Scientific Publications 2005
2005. "Chemistry - Oxygen Vacancies and Catalysis on Ceria Surfaces." Science 309(5735):713-714. Abstract Chemistry occurring at the surface of metal oxides is critical in a variety of industrial applications including catalysis and photocatalysis, optical display technology, solar energy devices and corrosion prevention. Defects have long been recognized to be the most reactive sites on the surfaces of many oxide materials. The most common types of defects present on the surfaces of metal oxides are oxygen vacancies and step edges. The nature of surface oxygen vacancies, and their number, distribution and diffusion across the surface of oxides, are thus issues of major scientific importance. One of the most interesting oxides in this respect is CeO2, since oxygen vacancies play the key role in giving this material it’s industrially important “oxygen-storage capacity.” This capacity makes modern automotive exhaust treatment catalysts containing CeO2 much more effective than their predecessors without CeO2. Ceria is also well known as a support which enhances the performance of transition metal catalysts, relative to other oxide supports, in a variety of other reactions including water-gas shift, steam reforming of oxygenates and PROX 1-7, all of which hold promise for enabling a hydrogen economy 1. Related to ceria’s facile redox capacity (ability to rapidly form and eliminate oxygen vacancy defects) is the poorly understood observation that some less reducible oxides, such as zirconia (ZrO2), are used as additives that actually enhance this “oxygen storage” property of CeO2. In this issue, Esch and coworkers in Trieste, Italy report an exciting study that for the first time clearly elucidates the structure, distribution and formation of oxygen vacancies on a cerium oxide surface 8. They have elegantly combined beautiful, atomic-resolution imaging using scanning-tunneling microscopy (STM) on a ceria surface with state-of-the-art quantum mechanical calculations using Density Functional Theory (DFT) to raise our understanding of CeO2 surfaces to a much higher level. They show that surface oxygen vacancies on CeO2(111) are immobile at room temperature, but at higher temperatures linear clusters of these vacancies are formed which expose exclusively Ce3+ ions to gas-phase reactants. The resulting exposed Ce3+ ions are thus grouped into rather large ensembles, with the sites immediately adjacent to these vacancy clusters remaining as pure Ce4+ ions. The authors further show that one subsurface oxygen vacancy is required to nucleate each such vacancy cluster. Guided by this knowledge, they performed DFT calculations that suggest an exciting new explanation for the role of Zr promoters in ceria-based catalysts: to enable growth of these linear vacancy chains without the need for a subsurface vacancy, which is energetically more costly. It should be noted that Namai et al. 9,10 also recently reported such linear vacancy clusters on CeO2(111), for which Esch et al. now provide much needed atomic-level structural detail.
2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4(5):1687-1698. Abstract We evaluate statistical models used in two-hypothesis tests for identifying peptides from tandem mass spectrometry data. The null hypothesis H0 that a peptide matches a spectrum by chance requires information on the probability of by-chance matches between peptide fragments and peaks in the spectrum. Likewise, the alternate hypothesis HA that the spectrum is due to a particular peptide requires probabilities that the peptide fragments would indeed be observed if it was the causative agent. We compare models for these probabilities by determining the identification rates produced by the models using an independent data set. The initial models use different probabilities depending on fragment ion type, but uniform probabilities for each ion type across all of the labile bonds along the backbone. More sophisticated models for probabilities under both HA and H0 are introduced that do not assume uniform probabilities for each ion type. In addition, the performance of these models using a standard likelihood model is compared to an information theory approach derived from the likelihood model. Also, a simple but effective model for incorporating peak intensities is described. Finally, a support-vector machine is used to discriminate between incorrect hits and correct identifications based on multiple characteristics of the scoring functions. The results are shown to reduce the misidentification rate by 10-fold when compared to a standard cross-correlation based approach.
2005. "Design of Micro-Scale Fuel Processors Assisted By Numerical Modeling." AIChE Journal 51(3):982-988. Abstract A methanol steam reformer and a selective carbon monoxide methanator have been mathematically described with a three-dimensional pseudo-homogenous model based on fundamental conservation laws of mass and energy. Results provide temperature distributions in a mili-watt scale fuel processor, which is used for reactor design. The tailored temperature profile allows the steam reformer and the CO methanator be operated at their preferred temperatures so that high selectivities can be achieved. The optimized reactor configuration and process conditions give high energy efficiency in generating low-CO-content hydrogen-rich gas stream for the miniature fuel cell applications. The precision of model has been validated with experimental observations.
2005. "Heterogeneous Reactor Model for Steam Reforming of Methane in a Microchannel Reactor with Microstructured Catalysts." Catalysis Today 110(1-2):92-97. Abstract Microstructured catalysts used for methane steam reforming in microchannel reactors are mathematically described and experimentally demonstrated under realistic process conditions. A heterogeneous model has been developed with a graphical interface to represent the three dimensions of the microchannel reactor. Porous metal substrates (FeCrAlY) were used to form engineered catalysts with active precious metal (Rh) for methane steam reforming. Two types of structures were evaluated in the microchannel reactors and simulated with the developed heterogeneous reactor model. Local temperature and methane concentration profiles within the structures are illustrated to show the correlation of the catalyst structure and its performance. Such a modeling technique provides a convenient and flexible method to evaluate variables in designing more efficient catalysts for the highly endothermic steam reforming reactions, as the desired mass and heat transfer characteristics are achieved.
2005. "Kinetic analysis of complex reactions using FEMLAB." Chemical Engineering and Technology 28(6):649-654. doi:10.1002/ceat.200500027 Abstract A finite element method software FEMALB has been implemented to the kinetic analysis of complex reaction systems. The established protocol provides fast solutions to the coupled differential-algebraic equations. It shows significant advantages over the conventional coding process with the standard implicit Runge-Kutta (IRK) method. The accuracy and high efficiency have been demonstrated in the simulation of the reaction processes such as glucose/fructose hydrogenation and catalytic cracking of gasoil. As model validation, the numerical results showed satisfactory agreement with the exact solutions. With the powerful capability of solving large matrixes of differential equations (both ODE and PDE) with nonlinear algebraic constrains, such an algorithm has greatly reduced the coding labor in reaction mechanistic studies and provided a unique tool in reactor design and optimization.
2005. "Mechanisms of Methanol Decomposition on Platinum: A Combined Experimental and abInitio Approach." Journal of Physical Chemistry B 109(23):11622-11633. doi:10.1021/jp0501188 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 dual path mechanism for methanol decomposition on well-defined low Miller index platinum single crystal planes, Pt(111), Pt(110), and Pt(100), was studied using a combination of chronoamperometry, fast scan cyclic voltammetry, and theoretical methods. The main focus was on the electrode potential range when the adsorbed intermediate, COad, is stable. At such “CO stability” potentials, the decomposition proceeds through a pure dehydrogenation reaction, and the dual path mechanism is then independent of the electrodesubstrate surface structure. However, the threshold potential where the decomposition of methanol proceeds via parallel pathways, forming other than COad products, depends on the surface structure. This is rationalized theoretically. To gain insights into the controlling surface chemistry, density functional theory calculations for the energy of dehydrogenation were used to approximate the potential-dependent methanol dehydrogenation pathways over aqueous-solvated platinum interfaces.
2005. "Reaction Intermediates of Quinol Oxidation in a Photoactivatable System that Mimics Electron Transfer in the Cytochrome bc1 Complex." Journal of the American Chemical Society 127(12):4208-4215. doi:10.1021/ja043955g Abstract Current competing models for the two-electron oxidation of quinol (QH2) at the cytochrome bc1 complex and related complexes have different requirements for the reaction intermediate. At present, the intermediate species of the enzymatic oxidation process have not been observed or characterized, probably due to their transient nature. Here, we use a biomimetic oxidant, Ru(bpy)2(pbim)(PF6)2 (bpy = 2,2’-dipyridyl, pbim = 2-(2-benzimidazolate)pyridine) in an aprotic medium to probe the oxidation of the ubiquinol analogue, 2,3-dimethoxy-5-methyl-1,4-benzoquinol (UQH2-0), an the plastoquinol analogue, trimethyl-1,4-benzoquinol (TMQH2-0), using time-resolved and steady state spectroscopic techniques. This system qualitatively reproduces key features observed during ubiquinol oxidation by the mitochondrial cytochrome bc1 complex. Comparison of isotope dependent activation properties in the native and synthetic systems, as well as, analysis of the time-resolved direct-detection electron paramagnetic resonance signals in the synthetic system allows us to conclude that: 1) the initial and rate-limiting step in quinol oxidation, both in the biological and biomimetic systems, involves electron and proton transfer, probably via a proton coupled electron transfer mechanism; 2) a neutral semiquinone intermediate is formed in the biomimetic system; and 3) oxidation of the QH•/QH2 couple for UQH2-0, but not TMQH2-0, exhibits a non-classical primary deuterium kinetic isotope effect on its Arrhenius activation energy (GTS), where GTS for the protiated form is larger than for the deuterated form. The same behavior is observed during steady state turnover of the cyt bc¬1 complex using ubiquinol, but not plastoquinol, as a substrate, leading to the conclusion that similar chemical pathways are involved in both systems. The synthetic system is an unambiguous n=1 electron acceptor and it is thus inferred that sequential oxidation of ubiquinol (by two sequential n=1 processes) is more rapid than a truly concerted (n=2) oxidation in the cyt bc¬1 complex.
2005. "THE RESPIRATORY SUBSTRATE RHODOQUINOL INDUCES Q-CYCLE BYPASS REACTIONS IN THE YEAST CYTOCHROME bc1 COMPLEX - MECHANISTIC AND PHYSIOLOGICAL IMPLICATIONS." Journal of Biological Chemistry 280(41):34654-34660. doi:10.1074/jbc.m507616200 Abstract The mitochondrial cytochrome bc1 complex catalyzes the transfer of electrons from ubiquinol to cyt c, while generating a proton motive force for ATP synthesis, via the ‘Qcycle’ mechanism. Under certain conditions, electron flow through the Q-cycle is blocked at the level of a reactive intermediate in the quinol oxidase site of the enzyme, resulting in ‘bypass reactions’, some of which lead to superoxide production. Using analogs of the respiratory substrates, ubiquinol-3 and rhodoquinol-3, we show that the relative rates of Q-cycle bypass reactions in the Saccharomyces cerevisiae cyt bc1 complex are highly dependent, by a factor of up to one hundred-fold, on the properties of the substrate quinol. Our results suggest that the rate of Q-cycle bypass reactions is dependent on the steady state concentration of reactive intermediates produced at the quinol oxidase site of the enzyme. We conclude that normal operation of the Q-cycle requires a fairly narrow window of redox potentials, with respect to the quinol substrate, to allow normal turnover of the complex while preventing potentially damaging bypass reactions.
2005. "Large Molecules as Models for Small Particles in Aqueous Geochemistry Research." Journal of Nanoparticle Research 7(4-5):377-387. doi:10.1007/s11051-005-4718-8 Abstract Many questions that geochemists now pose about mineral surfaces concern the properties of individual molecular functional groups. These questions can be answered directly with large aqueous molecules where the positions of atoms can be determined with accuracy and related to the reactive properties. It is time to abandon this approach with colloidal solid suspensions and employ aqueous molecular clusters. The reactive properties of individual oxygens can be determined separately using these aqueous clusters in spectroscopic studies. These molecules are sufficiently large (1–5 nm) that they overlap in size with the smallest colloids, yet the bond lengths and atom positions can be determined unequivocally from X-ray structural studies. In this paper we present research on a 2-nm cluster that provides a particular useful example. These molecules, unlike surface structures that are inferred from bulk structures, allow direct comparison of experimental data with molecular simulations.
2005. "Structure, Band Offsets and Photochemistry at Epitaxial ⍺-Cr₂O₃/⍺-Fe₂O₃ Heterojunctions." Surface Science 587(3):L197-L207. Abstract We test the hypothesis that electron-hole pair separation following light absorption enhances photochemistry at oxide/oxide heterojunctions which exhibit a type II or staggered band alignment. We have used hole-mediated photodecomposition of trimethyl acetic acid chemisorbed on surfaces of heterojunctions made from epitaxial ⍺-Cr₂O₃ on ⍺-Fe₂O₃(0001) to monitor the effect of UV light of wavelength 385 nm (3.2 eV) in promoting photodissociation. Absorption of photons of energies between the bandgaps of ⍺-Cr₂O₃ (Eg = 4.8 eV) and ⍺-Fe₂O₃ (Eg = 2.1 eV) is expected to be strong only in the ⍺-Fe₂O₃ layer. The staggered band alignment should then promote the segregation of holes (electrons) to the ⍺-Cr₂O₃ (⍺-Fe₂O₃) layer. Surprisingly, we find that the ⍺-Cr₂O₃ surface alone promotes photodissociation of the molecule at hv = 3.2 eV, and that any effect of the staggered band alignment, if present, is masked. We propose that the inherent photoactivity of the ⍺-Cr₂O₃ (0001) surface results from the creation of bound excitons in the surface which destabilize the chemisorption bond in the molecule, resulting in photodecomposition.
2005. "Molecular Dynamic Simulation of Disorder Induced Amorphization in Pyrochlore." Physical Review Letters 94:025505. Abstract The defect accumulation of amorphization has been studied for the La2Zr2O7 pyrochlore by means of classical molecular dynamic simulations. Present calculations show that the accumulation of cation Frenkel pairs is the main driving parameter for the amorphization process, while the oxygen atoms simply rearrange around cations. Under Frenkel pair accumulation, the structure follows the pyrochlore-amorphous sequence. Present results consequently provide atomic-level interpretation to previous experimental irradiation observations of the two-step phase transitions.
2005. "Dynamic Motion of Helix A in the Amino-terminal Domain of Calmodulin is Stabilized Upon Calcium Activation." Biochemistry 44:905-914. Abstract Calcium-dependent changes in the internal dynamics and average structures of the opposing globular domains of calmodulin (CaM), as well as their relative spatial arrangement, contribute to the productive association between CaM and a range of different target proteins to affect their functional activation. To identify dynamic structural changes involving individual α-helical elements and their modulation by calcium activation, we have used site-directed mutagenesis to engineer a tetracysteine binding motif within helix A near the amino-terminus of calmodulin (CaM), permitting the selective and rigid attachment of the fluorescent probe 4’,5’-bis(1,3,2-dithioarsolan-2-yl) fluorescein (FlAsH) with full retention of function. The rigid tetracoordinate linkage of FlAsH to CaM, in conjunction with frequency-domain fluorescence anisotropy measurements, allows assessment of dynamic changes associated with calcium activation without interference from independent probe motion. Taking advantage of the large fluorescent enhancement associated with FlAsH binding to CaM, rates of FlAsH binding to apo- and calcium-activated CaM were 2500 ± 10 M-1 sec-1 and 187 ± 2 M-1 sec-1, respectively. There is no difference in the solvent accessibility of the bound FlAsH irrespective of calcium binding to CaM. Thus, given that FlAsH selectively labels disordered structures, the large difference in rates of FlAsH binding indicates that calcium binding stabilizes helix A. Frequency-domain anisotropy measurements of bound FlAsH indicate that prior to calcium activation, helix A undergoes large amplitude nanosecond motions. Following calcium activation, helix A becomes immobile, and structurally coupled to the overall rotation of CaM. We discuss these results in the context of a model that suggests stabilization of helix A relative to other domain elements in the CaM structure is critical to defining high-affinity binding clefts, and in promoting specific and ordered biding of the opposing lobes of CaM to target proteins.
2005. "Structural Uncoupling between Opposing Domains of Oxidized Calmodulin Underlies the Enhanced Binding Affinity and Inhibition of the Plasma Membrane Ca-ATPase." Biochemistry 44(12):4737-4747. doi:10.1021/bi0474113 Abstract Stabilization of the plasma membrane Ca-ATPase (PMCA) in an inactive conformation upon oxidation of multiple methionines in the calcium regulatory protein calmodulin (CaM) is part of an adaptive cellular response to minimize ATP utilization and the generation of reactive oxygen species (ROS) under conditions of oxidative stress. To differentiate oxidant-induced structural changes that selectively modify the amino-terminal domain of CaM from those that modulate the conformational coupling between the opposing domains, we have engineered a tetracysteine binding motif within helix A in the amino-terminal domain of calmodulin (CaM) that permits the selective and rigid attachment of the conformationally sensitive fluorescent probe 4,5-bis(1,3,2-dithioarsolan-2-yl)fluorescein-(1,2-ethanedithiol)2 (FlAsH-EDT2). The position of the FlAsH label in the amino-terminal domain provides a signal for monitoring its binding to the CaM-binding sequence of the PMCA. Following methionine oxidation, there is an enhanced binding affinity between the amino-terminal domain and the CaM-binding sequence of the PMCA. To identify oxidant-induced structural changes, we used frequency domain fluorescence anisotropy measurements to assess the structural coupling between helix A and the amino- and carboxyl-terminal domains of CaM. Helix A undergoes large amplitude motions in apo-CaM; following calcium activation, helix A is immobilized as part of a conformational switch that couples the opposing domains of CaM to stabilize the high-affinity binding cleft associated with target protein binding. Methionine oxidation disrupts the structural coupling between opposing globular domains of CaM, without affecting the calcium-dependent immobilization of helix A associated with activation of the amino-terminal domain to promote highaffinity binding to target proteins. We suggest that this selective disruption of the structural linkage between the opposing globular domains of CaM relieves steric constraints associated with high-affinity target binding, permitting the formation of new contact interactions between the amino-terminal domain and the CaMbinding sequence that stabilizes the PMCA in an inhibited conformation.
2005. "Characterization of the molecular iodine electronic wave functions and potential energy curves through hyperfine interactions in the B0+_u(3Pi_u) state." Journal of the Optical Society of America. B, Optical Physics 22(5):951-961. Abstract We present a high-resolution numerical analysis on the six electronic states that are coupled to the B state via hyperfine interactions in molecular iodine. The four hyperfine parameters, CB, δB, dB, and eqQB, are calculated using the available potential energy curves and the wave functions constructed from the separated-atom basis set. In the calculation, we are able to obtain a maximum separation of the contributions from all the six electronic states and compare each individual term with the high-precision spectroscopic data, providing an independent verification of the relevant electronic structure.
2005. "Fabrication and Luminescence of ZnS:Mn2+ Nanoflowers." Journal of Nanoscience and Nanotechnology 5(9):1309-1322. Abstract Visually striking nanoflowers composed of ZnS:Mn2+ nanoparticles are prepared and characterized. The configurations of these fractal structures are very sensitive to both the pH values of the particle solutions from which they are precipitated and the substrates on which they are deposited. At pH 2.2, the fractal structures resemble trees without leaves; at pH 7.7, they are tree-like with four arms and at pH 11.0 they resemble trees with 6 arms. High resolution transmission microscopy reveals that the nanoflowers are composed of ZnS:Mn2+ nanoparticles of 2-5 nm in size. X-ray photoelectron spectral data indicate that the sample compositions of nitrogen, chlorine, and sulfur vary gradually with pH values of the solutions. These changes may have an impact on both the fractal configuration and the luminescence properties. The emission spectra of the particle solutions at pH of 2.2 and 11.0 are similar with the emission maximum at 475 nm. As the pH value approaches 7.7, the emission spectral maximum shifts to longer wavelengths. At a pH value of 7.7, the emission peak wavelength is the reddest, 520 nm. The emission peak of the nanoflowers at a pH value of 9.3 is 510 nm, while the emission spectrum of the nanoflowers at 5.2 has two peaks at 500 nm and 440 nm, respectively. These blue-green emissions are attributed to defects and are the dominant luminescence from the nanoflowers. The emission from Mn2+ dopant is only observed in the delayed spectra of the fractal solid samples.
2005. "Structure and Luminescence of BaFBr:Eu2+ and BaFBr:Eu2+, Tb3+ Phosphors and Thin Films." Journal of Applied Physics 97(8):083506 (8 p.). Abstract The inclusionof Tb3+ ions doped into the storage phosphor BaFBr: Eu2+ results in increased purity of the host material as well as an improvement in the linearity of the photostimulated luminescence intensity versus the X-ray irradiation dose. Films produced by pulsed laser deposition (PLD) also show similar results, indicating that PLD is a powerful technique for producing high quality, high purity thin films. As a result, the PSL dose response is more linear in the thin films than in the powder samples. The emission intensity of Eu2+ in the phosphors increases with the increasing time of X-ray irradiation while the emission intensity of Tb3+ remains almost constant. This result may be explained by considering the reduction of impurity Eu3+ ions following trapping of the photoexcited electrons. The results demonstrate that these materials are not only potentially useful for medical imaging but also show promise for use in radiation dosimetry.
2005. "Upconversion Luminescence from CdSe Nanoparticles." Journal of Chemical Physics 122(22):224708 (7 pages). Abstract Efficient upconversion luminescence has been observed from CdSe nanoparticles ranging in size from 2.5 to 6 nm. The upconversion luminescence exhibits a near quadratic laser power dependence. Emissions from both excitons and trap states are observed in the upconversion and photoluminescence spectra, and in the upconversion luminescence the emission from the trap states is enhanced relative to trap state emission in the photoluminescence. The upconversion decay lifetimes are slightly longer than the photoluminescence decay lifetimes. Time-resolved spectral measurements indicate that this is due to the involvement of long decay components from surface or trap states. Both the photoluminescence and upconversion luminescence decrease in intensity with increasing temperature due mainly to thermal quenching. All the observations indicate that surface or trap states work as emitters rather than as intermediate states for upconversion luminescence and that two-photon absorption is the likely excitation mechanism.
2005. "Fluorescense Anisotropy Studies of Molecularly Imprinted Polymer Sensors." Luminescence 21(1):7-14. doi:10.1002/bio.874 Abstract Molecularly imprinted polymers (MIPs) are used as recognition elements in biochemical sensors. In a fluorescence-based MIP sensor system, it is difficult to distinguish the analyte fluorescence from the background fluorescence of the polymer itself. We studied steady-state fluorescence anisotropy of anthracene imprinted in a polymer (polyurethane) matrix. Vertically polarized excitation light was incident on MIP films coated on silicon wafers; vertically and horizontally polarized emission was measured. We compared the fluorescence anisotropy of MIPs with imprinted molecules, MIPs with the imprinted molecules extracted, MIPs with rebound molecules, and nonimprinted control polymers (without binding cavities). It is shown that differences in fluorescence anisotropy between the polymers and imprinted fluorescent molecules may provide a means to discriminate the fluorescence of analyte from that of the background polymer.
2005. "Theoretical Study of the Diels-Alder Reactions between Singlet (¹Δg) Oxygen and Acenes." Journal of Physical Chemistry A 109(33):7509-7518. doi:10.1021/jp0503009 Abstract The abstract for this journal article is not available at this time.
2005. "Preparation of a novel structured catalyst based on aligned carbon nanotube arrays for a microchannel Fischer-Tropsch synthesis reactor ." Catalysis Today 110(1-2):47-52. Abstract A novel catalyst microstructure based on aligned multiwall carbon nanotube arrays was synthesized. Its advanced heat and mass transport characteristics coupled with high surface area led to superior performances for Fischer-Tropsch synthesis in a microchannel chemical reactor. The fabrication of such a novel catalyst structure first involved metalorganic chemical vapor deposition (MOCVD) growth of a dense Al2O3 thin film over FeCrAlY foam substrate to enhance adhesion between catalyst layer and metal substrate. Aligned arrays of multiwall carbon nanotubes were grown over the substrate by catalytic decomposition of ethylene. These nanotube bundles were directly attached to the FeCrAlY substrate through a thin layer of oxide thin film. When the outer surfaces of nanobundles were coated with a catalyst layer, a unique hierarchical catalyst structure with nanoporous interstitials between the bundles was created. Thus, engineered catalysts based on such a novel hierarchical structure minimizes mass transfer encountered in the gas-liquid-solid three phase reactions. In addition, high thermal conductivity of carbon nanotube and the direct attachment of these nanobundles to the metal foam allow efficient heat removal from catalytic sites. The advanced heat and mass transfer on this novel structured catalyst was demonstrated in Fischer-Tropsch synthesis in a microchannel fixed bed reactor. The presence of carbon nanotube arrays improved dispersion of active metals and reduced mass transfer limitation, leading to a factor of four enhancement of Fischer-Tropsch synthesis activity. The improved temperature control with the carbon nanotube arrays also allows the Fischer-Tropsch synthesis being operated at temperatures as high as 265 oC without reaction runaway favoring methane formation.
2005. "Clay mineral weathering and contaminant dynamics in a casutic aqueous sytem II. Mineral transformation and microscale partitioning." Geochimica et Cosmochimica Acta 69(18):4437-4451. doi:10.1016/j/gvs/2005.04.004 Abstract Microscopic and spectroscopic studies were conducted to assess mineral transformation processes in aqueous suspensions of illite (Il), vermiculite (Vm) and montmorillonite (Mt) that were subjected to weathering in a simulated high-level radioactive tank waste leachate (0.05 m AlT, 2 m Na*, 1 m NO3 *, pH *14, Cs* and Sr2* present as co-contaminants). Time series (0 to 369 d) experiments were conducted at 298 K, with initial [Cs]0 and [Sr]0 concentrations from 10*5 to 10* mol kg*. Incongruent clay dissolution resulted in an accumulation of secondary aluminosilicate precipitates identified as nitrate-sodalite, nitrate-cancrinite and zeolite X, by molecular spectroscopy and electron microscopy (XRD, IR, NMR, SEM-EDS and TEM-EDS). Contaminant fate was dependent on competing uptake to parent clays and weathering products. TEM-EDS results indicated that high Il affinity for Cs was due to adsorption at frayed edge sites. The Il system also comprised Sr-rich aluminous precipitates after 369 d reaction time. In Mt systems, Cs and Sr were co-precipitated into increasingly recalcitrant spheroidal precipitates over the course of the experiment, whereas contaminant association with montmorillonite platelets was less prevalent. In contrast, Cs and Sr were found in association with weathered Vm particles despite the formation of spheroidal aluminosilicate precipitates that were comparable to those formed from Mt dissolution.
2005. "Clay mineral weathering and contaminant dynamics in a caustic aqueous system I. Wet chemistry and aging effects." Geochimica et Cosmochimica Acta 69(18):4425-4436. doi:10.1016/j.gca.2005.04.003 Abstract Abstract—Caustic high level radioactive waste induces mineral weathering reactions that can influence the fate of radionuclides released in the vicinity of leaking storage tanks. The uptake and release of CsI and SrII were studied in batch reactors of 2:1 layer-type silicates—illite (Il), vermiculite (Vm) and montmorillonite (Mt)—under geochemical conditions characteristic of leaking tank waste at the Hanford Site in WA (0.05 mAlT, 2 m Na*, 1 m NO3 *, pH *14, Cs and Sr present as co-contaminants). Time series (0 to 369 d) experiments were conducted at 298 K, with initial [Cs]0 and [Sr]0 concentrations from 10*5 to 10*3 mol kg*1. Clay mineral type affected the rates of (i) hydroxide promoted dissolution of Si, Al and Fe, (ii) precipitation of secondary solids and (iii) uptake of Cs and Sr. Initial Si release to solution followed the order Mt * Vm * Il. An abrupt decrease in soluble Si and/or Al after 33 d for Mt and Vm systems, and after 190 d for Il suspensions was concurrent with accumulation of secondary aluminosilicate precipitates. Strontium uptake exceeded that of Cs in both rate and extent, although sorbed Cs was generally more recalcitrant to subsequent desorption and dissolution. After 369 d reaction time, reacted Il, Vm and Mt solids retained up to 17, 47 and 14 mmol kg*1 (0.18, 0.24 and 0.02 *mol m*2) of Cs, and 0, 27 and 22 mmol kg*1 (0, 0.14 and 0.03 *molm*2) Sr, respectively, which were not removed in subsequent Mg exchange or oxalic acid dissolution reactions. Solubility of Al and Si decreased with initial Cs and Sr concentration in Mt and Il, but not in Vm. High co-contaminant sorption to the Vm clay, therefore, appears to diminish the influence of those ions on mineral transformation rates. Copyright © 2005 Elsevier Ltd
2005. "A Structural Model for the Membrane-Bound Form of the Juxtamembrane Domain of the Epidermal Growth Factor Receptor." Journal of Biological Chemistry 280(25):24043-24052. doi:10.1074/jbc.m502698200 Abstract The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family involved in the regulation of cellular proliferation and differentiation. Its juxtamembrane domain (JX), the region located between the transmembrane and kinase domains, plays important roles in receptor trafficking. Two sorting signals, a PXXP motif and a 658LL659 motif, are responsible for basolateral sorting in polarized epithelial cells, and a 679LL680 motif targets the ligand-activated receptor for lysosomal degradation. To understand the regulation of these signals, we characterized the structural properties of recombinant JX domain in aqueous solution and in dodecylphosphocholine (DPC) detergent. JX is inherently unstructured in aqueous solution, albeit a nascent helix encompasses the lysosomal sorting signal. In DPC micelles, structures derived from NMR data showed three amphipathic, helical segments. A large, internally inconsistent group of long range nuclear Overhauser effects suggest a close proximity of the helices, and the presence of significant conformational averaging. Models were determined for the average JX conformation using restraints representing the translational restriction due to micelle-surface adsorption, and the helix orientations were determined from residual dipolar couplings. Two equivalent average structural models were obtained that differ only in the relative orientation between first and second helices. In these models, the 658LL659 and 679LL680 motifs are located in the first and second helices and face the micelle surface, whereas the PXXP motif is located in a flexible helix-connecting region. The data suggest that the activity of these signals may be regulated by their membrane association and restricted accessibility in the intact receptor.
2005. "Dynamics of Water Trapped Between Hydrophobic Solutes." Journal of Physical Chemistry B 109(13):6422-6429. Abstract The abstract for this product is not available at this time.
2005. "Dynamics of Water Trapped between Hydrophobic Solutes." Journal of Physical Chemistry B 109(13):6422-6429. doi:10.1021/jp045439i Abstract We describe the model dynamical behavior of the solvent between two nanoscopic hydrophobic solutes. The dynamics of the vicinal water in various sized traps is found to be significantly different from bulk behavior. We consider the dynamics at normal temperature and pressure at three intersolute distances corresponding to the three solvent separated minima in the free energy profile between the solutes with attractions. These three states correspond to one, two, and three intervening layers of water molecules. Results are obtained from a molecular dynamics simulation at constant temperature and pressure (NPT) ensemble. Translational diffusion of water molecules trapped between the two solutes has been analyzed from the velocity correlation function as well as from the mean square displacement of the water molecules. The rotational behavior has been analyzed through the reorientational dynamics of the dipole moment vector of the water molecule by calculating both first and second rank dipole-dipole correlation functions. Both the translational and reorientational mobilities of water are found to be much slower at the smaller separation and increases as the separation between solutes becomes larger. The occupation time distribution functions calculated from the trajectories also show that the relaxation is much slower for the smallest intersolute separation as compared to other wider separations. The sublinear trend in mean square displacement and the stretched exponential decay of the relaxation of dipolar correlation and occupation distribution function indicate that the dynamical behavior of water in the confined region between two large hydrophobic solutes departs from usual Brownian behavior. This behavior is reminiscent of the behavior of water in the vicinity of protein surface clefts or trapped between two domains of a protein.
2005. "Local Density Profiles are Coupled to Solute Size and Attractive Potential for Nanoscopic Hydrophobic Solutes." Molecular Simulation 31(6-7):457-463. doi:10.1080/08927020500035457 Abstract We employ constant pressure molecular dynamics simulations to investigate the effects of solute size and solute-water dispersion interactions on the salvation behavior of nanoscopic hydrpophobic model solutes in water at normal temperature and pressure. The hydration behavior around a single planar atomic model solute as well as a pair of such solutes have been considered. The hydration water structure of a model nanoscopic solute with standard Lennard-Jones interaction is shown to be significantly different from that of their purely repulsive analogues. The density of water in the first salvation shell of a Lennard-Jones solute is much higher than that of bulk water and it remains almost unchanged with the increase of the solute dimensions from one to a few nanometers. On the other hand, for a purely repulsive analogue of the above model, solute hydration behavior shows a marked solute size dependence. The contact density of water in this case decreases with the increasing dimension of the solute. We also demonstrate the effect of solute-solvent attraction on the cavity formation in the inter solute region between two solutes with an inter solute separation of 6.8A, corresponding to the first solvent separated minimum in the free energy Profile as obtained in our earlier work.
2005. "On the Mechanism of Hydrophobic Association of Nanoscopic Solutes." Journal of the American Chemical Society 127(10):3556-3567. doi:10.1021/ja0441817 Abstract The abstract for this product is currently not available.
2005. "On the Mechanism of Hydrophobic Association of Nanoscopic Solutes." Journal of the American Chemical Society 127(10):3556-3567. Abstract The abstract for this product is not available at this time.
2005. "On the Mechanism of Hydrophobic Association ofNanoscopic Solutes." Journal of the American Chemical Society 127(10):3556-3567. doi:10.1021/ja0441817 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 hydration behavior of two planar nanoscopic hydrophobic solutes in liquid water at normal temperature and pressure is investigated by calculating the potential of mean force between them at constant pressure as a function of the solute-solvent interaction potential. The importance of the effect of weak attractive interactions between the solute atoms and the solvent on the hydration behavior is clearly demonstrated. We focus on the underlying mechanism behind the contrasting results obtained in various recent experimental and computational studies on water near hydrophobic solutes. The length scale where crossover from a solvent separated state to the contact pair state occurs is shown to depend on the solute sizes as well as on details of the solute-solvent interaction. We find the mechanism for attractive mean forces between the plates is very different depending on the nature of the solute-solvent interaction which has implications for the mechanism of the hydrophobic effect for biomolecules.
2005. "Optical properties of La-based high-K dielectric films." Journal of Vacuum Science and Technology A--Vacuum, Surfaces and Films 23(6):1676-1680. doi:10.1116/1.205655 Abstract We have characterized thin films of LaScO3 and LaAIO3 which were grown by molecular beam deposition on Si substrates. Samples of LaScO3 were also grown by pulsed laser deposition of MgO substrates. Using transmission studies between 1.5 and 6 eV, we have established that low temperature deposition leads to a reduced band gap with respect to the bulk crystal. Furthermore, using spectroscopic ellipsometry form 5 to 9 eV we observe substantial difference in near-band gap absorption between thin and thicker films for both materials. We obtain a band gap of 5.84 eV for the thinner film of LaAIO3, shereas we find a band gap of 6.33 eV for the thicker film of LaAIO3. Similarly we find band gaps of 5.5 and 5.9 eV, respectively, for thin and thick films of LaScO3
2005. "Differentiation of Spores of Bacillus Subtilis Grown in Different Media by Elemental Characterization using Time-of-Flight Secondary Ion Mass Spectrometry." Applied and Environmental Microbiology 71(11):6524-6530. Abstract We demonstrate the use of time of flight secondary ion mass spectrometry (ToF-SIMS) to infer the medium in which Bacillus subtilis spores were grown based on elemental signatures of the spores. Triplicate culture replicates grown in each of four different media were analyzed to obtain ToF-SIMS signatures comprised of 16 elemental intensities. The signatures were analyzed using ANOVA and principal components analysis (PCA). Confusion matrices constructed using nearest neighbor classification of the PCA scores confirmed the predictive utility of ToF-SIMS elemental signatures in identifying sporulation media. Application of this method will be of use in microbial forensics, and may also prove useful in the areas of food microbiology and astrobiology.
2005. "Determination of the Uranium Valence State in the Brannerite Structure using EELS, XPS, and EDX." Physics and Chemistry of Minerals 78(2):52-64. Abstract In this study, the valence states of uranium in synthetic and natural brannerite samples were studied using a combination of transmission electron microscopy-electron energy loss spectroscopy (TEM-EELS), scanning electron microscopy-energy dispersive xray analysis (SEM-EDX) and x-ray photoelectron spectroscopy (XPS) techniques. We used a set of five (UO2, CaUO4, SrCa2UO6, UTi2O6, Y0.5U0.5Ti2O6) U standard samples, including two synthetic brannerites, to calibrate the EELS branching ratio, M5/(M4 +M5), against the number of f electrons. The EELS data were collected at liquid nitrogen temperature in order to minimise the effects of electron beam reduction of U(VI) and U(V) .
2005. "Effects of Sediment Iron Mineral Composition on Microbially Mediated Changes in Divalent Metal Speciation: Importance of ferrihydrite." Geochimica et Cosmochimica Acta 69(7):1739-1759. Abstract Abstract Dissimilatory metal reducing bacteria (DMRB) can influence geochemical processes that subsequently affect the speciation the speciation and lability of metallic contaminants within natural environments. Most investigations into the effect of DMRB on sediment geochemistry utilise various synthetic oxides as the FeIII source (e.g. ferrihydrite, goethite, hematite, hydrous ferric oxide), providing for well-controlled experiments. However, these materials do not necessarily emulate the actual mineralogical composition of natural systems, nor do they account for the effect of sediment mineralogy on microbial activity and/or microbially induced geochemical processes. Our experiments with a divalent metal (ZnII) indicate that, while sediment mineralogy may have little effect on the net rate of microbial iron reduction, it does impact the resultant speciation of reduced iron and sediment associated transition metals. These data demonstrate that microbial reduction of synthetic goethite carrying previouslysorbed ZnII increased both [ZnII-aq] and the proportion of sorbed ZnII that is insoluble in 0.5 M HCl. Microbial reduction of FeIII in similarly treated iron-bearing clayey sediment (Fe-clay) and hematite sand had no similar effect. Mössbauer spectroscopy data indicate that small amounts of ferrihydrite present in the synthetic VHSA goethite are preferentially consumed during FeIII reduction, a process that may result from FeII-driven conversion of ferrihydrite to goethite. Microbial reduction of Fe-clay did not permanently alter iron speciation within the Fe-clay. Zinc k-edge XAS data collected for ZnII previously sorbed to VHSA goethite and Fe-clay indicate that microbial FeIII reduction altered ZnII bonding in fundamentally different ways for VHSA goethite and Fe-clay. In VHSA goethite, XANES data indicate ZnO6 octahedra in both sterile and reduced samples. EXAFS data indicate a slightly increased average Zn-O coordination number and a slightly higher degree of long range order in the reduced sample. This result may be consistent with enhanced ZnII substitution within goethite in the microbially reduced sample, though these data do not show the large increase in the degree of Zn-O-metal interactions expected to accompany this change. In Fe-clay, XANES data indicate that microbial FeIII reduction transforms Zn-O polyhedra from octahedral to tetrahedral coordination and leads to an increased degree of multiple scattering. EXAFS data indicate formation of a ZnCl2 moiety that may also incorporate some Zn-O bonds in the microbially reduced sample. These data indicate that, while many sedimentary iron minerals are easily reduced by DMRB, the geochemical effects of microbial FeIII reduction are highly dependent on sediment iron speciation. Thus, one must consider the effects of sediment mineralogy when investigating the effect of microbial processes on trace metal geochemistry.
2005. "Excess kinetic energy dissipation in materials." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 228(1-4):274-281. Abstract Molecular dynamics computer simulations are used to study the evolution of thermal spikes arising from PKAs in zircon and copper. The effects of thermostats employed to remove energy from the system is characterized and compared to the case where kinetic energy is not removed from the system. Strong effects on the trajectory of the collision sequence is found for zircon, but in contrast, little effects are found for copper.
2005. "Rotational Analysis of Several Bands in the High-Resolution Infrared Spectrum of Butadiene-1- 13C1: Assignment of Vibrational Fundamentals." Journal of Molecular Structure 742:21-29. Abstract Butadiene-113C1 was synthesized, and its high-resolution (0.002 cm-1) infrared spectrum was recorded for several bands in the mid-infrared region. A complete analysis of the rotational structure in the C-type bands at 900.0 and 909 cm-1 were performed. Of these latter two bands, which are of comparable intensity, the higher frequency one is largely CH2 out-of-plane wagging and the lower frequency one is largely 13CH2 out-of-plane wagging. Taken together these bands correlate with one infrared-active au fundamental and one Raman-active bg fundamental of butadiene. The ground state rotational constants are A=1.3887919(6), B=0.1436683(3), and C=0.1302251(3) cm-1, and upper state rotational constants are reported for the bands at 524.485 and 900.0 cm-1. Medium resolution infrared and Raman spectra gave a complete assignment of the vibrational fundamentals, including 11 fundamentals observed directly for the first time.
2005. "Amperometric Biosensors Based on Carbon Paste Electrodes Modified with Nanostructured Mixed-valence Manganese Oxides and Glucose Oxidase." Nanomedicine 1(2):130-135. Abstract Nanostructured multivalent manganese oxides octahedral molecular sieve (OMS), including cryptomelane-type manganese oxides and todorokite-type manganese oxides, were synthesized and evaluated for chemical sensing and biosensing at low operating potential. Both cryptomelane-type manganese oxides and todorokite-type manganese oxides are nanofibrous crystals with sub-nanometer open tunnels that provide a unique property for sensing applications. The electrochemical and electrocatalytic performance of OMS for the oxidation of H2O2 have been compared. Both cryptomelane-type manganese oxides and todorokite-type manganese oxides can be used to fabricate sensitive H2O2 sensors. Amperometric glucose biosensors are constructed by bulk modification of carbon paste electrodes (CPEs) with glucose oxidase as a biocomponent and nanostructured OMS as a mediator. A Nafion thin film was applied as an immobilization/encapsulation and protective layer. The biosensors were evaluated as an amperometric glucose detector at phosphate buffer solution with a pH 7.4 at an operating potential of 0.3 V (vs. Ag/AgCl). The biosensor is characterized by a well-reproducible amperometric response, linear signal-to-glucose concentration range up to 3.5 mM and 1.75 mM, and detection limits (S/N = 3) of 0.1 mM and 0.05 mM for todorokite-type manganese oxide and cryptomelane-type manganese oxide modified electrodes, respectively. The biosensors based on OMS exhibit considerable good reproducibility and stability, and the construction and renewal are simple and inexpensive.
2005. "Biosensors Based on Carbon Nanotubes/Nickel Hexacyanoferrate/Glucose Oxidase Nanocomposites." Journal of Biomedical Nanotechnology 1(3):320-327. Abstract Novel hybrid films based on carbon nanotubes (CNTs)/nickel hexacyanoferrate (NiHCF) nanocomposites were synthesized, characterized, and evaluated for chemical and bio-sensing properties. Nickel hexacyanoferrate particles were electrodeposited on the porous CNT thin-film to fabricate electrochemical sensors with improved sensitivity toward hydrogen peroxide. Transmission electron microscopy illustrated the deposition of nickel hexacyanoferrate nanoparticles on the surface of carbon nanotubes. The experimental results show the electrode modified with the hybrid nanocomposite film has higher electrocatalytic activity and stability for detection of hydrogen peroxide than the electrodes modified with carbon nanotube or nickel hexacyanoferrate alone. With glucose oxidase (GOx) as an enzyme model, we constructed a biosensor based on the CNTs/NiHCF/GOx nanocomposite. Excellent linear relationship up to 1.2 mM has been attained with a slope of 5.3 μA/mM for the glucose biosensor. The response time and detection limit (S/N = 3) of the biosensor was determined to be 10 s and 1 μM, respectively. The high sensitivity to glucose of the biosensor resulted from the high surface area of carbon nanotubes and excellent electrocatalytic activity of the modifiers. The biosensor also performed with excellent reproducibility and good stability.
2005. "Electrochemical Sensor Based on Carbon Paste Electrode Modified with Nanostructured Crypotomelane-Type Manganese Oxides for Detection of Heavy Metals." Sensor Letters 3(1):16-21. doi:10.1166/sl.2005.004 Abstract A carbon paste electrode modified with nanostructured crypotomelane type manganese oxides was evaluated as new electrochemical sensor for the detection of heavy metal ions in aqueous media. The crypotomelane type manganese oxides are nanofibrous crystals with sub-nanometer tunnels which provide excellent sites for ion-exchanges. The adsorptive stripping voltammetry (ASV) technique involves preconcentration of the metal ions into nanostructured crypotomelane type manganese oxides under an open circuit, then electrolysis of the preconcentrated species, followed by a square-wave potential sweep towards positive values. Factors affecting the preconcentration process were investigated using lead ion as the model analyte. The voltammetric responses increased with the preconcentration time from 2 to 30 min, and also linearly with lead ion concentrations ranging from 50 to 1200 ppb. The detection limits of target metal ion were 10 ppb after 4 min preconcentration and improved to 1 ppb after 20 min preconcentration. The potential for simultaneous detection of copper, silver and lead is also discussed.