Scientific Publications 2006
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2006. "Tertiary Structural Rearrangements upon Oxidation of Methionine145 in Calmodulin Promotes Targeted Proteasomal Degradation." Biophysical Journal 91(4):1480-1493. Abstract Mass spectrometry was used to identify possible linkages between the oxidation of specific methionines in calmodulin (CaM) and its degradation by the proteasome. Degradation of oxidized CaM (CaMox) occurs in a multistep process, which involves an initial cleavage that releases a large fragment (Q41-D131) and a carboxyl-terminus peptide (G132-K148) enriched in methionine sulfoxide [Met(O)] prior to rebinding and complete digestion. Rates of CaM degradation correlate with the oxidation of Met145, which is preferentially oxidized by hydrogen peroxide prior to the oxidation of Met144. The specificity of CaMox degradation was confirmed using CaM mutants in which the majority of methionines were replaced by leucines using site-directed mutagenesis, permitting the site-specific oxidation of Met144 or Met145. Oxidation of both Met144 and Met145 results in the selective degradation of CaMox by the proteasome with rates comparable to that observed for fully oxidized CaM. Oxidation of Met144 has little effect on proteolytic degradation; rather, oxidation of Met145 targets CaMox for proteasomal degradation. The selective oxidation of either Met144 or Met145 has little effect on the secondary structure of CaM; rather, oxidation-induced tertiary structural changes mediate the recognition and degradation of CaMox by the proteasome. Thus, oxidation of Met145 can function as a sensor that has the potential to regulate cellular metabolism through the targeted modulation of CaM abundance in response to oxidative stress.
2006. "Endogenously Nitrated Proteins in Mouse Brain: Links To Neurodegenerative Disease ." Biochemistry 45(26):8009-8022. doi:10.1021/bi060474w Abstract Increased nitrotyrosine modification of proteins has been documented in multiple pathologies in a variety of tissue types; emerging evidence suggests its additional role in redox regulation of normal metabolism. In order to identify proteins sensitive to nitrating conditions in vivo, a comprehensive proteomic dataset identifying 7,792 proteins from whole mouse brain, generated by LC/LC-MS/MS analyses, was used to identify nitrated proteins. This analysis resulted in identification of 31 unique nitrotyrosine sites within 29 different proteins. Over half of the nitrated proteins identified have been reported to be involved in Parkinson’s disease, Alzheimer’s disease, or other neurodegenerative disorders. Similarly, nitrotyrosine immunoblots of whole brain homogenates show that treatment of mice with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), an experimental model of Parkinson’s disease, induces increased nitration of the same protein bands observed to be nitrated in brains of untreated animals. Comparing sequences and available high resolution structures around nitrated tyrosines with those of unmodified sites indicates a preference of nitration in vivo for surface accessible tyrosines in loops, characteristics consistent with peroxynitrite-induced tyrosine modification. More striking is the five-fold greater nitration of tyrosines having nearby basic sidechains, suggesting electrostatic attraction of basic groups with the negative charge of peroxynitrite. Together, these results suggest that elevated peroxynitrite generation plays a role in neurodegenerative changes in the brain and provides a predictive tool of functionally important sites of nitration.
2006. "Characterization of Ambient Aerosols in Mexico City during the MCMA-2003 Campaign with Aerosol Mass Spectrometry. Results from the CENICA Supersite." Atmospheric Chemistry and Physics 6:925-946. Abstract An Aerodyne Aerosol Mass Spectrometer (AMS) was deployed at the CENICA Supersite, while another was deployed in the Aerodyne Mobile Laboratory (AML) during the Mexico City Metropolitan Area field study (MCMA-2003) from March 29-May 4, 2003 to investigate particle concentrations, sources, and processes. This is the first of a series of papers reporting the AMS results from this campaign. The AMS provides real time information on mass concentration and composition of the non-refractory species in particulate matter less than 1 μm (NR PM1) with high time and size resolution. For the first time, we report field results from a beam width probe, which was used to study the shape and mixing state of the particles and to quantify potential losses of irregular particles due to beam broadening inside the AMS. Data from this probe show that no significant amount of irregular particles was lost due to excessive beam broadening. A comparison of the CENICA and AML AMSs measurements is presented, being the first published intercomparison between two quadrupole AMSs. The speciation, and mass concentrations reported by the two AMSs compared well. In order to account for the refractory material in the aerosol, we also present measurements of Black Carbon (BC) using an aethalometer and an estimate of the aerosol soil component obtained from PIXE analysis of filters. Comparisons of (AMS + BC + soil) mass concentration with other collocated particle instruments (a LASAIR Optical Particle Counter, a Tapered Element Oscillating Microbalance (TEOM) and a DustTrack Aerosol Monitor) are also presented. The comparisons show that the (AMS + BC + soil) mass concentration during MCMC-2003 is a good approximation to the total PM₂․₅ mass concentration.
2006. "Correlation among Channeling, Morphological and Micro-structural Properties in Epitaxial CeO2 Films." Electrochemical and Solid-State Letters 9(5):J17-J20. doi:10.1149/1.2186029 Abstract We report an evidence of a critical thickness at ~ 64 nm in epitaxial CeO2 films grown at 750 0C on YSZ substrates by dc magnetron sputtering where optimum ion channeling can be correlated with overall strain relaxation and film surface roughness. The occurrence of saturation in ion channeling yield, enhancement in the average surface roughness and relaxation in c-axis strain is clearly evident in thicker films beyond the critical thickness. Despite excellent surface smoothness and overall epitaxial growth, CeO2 films grown at 650 0C did not show optimum ion channeling properties due to high misfit dislocation and defect density. These results are discussed from a viewpoint of the need for such an optimum thickness to develop multilayers with smooth interfaces with relative overall lattice relaxation.
2006. "Proteome analysis of mitochondrial outer membrane from Neurospora crassa." Proteomics 6(1):72-80. doi:10.1002/pmic.200402084 Abstract The mitochondrial outer membrane mediates numerous interactions between the metabolic and genetic systems of mitochondria and the rest of the eukaryotic cell. We performed a proteomic study to discover novel functions of components of the mitochondrial outer membrane. Proteins of highly pure outer membrane vesicles (OMV) from Neurospora crassa were identified by a combination of liquid chromatography tandem mass spectrometry of tryptic peptide digests and gel electrophoresis of solubilized OMV proteins, followed by their identification using MALDI-MS peptide fingerprinting. Among the 30 proteins found in at least three of four separate analyses were 23 proteins with known functions in the outer membrane. These included components of the import machinery (the TOM and TOB complexes), a pore-forming component (Porin), and proteins that control fusion and fission of the organelle. In addition, proteins playing a role in various biosynthetic pathways, whose intracellular location had not been established previously, could be localized to the mitochondrial outer membrane. Thus, the proteome of the outer membrane can help in identifying new mitochondria-related functions.
2006. "Microbial Reduction of Fe(III) in the Fithian and Muloorina Illites : Contrasting Extents and Rates of Bioreduction." Clays and Clay Minerals 54(1):67-79. doi:10.1346/CCMN.2006.0540109 Abstract This study was undertaken to investigate the rate and extent of reduction of Fe(III) in two different illite samples, Muloorina and Fithian, by facultative anaerobe, Shewanella putrefaciens CN32. The Fithian illite (API reference illite from Illinois) is relatively pure with only a trace amount of goethite. The starting material contained 4% of Fe, 19% of which is Fe(II) as determined by Mössbauer spectroscopy. Mössbauer spectroscopy also confirmed the presence of two different sites for Fe(III) in the illite structure. The surface area of the Fithian illite is 85.31 m2/g. The Muloorina illite, attained from Lake Eyre, S. Australia, has a surface area of 107.68 m2/g. The <0.2 µm size fraction was separated from a rock containing the Muloorina illite and used for bioreduction experiment. This size fraction is pure with no other Fe-containing minerals. The starting material contained 9.2% Fe, 93% of which is Fe(III) as determined by chemical and Mössbauer methods. A subsurface iron-reducing bacterium, Shewenella putrefactions CN32, was used in the illite reduction experiments. For both bioreduction experiments, illite suspensions of 10 mg/mL were made in bicarbonate buffer and experimental tubes were inoculated with about 4.0 x 10-6-6.0 x 10-7 CN32 cells. In selected treatments, antraquinone-2,6-disulfonate (AQDS) was included as an electron shuttle to facilitate bioreduction while lactate was used as an electron donor. Controls were identical but no cells were added. Fe(II) production at various time points was determined by Ferrozine assay. Aqueous concentrations of major elements, Si, Al, Mg, and Fe were measured by direct current plasma emission spectroscopy. Lactate and its metabolic product acetate were measured by high performance liquid chromatography. Residual and biogenic solids were characterized by transmission electron microscopy, Mössbauer spectroscopy, and electron energy loss spectroscopy. The extent of reduction was much greater in the presence of AQDS for each illite sample, and the abiotic controls did not show any Fe(III) reduction. More importantly, the two illites exhibited contrasting extent and rate of bioreduction. Approximately 50-60% of Fe(III) in the Fithian illite (as measured by Ferrozine assay) was reduced within 4 days, whereas it took about two months to reduce 6-8% of Fe(III) in the Muloorina illite. In both cases, Fe(III) reduction was coupled with oxidation of lactate. The aqueous concentration of Fe increased over time and paralleled the trend of the biogenic Fe(II) production, but it accounted for only about 10% of total biogenic Fe(II), suggesting that most of bioproduced Fe(II) was either in biogenic solids or adsorbed onto solid surfaces. Intensive characterizations of residual and biogenic solids are underway to delineate the reasons for the differences in the bioreduction behavior of the two illite samples. Surface area does not account for the differences. We speculate that these differences are caused by different structural sites of Fe(III): there exists two structural sites for Fe(III) in the Fithian illite as opposed to one site for Fe(III) in the Muloorina illite. One of the two sites is unique to the Fithian illite, and this site may be responsible for the extensive reduction for this illite sample. This site may be accessible to bacteria and thus may subject to more bioreduction.
2006. "Isolation of a High-Affinity Functional Protein Complex between OmcA and MtrC: Two Outer Membrane Decaheme c-type Cytochromes of Shewanella oneidensis MR-1 ." Journal of Bacteriology 188(13):4705-4714. doi:10.1128/JB.01966-05 Abstract SUMMARY Shewanella oneidensis MR-1 is a facultatively anaerobic bacterium that is capable of using insoluble oxidized metals, such as manganese [Mn(III, IV)] and iron [Fe(III)] oxides and oxyhydroxides, as terminal electron acceptors during anaerobic respiration. The ability of S. oneidensis MR-1 to reduce oxidized Mn and/or Fe has previously been linked to OmcA and MtrC: two decaheme c-type cytochromes that are localized to the outer membrane. To investigate how the electron transport proteins OmcA and MtrC are organized, we expressed and purified recombinant OmcA and MtrC from wild type S. oneidensis MR-1 as well as a mutant that lacked OmcA and MtrC (ΔomcA/mtrC). After purification to the nearly electrophoretic homogeneity from the ΔomcA/mtrC mutant, the recombinant OmcA and MtrC exhibited the characteristics of c-type cytochromes, and each of their polypeptides was confirmed to contain 10 hemes. When purified from wild type cells, endogenous MtrC or OmcA was always co-purified with recombinant OmcA or MtrC, respectively. Fluorescence polarization experiment showed that recombinant OmcA bound to the FlAsH-labeled MtrC with a dissociation constant of 7 ×10-7 M. The purified recombinant OmcA or MtrC alone displayed intrinsic ferric reductase activity with NADH used as an electron donor. Ferric reductase specific activity increased by 35 to 41% when nearly equimolar concentrations of OmcA and MtrC were assayed relative to the two proteins assayed independently. These results demonstrate that OmcA and MtrC directly interact with each other to form a stable complex with high ferric reductase activity.
2006. "Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from RAW 264.7 Macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages." Journal of Biological Chemistry 281:29131-29140. doi:10.1074/jbc.M604640200 Abstract ABSTRACT: To evade host resistance mechanisms, Salmonella enterica serovar Typhimurium (STM), a facultative intracellular pathogen, must alter its proteome following macrophage infection. To identify new colonization and virulence factors that mediate STM pathogenesis, we have isolated STM cells from RAW 264.7 macrophages at various time-points following infection and used a liquid chromatography-mass spectrometry (LC-MS)-based proteomic approach to detect the changes in STM protein abundances. Because host resistance to STM infection is strongly modulated by the expression of a functional host resistant regulator, i.e., natural resistance associated macrophage protein 1 (Nramp1, also called Slc11a1), we have also examined the effects of Nramp1 activity on the changes of STM protein abundances. A total of 315 STM proteins have been identified from isolated STM cells, which are largely house-keeping proteins whose abundances remain relatively constant during the time-course of infection. However, 39 STM proteins are strongly induced after infection, suggesting their involvement in modulating colonization and infection. Of the 39 induced proteins, 6 proteins are specifically modulated by Nramp1 activity, including STM3117, as well as STM3118-3119 whose time-dependent abundance changes were confirmed using Western blot analysis. Deletion of the gene encoding STM3117 resulted in a dramatic reduction in the ability of STM to colonize wild-type RAW 264.7 macrophages, demonstrating a critical involvement of STM3117 in promoting the replication of STM inside macrophages. The predicted function common for STM3117-3119 is biosynthesis and modification of the peptidoglycan layer of STM cell wall, emphasizing their important roles in the colonization of macrophages by Salmonella.
2006. "Synthesis of Room-Temperature Ferromagnetic Cr-doped TiO₂(110) Rutile Single Crystals using Ion Implantation." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 242(1-2):198-200. doi:10.1016/j.nimb.2005.08.149 Abstract Ferromagnetic Cr-doped rutile TiO₂ single crystals were synthesized by high-temperature ion implantation. The associated structural, compositional and magnetic properties were studied by x-ray photoelectron spectroscopy, Rutherford backscattering spectrometry, proton induced x-ray emission, x-ray diffraction, Cr K- and L-shell near-edge x-ray absorption spectroscopy, and vibrating sample magnetometry. Cr was distributed uniformly to the depth of about 300 nm with an average concentration of ~1 at. %. The samples are semiconducting and ferromagnetic as implanted, with a saturation magnetization of 0.29B/Cr atom at room temperature. Cr is in a formal oxidation state of +3 throughout the implanted region, and no CrO₂ is detected.
2006. "Quantification of Dopant Concentrations in Diluted Magnetic Semiconductors using Ion Beam Techniques." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 249(1-2):402-405. doi:10.1016/j.nimb.2006.04.038 Abstract It has recently been demonstrated that magnetically doped TiO2 and SnO2 show ferromagnetism at room-temperature and Curie temperatures above room temperature. However, accurate knowledge of dopant concentrations is necessary to quantify magnetic moments in these materials. Rutherford Backscattering spectrometry (RBS) is one of the powerful techniques to quantify magnetic transition metal dopant concentrations in these materials. However, in some cases, the interference of RBS signals for different dopants and substrate elements in these materials makes analysis difficult. In this work, we demonstrate that particle induced x-ray emission (PIXE) can be successfully used to quantify the magnetic transition element dopants in several room temperature ferromagnetic materials synthesized using three different synthesis methods: oxygen plasma assisted molecular beam epitaxy, ion implantation and wet chemical methods.
2006. "Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms ." Journal of Physical Chemistry A 110(8):2663-2673. doi:10.1021/jp055349t Abstract Technologies for separating and characterizing ions based on their transport properties in gases have been around for three decades. The early method of ion mobility spectrometry (IMS) distinguished ions by absolute mobility that depends on the collision cross section with buffer gas atoms. The more recent technique of field asymmetric waveform IMS (FAIMS) measures the difference between mobilities at high and low electric fields. Coupling IMS and FAIMS to soft ionization sources and mass spectrometry (MS) has greatly expanded their utility, enabling new applications in biomedical and nanomaterials research. Here, we show that time-dependent electric fields comprising more than two intensity levels could, in principle, effect an infinite number of distinct differential separations based on the higher-order terms of expression for ion mobility. These analyses could employ the hardware and operational procedures similar to those utilized in FAIMS. Methods up to the 4th or 5th order (where conventional IMS is 1st order and FAIMS is 2nd order) should be practical at field intensities accessible in ambient air, with still higher orders potentially achievable in insulating gases. Available experimental data suggest that higher-order separations should be largely orthogonal to each other and to FAIMS, IMS, and MS.
2006. "Degradation Mechanisms of La-Sr-Co-Fe-O3 SOFC Cathodes." Electrochemical and Solid-State Letters 9(10):A478-A481. Abstract The long-term stability of anode-supported YSZ electrolyte SOFCs utilizing (La0.6Sr0.4)0.98Co0.2Fe0.8O3- (LSCF-6428) cathodes was assessed. Samples tested for 500 hours at 750ºC and 0.7V indicated ≈50% degradation. While scanning electron microscopy (SEM) and energy dispersive x-ray (EDX) analysis indicated no obvious microstructural or chemical phenomena that could explain the high degradation, x-ray photon spectroscopy (XPS) revealed that enrichment of Sr at the cathode-electrolyte and cathode-current collector interfaces was at least partially responsible for the observed degradation.
2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling ." Electrophoresis 27(13):2722-2733. doi:10.1002/elps.200600037 Abstract Bottom-up proteomics (analyzing peptides that result from protein digestion) has demonstrated capability for broad proteome coverage and good throughput. However, due to incomplete sequence coverage, this approach is not ideally suited to the study of modified proteins. The modification complement of a protein can best be elucidated by analyzing the intact protein. Two-dimensional gel electrophoresis, typically coupled with the analysis of peptides that result from in-gel digestion, is the most frequently applied protein separation technique in MS-based proteomics. As an alternative, numerous column-based liquid phase techniques, which are generally more amenable to automation, are being investigated. In this work, the combination of size exclusion chromatography (SEC) fractionation with reversed-phase liquid chromatography (RPLC)-Fourier-transform ion cyclotron resonance (FTICR)-mass spectrometry (MS) is compared with the combination of RPLC fractionation with capillary isoelectric focusing (CIEF)-FTICR-MS for the analysis of the Shewanella oneidensis proteome. SEC-RPLC-FTICR-MS allowed the detection of 297 proteins, as opposed to 166 using RPLC-CIEF-FTICR-MS, indicating that approaches based on LC-MS provide better coverage. However, there were significant differences in the sets of proteins detected and both approaches provide a basis for accurately quantifying changes in protein and modified protein abundances.
2006. "Realistic Quantitative Descriptions of Electron Transfer Reactions: Diabatic Free-EnergySurfaces from First-Principles Molecular Dynamics." Physical Review Letters 97(028303):1-4. doi:10.1103/PhysRevLett.97.028303 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 general approach to calculate the diabatic surfaces for electron-transfer reactions is presented, based on first-principles molecular dynamics of the active centers and their surrounding medium. The excitation energy corresponding to the transfer of an electron at any given ionic configuration (the Marcus energy gap) is accurately assessed within ground-state density-functional theory via a novel penalty functional for oxidation-reduction reactions that appropriately acts on the electronic degrees of freedom alone. The selfinteraction error intrinsic to common exchange-correlation functionals is also corrected by the same penalty functional. The diabatic free-energy surfaces are then constructed from umbrella sampling on large ensembles of configurations. As a paradigmatic case study, the self-exchange reaction between ferrous and ferric ions in water is studied in detail.
2006. "Electronic Coupling between Heme Electron-Transfer Centers and Its Decay with Distance Depends Strongly on Relative Orientation." Journal of Physical Chemistry B 110(31):15582-15588. doi:10.1021/jp057068r Abstract A method for calculating the electron-transfer matrix element VRP using density functional theory Kohn-Sham orbitals is presented and applied to heme dimers of varying relative orientation. The electronic coupling decays with increased iron separation according to VRP ) V0RP exp(-βr/2) with a distance dependence parameter β ≈ 2 Å-1 for hemes with parallel porphyrins and either 1.1 or 4.0 Å-1 when the porphyrin planes are perpendicular, depending on the alignment of the iron dл orbital. These findings are used to interpret the observed orientation of the hemes in tetraheme redox proteins such as Flavocytochrome c3 fumarate reductase (Ifc3, PDB code 1QJD) of Shewanella frigidimarina, another flavocytochrome from the same bacterium (Fcc3, 1E39) and a small tetraheme cytochrome of Shewanella oneidensis strain MR1 (1M1P). Our results show that shifting and rotating the hemes controls the adiabaticity of the three electron hopping steps.
2006. "The Effect of the Incident Collision Energy on the Phase and Crystallization Kinetics of Vapor Deposited Water Films." Journal of Chemical Physics 124(11):114710 (7 pages). Abstract Molecular beam techniques are used to grow water films on Pt(111) with incident collision energies from 5 to 205 kJ/mole. The effect of the incident collision energy on the phase of vapor deposited water films and their subsequent crystallization kinetics are studied using temperature-programmed desorption and FTIR spectroscopy. We find that for films deposited at substrate temperatures below 110 K, the incident kinetic energy (up to 205 kJ/mole) has no effect on the initial phase of the deposited film or its crystallization kinetics. Above 110 K, the substrate temperature does affect the phase and crystallization kinetics of the deposited films but this result is also independent of the incident collision energy. The presence of a crystalline ice does affect the crystallization of ASW but this effect is also independent of the incident beam energy. These results suggest that the crystallization of amorphous solid water requires cooperative motion of several water molecules.
2006. "Low-LET Bystander Responses in Gap Junction Null Human Colon Carcinoma Cells (RK036)." Radiation Research 166(4):688-689. Abstract Combined with sensitive molecular techniques, the microbeam has proven extremely useful in studying radiation biology. This technology allows individual cells, or selected groups of cells, to be irradiated at specific doses and dose rates. Such capabilities lend themselves well to studies of low dose responses, delayed and non-targeted bystander effects of radiation. High-linear energy transfer (LET) microbeams mimic heavy energetic particles such as the α-particles associated with radon exposure and have been used in numerous biological studies. Several low-LET microbeams have also been developed (reviewed in. One such low-LET microbeam, developed at the Pacific Northwest National Laboratory and currently located at the University of Maryland Radiation Oncology Research Laboratory, uses a variable energy electron source to mimic low-LET radiation and allows observation of how x-rays and γ-rays affect mammalian cells.
2006. "Acid Initiation of Ammonia-Borane Dehydrogenation for Hydrogen Storage." Angewandte Chemie International Edition 46(5):746-749. doi:10.1002/anie.200603285 Abstract An abstract for this journal article is not available at this time.
2006. "Toward an Accurate Determination of 195Pt Chemical Shifts by DensityFunctional Computations: The Importance of Unspecific Solvent Effectsand the Dependence of Pt Magnetic Shielding Constants on StructuralParameters." Inorganic Chemistry 45(8):3316-3324. doi:10.1021/ic052143y Abstract Density functional theory using the zero-order regular approximate two-component relativistic Hamiltonian has been applied to calculate the 195Pt chemical shifts for the complexes [PtCl6]2-, [PtCl4]2-, and [Pt2(NH3)2Cl2((CH3)3CCONH)2- (CH2COCH3)]Cl. It is demonstrated that, in contrast to recent findings by other authors, platinum chemical shift calculations require not only a basis set beyond polarized triple-ú quality for the metal atom but also, in principle, the consideration of explicit solvent molecules in addition to a continuum model for the first two complexes. We find that the inclusion of direct solvent-solute interactions at the quantum mechanical level is important for obtaining reasonable results despite that fact that these solvent effects are rather nonspecific. The importance of solvent effects has also implications on how experimental data should be interpreted. Further, in contrast to several previous studies of heavy-metal NMR parameters, functionals beyond the local density approximation were required both in the geometry optimization and the NMR calculations to obtain reasonable agreement between the computed and experimental NMR data. This comes with the disadvantage, however, of increased Pt-ligand bond distances leading to less good agreement with experiment for structural data. A detailed analysis of the results for the two chloroplatinate complexes is presented. The same computational procedure has then been applied to the dinuclear Pt(III) complex. Chemical shifts have been calculated with respect to both [PtCl6]2- and [PtCl4]2- chosen as the NMR reference, yielding good agreement with experiment. The determination of preferred solvent locations around the complexes studied turned out to be important for reproducing experimental data.
2006. "A Study of Pore Geometry Effects on Anisotropy in Hydraulic Permeability Using the Lattice-Boltzmann Method." Advances in Water Resources 29(9):1328-1340. Abstract We hypothesize that anisotropy in soil properties arises from pore-scale heterogeneity caused by the alignment of aspherical soil particles. We developed a method to predict the permeability tensor from particle shape and packing structure. Digital geometry maps were created for the pore space in regular cubic and random packs of particles with various aspect ratios using a numerical packing algorithm. The lattice-Boltzmann method was used to simulate saturated flow through these packs, and the effect of particle shape and degree of alignment on the permeability tensor was characterized. Results show that the degree of anisotropy in permeability depends not only upon particle shape and alignment, but also on the three-dimensional structure of the pack. In random packs, more oblate particles and higher degrees of particle alignment lead to reduced permeability perpendicular to the direction of particle alignment compared to the direction parallel to particle alignment.
2006. "Luminescence Temperature and Pressure Studies of Zn2SiO4 Phosphors Doped with Mn2+ and Eu3+ Ions." Journal of Luminescence 116(1-2):117-126. Abstract Zn2SiO4:Mn2+, Zn2SiO4:Mn3+, and Zn2SiO4:Mn2+, Eu3+ phosphors were prepared by a sol-gel process and their luminescence spectra were investigated. The emission bands from intra-ion transitions of Mn2+ and Eu3+ samples were studied as a function of pressure. The pressure coefficient of Mn2+ emission was found to be -25.3±0.5 and -28.5±0.9 neV/GPa for Zn2SiO4:Mn2+ and Zn2SiO4:Mn2+, Eu3+, emission shows only weak pressure dependence. The pressure dependences of the Mn2+ and Eu3+ emissions in Zn2SiO4:Mn2+, Eu3+ are slightly different from that in Zn2SiO4:Mn2+ and Zn2SiO4:Mn3+ samples, which can be attributed to the co-doping of Mn2+ and Eu3+ ions. The Mn2+ emission in the two samples, however, exhibits analogous temperature dependence and similar luminescence lifetimes, indicating no energy transfer from Mn2+ to Eu3+ occurs.
2006. "Pressure Dependence of the Near-Band-Edge Photoluminescence from ZnO Microds at Low Temperature." The Journal of Physics and Chemistry of Solids 67(11):2376-2381. Abstract The temperature and pressure dependences of band-edge photoluminescence from ZnO mico-rods have been investigated. The energy separation between the free exciton (FX) and its first order phonon replica (FX-1LO) decreases at a rate of kBT with increasing temperature. The intensity ratio of the FX-1LO to the bound exciton (BX) emission is found to decrease slightly with increasing pressure. All of the exciton emission peaks show a blue shift with increasing pressure. The pressure coefficient of the FX transition, longitudinal optical (LO) phonon energy, and binding energy of BX are estimated to be 21.4, 0.5, and 0.9 meV/GPa, respectively.
2006. "Temperature and pressure dependences of the Copper-related Green Emission in ZnO Microrods." Journal of Applied Physics 100(1):013107-1 - 013107-6. doi:10.1063/1.2206705 Abstract We investigate the temperature and pressure dependence of the green, Cu2+-related photoluminescence (PL) from tetrapod-like ZnO micro-rods. The temperature dependence of the green emission energy follows the changes in the band gap from 10-200 K, but deviates from this behavior above 200 K. The pressure dependence of the defect-related green band (25±5 meV/GPa) is similar to that of the band gap of ZnO, which is far larger than reported previously.
2006. "Reduction of Stored NOx on Pt/Al₂O₃ and Pt/BaO/Al₂O₃ Catalysts with H₂ and CO." Journal of Catalysis 239(1):51-64. doi:10.1016/j.jcat.2006.01.014 Abstract In situ FTIR spectroscopy coupled with mass spectrometry, and time resolved X-ray diffraction were used to study the efficiency of nitrate reduction with CO and H₂ on Pt/Al₂O₃ and Pt/BaO/Al₂O₃ NOx storage-reduction (NSR) catalysts. Surface nitrates were generated by NO₂ adsorption and their reduction efficiencies were examined on the catalysts together with the analysis of the gas phase composition in the presence of the two different reductants. H₂ was found to be a more effective reducing agent than CO. In particular, the reduction of surface nitrates proceeds very efficiently with H₂ even at low temperatures (~420 K). During reduction with CO, isocyanates were observed to form on every catalyst component. These surface isocyanates, however, readily react with water to form CO₂ and ammonia. The thus formed NH₃, in turn, reacts with stored NOx at higher temperatures (>473K) to produce N₂. In the absence of H₂O, the NCO species are stable to high temperatures, and removed only from the catalyst when they react with NOx thermal decomposition products to form N₂ and CO₂. The results of this study point to a complex reaction mechanism that involves the removal of surface oxygen atoms from the Pt particles by either H₂ or CO, the direct reduction of stored NOx with H₂ (low temperature NOx reduction), the formation and the subsequent hydrolysis of NCO species, as well as the direct reaction of NCO with decomposing NOx (high temperature NOx reduction).
2006. "Effects of Ba loading and calcination temperature on BaAl2O4 formation for BaO/Al2O3 NOx Storage and Reduction Catalysts." Catalysis Today 114(1):86-93. doi:10.1016/j.cattod.2006.02.016 Abstract The effect of thermal treatment on the structure and chemical properties of Ba-oxide-based NOx storage/reduction catalysts with different Ba loadings was investigated using BET, TEM, EDS, TPD and FTIR techniques. On the basis of the present and previously reported results, we propose that moderate (< ~873 K) temperature calcinations result in a single monolayer (ML) ‘coating’ of BaO on the alumina surface. At high Ba loading in excess of that required for a full monolayer ‘coating’ (> 8 wt.% BaO), small (~5 nm) particles of ‘bulk’ BaO are present on top of the 1 ML BaO/Al2O3 surface. We did not observe any detectable morphological changes upon higher temperature thermal treatment of 2 and 8 wt% BaO/Al2O3 samples, while dramatic changes occurred for the 20 wt% sample. In this latter case, the transformations included BaAl2O4 formation at the expense of the bulk BaO phase. In particular, we conclude that the surface (ML) BaO phase is quite stable against thermal treatment, while the bulk phase provides the source of Ba for BaAl2O4 formation.
2006. "Characterization of NOx Species in Dehydrated and Hydrated Na- and Ba-Y, FAU Zeolites Formed in NO₂ Adsorption." Journal of Electron Spectroscopy and Related Phenomena 150(2-3):164-170. doi:10.1016/j.elspec.2005.05.007 Abstract Adsorbed ionic NOx species formed upon the interaction of NO₂ with dehydrated or hydrated Na-, and Ba-Y, FAU zeolites were characterized using FTIR/TPD, solid state NMR, and XANES techniques. NO₂ disproportionates on both dehydrated catalyst materials forming NO⁺ and NO₃⁻ species. These ionic species are stabilized by their interactions with the negatively charged zeolite framework and the charge compensating cations (Na⁺ and Ba²⁺), respectively. Although the nature of the adsorbed NOx species formed on the two catalysts is similar, their thermal stabilities are strongly dependent on the charge compensating cations. In the presence of water in the channels of these zeolite materials new paths open for reactions between NO⁺ and H₂O, and NO₂ and H₂O, resulting in significant changes in the adsorbed ionic species observed. These combined spectroscopic investigations afforded the understanding of the interactions between water and the NO₂ on these zeolite catalysts.
