β-strands running along the back of the protein that act like a hinge during domain motion. This motion may require relatively little energy since total contact area between the domains is the same whether the protein is in the open or closed conformation. Consistent with the pH dependency of iron binding, the main trigger for iron release is likely the histidine in the iron-binding site. Finally, neither FutA1 nor FutA2 binds iron as a siderophore complex or in the presence of anions and both preferentially bind ferrous over ferric ions.
2007. "The Structure of a Cyanobacterial Bicarbonate Transport Protein, CmpA." Journal of Biological Chemistry 282(4):2606-2614. doi:10.1074/jbc.M610222200 Abstract Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of the food chain by fixing carbon and nitrogen into cellular biomass. To compensate for the low selectivity of Rubisco for CO₂ over O₂, Cyanobacteria have developed highly efficient CO₂concentrating machinery of which the ABC transport system CmpABCD from Synechocystis PCC 6803 is one component. Here we describe the structure of the bicarbonate binding protein, CmpA, in the absence and presence of bicarbonate and carbonic acid. CmpA is highly homologous to the nitrate transport protein, NrtA. CmpA binds carbonic acid at the entrance to the ligand-binding pocket whereas bicarbonate binds in nearly an identical location compared to nitrate binding to NrtA. Unexpectedly, bicarbonate binding is accompanied by a metal ion, identified as Ca²⁺ via inductively coupled plasma optical emission spectrometry. The binding of bicarbonate and metal is highly cooperative and suggests that CmpA co-transports bicarbonate and calcium.
2007. "Chemical Sputtering by Impact of Excited Molecules." Europhysics Letters 77:33002-p1-p6. doi:10.1209/0295-5075/77/3300 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We study chemical sputtering of deuterated amorphous carbon surfaces by D atoms, vibrationally excited D2, and dissociating D3 molecules, in a range of impact energies, 7.5–30 eV/D. We analyze the role of the internal state, i.e. the vibrationally excited and dissociating states of the neutral molecules resulting from above-surface neutralization of impacting molecular ions in typical sputtering experiments. The sputtering yields are shown to considerably increase with the internal vibrational energy at the lowest impact energies. By comparison of calculated and measured yields we draw conclusions regarding the possible mechanisms for neutralization.
2007. "Chemical Sputtering from Amorphous Carbon under Bombardment by Deuterium Atoms and Molecules." New Journal of Physics 9(209):1-25. doi:10.1088/1367-2630/9/7/209 Abstract The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. We perform classical molecular dynamics simulations of the chemical sputtering of deuterated amorphous carbon surfaces by D and D2, at energies of 7.5–30 eVD−1. Particular attention is paid to the preparation of the target surfaces for varying impact projectile fluence, energy and species, to the vibrational state of D2 projectiles, as well as to the variation in sputtering yields with target surface and impact projectile. The methane and acetylene sputtering yields per deuteron, obtained with atomic and molecular projectiles, agree quantitatively with recent experimental values.We study the distribution of sputtered species, as well as their kinetic energy and angular spectra.
2007. "Hierarchical Assembly of Inorganic Nanostructure Building Blocks to Octahedral Superstructures – A True Template-Free Self-Assembly." Nanotechnology 18(7):075303. doi:10.1088/0957-4484/18/7/075303 Abstract Time dependent size and shape evolution of nanomaterials has gained a significant interest. A room temperature, template free, wet chemical synthesis of ceria nanoparticles and their long term aging characteristics are reported. High Resolution Transmission Electron Microscopy and UV visible spectroscopy techniques are used to observe the variation in size, structure and oxidation state as a function of time. The morphology variation and the hierarchical assembly of nanostructures are imputed to the inherent structural aspects of cerium oxide. This communication also emphasizes the need for long term aging studies of nanomaterials in various solvents for multiple functionalities.
2007. "Penta-coordinated Al3+ ions as preferential nucleation sites for BaO on γ-Al2O3: an ultra-high magnetic field 27Al MAS NMR study." Journal of Catalysis 251(2):189-194. doi:10.1016/j.jcat.2007.06.029 Abstract In this paper, we report the first observation of preferential anchoring of an impregnated catalytic phase onto penta-coordinated Al3+ sites on the surface of γ Al2O3. The interaction of barium oxide with a γ alumina support was investigated by high resolution solid state 27Al magic angle spinning NMR at an ultra-high magnetic field of 21.1T and at sample spinning rates of up to 23 kHz. Under these experimental conditions, a peak in the NMR spectrum at ~ 23 ppm with relatively low intensity, assigned to 5-coordinated Al3+ ions, is clearly distinguished from the two other peaks representing Al3+ ions in tetra-, and octahedral coordination sites. Spin-lattice 27Al relaxation time measurements clearly show that these penta-coordinated Al3+ sites are located on the surface of the γ alumina support. BaO deposition onto this γ alumina sample resulted in the loss of intensity of the 23 ppm peak. The intensity loss observed was linearly proportional to the amount of BaO deposited. The results of this study strongly suggest that, at least for BaO, these penta-coordinated Al3+ ions are the nucleation sites.
