Scientific Publications 2007
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2007. "Fabrication of SiO2 Microdisk Arrays for Optics and Light Trapping Experiments." Microelectronic Engineering 84(12):2799-2803. doi:10.1016/j.mee.2007.02.001 Abstract We present a simple silicon based microfabrication process that produces an array of SiO2 microdisks using UV lithography. High-resolution SEM images of these structures indicate a smooth outer microdisk cavity surface. Photoemission measurements were performed at different spots on the microdisk and compared with measurements inside the cavity. A silicon to oxygen atomic concentration ratio of 1:2 obtained during depth profiling confirms that the entire microdisk is made up of stoichometric SiO2. In contrast, the inner cavity is mostly silicon with native oxide on top. We discuss the usefulness of SiO2 microdisks in optics for light trapping experiments.
2007. "Nucleation and Growth of MOCVD Grown (Cr, Zn)O Films – Uniform Doping vs. Secondary Phase Formation." Journal of the Electrochemical Society 154(3):D134-D138. doi:10.1149/1.2424422 Abstract We report a detailed study of chromium solubility and secondary phase formation in MOCVD grown (Cr, Zn)O-based films on silicon (100). Simultaneous deposition of 0.15M Cr(TMHD) and 0.025M Zn(TMHD) based precursors in an oxidizing environment with a flow ratio of 1:10 resulted in secondary phase formation rather than uniform Cr doping. Based on several surface and micro-structural techniques, we have identified nano-crystalline ZnCr2O4 and disordered Cr2O3 as the secondary Cr-containing phases that nucleate. Analysis suggests that ZnCr2O4 crystallites are dispersed throughout the film and that disordered Cr2O3 layer may form at the interface. These results reveal a strong tendency for Cr to exist in octahedral, rather than tetrahedral coordination.
2007. "Distal Charge Transport in Peptides." Angewandte Chemie International Edition 46:2-17. doi:10.1002/anie.200601623 Abstract An abstract for this journal article is not available at this time.
2007. "IO strategies and data services for petascale data sets from a global cloud resolving model." Journal of Physics: Conference Series 78:Art. No. 012089. doi:10.1088/1742-6596/78/1/012089 Abstract Global cloud resolving models at 4km resolutions or less create significant challenges in generation of simulation data, data storage, data management, and post-simulation analysis and visualization. To support efficient model output as well as data analysis, new models for IO and data organization must be evaluated. The model we are supporting, the Global Cloud Resolving Model being developed at Colorado State University, uses a geodesic grid. The non-monotonic nature of the grid's coordinate variables requires enhancements to existing data processing tools and community standards for describing and manipulating grids. The resolution, size and extent of the data suggest the need for parallel analysis tools and allow for the possibility of new techniques in data mining, filtering and comparison to observations. We describe the challenges posed by various aspects of data generation, management, and analysis, our work exploring IO strategies for the model, and a preliminary architecture, web portal, and tool enhancements which, when complete, will enable broad community access to the data sets in a way that is familiar to the community.
2007. "Process Integration, data management, and visualizationframework for subsurface sciences." Journal of Physics: Conference Series 78:012064, 1-5. doi:10.1088/1742-6596/78/1/012064 Abstract Applying subsurface simulation codes to understand heterogeneous flow and transport problems is a complex process potentially involving multiple models, multiple scales, and spanning multiple scientific disciplines. For each model used, the process may involve steps such as changing the model, acquiring and preparing input data sources, configuring the model, executing the model on a remote supercomputer, validating the results, and performing calibration and sensitivity analysis all before predictive modeling can be applied to important environmental remediation problems. This process involves many tools, scripts and data sources usually shared only though informal channels. Additionally, the process contains many sub-processes that are repeated frequently and could be automated and shared. Finally, keeping records of the models, processes, and correlation between inputs and outputs is currently manual, time consuming and error prone. We are developing a software framework that integrates a workflow execution environment, shared data repository, and analysis and visualization tools to support development and use of new hybrid subsurface simulation codes. We are taking advantage of recent advances in scientific process automation using the Kepler system and advances in data services based on content management. Extensibility and flexibility are underlying design considerations to support the constantly changing set of tools, scripts, and models available. We describe the architecture and components of this system with early examples of applying it to a continuum subsurface model.
2007. "The effect of U(VI) bioreduction kinetics on subsequent reoxidation of biogenic U(IV)." Geochimica et Cosmochimica Acta 71(19):4644-4654. doi:10.1016/j.gca.2007.07.021 Abstract Microbially mediated in situ reduction of soluble U(VI) to insoluble U(IV) (as UO2) has been proposed as a means of preventing the migration of that radionuclide with groundwater, but preventing the oxidative resolubilization of U has proven difficult. We hypothesized that relatively slow rates of U(VI) bioreduction would yield larger UO2 precipitates that would be more resistant to oxidation than those produced by rapid U(VI) bioreduction. We manipulated U(VI) bioreduction rates by varying the density of Shewanella putrefaciens CN32 added to U(VI) containing solutions with lactate as an electron donor. Characterization of biogenic UO2 particles by extended X-ray absorption fine-structure spectroscopy and transmission electron microscopy revealed that UO2 nanoparticles formed by relatively slow rates of U(VI) reduction were larger and more highly aggregated than those formed by relatively rapid U(VI) reduction. UO2 particles formed at various rates were incubated under a variety of abiotically and biologically oxidizing conditions. In all cases, UO2 that was formed by relatively slow U(VI) reduction was oxidized at a slower rate and to a lesser extent than UO2 formed by relatively rapid U(VI) bioreduction, suggesting that the stability of UO2 in situ may be enhanced by stimulation of relatively slow rates of U(VI) reduction.
2007. "Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry." Journal of Proteome Research 6(2):602-610. doi:10.1021/pr060354a Abstract We investigated the combination of weak anion exchange (WAX) fractionation and on-line reversed phase liquid chromatography (RPLC) separation using a 12 T FTICR mass spectrometer for the detection of intact proteins from a Shewanella oneidensis MR-1 cell lysate. 715 intact proteins were detected and the combined results from the WAX fractions and the unfractionated cell lysate were aligned using LC-MS features to facilitate protein abundance measurements. Protein identifications and post translational modifications were assigned for ~10% of the detected proteins by comparing intact protein mass measurements to proteins identified in peptide MS/MS analysis of an aliquot of the same fraction. Intact proteins were also detected for S. oneidensis lysates obtained from cells grown on 13C, 15N depleted media under aerobic and sub-oxic conditions. This work aimed at optimizing intact protein detection for profiling proteins at a level that incorporates their modification complement. The strategy can be readily applied for measuring differential protein abundances, and provides a platform for high-throughput selection of biologically relevant targets for further characterization.
2007. "XPS of fast-frozen hematite colloids in NaCl aqueous solutions: I. Evidence for the formation of multiple layers of hydrated sodium and chloride ions induced by the {001} basal plane." Journal of Physical Chemistry C 111(49):18307-18316. doi:10.1021/jp075321c Abstract The influence of the {001} basal plane of hematite on the composition of fast-frozen centrifuged wet pastes of hematite prepared at pH 4 and 9 and at ionic strengths of 0, 10 and 100 mM NaCl was investigated by x-ray photoelectron spectroscopy. Two hematite preparations consisted of micrometer-sized platelets with 42% (HEM-1) and 95% (HEM-8) of the surface terminated by the {001} basal plane. A third preparation of spherical shape with no recognizable crystal plane (HEM-control) was used as a control to these experiments. All hematite samples responded to changes in pH and ionic strength, showing that acid/base reactions of surface hydroxyl groups control the composition of the paste. The HEM-1 and HEM-8 sample exhibited divergent properties at the highest ionic strength (100 mM) with energy loss features in the Na 1s and Cl 2p spectra and an important water content. As the spectra were typical of hydrated Na+ and Cl- ions and that the surface concentrations were unusually large, the HEM-1 and HEM-8 samples are proposed to induce the formation of a three-dimensional distribution of these ions in the paste. The sodium, chloride and water content was also correlated to the fraction of the {001} basal plane present in the sample and provided evidence for an approximate stochiometric Na:Cl:H2O ratio of 1:1:2. The {001} basal plane of hematite is consequently proposeD to be the cause of this feature.
2007. "Synthesis and Characterization of Phosphate-coated Mesoporous Titania and Cd-doping of Same via Ion-Exchange." Inorganic Chemistry Communications 10(6):642-645. doi:10.1016/j.inoche.2007.02.016 Abstract Phosphate-based mesoporous TiO2 materials were prepared by surfactant-directed method using an alkylphosphate surfactant, which produced a mesoporous titania with high surface area (~200 m2/g) and a phosphate monolayer interface. Calcination of the as-synthesized greenbody in an ozone atmosphere generated materials with higher surface area, and higher purity, than did calcination in air. These interfacial phosphate groups are convenient functionality for chemically modifying the surface via ion-exchange processes. High doping ratios of P/Ti (0.47-0.69) and Cd/P (0.37-0.40) were observed. Materials were characterized by XRD, FE-SEM, TEM, and XPS.
2007. "Grid-based Numerical Hartree-Fock Solutions of Polyatomic Molecules." Physical Review. A. 76:040503R. doi:10.1103/PhysRevA.76.040503 Abstract Numerical solutions of the Hartree-Fock _HF_ equation of polyatomic molecules have been obtained by an extension of the numerical density-functional method of Becke and Dickson _J. Chem. Phys. 89, 2993 1988; 92, 3610 1990. A finite-difference method has been used to solve Poisson’s equation for the Coulomb and exchange potentials and to evaluate the action of the Laplace operator on numerical orbitals expanded on an interlocking multicenter quadrature grid. Basis-set-limit HF results for an atom and diatomic and triatomic molecules are presented with the total energies and the highest occupied orbital energies converged to within 10−5 Hartree without any extrapolation.
2007. "Bimodal Energy Distributions in the Scattering of Ar+ Ions from Modified Surfaces at Hyperthermal Energies." Chemical Physics Letters 449(1-3):53-56. doi:10.1016/j.cplett.2007.10.043 Abstract Collisions of Ar+ ions with three different surfaces (self assembled monolayer of fluorinated alkyl thiol, vapor deposited thin films of diamond and LiF) have been studied by mass and energy resolved ion-scattering spectrometry. Kinetic energy distributions of scattered ions measured as a function of ion’s initial kinetic energy and scattering angle show a single peak at the lowest energy (~25 eV) corresponding to the loss of a small amount (~6 – 9 eV) of kinetic energy by the Ar+ ions. However, as the collision energy is increased, two energetically and spatially distinct peaks are observed in the kinetic energy spectra. These two processes correspond to the low energy loss process as mentioned above and a very high energy loss process approaching close to the initial kinetic energy of the Ar+ ion. As the ion energy is increased further, the low energy process disappears and the total intensity of scattered ions decreases significantly. The low energy loss peak is interpreted as due to the interaction of the Ar+ ions with the self assembled monolayer surface acting as a bulk surface. All three surfaces behave in the same manner with only minor differences in the thresholds for the high energy loss process.
2007. "Fragmentation dynamics of CS22+ on collision with a self assembled monolayer surface." Chemical Physics Letters 448(4-6):156-158. doi:10.1016/j.cplett.2007.09.083 Abstract Surface-induced dissociation of doubly charged CS22+ ions in collision with a self assembled monolayer surface of fluorinated alkyl thiol on gold 111 crystal has been studied on a beam scattering instrument. Two energetically distinct processes, corresponding to the Coulomb explosion and charge transfer induced dissociation have been observed and the latter process dominates the dissociation process.
2007. "Scaling of the Resolving Power and Sensitivity for Planar FAIMS and Mobility-Based Discrimination in Flow- and Field- Driven Analyzers." Journal of the American Society for Mass Spectrometry 18(9):1672?1681. doi:10.1016/j.jasms.2007.06.013 Abstract Continuing rapid development of the technology and applications of field asymmetric waveform ion mobility spectrometry (FAIMS) calls for better understanding of the limitations of this method and factors that govern them. While key performance metrics such as resolution and ion transmission efficiency had been calculated for specific cases using numerical simulations, the underlying physical trends remained obscure. Here we determine that the resolving power of planar FAIMS scales as the square root of separation time and sensitivity drops exponentially at the rate controlled by absolute ion mobility and several instrumental parameters. A strong dependence of ion transmission on mobility causes severe discrimination against species with higher mobility, presenting particular problems for analyses of complex mixtures. While the time evolution of resolution and sensitivity is virtually identical in existing FAIMS systems driven by gas flow and proposed devices driven by electric field, the distributions of separation times are not. The inverse correlation between mobility (and thus diffusion speed) and residence time for a particular species in field-driven FAIMS greatly reduces the mobility-based discrimination and provides much more uniform separations.
2007. "Distortion of Ion Structures by Field AsymmetricWaveform Ion Mobility Spectrometry." Analytical Chemistry 79(4):1523-1528. doi:10.1021/ac061306c Abstract Field asymmetric waveform ion mobility spectrometry (FAIMS) is emerging as a major analytical tool, especially in conjunction with mass spectrometry (MS) and/or conventional ion mobility spectrometry (IMS). In particular, FAIMS is used to separate protein or peptide conformers prior to characterization by IMS, MS/MS, or H/D exchange. High electric fields in FAIMS induce ion heating, previously estimated at <10 0C on average and believed too weak to affect ion geometries. Here we use a FAIMS/IMS/MS system to compare the IMS spectra for ESI-generated ubiquitin ions that have and have not passed FAIMS, and find that some unfolding occurs for all charge states. The analysis of those data and their comparison with reported protein unfolding in a Paul trap indicate that at least some structural transitions observed in FAIMS, or previously in an ion trap, are not spontaneous. The observed unfolding is overall similar to that produced by heating of ~40 - 50 0C above room temperature, consistent with the calculated heating of ions at FAIMS waveform peaks. Hence the isomerization in FAIMS likely proceeds in steps during “hot” periods, especially right after ions entering the device. That process distorts ion geometries and causes ion losses by a “self-cleaning” mechanism, and thus should be suppressed as much as possible. We propose achieving that via cooling FAIMS by the amount of ion heating; in most relevant cases cooling by ~75 0C should suffice.
2007. "Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles." Protein Science 16(2):299-308. 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. MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Comparative unrestrained molecular dynamics simulations on the 1/2 peptide binding domains performed in the presence of bound peptides resulted in structures in close agreement with experiments for both alleles. In the absence of peptides, allele-specific conformational changes occurred in the first segment of the 2-helix that flanks the peptide C-terminal binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a shift toward an altered F-pocket structure deviating significantly from the bound form was observed. Subsequent free energy simulations on induced F-pocket opening in B*4402 confirmed a conformation that deviated significantly from the bound structure. For B*4405, a free energy minimum close to the bound structure was found. The simulations suggest that B*4405 has a greater tendency to adopt a peptide receptive conformation in the absence of peptide, allowing tapasin-independent peptide loading. A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles.
2007. "Car–Parrinello molecular dynamics in the DFT + U formalism:Structure and energetics of solvated ferrous and ferric ions." Journal of Electroanalytical Chemistry 607(1-2):107-112. doi:10.1016/j.jelechem.2007.01.008 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 implemented a rotationally-invariant Hubbard U extension to density-functional theory in the Car–Parrinello molecular dynamics framework, with the goal of bringing the accuracy of the DFT + U approach to finite-temperature simulations, especially for liquids or solids containing transition-metal ions. First, we studied the effects on the Hubbard U on the static equilibrium structure of the hexaaqua ferrous and ferric ions, and the inner-sphere reorganization energy for the electron-transfer reaction between aqueous ferrous and ferric ions. It is found that the reorganization energy is increased, mostly as a result of the Fe–O distance elongation in the hexa-aqua ferrous ion. Second, we performed a first-principles molecular dynamics study of the solvation structure of the two aqueous ferrous and ferric ions. The Hubbard term is found to change the Fe–O radial distribution function for the ferrous ion, while having a negligible effect on the aqueous ferric ion. Moreover, the frequencies of vibrations between Fe and oxygen atoms in the first-solvation shell are shown to be unaffected by the Hubbard corrections for both ferrous and ferric ions.
2007. "Identification of a Denitrase Activity Against Calmodulin in Activated Macrophages Using High-Field Liquid Chromatography - FTICR Mass Spectrometry." Biochemistry 46(37):10498-10505. Abstract We have identified a denitrase activity in macrophages that is upregulated following macrophage activation, which is shown by mass spectrometry to recognize nitrotyrosines in the calcium signaling protein calmodulin (CaM) and convert them to their native tyrosine structure without the formation of any aminotyrosine. Comparable extents of methionine sulfoxide reduction are also observed that are catalyzed by endogenous methionine sulfoxide reductases. Competing with repair processes, oxidized CaM is a substrate for a peptidase activity that results in the selective cleavage of the C-terminus lysine (i.e., Lys148) that is expected to diminish CaM function. Thus, competing repair and peptidase activities define the abundances and functionality of CaM to modulate cellular metabolism in response to oxidative stress, where the presence of the truncated CaM species provides a useful biomarker for the transient appearance of oxidized CaM.
2007. "The Isolated Sixth Gelsolin Repeat and Headpiece Domain of Villin Bundle F-Actin in the Presence of Calcium and Are Linked by a 40-Residue Unstructured Sequence ." Biochemistry 46(25):7488-7496. doi:10.1021/bi700110v Abstract Villin is an F-actin regulating, modular protein with a gelsolin-like core and a distinct C-terminal 'headpiece’ domain. Localized in the microvilli of the absorptive epithelium, villin can bundle F-actin and, at higher calcium concentration, is capable of a gelsolin-like F-actin severing. The headpiece domain can, in isolation, bind F-actin and is crucial for F-actin bundling by villin. While the three-dimensional structure of the isolated headpiece is known, its conformation in the context of attachment to the villin core remains unexplored. Furthermore, the dynamics of the linkage of headpiece to the core has not been determined. To address these issues, we employ a 208 residue modular fragment of villin, D6-HP, which consists of the sixth gelsolin-like domain of villin (D6) and the headpiece (HP). We demonstrate that this protein fragment requires calcium for structural stability and, surprisingly, is capable of Ca2+-dependent F-actin bundling, suggesting that D6 contains a cryptic F-actin binding site. NMR resonance assignments and 15N-relaxation measurements of D6-HP in 5 mM Ca2+ demonstrate that D6-HP consists of two independent structural domains (D6 and HP) connected by an unfolded 40-residue linker sequence. The headpiece domain in D6-HP retains its structure and interacts with D6 domain only through the linker sequence without engaging in other interactions. Chemical shift values indicate essentially the same secondary structure elements for the D6 domain in D6-HP as in the highly homologous gelsolin domain 6. Thus, the headpiece domain of villin is structurally and functionally independent from the core domain.
2007. "Formation of Supercooled Liquid Solutions from Nanoscale Amorphous Solid Films of Methanol and Ethanol." Journal of Chemical Physics 127(24):Art. No. 244705. doi:10.1063/1.2819140 Abstract Molecular beam techniques are used to create layered nanoscale composite films of amorphous methanol and ethanol at 20 K. The films are then heated and temperature programmed desorption (TPD) and FTIR spectroscopy are used to observe the mixing, desorption, and crystallization behavior from the initially unmixed amorphous layers. We find that after heating above Tg, the layers completely intermix to form a deeply supercooled liquid solution. Modeling of the desorption kinetics shows that the supercooled liquid films behave as ideal solutions. Deviations from ideal solution desorption behavior are observed when the metastable supercooled solution remains for longer times in regions of the phase diagram where crystallization is thermodynamically favorable. In those cases, the finite lifetime of the metastable solutions results in the precipitation of crystalline solids. Finally, in very thick films at temperatures and compositions where a stable liquid should exist, we unexpectedly observe deviations from ideal solution behavior. Visual inspection of the sample indicates that these apparent departures from ideality arise from dewetting of the liquid film from the substrate. We conclude that compositionally tailored nanoscale amorphous films provide a useful means for preparing and examining deeply-supercooled solutions in metastable regions of the phase diagram.
2007. "Molecular Dynamics of Organophosphorous Hydrolases Bound to the Nerve Agent Soman." Journal of Chemical Theory and Computation 3(4):1569-1579. Abstract The organophosphorous hydrolase (OPH) from Pseudomonas diminuta is capable of degrading extremely toxic organophosphorous compounds with a high catalytic turnover and broad substrate specificity. The potential use of this enzyme for the detection and detoxification of warfare nerve agents has spurred efforts to engineer mutants of enhanced catalytic activity and modified stereospecificity towards the most toxic forms of organophosphate nerve agents. Molecular dynamics simulations of the wild-type OPH and the complexes between the wild-type and the triple-mutant H254G/H257W/L303R forms and the substrate SpSc-soman have been carried out to enhance our molecular level understanding of its reaction mechanism. Comparison of the three simulations indicate that substrate binding induces conformational changes of the loops near the active site, suggesting an induced-fit mechanism. Likewise, the coordination of the zinc cations in the active site of the enzyme differs between the free enzyme and the complexes. In the absence of the substrate, the more exposed b-zinc is hexa-coordinated and the less exposed a-zinc is penta-coordinated. In the presence of the substrate, the b- zinc atom can be both penta- or hexa-coordinated while the a-zinc atom is tetra-coordinated. In addition, binding energies were calculated from electrostatic properties obtained by solution of the Poisson-Boltzmann equation combined with a surface area-dependent apolar contribution. The calculations indicate that the binding of SpSc-soman to OPH is driven by nonpolar interactions while electrostatic interactions determine binding specificity. These results provide a qualitative, molecular-level explanation for 2 the three-fold increase in catalytic efficiency of the triple-mutant towards SpSc-soman. Keywords: organophosphorous hydrolase, phosphotriesterase, nerve agents, soman, molecular dynamics, Poisson-Boltzmann equation, continuum electrostatics, metalloprotein.
2007. "Effect of Hydrophobic Primary Organic Aerosols on Secondary Organic Aerosol Formation from Ozonolysis of α-Pinene." Geophysical Research Letters 34(20):Paper # L20803. doi:10.1029/2007GL030720 Abstract Semi-empirical secondary organic aerosol (SOA) models typically assume a well-mixed organic aerosol phase even in the presence of hydrophobic primary organic aerosols (POA). This assumption significantly enhances the modeled SOA yields as additional organic mass is made available to absorb greater amounts of oxidized secondary organic gases than otherwise. We investigate the applicability of this critical assumption by measuring SOA yields from ozonolysis of α-pinene (a major biogenic SOA precursor) in a smog chamber in the absence and in the presence of dioctyl phthalate (DOP) and lubricating oil seed aerosol. These particles serve as surrogates for urban hydrophobic POA. The results show that these POA did not enhance the SOA yields. If these results are found to apply to other biogenic SOA precursors, then the semi-empirical models used in many global models would predict significantly less biogenic SOA mass and display reduced sensitivity to anthropogenic POA emissions than previously thought.
2007. "In situ solid state B-11 MAS-NMR studies of the thermal decomposition of ammonia borane: mechanistic studies of the hydrogen release pathways from a solid state hydrogen storage material." Physical Chemistry Chemical Physics. PCCP 9(15):1831-1836. doi:10.1039/b617781f Abstract The mechanism of hydrogen release from solid state ammonia borane (AB) has been investigated via in situ solid state 11B{1H} MAS-NMR techniques in external fields of 7.06 T and 18.8 T at a decomposition temperature of 88 oC, well below the reported melting point. The decomposition of AB is well described by an induction, nucleation and growth mechanistic pathway. During the induction period, little hydrogen is released from AB; however, a new species identified as a mobile phase of AB is observed in the 11B NMR spectra. Subsequent to induction, at reaction times when hydrogen is initially being released, three additional species are observed: the diammoniate of diborane (DADB), [(NH3)2BH2]+[BH4]-, and two BH2N2 species believed to be the linear (NH3BH2NH2BH3) and cyclic dimer (NH2BH2)2 of aminoborane. At longer reaction times the sharper features are replaced by broad, structureless peaks of a complex polymeric aminoborane (PAB) containing both BH2N2 and BHN3 species. We propose the following mechanistic model for the induction, nucleation and growth for AB decomposition leading to formation of hydrogen: (1) an induction period that yields a mobile phase of AB caused by disruption of the dihydrogen bonds, (2) nucleation that yields reactive DADB from the mobile AB and (3) growth that includes a bimolecular reaction between DADB and AB to release the stored hydrogen. Support for this work by the U.S. Department of Energy, Office of Science, Basic Energy Sciences is gratefully acknowledged. A portion of the research described in this paper was performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.
2007. "In Vitro Cell Culture Infectivity Assay for Human Noroviruses." Emerging Infectious Diseases 13(3):396-403. Abstract Human noroviruses (NoV) cause severe, self-limiting gastroenteritis that typically lasts 24 - 48 hours. The true nature of NoV pathogenesis remains unknown due to the lack of suitable tissue culture or animal models. Here we show, for the first time, that NoV can infect and replicate in an organoid, three-dimensional (3-D) model of human small intestinal epithelium (INT-407). Cellular differentiation for this model was achieved by growing the cells in 3-D on porous collagen I-coated microcarrier beads under conditions of physiological fluid shear in rotating wall vessel bioreactors. Microscopy, PCR, and fluorescent in-situ hybridization were employed to provide evidence of NoV infection. CPE and norovirus RNA was detected at each of the five cell passages for both genogroup I and II viruses. Our results demonstrate that the highly differentiated 3-D cell culture model can support the natural growth of human noroviruses, whereas previous attempts using differentiated monolayer cultures failed.
2007. "Methane Production by Deuterium Impact at Carbon Surfaces." Nuclear Instruments and Methods in Physics Research. Section B, Beam Interactions with Materials and Atoms 255(1):202-207. 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. Molecular dynamics simulations have been performed of the sputtering of both deuterated amorphous carbon and graphite surfaces by D2 molecules at impact energies ranging from 7.5 to 30 eV/D. These simulations were done under conditions that replicate, as closely as possible, prior experimental investigations of D+ 2 impacts on ATJ graphite. The substrate structure is heavily modified by cumulative impacts, and the sputtering yields change with increasing fluence. For the graphite sample, the surface continues to evolve up to the highest fluences studied, 3.8 × 1020 D/m2. For the deuterated amorphous carbon surface, however, the sample reaches a steady state at fluences of less than 1×1020 D/m2, at which point the structure and sputtering yields change slowly, aside from statistical fluctuations. The structure of this ensemble of steady-state surfaces is examined in detail, and is highly supersaturated with deuterium, with an enrichment in sp3 carbon. The yields of the hydrocarbons sputtered from this set of surfaces show good agreement with experiment, and are significantly larger than those from the unmodified, bulk-like amorphous carbon surface, where atomic and radical species dominate. These simulations indicate that it is both feasible and necessary to perform sputtering simulations on surfaces that have been dynamically created by impacts, if meaningful comparison with experiment is desired.
2007. "Pd2@Sn18(4-): Fusion of Two Endohedral Stannaspherenes." Journal of the American Chemical Society 129(31):9560-9561. doi:10.1021/ja0728674 Abstract One of the major objectives of cluster science is to discover stable atomic clusters, which may be used as building blocks for clusterassembled materials. The discovery and bulk synthesis of the fullerenes1,2 have sprouted new research disciplines in chemistry and nanoscience and precipitated intense interests to search for other similar stable clusters. However, despite major research efforts, no other analogous gas-phase clusters have been found and yielded to bulk syntheses. Recently, a 12-atom Sn cluster (Sn12 2-), named stannaspherene, was discovered serendipitously to be a highly stable icosahedral cage during gas-phase photoelectron spectroscopic experiment.3 Stannaspherene has a diameter of 6.1 Å, which is large enough to entrap a foreign atom and suggests possibilities to create endohedral stannaspherenes analogous to the endohedral fullerenes. Indeed, we have shown recently that stannaspherene can trap all transition-metal atoms, as well as f-block elements, giving rise to a whole new class of endohedral clusters.4 The endohedral stannaspherenes may even rival the fullerenes, which cannot trap transition-metal atoms other than the rare-earth and f-block atoms,5 and be used as building blocks for novel cluster-assembled materials with tunable magnetic and electronic properties. We have found further that Pb12 2- (plumbaspherene)6 is also a highly stable icosahedral cage cluster in the gas phase with a diameter (6.3 Å) slightly larger than that of stannaspherene and should also be able to trap a variety of foreign atoms. Indeed, an endohedral AlPb12 + cluster has been observed as a stable gaseous species,7 which can be formulated as Al3+@Pb12 2-. Very interestingly, Eichhorn and co-workers have synthesized a series of endohedral cage compounds, M@Pb12 2- (M ) Ni, Pd, Pt), through chemical reactions of K4Pb9 and ML4 (M ) Pt, Pd, L ) PPh3) in ethylenediamine (ED) and crystallized them as (2,2,2-crypt)K+ salts.
2007. "Water-induced morphology changes in BaO/γ-Al2O3 NOx storage materials." Chemical Communications 2007(9):984-986. doi:10.1039/b613674e Abstract Exposure of NO2-saturated BaO/γ-Al2O3 NOx storage materials to H2O vapour results in the conversion of surface nitrates to Ba(NO3)2 crystallites, causing dramatic morphological changes in the Ba-containing phase, demonstrating a role for water in affecting the NOx storage/reduction properties of these materials.
2007. "Water-induced morphology changes in BaO/γ-Al2O3 NOx storage materials: an FTIR, TPD, and time-resolved synchrotron XRD study." Journal of Physical Chemistry C 111(12):4678-4687. doi:10.1021/jp067932v Abstract The effect of water on the morphology of BaO/Al2O3-based NOx storage materials was investigated using Fourier transform infrared spectroscopy, temperature programmed desorption, and time-resolved synchrotron X-ray diffraction techniques. The results of this multi-spectroscopy study reveal that, in the presence of water, surface Ba-nitrates convert to bulk nitrates, and water facilitates the formation of large Ba(NO3)2 particles. This process is completely reversible, i.e. after the removal of water from the storage material a significant fraction of the bulk nitrates re-convert to surface nitrates. NO2 exposure of a H2O-containing (wet) BaO/Al2O3 sample results in the formation of nitrites and bulk nitrates exclusively, i.e. no surface nitrates form. After further exposure to NO2, the nitrites completely convert to bulk nitrates. The amount of NOx taken up by the storage material is, however, essentially unaffected by the presence of water, regardless of whether the water was dosed prior to or after NO2 exposure. Based on the results of this study we are now able to explain most of the observations reported in the literature on the effect of water on NOx uptake on similar storage materials.
2007. "The effect of H2O on the adsorption of NO2 on γ-Al2O3: an in situ FTIR/MS study." Journal of Physical Chemistry C 111(6):2661-2669. doi:10.1021/jp066326x Abstract The effect of water on the adsorption of NO2 onto a γ-Al2O3 catalyst support surface was investigated using Fourier transform infrared spectroscopy (FTIR) and mass spectrometry (MS). Upon room temperature exposure of the alumina surface to small amounts of NO2, nitrites and nitrates are formed, and at higher NO2 doses only nitrates are observed. The surface nitrates formed were of bridging monodentate, bridging bidentate, and monodentate configuration. At elevated NO2 pressures, the surface hydroxyls were consumed in their reaction with NO2 giving primarily bridge-bound nitrates. A significant amount of weakly adsorbed N2O3 was seen as well. Exposure of the NO2-saturated γ-Al2O3 surface to H2O resulted in the desorption of some NO2 + NO as H2O interacted with the weakly-held N2O3, while the bridging monodentate surface nitrates converted into monodentate nitrates. The conversion of these oxide-bound nitrates to water-solvated nitrates was observed at high water doses when the presence of liquid-like water is expected on the surface. The addition of H2O to the NO2-saturated γ-Al2O3 did not affect the amount of NOx strongly adsorbed on the support surface. In particular, no NOx desorption was observed when the NO2-saturated sample was heated to 573K prior to room temperature H2O exposure. The effect of water is completely reversible; i.e., during TPD experiments following NO2 and H2O coadsorption, the same IR spectra were observed at temperatures above that required for H2O desorption as seen for NO2 adsorption only experiments.
